Switch to flit

.azure-pipelines.yml

@@ -28,8 +28,8 @@ jobs:
 
   - task: Cache@2
     inputs:
-      key: '"python $(python.version)" | "$(Agent.OS)" | requirements.txt'
-      restoreKeys: | 
+      key: '"python $(python.version)" | "$(Agent.OS)" | pyproject.toml'
+      restoreKeys: |
         python | "$(Agent.OS)"
         python
       path: $(PIP_CACHE_DIR)
@@ -42,8 +42,9 @@ jobs:
 
   - script: |
       python -m pip install --upgrade pip
+      pip install -r .pip-2033.txt
       pip install pytest-cov wheel
-      pip install -e .[dev,doc,test,louvain,leiden,magic,scvi,harmony,scrublet,scanorama]
+      pip install .[dev,doc,test,louvain,leiden,magic,scvi,harmony,scrublet,scanorama]
     displayName: 'Install dependencies'
 
   - script: |
@@ -102,6 +103,7 @@ jobs:
     displayName: 'Display installed versions'
 
   - script: |
-      python setup.py sdist bdist_wheel
+      pip install flit
+      flit build
       twine check dist/*
     displayName: 'Build & Twine check'

.pip-2033.txt

@@ -0,0 +1,4 @@
+# Flit mangles the +local part of the version spec in compliance with PEP 427,
+# but pip 20.3.4 started expecting wheel filenames to contain the local part unmangled.
+# https://github.com/pypa/pip/issues/9628
+pip==20.3.3

.readthedocs.yml

@@ -6,6 +6,7 @@ sphinx:
 python:
   version: 3.8
   install:
+  - requirements: .pip-2033.txt
   - method: pip
     path: .
     extra_requirements:

.travis.yml

@@ -11,7 +11,6 @@ matrix:
     - pip install .[dev,doc]
     script:
     - black . --check --diff
-    - python setup.py check --restructuredtext --strict
     - rst2html.py --halt=2 README.rst >/dev/null
     after_success: skip
   - name: "anndata dev"

docs/conf.py

@@ -1,6 +1,5 @@
 import os
 import sys
-import warnings
 from pathlib import Path
 from datetime import datetime
 

docs/installation.rst

@@ -7,7 +7,7 @@ If you do not have a working installation of Python 3.6 (or later), consider
 installing Miniconda_ (see `Installing Miniconda`_). Then run::
 
     conda install seaborn scikit-learn statsmodels numba pytables
-    conda install -c conda-forge python-igraph leidenalg	
+    conda install -c conda-forge python-igraph leidenalg
 
 Pull Scanpy from `PyPI <https://pypi.org/project/scanpy>`__ (consider using ``pip3`` to access Python 3)::
 
@@ -35,21 +35,40 @@ 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::
 
-    pip install -e .
+    flit install -s --deps=develop  # from an activated venv or conda env
+    # or
+    flit install -s --deps=develop --python path/to/venv/bin/python
 
-If you intend to do development work, there are some extra dependencies you'll want.
-These can be install with `scanpy` via::
+.. _on GitHub: https://github.com/theislab/scanpy
 
-    pip install -e ".[dev,doc,test]"
+.. note::
 
-.. _on GitHub: https://github.com/theislab/scanpy
+   Due to a `bug in pip`_, packages installed by `flit` can be uninstalled by normal pip operations.
+   For now, you can avoid this by using::
+
+       pip install -e ".[dev,doc,test]"
+
+.. _bug in pip: https://github.com/pypa/pip/issues/9670
+
+If you want to let conda_ handle the installations of dependencies, do::
+
+    pip install beni
+    beni pyproject.toml > environment.yml
+    conda env create -f environment.yml
+    conda activate scanpy
+    flit install -s --deps=develop  # or: pip install -e ".[dev,doc,test]"
+
+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
 
 Docker
 ~~~~~~
-If you're using Docker_, you can use the minimal `fastgenomics/scanpy`_ image from the Docker Hub.
+If you're using Docker_, you can use e.g. the image `gcfntnu/scanpy`_ from Docker Hub.
 
 .. _Docker: https://en.wikipedia.org/wiki/Docker_(software)
-.. _fastgenomics/scanpy: https://hub.docker.com/r/fastgenomics/scanpy
+.. _gcfntnu/scanpy: https://hub.docker.com/r/gcfntnu/scanpy
 .. _bioconda: https://bioconda.github.io/
 
 Troubleshooting
@@ -78,6 +97,8 @@ Download those and install them using `pip install ./path/to/file.whl`
 .. _compiling igraph: https://stackoverflow.com/q/29589696/247482
 .. _unofficial binaries: https://www.lfd.uci.edu/~gohlke/pythonlibs/
 
+.. _conda:
+
 Installing Miniconda
 ~~~~~~~~~~~~~~~~~~~~
 After downloading Miniconda_, in a unix shell (Linux, Mac), run

docs/release-notes/1.8.0.rst

@@ -3,6 +3,11 @@
 
 .. rubric:: Features
 
+- Switched to flit_ for building and deploying the package,
+  a simple tool with an easy to understand command line interface and metadata.
+
+.. _flit: https://flit.readthedocs.io/en/latest/
+
 .. rubric:: External tools
 
