diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0e7ad6b95b..103d53e3d6 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -70,12 +70,15 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} + - uses: yezz123/setup-uv@v4 + with: + uv-version: "0.3.0" - name: Install standalone dependencies only run: | - pip install -e .[all] + uv sync --locked --extra all - name: Test importing Flax run: | - python -c "import flax" + uv run python -c "import flax" tests: name: Run Tests needs: [cancel-previous, pre-commit, commit-count, test-import] @@ -101,51 +104,40 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - - name: Get week and year - id: date_key - run: echo "DATE=$(date +%j)" >> $GITHUB_OUTPUT - # TODO(cgarciae): caching is breaking the install step, disabling for now. - # - name: Cached virtual environment - # id: venv_cache - # uses: actions/cache@v3 - # with: - # path: venv - # key: pip-${{ steps.setup_python.outputs.python-version }}-${{ steps.date_key.outputs.DATE }}-${{ hashFiles('**/requirements.txt', 'pyproject.toml') }} + - uses: yezz123/setup-uv@v4 + with: + uv-version: "0.3.0" + - name: Cached virtual environment + id: venv_cache + uses: actions/cache@v3 + with: + path: venv + key: pip-${{ steps.setup_python.outputs.python-version }}-${{ hashFiles('uv.lock') }} - name: Install Dependencies for cache if: steps.venv_cache.outputs.cache-hit != 'true' run: | - if [ -d "venv" ]; then rm -rf venv; fi - python3 -m venv venv - venv/bin/python3 -m pip install .[all,testing] - venv/bin/python3 -m pip install tensorflow_datasets[dev] - venv/bin/python3 -m pip install -r docs/requirements.txt - - name: Install Flax + if [ -d ".venv" ]; then rm -rf .venv; fi + uv sync --locked --all-extras + - name: Check lockfile run: | - venv/bin/python3 -m pip install -e .[all,testing] + uv sync --locked --all-extras - name: Install JAX run: | if [[ "${{ matrix.jax-version }}" == "newest" ]]; then - venv/bin/python3 -m pip install -U jax jaxlib + uv pip install -U jax jaxlib else - venv/bin/python3 -m pip install "jax==${{ matrix.jax-version }}" "jaxlib==${{ matrix.jax-version }}" + uv pip install "jax==${{ matrix.jax-version }}" "jaxlib==${{ matrix.jax-version }}" fi - - name: Cached mypy cache - id: mypy_cache - uses: actions/cache@v3 - if: matrix.test-type == 'mypy' - with: - path: .mypy_cache - key: mypy-${{ steps.setup_python.outputs.python-version }}-${{ steps.date_key.outputs.DATE }} - name: Test with ${{ matrix.test-type }} run: | if [[ "${{ matrix.test-type }}" == "doctest" ]]; then - tests/run_all_tests.sh --no-pytest --no-pytype --no-mypy --use-venv + uv run tests/run_all_tests.sh --only-doctest elif [[ "${{ matrix.test-type }}" == "pytest" ]]; then - tests/run_all_tests.sh --no-doctest --no-pytype --no-mypy --with-cov --use-venv + uv run tests/run_all_tests.sh --only-pytest elif [[ "${{ matrix.test-type }}" == "pytype" ]]; then - tests/run_all_tests.sh --no-doctest --no-pytest --no-mypy --use-venv + uv run tests/run_all_tests.sh --only-pytype elif [[ "${{ matrix.test-type }}" == "mypy" ]]; then - tests/run_all_tests.sh --no-doctest --no-pytest --no-pytype --use-venv + uv run tests/run_all_tests.sh --only-mypy else echo "Unknown test type: ${{ matrix.test-type }}" exit 1 diff --git a/.readthedocs.yml b/.readthedocs.yml index d466631bbb..89a5ee8339 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -23,4 +23,9 @@ formats: # Optionally set the version of Python and requirements required to build your docs python: install: - - requirements: docs/requirements.txt + - method: pip + path: . + extra_requirements: + - all + - testing + - docs diff --git a/docs/contributing.md b/docs/contributing.md index c9b6d4391e..72c48ae1af 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -58,9 +58,14 @@ To contribute code to Flax on GitHub, follow these steps: ```bash git clone https://github.com/YOUR_USERNAME/flax cd flax - pip install -e ".