Misc/tox

.github/workflows/lint.yml

@@ -8,31 +8,38 @@ on:
   pull_request:
     branches: [main]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   lint:
-    runs-on: ${{ matrix.os }}
+    name: Lint ${{ matrix.lint-kind }}
+    runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python: [3.8]
-        os: [ubuntu-latest]
+        lint-kind: [code, docs]
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python }}
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python }}
-
-    - uses: actions/cache@v3
-      with:
-        path: ~/.cache/pre-commit
-        key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
+        python-version: '3.10'
 
-    - name: Install pip dependencies
+    - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pre-commit
+        python -m pip install tox
+
+    - name: Install PyEnchant
+      if: ${{ matrix.lint-kind == 'docs' }}
+      run: |
+        sudo apt update -y
+        sudo apt install libenchant-2-dev
+        python -m pip install pyenchant
 
-    - name: Lint
+    - name: Lint ${{ matrix.lint-kind }}
       run: |
-        pre-commit run --all-files --show-diff-on-failure
+        tox -e lint-${{ matrix.lint-kind }}

.github/workflows/publish.yml

@@ -0,0 +1,29 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox
+
+    - name: Build package
+      run: tox -e build-package
+
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}
+        verbose: true

.github/workflows/tests.yml

@@ -8,57 +8,73 @@ on:
   pull_request:
     branches: [main]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  build-and-test:
+  fast-tests:
+    name: Fast tests Python 3.9 on ubuntu-latest
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install tox
+
+    - name: Setup environment
+      run: |
+        tox -e py39 --notest -v
+
+    - name: Run tests
+      run: |
+        tox -e py39 --skip-pkg-install -- -m fast --memray -n auto -vv
+
+  tests:
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8]
+        python-version: ['3.8', '3.10', '3.11']
         os: [ubuntu-latest]
-        test_mark: [fast, all]
+        include:
+        - python-version: '3.9'
+          os: macos-latest
 
     steps:
     - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
-      if: runner.os == 'Linux'
-      run: |
-        sudo apt install libsuitesparse-dev
-
-    - name: Build
-      run: |
-        set -xe
-        python -VV
-        pip install --upgrade pip
-        pip install pytest-memray
-        pip install -e '.[test,experimental]'
-
-    - name: Print versions
       run: |
-        python -VV
-        python -c "import jax; print('jax==', jax.__version__)"
-        python -c "import jaxlib; print('jaxlib==', jaxlib.__version__)"
+        python -m pip install --upgrade pip
+        python -m pip install tox
 
-    - name: Run fast tests
-      if: ${{ matrix.test_mark == 'fast' }}
+    - name: Setup environment
       run: |
-        python -m pytest --cov=ott --cov-append --cov-report=xml --cov-report=term-missing --cov-config=pyproject.toml --memray -m fast -n auto
+        tox -e py${{ matrix.python-version }} --notest -v
 
-    - name: Run all tests
-      if: ${{ matrix.test_mark == 'all' }}
+    - name: Run tests
       run: |
-        python -m pytest --cov=ott --cov-append --cov-report=xml --cov-report=term-missing --cov-config=pyproject.toml --memray
+        tox -e py${{ matrix.python-version }} --skip-pkg-install
+      env:
+        PYTEST_ADDOPTS: --memray --durations 10 -vv
 
     - name: Upload coverage
       uses: codecov/codecov-action@v3
       with:
         files: ./coverage.xml
-        flags: tests-${{ matrix.test_mark }}
+        flags: tests-${{ matrix.os }}-${{ matrix.python-version }}
         name: unittests
         env_vars: OS,PYTHON
         fail_ci_if_error: false

.pre-commit-config.yaml

@@ -12,14 +12,14 @@ repos:
   - id: yapf
     additional_dependencies: [toml]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.0
+  rev: 1.6.1
   hooks:
   - id: nbqa-pyupgrade
     args: [--py38-plus]
   - id: nbqa-black
   - id: nbqa-isort
 - repo: https://github.com/PyCQA/isort
-  rev: 5.11.4
+  rev: 5.12.0
   hooks:
   - id: isort
 - repo: https://github.com/asottile/yesqa
@@ -33,7 +33,7 @@ repos:
     - flake8-bugbear
     - flake8-blind-except
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.5.0
+  rev: v2.6.0
   hooks:
   - id: pretty-format-yaml
     args: [--autofix, --indent, '2']

CONTRIBUTING.md

@@ -1,5 +1,4 @@
 # Contributing to OTT
-
 We'd love to accept your contributions to this project.
 