 .. rubric:: Performance enhancements

pyproject.toml

@@ -1,16 +1,119 @@
 [build-system]
-requires = ['setuptools', 'setuptools_scm', 'wheel', 'pytoml']
-build-backend = 'setuptools.build_meta'
+build-backend = 'flit_core.buildapi'
+requires = [
+    'flit_core >=2,<4',
+    'setuptools_scm',
+    'pytoml',
+    'importlib_metadata>=0.7; python_version < "3.8"',
+    # setup.py stuff
+    'packaging',
+]
 
-# uses the format of tool.flit.metadata because we’ll move to it anyway
-[tool.scanpy]
-author = """
+[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/' }
+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 :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'Topic :: Scientific/Engineering :: Visualization',
+]
+requires-python = '>=3.6'
+requires = [
+    'anndata>=0.7.4',
+    # numpy needs a version due to #1320
+    '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>=0.21.2',
+    'statsmodels>=0.10.0rc2',
+    'patsy',
+    'networkx>=2.3',
+    'natsort',
+    'joblib',
+    'numba>=0.41.0',
+    'umap-learn>=0.3.10',
+    'legacy-api-wrap',
+    'packaging',
+    'sinfo',
+    # for getting the stable version
+    'importlib_metadata>=0.7; python_version < "3.8"',
+]
+
+[tool.flit.metadata.requires-extra]
+louvain = ['python-igraph', 'louvain>=0.6,!=0.6.2']
+leiden = ['python-igraph', 'leidenalg']
+bbknn = ['bbknn']
+scvi = ['scvi==0.6.7']
+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',
+]
+doc = [
+    'sphinx>=3.2',
+    'sphinx-rtd-theme>=0.3.1',
+    'sphinx-autodoc-typehints',
+    'readthedocs-sphinx-search',
+    'scanpydoc>=0.5',
+    'typing_extensions; python_version < "3.8"',  # for `Literal`
+]
+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',
+]
+
+[tool.flit.scripts]
+scanpy = 'scanpy.cli:console_main'
+
+[tool.flit.sdist]
+exclude = [
+    'scanpy/tests',
+    'setup.py',
+]
 
 [tool.pytest.ini_options]
 python_files = 'test_*.py'

scanpy/__init__.py

@@ -1,43 +1,42 @@
 """Single-Cell Analysis in Python."""
 
-from ._metadata import __version__, __author__, __email__
-
-from ._utils import check_versions
-
-check_versions()
-del check_versions
-
-# the actual API
-from ._settings import (
-    settings,
-    Verbosity,
-)  # start with settings as several tools are using it
-from . import tools as tl
-from . import preprocessing as pp
-from . import plotting as pl
-from . import datasets, logging, queries, external, get
-
-from anndata import AnnData, concat
-from anndata import (
-    read_h5ad,
-    read_csv,
-    read_excel,
-    read_hdf,
-    read_loom,
-    read_mtx,
-    read_text,
-    read_umi_tools,
-)
-from .readwrite import read, read_10x_h5, read_10x_mtx, write, read_visium
-from .neighbors import Neighbors
-
-set_figure_params = settings.set_figure_params
-
-# has to be done at the end, after everything has been imported
-import sys
-
-sys.modules.update({f'{__name__}.{m}': globals()[m] for m in ['tl', 'pp', 'pl']})
-from ._utils import annotate_doc_types
-
-annotate_doc_types(sys.modules[__name__], 'scanpy')
-del sys, annotate_doc_types
+from ._metadata import __version__, __author__, __email__, within_flit
+
+if not within_flit():  # see function docstring on why this is there
+    from ._utils import check_versions
+
+    check_versions()
+    del check_versions, within_flit
+
+    # the actual API
+    # (start with settings as several tools are using it)
+    from ._settings import settings, Verbosity
+    from . import tools as tl
+    from . import preprocessing as pp
+    from . import plotting as pl
+    from . import datasets, logging, queries, external, get
+
+    from anndata import AnnData, concat
+    from anndata import (
+        read_h5ad,
+        read_csv,
+        read_excel,
+        read_hdf,
+        read_loom,
+        read_mtx,
+        read_text,
+        read_umi_tools,
+    )
+    from .readwrite import read, read_10x_h5, read_10x_mtx, write, read_visium
+    from .neighbors import Neighbors
+
+    set_figure_params = settings.set_figure_params
+
+    # has to be done at the end, after everything has been imported
+    import sys
+
+    sys.modules.update({f'{__name__}.{m}': globals()[m] for m in ['tl', 'pp', 'pl']})
+    from ._utils import annotate_doc_types
+
+    annotate_doc_types(sys.modules[__name__], 'scanpy')
+    del sys, annotate_doc_types