ci: add tests for python 3.12

This commit also refactors all the requirement files into optional dependencies bundles in the pyproject file
cds-astro · Nov 8, 2023 · 396f593 · 396f593
1 parent 96cf964
commit 396f593
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Showing 14 changed files with 102 additions and 157 deletions.
diff --git a/.github/workflows/cov-and-doc.yml b/.github/workflows/cov-and-doc.yml
@@ -15,13 +15,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: "Checkout branch ${{ github.head_ref }}"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
       - name: "Set up Python on Ubuntu"
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
             # Test Rust code
       - name: "Test with coverage, build and test doc"
         run: |
@@ -37,12 +37,12 @@ jobs:
           # Build and install mocpy
           maturin develop --release
           # Install pytest-cov, needed to test with coverage
-          pip install -r requirements/tests.txt
+          pip install .[dev]
           pip install pytest-cov
           # Run test with coverage and doctests
           python -m pytest -v -s --doctest-modules python/mocpy --cov-report=term --cov=python/mocpy
           # Install dependencies needed to build the docs
-          pip install -r requirements/docs.txt
+          pip install .[docs]
           sudo apt-get install pandoc
           # Compile the docs and run the test examples
           cd ./docs

diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -11,13 +11,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: "Checkout branch ${{ github.head_ref }}"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
       - name: "Set up Python on Ubuntu"
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: "Build doc"
         run: |
           # Build the doc
@@ -31,7 +31,7 @@ jobs:
           # - Build and install mocpy
           maturin develop --release
           # - Install dependencies needed to build the docs
-          pip install -r requirements/docs.txt
+          pip install .[docs]
           sudo apt-get install pandoc
           # - Build the doc: once done, it is in docs/_build/html/
           cd ./docs
@@ -40,8 +40,8 @@ jobs:
           # Switch off the virtualenv
           deactivate
       - name: "Publish doc on github pages (commit on branch gh-pages)"
-        uses: JamesIves/github-pages-deploy-action@4.4.3
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages
           folder: docs/_build/html/
-            
+
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -28,7 +28,7 @@ jobs:
        run: |
          source $HOME/.cargo/env
          rustup target add wasm32-unknown-emscripten
-         for PYBIN in /opt/python/cp3[78910]*/bin; do
+         for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
            "${PYBIN}/pip" install --upgrade pip
            "${PYBIN}/pip" install maturin
            "${PYBIN}/maturin" publish -i "${PYBIN}/python" --skip-existing --compatibility manylinux2014 --username "$MATURIN_USERNAME"
@@ -47,10 +47,10 @@ jobs:
       img: quay.io/pypa/manylinux2014_i686
     steps:
      - name: Checkout
-       uses: actions/checkout@v3
+       uses: actions/checkout@v4
      - name: "Set up QEMU"
        id: qemu
-       uses: docker/setup-qemu-action@v1
+       uses: docker/setup-qemu-action@v3
      - name: Install dependencies
        run: |
          docker run --rm -v ${{ github.workspace }}:/ws:rw --workdir=/ws \
@@ -59,7 +59,7 @@ jobs:
          ${{ env.img }} \
          bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y && \
            source $HOME/.cargo/env && \
-           for PYBIN in /opt/python/cp3[8910]*/bin; do
+           for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
              echo "Loop on PYBIN: $PYBIN"
              "${PYBIN}/pip" install --upgrade pip
              "${PYBIN}/pip" install maturin
@@ -76,10 +76,10 @@ jobs:
       img: quay.io/pypa/manylinux2014_aarch64
     steps:
      - name: Checkout
-       uses: actions/checkout@v3
+       uses: actions/checkout@v4
      - name: "Set up QEMU"
        id: qemu
-       uses: docker/setup-qemu-action@v1
+       uses: docker/setup-qemu-action@v3
      - name: Install dependencies
        run: |
          docker run --rm -v ${{ github.workspace }}:/ws:rw --workdir=/ws \
@@ -88,7 +88,7 @@ jobs:
          ${{ env.img }} \
          bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- --default-host aarch64-unknown-linux-gnu -y && \
            source $HOME/.cargo/env && \
-           for PYBIN in /opt/python/cp3[78910]*/bin; do
+           for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
              echo "Loop on PYBIN: $PYBIN"
              "${PYBIN}/pip" install maturin
              "${PYBIN}/maturin" -V
@@ -104,10 +104,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11','3.12']
     steps:
      # Checkout the project
-     - uses: actions/checkout@v3
+     - uses: actions/checkout@v4
      #  Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
      - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
        uses: actions/setup-python@v4
@@ -139,10 +139,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
      # Checkout the project
-     - uses: actions/checkout@v3
+     - uses: actions/checkout@v4
      #  Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
      - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
        uses: actions/setup-python@v4

diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml
@@ -1,23 +1,22 @@
 name: notebooks-mocpy
 on: workflow_dispatch
-jobs:  
+jobs:
   # Run the notebooks. This add more examples to test the code with.
-  # This workflow should not block the deployment pipeline. 
+  # This workflow should not block the deployment pipeline.
   run-notebooks:
     runs-on: ubuntu-latest
     steps:
       - name: "Checkout branch ${{ github.head_ref }}"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
-      - name: "Set up Python 3.8 on Ubuntu"
+      - name: "Set up Python 3.12 on Ubuntu"
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
-            # Test Rust code
+          python-version: 3.12
       - name: "Run notebooks"
         run: |
-          # Install virtualenv     
+          # Install virtualenv
           pip install virtualenv
           # Create and activate a new virtualenv
           virtualenv mocpy-env
@@ -29,7 +28,7 @@ jobs:
           # Build and install mocpy
           maturin develop --release
           # Install pytest-cov, needed to test with coverage
-          pip install -r requirements/notebooks.txt
+          pip install .[notebooks]
           # Add the mocpy-env environnement as a jupyter kernel
           python -m ipykernel install --user --name mocpy-env
           # Run the notebooks under that kernel

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -29,7 +29,7 @@ jobs:
      - name: "Build and test wheels"
        run: |
          source $HOME/.cargo/env
-         for PYBIN in /opt/python/cp{37,38,39,310,311}-*/bin; do
+         for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
            echo "Loop on PYBIN: $PYBIN"
            # With maturin develop, we have to use virtualenv
            "${PYBIN}/pip" install virtualenv
@@ -39,7 +39,7 @@ jobs:
            pip install maturin
            maturin build --release --compatibility manylinux2014
            maturin develop --release
-           pip install -r requirements/tests.txt
+           pip install .[dev]
            python -m pytest -v -s python/mocpy
            pip freeze > requirements-uninstall.txt
            pip uninstall -r requirements-uninstall.txt -y
@@ -51,11 +51,11 @@ jobs:
     runs-on: macOS-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
      # Checkout the project
      - name: "Checkout branch ${{ github.head_ref }}"
-       uses: actions/checkout@v3
+       uses: actions/checkout@v4
        with:
          ref: ${{ github.head_ref }}
      # Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
@@ -77,7 +77,7 @@ jobs:
          maturin build --release --target universal2-apple-darwin
          maturin develop --release
          # Install dependencies
-         pip install -r requirements/tests.txt
+         pip install .[dev]
          # Run tests
          python -m pytest -v -s python/mocpy
          # Clean
@@ -90,11 +90,11 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
       # Checkout the project
       - name: "Checkout branch ${{ github.head_ref }}"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
       # Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
@@ -114,7 +114,7 @@ jobs:
           pip install maturin
           maturin develop --release
           # Install dependencies
-          pip install -r requirements\tests.txt
+          pip install .[dev]
           # Run tests
           python -m pytest -v -s python\mocpy
           deactivate
diff --git a/README.rst b/README.rst
@@ -77,17 +77,26 @@ Latest stable version
 - from conda ``conda install -c conda-forge mocpy``
 - from this repository
 
-Developpement version
-*********************
+Unreleased latest version
+*************************
 .. code::
 
    git clone https://github.com/cds-astro/mocpy.git
    cd mocpy
    pip install .
- 
+
 Note that the point is important.
-
+
+To run the notebooks
+********************
+
+The example notebooks require additional dependencies. They can be installed with
+
+.. code::
+
+    pip install mocpy[notebooks]
+
 For use in pyodide
 ******************
 
