{"id":31870,"name":"virtual_rainforest","ecosystem":"submodules","repository_url":null,"issues_count":24,"created_at":"2025-06-07T10:37:06.438Z","updated_at":"2025-06-07T10:37:06.438Z","purl":"pkg:submodules/virtual_rainforest","unique_repositories_count":1,"unique_repositories_count_past_30_days":1,"recent_issues":[{"uuid":"3683123391","node_id":"PR_kwDOKCm6f862dYX0","number":147,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `035163b`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-12-08T19:05:33.000Z","author_association":null,"state_reason":null,"created_at":"2025-12-01T22:26:17.000Z","updated_at":"2025-12-08T19:05:34.000Z","time_to_close":592756,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`035163b`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `035163b`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/035163b20b50b956988a7fbfa664f47be83d8c98\"\u003e\u003ccode\u003e035163b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1163\"\u003e#1163\u003c/a\u003e from ImperialCollegeLondon/bugfix/symbiotic_supply_l...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/274facff06b09a870042a2227f30e20e98599eaf\"\u003e\u003ccode\u003e274facf\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into bugfix/symbiotic_supply_limits\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c7ed97185b4299412f3c43feb4575001bf3923b7\"\u003e\u003ccode\u003ec7ed971\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1166\"\u003e#1166\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6e96b087ede617c689d8c4ede83b7da17218885f\"\u003e\u003ccode\u003e6e96b08\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9779436506b8234c5a409b4859e5a0955ab0aeb5\"\u003e\u003ccode\u003e9779436\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1167\"\u003e#1167\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-55c...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/279b12089dd6991965c294c92460269ffaec3da0\"\u003e\u003ccode\u003e279b120\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-mermaid from 1.1.0 to 1.2.3 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1bcbca88e3b4109ccd84dc971f4f892833a70428\"\u003e\u003ccode\u003e1bcbca8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1165\"\u003e#1165\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/416908faa870e81c493938fa89774e1edc00d23f\"\u003e\u003ccode\u003e416908f\u003c/code\u003e\u003c/a\u003e Bump pydantic from 2.12.4 to 2.12.5 in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/77524da427af732d2ff9bf04c38c2dcd4003fc2a\"\u003e\u003ccode\u003e77524da\u003c/code\u003e\u003c/a\u003e Added TODO about air temperatures not being populated on init to the AbioticS...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/80b3f00448a36fd7a218e04878ec2c5523c923dd\"\u003e\u003ccode\u003e80b3f00\u003c/code\u003e\u003c/a\u003e Merge branch 'bugfix/symbiotic_supply_limits' of \u003ca href=\"https://github.com/ImperialC\"\u003ehttps://github.com/ImperialC\u003c/a\u003e...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...035163b20b50b956988a7fbfa664f47be83d8c98\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/147","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/147","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/147/packages"},{"uuid":"3660243726","node_id":"PR_kwDOKCm6f861RUmT","number":146,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `12e54e5`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-12-01T22:26:20.000Z","author_association":null,"state_reason":null,"created_at":"2025-11-24T19:28:28.000Z","updated_at":"2025-12-01T22:26:22.000Z","time_to_close":615472,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`12e54e5`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `12e54e5`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/12e54e5278e59feb00805056a8eabd3730379576\"\u003e\u003ccode\u003e12e54e5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1160\"\u003e#1160\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/fa1a83be7fc419f567db7aa035ee65a73bd0b5aa\"\u003e\u003ccode\u003efa1a83b\u003c/code\u003e\u003c/a\u003e Bump actions/checkout from 5 to 6\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c998837aead47212a89b352cd2cf8453a240a6ff\"\u003e\u003ccode\u003ec998837\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1158\"\u003e#1158\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4f402ec5bd83d5e2fa9ef55b7dff15cd062ccaa9\"\u003e\u003ccode\u003e4f402ec\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7f2b197d916e368ee8a49d66a9c13a356c4eba0c\"\u003e\u003ccode\u003e7f2b197\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1159\"\u003e#1159\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-a4c...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d7a6824d0fb50fee80b1d8f446c908f0970d233f\"\u003e\u003ccode\u003ed7a6824\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-mermaid from 1.0.0 to 1.1.0 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f0228b7b16e6914ba0ea256c50aa0c3fdc97fcb3\"\u003e\u003ccode\u003ef0228b7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1157\"\u003e#1157\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a07cf4f0542b11b47ddbd887bfefd63457a48fe6\"\u003e\u003ccode\u003ea07cf4f\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/98f2629b71c3e8939a26c157c98b331bf4ff00d3\"\u003e\u003ccode\u003e98f2629\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1156\"\u003e#1156\u003c/a\u003e from ImperialCollegeLondon/484-abiotic-simple---atmo...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/31a5ff5f6444c9ef18555970ed7e329b39c15734\"\u003e\u003ccode\u003e31a5ff5\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 484-abiotic-simple---atmospheric-pressure-and-co2...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...12e54e5278e59feb00805056a8eabd3730379576\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/146","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/146","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/146/packages"},{"uuid":"3609325012","node_id":"PR_kwDOKCm6f86ymfdS","number":143,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `f93d9d2`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-11-17T19:07:50.000Z","author_association":null,"state_reason":null,"created_at":"2025-11-10T19:06:52.000Z","updated_at":"2025-11-17T19:07:52.000Z","time_to_close":604858,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`f93d9d2`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `f93d9d2`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f93d9d2be3cf0dbd97e9c0145f81293aad3510df\"\u003e\u003ccode\u003ef93d9d2\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1145\"\u003e#1145\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/aa78dde96620ef97461a2f51d3f8073494b4bae0\"\u003e\u003ccode\u003eaa78dde\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/03935e099aac52b5cb3ced8a36adf166a1ab346e\"\u003e\u003ccode\u003e03935e0\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1144\"\u003e#1144\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d131e3a232c19e6934408a3481b668758e31b1d7\"\u003e\u003ccode\u003ed131e3a\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0fefce4ec5b873213e683a27575fa119075dfe9a\"\u003e\u003ccode\u003e0fefce4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1143\"\u003e#1143\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4deec5a9d9cfc9f7f0ab31f8e727c411aef5e6a8\"\u003e\u003ccode\u003e4deec5a\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1a0ea4b40b5210245390906ea118bea42d895717\"\u003e\u003ccode\u003e1a0ea4b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1138\"\u003e#1138\u003c/a\u003e from ImperialCollegeLondon/1136-simplify-model-regis...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e95f355caddd1d59a55381ba4079e44a2895828d\"\u003e\u003ccode\u003ee95f355\u003c/code\u003e\u003c/a\u003e Adding naming convention notes, test fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/71064bc45ec7654081b27338dcfac30d2b58a422\"\u003e\u003ccode\u003e71064bc\u003c/code\u003e\u003c/a\u003e Removing docs on root import of BaseModel\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f6beff384eed827d98bf6a53d6236573d46b60cd\"\u003e\u003ccode\u003ef6beff3\u003c/code\u003e\u003c/a\u003e Forgot to add file\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...f93d9d2be3cf0dbd97e9c0145f81293aad3510df\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/143","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/143","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/143/packages"},{"uuid":"2891492585","node_id":"PR_kwDOKCm6f86sWKzp","number":130,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `7dc6f06`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-10-06T19:05:57.000Z","updated_at":"2025-10-06T19:05:58.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`7dc6f06`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `7dc6f06`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7dc6f060ccf25bd62a2564dc4c79fa87c450064d\"\u003e\u003ccode\u003e7dc6f06\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1074\"\u003e#1074\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b34184ea0ea3f6649f952fc95b7d1f94df98f8cb\"\u003e\u003ccode\u003eb34184e\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/745f4b3a7b1c59e638a0c10a45524a079e443ab0\"\u003e\u003ccode\u003e745f4b3\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1066\"\u003e#1066\u003c/a\u003e from ImperialCollegeLondon/1041-move-initial-plant-c...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/537d26314b06e5bdcee1a2614ace53df3644299a\"\u003e\u003ccode\u003e537d263\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 1041-move-initial-plant-cohort-data\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/10d4bc4566d59780dc01d7aa72c0ddc0f7cae810\"\u003e\u003ccode\u003e10d4bc4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1043\"\u003e#1043\u003c/a\u003e from ImperialCollegeLondon/1033-bug-in-accumulated-r...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/8388d9f22eba1a6675024b6ca0c1724fce1090e9\"\u003e\u003ccode\u003e8388d9f\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 1033-bug-in-accumulated-runoff\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c616b53911fa47a080a4825e76668f49f31c68fe\"\u003e\u003ccode\u003ec616b53\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1072\"\u003e#1072\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c7b2c7a97b27b2a03434d5f3ef2204c032e50bb5\"\u003e\u003ccode\u003ec7b2c7a\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9ad8b0e251cd7db4ae21509b8aa8e5f6b287f660\"\u003e\u003ccode\u003e9ad8b0e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1071\"\u003e#1071\u003c/a\u003e from ImperialCollegeLondon/1058-integrate-subcanopy-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/88ee1cb92062bf653001d01441ae78f4c01287ab\"\u003e\u003ccode\u003e88ee1cb\u003c/code\u003e\u003c/a\u003e Started removing subcanopy uptake from the appropriate soil pools\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...7dc6f060ccf25bd62a2564dc4c79fa87c450064d\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/130","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/130","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/130/packages"},{"uuid":"2830331762","node_id":"PR_kwDOKCm6f86os29y","number":120,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `09332ea`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-09-22T19:06:11.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-15T19:05:46.000Z","updated_at":"2025-09-22T19:06:11.000Z","time_to_close":604825,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`09332ea`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `09332ea`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/09332ea49372a979204d12ab9801c8f4839ff6f7\"\u003e\u003ccode\u003e09332ea\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1042\"\u003e#1042\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/41be846eba77e7a24666ba3f169b02849c435350\"\u003e\u003ccode\u003e41be846\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/35ef062043a3874ecd759c4c89d48cfbbd6560f7\"\u003e\u003ccode\u003e35ef062\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1030\"\u003e#1030\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ed74b101b28c493155e13a60c8e5f5b298f48f00\"\u003e\u003ccode\u003eed74b10\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into dependabot/pip/development-dependencies-47fb0c18d6\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a7d8b1680733def8ee0eb3ced9cc61ff27140b93\"\u003e\u003ccode\u003ea7d8b16\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1031\"\u003e#1031\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/588a4222dc16683374b82637b145ee57ddcfb227\"\u003e\u003ccode\u003e588a422\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/53410d88e2f014895d0174a3a938c0b5252d54f7\"\u003e\u003ccode\u003e53410d8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1029\"\u003e#1029\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ded6d49a5d2c2da1b0627374cc9e80ac7a5698b5\"\u003e\u003ccode\u003eded6d49\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group across 1 directory with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/81dc7e64d8a45cc6f882decb5b5bcc5621cfce96\"\u003e\u003ccode\u003e81dc7e6\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into dependabot/github_actions/actions/setup-python-6\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/502b88d18011f04bb84903d51a92cb568fe829a2\"\u003e\u003ccode\u003e502b88d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/827\"\u003e#827\u003c/a\u003e from ImperialCollegeLondon/824-recruitment-of-new-tre...