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

pyproject.toml

@@ -2,7 +2,120 @@
 requires = ["setuptools>=42.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
-# pyproject.toml file content
+[project]
+name = "harpy-analysis"
+version = "0.0.2"
+description = "single-cell spatial proteomics analysis that makes you happy"
+readme = "README.md"
+requires-python = ">=3.10,<3.13"
+license = { file = "LICENSE" }
+authors = [
+    { name = "dambi" }
+]
+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"
+]
+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"]

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 harpy import plot as pl  # noqa: E402
+from harpy import points as pt  # noqa: E402
+from harpy import shape as sh  # noqa: E402
+from harpy import table as tb  # noqa: E402