pep-621 pyproject.toml (scverse#2042)

* Initial pep-621 commit * Add content-type to readme * Update metadata retrieval * Update `__author__` field usage in docs It was getting pretty unwieldy and out of date anyways. * Require flit>=3.4 to allow editable installs * Update phil’s maintainer email * update install instructions * Clean up for install instructions * Remove setup.py * Syntax highlighting Co-authored-by: Philipp A <[email protected]>
The-Dev-Effect · Dec 6, 2021 · 50f015b · 50f015b
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diff --git a/docs/conf.py b/docs/conf.py
@@ -23,8 +23,8 @@
 
 # General information
 project = 'Scanpy'
-author = scanpy.__author__
-copyright = f'{datetime.now():%Y}, {author}.'
+author = 'Scanpy development team'
+copyright = f'{datetime.now():%Y}, the Scanpy development team.'
 version = scanpy.__version__.replace('.dirty', '')
 release = version
 

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -4,19 +4,25 @@ Installation
 Anaconda
 ~~~~~~~~
 If you do not have a working installation of Python 3.6 (or later), consider
-installing Miniconda_ (see `Installing Miniconda`_). Then run::
+installing Miniconda_ (see `Installing Miniconda`_). Then run:
+
+.. code:: shell
 
     conda install -c conda-forge scanpy python-igraph leidenalg
 
-Pull Scanpy from `PyPI <https://pypi.org/project/scanpy>`__ (consider using ``pip3`` to access Python 3)::
+Pull Scanpy from `PyPI <https://pypi.org/project/scanpy>`__ (consider using ``pip3`` to access Python 3):
+
+.. code:: shell
 
     pip install scanpy
 
 .. _from PyPI: https://pypi.org/project/scanpy
 
 PyPI only
 ~~~~~~~~~
-If you prefer to exclusively use PyPI run::
+If you prefer to exclusively use PyPI run:
+
+.. code:: shell
 
     pip install 'scanpy[leiden]'
 
@@ -30,17 +36,33 @@ parts of scanpy but aren't requirements: python-igraph_ [Csardi06]_ and leiden_
 
 Development Version
 ~~~~~~~~~~~~~~~~~~~
-To work with the latest version `on GitHub`_: clone the repository and `cd` into
-its root directory. To install using symbolic links (stay up to date with your
-cloned version after you update with `git pull`) call::
+To work with the latest version `on GitHub`_: clone the repository and `cd` into its root directory.
+
+.. code:: shell
+
+   gh repo clone theislab/scanpy
+   cd scanpy
+
+If you are using `pip>=21.3`, an editable install can be made:
+
+.. code:: shell
+
+   pip install -e '.[dev,doc,test]'
+
+For older versions of `pip`, flit_ can be used directly.
+To install using symbolic links (stay up to date with your cloned version after you update with `git pull`) call:
+
+.. code:: shell
 
     flit install -s --deps=develop  # from an activated venv or conda env
     # or
     flit install -s --deps=develop --python path/to/venv/bin/python
 
 .. _on GitHub: https://github.com/theislab/scanpy
 
-If you want to let conda_ handle the installations of dependencies, do::
+If you want to let conda_ handle the installations of dependencies, do:
+
+.. code:: shell
 
     pip install beni
     beni pyproject.toml > environment.yml
@@ -52,10 +74,9 @@ On Windows, you might have to use `flit install --pth-file`
 if you are not able to give yourself the `create symbolic links`_ privilege.
 
 .. _create symbolic links: https://docs.microsoft.com/en-us/windows/security/threat-protection/security-policy-settings/create-symbolic-links
+.. _flit: https://flit.readthedocs.io/en/latest/
 
-.. note::
-
-    `pip install -e` still works, but may not in future versions.
+For instructions on how to work with the code, see the :ref:`contributing guide <contribution-guide>`.
 
 Docker
 ~~~~~~
@@ -67,7 +88,9 @@ If you're using Docker_, you can use e.g. the image `gcfntnu/scanpy`_ from Docke
 