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...09332ea49372a979204d12ab9801c8f4839ff6f7\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/120","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/120","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/120/packages"},{"uuid":"2774881495","node_id":"PR_kwDOKCm6f86lZVTX","number":111,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `47ce912`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-26T11:55:50.000Z","updated_at":"2025-08-26T11:55:51.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`47ce912`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `47ce912`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/47ce9123c7db7b819220f0698fe79b489663ecaa\"\u003e\u003ccode\u003e47ce912\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1008\"\u003e#1008\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/eccb818aba91abc655618a5f9bf3cb6ad61c0594\"\u003e\u003ccode\u003eeccb818\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/bff4ac242960a015112ff048803e7a40542dcc44\"\u003e\u003ccode\u003ebff4ac2\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1007\"\u003e#1007\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7f23e7d2800ff87db59140933796c0f435e8094b\"\u003e\u003ccode\u003e7f23e7d\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/61f557aaf994e9c685c01afc930c7d2daf2a9f8e\"\u003e\u003ccode\u003e61f557a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1005\"\u003e#1005\u003c/a\u003e from ImperialCollegeLondon/1002-bulk-density-is-defi...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a0cd133cd0cabb2ad1e9d9084dc6d05ccbc6f729\"\u003e\u003ccode\u003ea0cd133\u003c/code\u003e\u003c/a\u003e Removed bulk density from the soil model as it isn't actually used\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/8e4416d867f21f43a000f9ecc4ef8780586cf7cd\"\u003e\u003ccode\u003e8e4416d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1004\"\u003e#1004\u003c/a\u003e from ImperialCollegeLondon/536-add-check-for-nan-val...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/981e29bd8383ef43c5c7e33c192fabb51bce0939\"\u003e\u003ccode\u003e981e29b\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 536-add-check-for-nan-values-before-running-the-s...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/bd4934139aa1cde5d791973f9416a987c09e3d19\"\u003e\u003ccode\u003ebd49341\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1001\"\u003e#1001\u003c/a\u003e from ImperialCollegeLondon/979-integration-of-the-li...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/52474f4a4ad1e87ea524e8303cc5c7d3ac99972b\"\u003e\u003ccode\u003e52474f4\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 979-integration-of-the-litter-model-needs-to-be-i...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...47ce9123c7db7b819220f0698fe79b489663ecaa\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/111","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/111","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/111/packages"},{"uuid":"2755310681","node_id":"PR_kwDOKCm6f86kOrRZ","number":109,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `c051224`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-19T06:19:15.000Z","updated_at":"2025-08-19T06:19:16.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`c051224`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `c051224`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c05122447b364fd77f31c4be7ec4021a6a1c492b\"\u003e\u003ccode\u003ec051224\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1003\"\u003e#1003\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5b06dcb9fdd3804619d790140123641e8508072b\"\u003e\u003ccode\u003e5b06dcb\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/48c3562b9824443f29e04da4aa84f0e66cdcfa7b\"\u003e\u003ccode\u003e48c3562\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1000\"\u003e#1000\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ca55541dd110ffca233eaaf1a305c3cd5a5cd23c\"\u003e\u003ccode\u003eca55541\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/266dbe60687aee96eb336be760a10af39d53eae0\"\u003e\u003ccode\u003e266dbe6\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/990\"\u003e#990\u003c/a\u003e from ImperialCollegeLondon/989-foraging-methods-refac...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/02702b328de26787775eabc40ba0bfb30e4180aa\"\u003e\u003ccode\u003e02702b3\u003c/code\u003e\u003c/a\u003e Removed some unecessary error checks.\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/befc645859b78aee17b9ca342e5773c81d2580b7\"\u003e\u003ccode\u003ebefc645\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 989-foraging-methods-refactor-to-reduce-resuse\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3b4c74a6aba9842e3556bbd1119f95369476c7c2\"\u003e\u003ccode\u003e3b4c74a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/994\"\u003e#994\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0c76fc47a7a72ecf78197b86834fc1198123beff\"\u003e\u003ccode\u003e0c76fc4\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d026cee2625f77320f55ecd7e978c27c6872ed48\"\u003e\u003ccode\u003ed026cee\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/993\"\u003e#993\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions/...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...c05122447b364fd77f31c4be7ec4021a6a1c492b\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/109","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/109","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/109/packages"},{"uuid":"2737491022","node_id":"PR_kwDOKCm6f86jKsxO","number":104,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `3b4c74a`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-08-19T06:19:17.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-12T03:01:39.000Z","updated_at":"2025-08-19T06:19:17.000Z","time_to_close":616658,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3b4c74a`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3b4c74a`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3b4c74a6aba9842e3556bbd1119f95369476c7c2\"\u003e\u003ccode\u003e3b4c74a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/994\"\u003e#994\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0c76fc47a7a72ecf78197b86834fc1198123beff\"\u003e\u003ccode\u003e0c76fc4\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d026cee2625f77320f55ecd7e978c27c6872ed48\"\u003e\u003ccode\u003ed026cee\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/993\"\u003e#993\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions/...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4dee4e807eb20a17ee21d5fe80112d609f5b6c4b\"\u003e\u003ccode\u003e4dee4e8\u003c/code\u003e\u003c/a\u003e Bump actions/download-artifact from 4 to 5\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ec777d3ae33d37a77df1f7a23e48e97c03b15311\"\u003e\u003ccode\u003eec777d3\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/992\"\u003e#992\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3071e5e23f58077feead5a88cc5929efb23bbe80\"\u003e\u003ccode\u003e3071e5e\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 6 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3f830d43bdba60defb4e742dcc86822caf1a484f\"\u003e\u003ccode\u003e3f830d4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/947\"\u003e#947\u003c/a\u003e from ImperialCollegeLondon/814-microbial-community-do...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/399c54cf1563b7c817f919c3aab041eb0caafc85\"\u003e\u003ccode\u003e399c54c\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 814-microbial-community-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0861c9548d48dbea1033604e1631501bb653df77\"\u003e\u003ccode\u003e0861c95\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/985\"\u003e#985\u003c/a\u003e from ImperialCollegeLondon/release/v0.1.1a12\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c54ba454b0386318c9e74d02d18b8445f2e6726f\"\u003e\u003ccode\u003ec54ba45\u003c/code\u003e\u003c/a\u003e Dumping abatilo poetry action\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3b4c74a6aba9842e3556bbd1119f95369476c7c2\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/104","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/104","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/104/packages"},{"uuid":"2719680150","node_id":"PR_kwDOKCm6f86iGwaW","number":103,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `0c4f449`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-05T02:45:55.000Z","updated_at":"2025-08-05T02:45:56.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`0c4f449`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `0c4f449`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0c4f44998500e3a5766a8e8b96e84de171a4516a\"\u003e\u003ccode\u003e0c4f449\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/984\"\u003e#984\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7df4f00ecd12394b99693fc1746de5cd66709ff5\"\u003e\u003ccode\u003e7df4f00\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3df9e7ac3048228b8d3df58349d7232459b62e2b\"\u003e\u003ccode\u003e3df9e7a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/981\"\u003e#981\u003c/a\u003e from ImperialCollegeLondon/980-unpin-the-update-inter...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d9d13f35fa46d983b203325cd3261381a0fa8495\"\u003e\u003ccode\u003ed9d13f3\u003c/code\u003e\u003c/a\u003e Updates from \u003ca href=\"https://github.com/vgro\"\u003e\u003ccode\u003e@​vgro\u003c/code\u003e\u003c/a\u003e comments\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2a13f4ba5945dff490179729d24b6d7796f11f0b\"\u003e\u003ccode\u003e2a13f4b\u003c/code\u003e\u003c/a\u003e pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7f679d1f4d2575d87a976f899218669ec4c4f2d5\"\u003e\u003ccode\u003e7f679d1\u003c/code\u003e\u003c/a\u003e More typing fixes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e91c152ca5f70ff0e42a01ab9bcb5358e6397f2f\"\u003e\u003ccode\u003ee91c152\u003c/code\u003e\u003c/a\u003e Restoring old pre-commit mypy settings - not sure why they disappeared\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5fe1fe68d6025e4e29f517e293d52e389611c474\"\u003e\u003ccode\u003e5fe1fe6\u003c/code\u003e\u003c/a\u003e mypy fixes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/05e0874fbf0a47f4832c051d24ea952b65c86b27\"\u003e\u003ccode\u003e05e0874\u003c/code\u003e\u003c/a\u003e Adding types-tabulate to pre-commit\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0cde14d6012e24043db5b39615f738eb92a176d1\"\u003e\u003ccode\u003e0cde14d\u003c/code\u003e\u003c/a\u003e Adding types-tabulate - not sure why this is needed now\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...0c4f44998500e3a5766a8e8b96e84de171a4516a\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/103","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/103","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/103/packages"},{"uuid":"2683267681","node_id":"PR_kwDOKCm6f86f72ph","number":98,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `7988df5`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-08-05T02:45:57.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-07-21T21:51:12.000Z","updated_at":"2025-08-05T02:45:57.000Z","time_to_close":1227285,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`7988df5`","repository_url":null}],"path":null,"ecosystem":"submodules"},"body":"\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/98","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/98","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/98/packages"},{"uuid":"2665641546","node_id":"PR_kwDOKCm6f86e4nZK","number":97,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `3be034e`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-07-14T23:36:25.000Z","updated_at":"2025-07-14T23:36:26.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3be034e`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3be034e`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3be034ed11c208002276d7e8d3f0ad26fde93443\"\u003e\u003ccode\u003e3be034e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/951\"\u003e#951\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7284d54ec6b04fb70b82209dbd379990b4aae117\"\u003e\u003ccode\u003e7284d54\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6fabd1511271dfe251bd6b9a70946a1fff0cbfa6\"\u003e\u003ccode\u003e6fabd15\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/946\"\u003e#946\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/caa09ddab1fdb73a3ed2bd245896250832ecd917\"\u003e\u003ccode\u003ecaa09dd\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d71b8e35b7ec37269ee766df867185428773b5ff\"\u003e\u003ccode\u003ed71b8e3\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/938\"\u003e#938\u003c/a\u003e from ImperialCollegeLondon/937-add-vertical-structure...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7034bcecaf867ac367a4f7fabd3d241e3ba734a2\"\u003e\u003ccode\u003e7034bce\u003c/code\u003e\u003c/a\u003e typos fixed\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/385a5bad321ce27edab3b1ecd35052a39d7e4b81\"\u003e\u003ccode\u003e385a5ba\u003c/code\u003e\u003c/a\u003e Merge branch '937-add-vertical-structure-graphic-to-hydrology-model' of https...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/837313f548fc911321378a3eec35c2b23c5dc6d6\"\u003e\u003ccode\u003e837313f\u003c/code\u003e\u003c/a\u003e replaced bucket model graph to account for throughflow\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/da7f1cbbf8c60ddc008e7a38902bb901ee29fb28\"\u003e\u003ccode\u003eda7f1cb\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 937-add-vertical-structure-graphic-to-hydrology-m...