diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml index cf13062b..2e7e358c 100644 --- a/.github/workflows/publish.yaml +++ b/.github/workflows/publish.yaml @@ -12,11 +12,15 @@ jobs: - uses: actions/setup-python@v5 with: python-version: "3.12" - - name: Install Poetry - uses: snok/install-poetry@v1 - - name: Publish + - name: Install uv + run: | + pip install uv + - name: Build and Publish env: PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }} run: | - poetry config pypi-token.pypi $PYPI_TOKEN - poetry publish --build + uv build + uv publish --token $PYPI_TOKEN + +# poetry config pypi-token.pypi $PYPI_TOKEN +# poetry publish --build diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml index 6775764d..d84fa611 100644 --- a/.github/workflows/pytest.yaml +++ b/.github/workflows/pytest.yaml @@ -13,29 +13,25 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.12" - - - name: Run Poetry Image - uses: abatilo/actions-poetry@v2.0.0 + - name: Install uv + uses: astral-sh/setup-uv@v5 + + - name: "Set up Python" + uses: actions/setup-python@v5 with: - poetry-version: 1.2.2 + python-version-file: "pyproject.toml" - - name: Install package - run: | - poetry --version - poetry install --all-extras + - name: Install the project + run: uv sync --all-extras --no-extra cuda --dev - name: Unit Tests run: | - poetry run coverage run -m pytest -k "not slow" - poetry run coverage report + uv run coverage run -m pytest -k "not slow" + uv run coverage report - name: Coverage Report run: | - poetry run coverage report -m >> $GITHUB_STEP_SUMMARY + uv run coverage report -m >> $GITHUB_STEP_SUMMARY # - name: Regression Tests # run: | diff --git a/.readthedocs.yaml b/.readthedocs.yaml index a5783eea..ef0d27ee 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,9 +11,12 @@ build: python: "3.12" jobs: post_install: - - pip install poetry - - poetry config virtualenvs.create false - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs #poetry install --with=docs + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - uv venv $READTHEDOCS_VIRTUALENV_PATH + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv --preview pip install .[docs] + # - python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs/source $READTHEDOCS_OUTPUT/html # Build documentation in the docs/ directory with Sphinx sphinx: diff --git a/README.md b/README.md index 391e6044..96ef510e 100644 --- a/README.md +++ b/README.md @@ -17,20 +17,12 @@ Apax is available on PyPI with a CPU version of JAX. pip install apax ``` -For more detailed instructions, please refer to the [documentation](https://apax.readthedocs.io/en/latest/). - - -### CUDA Support -If you want to enable GPU support (only on Linux), please overwrite the jaxlib version: - -CUDA 12: +If you want to enable GPU support (only on Linux), please run ```bash -pip install -U "jax[cuda12]" +pip install "apax[cuda]" ``` -See the [Jax installation instructions](https://github.com/google/jax#installation) for more details. - - +For more detailed instructions, please refer to the [documentation](https://apax.readthedocs.io/en/latest/). ## Usage diff --git a/apax/train/checkpoints.py b/apax/train/checkpoints.py index 1b2bc7ae..ab294b83 100644 --- a/apax/train/checkpoints.py +++ b/apax/train/checkpoints.py @@ -69,12 +69,15 @@ def create_params(model, rng_key, sample_input: tuple, n_models: int): def load_state(state, ckpt_dir): + ckpt_dir = Path(ckpt_dir) start_epoch = 0 target = {"model": state, "epoch": 0} - checkpoints_exist = Path(ckpt_dir).is_dir() + checkpoints_exist = ckpt_dir.is_dir() if checkpoints_exist: log.info("Loading checkpoint") - raw_restored = checkpoints.restore_checkpoint(ckpt_dir, target=target, step=None) + raw_restored = checkpoints.restore_checkpoint( + ckpt_dir.resolve(), target=target, step=None + ) state = raw_restored["model"] start_epoch = raw_restored["epoch"] + 1 log.info("Successfully restored checkpoint from epoch %d", raw_restored["epoch"]) diff --git a/docs/source/conf.py b/docs/source/conf.py index 89982603..54af9ca2 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -15,7 +15,7 @@ project = "Apax" copyright = "2023, Moritz Schäfer, Nico Segreto, Johannes Kästner" author = "Moritz Schäfer, Nico Segreto, Johannes Kästner" -release = "0.7.0" +release = "0.10.0" # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration diff --git a/docs/source/getting_started/install.rst b/docs/source/getting_started/install.rst index f54f82a8..63f5848c 100644 --- a/docs/source/getting_started/install.rst +++ b/docs/source/getting_started/install.rst @@ -2,63 +2,99 @@ Installation ============ -From PyPI (soon) +The standard installation installs the CPU version of Apax. To enable GPU +support (available only on **Linux**), install Apax with the extra CUDA +dependencies. See the +`Jax installation instructions `_ +for more details. + +From PyPI +--------- + +**CPU:** .. highlight:: bash .. code-block:: bash pip install apax +**GPU:** + +.. highlight:: bash +.. code-block:: bash + + pip install "apax[cuda]" From GitHub ----------- -If you would like to have a pre-release version, -you can install Apax from GitHub directly +For a pre-release version, install Apax directly from GitHub. + +**CPU:** .. highlight:: bash .. code-block:: bash pip install git+https://github.com/apax-hub/apax.git +**GPU:** + +.. highlight:: bash +.. code-block:: bash + + pip install apax[cuda] git+https://github.com/apax-hub/apax.git For Developers -------------- -As a developer, you first need to install Poetry_. -You can obtain it by running +To set up a development environment, first install `uv`_. .. highlight:: bash .. code-block:: bash - curl -sSL https://install.python-poetry.org | python3 - + pip install uv -You can then clone and install the project. +Then clone the project from GitHub, .. highlight:: bash .. code-block:: bash git clone https://github.com/apax-hub/apax.git cd - poetry install +and install it. -========================= -CUDA Support (Linux only) -========================= +**CPU:** -Note that all of the above only install the CPU version. -If you want to enable GPU support, please overwrite the jaxlib version: +.. highlight:: bash +.. code-block:: bash + + uv sync --all-extras --no-extra cuda -CUDA 12: +**GPU:** .. highlight:: bash .. code-block:: bash - pip install -U "jax[cuda12]" + uv sync --extra cuda + +Extra Dependencies +------------------ -See the `Jax installation instructions `_ for more details. +If you want to use Apax in the IPSuite framework and use the predefined +`apax.nodes`, you can install the extra dependencies for IPSuite: + +.. highlight:: bash +.. code-block:: bash + + pip install "apax[ipsuite]" + +Additionally, you have the option to install the extra dependencies for MLFlow: + +.. highlight:: bash +.. code-block:: bash + pip install "apax[mlflow]" -.. _Poetry: https://python-poetry.org/ +.. _uv: https://astral.sh/blog/uv diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 03e2cfa6..00000000 --- a/poetry.lock +++ /dev/null @@ -1,7322 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. - 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"ipsuite>=0.2.3", +] + +docs = [ + "sphinx>=7.2.6", + "sphinx-rtd-theme>=1.3.0", + "myst-parser>=2.0.0", + "sphinx-copybutton>=0.5.2", + "furo>=2023.9.10", + "nbsphinx>=0.9.3", + "nbsphinx-link>=1.3.0", + "ipykernel>=6.29.3", + "pandoc>=2.3", +] + +[dependency-groups] +dev = [ + "coverage>=7.6.10", + "matplotlib>=3.10.0", + "pre-commit>=4.0.1", + "pytest>=8.3.4", + "pytest-cov>=6.0.0", +] +lint = [ + "ruff>=0.9.1", +] + + + +[project.scripts] apax = 'apax.cli.apax_app:app' -[tool.poetry.group.dev.dependencies] -pytest = "^7.2.0" -pytest-cov = "^4.0.0" -pytest-xdist = "^3.0.2" -coverage = {extras = ["toml"], version = "^6.4.2"} -matplotlib = "^3.6.2" -pre-commit = "^2.20.0" -ruff = "^0.5" - -[tool.poetry.group.docs.dependencies] -sphinx = "^7.2.6" -sphinx-rtd-theme = "^1.3.0" -myst-parser = "^2.0.0" -sphinx-copybutton = "^0.5.2" -furo = "^2023.9.10" -nbsphinx = "^0.9.3" -nbsphinx-link = "^1.3.0" -ipykernel = "^6.29.3" -pandoc = "^2.3" [build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" -[tool.pytest.ini_options] -filterwarnings = ["ignore::FutureWarning:jax.*scatter",] -markers = [ - "slow: mark a test as slow and should only run explicitly" + +[tool.ruff] +line-length = 90 + +[tool.ruff.lint] +select = ["E", "F", "C", "I", "E"] +extend-ignore = [ + "E501", "E731", "E741", "E402", "F841", "F811", "C901", "E203", "E402" ] [tool.coverage.run] @@ -78,11 +96,8 @@ directory = "coverage_html_report" [tool.coverage.report] show_missing = true -[tool.ruff] -line-length = 90 - -[tool.ruff.lint] -select = ["E", "F", "C", "I", "E"] -extend-ignore = [ - "E501", "E731", "E741", "E402", "F841", "F811", "C901", "E203", "E402" +[tool.pytest.ini_options] +filterwarnings = ["ignore::FutureWarning:jax.*scatter",] +markers = [ + "slow: mark a test as slow and should only run explicitly" ] diff --git a/tests/nodes/test_n_model.py b/tests/nodes/test_n_model.py index e5e01853..bffcc4ef 100644 --- a/tests/nodes/test_n_model.py +++ b/tests/nodes/test_n_model.py @@ -62,9 +62,7 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose): save_config_with_seed(tmp_path / "example2.yaml", seed=2) proj = zntrack.Project(automatic_node_names=True) - thermostat = ips.calculators.LangevinThermostat( - time_step=1.0, temperature=100.0, friction=0.01 - ) + thermostat = ips.LangevinThermostat(time_step=1.0, temperature=100.0, friction=0.01) with proj: data = AddData(file=get_md22_stachyose, stop=100) model1 = Apax( @@ -74,7 +72,7 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose): data=data.frames, validation_data=data.frames, config="example2.yaml" ) ensemble = ApaxEnsemble(models=[model1, model2]) - md = ips.calculators.ASEMD( + md = ips.ASEMD( data=data.frames, model=ensemble, thermostat=thermostat, @@ -82,23 +80,21 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose): sampling_rate=1, ) - uncertainty_selection = ips.configuration_selection.ThresholdSelection( - data=md, n_configurations=1, threshold=0.0001 + uncertainty_selection = ips.ThresholdSelection( + data=md.frames, n_configurations=1, threshold=0.0001 ) selection_batch_size = 3 kernel_selection = apax.nodes.BatchKernelSelection( - data=md.atoms, + data=md.frames, train_data=data.frames, models=[model1, model2], n_configurations=selection_batch_size, processing_batch_size=4, ) - prediction = ips.analysis.Prediction(data=kernel_selection.frames, model=ensemble) - analysis = ips.analysis.PredictionMetrics( - x=kernel_selection.frames, y=prediction.atoms - ) + prediction = ips.Prediction(data=kernel_selection.frames, model=ensemble) + analysis = ips.PredictionMetrics(x=kernel_selection.frames, y=prediction.frames) proj.repro() @@ -110,7 +106,7 @@ def test_n_train_2_model(tmp_path, get_md22_stachyose): assert atoms.get_potential_energy() < 0 - uncertainties = [x.calc.results["energy_uncertainty"] for x in md.atoms] - assert [md.atoms[np.argmax(uncertainties)]] == 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