From 7a554b0c04b12499d34704f615a03b0b4213308a Mon Sep 17 00:00:00 2001 From: Benjamin Rombaut Date: Thu, 23 Jan 2025 14:44:24 +0100 Subject: [PATCH] Remove setup.cfg (#87) * add contents of setup.cfg to pyproject.toml * add lockfiles * remove setup.cfg and MANIFEST * remove relative import * revert hatchling backend --- MANIFEST.in | 5 - pixi.lock | 12709 ++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 145 +- setup.cfg | 132 - src/harpy/__init__.py | 12 +- uv.lock | 5753 ++++++++++++++++++ 6 files changed, 18611 insertions(+), 145 deletions(-) delete mode 100644 MANIFEST.in create mode 100644 pixi.lock delete mode 100644 setup.cfg create mode 100644 uv.lock diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index f3155af7..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1,5 +0,0 @@ -include LICENSE -include README.md - -recursive-exclude * __pycache__ -recursive-exclude * *.py[co] diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..be343688 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,12709 @@ +version: 6 +environments: + cli: + channels: + - 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Pre-Alpha", + "Framework :: napari", + "Intended Audience :: Developers", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Software Development :: Testing" +] +dependencies = [ + "spatialdata>=0.2.6", + "xarray>=2024.10.0", + "ome-zarr>=0.9.0", + "scanpy>=1.9.1", + "voronoi-diagram-for-polygons>=0.1.6", + "rasterio>=1.3.2", + "seaborn>=0.12.2", + "leidenalg>=0.9.1", + "geopandas>=1.0.1", + "omegaconf==2.3.0", + "nptyping", + "magicgui", + "pyrootutils", + "universal_pathlib", + "datasets", + "crick", + "spatialdata_io>=0.1.6", +] + +# TODO: change to dependency-groups once pip has support https://github.com/pypa/pip/issues/12963 +[project.optional-dependencies] +plugin = [ + "napari>=0.4.18", + "hydra-core>=1.2.0", + "hydra-colorlog>=1.2.0", + "napari-spatialdata>=0.2.6", + "squidpy>=1.5.0", + "cellpose>=2.2.3", + "pytest-qt" +] +testing = [ + "hydra-core>=1.2.0", + "hydra-colorlog>=1.2.0", + "cellpose>=2.2.3", + "squidpy>=1.5.0", + "datasets", + "jax>=0.4.6", + "jaxlib>=0.4.6", + "basicpy>=1.0.0", + "opencv-python", + "pytest", + "pytest-cov", + "tox", + "nbconvert" +] +cli = [ + "hydra-core>=1.2.0", + "hydra-colorlog>=1.2.0", + "submitit>=1.4.5", + "hydra-submitit-launcher>=1.2.0" +] +docs = [ + "sphinx>=4.5", + "sphinx-book-theme>=1.0.0", + "sphinx_rtd_theme", + "myst-nb", + "sphinxcontrib-bibtex>=1.0.0", + "sphinx-autodoc-typehints", + "sphinx-design", + "ipython>=8.6.0", + "sphinx-copybutton" +] +clustering = [ + "scikit-learn>=1.3.1", + "datasets", + "textalloc", + "joypy", + "bokeh", + "spatialdata-plot>=0.2.0" +] +instanseg = [ + # TODO: wait for 0.0.7 release that drops AICSImageIO dependency + # "instanseg-torch>=0.0.7" + "instanseg-torch @ git+https://github.com/instanseg/instanseg" +] + +[project.urls] +"Bug Tracker" = "https://github.com/saeyslab/harpy/issues" +"Documentation" = "https://github.com/saeyslab/harpy#README.md" +"Source Code" = "https://github.com/saeyslab/harpy" +"User Support" = "https://github.com/saeyslab/harpy/issues" + +[project.scripts] +harpy = "harpy.single:main" + +[project.entry-points."napari.manifest"] +harpy = "harpy:napari.yaml" + [tool.coverage.run] omit = ["src/harpy/_tests/*", "experiments/*", "src/harpy/widgets/*", "docs/*" ] @@ -51,6 +164,13 @@ ignore = [ ] extend-include = ["*.ipynb"] +[tool.hatch.build.targets.wheel] +packages = ["src/harpy"] + +[tool.hatch] +# TODO: remove once instanseg-torch is released +metadata.allow-direct-references = true + [tool.ruff.pydocstyle] convention = "numpy" @@ -60,6 +180,27 @@ convention = "numpy" "*/__init__.py" = ["F401"] "**/test_data/*" = ["ALL"] - [tool.pytest.ini_options] testpaths = ['src/harpy/_tests'] + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["osx-arm64", "linux-64"] + +[tool.pixi.dependencies] +# add some dependencies, which will fetch them from conda instead of pypi +# needed to avoid gdal build step when installing rasterio +rasterio = ">=1.3.2" +# bioio = "*" +# numba = "*" + +[tool.pixi.environments] +# add