diff --git a/.coveragerc_omit b/.coveragerc_omit index b2036261..e70d702e 100644 --- a/.coveragerc_omit +++ b/.coveragerc_omit @@ -1,16 +1,16 @@ [run] omit = - vitessce/config.py - vitessce/export.py - vitessce/file_def_utils.py - vitessce/routes.py - vitessce/widget.py - vitessce/wrappers.py - vitessce/repr.py - vitessce/utils.py - vitessce/data_utils/anndata.py - vitessce/data_utils/ome.py - vitessce/data_utils/entities.py - vitessce/data_utils/multivec.py - vitessce/widget_plugins/demo_plugin.py - vitessce/widget_plugins/spatial_query.py \ No newline at end of file + src/vitessce/config.py + src/vitessce/export.py + src/vitessce/file_def_utils.py + src/vitessce/routes.py + src/vitessce/widget.py + src/vitessce/wrappers.py + src/vitessce/repr.py + src/vitessce/utils.py + src/vitessce/data_utils/anndata.py + src/vitessce/data_utils/ome.py + src/vitessce/data_utils/entities.py + src/vitessce/data_utils/multivec.py + src/vitessce/widget_plugins/demo_plugin.py + src/vitessce/widget_plugins/spatial_query.py \ No newline at end of file diff --git a/.envrc b/.envrc deleted file mode 100644 index 40ee06b8..00000000 --- a/.envrc +++ /dev/null @@ -1 +0,0 @@ -use conda vitessce-python-dev \ No newline at end of file diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 101a0fc2..f5cfda07 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -16,28 +16,22 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 + - uses: astral-sh/setup-uv@v3 + with: + version: "latest" - name: Install system dependencies run: | sudo apt-get update sudo apt-get install -y pandoc - - uses: actions/setup-python@v2 - with: - python-version: '3.9' - name: Install vitessce - run: pip install -e .[dev,docs,all] + run: uv sync --extra dev --extra docs --extra all - name: Run tests - run: pytest + run: uv run pytest - name: Build a binary wheel and a source tarball - run: >- - python -m - build - --sdist - --wheel - --outdir dist/ - . + run: uv build --sdist --wheel - name: Build docs run: | - make html + uv run make html touch docs-dist/html/.nojekyll - uses: actions/upload-pages-artifact@v1 with: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 2697cb06..c5a5f282 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -7,12 +7,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 + - uses: astral-sh/setup-uv@v3 + with: + version: "latest" - name: Install system dependencies run: | sudo apt-get update sudo apt-get install -y pandoc - - uses: actions/setup-python@v2 - with: - python-version: '3.9' - - run: pip install -e .[docs,all] - - run: make html + - run: uv sync --extra docs --extra all + - run: uv run make html diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 42915059..16c3401c 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -7,9 +7,8 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: astral-sh/setup-uv@v3 with: - python-version: '3.9' - architecture: 'x64' - - run: pip install .[dev] - - run: flake8 + version: "latest" + - run: uv sync --extra dev + - run: uv run flake8 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 2dddba77..f3c58cec 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -7,19 +7,21 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - version: ['3.9', '3.12'] + version: ['3.10', '3.12'] steps: - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: astral-sh/setup-uv@v3 with: - python-version: ${{ matrix.version }} + version: "latest" + env: + UV_PYTHON: ${{ matrix.version }} - name: Install vitessce - run: pip install -e .[dev,all] + run: uv sync --extra dev --extra all - name: Run tests and report coverage with omits run: | - coverage run --rcfile .coveragerc_omit --module pytest && \ - coverage report --show-missing --fail-under 100 + uv run coverage run --rcfile .coveragerc_omit --module pytest && \ + uv run coverage report --show-missing --fail-under 100 - name: Run tests and report coverage without omits run: | - coverage run --rcfile .coveragerc_real --module pytest && \ - coverage report --show-missing + uv run coverage run --rcfile .coveragerc_real --module pytest && \ + uv run coverage report --show-missing diff --git a/.github/workflows/test_demos.yml b/.github/workflows/test_demos.yml index aba56104..59ccd9c0 100644 --- a/.github/workflows/test_demos.yml +++ b/.github/workflows/test_demos.yml @@ -7,15 +7,11 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: astral-sh/setup-uv@v3 with: - python-version: '3.9' - - run: | - pip install "pulp==2.7.0" - pip install snakemake - pip install pyyaml + version: "latest" - name: Install vitessce - run: pip install -e .