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‎.gitignore‎

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@@ -33,6 +33,7 @@ __pycache__/
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/scanpy.egg-info/
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/*-env/
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/env-*/
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/setup.py
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# OS stuff
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.DS_Store

‎.travis.yml‎

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script:
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- black . --check --diff
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- python -m scanpy.tests.blackdiff 10
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- python setup.py check --restructuredtext --strict
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- rst2html.py --halt=2 README.rst >/dev/null
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after_success: skip
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- name: "anndata dev"

‎MANIFEST.in‎

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‎docs/conf.py‎

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import os
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import sys
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import warnings
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from pathlib import Path
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from datetime import datetime
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‎docs/installation.rst‎

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@@ -7,7 +7,7 @@ If you do not have a working installation of Python 3.6 (or later), consider
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installing Miniconda_ (see `Installing Miniconda`_). Then run::
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conda install seaborn scikit-learn statsmodels numba pytables
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conda install -c conda-forge python-igraph leidenalg
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conda install -c conda-forge python-igraph leidenalg
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Pull Scanpy from `PyPI <https://pypi.org/project/scanpy>`__ (consider using ``pip3`` to access Python 3)::
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its root directory. To install using symbolic links (stay up to date with your
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cloned version after you update with `git pull`) call::
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pip install -e .
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flit install -s # from an activated venv or conda env
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# or
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flit install -s --python path/to/venv/bin/python
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.. _on GitHub: https://github.com/theislab/scanpy
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If you want to let conda_ handle the installations of dependencies, do::
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pip install beni
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beni pyproject.toml > environment.yml
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conda env create -f environment.yml
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conda activate scanpy
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flit install -s
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On Windows, you might have to use `flit install --pth-file`
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if you are not able to give yourself the `create symbolic links`_ privilege.
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Be aware that a `conda bug`_ might prevent `conda list` from working then.
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.. _create symbolic links: https://docs.microsoft.com/en-us/windows/security/threat-protection/security-policy-settings/create-symbolic-links
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.. _conda bug: https://github.com/conda/conda/issues/9074
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Docker
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~~~~~~
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If you're using Docker_, you can use the minimal `fastgenomics/scanpy`_ image from the Docker Hub.
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.. _compiling igraph: https://stackoverflow.com/q/29589696/247482
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.. _unofficial binaries: https://www.lfd.uci.edu/~gohlke/pythonlibs/
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.. _conda:
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Installing Miniconda
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~~~~~~~~~~~~~~~~~~~~
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After downloading Miniconda_, in a unix shell (Linux, Mac), run

‎pyproject.toml‎

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[build-system]
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requires = ['setuptools', 'setuptools_scm', 'wheel', 'pytoml']
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build-backend = 'setuptools.build_meta'
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build-backend = 'flit_core.buildapi'
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requires = [
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'flit_core >=2,<4',
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'setuptools_scm',
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'pytoml',
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'importlib_metadata>=0.7; python_version < "3.8"',
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]
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# uses the format of tool.flit.metadata because we’ll move to it anyway
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[tool.scanpy]
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author = '''
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Alex Wolf, Philipp Angerer, Fidel Ramirez, Isaac Virshup,
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Sergei Rybakov, Gokcen Eraslan, Tom White, Malte Luecken,
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Davide Cittaro, Tobias Callies, Marius Lange, Andrés R. Muñoz-Rojas
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'''
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[tool.flit.metadata]
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module = 'scanpy'
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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'
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# We don’t need all emails, the main authors are sufficient.
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author-email = 'f.alex.wolf@gmx.de, philipp.angerer@helmholtz-muenchen.de'
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description-file = 'README.rst'
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home-page = 'http://github.com/theislab/scanpy'
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urls = { Documentation = 'https://scanpy.readthedocs.io/' }
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classifiers = [
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'License :: OSI Approved :: BSD License',
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'Development Status :: 5 - Production/Stable',
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'Environment :: Console',
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'Framework :: Jupyter',
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'Intended Audience :: Developers',
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'Intended Audience :: Science/Research',
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'Natural Language :: English',
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'Operating System :: MacOS :: MacOS X',
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'Operating System :: Microsoft :: Windows',
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'Operating System :: POSIX :: Linux',
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'Programming Language :: Python :: 3',
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'Programming Language :: Python :: 3.6',
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'Programming Language :: Python :: 3.7',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Scientific/Engineering :: Visualization',
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]
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requires-python = '>=3.6'
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requires = [
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'anndata>=0.7.4',
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# numpy needs a version due to #1320
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'numpy>=1.17.0',
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# Matplotlib 3.1 causes an error in 3d scatter plots (https://github.com/matplotlib/matplotlib/issues/14298)
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# But matplotlib 3.0 causes one in heatmaps
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'matplotlib>=3.1.2',
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'pandas>=0.21',
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'scipy>=1.4',
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'seaborn',
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'h5py>=2.10.0',
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'tables',
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'tqdm',
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'scikit-learn>=0.21.2',
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'statsmodels>=0.10.0rc2',
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'patsy',
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'networkx>=2.3',
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'natsort',
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'joblib',
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'numba>=0.41.0',
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'umap-learn>=0.3.10',
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'legacy-api-wrap',
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'packaging',
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'sinfo',
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# for getting the stable version
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'importlib_metadata>=0.7; python_version < "3.8"',
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]
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[tool.flit.metadata.requires-extra]
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louvain = ['python-igraph', 'louvain>=0.6,!=0.6.2']
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leiden = ['python-igraph', 'leidenalg']
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bbknn = ['bbknn']
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scvi = ['scvi>=0.6.5']
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rapids = ['cudf>=0.9', 'cuml>=0.9', 'cugraph>=0.9']
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magic = ['magic-impute>=2.0']
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skmisc = ['scikit-misc>=0.1.3']
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harmony = ['harmonypy']
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dev = [
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# getting the dev version
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'setuptools_scm',
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'pytoml',
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# static checking
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'black>=20.8b1',
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'docutils',
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]
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doc = [
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'sphinx<3.1, >3',
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'sphinx-rtd-theme>=0.3.1',
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'sphinx-autodoc-typehints',
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'scanpydoc>=0.5',
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'typing_extensions; python_version < "3.8"', # for `Literal`
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]
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test = [
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'pytest>=4.4',
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'dask[array]!=2.17.0',
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'fsspec',
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'zappy',
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'zarr',
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'profimp',
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]
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[tool.flit.scripts]
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scanpy = 'scanpy.cli:console_main'
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[tool.flit.sdist]
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exclude = ['scanpy/tests']
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[tool.pytest.ini_options]
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python_files = 'test_*.py'

‎requirements.txt‎

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‎scanpy/__init__.py‎

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

‎scanpy/_metadata.py‎

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import traceback
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from pathlib import Path
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here = Path(__file__).parent
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import pytoml
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proj = pytoml.loads((here.parent / 'pyproject.toml').read_text())
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metadata = proj['tool']['scanpy']
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metadata = proj['tool']['flit']['metadata']
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__version__ = get_version(root='..', relative_to=__file__)
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__author__ = metadata['author']
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__version__ = metadata['Version']
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__author__ = metadata['Author']
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__email__ = metadata['Author-email']
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def within_flit():
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for frame in traceback.extract_stack():
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if frame.name == 'get_docstring_and_version_via_import':
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return True
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return False

‎setup.py‎

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