blacken everything without too many line changes (scverse#841)

.travis.yml

@@ -1,10 +1,13 @@
 dist: xenial
 language: python
+stages:
+    - name: static analysis
+    - name: test
 python:
   - '3.6'
   - '3.7'
   #- '3.8-dev' # https://github.com/numpy/numpy/issues/13790
-cache: 
+cache:
   - pip
   - directories: data
 install:
@@ -16,3 +19,11 @@ script:
   - pytest --ignore=scanpy/tests/_images
   - python setup.py check --restructuredtext --strict
   - rst2html.py --halt=2 README.rst >/dev/null
+jobs:
+  include:
+    - stage: static analysis
+      python: "3.7"
+      script:
+        - black . --check --diff
+        - python -m scanpy.tests.blackdiff 10
+      after_success: skip

conftest.py

@@ -13,9 +13,11 @@ def pytest_addoption(parser):
 
 def pytest_collection_modifyitems(config, items):
     run_internet = config.getoption("--internet-tests")
-    skip_internet = pytest.mark.skip(reason="need --internet-tests option to run")
+    skip_internet = pytest.mark.skip(
+        reason="need --internet-tests option to run"
+    )
     for item in items:
         # All tests marked with `pytest.mark.internet` get skipped unless
         # `--run-internet` passed
         if not run_internet and ("internet" in item.keywords):
-            item.add_marker(skip_internet)
+            item.add_marker(skip_internet)

docs/conf.py

@@ -5,12 +5,14 @@
 from datetime import datetime
 
 import matplotlib  # noqa
+
 # Don’t use tkinter agg when importing scanpy → … → matplotlib
 matplotlib.use('agg')
 
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE.parent))
 import scanpy  # noqa
+
 with warnings.catch_warnings():
     warnings.filterwarnings('ignore', category=FutureWarning)
     import scanpy.api
@@ -83,7 +85,10 @@
     scvelo=('https://scvelo.readthedocs.io/en/stable/', None),
     seaborn=('https://seaborn.pydata.org/', None),
     sklearn=('https://scikit-learn.org/stable/', None),
-    scanpy_tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest', None),
+    scanpy_tutorials=(
+        'https://scanpy-tutorials.readthedocs.io/en/latest',
+        None,
+    ),
 )
 
 
@@ -92,20 +97,21 @@
 
 html_theme = 'sphinx_rtd_theme'
 html_theme_options = dict(
-    navigation_depth=4,
-    logo_only=True,           # Only show the logo
+    navigation_depth=4, logo_only=True  # Only show the logo
 )
 html_context = dict(
-    display_github=True,      # Integrate GitHub
-    github_user='theislab',   # Username
-    github_repo='scanpy',     # Repo name
+    display_github=True,  # Integrate GitHub
+    github_user='theislab',  # Username
+    github_repo='scanpy',  # Repo name
     github_version='master',  # Version
-    conf_py_path='/docs/',    # Path in the checkout to the docs root
+    conf_py_path='/docs/',  # Path in the checkout to the docs root
 )
 html_static_path = ['_static']
 html_show_sphinx = False
 html_logo = '_static/img/Scanpy_Logo_RGB.png'
-gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(html_context)
+gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(
+    html_context
+)
 
 
 def setup(app):
@@ -115,19 +121,24 @@ def setup(app):
     app.connect('build-finished', show_param_warnings)
     app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}'))
 
+
 # -- Options for other output formats ------------------------------------------
 
 
 htmlhelp_basename = f'{project}doc'
 doc_title = f'{project} Documentation'
-latex_documents = [
-    (master_doc, f'{project}.tex', doc_title, author, 'manual'),
-]
-man_pages = [
-    (master_doc, project, doc_title, [author], 1)
-]
+latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')]
+man_pages = [(master_doc, project, doc_title, [author], 1)]
 texinfo_documents = [
-    (master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous'),
+    (
+        master_doc,
+        project,
+        doc_title,
+        author,
+        project,
+        'One line description of project.',
+        'Miscellaneous',
+    )
 ]
 
