Switch to flit (#478)

This reverts commit f8ed61f.

Author: flying-sheep

.gitignore

@@ -9,6 +9,7 @@ __pycache__/
 /build/
 /dist/
 /*.egg-info/
+/setup.py
 
 # Tests and coverage
 /.pytest_cache/

.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:

MANIFEST.in

@@ -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/__init__.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

anndata/_metadata.py

@@ -1,12 +1,83 @@
 [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 = '[email protected], [email protected]'
+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 breaks tests, https://github.com/pandas-dev/pandas/issues/35446
+    'pandas>=1.0,!=1.1',
+    'numpy>=1.15',
+    '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']
 
 [tool.coverage.run]
 source = ['anndata']