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/92145eb10b9790ae3d89aa054985d8249ded8a2b\"\u003e\u003ccode\u003e92145eb\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/942\"\u003e#942\u003c/a\u003e from ImperialCollegeLondon/feature/publication_workfl...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3be034ed11c208002276d7e8d3f0ad26fde93443\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/97","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/97","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/97/packages"},{"uuid":"2630293586","node_id":"PR_kwDOKCm6f86cxxhS","number":92,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `4e6ce4e`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-30T22:24:04.000Z","updated_at":"2025-06-30T22:24:05.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`4e6ce4e`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `4e6ce4e`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4e6ce4ed43cf6e5b2514650c5807ad0a039e0745\"\u003e\u003ccode\u003e4e6ce4e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/922\"\u003e#922\u003c/a\u003e from ImperialCollegeLondon/918-update-pyrealm-version\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3471fd0cb1fb64641e86dcf003017246fa317fae\"\u003e\u003ccode\u003e3471fd0\u003c/code\u003e\u003c/a\u003e Resolving poetry.lock\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c5a08892bfdea5b9e4ea384212f0d5e6c2d7cbf7\"\u003e\u003ccode\u003ec5a0889\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/926\"\u003e#926\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-c732...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/541bf64d51c41e487d332dbc5e419a217f5839b3\"\u003e\u003ccode\u003e541bf64\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-bibtex from 2.6.4 to 2.6.5 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a87faa90e9f68d323f14cc2625033c7762a2bcda\"\u003e\u003ccode\u003ea87faa9\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/925\"\u003e#925\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/52b70db250f34fcbb5f2af96b4e742463131d2ed\"\u003e\u003ccode\u003e52b70db\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/75fc2baa3a61b697027bbdfa186c33a2a082a175\"\u003e\u003ccode\u003e75fc2ba\u003c/code\u003e\u003c/a\u003e Merge branch '918-update-pyrealm-version' of \u003ca href=\"https://github.com/ImperialColle\"\u003ehttps://github.com/ImperialColle\u003c/a\u003e...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f4aa114ce3f69a3f8bc31492632525a51967a07b\"\u003e\u003ccode\u003ef4aa114\u003c/code\u003e\u003c/a\u003e Comment tweaks\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c8b4b71ff705de7ed00e4f0fd215e40987143cc9\"\u003e\u003ccode\u003ec8b4b71\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 918-update-pyrealm-version\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e11d18b59c237162cc640555e564f50dba7f2a3c\"\u003e\u003ccode\u003ee11d18b\u003c/code\u003e\u003c/a\u003e Hacking tree stems to prevent D \u0026lt;= 0\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...4e6ce4ed43cf6e5b2514650c5807ad0a039e0745\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/92","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/92","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/92/packages"},{"uuid":"2612881239","node_id":"PR_kwDOKCm6f86bvWdX","number":91,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `3bd0e9b`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-23T21:52:23.000Z","updated_at":"2025-06-23T21:52:24.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3bd0e9b`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3bd0e9b`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3bd0e9bf857fa7268a87732fd757df951b681bcb\"\u003e\u003ccode\u003e3bd0e9b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/915\"\u003e#915\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-fa20...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ba1e0cd0ccf302f98f5281285a30dd8f2cdc72c8\"\u003e\u003ccode\u003eba1e0cd\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-bibtex from 2.6.3 to 2.6.4 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/88667f83c41c2502869abf5e85d8bd03ee57b177\"\u003e\u003ccode\u003e88667f8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/914\"\u003e#914\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d35bb77ab74fe19ef32d3066b18b6826c88e57df\"\u003e\u003ccode\u003ed35bb77\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/21a56362089d6b864070859ed2022bd06613a032\"\u003e\u003ccode\u003e21a5636\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/906\"\u003e#906\u003c/a\u003e from ImperialCollegeLondon/888-animal-model---foragin...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1843cb7037579d1d615f7b29951af414b3e90520\"\u003e\u003ccode\u003e1843cb7\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 888-animal-model---foraging-time-budget\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/422be4cd156cc169a41dd6ad9f4c82d9711d6712\"\u003e\u003ccode\u003e422be4c\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/903\"\u003e#903\u003c/a\u003e from ImperialCollegeLondon/902-better-control-of-ve_r...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7eb42153147a5795ce6eddfccf0b9b76f9ec1962\"\u003e\u003ccode\u003e7eb4215\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 902-better-control-of-ve_run-screen-output\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a90a7b85fb90609b59532218e765f1ad5c6e0f76\"\u003e\u003ccode\u003ea90a7b8\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 888-animal-model---foraging-time-budget\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/730109dadafce92a4cfa731ac2f131eb7070493b\"\u003e\u003ccode\u003e730109d\u003c/code\u003e\u003c/a\u003e Revised tests for foraging.\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3bd0e9bf857fa7268a87732fd757df951b681bcb\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/91","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/91","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/91/packages"},{"uuid":"2597033191","node_id":"PR_kwDOKCm6f86ay5Tn","number":86,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `c2aa4b5`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-16T22:07:35.000Z","updated_at":"2025-06-16T22:07:36.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`c2aa4b5`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `c2aa4b5`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c2aa4b52c34ee6db05cb0862378d7eafcdc9eeab\"\u003e\u003ccode\u003ec2aa4b5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/894\"\u003e#894\u003c/a\u003e from ImperialCollegeLondon/887-animal-model---handlin...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/46ea0a83d90ae5efda50626ed32f89794577b309\"\u003e\u003ccode\u003e46ea0a8\u003c/code\u003e\u003c/a\u003e Rerouted update_cohort_bookkeeping to use the community level methods instead...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c9057261ab8face4e331f44e6ff8bf5b2eede247\"\u003e\u003ccode\u003ec905726\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 887-animal-model---handling-starvation-during-ont...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5a4188956acb15add6ca0bc341ae518a849f9fdc\"\u003e\u003ccode\u003e5a41889\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/893\"\u003e#893\u003c/a\u003e from ImperialCollegeLondon/890-mycorrhizal-fungi-shou...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2e02f976fa18ab14ede59e52884aa4f88015620a\"\u003e\u003ccode\u003e2e02f97\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 890-mycorrhizal-fungi-should-be-obligate-rather-t...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3327f933aebe72a9be72d84a4d7fb0e875ac7dd8\"\u003e\u003ccode\u003e3327f93\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/896\"\u003e#896\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0b54a9d2235c8f266fddb81c580b4806fb780c3b\"\u003e\u003ccode\u003e0b54a9d\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f649836fdb635f68152daf9c9b0f0c77972ae903\"\u003e\u003ccode\u003ef649836\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/895\"\u003e#895\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/90a0b893d61b13a10a5ef0b58d4491d75b882dd8\"\u003e\u003ccode\u003e90a0b89\u003c/code\u003e\u003c/a\u003e Bump xarray in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e41b430f310230c66ca93f9efa79702f547c3e5c\"\u003e\u003ccode\u003ee41b430\u003c/code\u003e\u003c/a\u003e Added test for handle_ontogeny.\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...c2aa4b52c34ee6db05cb0862378d7eafcdc9eeab\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/86","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/86","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/86/packages"},{"uuid":"2579262471","node_id":"PR_kwDOKCm6f86ZvGwH","number":84,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `7c06369`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-06-16T22:07:37.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-09T19:32:00.000Z","updated_at":"2025-06-16T22:07:37.000Z","time_to_close":614137,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`7c06369`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `7c06369`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7c06369ba3fb9cff9c6d2548b7274684bc1433f7\"\u003e\u003ccode\u003e7c06369\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/889\"\u003e#889\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/14eaac7d4c5211f36ba9a356312446a467a8e120\"\u003e\u003ccode\u003e14eaac7\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/36041884332c058b1e3b3abe719b53f93475442f\"\u003e\u003ccode\u003e3604188\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/886\"\u003e#886\u003c/a\u003e from ImperialCollegeLondon/885-need-to-handle-zero-ra...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/39717b4308fcff5fbd94d2355e937a583a227fc3\"\u003e\u003ccode\u003e39717b4\u003c/code\u003e\u003c/a\u003e Added handling so that carbon limitation is calculated coreectly when max rat...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2632c709a12ff5054c2f6ae33c51e208471c0d54\"\u003e\u003ccode\u003e2632c70\u003c/code\u003e\u003c/a\u003e Added step to ignore divide by zero warnings when they had already been handl...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9b23fa5e9a64014402c20e30955212b93a4b8d27\"\u003e\u003ccode\u003e9b23fa5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/884\"\u003e#884\u003c/a\u003e from ImperialCollegeLondon/883-soil-model-implementat...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d3b70289280fb4ce3b905f83cec28eef1f26c93b\"\u003e\u003ccode\u003ed3b7028\u003c/code\u003e\u003c/a\u003e Changed var_populated_by_update section of soil implementation docs to reflec...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9edcb351c52e6c189da57da9397c75d0fc044f63\"\u003e\u003ccode\u003e9edcb35\u003c/code\u003e\u003c/a\u003e Added basic page for implementation with output variables and a TODO about fi...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5e3ceef60e6614b560dc50f8e98cec7e1a0dc6a6\"\u003e\u003ccode\u003e5e3ceef\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/881\"\u003e#881\u003c/a\u003e from ImperialCollegeLondon/770-function-to-calculate-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f3d12f3bdda5127392871fc202087818621e0b5f\"\u003e\u003ccode\u003ef3d12f3\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 770-function-to-calculate-the-effective-saturatio...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...7c06369ba3fb9cff9c6d2548b7274684bc1433f7\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/84","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/84","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/84/packages"},{"uuid":"3111389571","node_id":"PR_kwDOKCm6f86YsMxz","number":82,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `3c5d746`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-06-09T19:32:03.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-02T19:37:26.000Z","updated_at":"2025-06-09T19:32:03.000Z","time_to_close":604477,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3c5d746`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3c5d746`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3c5d7468bc42ea6d078e5c8bf98dd312e61bec97\"\u003e\u003ccode\u003e3c5d746\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/878\"\u003e#878\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c8bcab5d6a16fb887d88e4298b0929464f94af89\"\u003e\u003ccode\u003ec8bcab5\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group across 1 directory with 8 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a207634a98c6d3ef59e0d6569d1bf23844ba7a7f\"\u003e\u003ccode\u003ea207634\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/877\"\u003e#877\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/125934847efacb6d83c22ffb94453f6577d5da97\"\u003e\u003ccode\u003e1259348\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group across 1 directory with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6f36cfd933ca41243fdc1e6a492aae479e6f7a48\"\u003e\u003ccode\u003e6f36cfd\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/752\"\u003e#752\u003c/a\u003e from ImperialCollegeLondon/662-improve-soil-nutrient-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/667e0291019d2e57b1f149445164b3e62b1a59dd\"\u003e\u003ccode\u003e667e029\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/abd205db5f848479d3d0315b29ea012bf5db6096\"\u003e\u003ccode\u003eabd205d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/767\"\u003e#767\u003c/a\u003e from ImperialCollegeLondon/feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/43f7b8c08428cf61466cf13db48e754a4fe60e47\"\u003e\u003ccode\u003e43f7b8c\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6d2a2aeb4f3d48719d655c2f40f24d6d3e46d279\"\u003e\u003ccode\u003e6d2a2ae\u003c/code\u003e\u003c/a\u003e Changed first subheading so that it's meaningfully distinct from the page title\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/35bb8c7c5f6946c706db6f0656cb479d13a6832c\"\u003e\u003ccode\u003e35bb8c7\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3c5d7468bc42ea6d078e5c8bf98dd312e61bec97\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/82","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/82","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/82/packages"},{"uuid":"2544715906","node_id":"PR_kwDOKCm6f86XrUiC","number":79,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `6f36cfd`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-26T19:21:09.000Z","updated_at":"2025-05-26T19:21:10.