[dev,all] + run: uv sync --extra dev --extra all --extra demos - name: Run tests working-directory: ./demos - run: snakemake -j 1 --dry-run + run: uv run snakemake -j 1 --dry-run diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..7c7a975f --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.10 \ No newline at end of file diff --git a/README.md b/README.md index 0cd244e1..14b00f06 100644 --- a/README.md +++ b/README.md @@ -28,9 +28,7 @@ For a development installation (requires NodeJS and NPM), $ git clone https://github.com/vitessce/vitessce-python.git $ cd vitessce-python - $ conda env create -f environment.yml - $ conda activate vitessce-python-dev - $ pip install -e ".[dev,docs,all]" + $ uv sync --extra dev --extra docs --extra all ### Conda environments @@ -43,8 +41,8 @@ In this repository, there are multiple conda environments for different purposes ## Linting and testing ```sh -flake8 -pytest +uv run flake8 +uv run pytest ``` ### Formatting @@ -52,20 +50,20 @@ pytest One file: ```sh -autopep8 --in-place --aggressive ./path/to/file.py +uv run autopep8 --in-place --aggressive ./path/to/file.py ``` All `.py` files: ```sh -find . -name '*.py' -exec autopep8 --in-place --aggressive '{}' \; +find . -name '*.py' -exec uv run autopep8 --in-place --aggressive '{}' \; ``` ## Documentation ```sh -make html +uv run make html ``` diff --git a/docs/notebooks/.envrc b/docs/notebooks/.envrc deleted file mode 100644 index ec2131bf..00000000 --- a/docs/notebooks/.envrc +++ /dev/null @@ -1 +0,0 @@ -use conda vitessce-python-notebooks \ No newline at end of file diff --git a/docs/notebooks/README.md b/docs/notebooks/README.md index bcdd6996..c1dc3e17 100644 --- a/docs/notebooks/README.md +++ b/docs/notebooks/README.md @@ -8,15 +8,13 @@ Some of the example notebooks rely on external single-cell data analysis package ```sh cd docs/notebooks -conda env create -f environment.yml -conda activate vitessce-python-notebooks -pip install -e "../..[dev]" +uv sync --extra dev --extra docs --extra all ``` ## Run ```sh -jupyter lab +uv run jupyter lab ``` ## Troubleshooting diff --git a/environment.yml b/environment.yml deleted file mode 100644 index d78ca0d2..00000000 --- a/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: vitessce-python-dev -channels: - - defaults - - conda-forge -dependencies: - - python==3.9 - - pip diff --git a/pyproject.toml b/pyproject.toml index 328a1f9e..5f9a872e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [build-system] -requires = ["setuptools>=67.0", "wheel>=0.38.4"] -build-backend = "setuptools.build_meta" +requires = ["hatchling"] +build-backend = "hatchling.build" [project] name = "vitessce" @@ -11,7 +11,7 @@ authors = [ description = "Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce" readme = "README.md" license = {file = "LICENSE"} -requires-python = ">=3.9" +requires-python = ">=3.10" keywords = ["ipython", "jupyter", "widgets"] classifiers = [ 'Development Status :: 4 - Beta', @@ -31,9 +31,11 @@ dependencies = [ 'negspy>=0.2.24', 'pandas>=1.1.2', 'black>=21.11b1', - 'numpy>=1.21.2,<2.0', - 'anndata>=0.7.8,<0.11', - 'scanpy>=1.9.3', + 'numpy>=1.21.2', + 'anndata>=0.7.8', + # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not + # Reference: https://github.com/scverse/scanpy/pull/3115/files + 'scanpy>=1.10.2', 'ome-zarr>=0.8.3', 'tifffile>=2020.10.1', 'jsonschema>=3.2', @@ -41,14 +43,7 @@ dependencies = [ ] [project.optional-dependencies] -dev = [ - 'build==0.1.0', - 'pytest>=6.2.4', - 'loompy>=3.0.6', - 'coverage>=6.3.2', - 'flake8==3.8.4', - 'spatialdata>=0.2.2', -] +dev = [] docs = [ 'sphinx==4.2.0', 'sphinx-rtd-theme==1.0.0', @@ -79,7 +74,7 @@ all = [ 'uvicorn>=0.17.0', 'ujson>=4.0.1', 'starlette==0.14.0', - 'generate-tiff-offsets>=0.1.7', + 'generate-tiff-offsets>=0.1.8', 'kerchunk>=0.2.6', 'fsspec', @@ -93,9 +88,46 @@ building = [] testing = [] linting = [] notebook = [] +demos = [ + "pulp==2.7.0", + "snakemake", + "pyyaml", +] + +[dependency-groups] +dev = [ + 'build==0.1.0', + 'pytest>=6.2.4', + 'loompy>=3.0.6', + 'coverage>=6.3.2', + 'flake8==3.8.4', + #'spatialdata>=0.2.2', + 'jupyterlab', + 'numba>=0.53.0', + 'jupyterlab>=3', + 'boto3>=1.16.30', + 'scikit-misc>=0.1.3', +] + +[tool.uv] +default-groups = ["dev"] +override-dependencies = [ + 'starlette==0.14.0' +] + +[tool.hatch.build] +exclude = [".github", "docs", "demos", "binder"] [project.urls] repository = "https://github.com/vitessce/vitessce-python" [tool.setuptools] packages = ["vitessce", "vitessce.data_utils", "vitessce.widget_plugins"] +package-dir = {"" = "src"} + +# Reference: https://stackoverflow.com/a/50156706 +[tool.pytest.ini_options] +pythonpath = ["src"] +testpaths = ["tests"] +addopts = ["--doctest-modules", "--verbose", "--ignore=docs", "--ignore=demos"] + diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index d52d0f7c..00000000 --- a/pytest.ini +++ /dev/null @@ -1,2 +0,0 @@ -[pytest] -addopts = --doctest-modules --verbose --ignore=docs --ignore=demos \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 09602d86..28370066 100644 --- a/setup.cfg +++ b/setup.cfg @@ -4,9 +4,9 @@ universal=1 [flake8] per-file-ignores = # Special case: names are reimported from __init__.py, so unused imports are expected. - vitessce/__init__.py: F401 - vitessce/data_utils/__init__.py: F401 - vitessce/widget_plugins/__init__.py: F401 + src/vitessce/__init__.py: F401 + src/vitessce/data_utils/__init__.py: F401 + src/vitessce/widget_plugins/__init__.py: F401 ignore = # Ignore line too long E501, @@ -20,6 +20,10 @@ ignore = E128 exclude = ./js/node_modules/, + ./docs/, + ./demos/, + ./binder/, + ./.venv/, ./docs/notebooks/.ipynb_checkpoints/, ./build/, ./.ipynb_checkpoints/ \ No newline at end of file diff --git a/vitessce/__init__.py b/src/vitessce/__init__.py similarity index 100% rename from vitessce/__init__.py rename to src/vitessce/__init__.py diff --git a/vitessce/config.py b/src/vitessce/config.py similarity index 100% rename from vitessce/config.py rename to src/vitessce/config.py diff --git a/vitessce/config_converter.py b/src/vitessce/config_converter.py similarity index 100% rename from vitessce/config_converter.py rename to src/vitessce/config_converter.py diff --git a/vitessce/constants.py b/src/vitessce/constants.py similarity index 100% rename from vitessce/constants.py rename to src/vitessce/constants.py diff --git a/vitessce/data_utils/__init__.py b/src/vitessce/data_utils/__init__.py similarity index 100% rename from vitessce/data_utils/__init__.py rename to src/vitessce/data_utils/__init__.py diff --git a/vitessce/data_utils/anndata.py b/src/vitessce/data_utils/anndata.py similarity index 100% rename from vitessce/data_utils/anndata.py rename to src/vitessce/data_utils/anndata.py diff --git a/vitessce/data_utils/entities.py b/src/vitessce/data_utils/entities.py similarity index 100% rename from vitessce/data_utils/entities.py rename to src/vitessce/data_utils/entities.py diff --git a/vitessce/data_utils/multivec.py b/src/vitessce/data_utils/multivec.py similarity index 100% rename from vitessce/data_utils/multivec.py rename to src/vitessce/data_utils/multivec.py diff --git a/vitessce/data_utils/ome.py b/src/vitessce/data_utils/ome.py similarity index 100% rename from vitessce/data_utils/ome.py rename to src/vitessce/data_utils/ome.py diff --git a/vitessce/export.py b/src/vitessce/export.py similarity index 100% rename from vitessce/export.py rename to src/vitessce/export.py diff --git a/vitessce/file_def_utils.py b/src/vitessce/file_def_utils.py similarity index 100% rename from vitessce/file_def_utils.py rename to src/vitessce/file_def_utils.py diff --git a/vitessce/repr.py b/src/vitessce/repr.py similarity index 100% rename from vitessce/repr.py rename to src/vitessce/repr.py diff --git a/vitessce/routes.py b/src/vitessce/routes.py similarity index 100% rename from vitessce/routes.py rename to src/vitessce/routes.py diff --git a/vitessce/utils.py b/src/vitessce/utils.py similarity index 100% rename from vitessce/utils.py rename to src/vitessce/utils.py diff --git a/vitessce/widget.py b/src/vitessce/widget.py similarity index 100% rename from vitessce/widget.py rename to src/vitessce/widget.py diff --git a/vitessce/widget_plugins/__init__.py b/src/vitessce/widget_plugins/__init__.py similarity index 100% rename from vitessce/widget_plugins/__init__.py rename to src/vitessce/widget_plugins/__init__.py diff --git a/vitessce/widget_plugins/demo_plugin.py b/src/vitessce/widget_plugins/demo_plugin.py similarity index 100% rename from vitessce/widget_plugins/demo_plugin.py rename to src/vitessce/widget_plugins/demo_plugin.py diff --git a/vitessce/widget_plugins/spatial_query.py b/src/vitessce/widget_plugins/spatial_query.py similarity index 100% rename from vitessce/widget_plugins/spatial_query.py rename to src/vitessce/widget_plugins/spatial_query.py diff --git a/vitessce/wrappers.py b/src/vitessce/wrappers.py similarity index 100% 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