 
@@ -136,20 +147,28 @@ def setup(app):
 
 def insert_function_images(app, what, name, obj, options, lines):
     path = Path(__file__).parent / 'api' / f'{name}.png'
-    if what != 'function' or not path.is_file(): return
-    lines[0:0] = [f'.. image:: {path.name}', '   :width: 200', '   :align: right', '']
+    if what != 'function' or not path.is_file():
+        return
+    lines[0:0] = [
+        f'.. image:: {path.name}',
+        '   :width: 200',
+        '   :align: right',
+        '',
+    ]
 
 
 # -- GitHub links --------------------------------------------------------------
 
 
 def autolink(url_template, title_template='{}'):
     from docutils import nodes
+
     def role(name, rawtext, text, lineno, inliner, options={}, content=[]):
         url = url_template.format(text)
         title = title_template.format(text)
         node = nodes.reference(rawtext, title, refuri=url, **options)
         return [node], []
+
     return role
 
 
@@ -171,7 +190,9 @@ def process_return(lines):
 
 
 def scanpy_parse_returns_section(self, section):
-    lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
+    lines_raw = list(
+        process_return(self._dedent(self._consume_to_next_section()))
+    )
     lines = self._format_block(':returns: ', lines_raw)
     if lines and lines[-1]:
         lines.append('')
@@ -190,15 +211,20 @@ def scanpy_parse_returns_section(self, section):
 
 def scanpy_log_param_types(self, fields, field_role='param', type_role='type'):
     for _name, _type, _desc in fields:
-        if not _type: continue
+        if not _type:
+            continue
         set_item = r"`'[a-z0-9_.-]+'`"
-        if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type): continue
-        param_warnings.setdefault((self._name, self._obj), []).append((_name, _type))
+        if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type):
+            continue
+        param_warnings.setdefault((self._name, self._obj), []).append(
+            (_name, _type)
+        )
     return _format_docutils_params_orig(self, fields, field_role, type_role)
 
 
 def show_param_warnings(app, exception):
     import inspect
+
     for (fname, fun), params in param_warnings.items():
         _, line = inspect.getsourcelines(fun)
         file_name = inspect.getsourcefile(fun)
@@ -207,7 +233,9 @@ def show_param_warnings(app, exception):
             f'\nParameters in `{fname}` not set-like: {{`elm-1`, `s_el.2`}}.\n'
             'Convert to this format or replace with type annotations:\n'
             + params_str,
-            UserWarning, file_name, line,
+            UserWarning,
+            file_name,
+            line,
         )
 
 
@@ -220,19 +248,23 @@ def show_param_warnings(app, exception):
 # Just do the following to see the rst of a function:
 # rm -f _build/doctrees/api/scanpy.<what_you_want>.doctree; DEBUG=1 make html
 import os
+
 if os.environ.get('DEBUG') is not None:
     import sphinx.ext.napoleon
+
     pd = sphinx.ext.napoleon._process_docstring
+
     def pd_new(app, what, name, obj, options, lines):
         pd(app, what, name, obj, options, lines)
         print(*lines, sep='\n')
+
     sphinx.ext.napoleon._process_docstring = pd_new
 
 
 # -- Suppress link warnings ----------------------------------------------------
 
 qualname_overrides = {
-    "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
+    "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric"
 }
 
 nitpick_ignore = [
@@ -243,8 +275,13 @@ def pd_new(app, what, name, obj, options, lines):
 ]
 
 for mod_name in [
-    'pp', 'tl', 'pl',
-    'queries', 'logging', 'datasets', 'export_to',
+    'pp',
+    'tl',
+    'pl',
+    'queries',
+    'logging',
+    'datasets',
+    'export_to',
     None,
 ]:
     if mod_name is None:

pyproject.toml

@@ -1,3 +1,80 @@
 [build-system]
 requires = ['setuptools', 'setuptools_scm', 'wheel']
 build-backend = 'setuptools.build_meta'
+
+[tool.black]
+line-length = 80
+target-version = ['py36']
+skip-string-normalization = true
+exclude = '''
+/build/.*
+|/scanpy/(
+    get
+    |__init__
+    |cli
+    |logging
+    |readwrite
+    |_utils
+    |_settings
+    |neighbors/__init__
+    |api/(__init__|pp|pl|datasets)
+    |external/(exporting|tl/_palantir)
+    |datasets/(__init__|_ebi_expression_atlas)
+    |preprocessing/(
+        __init__
+        |_qc
+        |_combat
+        |_simple
+        |_recipes
+        |_normalization
+        |_highly_variable_genes
+        |_deprecated/highly_variable_genes
+    )
+    |tools/(
+        _dpt
+        |_sim
+        |_paga
+        |_tsne
+        |_umap
+        |_utils
+        |_leiden
+        |_louvain
+        |_tsne_fix
+        |_top_genes
+        |_dendrogram
+        |_draw_graph
+        |_score_genes
+        |_utils_clustering
+        |_rank_genes_groups
+        |_embedding_density
+        |_marker_gene_overlap
+    )
+    |plotting/(
+        __init__
+        |palettes
+        |_anndata
+        |_utils
+        |_preprocessing
+        |_tools/(scatterplots|__init__|paga)
+    )
+    |tests/(
+        test_get
+        |test_pca
+        |test_docs
+        |test_binary
+        |test_combat
+        |test_plotting
+        |test_read_10x
+        |test_neighbors
+        |test_readwrite
+        |test_clustering
+        |test_qc_metrics
+        |test_score_genes
+        |test_preprocessing
+        |test_rank_genes_groups
+        |test_marker_gene_overlap
+        |test_highly_variable_genes
+        |test_rank_genes_groups_logreg
+        |notebooks/(test_paga_paul15_subsampled|test_pbmc3k)
+    )
+).py'''

scanpy/__main__.py

@@ -1,2 +1,3 @@
 from .cli import console_main
+
 console_main()

scanpy/api/tl.py

@@ -4,7 +4,12 @@
 from ..tools._diffmap import diffmap
 from ..tools._draw_graph import draw_graph
 
-from ..tools._paga import paga, paga_degrees, paga_expression_entropies, paga_compare_paths
+from ..tools._paga import (
+    paga,
+    paga_degrees,
+    paga_expression_entropies,
+    paga_compare_paths,
+)
 from ..tools._rank_genes_groups import rank_genes_groups
 from ..tools._dpt import dpt
 from ..tools._leiden import leiden

scanpy/external/__init__.py

@@ -5,6 +5,7 @@
 
 import sys
 from .. import _utils
+
 _utils.annotate_doc_types(sys.modules[__name__], 'scanpy')
 del sys, _utils
 

scanpy/external/pp/_bbknn.py

@@ -22,7 +22,7 @@ def bbknn(
     trim: Optional[int] = None,
     n_trees: int = 10,
     use_faiss: bool = True,
-    set_op_mix_ratio: float = 1.,
+    set_op_mix_ratio: float = 1.0,
     local_connectivity: int = 1,
     **kwargs,
 ) -> AnnData:

scanpy/external/pp/_dca.py

@@ -12,7 +12,7 @@ def dca(
     log1p=True,
     # network args
     hidden_size=(64, 32, 64),
-    hidden_dropout=0.,
+    hidden_dropout=0.0,
     batchnorm=True,
     activation='relu',
     init='glorot_uniform',
@@ -138,7 +138,9 @@ def dca(
     try:
         from dca.api import dca
     except ImportError:
-        raise ImportError('Please install dca package (>= 0.2.1) via `pip install dca`')
+        raise ImportError(
+            'Please install dca package (>= 0.2.1) via `pip install dca`'
+        )
 
     return dca(
         adata,

scanpy/external/pp/_magic.py

@@ -147,8 +147,9 @@ def magic(
         time=start,
         deep=(
             "added\n    'X_magic', PCA on MAGIC coordinates (adata.obsm)"
-            if name_list == "pca_only" else ''
-        )
+            if name_list == "pca_only"
+            else ''
+        ),
     )
     # update AnnData instance
     if name_list == "pca_only":