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`6f36cfd`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `6f36cfd`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6f36cfd933ca41243fdc1e6a492aae479e6f7a48\"\u003e\u003ccode\u003e6f36cfd\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/752\"\u003e#752\u003c/a\u003e from ImperialCollegeLondon/662-improve-soil-nutrient-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/667e0291019d2e57b1f149445164b3e62b1a59dd\"\u003e\u003ccode\u003e667e029\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/abd205db5f848479d3d0315b29ea012bf5db6096\"\u003e\u003ccode\u003eabd205d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/767\"\u003e#767\u003c/a\u003e from ImperialCollegeLondon/feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/43f7b8c08428cf61466cf13db48e754a4fe60e47\"\u003e\u003ccode\u003e43f7b8c\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6d2a2aeb4f3d48719d655c2f40f24d6d3e46d279\"\u003e\u003ccode\u003e6d2a2ae\u003c/code\u003e\u003c/a\u003e Changed first subheading so that it's meaningfully distinct from the page title\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/35bb8c7c5f6946c706db6f0656cb479d13a6832c\"\u003e\u003ccode\u003e35bb8c7\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/af805f4d72b52528def649a5e539d0315dbbdde0\"\u003e\u003ccode\u003eaf805f4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/870\"\u003e#870\u003c/a\u003e from ImperialCollegeLondon/869-avoid-division-by-zero...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/37947a244c77691c8dfedbb9222e0f4c5adf4284\"\u003e\u003ccode\u003e37947a2\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/82c3619a1275d15b561f4e804ee539665e1f5925\"\u003e\u003ccode\u003e82c3619\u003c/code\u003e\u003c/a\u003e minor tweaks to heading hierarchy and wording to be consistent\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3fb2ff1b2852f48886c0039596966470067de872\"\u003e\u003ccode\u003e3fb2ff1\u003c/code\u003e\u003c/a\u003e added conditional statement to avoid division by zero\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...6f36cfd933ca41243fdc1e6a492aae479e6f7a48\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/79","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/79","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/79/packages"},{"uuid":"2529573080","node_id":"PR_kwDOKCm6f86WxjjY","number":76,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `aa95eca`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-05-26T19:21:12.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-19T19:15:49.000Z","updated_at":"2025-05-26T19:21:12.000Z","time_to_close":605123,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`aa95eca`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `aa95eca`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/aa95eca74460a15189d045f6f800df275b0abddd\"\u003e\u003ccode\u003eaa95eca\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/865\"\u003e#865\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/451edbcd2fa5bda6aa0ed17b44c97788a1486b49\"\u003e\u003ccode\u003e451edbc\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/522864b60c00006ce96d9440f145b9ed3a7d028a\"\u003e\u003ccode\u003e522864b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/864\"\u003e#864\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ae68856e1eeafef64e35aad20ece358947393965\"\u003e\u003ccode\u003eae68856\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b490690cbb0156a62509786d8f9f144aa12c5ab2\"\u003e\u003ccode\u003eb490690\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/860\"\u003e#860\u003c/a\u003e from ImperialCollegeLondon/704-the-plantsmodel-is-pre...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2aa2bdd0b26127aaee9fed1344d3a8856c570ab8\"\u003e\u003ccode\u003e2aa2bdd\u003c/code\u003e\u003c/a\u003e documentation updated\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/dbfe9e4caa7606bd445f4c58a025f8682ea207d7\"\u003e\u003ccode\u003edbfe9e4\u003c/code\u003e\u003c/a\u003e added canopy_evaporation to conftest\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a38024fd5d790ab6c8adf731a2926ddac8cd2fb7\"\u003e\u003ccode\u003ea38024f\u003c/code\u003e\u003c/a\u003e updated hydrology model to transpiration\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/55107956c9f4c6c1033e711dac3197904984e3f0\"\u003e\u003ccode\u003e5510795\u003c/code\u003e\u003c/a\u003e changed to transpiration in plant model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/356056bb33f35834093e9886a071fadd011bc1ec\"\u003e\u003ccode\u003e356056b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/856\"\u003e#856\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...aa95eca74460a15189d045f6f800df275b0abddd\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/76","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/76","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/76/packages"},{"uuid":"3057974811","node_id":"PR_kwDOKCm6f86V5Drc","number":75,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `356056b`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-05-19T19:15:51.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-12T19:53:01.000Z","updated_at":"2025-05-19T19:15:52.000Z","time_to_close":602570,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`356056b`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `356056b`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/356056bb33f35834093e9886a071fadd011bc1ec\"\u003e\u003ccode\u003e356056b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/856\"\u003e#856\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c5633a5c88ddd28bf811296fcb3e59fb00c171c0\"\u003e\u003ccode\u003ec5633a5\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/691fd3422f3fd2946e7848cd9fe3a25596babe31\"\u003e\u003ccode\u003e691fd34\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/854\"\u003e#854\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b6e238aa82ef9f14141384ebaf7d1c721c340542\"\u003e\u003ccode\u003eb6e238a\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/15ac423ccd4371756a1581bf3ede5870e07a7ee9\"\u003e\u003ccode\u003e15ac423\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/853\"\u003e#853\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/af138702a42bf90da6d7d37f8e49655d2ea86616\"\u003e\u003ccode\u003eaf13870\u003c/code\u003e\u003c/a\u003e Bump scipy from 1.15.2 to 1.15.3 in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/04bcf1299e22815966e3567603b949440bf5e457\"\u003e\u003ccode\u003e04bcf12\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/850\"\u003e#850\u003c/a\u003e from ImperialCollegeLondon/849-remove-duplicated-cons...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/dce08d39cf94080ad33aca553685cf74ed2cd7bc\"\u003e\u003ccode\u003edce08d3\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 849-remove-duplicated-constant\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/bd4c1f6e45aa93eb9d00a90ff0fbad42f9648654\"\u003e\u003ccode\u003ebd4c1f6\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/852\"\u003e#852\u003c/a\u003e from ImperialCollegeLondon/851-busted-value-of-tmodel...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ba2fdeb8f93ca442fac78340908a798f55e5942c\"\u003e\u003ccode\u003eba2fdeb\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 849-remove-duplicated-constant\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...356056bb33f35834093e9886a071fadd011bc1ec\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/75","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/75","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/75/packages"},{"uuid":"3040619534","node_id":"PR_kwDOKCm6f86U_RDg","number":70,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `4e823b8`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-05-12T19:53:04.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-05T19:30:36.000Z","updated_at":"2025-05-12T19:53:04.000Z","time_to_close":606148,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`4e823b8`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `4e823b8`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4e823b8c4d5d46f91f3aab169d2ffc4c0c5f3003\"\u003e\u003ccode\u003e4e823b8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/841\"\u003e#841\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c6181ad0435eb658f8ce5232418316124771145e\"\u003e\u003ccode\u003ec6181ad\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b6d4cd09399dbd0ef8a56cf997cc006becc21005\"\u003e\u003ccode\u003eb6d4cd0\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/840\"\u003e#840\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/8627b9f1faa7ed6975af2f3753fd77061de049bd\"\u003e\u003ccode\u003e8627b9f\u003c/code\u003e\u003c/a\u003e Bump ruff from 0.11.7 to 0.11.8 in the development-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a405a7c8a68fd3b3a135cb26b1a4269996bfd313\"\u003e\u003ccode\u003ea405a7c\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/839\"\u003e#839\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1c59b77c067e87f59bb21c62a77a8deadc4c2465\"\u003e\u003ccode\u003e1c59b77\u003c/code\u003e\u003c/a\u003e Bump xarray in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/343bbcdf45f5c05145fbe14026132f23b56c98ce\"\u003e\u003ccode\u003e343bbcd\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/838\"\u003e#838\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a97625a8f2da32fa120e9b75937712d3928ee6d3\"\u003e\u003ccode\u003ea97625a\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] auto fixes from pre-commit.com hooks\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5ef9e55638012e367ef52dd3d91f52fa5abaca1d\"\u003e\u003ccode\u003e5ef9e55\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1b8e57f3ca95682d5f3b071c063385fa3561f92a\"\u003e\u003ccode\u003e1b8e57f\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/837\"\u003e#837\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...4e823b8c4d5d46f91f3aab169d2ffc4c0c5f3003\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/70","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/70","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/70/packages"}],"issue_packages":[{"old_version":"`78b18b5`","new_version":"`035163b`","update_type":null,"path":null,"pr_created_at":"2025-12-01T22:26:17.000Z","version_change":"`78b18b5` → `035163b`","issue":{"uuid":"3683123391","node_id":"PR_kwDOKCm6f862dYX0","number":147,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `035163b`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-12-08T19:05:33.000Z","author_association":null,"state_reason":null,"created_at":"2025-12-01T22:26:17.000Z","updated_at":"2025-12-08T19:05:34.000Z","time_to_close":592756,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`035163b`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `035163b`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/035163b20b50b956988a7fbfa664f47be83d8c98\"\u003e\u003ccode\u003e035163b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1163\"\u003e#1163\u003c/a\u003e from ImperialCollegeLondon/bugfix/symbiotic_supply_l...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/274facff06b09a870042a2227f30e20e98599eaf\"\u003e\u003ccode\u003e274facf\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into bugfix/symbiotic_supply_limits\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c7ed97185b4299412f3c43feb4575001bf3923b7\"\u003e\u003ccode\u003ec7ed971\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1166\"\u003e#1166\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6e96b087ede617c689d8c4ede83b7da17218885f\"\u003e\u003ccode\u003e6e96b08\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9779436506b8234c5a409b4859e5a0955ab0aeb5\"\u003e\u003ccode\u003e9779436\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1167\"\u003e#1167\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-55c...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/279b12089dd6991965c294c92460269ffaec3da0\"\u003e\u003ccode\u003e279b120\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-mermaid from 1.1.0 to 1.2.3 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1bcbca88e3b4109ccd84dc971f4f892833a70428\"\u003e\u003ccode\u003e1bcbca8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1165\"\u003e#1165\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/416908faa870e81c493938fa89774e1edc00d23f\"\u003e\u003ccode\u003e416908f\u003c/code\u003e\u003c/a\u003e Bump pydantic from 2.12.4 to 2.12.5 in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/77524da427af732d2ff9bf04c38c2dcd4003fc2a\"\u003e\u003ccode\u003e77524da\u003c/code\u003e\u003c/a\u003e Added TODO about air temperatures not being populated on init to the AbioticS...