Namespaces

.github/dependabot.yml

@@ -0,0 +1,11 @@
+---
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    groups:
+      github-actions:
+        patterns:
+          - '*'

.github/workflows/main.yaml

@@ -25,38 +25,43 @@ jobs:
         environment:
           - py311
           - py312
-          # - py312-jax
+          - py313
+          - py313-jax
         exclude:
           - os: macos-latest
-            environment: py311
+            environment: py311, py312
           - os: windows-latest
-            environment: py311
+            environment: py311, py312
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/[email protected].1
+      - uses: prefix-dev/[email protected].10
         with:
-          pixi-version: v0.34.0
+          pixi-version: v0.49.0
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
           frozen: true
           environments: ${{ matrix.environment }}
-      - name: Run tests on Linux (with NumPy backend)
-        # Ignore MacOS for being slow -- no reason that would break if JAX works.
-        if: runner.os == 'Linux'
-        run: pixi run -e ${{ matrix.environment }} pytest --cov=./ --cov-report=xml
-        shell: bash -el {0}
       - name: Configure dot on macOS
         if: runner.os == 'macOS'
         run: pixi run -e ${{ matrix.environment }} dot -c
-      - name: Run tests on macOS & Windows (with JAX backend)
-        # TODO: remove exclusion of Linux once --use-jax is fixed.
+      - name: Run tests on Linux (with NumPy backend and without coverage)
+        if: matrix.environment == 'py311' || matrix.environment == 'py312'
+        run: pixi run -e ${{ matrix.environment }} tests
+        shell: bash -el {0}
+      - name: Run tests on Linux (with NumPy backend and coverage)
+        if: runner.os == 'Linux' && matrix.environment == 'py313'
+        run: pixi run -e ${{ matrix.environment }} tests --cov=./ --cov-report=xml
+        shell: bash -el {0}
+      - name: Run tests on MacOS / Windows (with NumPy backend and without coverage)
         if: runner.os != 'Linux'
-        run: pixi run -e ${{ matrix.environment }} pytest
-        # TODO: add to the end of previous line to actually run with Jax backend
-        # --use-jax
+        run: pixi run -e ${{ matrix.environment }} tests
+        shell: bash -el {0}
+      - name: Run tests with JAX backend
+        if: matrix.environment == 'py313-jax'
+        run: pixi run -e ${{ matrix.environment }} tests-jax
         shell: bash -el {0}
       - name: Upload coverage reports
-        if: runner.os == 'Linux' && matrix.environment == 'py312'
+        if: runner.os == 'Linux' && matrix.environment == 'py313'
         uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/publish-to-pypi.yaml

@@ -6,9 +6,9 @@ jobs:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.12'
       - name: Install pypa/build

.gitignore

@@ -72,3 +72,4 @@ docs/_build
 docs/tutorials/sandbox_cz.ipynb
 _version.py
 .pixi/
+prof/

.pre-commit-config.yaml

@@ -38,11 +38,11 @@ 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: v0.7.2
+    rev: v0.12.2
     hooks:
       # Run the linter.
       - id: ruff
@@ -57,14 +57,14 @@ repos:
           - python
           - jupyter
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.0
+    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: 0.7.18
+    rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -75,7 +75,7 @@ repos:
           - '88'
         files: (README\.md)
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.18
+    rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -86,14 +86,30 @@ repos:
           - '88'
         files: (docs/.|CHANGES.md|CODE_OF_CONDUCT.md)
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         args:
           - --ignore-missing-imports
           - --config=pyproject.toml
+          - --allow-redefinition-new
+          - --local-partial-types
         additional_dependencies:
           - types-PyYAML
           - types-pytz
+          - numpy >= 2
+          - jaxtyping
+          # - dags >= 0.3
+          - optree >= 0.15
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.33.2
+    hooks:
+      - id: check-jsonschema
+        name: Validate JSON/YAML files against schema
+        entry: check-jsonschema
+        language: python
+        files: ^src/_gettsim/.*\.(yaml|yml)$
+        args:
+          - --schemafile=docs/geps/params-schema.json
 ci:
   autoupdate_schedule: monthly

.readthedocs.yaml

@@ -3,10 +3,15 @@ version: 2
 build:
   os: ubuntu-lts-latest
   tools:
-    python: mambaforge-latest
-conda:
-  environment: docs/rtd_environment.yml
-sphinx:
-  builder: html
-  configuration: docs/conf.py
-  fail_on_warning: false
+    python: '3.13'
+  jobs:
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+    install:
+        # assuming you have an environment called "docs"
+      - pixi install -e docs
+    build:
+      html:
+        - pixi run -e docs sphinx-build -T -b html docs $READTHEDOCS_OUTPUT/html