[all]" - pip install -e ".[testing]" - pip install -r docs/requirements.txt + pip install -e ".[all,testing,docs]" + ``` + + You can also use [uv](https://docs.astral.sh/uv/) to setup + the development environment: + + ```bash + uv sync --all-extras ``` 5. Set up pre-commit hooks, this will run some automated checks during each `git` commit and @@ -130,6 +135,20 @@ To contribute code to Flax on GitHub, follow these steps: You can learn more in GitHub's [Creating a pull request from a fork ](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork). documentation. +### Adding or updating dependencies + +To add or update dependencies, you must use `uv` after +updating the `pyproject.toml` file to ensure that the `uv.lock` file is up-to-date. + +```bash +uv sync --all-extras +``` +Alternatively use can use `uv add` to add or update the dependencies automatically, for example: + +```bash +uv add 'some-package>=1.2.3' +``` + ### Updating Jupyter Notebooks We use [jupytext](https://jupytext.readthedocs.io/) to maintain two synced copies of docs diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index f03ca74052..0000000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,36 +0,0 @@ -sphinx>=3.3.1 -sphinx-book-theme -Pygments>=2.6.1 -jax>=0.4 -jaxlib -numpy>1.22 -numpy>=1.23.2; python_version>='3.11' -numpy>=1.26.0; python_version>='3.12' - -ipykernel -myst_nb -recommonmark -ipython_genutils -sphinx-design -jupytext==1.13.8 -dm-haiku -treescope>=0.1.1; python_version>='3.10' - -# Need to pin docutils to 0.16 to make bulleted lists appear correctly on -# ReadTheDocs: https://stackoverflow.com/a/68008428 -docutils==0.16 - -# The next packages are for notebooks. -matplotlib -scikit-learn -# Must install flax itself for notebook execution and autodocs to work. -. -# The next packages are used in testcode blocks. -ml_collections -tensorflow -tensorflow_datasets -tensorflow_text>=2.11.0 # WMT example - -# notebooks -einops - diff --git a/flax/nnx/examples/lm1b/input_pipeline_test.py b/flax/nnx/examples/lm1b/input_pipeline_test.py index e6287fac07..3ce21d6648 100644 --- a/flax/nnx/examples/lm1b/input_pipeline_test.py +++ b/flax/nnx/examples/lm1b/input_pipeline_test.py @@ -16,10 +16,11 @@ import pathlib import tempfile -import input_pipeline -import tensorflow_datasets as tfds from absl.testing import absltest +import tensorflow_datasets as tfds + from configs import default +import input_pipeline # We just use different values here to verify that the input pipeline uses the # the correct value for the 3 different datasets. @@ -29,6 +30,7 @@ class InputPipelineTest(absltest.TestCase): + def setUp(self): super().setUp() self.train_ds, self.eval_ds, self.predict_ds = self._get_datasets() diff --git a/pyproject.toml b/pyproject.toml index 94a2ca56cc..41506fec32 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,10 +11,10 @@ authors = [ {name = "Flax team", email = "flax-dev@google.com"}, ] dependencies = [ - "numpy>=1.22", "numpy>=1.23.2; python_version>='3.11'", "numpy>=1.26.0; python_version>='3.12'", - "jax>=0.4.27", # keep in sync with jax-version in .github/workflows/build.yml + # keep in sync with jax-version in .github/workflows/build.yml + "jax>=0.4.27", "msgpack", "optax", "orbax-checkpoint", @@ -40,7 +40,7 @@ all = [ "matplotlib", # only needed for tensorboard export ] testing = [ - "clu", # All examples. + "clu", "clu<=0.0.9; python_version<'3.10'", "einops", "gymnasium[atari, accept-rom-license]", @@ -55,16 +55,42 @@ testing = [ "pytest-custom_exit_code", "pytest-xdist", "pytype", - "sentencepiece", # WMT/LM1B examples - "tensorflow_text>=2.11.0", # WMT/LM1B examples + # WMT/LM1B examples + "sentencepiece", + "tensorflow_text>=2.11.0; platform_system!