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/80b3f00448a36fd7a218e04878ec2c5523c923dd\"\u003e\u003ccode\u003e80b3f00\u003c/code\u003e\u003c/a\u003e Merge branch 'bugfix/symbiotic_supply_limits' of \u003ca href=\"https://github.com/ImperialC\"\u003ehttps://github.com/ImperialC\u003c/a\u003e...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...035163b20b50b956988a7fbfa664f47be83d8c98\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/147","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/147","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/147/packages"}},{"old_version":"`78b18b5`","new_version":"`12e54e5`","update_type":null,"path":null,"pr_created_at":"2025-11-24T19:28:28.000Z","version_change":"`78b18b5` → `12e54e5`","issue":{"uuid":"3660243726","node_id":"PR_kwDOKCm6f861RUmT","number":146,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `12e54e5`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-12-01T22:26:20.000Z","author_association":null,"state_reason":null,"created_at":"2025-11-24T19:28:28.000Z","updated_at":"2025-12-01T22:26:22.000Z","time_to_close":615472,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`12e54e5`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `12e54e5`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/12e54e5278e59feb00805056a8eabd3730379576\"\u003e\u003ccode\u003e12e54e5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1160\"\u003e#1160\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/fa1a83be7fc419f567db7aa035ee65a73bd0b5aa\"\u003e\u003ccode\u003efa1a83b\u003c/code\u003e\u003c/a\u003e Bump actions/checkout from 5 to 6\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c998837aead47212a89b352cd2cf8453a240a6ff\"\u003e\u003ccode\u003ec998837\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1158\"\u003e#1158\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4f402ec5bd83d5e2fa9ef55b7dff15cd062ccaa9\"\u003e\u003ccode\u003e4f402ec\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7f2b197d916e368ee8a49d66a9c13a356c4eba0c\"\u003e\u003ccode\u003e7f2b197\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1159\"\u003e#1159\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-a4c...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d7a6824d0fb50fee80b1d8f446c908f0970d233f\"\u003e\u003ccode\u003ed7a6824\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-mermaid from 1.0.0 to 1.1.0 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f0228b7b16e6914ba0ea256c50aa0c3fdc97fcb3\"\u003e\u003ccode\u003ef0228b7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1157\"\u003e#1157\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a07cf4f0542b11b47ddbd887bfefd63457a48fe6\"\u003e\u003ccode\u003ea07cf4f\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/98f2629b71c3e8939a26c157c98b331bf4ff00d3\"\u003e\u003ccode\u003e98f2629\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1156\"\u003e#1156\u003c/a\u003e from ImperialCollegeLondon/484-abiotic-simple---atmo...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/31a5ff5f6444c9ef18555970ed7e329b39c15734\"\u003e\u003ccode\u003e31a5ff5\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 484-abiotic-simple---atmospheric-pressure-and-co2...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...12e54e5278e59feb00805056a8eabd3730379576\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/146","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/146","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/146/packages"}},{"old_version":"`78b18b5`","new_version":"`f93d9d2`","update_type":null,"path":null,"pr_created_at":"2025-11-10T19:06:52.000Z","version_change":"`78b18b5` → `f93d9d2`","issue":{"uuid":"3609325012","node_id":"PR_kwDOKCm6f86ymfdS","number":143,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `f93d9d2`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-11-17T19:07:50.000Z","author_association":null,"state_reason":null,"created_at":"2025-11-10T19:06:52.000Z","updated_at":"2025-11-17T19:07:52.000Z","time_to_close":604858,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`f93d9d2`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `f93d9d2`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f93d9d2be3cf0dbd97e9c0145f81293aad3510df\"\u003e\u003ccode\u003ef93d9d2\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1145\"\u003e#1145\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/aa78dde96620ef97461a2f51d3f8073494b4bae0\"\u003e\u003ccode\u003eaa78dde\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/03935e099aac52b5cb3ced8a36adf166a1ab346e\"\u003e\u003ccode\u003e03935e0\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1144\"\u003e#1144\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d131e3a232c19e6934408a3481b668758e31b1d7\"\u003e\u003ccode\u003ed131e3a\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0fefce4ec5b873213e683a27575fa119075dfe9a\"\u003e\u003ccode\u003e0fefce4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1143\"\u003e#1143\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4deec5a9d9cfc9f7f0ab31f8e727c411aef5e6a8\"\u003e\u003ccode\u003e4deec5a\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1a0ea4b40b5210245390906ea118bea42d895717\"\u003e\u003ccode\u003e1a0ea4b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1138\"\u003e#1138\u003c/a\u003e from ImperialCollegeLondon/1136-simplify-model-regis...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e95f355caddd1d59a55381ba4079e44a2895828d\"\u003e\u003ccode\u003ee95f355\u003c/code\u003e\u003c/a\u003e Adding naming convention notes, test fix\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/71064bc45ec7654081b27338dcfac30d2b58a422\"\u003e\u003ccode\u003e71064bc\u003c/code\u003e\u003c/a\u003e Removing docs on root import of BaseModel\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f6beff384eed827d98bf6a53d6236573d46b60cd\"\u003e\u003ccode\u003ef6beff3\u003c/code\u003e\u003c/a\u003e Forgot to add file\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...f93d9d2be3cf0dbd97e9c0145f81293aad3510df\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/143","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/143","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/143/packages"}},{"old_version":"`78b18b5`","new_version":"`7dc6f06`","update_type":null,"path":null,"pr_created_at":"2025-10-06T19:05:57.000Z","version_change":"`78b18b5` → `7dc6f06`","issue":{"uuid":"2891492585","node_id":"PR_kwDOKCm6f86sWKzp","number":130,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `7dc6f06`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-10-06T19:05:57.000Z","updated_at":"2025-10-06T19:05:58.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`7dc6f06`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `7dc6f06`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7dc6f060ccf25bd62a2564dc4c79fa87c450064d\"\u003e\u003ccode\u003e7dc6f06\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1074\"\u003e#1074\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b34184ea0ea3f6649f952fc95b7d1f94df98f8cb\"\u003e\u003ccode\u003eb34184e\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/745f4b3a7b1c59e638a0c10a45524a079e443ab0\"\u003e\u003ccode\u003e745f4b3\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1066\"\u003e#1066\u003c/a\u003e from ImperialCollegeLondon/1041-move-initial-plant-c...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/537d26314b06e5bdcee1a2614ace53df3644299a\"\u003e\u003ccode\u003e537d263\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 1041-move-initial-plant-cohort-data\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/10d4bc4566d59780dc01d7aa72c0ddc0f7cae810\"\u003e\u003ccode\u003e10d4bc4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1043\"\u003e#1043\u003c/a\u003e from ImperialCollegeLondon/1033-bug-in-accumulated-r...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/8388d9f22eba1a6675024b6ca0c1724fce1090e9\"\u003e\u003ccode\u003e8388d9f\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 1033-bug-in-accumulated-runoff\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c616b53911fa47a080a4825e76668f49f31c68fe\"\u003e\u003ccode\u003ec616b53\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1072\"\u003e#1072\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c7b2c7a97b27b2a03434d5f3ef2204c032e50bb5\"\u003e\u003ccode\u003ec7b2c7a\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9ad8b0e251cd7db4ae21509b8aa8e5f6b287f660\"\u003e\u003ccode\u003e9ad8b0e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1071\"\u003e#1071\u003c/a\u003e from ImperialCollegeLondon/1058-integrate-subcanopy-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/88ee1cb92062bf653001d01441ae78f4c01287ab\"\u003e\u003ccode\u003e88ee1cb\u003c/code\u003e\u003c/a\u003e Started removing subcanopy uptake from the appropriate soil pools\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...7dc6f060ccf25bd62a2564dc4c79fa87c450064d\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/130","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/130","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/130/packages"}},{"old_version":"`78b18b5`","new_version":"`09332ea`","update_type":null,"path":null,"pr_created_at":"2025-09-15T19:05:46.000Z","version_change":"`78b18b5` → `09332ea`","issue":{"uuid":"2830331762","node_id":"PR_kwDOKCm6f86os29y","number":120,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `09332ea`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-09-22T19:06:11.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-15T19:05:46.000Z","updated_at":"2025-09-22T19:06:11.000Z","time_to_close":604825,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`09332ea`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `09332ea`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/09332ea49372a979204d12ab9801c8f4839ff6f7\"\u003e\u003ccode\u003e09332ea\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1042\"\u003e#1042\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/41be846eba77e7a24666ba3f169b02849c435350\"\u003e\u003ccode\u003e41be846\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/35ef062043a3874ecd759c4c89d48cfbbd6560f7\"\u003e\u003ccode\u003e35ef062\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1030\"\u003e#1030\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ed74b101b28c493155e13a60c8e5f5b298f48f00\"\u003e\u003ccode\u003eed74b10\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into dependabot/pip/development-dependencies-47fb0c18d6\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a7d8b1680733def8ee0eb3ced9cc61ff27140b93\"\u003e\u003ccode\u003ea7d8b16\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1031\"\u003e#1031\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/588a4222dc16683374b82637b145ee57ddcfb227\"\u003e\u003ccode\u003e588a422\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/53410d88e2f014895d0174a3a938c0b5252d54f7\"\u003e\u003ccode\u003e53410d8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1029\"\u003e#1029\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ded6d49a5d2c2da1b0627374cc9e80ac7a5698b5\"\u003e\u003ccode\u003eded6d49\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group across 1 directory with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/81dc7e64d8a45cc6f882decb5b5bcc5621cfce96\"\u003e\u003ccode\u003e81dc7e6\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into dependabot/github_actions/actions/setup-python-6\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/502b88d18011f04bb84903d51a92cb568fe829a2\"\u003e\u003ccode\u003e502b88d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/827\"\u003e#827\u003c/a\u003e from ImperialCollegeLondon/824-recruitment-of-new-tre...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...09332ea49372a979204d12ab9801c8f4839ff6f7\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/120","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/120","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/120/packages"}},{"old_version":"`78b18b5`","new_version":"`47ce912`","update_type":null,"path":null,"pr_created_at":"2025-08-26T11:55:50.000Z","version_change":"`78b18b5` → `47ce912`","issue":{"uuid":"2774881495","node_id":"PR_kwDOKCm6f86lZVTX","number":111,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `47ce912`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-26T11:55:50.000Z","updated_at":"2025-08-26T11:55:51.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`47ce912`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `47ce912`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/47ce9123c7db7b819220f0698fe79b489663ecaa\"\u003e\u003ccode\u003e47ce912\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1008\"\u003e#1008\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/eccb818aba91abc655618a5f9bf3cb6ad61c0594\"\u003e\u003ccode\u003eeccb818\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/bff4ac242960a015112ff048803e7a40542dcc44\"\u003e\u003ccode\u003ebff4ac2\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1007\"\u003e#1007\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7f23e7d2800ff87db59140933796c0f435e8094b\"\u003e\u003ccode\u003e7f23e7d\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/61f557aaf994e9c685c01afc930c7d2daf2a9f8e\"\u003e\u003ccode\u003e61f557a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1005\"\u003e#1005\u003c/a\u003e from ImperialCollegeLondon/1002-bulk-density-is-defi...