Centralize setup information (scverse#1381)

.readthedocs.yml

@@ -1,4 +1,12 @@
+version: 2
 build:
   image: latest
+sphinx:
+  configuration: docs/conf.py
 python:
   version: 3.6
+  install:
+  - method: pip
+    path: .
+    extra_requirements:
+    - doc

.travis.yml

@@ -2,31 +2,32 @@ dist: xenial
 language: python
 matrix:
   include:
-    - name: "static analysis"
-      python: "3.7"
-      script:
-        - black . --check --diff
-        - python -m scanpy.tests.blackdiff 10
-      after_success: skip
-    - name: "anndata dev"
-      python: "3.7"
-      install:
-        - pip install docutils sphinx
-        - pip install -e .[test,louvain,leiden,magic,scvi,harmony,skmisc]
-        - pip install git+https://github.com/theislab/anndata
+  - name: "static analysis"
+    python: "3.7"
+    install:
+    - pip install .[dev,doc]
+    script:
+    - black . --check --diff
+    - python -m scanpy.tests.blackdiff 10
+    - python setup.py check --restructuredtext --strict
+    - rst2html.py --halt=2 README.rst >/dev/null
+    after_success: skip
+  - name: "anndata dev"
+    python: "3.7"
+    install:
+    - pip install .[dev,test,louvain,leiden,magic,scvi,harmony,skmisc]
+    - pip install git+https://github.com/theislab/anndata
 python:
-  - '3.6'
-  - '3.7'
-  #- '3.8-dev' # https://github.com/numpy/numpy/issues/13790
+- '3.6'
+- '3.7'
+#- '3.8-dev' # https://github.com/numpy/numpy/issues/13790
 cache:
-  - pip
-  - directories: data
+- pip
+- directories:
+  - data
 install:
-  - pip install docutils sphinx
-  - pip install -e .[test,louvain,leiden,magic,scvi,harmony,skmisc]
+- pip install .[dev,test,louvain,leiden,magic,scvi,harmony,skmisc]
 env:
-  - MPLBACKEND=Agg
+- MPLBACKEND=Agg
 script:
-  - pytest --ignore=scanpy/tests/_images
-  - python setup.py check --restructuredtext --strict
-  - rst2html.py --halt=2 README.rst >/dev/null
+- pytest --ignore=scanpy/tests/_images

pyproject.toml

@@ -1,7 +1,25 @@
 [build-system]
-requires = ['setuptools', 'setuptools_scm', 'wheel']
+requires = ['setuptools', 'setuptools_scm', 'wheel', 'pytoml']
 build-backend = 'setuptools.build_meta'
 
+# uses the format of tool.flit.metadata because we’ll move to it anyway
+[tool.scanpy]
+author = '''
+Alex Wolf, Philipp Angerer, Fidel Ramirez, Isaac Virshup,
+Sergei Rybakov, Gokcen Eraslan, Tom White, Malte Luecken,
+Davide Cittaro, Tobias Callies, Marius Lange, Andrés R. Muñoz-Rojas
+'''
+# We don’t need all emails, the main authors are sufficient.
+author-email = '[email protected], [email protected]'
+
+[tool.pytest.ini_options]
+python_files = 'test_*.py'
+testpaths = 'scanpy/tests/'
+xfail_strict = true
+markers = [
+    'internet: tests which rely on internet resources (enable with `--internet-tests`)',
+]
+
 [tool.black]
 line-length = 88
 target-version = ['py36']

requirements.txt

@@ -20,6 +20,5 @@ joblib
 numba>=0.41.0
 umap-learn>=0.3.10
 legacy-api-wrap
-setuptools_scm
 packaging
 sinfo

scanpy/__init__.py

@@ -1,35 +1,10 @@
-# some technical stuff
-import sys
-from ._utils import pkg_version, check_versions, annotate_doc_types
+"""Single-Cell Analysis in Python."""
 
-__author__ = ', '.join([
-    'Alex Wolf',
-    'Philipp Angerer',
-    'Fidel Ramirez',
-    'Isaac Virshup',
-    'Sergei Rybakov',
-    'Gokcen Eraslan',
-    'Tom White',
-    'Malte Luecken',
-    'Davide Cittaro',
-    'Tobias Callies',
-    'Marius Lange',
-    'Andrés R. Muñoz-Rojas',
-])
-__email__ = ', '.join([
-    '[email protected]',
-    '[email protected]',
-    # We don’t need all, the main authors are sufficient.
-])
-try:
-    from setuptools_scm import get_version
-    __version__ = get_version(root='..', relative_to=__file__)
-    del get_version
-except (LookupError, ImportError):
-    __version__ = str(pkg_version(__name__))
+from ._metadata import __version__, __author__, __email__
 
+from ._utils import check_versions
 check_versions()
-del pkg_version, check_versions
+del check_versions
 
 # the actual API
 from ._settings import settings, Verbosity  # start with settings as several tools are using it
@@ -46,5 +21,7 @@
 set_figure_params = settings.set_figure_params
 