 There are many ways to contribute to OTT, with the most common ones being contribution of code, documentation
@@ -8,49 +7,55 @@ to the project, participating in discussions or raising issues.
 ## Contributing code or documentation
 1. fork the repository using the **Fork** button on GitHub or the following
    [link](https://github.com/ott-jax/ott/fork)
-2. ```bash
+2. ```shell
    git clone https://github.com/<YOUR_USERNAME>/ott
    cd ott
-   pip install -e .'[dev,test]'
+   pip install -e .'[dev]'
    pre-commit install
    ```
 
 When committing changes, sometimes you might want or need to bypass the pre-commit checks. This can be
 done via the ``--no-verify`` flag as:
-```bash
-git commit --no-verify -m "The commit message"
+```shell
+git commit --no-verify -m "<SOME_COMMIT_MESSAGE>"
 ```
 
 ## Running tests
-In order to run tests, you can:
-```bash
-pytest  # run all tests
-pytest -m fast  # run only fast tests
-pytest tests/core/sinkhorn_test.py  # only test within a specific file
-pytest -k "test_euclidean_point_cloud"  # only tests which contain the expression
+In order to run tests, we utilize [tox](https://tox.wiki/):
+```shell
+tox run  # run linter and all tests on all available Python versions
+tox run -- -n auto -m fast  # run linter and fast tests in parallel
+tox -e py38  # run all tests on Python3.8
+tox -e py39 -- -k "test_euclidean_point_cloud"  # run tests matching the expression on Python3.9
+tox -e py310 -- --memray  # test also memory on Python3.10
 ```
+Alternatively, tests can be also run using the [pytest](https://docs.pytest.org/):
+```shell
+python -m pytest
+```
+This requires the ``'[test]'`` extra requirements to be installed as ``pip install -e.'[test]'``.
 
-In order to run memory related tests (used for low-rank solvers/geometries and online point clouds), we utilize
-[pytest-memray](https://github.com/bloomberg/pytest-memray) (current available only on Linux).
-Whenever running the ``pytest`` commands mentioned above, the ``--memray`` option needs to be specified as well.
-
-Lastly, to the run notebook regression tests, use ``pytest -m notebook``. Cell execution limit can be adjusted
-using ``--notebook-cell-timeout=...`` (in seconds), Jupyter kernel name can be set using ``--kernel-name=...``.
-
-## Building documentation
+## Documentation
 From the root of the repository, run:
-```bash
-pip install -e.'[docs]'
-cd docs
-make html  # use `-j 4` to run using 4 jobs
-<your favorite browser> _build/html/index.html
-# run `make clean` to remove generated files
+```shell
+tox -e build-docs  # build documentation
+tox -e clean-docs  # remove documentation
+tox -e lint-docs  # run spellchecker and linkchecker
+```
+Installing ``pyEnchant`` is required to run spellchecker, please refer to the
+[installation instructions](https://pyenchant.github.io/pyenchant/install.html). On macOS Silicon, it may be necessary
+to also set ``PYENCHANT_LIBRARY_PATH`` environment variable.
+
+## Building the package
+The package can be built using:
+```shell
+tox -e build-package
 ```
+Afterwards, the built package will be located under ``dist/``.
 
 ## Code reviews
-
-All submissions, including submissions by project members, require review. We
-use GitHub pull requests for this purpose. Consult
+All submissions, including submissions by project members, require review. We use GitHub
+[pull requests](https://github.com/ott-jax/ott/pulls) for this purpose. Consult
 [GitHub Help](https://help.github.com/articles/about-pull-requests/) for more information on using pull requests.
 
 # Community Guidelines