Switch to flit

.travis.yml

@@ -8,17 +8,16 @@ matrix:
   include:
   - name: static analysis
     python: "3.7"
-    install: pip install .[dev,doc]
+    install: pip install .[dev]
     script:
     - black . --check --diff
-    - python setup.py check --restructuredtext --strict
     - rst2html.py --halt=2 README.rst >/dev/null
     after_success: skip
 python:
 - "3.6"
 - "3.7"
 install:
-- pip install -e .[dev,test]
+- pip install .[dev,test]
 script:
 - pytest --cov=. --cov-report=xml
 after_success:

anndata/__init__.py

@@ -1,21 +1,23 @@
 """Annotated multivariate observation data."""
 
-from ._metadata import __version__, __author__, __email__
+from ._metadata import __version__, __author__, __email__, within_flit
 
-from ._core.anndata import AnnData, ImplicitModificationWarning
-from ._core.merge import concat
-from ._core.raw import Raw
-from ._io import (
-    read_h5ad,
-    read_loom,
-    read_hdf,
-    read_excel,
-    read_umi_tools,
-    read_csv,
-    read_text,
-    read_mtx,
-    read_zarr,
-)
+if not within_flit():
+    del within_flit
+    from ._core.anndata import AnnData, ImplicitModificationWarning
+    from ._core.merge import concat
+    from ._core.raw import Raw
+    from ._io import (
+        read_h5ad,
+        read_loom,
+        read_hdf,
+        read_excel,
+        read_umi_tools,
+        read_csv,
+        read_text,
+        read_mtx,
+        read_zarr,
+    )
 
-# backwards compat / shortcut for default format
-from ._io import read_h5ad as read
+    # backwards compat / shortcut for default format
+    from ._io import read_h5ad as read

anndata/_metadata.py

@@ -1,14 +1,34 @@
+import traceback
 from pathlib import Path
 
 here = Path(__file__).parent
 
+
+def refresh_entry_points():
+    """\
+    Under some circumstances, (e.g. when installing a PEP 517 package via pip),
+    pkg_resources.working_set.entries is stale. This tries to fix that.
+    See https://github.com/pypa/setuptools_scm/issues/513
+    """
+    try:
+        import sys
+        import pkg_resources
+
+        ws: pkg_resources.WorkingSet = pkg_resources.working_set
+        for entry in sys.path:
+            ws.add_entry(entry)
+    except Exception:
+        pass
+
+
 try:
     from setuptools_scm import get_version
     import pytoml
 
     proj = pytoml.loads((here.parent / "pyproject.toml").read_text())
-    metadata = proj["tool"]["anndata"]
+    metadata = proj["tool"]["flit"]["metadata"]
 
+    refresh_entry_points()
     __version__ = get_version(root="..", relative_to=__file__)
     __author__ = metadata["author"]
     __email__ = metadata["author-email"]
@@ -22,3 +42,16 @@
     __version__ = meta["Version"]
     __author__ = meta["Author"]
     __email__ = meta["Author-email"]
+
+
+def within_flit():
+    """\
+    Checks if we are being imported by flit.
+    This is necessary so flit can import __version__ without all depedencies installed.
+    There are a few options to make this hack unnecessary, see:
+    https://github.com/takluyver/flit/issues/253#issuecomment-737870438
+    """
+    for frame in traceback.extract_stack():
+        if frame.name == "get_docstring_and_version_via_import":
+            return True
+    return False

pyproject.toml

@@ -1,12 +1,85 @@
 [build-system]
-requires = ['setuptools', 'setuptools_scm', 'wheel', 'pytoml']
-build-backend = 'setuptools.build_meta'
+build-backend = 'flit_core.buildapi'
+requires = [
+    'flit_core >=3.1,<4',
+    'setuptools_scm',
+    'pytoml',
+    'importlib_metadata>=0.7; python_version < "3.8"',
+]
 
-# uses the format of tool.flit.metadata because we’ll move to it anyway
-[tool.anndata]
+[tool.flit.metadata]
+module = 'anndata'
 author = 'Philipp Angerer, Alex Wolf, Isaac Virshup, Sergei Rybakov'
 # We don’t need all emails, the main authors are sufficient.
 author-email = 'phil.angerer@gmail.com, f.alex.wolf@gmx.de'
+description-file = 'README.rst'
+home-page = 'http://github.com/theislab/anndata'
+urls = { Documentation = 'https://anndata.readthedocs.io/' }
+classifiers = [
+    'License :: OSI Approved :: BSD License',
+    'Environment :: Console',
+    'Framework :: Jupyter',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'Natural Language :: English',
+    'Operating System :: MacOS :: MacOS X',
+    'Operating System :: Microsoft :: Windows',
+    'Operating System :: POSIX :: Linux',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'Topic :: Scientific/Engineering :: Visualization',
+]
+requires-python = '>=3.6'
+requires = [
+    'pandas>=1.1.1',  # pandas <1.1.1 has pandas/issues/35446
+    'numpy>=1.16.5',  # required by pandas 1.x
+    'scipy~=1.0',
+    'h5py',
+    'natsort',
+    'packaging>=20',
+    'xlrd<2.0',  # xlsx format not support anymore from v2.0, see pandas/issues/38524
+    # for getting the stable version
+    'importlib_metadata>=0.7; python_version < "3.8"',
+]
+
+[tool.flit.metadata.requires-extra]
+dev = [
+    # dev version generation
+    'setuptools_scm',
+    'pytoml',
+    # static checking
+    'black>=20.8b1',
+    'docutils',
+]
+doc = [
+    # Sphinx 2 has nicer looking sections
+    'sphinx>=2.0.1',
+    'sphinx-rtd-theme',
+    'sphinx-autodoc-typehints>=1.11.0',
+    'sphinx_issues',
+    'scanpydoc>=0.5',
+    'typing_extensions; python_version < "3.8"',
+]
+test = [
+    'loompy>=3.0.5',
+    'pytest>=6.0',
+    'pytest-cov>=2.10',
+    'zarr',
+    'matplotlib',
+    'sklearn',
+    'xlrd',
+    'joblib',
+    'boltons',
+    'scanpy',
+]
+
+[tool.flit.sdist]
+exclude = [
+    'anndata/tests',
+    'setup.py',
+]
 