 Troubleshooting
 ~~~~~~~~~~~~~~~
-If you get a `Permission denied` error, never use `sudo pip`. Instead, use virtual environments or::
+If you get a `Permission denied` error, never use `sudo pip`. Instead, use virtual environments or:
+
+.. code:: shell
 
     pip install --user scanpy
 
@@ -76,7 +99,9 @@ If you get a `Permission denied` error, never use `sudo pip`. Instead, use virtu
 - `brew install igraph`
 - If python-igraph still fails to install, see the question on `compiling igraph`_.
   Alternatively consider installing gcc via `brew install gcc --without-multilib`
-  and exporting the required variables::
+  and exporting the required variables:
+
+  .. code:: shell
 
       export CC="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X"
       export CXX="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X"

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,136 +1,153 @@
 [build-system]
-build-backend = 'flit_core.buildapi'
+build-backend = "flit_core.buildapi"
 requires = [
-    'flit_core >=3.1,<4',
-    'setuptools_scm',
-    'pytoml',
-    'importlib_metadata>=0.7; python_version < "3.8"',
+    "flit_core >=3.4,<4",
+    "setuptools_scm",
+    "tomli",
+    "importlib_metadata>=0.7; python_version < '3.8'",
     # setup.py stuff
-    'packaging',
+    "packaging",
 ]
 
-[tool.flit.metadata]
-module = '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]'
-description-file = 'README.rst'
-home-page = 'http://github.com/theislab/scanpy'
-urls = { Documentation = 'https://scanpy.readthedocs.io/' }
+[project]
+name = "scanpy"
+description = "Single-Cell Analysis in Python."
+requires-python = ">=3.7"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Alex Wolf"},
+    {name = "Philipp Angerer"},
+    {name = "Fidel Ramirez"},
+    {name = "Isaac Virshup"},
+    {name = "Sergei Rybakov"},
+    {name = "Gokcen Eraslan"},
+    {name = "Tom White"},
+    {name = "Malte Luecken"},
+    {name = "Davide Cittaro"},
+    {name = "Tobias Callies"},
+    {name = "Marius Lange"},
+    {name = "Andrés R. Muñoz-Rojas"},
+]
+maintainers = [
+    {name = "Isaac Virshup", email = "[email protected]"},
+    {name = "Philipp Angerer", email = "[email protected]"},
+    {name = "Alex Wolf", email = "[email protected]"},
+]
+readme = {file = "README.rst", content-type="text/x-rst"}
 classifiers = [
-    'License :: OSI Approved :: BSD License',
-    'Development Status :: 5 - Production/Stable',
-    '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 :: 3.7',
-    'Programming Language :: Python :: 3.8',
-    'Programming Language :: Python :: 3.9',
-    'Topic :: Scientific/Engineering :: Bio-Informatics',
-    'Topic :: Scientific/Engineering :: Visualization',
+    "License :: OSI Approved :: BSD License",
+    "Development Status :: 5 - Production/Stable",
+    "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 :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
 ]
-requires-python = '>=3.7'
-requires = [
-    'anndata>=0.7.4',
+dependencies = [
+    "anndata>=0.7.4",
     # numpy needs a version due to #1320
-    'numpy>=1.17.0',
+    "numpy>=1.17.0",
     # Matplotlib 3.1 causes an error in 3d scatter plots (https://github.com/matplotlib/matplotlib/issues/14298)
     # But matplotlib 3.0 causes one in heatmaps
-    'matplotlib>=3.1.2',
-    'pandas>=0.21',
-    'scipy>=1.4',
-    'seaborn',
-    'h5py>=2.10.0',
-    'tables',
-    'tqdm',
-    'scikit-learn>=0.22',
-    'statsmodels>=0.10.0rc2',
-    'patsy',
-    'networkx>=2.3',
-    'natsort',
-    'joblib',
-    'numba>=0.41.0',
-    'umap-learn>=0.3.10',
-    'packaging',
-    'sinfo',
+    "matplotlib>=3.1.2",
+    "pandas>=0.21",
+    "scipy>=1.4",
+    "seaborn",
