v0.2 - refactoring, fixes, and enhancements

.github/workflows/pythonpackage.yml

@@ -23,23 +23,24 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install tools
-      run: python -m pip install --upgrade pip
     - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install uv
+        uv venv
+        source .venv/bin/activate
+        uv pip install ruff pytest
+        uv pip install .[dev,test,atac]
+    - name: Install dev dependencies
       run: >
-        pip install
-        ".[test]"
+        uv pip install
         git+https://github.com/bioFAM/mofapy2
         git+https://github.com/scverse/mudata
-    - name: List dependencies
-      run: |
-        pip list
-    - name: Lint with flake8
+    - name: Ruff check
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        source .venv/bin/activate
+        ruff check src/muon
     - name: Test with pytest
       run: |
-        pytest
+        source .venv/bin/activate
+        python -m pytest

.gitignore

@@ -29,6 +29,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+src/muon/_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

pyproject.toml

@@ -1,13 +1,19 @@
 [build-system]
-requires = ["flit_core >=2,<4"]
-build-backend = "flit_core.buildapi"
+build-backend = "hatchling.build"
+requires = ["hatchling", "hatch-vcs"]
 
-[tool.flit.metadata]
-module = "muon"
-author = "Danila Bredikhin"
-author-email = "danila.bredikhin@embl.de"
-description-file = "README.md"
-home-page = "https://github.com/scverse/muon"
+[project]
+name = "muon"
+description = "Multimodal omics analysis framework"
+requires-python = ">= 3.10"
+license = "BSD-3-Clause"
+authors = [
+    { name = "Danila Bredikhin" },
+]
+maintainers = [
+    { name = "Danila Bredikhin", email = "danila@stanford.edu" },
+]
+readme = "README.md"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: BSD License",
@@ -16,49 +22,100 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Intended Audience :: Science/Research"
 ]
-requires-python = ">= 3.10"
-requires = [
+dependencies = [
     "numpy",
     "pandas",
     "matplotlib",
     "seaborn",
     "h5py",
-    "anndata",
+    "anndata >= 0.10.8",
     "scanpy",
     "scikit-learn",
     "umap-learn",
-    "numba",
+    "numba >= 0.57",
     "protobuf",
     "tqdm",
     "mudata",
 ]
+dynamic = ["version"]
 
-[tool.flit.metadata.requires-extra]
+[project.urls]
+Documentation = "https://muon.readthedocs.io/en/latest/"
+Source = "https://github.com/scverse/muon"
+Home-page = "https://muon.scverse.org/"
+
+[project.optional-dependencies]
+dev = [
+    "setuptools_scm",
+]
 docs = [
-    "sphinx >= 4.0",
-    "pydata-sphinx-theme==0.8.1",
-    "sphinx-book-theme==0.3.3",
+    "sphinx",
+    "sphinx-book-theme",
+    "pydata-sphinx-theme",
     "readthedocs-sphinx-search",
     "nbsphinx",
-    "sphinx_automodapi"
-]
-atac = [
-    "pybedtools",
-    "pysam"
+    "sphinx_automodapi",
+    "recommonmark"
 ]
 test = [
     "pytest",
-    "flake8",
     "mofapy2",
+    "zarr < 3",  # anndata compat
+]
+# TODO: replace by a single depencency - chame
+atac = [
+    "pybedtools",
+    "pysam",
 ]
 
-[tool.flit.metadata.urls]
-Documentation = "https://muon.readthedocs.io/en/latest/"
-
-[tool.flit.sdist]
-exclude = [".github", "docs/build"]
-
+[tool.pytest.ini_options]
+python_files = "test_*.py"
+testpaths = [
+    "./tests", # unit tests
+]
 
 [tool.black]
 line-length = 100
-target-version = ['py37']
+target-version = ['py39']
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/muon/_version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/muon"]
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "/.github",
+  "/docs",
+]
+
+[tool.ruff]
+src = ["src"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
+select = [
+    "E",   # Error detected by Pycodestyle
+    "F",   # Errors detected by Pyflakes
+    "W",   # Warning detected by Pycodestyle
+    "UP",  # pyupgrade
+    "I",   # isort
+    "TCH", # manage type checking blocks
+    "ICN", # Follow import conventions
+    "PTH", # Pathlib instead of os.path
+    "PT",  # Pytest conventions
+]
+ignore = [
+    # line too long -> we accept long comment lines; formatter gets rid of long code lines
+    "E501",
+    # Do not assign a lambda expression, use a def -> AnnData allows lambda expression assignments,
+    "E731",
+    # allow I, O, l as variable names -> I is the identity matrix, i, j, k, l is reasonable indexing notation
+    "E741",
+]

src/muon/__init__.py

@@ -0,0 +1,61 @@
+"""Multimodal omics analysis framework"""
+
+try:  # See https://github.com/maresb/hatch-vcs-footgun-example
+    from setuptools_scm import get_version
+
+    __version__ = get_version(root="../..", relative_to=__file__)
+except (ImportError, LookupError):
+    try:
+        from ._version import __version__
+    except ModuleNotFoundError:
+        raise RuntimeError("muon is not correctly installed. Please install it, e.g. with pip.")
+
+
+from mudata import MuData
+from mudata._core.io import (
+    read,
+    read_anndata,
+    read_h5ad,
+    read_h5mu,
+    read_zarr,
+    write_anndata,
+    write_h5ad,
+    write_h5mu,
+    write_zarr,
+)
+
+from . import _atac as atac
+from . import _prot as prot
+from . import _rna as rna
+from ._core import plot as pl
+from ._core import preproc as pp
+from ._core import tools as tl
+from ._core import utils
+from ._core.config import set_options
+from ._core.io import read_10x_h5, read_10x_mtx
+
+__all__ = [
+    "__version__",
+    "MuData",
+    "pp",
+    "tl",
+    "pl",
+    "utils",
+    # mudata I/O
+    "read_h5mu",
+    "read_h5ad",
+    "read_anndata",
+    "read_zarr",
+    "write_h5mu",
+    "write_h5ad",
+    "write_anndata",
+    "write_zarr",
+    "read",
+    # muon I/O
+    "read_10x_h5",
+    "read_10x_mtx",
+    "set_options",
+    "atac",
+    "prot",
+    "rna",
+]

src/muon/_atac/__init__.py

@@ -0,0 +1,6 @@
+from . import plot as pl
+from . import preproc as pp
+from . import tools as tl
+from .io import read_10x_h5, read_10x_mtx, read_snap
+
+__all__ = ["pp", "tl", "pl", "read_10x_h5", "read_10x_mtx", "read_snap"]