 [tool.coverage.run]
 source = ['anndata']

setup.py

@@ -1,74 +1,73 @@
+"""Temporary setuptools bridge
+Don't use this except if you have a deadline or you encounter a bug.
+"""
+import re
 import sys
+from warnings import warn
 
-if sys.version_info < (3, 6):
-    sys.exit("anndata requires Python >= 3.6")
+import setuptools
 from pathlib import Path
 
-from setuptools import setup, find_namespace_packages
+from flit_core import common, config
+from setuptools_scm.integration import find_files
 
-try:
-    import pytoml
-except ImportError:
-    sys.exit("Please use `pip install .` or install pytoml first.")
 
-proj = pytoml.loads(Path("pyproject.toml").read_text())
-metadata = proj["tool"]["anndata"]
-
-setup(
-    name="anndata",
-    use_scm_version=True,
-    setup_requires=["setuptools_scm"],
-    description="Annotated Data.",
-    long_description=Path("README.rst").read_text("utf-8"),
-    url="http://github.com/theislab/anndata",
-    author=metadata["author"],
-    author_email=metadata["author-email"],
-    license="BSD-3-Clause",
-    install_requires=[
-        l.strip() for l in Path("requirements.txt").read_text("utf-8").splitlines()
-    ],
-    extras_require=dict(
-        dev=["setuptools_scm", "pytoml", "black>=20.8b1"],
-        doc=[
-            # Sphinx 2 has nicer looking sections
-            "sphinx>=2.0.1",
-            "sphinx-rtd-theme",
-            "sphinx-autodoc-typehints>=1.11.0",
-            "sphinx_issues",
-            "scanpydoc>=0.5",
-            'typing_extensions; python_version < "3.8"',
-        ],
-        test=[
-            "loompy>=3.0.5",
-            "pytest>=4.6",
-            "pytest-cov>=2.10",
-            "docutils",  # for rst2html.py
-            "zarr",
-            "matplotlib",
-            "sklearn",
-            "xlrd<2",
-            "joblib",
-            "boltons",
-            "scanpy",
-        ],
-    ),
-    python_requires=">=3.6",
-    packages=find_namespace_packages(include=["anndata", "anndata.*"]),
-    include_package_data=True,
-    zip_safe=False,
-    classifiers=[
-        "Environment :: Console",
-        "Framework :: Jupyter",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "Natural Language :: English",
-        "Operating System :: MacOS :: MacOS X",
-        "Operating System :: Microsoft :: Windows",
-        "Operating System :: POSIX :: Linux",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Topic :: Scientific/Engineering :: Visualization",
-    ],
+field_map = dict(
+    description="summary",
+    long_description="description",
+    long_description_content_type="description_content_type",
+    python_requires="requires_python",
+    url="home_page",
+    **{
+        n: n
+        for n in ["name", "version", "author", "author_email", "license", "classifiers"]
+    },
 )
+
+
+def setup_args(config_path=Path("pyproject.toml")):
+    cfg = config.read_flit_config(config_path)
+    module = common.Module(cfg.module, config_path.parent)
+    metadata = common.make_metadata(module, cfg)
+    kwargs = {}
+    for st_field, metadata_field in field_map.items():
+        val = getattr(metadata, metadata_field, None)
+        if val is not None:
+            kwargs[st_field] = val
+        else:
+            msg = f"{metadata_field} not found in {dir(metadata)}"
+            assert metadata_field in {"license"}, msg
+    kwargs["packages"] = setuptools.find_packages(include=[metadata.name + "*"])
+    if metadata.requires_dist:
+        kwargs["install_requires"] = [
+            req for req in metadata.requires_dist if "extra ==" not in req
+        ]
+    if cfg.reqs_by_extra:
+        kwargs["extras_require"] = cfg.reqs_by_extra
+    scripts = cfg.entrypoints.get("console_scripts")
+    if scripts is not None:
+        kwargs["entry_points"] = dict(
+            console_scipts=[" = ".join(ep) for ep in scripts.items()]
+        )
+    kwargs["include_package_data"] = True
+    kwargs["package_data"] = {
+        module.name: [
+            re.escape(f[len(module.name) + 1 :]) for f in find_files(module.path)
+        ]
+    }
+    return kwargs
+
+
+if __name__ == "__main__":
+    if "develop" in sys.argv:
+        msg = (
+            "Please use `flit install -s` or `flit install --pth-file` "
+            "instead of `pip install -e`/`python setup.py develop` "
+            "once https://github.com/pypa/pip/issues/9670 is fixed."
+        )
+    elif "install" in sys.argv:
+        msg = 'Please use `pip install "$d"` instead of `python "$d/setup.py" install`'
+    else:
+        msg = "Please use `pip ...` or `flit ...` instead of `python setup.py ...`"
+    warn(msg, FutureWarning)
+    setuptools.setup(**setup_args())