 # has to be done at the end, after everything has been imported
+import sys
+from ._utils import annotate_doc_types
 annotate_doc_types(sys.modules[__name__], 'scanpy')
 del sys, annotate_doc_types

scanpy/_compat.py

@@ -1,3 +1,5 @@
+from packaging import version
+
 try:
     from typing import Literal
 except ImportError:
@@ -13,3 +15,19 @@ def __getitem__(cls, values):
 
         class Literal(metaclass=LiteralMeta):
             pass
+
+
+def pkg_metadata(package):
+    try:
+        from importlib.metadata import metadata as m
+    except ImportError:  # < Python 3.8: Use backport module
+        from importlib_metadata import metadata as m
+    return m(package)
+
+
+def pkg_version(package):
+    try:
+        from importlib.metadata import version as v
+    except ImportError:  # < Python 3.8: Use backport module
+        from importlib_metadata import version as v
+    return version.parse(v(package))

scanpy/_metadata.py

@@ -0,0 +1,21 @@
+from pathlib import Path
+
+here = Path(__file__).parent
+
+try:
+    from setuptools_scm import get_version
+    import pytoml
+
+    proj = pytoml.loads((here.parent / 'pyproject.toml').read_text())
+    metadata = proj['tool']['scanpy']
+
+    __version__ = get_version(root='..', relative_to=__file__)
+    __author__ = metadata['author']
+    __email__ = metadata['author-email']
+except (ImportError, LookupError, FileNotFoundError):
+    from ._compat import pkg_metadata
+
+    metadata = pkg_metadata(here.name)
+    __version__ = metadata['Version']
+    __author__ = metadata['Author']
+    __email__ = metadata['Author-email']

scanpy/_utils.py

@@ -15,7 +15,7 @@
 import numpy as np
 from numpy import random
 from scipy import sparse
-from anndata import AnnData
+from anndata import AnnData, __version__ as anndata_version
 from textwrap import dedent
 from packaging import version
 
@@ -36,19 +36,12 @@ class Empty(Enum):
 EPS = 1e-15
 
 
-def pkg_version(package):
-    try:
-        from importlib.metadata import version as v
-    except ImportError:  # < Python 3.8: Use backport module
-        from importlib_metadata import version as v
-    return version.parse(v(package))
-
-
 def check_versions():
-    anndata_version = pkg_version("anndata")
+    from ._compat import pkg_version
+
     umap_version = pkg_version("umap-learn")
 
-    if anndata_version < version.parse('0.6.10'):
+    if version.parse(anndata_version) < version.parse('0.6.10'):
         from . import __version__
 
         raise ImportError(

scanpy/tests/test_ingest.py

@@ -6,7 +6,7 @@
 
 import scanpy as sc
 from scanpy import settings
-from scanpy._utils import pkg_version
+from scanpy._compat import pkg_version
 
 
 X = np.array(

scanpy/tests/test_plotting.py

@@ -6,7 +6,7 @@
 from matplotlib.testing import setup
 from packaging import version
 
-from scanpy._utils import pkg_version
+from scanpy._compat import pkg_version
 
 setup()
 

scanpy/tools/_ingest.py

@@ -9,9 +9,10 @@
 from anndata import AnnData
 
 from .. import settings
-from ..neighbors import _rp_forest_generate
 from .. import logging as logg
-from .._utils import pkg_version, NeighborsView
+from ..neighbors import _rp_forest_generate
+from .._utils import NeighborsView
+from .._compat import pkg_version
 
 ANNDATA_MIN_VERSION = version.parse("0.7rc1")
 

setup.py

@@ -6,11 +6,13 @@
 
 from setuptools import setup, find_packages
 
-
 try:
-    from scanpy import __author__, __email__
-except ImportError:  # Deps not yet installed
-    __author__ = __email__ = ''
+    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']['scanpy']
 
 setup(
     name='scanpy',
@@ -19,8 +21,8 @@
     description='Single-Cell Analysis in Python.',
     long_description=Path('README.rst').read_text('utf-8'),
     url='http://github.com/theislab/scanpy',
-    author=__author__,
-    author_email=__email__,
+    author=metadata['author'],
+    author_email=metadata['author-email'],
     license='BSD',
     python_requires='>=3.6',
     install_requires=[
@@ -33,11 +35,12 @@
         scvi=['scvi>=0.6.5'],
         rapids=['cudf>=0.9', 'cuml>=0.9', 'cugraph>=0.9'],
         magic=['magic-impute>=2.0'],
-        skmisc=["scikit-misc>=0.1.3"],
+        skmisc=['scikit-misc>=0.1.3'],
         harmony=['harmonypy'],
+        dev=['setuptools_scm', 'pytoml', 'black'],
         doc=[
-            'sphinx',
-            'sphinx_rtd_theme',
+            'sphinx<3.1, >3',
+            'sphinx_rtd_theme>=0.3.1',
             'sphinx_autodoc_typehints',
             'scanpydoc>=0.5',
             'typing_extensions; python_version < "3.8"',  # for `Literal`
@@ -48,7 +51,6 @@
             'fsspec',
             'zappy',
             'zarr',
-            'black',
             'profimp',
         ],
     ),