='Darwin'", "tensorflow_datasets", "tensorflow>=2.12.0", # to fix Numpy np.bool8 deprecation error "torch", - "nbstripout", - "black[jupyter]==23.7.0", - # "pyink==23.5.0", # disabling pyink fow now "treescope>=0.1.1; python_version>='3.10'", ] +docs = [ + "sphinx>=3.3.1", + "sphinx-book-theme", + "Pygments>=2.6.1", + "ipykernel", + "myst_nb", + "nbstripout", + "recommonmark", + "ipython_genutils", + "sphinx-design", + "jupytext==1.13.8", + "dm-haiku", + + # Need to pin docutils to 0.16 to make bulleted lists appear correctly on + # ReadTheDocs: https://stackoverflow.com/a/68008428 + "docutils==0.16", + + # The next packages are for notebooks. + "matplotlib", + "scikit-learn", + # The next packages are used in testcode blocks. + "ml_collections", + # notebooks + "einops", +] +dev = [ + "pre-commit>=3.8.0", +] [project.urls] homepage = "https://github.com/google/flax" @@ -151,6 +177,10 @@ filterwarnings = [ "ignore:.*jax.xla_computation is deprecated.*:DeprecationWarning", # Orbax warnings inside deprecated `flax.training` package. "ignore:.*Couldn't find sharding info under RestoreArgs.*:UserWarning", + # numpy: RuntimeWarning: invalid value encountered in cast + "ignore:.*invalid value encountered in cast.*:RuntimeWarning", + # numpy: RuntimeWarning: divide by zero encountered in {not_}equal + "ignore:.*divide by zero encountered in.*:RuntimeWarning", ] [tool.coverage.report] @@ -190,3 +220,4 @@ unfixable = [] [tool.ruff.format] indent-style = "space" quote-style = "single" + diff --git a/tests/run_all_tests.sh b/tests/run_all_tests.sh index a130c26caf..fb1fb318f9 100755 --- a/tests/run_all_tests.sh +++ b/tests/run_all_tests.sh @@ -1,10 +1,11 @@ #!/bin/bash +# export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python PYTEST_OPTS= -RUN_DOCTEST=true -RUN_MYPY=true -RUN_PYTEST=true -RUN_PYTYPE=true +RUN_DOCTEST=false +RUN_MYPY=false +RUN_PYTEST=false +RUN_PYTYPE=false GH_VENV=false for flag in "$@"; do @@ -17,17 +18,17 @@ case $flag in echo " --with-cov: Also generate pytest coverage." exit ;; - --no-doctest) - RUN_DOCTEST=false + --only-doctest) + RUN_DOCTEST=true ;; - --no-pytest) - RUN_PYTEST=false + --only-pytest) + RUN_PYTEST=true ;; - --no-pytype) - RUN_PYTYPE=false + --only-pytype) + RUN_PYTYPE=true ;; - --no-mypy) - RUN_MYPY=false + --only-mypy) + RUN_MYPY=true ;; --use-venv) GH_VENV=true @@ -39,9 +40,17 @@ case $flag in esac done +# if neither --only-doctest, --only-pytest, --only-pytype, --only-mypy is set, run all tests +if ! $RUN_DOCTEST && ! $RUN_PYTEST && ! $RUN_PYTYPE && ! $RUN_MYPY; then + RUN_DOCTEST=true + RUN_PYTEST=true + RUN_PYTYPE=true + RUN_MYPY=true +fi + # Activate cached virtual env for github CI if $GH_VENV; then - source $(dirname "$0")/../venv/bin/activate + source $(dirname "$0")/../.venv/bin/activate fi echo "====== test config =======" diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000000..5dbc9e8070 --- /dev/null +++ b/uv.lock @@ -0,0 +1,3712 @@ +version = 1 +requires-python = ">=3.10" +resolution-markers = [ + "python_full_version < '3.11' and 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