environments given features of dependency-groups +plugin = ["plugin"] +testing = ["testing"] +cli = ["cli"] +docs = ["docs"] +clustering = ["clustering"] +# TODO fix "instanseg-torch==0.0.6 depends on bioio>=1.1.0,<1.2.dev0 and numpy==2.2.2, +# we can conclude that instanseg-torch==0.0.6 cannot be used" +# instanseg = ["instanseg"] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index a5780d0f..00000000 --- a/setup.cfg +++ /dev/null @@ -1,132 +0,0 @@ -[metadata] -name = harpy-analysis -author = dambi -version = 0.0.2 -description = single-cell spatial proteomics analysis that makes you happy -long_description = file: README.md -long_description_content_type = text/markdown -url = https://github.com/saeyslab/harpy -license = BSD-3-Clause -license_file = LICENSE -license_files = LICENSE -classifiers = - Development Status :: 2 - Pre-Alpha - Framework :: napari - Intended Audience :: Developers - License :: OSI Approved :: BSD License - Operating System :: OS Independent - Programming Language :: Python - Programming Language :: Python :: 3 - Programming Language :: Python :: 3 :: Only - Programming Language :: Python :: 3.9 - Programming Language :: Python :: 3.10 - Programming Language :: Python :: 3.11 - Programming Language :: Python :: 3.12 - Topic :: Software Development :: Testing -project_urls = - Bug Tracker = https://github.com/saeyslab/harpy/issues - Documentation = https://github.com/saeyslab/harpy#README.md - Source Code = https://github.com/saeyslab/harpy - User Support = https://github.com/saeyslab/harpy/issues - -[options] -packages = find: -install_requires = - spatialdata>=0.2.6 - xarray>=v2024.10.0 - ome-zarr>=0.9.0 - scanpy>=1.9.1 - voronoi-diagram-for-polygons>=0.1.6 - rasterio>=1.3.2 - seaborn>=0.12.2 - leidenalg>=0.9.1 - geopandas>=1.0.1 - omegaconf==2.3.0 - nptyping - magicgui - pyrootutils - universal_pathlib - datasets - crick - spatialdata_io>=0.1.6 - #spatialdata_io @ git+https://github.com/ArneDefauw/spatialdata-io.git@visium_hd -python_requires = >=3.8 -include_package_data = True -package_dir = - =src - -[options.packages.find] -where = src - -[options.entry_points] -console_scripts = - harpy = harpy.single:main -napari.manifest = - harpy = harpy:napari.yaml - -[options.extras_require] -plugin = - napari>=0.4.18 - hydra-core>=1.2.0 - hydra-colorlog>=1.2.0 - napari-spatialdata>=0.2.6 - squidpy>=1.5.0 - cellpose>=2.2.3 - pytest-qt - -testing = - hydra-core>=1.2.0 - hydra-colorlog>=1.2.0 - cellpose>=2.2.3 - squidpy>=1.5.0 - datasets - jax>=0.4.6 - jaxlib>=0.4.6 - basicpy>=1.0.0 - opencv-python - pytest - pytest-cov - tox - nbconvert - -cli = - hydra-core>=1.2.0 - hydra-colorlog>=1.2.0 - submitit>=1.4.5 - hydra-submitit-launcher>=1.2.0 - -docs = - sphinx>=4.5 - sphinx-book-theme>=1.0.0 - sphinx_rtd_theme - myst-nb - sphinxcontrib-bibtex>=1.0.0 - sphinx-autodoc-typehints - sphinx-design - # For notebooks - ipython>=8.6.0 - sphinx-copybutton - -clustering = - scikit-learn>=1.3.1 - #flowsom @ git+https://git@github.com/saeyslab/FlowSOM_Python # wait for release. Pypi does not support git+ dependencies - datasets - textalloc - joypy - # For dask cluster dashboard - bokeh - # For visualization - spatialdata-plot>=0.2.0 - #napari-clusters-plotter>=0.7.3 # can not be installed alongside harpy plugin - #napari-convpaint @ git+ssh://git@github.com/guiwitz/napari-convpaint.git - -instanseg = - instanseg-torch - -[options.package_data] -* = *.yaml - -[flake8] -max-line-length = 88 -select = C,E,F,W,B,B950 -extend-ignore = E203, E501 diff --git a/src/harpy/__init__.py b/src/harpy/__init__.py index 18f66531..49b71433 100644 --- a/src/harpy/__init__.py +++ b/src/harpy/__init__.py @@ -11,13 +11,13 @@ except ImportError: pass -from . import ( # noqa: E402 +from harpy import ( # noqa: E402 datasets, io, utils, ) -from . import image as im # noqa: E402 -from . import plot as pl # noqa: E402 -from . import points as pt # noqa: E402 -from . import shape as sh # noqa: E402 -from . import table as tb # noqa: E402 +from harpy import image as im # noqa: E402 +from 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