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a0cd133cd0cabb2ad1e9d9084dc6d05ccbc6f729\"\u003e\u003ccode\u003ea0cd133\u003c/code\u003e\u003c/a\u003e Removed bulk density from the soil model as it isn't actually used\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/8e4416d867f21f43a000f9ecc4ef8780586cf7cd\"\u003e\u003ccode\u003e8e4416d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1004\"\u003e#1004\u003c/a\u003e from ImperialCollegeLondon/536-add-check-for-nan-val...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/981e29bd8383ef43c5c7e33c192fabb51bce0939\"\u003e\u003ccode\u003e981e29b\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 536-add-check-for-nan-values-before-running-the-s...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/bd4934139aa1cde5d791973f9416a987c09e3d19\"\u003e\u003ccode\u003ebd49341\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1001\"\u003e#1001\u003c/a\u003e from ImperialCollegeLondon/979-integration-of-the-li...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/52474f4a4ad1e87ea524e8303cc5c7d3ac99972b\"\u003e\u003ccode\u003e52474f4\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 979-integration-of-the-litter-model-needs-to-be-i...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...47ce9123c7db7b819220f0698fe79b489663ecaa\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/111","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/111","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/111/packages"}},{"old_version":"`78b18b5`","new_version":"`c051224`","update_type":null,"path":null,"pr_created_at":"2025-08-19T06:19:15.000Z","version_change":"`78b18b5` → `c051224`","issue":{"uuid":"2755310681","node_id":"PR_kwDOKCm6f86kOrRZ","number":109,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `c051224`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-19T06:19:15.000Z","updated_at":"2025-08-19T06:19:16.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`c051224`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `c051224`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c05122447b364fd77f31c4be7ec4021a6a1c492b\"\u003e\u003ccode\u003ec051224\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1003\"\u003e#1003\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5b06dcb9fdd3804619d790140123641e8508072b\"\u003e\u003ccode\u003e5b06dcb\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/48c3562b9824443f29e04da4aa84f0e66cdcfa7b\"\u003e\u003ccode\u003e48c3562\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/1000\"\u003e#1000\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/developmen...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ca55541dd110ffca233eaaf1a305c3cd5a5cd23c\"\u003e\u003ccode\u003eca55541\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/266dbe60687aee96eb336be760a10af39d53eae0\"\u003e\u003ccode\u003e266dbe6\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/990\"\u003e#990\u003c/a\u003e from ImperialCollegeLondon/989-foraging-methods-refac...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/02702b328de26787775eabc40ba0bfb30e4180aa\"\u003e\u003ccode\u003e02702b3\u003c/code\u003e\u003c/a\u003e Removed some unecessary error checks.\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/befc645859b78aee17b9ca342e5773c81d2580b7\"\u003e\u003ccode\u003ebefc645\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 989-foraging-methods-refactor-to-reduce-resuse\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3b4c74a6aba9842e3556bbd1119f95369476c7c2\"\u003e\u003ccode\u003e3b4c74a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/994\"\u003e#994\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0c76fc47a7a72ecf78197b86834fc1198123beff\"\u003e\u003ccode\u003e0c76fc4\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d026cee2625f77320f55ecd7e978c27c6872ed48\"\u003e\u003ccode\u003ed026cee\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/993\"\u003e#993\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions/...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...c05122447b364fd77f31c4be7ec4021a6a1c492b\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/109","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/109","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/109/packages"}},{"old_version":"`78b18b5`","new_version":"`3b4c74a`","update_type":null,"path":null,"pr_created_at":"2025-08-12T03:01:39.000Z","version_change":"`78b18b5` → `3b4c74a`","issue":{"uuid":"2737491022","node_id":"PR_kwDOKCm6f86jKsxO","number":104,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `3b4c74a`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-08-19T06:19:17.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-12T03:01:39.000Z","updated_at":"2025-08-19T06:19:17.000Z","time_to_close":616658,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3b4c74a`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3b4c74a`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3b4c74a6aba9842e3556bbd1119f95369476c7c2\"\u003e\u003ccode\u003e3b4c74a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/994\"\u003e#994\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0c76fc47a7a72ecf78197b86834fc1198123beff\"\u003e\u003ccode\u003e0c76fc4\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d026cee2625f77320f55ecd7e978c27c6872ed48\"\u003e\u003ccode\u003ed026cee\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/993\"\u003e#993\u003c/a\u003e from ImperialCollegeLondon/dependabot/github_actions/...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4dee4e807eb20a17ee21d5fe80112d609f5b6c4b\"\u003e\u003ccode\u003e4dee4e8\u003c/code\u003e\u003c/a\u003e Bump actions/download-artifact from 4 to 5\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ec777d3ae33d37a77df1f7a23e48e97c03b15311\"\u003e\u003ccode\u003eec777d3\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/992\"\u003e#992\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3071e5e23f58077feead5a88cc5929efb23bbe80\"\u003e\u003ccode\u003e3071e5e\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 6 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3f830d43bdba60defb4e742dcc86822caf1a484f\"\u003e\u003ccode\u003e3f830d4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/947\"\u003e#947\u003c/a\u003e from ImperialCollegeLondon/814-microbial-community-do...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/399c54cf1563b7c817f919c3aab041eb0caafc85\"\u003e\u003ccode\u003e399c54c\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 814-microbial-community-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0861c9548d48dbea1033604e1631501bb653df77\"\u003e\u003ccode\u003e0861c95\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/985\"\u003e#985\u003c/a\u003e from ImperialCollegeLondon/release/v0.1.1a12\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c54ba454b0386318c9e74d02d18b8445f2e6726f\"\u003e\u003ccode\u003ec54ba45\u003c/code\u003e\u003c/a\u003e Dumping abatilo poetry action\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3b4c74a6aba9842e3556bbd1119f95369476c7c2\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/104","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/104","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/104/packages"}},{"old_version":"`78b18b5`","new_version":"`0c4f449`","update_type":null,"path":null,"pr_created_at":"2025-08-05T02:45:55.000Z","version_change":"`78b18b5` → `0c4f449`","issue":{"uuid":"2719680150","node_id":"PR_kwDOKCm6f86iGwaW","number":103,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `0c4f449`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-08-05T02:45:55.000Z","updated_at":"2025-08-05T02:45:56.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`0c4f449`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `0c4f449`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0c4f44998500e3a5766a8e8b96e84de171a4516a\"\u003e\u003ccode\u003e0c4f449\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/984\"\u003e#984\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7df4f00ecd12394b99693fc1746de5cd66709ff5\"\u003e\u003ccode\u003e7df4f00\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3df9e7ac3048228b8d3df58349d7232459b62e2b\"\u003e\u003ccode\u003e3df9e7a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/981\"\u003e#981\u003c/a\u003e from ImperialCollegeLondon/980-unpin-the-update-inter...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d9d13f35fa46d983b203325cd3261381a0fa8495\"\u003e\u003ccode\u003ed9d13f3\u003c/code\u003e\u003c/a\u003e Updates from \u003ca href=\"https://github.com/vgro\"\u003e\u003ccode\u003e@​vgro\u003c/code\u003e\u003c/a\u003e comments\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2a13f4ba5945dff490179729d24b6d7796f11f0b\"\u003e\u003ccode\u003e2a13f4b\u003c/code\u003e\u003c/a\u003e pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7f679d1f4d2575d87a976f899218669ec4c4f2d5\"\u003e\u003ccode\u003e7f679d1\u003c/code\u003e\u003c/a\u003e More typing fixes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e91c152ca5f70ff0e42a01ab9bcb5358e6397f2f\"\u003e\u003ccode\u003ee91c152\u003c/code\u003e\u003c/a\u003e Restoring old pre-commit mypy settings - not sure why they disappeared\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5fe1fe68d6025e4e29f517e293d52e389611c474\"\u003e\u003ccode\u003e5fe1fe6\u003c/code\u003e\u003c/a\u003e mypy fixes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/05e0874fbf0a47f4832c051d24ea952b65c86b27\"\u003e\u003ccode\u003e05e0874\u003c/code\u003e\u003c/a\u003e Adding types-tabulate to pre-commit\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0cde14d6012e24043db5b39615f738eb92a176d1\"\u003e\u003ccode\u003e0cde14d\u003c/code\u003e\u003c/a\u003e Adding types-tabulate - not sure why this is needed now\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...0c4f44998500e3a5766a8e8b96e84de171a4516a\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/103","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/103","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/103/packages"}},{"old_version":"`78b18b5`","new_version":"`7988df5`","update_type":null,"path":null,"pr_created_at":"2025-07-21T21:51:12.000Z","version_change":"`78b18b5` → `7988df5`","issue":{"uuid":"2683267681","node_id":"PR_kwDOKCm6f86f72ph","number":98,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `7988df5`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-08-05T02:45:57.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-07-21T21:51:12.000Z","updated_at":"2025-08-05T02:45:57.000Z","time_to_close":1227285,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`7988df5`","repository_url":null}],"path":null,"ecosystem":"submodules"},"body":"\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/98","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/98","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/98/packages"}},{"old_version":"`78b18b5`","new_version":"`3be034e`","update_type":null,"path":null,"pr_created_at":"2025-07-14T23:36:25.000Z","version_change":"`78b18b5` → `3be034e`","issue":{"uuid":"2665641546","node_id":"PR_kwDOKCm6f86e4nZK","number":97,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `3be034e`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-07-14T23:36:25.000Z","updated_at":"2025-07-14T23:36:26.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3be034e`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3be034e`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3be034ed11c208002276d7e8d3f0ad26fde93443\"\u003e\u003ccode\u003e3be034e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/951\"\u003e#951\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7284d54ec6b04fb70b82209dbd379990b4aae117\"\u003e\u003ccode\u003e7284d54\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6fabd1511271dfe251bd6b9a70946a1fff0cbfa6\"\u003e\u003ccode\u003e6fabd15\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/946\"\u003e#946\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/caa09ddab1fdb73a3ed2bd245896250832ecd917\"\u003e\u003ccode\u003ecaa09dd\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d71b8e35b7ec37269ee766df867185428773b5ff\"\u003e\u003ccode\u003ed71b8e3\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/938\"\u003e#938\u003c/a\u003e from ImperialCollegeLondon/937-add-vertical-structure...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7034bcecaf867ac367a4f7fabd3d241e3ba734a2\"\u003e\u003ccode\u003e7034bce\u003c/code\u003e\u003c/a\u003e typos fixed\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/385a5bad321ce27edab3b1ecd35052a39d7e4b81\"\u003e\u003ccode\u003e385a5ba\u003c/code\u003e\u003c/a\u003e Merge branch '937-add-vertical-structure-graphic-to-hydrology-model' of https...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/837313f548fc911321378a3eec35c2b23c5dc6d6\"\u003e\u003ccode\u003e837313f\u003c/code\u003e\u003c/a\u003e replaced bucket model graph to account for throughflow\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/da7f1cbbf8c60ddc008e7a38902bb901ee29fb28\"\u003e\u003ccode\u003eda7f1cb\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 937-add-vertical-structure-graphic-to-hydrology-m...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/92145eb10b9790ae3d89aa054985d8249ded8a2b\"\u003e\u003ccode\u003e92145eb\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/942\"\u003e#942\u003c/a\u003e from ImperialCollegeLondon/feature/publication_workfl...