Merge branch 'develop' into feature/organic_phosphorus

ImperialCollegeLondon · Jan 6, 2025 · f129175 · f129175
2 parents 54bbb2d + 39f9a0e
commit f129175
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -36,7 +36,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Install Poetry
-      uses: abatilo/actions-poetry@v3.0.1
+      uses: abatilo/actions-poetry@v4.0.0
       with:
         poetry-version: 1.5.1
 
@@ -71,7 +71,7 @@ jobs:
           python-version: "3.10"
 
       - name: Install Poetry
-        uses: abatilo/actions-poetry@v3.0.1
+        uses: abatilo/actions-poetry@v4.0.0
         with:
           poetry-version: 1.5.1
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,22 +5,22 @@ repos:
       - id: check-merge-conflict
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.8.4
     hooks:
       - id: ruff        #  Run the linter.
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format #  Run the formatter.
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.11.2"
+    rev: "v1.14.0"
     hooks:
       - id: mypy
-        additional_dependencies: [types-jsonschema, xarray, types-tabulate, numpy]
+        additional_dependencies: [types-jsonschema, xarray, types-tabulate, numpy==2.1.3]
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.42.0
+    rev: v0.43.0
     hooks:
     - id: markdownlint
   - repo: https://github.com/mwouts/jupytext
-    rev: v1.16.4b
+    rev: v1.16.6
     hooks:
     - id: jupytext
       args: [--pipe, black]

diff --git a/docs/source/_toc.yaml b/docs/source/_toc.yaml
@@ -147,8 +147,6 @@ subtrees:
             entries:
               - file: api/models/animal/animal_cohorts
                 title: The animal_cohorts submodule
-              - file: api/models/animal/animal_communities
-                title: The animal_communities submodule
               - file: api/models/animal/animal_model
                 title: The animal_model submodule
               - file: api/models/animal/animal_traits

diff --git a/docs/source/api/core.md b/docs/source/api/core.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/axes.md b/docs/source/api/core/axes.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/base_model.md b/docs/source/api/core/base_model.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/config.md b/docs/source/api/core/config.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/constants.md b/docs/source/api/core/constants.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/constants_class.md b/docs/source/api/core/constants_class.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/constants_loader.md b/docs/source/api/core/constants_loader.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/core_components.md b/docs/source/api/core/core_components.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/data.md b/docs/source/api/core/data.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/exceptions.md b/docs/source/api/core/exceptions.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/grid.md b/docs/source/api/core/grid.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/logger.md b/docs/source/api/core/logger.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/readers.md b/docs/source/api/core/readers.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/registry.md b/docs/source/api/core/registry.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/schema.md b/docs/source/api/core/schema.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/utils.md b/docs/source/api/core/utils.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/core/variables.md b/docs/source/api/core/variables.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/example_data.md b/docs/source/api/example_data.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/main.md b/docs/source/api/main.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models.md b/docs/source/api/models.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic.md b/docs/source/api/models/abiotic.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic/abiotic_constants.md b/docs/source/api/models/abiotic/abiotic_constants.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic/abiotic_model.md b/docs/source/api/models/abiotic/abiotic_model.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic/abiotic_tools.md b/docs/source/api/models/abiotic/abiotic_tools.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic/conductivities.md b/docs/source/api/models/abiotic/conductivities.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic/energy_balance.md b/docs/source/api/models/abiotic/energy_balance.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic/soil_energy_balance.md b/docs/source/api/models/abiotic/soil_energy_balance.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic/wind.md b/docs/source/api/models/abiotic/wind.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic_simple.md b/docs/source/api/models/abiotic_simple.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic_simple/abiotic_simple_constants.md b/docs/source/api/models/abiotic_simple/abiotic_simple_constants.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic_simple/abiotic_simple_model.md b/docs/source/api/models/abiotic_simple/abiotic_simple_model.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/abiotic_simple/microclimate.md b/docs/source/api/models/abiotic_simple/microclimate.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/animal.md b/docs/source/api/models/animal.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/animal/animal_cohorts.md b/docs/source/api/models/animal/animal_cohorts.md
@@ -7,7 +7,7 @@ jupytext:
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diff --git a/docs/source/api/models/animal/animal_communities.md b/docs/source/api/models/animal/animal_communities.md