+    "h5py>=2.10.0",
+    "tables",
+    "tqdm",
+    "scikit-learn>=0.22",
+    "statsmodels>=0.10.0rc2",
+    "patsy",
+    "networkx>=2.3",
+    "natsort",
+    "joblib",
+    "numba>=0.41.0",
+    "umap-learn>=0.3.10",
+    "packaging",
+    "sinfo",
     # for getting the stable version
-    'importlib_metadata>=0.7; python_version < "3.8"',
+    "importlib_metadata>=0.7; python_version < '3.8'",
 ]
+dynamic = ["version"]
 
-[tool.flit.metadata.requires-extra]
-louvain = ['python-igraph', 'louvain>=0.6,!=0.6.2']
-leiden = ['python-igraph', 'leidenalg']
-bbknn = ['bbknn']
-rapids = ['cudf>=0.9', 'cuml>=0.9', 'cugraph>=0.9']
-magic = ['magic-impute>=2.0']
-skmisc = ['scikit-misc>=0.1.3']
-harmony = ['harmonypy']
-scanorama = ['scanorama']
-scrublet = ['scrublet']
-dev = [
-    # getting the dev version
-    'setuptools_scm',
-    'pytoml',
-    # static checking
-    'black>=20.8b1',
-    'docutils',
+[project.urls]
+Documentation = "https://scanpy.readthedocs.io/"
+Source = "https://github.com/theislab/scanpy"
+Home-page = "https://scanpy.org"
+
+[project.scripts]
+scanpy = "scanpy.cli:console_main"
+
+[project.optional-dependencies]
+test = [
+    "pytest>=4.4",
+    "pytest-nunit",
+    "dask[array]!=2.17.0",
+    "fsspec",
+    "zappy",
+    "zarr",
+    "profimp",
+    # Test the metadata while this exists: https://github.com/takluyver/flit/issues/387
+    "flit_core",
 ]
 doc = [
-    'sphinx>=4.1,<4.2',
-    'sphinx-rtd-theme>=0.3.1',
-    'sphinx-autodoc-typehints',
-    'scanpydoc>=0.7.3',
-    'typing_extensions; python_version < "3.8"',  # for `Literal`
-    'python-igraph',
+    "sphinx>=4.1,<4.2",
+    "sphinx-rtd-theme>=0.3.1",
+    "sphinx-autodoc-typehints",
+    "scanpydoc>=0.7.3",
+    "typing_extensions; python_version < '3.8'",  # for `Literal`
+    "python-igraph",
 ]
-test = [
-    'pytest>=4.4',
-    'pytest-nunit',
-    'dask[array]!=2.17.0',
-    'fsspec',
-    'zappy',
-    'zarr',
-    'profimp',
-    # Test the metadata while this exists: https://github.com/takluyver/flit/issues/387
-    'flit_core',
+dev = [
+    # getting the dev version
+    "setuptools_scm",
+    # static checking
+    "black>=20.8b1",
+    "docutils",
 ]
-
-[tool.flit.scripts]
-scanpy = 'scanpy.cli:console_main'
+louvain = ["python-igraph", "louvain>=0.6,!=0.6.2"]
+leiden = ["python-igraph", "leidenalg"]
+bbknn = ["bbknn"]
+rapids = ["cudf>=0.9", "cuml>=0.9", "cugraph>=0.9"]
+magic = ["magic-impute>=2.0"]
+skmisc = ["scikit-misc>=0.1.3"]
+harmony = ["harmonypy"]
+scanorama = ["scanorama"]
+scrublet = ["scrublet"]
 
 [tool.flit.sdist]
 exclude = [
-    'scanpy/tests',
-    'setup.py',
+    "scanpy/tests",
+    "setup.py",
 ]
 
 [tool.pytest.ini_options]
-python_files = 'test_*.py'
-testpaths = 'scanpy/tests/'
+python_files = "test_*.py"
+testpaths = "scanpy/tests/"
 xfail_strict = true
-nunit_attach_on = 'fail'
+nunit_attach_on = "fail"
 markers = [
-    'internet: tests which rely on internet resources (enable with `--internet-tests`)',
+    "internet: tests which rely on internet resources (enable with `--internet-tests`)",
 ]
 
 [tool.coverage.run]
-source = ['scanpy']
-omit = ['*/tests/*']
+source = ["scanpy"]
+omit = ["*/tests/*"]
 
 [tool.black]
 line-length = 88
-target-version = ['py37']
+target-version = ["py37"]
 skip-string-normalization = true
-exclude = '''
+exclude = """
 /build/.*
-'''
+"""
diff --git a/scanpy/__init__.py b/scanpy/__init__.py
@@ -1,6 +1,6 @@
 """Single-Cell Analysis in Python."""
 
-from ._metadata import __version__, __author__, __email__, within_flit
+from ._metadata import __version__, within_flit
 
 if not within_flit():  # see function docstring on why this is there
     from ._utils import check_versions