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3be034ed11c208002276d7e8d3f0ad26fde93443\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/97","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/97","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/97/packages"}},{"old_version":"`78b18b5`","new_version":"`4e6ce4e`","update_type":null,"path":null,"pr_created_at":"2025-06-30T22:24:04.000Z","version_change":"`78b18b5` → `4e6ce4e`","issue":{"uuid":"2630293586","node_id":"PR_kwDOKCm6f86cxxhS","number":92,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `4e6ce4e`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-30T22:24:04.000Z","updated_at":"2025-06-30T22:24:05.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`4e6ce4e`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `4e6ce4e`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4e6ce4ed43cf6e5b2514650c5807ad0a039e0745\"\u003e\u003ccode\u003e4e6ce4e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/922\"\u003e#922\u003c/a\u003e from ImperialCollegeLondon/918-update-pyrealm-version\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3471fd0cb1fb64641e86dcf003017246fa317fae\"\u003e\u003ccode\u003e3471fd0\u003c/code\u003e\u003c/a\u003e Resolving poetry.lock\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c5a08892bfdea5b9e4ea384212f0d5e6c2d7cbf7\"\u003e\u003ccode\u003ec5a0889\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/926\"\u003e#926\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-c732...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/541bf64d51c41e487d332dbc5e419a217f5839b3\"\u003e\u003ccode\u003e541bf64\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-bibtex from 2.6.4 to 2.6.5 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a87faa90e9f68d323f14cc2625033c7762a2bcda\"\u003e\u003ccode\u003ea87faa9\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/925\"\u003e#925\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/52b70db250f34fcbb5f2af96b4e742463131d2ed\"\u003e\u003ccode\u003e52b70db\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/75fc2baa3a61b697027bbdfa186c33a2a082a175\"\u003e\u003ccode\u003e75fc2ba\u003c/code\u003e\u003c/a\u003e Merge branch '918-update-pyrealm-version' of \u003ca href=\"https://github.com/ImperialColle\"\u003ehttps://github.com/ImperialColle\u003c/a\u003e...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f4aa114ce3f69a3f8bc31492632525a51967a07b\"\u003e\u003ccode\u003ef4aa114\u003c/code\u003e\u003c/a\u003e Comment tweaks\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c8b4b71ff705de7ed00e4f0fd215e40987143cc9\"\u003e\u003ccode\u003ec8b4b71\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 918-update-pyrealm-version\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e11d18b59c237162cc640555e564f50dba7f2a3c\"\u003e\u003ccode\u003ee11d18b\u003c/code\u003e\u003c/a\u003e Hacking tree stems to prevent D \u0026lt;= 0\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...4e6ce4ed43cf6e5b2514650c5807ad0a039e0745\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/92","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/92","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/92/packages"}},{"old_version":"`78b18b5`","new_version":"`3bd0e9b`","update_type":null,"path":null,"pr_created_at":"2025-06-23T21:52:23.000Z","version_change":"`78b18b5` → `3bd0e9b`","issue":{"uuid":"2612881239","node_id":"PR_kwDOKCm6f86bvWdX","number":91,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `3bd0e9b`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-23T21:52:23.000Z","updated_at":"2025-06-23T21:52:24.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3bd0e9b`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3bd0e9b`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3bd0e9bf857fa7268a87732fd757df951b681bcb\"\u003e\u003ccode\u003e3bd0e9b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/915\"\u003e#915\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/sphinx-fa20...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ba1e0cd0ccf302f98f5281285a30dd8f2cdc72c8\"\u003e\u003ccode\u003eba1e0cd\u003c/code\u003e\u003c/a\u003e Bump sphinxcontrib-bibtex from 2.6.3 to 2.6.4 in the sphinx group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/88667f83c41c2502869abf5e85d8bd03ee57b177\"\u003e\u003ccode\u003e88667f8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/914\"\u003e#914\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d35bb77ab74fe19ef32d3066b18b6826c88e57df\"\u003e\u003ccode\u003ed35bb77\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/21a56362089d6b864070859ed2022bd06613a032\"\u003e\u003ccode\u003e21a5636\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/906\"\u003e#906\u003c/a\u003e from ImperialCollegeLondon/888-animal-model---foragin...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1843cb7037579d1d615f7b29951af414b3e90520\"\u003e\u003ccode\u003e1843cb7\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 888-animal-model---foraging-time-budget\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/422be4cd156cc169a41dd6ad9f4c82d9711d6712\"\u003e\u003ccode\u003e422be4c\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/903\"\u003e#903\u003c/a\u003e from ImperialCollegeLondon/902-better-control-of-ve_r...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7eb42153147a5795ce6eddfccf0b9b76f9ec1962\"\u003e\u003ccode\u003e7eb4215\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 902-better-control-of-ve_run-screen-output\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a90a7b85fb90609b59532218e765f1ad5c6e0f76\"\u003e\u003ccode\u003ea90a7b8\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 888-animal-model---foraging-time-budget\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/730109dadafce92a4cfa731ac2f131eb7070493b\"\u003e\u003ccode\u003e730109d\u003c/code\u003e\u003c/a\u003e Revised tests for foraging.\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3bd0e9bf857fa7268a87732fd757df951b681bcb\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/91","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/91","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/91/packages"}},{"old_version":"`78b18b5`","new_version":"`c2aa4b5`","update_type":null,"path":null,"pr_created_at":"2025-06-16T22:07:35.000Z","version_change":"`78b18b5` → `c2aa4b5`","issue":{"uuid":"2597033191","node_id":"PR_kwDOKCm6f86ay5Tn","number":86,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `c2aa4b5`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-16T22:07:35.000Z","updated_at":"2025-06-16T22:07:36.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`c2aa4b5`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `c2aa4b5`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c2aa4b52c34ee6db05cb0862378d7eafcdc9eeab\"\u003e\u003ccode\u003ec2aa4b5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/894\"\u003e#894\u003c/a\u003e from ImperialCollegeLondon/887-animal-model---handlin...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/46ea0a83d90ae5efda50626ed32f89794577b309\"\u003e\u003ccode\u003e46ea0a8\u003c/code\u003e\u003c/a\u003e Rerouted update_cohort_bookkeeping to use the community level methods instead...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c9057261ab8face4e331f44e6ff8bf5b2eede247\"\u003e\u003ccode\u003ec905726\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 887-animal-model---handling-starvation-during-ont...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5a4188956acb15add6ca0bc341ae518a849f9fdc\"\u003e\u003ccode\u003e5a41889\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/893\"\u003e#893\u003c/a\u003e from ImperialCollegeLondon/890-mycorrhizal-fungi-shou...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2e02f976fa18ab14ede59e52884aa4f88015620a\"\u003e\u003ccode\u003e2e02f97\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 890-mycorrhizal-fungi-should-be-obligate-rather-t...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3327f933aebe72a9be72d84a4d7fb0e875ac7dd8\"\u003e\u003ccode\u003e3327f93\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/896\"\u003e#896\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/0b54a9d2235c8f266fddb81c580b4806fb780c3b\"\u003e\u003ccode\u003e0b54a9d\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f649836fdb635f68152daf9c9b0f0c77972ae903\"\u003e\u003ccode\u003ef649836\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/895\"\u003e#895\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/90a0b893d61b13a10a5ef0b58d4491d75b882dd8\"\u003e\u003ccode\u003e90a0b89\u003c/code\u003e\u003c/a\u003e Bump xarray in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/e41b430f310230c66ca93f9efa79702f547c3e5c\"\u003e\u003ccode\u003ee41b430\u003c/code\u003e\u003c/a\u003e Added test for handle_ontogeny.\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...c2aa4b52c34ee6db05cb0862378d7eafcdc9eeab\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/86","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/86","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/86/packages"}},{"old_version":"`78b18b5`","new_version":"`7c06369`","update_type":null,"path":null,"pr_created_at":"2025-06-09T19:32:00.000Z","version_change":"`78b18b5` → `7c06369`","issue":{"uuid":"2579262471","node_id":"PR_kwDOKCm6f86ZvGwH","number":84,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `7c06369`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-06-16T22:07:37.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-09T19:32:00.000Z","updated_at":"2025-06-16T22:07:37.000Z","time_to_close":614137,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`7c06369`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `7c06369`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/7c06369ba3fb9cff9c6d2548b7274684bc1433f7\"\u003e\u003ccode\u003e7c06369\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/889\"\u003e#889\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/14eaac7d4c5211f36ba9a356312446a467a8e120\"\u003e\u003ccode\u003e14eaac7\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 5 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/36041884332c058b1e3b3abe719b53f93475442f\"\u003e\u003ccode\u003e3604188\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/886\"\u003e#886\u003c/a\u003e from ImperialCollegeLondon/885-need-to-handle-zero-ra...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/39717b4308fcff5fbd94d2355e937a583a227fc3\"\u003e\u003ccode\u003e39717b4\u003c/code\u003e\u003c/a\u003e Added handling so that carbon limitation is calculated coreectly when max rat...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2632c709a12ff5054c2f6ae33c51e208471c0d54\"\u003e\u003ccode\u003e2632c70\u003c/code\u003e\u003c/a\u003e Added step to ignore divide by zero warnings when they had already been handl...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9b23fa5e9a64014402c20e30955212b93a4b8d27\"\u003e\u003ccode\u003e9b23fa5\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/884\"\u003e#884\u003c/a\u003e from ImperialCollegeLondon/883-soil-model-implementat...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/d3b70289280fb4ce3b905f83cec28eef1f26c93b\"\u003e\u003ccode\u003ed3b7028\u003c/code\u003e\u003c/a\u003e Changed var_populated_by_update section of soil implementation docs to reflec...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/9edcb351c52e6c189da57da9397c75d0fc044f63\"\u003e\u003ccode\u003e9edcb35\u003c/code\u003e\u003c/a\u003e Added basic page for implementation with output variables and a TODO about fi...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5e3ceef60e6614b560dc50f8e98cec7e1a0dc6a6\"\u003e\u003ccode\u003e5e3ceef\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/881\"\u003e#881\u003c/a\u003e from ImperialCollegeLondon/770-function-to-calculate-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/f3d12f3bdda5127392871fc202087818621e0b5f\"\u003e\u003ccode\u003ef3d12f3\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 770-function-to-calculate-the-effective-saturatio...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...7c06369ba3fb9cff9c6d2548b7274684bc1433f7\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/84","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/84","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/84/packages"}},{"old_version":"`78b18b5`","new_version":"`3c5d746`","update_type":null,"path":null,"pr_created_at":"2025-06-02T19:37:26.000Z","version_change":"`78b18b5` → `3c5d746`","issue":{"uuid":"3111389571","node_id":"PR_kwDOKCm6f86YsMxz","number":82,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `3c5d746`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-06-09T19:32:03.