Endogenize investments

.github/workflows/main.yml

@@ -23,51 +23,27 @@ jobs:
           - macos-latest
           - windows-latest
         python-version:
-          - '3.12'
+          - '3.13'
     steps:
-      - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.0
+      - uses: actions/checkout@v5
+      - uses: prefix-dev/setup-pixi@v0.9.1
         with:
-          pixi-version: v0.29.0
+          pixi-version: v0.56.0
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
           environments: test-cpu
           activate-environment: true
+          frozen: true
       - name: Run pytest
+        if: runner.os != 'Linux' || matrix.python-version != '3.13'
+        shell: bash -l {0}
+        run: pixi run -e test-cpu tests
+      - name: Run pytest with coverage
+        if: runner.os == 'Linux' && matrix.python-version == '3.13'
         shell: bash -l {0}
         run: pixi run -e test-cpu tests-with-cov
       - name: Upload coverage report
-        if: runner.os == 'Linux' && matrix.python-version == '3.12'
-        uses: codecov/codecov-action@v4
+        if: runner.os == 'Linux' && matrix.python-version == '3.13'
+        uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-  # run-mypy:
-  #   name: Run mypy on Python 3.12
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     fail-fast: false
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - uses: prefix-dev/setup-pixi@v0.8.0
-  #       with:
-  #         pixi-version: v0.28.2
-  #         cache: true
-  #         cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
-  #         environments: mypy
-  #     - name: Run mypy
-  #       shell: bash -l {0}
-  #       run: pixi run mypy
-  # run-explanation-notebooks:
-  #   name: Run explanation notebooks on Python 3.12
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - uses: prefix-dev/setup-pixi@v0.8.0
-  #       with:
-  #         pixi-version: v0.28.2
-  #         cache: true
-  #         cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
-  #         environments: test
-  #     - name: Run explanation notebooks
-  #       shell: bash -l {0}
-  #       run: pixi run -e test explanation-notebooks

.pre-commit-config.yaml

@@ -6,11 +6,11 @@ repos:
       - id: check-useless-excludes
       # - id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.17.0
+    rev: 1.18.0
     hooks:
       - id: yamlfix
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args:
@@ -37,11 +37,11 @@ repos:
       - id: check-ast
       - id: check-docstring-first
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
+    rev: v1.37.1
     hooks:
       - id: yamllint
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.13.3
     hooks:
       # Run the linter.
       - id: ruff
@@ -59,14 +59,14 @@ repos:
           - pyi
           - jupyter
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args:
           - --extra-keys
           - metadata.kernelspec metadata.language_info.version metadata.vscode
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies:

docs/source/getting_started/tutorial.ipynb

@@ -23,6 +23,13 @@
     "from skillmodels.maximization_inputs import get_maximization_inputs"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

docs/source/how_to_guides/model_specs.rst

@@ -96,14 +96,8 @@ Any python string is possible as factor name. The values are dictionaries with t
 entries:
 
 - measurements: A nested list that is as long as the number of periods of the model.
-  Each sublist contains the names of the measurements in that period. If A factor has
-  no measurements in a period, it has to be an empty list. If a factor only has
-  measurements up to a certain period you can leave out the empty lists at the end. In
-  the example this is done for factor 3. Note that even in that case, the measurements
-  have to be specified as nested list. If a factor only starts having measurements in
-  some period, you still have to specify the empty lists for all periods before that
-  period.
-
+  Each sublist contains the names of the measurements in that period. If a factor has
+  no measurements in a period, it has to be an empty list.
 
 - normalizations: This entry is optional. It is a dictionary that can have the keys
   ``"loadings"`` and ``"intercepts"``. The values are lists of dictionaries. The list
@@ -114,7 +108,7 @@ entries:
 - transition_equation: A string with the name of a pre-implemented transition equation
   or a custom transition equation. Pre-implemented transition equations are
   linear, log_ces (in the known location and scale version), constant and translog.
-  The example model dictionary only uses pre-implement transition functions.
+  The example model dictionary only uses pre-implemented transition functions.
 
   To see how to use custom transition functions, assume that the yaml file shown above
   has been loaded into a python dictionary called ``model`` and look at the following