-Wheels that run in pyodide can be downloaded from `this repository assets <https://github.com/cds-astro/mocpy/releases/download/v0.12.3/mocpy-0.12.3-cp310-cp310-emscripten_3_1_27_wasm32.whl>`__. This is not fully tested. 
+Wheels that run in pyodide can be downloaded from `this repository assets <https://github.com/cds-astro/mocpy/releases/download/v0.12.3/mocpy-0.12.3-cp310-cp310-emscripten_3_1_27_wasm32.whl>`__. This is not fully tested.
diff --git a/docs/contribute.rst b/docs/contribute.rst
@@ -10,24 +10,24 @@ interpreter and package manager.
 Setting up the environment
 --------------------------
 
-There is two ways to set up an environment.
+Here we highlight two ways to set up an environment.
 Using conda (installed from miniconda or anaconda) or
-using the pip package called
+using the pip package
 `virtualenv <https://python-guide-pt-br.readthedocs.io/fr/latest/dev/virtualenvs.html>`__ .
-Choose the one you prefer.
+Choose the one you prefer, or your own one.
 
 Using conda
 ~~~~~~~~~~~
 
 - Set up the conda environment and activate it::
 
-    conda env create -q python=3.8 -f <path_to_mocpy>/requirements/environment.yml -n mocpy-env
-    source activate mocpy-env
+    conda create -n mocpy-dev python==3.12.*
+    source activate mocpy-dev
 
 - Once you are done with your developments you can
   deactivate your conda environment::
 
-    source deactivate
+    conda deactivate
 
 Using virtualenv
 ~~~~~~~~~~~~~~~~
@@ -53,9 +53,9 @@ along with a new empty pip package manager.
 opens a session with the ``mocpy-env`` interpreter.
 
 - You can now install all the necessary pip packages
-  for developping and testing MOCpy::
+  for developing and testing MOCpy::
 
-    pip install -r <path_to_mocpy_repo>/requirements/contributing.txt
+    pip install .[dev]
 
 - Once you are done with your developments you can deactivate the virtual env::
 
@@ -68,7 +68,7 @@ Pre-commits setup
 
     pre-commit install
 
-It will run linting and formating tests at each of your commits.
+It will run linting and formatting tests at each of your commits.
 
 Now build package
 -----------------
@@ -83,7 +83,8 @@ Now build package
 
 This step will inform you of any issue in the rust part.
 
-- After a new version of mocpy goes out, if a ``maturin develop --release`` does not actualise your ``Cargo.toml`` file, you might need to before executing the ``maturin`` command again::
+- After a new version of mocpy goes out, if a ``maturin develop --release`` does not actualize your
+``Cargo.toml`` file, you might need to before executing the ``maturin`` command again::
 
     rm Cargo.lock && cargo clean
 
@@ -102,29 +103,28 @@ Once your environment is set up and activated you can run the tests
 
 - When contributing to the notebooks::
 
-    python -m pip install -r requirements/notebooks.txt
+    python -m pip install .[notebooks]
     python -m pytest --nbmake -n=auto "./notebooks"
 
-You also can have a html output of the coverage. For that set ``--cov-report=html``,
-this will generate an ``htmlcov`` folder where all the static html files can be found.
+You also can have a html output of the coverage with the flag ``--cov-report=html``.
+This will generate an ``htmlcov`` folder where all the static html files can be found.
 
 
 Building the documentation
 --------------------------
 
-To see the documentation locally, you'll need to install the python packages in
-:file:`requirements/docs.txt` and the pandoc software.
+To see the documentation locally, you'll need to install the additional python dependencies with
 
-- To build the docs from the repo directory::
+    pip install .[docs]
 
-    cd docs
-    make html
-    cd ..
+and the pandoc software (``sudo apt-get install pandoc`` on ubuntu,
+``choco install pandoc`` on windows, ``brew install pandoc`` on mac,
+``pacman -S haskell-pandoc`` on arch).
 
-- Other API examples found in the documentation can be run with::
+- To build the docs from the repo directory::
 
     cd docs
-    make doctest
+    make html
     cd ..
 
 You will find the html index file in the :file:`docs/_build/html` folder.