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-06-02T19:37:26.000Z","updated_at":"2025-06-09T19:32:03.000Z","time_to_close":604477,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`3c5d746`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `3c5d746`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3c5d7468bc42ea6d078e5c8bf98dd312e61bec97\"\u003e\u003ccode\u003e3c5d746\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/878\"\u003e#878\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c8bcab5d6a16fb887d88e4298b0929464f94af89\"\u003e\u003ccode\u003ec8bcab5\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group across 1 directory with 8 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a207634a98c6d3ef59e0d6569d1bf23844ba7a7f\"\u003e\u003ccode\u003ea207634\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/877\"\u003e#877\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/125934847efacb6d83c22ffb94453f6577d5da97\"\u003e\u003ccode\u003e1259348\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group across 1 directory with 3 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6f36cfd933ca41243fdc1e6a492aae479e6f7a48\"\u003e\u003ccode\u003e6f36cfd\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/752\"\u003e#752\u003c/a\u003e from ImperialCollegeLondon/662-improve-soil-nutrient-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/667e0291019d2e57b1f149445164b3e62b1a59dd\"\u003e\u003ccode\u003e667e029\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/abd205db5f848479d3d0315b29ea012bf5db6096\"\u003e\u003ccode\u003eabd205d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/767\"\u003e#767\u003c/a\u003e from ImperialCollegeLondon/feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/43f7b8c08428cf61466cf13db48e754a4fe60e47\"\u003e\u003ccode\u003e43f7b8c\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6d2a2aeb4f3d48719d655c2f40f24d6d3e46d279\"\u003e\u003ccode\u003e6d2a2ae\u003c/code\u003e\u003c/a\u003e Changed first subheading so that it's meaningfully distinct from the page title\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/35bb8c7c5f6946c706db6f0656cb479d13a6832c\"\u003e\u003ccode\u003e35bb8c7\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...3c5d7468bc42ea6d078e5c8bf98dd312e61bec97\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/82","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/82","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/82/packages"}},{"old_version":"`78b18b5`","new_version":"`6f36cfd`","update_type":null,"path":null,"pr_created_at":"2025-05-26T19:21:09.000Z","version_change":"`78b18b5` → `6f36cfd`","issue":{"uuid":"2544715906","node_id":"PR_kwDOKCm6f86XrUiC","number":79,"state":"open","title":"Bump virtual_rainforest from `78b18b5` to `6f36cfd`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-26T19:21:09.000Z","updated_at":"2025-05-26T19:21:10.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`6f36cfd`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `6f36cfd`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6f36cfd933ca41243fdc1e6a492aae479e6f7a48\"\u003e\u003ccode\u003e6f36cfd\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/752\"\u003e#752\u003c/a\u003e from ImperialCollegeLondon/662-improve-soil-nutrient-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/667e0291019d2e57b1f149445164b3e62b1a59dd\"\u003e\u003ccode\u003e667e029\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/abd205db5f848479d3d0315b29ea012bf5db6096\"\u003e\u003ccode\u003eabd205d\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/767\"\u003e#767\u003c/a\u003e from ImperialCollegeLondon/feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/43f7b8c08428cf61466cf13db48e754a4fe60e47\"\u003e\u003ccode\u003e43f7b8c\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 662-improve-soil-nutrient-documentation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/6d2a2aeb4f3d48719d655c2f40f24d6d3e46d279\"\u003e\u003ccode\u003e6d2a2ae\u003c/code\u003e\u003c/a\u003e Changed first subheading so that it's meaningfully distinct from the page title\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/35bb8c7c5f6946c706db6f0656cb479d13a6832c\"\u003e\u003ccode\u003e35bb8c7\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/af805f4d72b52528def649a5e539d0315dbbdde0\"\u003e\u003ccode\u003eaf805f4\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/870\"\u003e#870\u003c/a\u003e from ImperialCollegeLondon/869-avoid-division-by-zero...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/37947a244c77691c8dfedbb9222e0f4c5adf4284\"\u003e\u003ccode\u003e37947a2\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into feature/improved_cue_model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/82c3619a1275d15b561f4e804ee539665e1f5925\"\u003e\u003ccode\u003e82c3619\u003c/code\u003e\u003c/a\u003e minor tweaks to heading hierarchy and wording to be consistent\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/3fb2ff1b2852f48886c0039596966470067de872\"\u003e\u003ccode\u003e3fb2ff1\u003c/code\u003e\u003c/a\u003e added conditional statement to avoid division by zero\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...6f36cfd933ca41243fdc1e6a492aae479e6f7a48\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/79","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/79","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/79/packages"}},{"old_version":"`78b18b5`","new_version":"`aa95eca`","update_type":null,"path":null,"pr_created_at":"2025-05-19T19:15:49.000Z","version_change":"`78b18b5` → `aa95eca`","issue":{"uuid":"2529573080","node_id":"PR_kwDOKCm6f86WxjjY","number":76,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `aa95eca`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-05-26T19:21:12.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-19T19:15:49.000Z","updated_at":"2025-05-26T19:21:12.000Z","time_to_close":605123,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`aa95eca`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `aa95eca`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/aa95eca74460a15189d045f6f800df275b0abddd\"\u003e\u003ccode\u003eaa95eca\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/865\"\u003e#865\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/451edbcd2fa5bda6aa0ed17b44c97788a1486b49\"\u003e\u003ccode\u003e451edbc\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/522864b60c00006ce96d9440f145b9ed3a7d028a\"\u003e\u003ccode\u003e522864b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/864\"\u003e#864\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ae68856e1eeafef64e35aad20ece358947393965\"\u003e\u003ccode\u003eae68856\u003c/code\u003e\u003c/a\u003e Bump the production-dependencies group with 2 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b490690cbb0156a62509786d8f9f144aa12c5ab2\"\u003e\u003ccode\u003eb490690\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/860\"\u003e#860\u003c/a\u003e from ImperialCollegeLondon/704-the-plantsmodel-is-pre...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/2aa2bdd0b26127aaee9fed1344d3a8856c570ab8\"\u003e\u003ccode\u003e2aa2bdd\u003c/code\u003e\u003c/a\u003e documentation updated\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/dbfe9e4caa7606bd445f4c58a025f8682ea207d7\"\u003e\u003ccode\u003edbfe9e4\u003c/code\u003e\u003c/a\u003e added canopy_evaporation to conftest\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a38024fd5d790ab6c8adf731a2926ddac8cd2fb7\"\u003e\u003ccode\u003ea38024f\u003c/code\u003e\u003c/a\u003e updated hydrology model to transpiration\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/55107956c9f4c6c1033e711dac3197904984e3f0\"\u003e\u003ccode\u003e5510795\u003c/code\u003e\u003c/a\u003e changed to transpiration in plant model\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/356056bb33f35834093e9886a071fadd011bc1ec\"\u003e\u003ccode\u003e356056b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/856\"\u003e#856\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...aa95eca74460a15189d045f6f800df275b0abddd\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/76","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/76","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/76/packages"}},{"old_version":"`78b18b5`","new_version":"`356056b`","update_type":null,"path":null,"pr_created_at":"2025-05-12T19:53:01.000Z","version_change":"`78b18b5` → `356056b`","issue":{"uuid":"3057974811","node_id":"PR_kwDOKCm6f86V5Drc","number":75,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `356056b`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-05-19T19:15:51.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-12T19:53:01.000Z","updated_at":"2025-05-19T19:15:52.000Z","time_to_close":602570,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`356056b`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `356056b`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/356056bb33f35834093e9886a071fadd011bc1ec\"\u003e\u003ccode\u003e356056b\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/856\"\u003e#856\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c5633a5c88ddd28bf811296fcb3e59fb00c171c0\"\u003e\u003ccode\u003ec5633a5\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/691fd3422f3fd2946e7848cd9fe3a25596babe31\"\u003e\u003ccode\u003e691fd34\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/854\"\u003e#854\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b6e238aa82ef9f14141384ebaf7d1c721c340542\"\u003e\u003ccode\u003eb6e238a\u003c/code\u003e\u003c/a\u003e Bump the development-dependencies group with 4 updates\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/15ac423ccd4371756a1581bf3ede5870e07a7ee9\"\u003e\u003ccode\u003e15ac423\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/853\"\u003e#853\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/af138702a42bf90da6d7d37f8e49655d2ea86616\"\u003e\u003ccode\u003eaf13870\u003c/code\u003e\u003c/a\u003e Bump scipy from 1.15.2 to 1.15.3 in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/04bcf1299e22815966e3567603b949440bf5e457\"\u003e\u003ccode\u003e04bcf12\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/850\"\u003e#850\u003c/a\u003e from ImperialCollegeLondon/849-remove-duplicated-cons...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/dce08d39cf94080ad33aca553685cf74ed2cd7bc\"\u003e\u003ccode\u003edce08d3\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 849-remove-duplicated-constant\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/bd4c1f6e45aa93eb9d00a90ff0fbad42f9648654\"\u003e\u003ccode\u003ebd4c1f6\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/852\"\u003e#852\u003c/a\u003e from ImperialCollegeLondon/851-busted-value-of-tmodel...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/ba2fdeb8f93ca442fac78340908a798f55e5942c\"\u003e\u003ccode\u003eba2fdeb\u003c/code\u003e\u003c/a\u003e Merge branch 'develop' into 849-remove-duplicated-constant\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...356056bb33f35834093e9886a071fadd011bc1ec\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/75","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/75","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/75/packages"}},{"old_version":"`78b18b5`","new_version":"`4e823b8`","update_type":null,"path":null,"pr_created_at":"2025-05-05T19:30:36.000Z","version_change":"`78b18b5` → `4e823b8`","issue":{"uuid":"3040619534","node_id":"PR_kwDOKCm6f86U_RDg","number":70,"state":"closed","title":"Bump virtual_rainforest from `78b18b5` to `4e823b8`","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":"2025-05-12T19:53:04.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-05-05T19:30:36.000Z","updated_at":"2025-05-12T19:53:04.000Z","time_to_close":606148,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"virtual_rainforest","old_version":"`78b18b5`","new_version":"`4e823b8`","repository_url":"https://github.com/ImperialCollegeLondon/virtual_rainforest"}],"path":null,"ecosystem":"submodules"},"body":"Bumps [virtual_rainforest](https://github.com/ImperialCollegeLondon/virtual_rainforest) from `78b18b5` to `4e823b8`.\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/4e823b8c4d5d46f91f3aab169d2ffc4c0c5f3003\"\u003e\u003ccode\u003e4e823b8\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/841\"\u003e#841\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/c6181ad0435eb658f8ce5232418316124771145e\"\u003e\u003ccode\u003ec6181ad\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/b6d4cd09399dbd0ef8a56cf997cc006becc21005\"\u003e\u003ccode\u003eb6d4cd0\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/840\"\u003e#840\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/8627b9f1faa7ed6975af2f3753fd77061de049bd\"\u003e\u003ccode\u003e8627b9f\u003c/code\u003e\u003c/a\u003e Bump ruff from 0.11.7 to 0.11.8 in the development-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a405a7c8a68fd3b3a135cb26b1a4269996bfd313\"\u003e\u003ccode\u003ea405a7c\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/839\"\u003e#839\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/production-...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1c59b77c067e87f59bb21c62a77a8deadc4c2465\"\u003e\u003ccode\u003e1c59b77\u003c/code\u003e\u003c/a\u003e Bump xarray in the production-dependencies group\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/343bbcdf45f5c05145fbe14026132f23b56c98ce\"\u003e\u003ccode\u003e343bbcd\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/838\"\u003e#838\u003c/a\u003e from ImperialCollegeLondon/pre-commit-ci-update-config\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/a97625a8f2da32fa120e9b75937712d3928ee6d3\"\u003e\u003ccode\u003ea97625a\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] auto fixes from pre-commit.com hooks\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/5ef9e55638012e367ef52dd3d91f52fa5abaca1d\"\u003e\u003ccode\u003e5ef9e55\u003c/code\u003e\u003c/a\u003e [pre-commit.ci] pre-commit autoupdate\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_ecosystem/commit/1b8e57f3ca95682d5f3b071c063385fa3561f92a\"\u003e\u003ccode\u003e1b8e57f\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/ImperialCollegeLondon/virtual_rainforest/issues/837\"\u003e#837\u003c/a\u003e from ImperialCollegeLondon/dependabot/pip/development...\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/ImperialCollegeLondon/virtual_rainforest/compare/78b18b51895efb95ff57ee2ff021b355e2c8df6e...4e823b8c4d5d46f91f3aab169d2ffc4c0c5f3003\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)\n- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)\n\n\n\u003c/details\u003e","html_url":"https://github.com/ImperialCollegeLondon/virtual_ecosystem_snakemake_template/pull/70","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/ImperialCollegeLondon%2Fvirtual_ecosystem_snakemake_template/issues/70","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/70/packages"}}]}