chore: update code base for Python 3.13 ; add uv migration and make it compatible with pyodide 2024, used by Marimo

.github/workflows/check.yml

@@ -15,13 +15,15 @@ jobs:
     name:  Run lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
         with:
-          python-version: 3.11
-      - name: Install tox
-        run: python -m pip install tox
+          version: "0.11.16"
+          python-version: "3.11"
+          enable-cache: true
+      - name: Install tox with tox-uv
+        run: uv tool install tox --with tox-uv
       - name: check-manifest
         run: tox -e check-manifest
       - name: flake8
@@ -39,26 +41,28 @@ jobs:
       fail-fast: false
       matrix:
         py:
+          - "3.14"
+          - "3.13"
           - "3.12"
           - "3.11"
-          - "3.10"
-          - "3.9"
         os:
           - ubuntu-latest
           - macos-13
           - windows-latest
     env:
       MPLBACKEND: Agg  # https://github.com/orgs/community/discussions/26434
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - name: Setup python for test ${{ matrix.py }}
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
         with:
+          version: "0.11.16"
           python-version: ${{ matrix.py }}
-      - name: Install tox
-        run: python -m pip install tox-gh>=1.2
+          enable-cache: true
+      - name: Install tox with tox-uv
+        run: uv tool install tox --with tox-uv
       - name: Setup test suite
         run: tox -vv --notest
       - name: Run test suite

.github/workflows/documentation.yml

@@ -12,34 +12,32 @@ jobs:
     name: Test if documentation can be rendered
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
         with:
-          python-version: 3.11
-      - name: Install package and sphinx
-        run: |
-          pip install .
-          pip install sphinx>=4.5 sphinx-book-theme pytest sphinx_gallery plotly
-          sphinx-build -b doctest doc .
+          version: "0.11.16"
+          enable-cache: true
+      - name: Install the project
+        run: uv sync --locked --all-extras --extra doc
+      - name: Run doctest
+        run: uv run sphinx-build -b doctest doc .
   docdeploy:
     name: Render the documentation and push it to gh-pages
     runs-on: ubuntu-latest
     needs: doctest
     if: ${{github.ref == 'refs/heads/main'}}
     steps:
-      - uses: actions/checkout@v4
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
         with:
-          python-version: 3.11
-      - name: Install package and sphinx
-        run: |
-          pip install .
-          pip install sphinx>=4.5 sphinx-book-theme pytest sphinx_gallery plotly
+          version: "0.11.16"
+          enable-cache: true
+      - name: Install the project
+        run: uv sync --locked --all-extras --extra doc
       - name: Sphinx build
-        run: |
-          sphinx-build doc _build
+        run: uv run sphinx-build doc _build
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
         with:

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

@@ -10,17 +10,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - uses: actions/checkout@v6
+    - name: Install uv
+      uses: astral-sh/setup-uv@v8.1.0
       with:
-        python-version: "3.x"
-    - name: Install dependencies
-      run: |
-        python3 -m pip install --upgrade pip
-        python3 -m pip install build twine
+        version: "0.11.16"
+        enable-cache: true
     - name: Build a binary wheel and a source tarball
-      run: python3 -m build
+      run: uv build
     - name: Store the distribution packages
       uses: actions/upload-artifact@v4
       with:
@@ -46,8 +43,12 @@ jobs:
       with:
         name: resourcecode
         path: dist/
+    - name: Install uv
+      uses: astral-sh/setup-uv@v8.1.0
+      with:
+        version: "0.11.16"
     - name: Publish Resourcecode 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      run: uv publish
 
   github-release:
     name: >-
@@ -62,7 +63,7 @@ jobs:
       id-token: write  # IMPORTANT: mandatory for sigstore
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Download all the dists
       uses: actions/download-artifact@v4
       with:
@@ -113,8 +114,9 @@ jobs:
       with:
         name: resourcecode
         path: dist/
-    - name: Publish Resourcecode 📦 to TestPyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+    - name: Install uv
+      uses: astral-sh/setup-uv@v8.1.0
       with:
-        repository-url: https://test.pypi.org/legacy/
-        verbose: true
+        version: "0.11.16"
+    - name: Publish Resourcecode 📦 to TestPyPI
+      run: uv publish --token ${{ secrets.TEST_PYPI_TOKEN }} --publish-url https://test.pypi.org/legacy/

.gitignore

@@ -1,192 +1,6 @@
-# Created by https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks
-# Edit at https://www.toptal.com/developers/gitignore?templates=python,jupyternotebooks
+# uv
+uv.lock
+.venv/
 
-### JupyterNotebooks ###
-# gitignore template for Jupyter Notebooks
-# website: http://jupyter.org/
-
-.ipynb_checkpoints
-*/.ipynb_checkpoints/*
-
-# IPython
-profile_default/
-ipython_config.py
-
-# Remove previous ipynb_checkpoints
-#   git rm -r .ipynb_checkpoints/
-
-### Python ###
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-.doctrees/*
-public/*
-output.txt
-
-# Sphinx documentation
-doc/_build/
-doc/auto_examples
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-tests/output/*.png
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-
-# IPython
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-
-# End of https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks
-
-#Additional stuff
-joss_paper/paper.log
-joss_paper/paper.Rmd
-joss_paper/paper.html
-joss_paper/paper.bib.bak
-joss_paper/paper.pdf
+# Jupyter checkpoints
+**/.ipynb_checkpoints/

MANIFEST.in

@@ -2,16 +2,19 @@ include LICENSE
 include CITATION.cff
 include tox.ini
 include mypy.ini
-include config/config.ini
-include dev_requirements.txt
 include fp_hs.png
 exclude .gitlab-ci.yml .gitlab-ci-ifremer.yml
 include *.md
+include uv.lock
+include *.txt
 
+recursive-include config *.ini
 recursive-include notebooks *.ipynb
+global-exclude **/.ipynb_checkpoints/*
 recursive-include resourcecode *.py
 recursive-include resourcecode/data *.feather *.json
 recursive-include resourcecode *.csv
+recursive-include resourcecode/config *.ini
 
 recursive-include examples *.py
 recursive-include examples *.rst
@@ -22,6 +25,7 @@ recursive-include CLA *.pdf
 
 recursive-exclude joss_paper *
 exclude joss_paper
+exclude dev_requirements.txt
 
 prune codes_to_migrate
 prune doc