Merge pull request #215 from scottclowe/sty_blacken

STY: Change code style to black
rochefort-lab · Jun 28, 2021 · 0829998 · 0829998
2 parents 742e1ea + ec7b531
commit 0829998
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,14 +1,33 @@
 repos:
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.9.1
     hooks:
-      - id: python-check-blanket-noqa
-      - id: python-no-log-warn
-      - id: rst-backticks
-      - id: rst-directive-colons
-        types: [text]
-      - id: rst-inline-touching-normal
-        types: [text]
+      - id: isort
+        name: isort
+        args: ["--profile", "black"]
+      - id: isort
+        name: isort (cython)
+        types: [cython]
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/psf/black
+    rev: 21.6b0
+    hooks:
+      - id: black
+        args:
+            - "--target-version=py27"
+            - "--target-version=py35"
+            - "--target-version=py36"
+            - "--target-version=py37"
+            - "--target-version=py38"
+            - "--target-version=py39"
+        types: [python]
+
+  - repo: https://github.com/asottile/blacken-docs
+    rev: v1.8.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==21.6b0]
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.4.0
@@ -20,6 +39,17 @@ repos:
     hooks:
       - id: black_nbconvert
 
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-no-log-warn
+      - id: rst-backticks
+      - id: rst-directive-colons
+        types: [text]
+      - id: rst-inline-touching-normal
+        types: [text]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.0.1
     hooks:

diff --git a/README.rst b/README.rst
@@ -1,21 +1,23 @@
 FISSA
 =====
 
-+------------------+----------------------------------------------------------+
-| Latest Release   | |PyPI badge| |Py Versions|                               |
-+------------------+----------------------------------------------------------+
-| License          | |License|                                                |
-+------------------+----------------------------------------------------------+
-| Documentation    | |readthedocs|                                            |
-+------------------+----------------------------------------------------------+
-| Build Status     | |Documentation| |GHA tests| |AppVeyor| |Codecov|         |
-+------------------+----------------------------------------------------------+
-| Interactive Demo | |Binder|                                                 |
-+------------------+----------------------------------------------------------+
-| Support          | |Gitter|                                                 |
-+------------------+----------------------------------------------------------+
-| Citation         | |DOI badge|                                              |
-+------------------+----------------------------------------------------------+
++------------------+----------------------------------------------------------------------+
+| Latest Release   | |PyPI badge| |Py Versions|                                           |
++------------------+----------------------------------------------------------------------+
+| License          | |License|                                                            |
++------------------+----------------------------------------------------------------------+
+| Documentation    | |readthedocs|                                                        |
++------------------+----------------------------------------------------------------------+
+| Build Status     | |Documentation| |GHA tests| |AppVeyor| |Codecov| |pre-commit-status| |
++------------------+----------------------------------------------------------------------+
+| Code style       | |black| |pre-commit|                                                 |
++------------------+----------------------------------------------------------------------+
+| Interactive Demo | |Binder|                                                             |
++------------------+----------------------------------------------------------------------+
+| Support          | |Gitter|                                                             |
++------------------+----------------------------------------------------------------------+
+| Citation         | |DOI badge|                                                          |
++------------------+----------------------------------------------------------------------+
 
 FISSA (Fast Image Signal Separation Analysis) is a Python package for
 decontaminating somatic signals from two-photon calcium imaging data.
@@ -389,3 +391,12 @@ with this program. If not, see http://www.gnu.org/licenses/.
 .. |License| image:: https://img.shields.io/pypi/l/fissa
    :target: https://raw.githubusercontent.com/rochefort-lab/fissa/master/LICENSE
    :alt: GPLv3 License
+.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
+   :target: https://github.com/pre-commit/pre-commit
+   :alt: pre-commit enabled
+.. |pre-commit-status| image:: https://results.pre-commit.ci/badge/github/rochefort-lab/fissa/master.svg
+   :target: https://results.pre-commit.ci/latest/github/rochefort-lab/fissa/master
+   :alt: pre-commit.ci status
+.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
+   :target: https://github.com/psf/black
+   :alt: black
diff --git a/docs/conf.py b/docs/conf.py
@@ -15,15 +15,17 @@
 import datetime
 import os
 import sys
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../'))
+
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # Can't import __meta__.py if the requirements aren't installed
 # due to imports in __init__.py. This is a workaround.
 def read(fname):
     return open(os.path.join(os.path.dirname(__file__), fname)).read()
 
+
 meta = {}
 exec(read("../fissa/__meta__.py"), meta)
 
@@ -35,73 +37,77 @@ def read(fname):
 project = meta["name"].upper()
 project_path = meta["path"]
 author = meta["author"]
-copyright = '{}, {}'.format(now.year, author)
+copyright = "{}, {}".format(now.year, author)
 
 
 # The full version, including alpha/beta/rc tags
 release = meta["version"]
 # The short X.Y version
-version = '.'.join(release.split('.')[0:2])
+version = ".".join(release.split(".")[0:2])
 
 
 # -- Automatically generate API documentation --------------------------------
 
+
 def run_apidoc(_):
     ignore_paths = [
-        os.path.join('..', project_path, 'tests'),
+        os.path.join("..", project_path, "tests"),
     ]
 
     argv = [
         "--force",  # Overwrite output files
         "--follow-links",  # Follow symbolic links
         "--separate",  # Put each module file in its own page
         "--module-first",  # Put module documentation before submodule
-        "-o", "source/packages",  # Output path
+        "-o",
+        "source/packages",  # Output path
         os.path.join("..", project_path),
     ] + ignore_paths
 
     try:
         # Sphinx 1.7+
         from sphinx.ext import apidoc
+
         apidoc.main(argv)
     except ImportError:
         # Sphinx 1.6 (and earlier)
         from sphinx import apidoc
+
         argv.insert(0, apidoc.__file__)
         apidoc.main(argv)
 
 
 def retitle_modules(_):
-    pth = 'source/packages/modules.rst'
+    pth = "source/packages/modules.rst"
     lines = open(pth).read().splitlines()
     # Overwrite the junk in the first two lines with a better title
-    lines[0] = 'API Reference'
-    lines[1] = '============='
-    open(pth, 'w').write('\n'.join(lines))
+    lines[0] = "API Reference"
+    lines[1] = "============="
+    open(pth, "w").write("\n".join(lines))
 
 
 def setup(app):
-    app.connect('builder-inited', run_apidoc)
-    app.connect('builder-inited', retitle_modules)
+    app.connect("builder-inited", run_apidoc)
+    app.connect("builder-inited", retitle_modules)
 
 
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-# needs_sphinx = '1.0'
+# needs_sphinx = "1.0"
 
 # Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
     "numpydoc",  # handle NumPy documentation formatted docstrings
 ]
 
@@ -129,19 +135,19 @@ def setup(app):
 }
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+# source_suffix = [".rst", ".md"]
+source_suffix = ".rst"
 
 # The encoding of source files.
 source_encoding = "utf-8"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -153,7 +159,7 @@ def setup(app):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
@@ -186,44 +192,38 @@ def setup(app):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #
 # The default sidebars (for documents that don't match any pattern) are
 # defined by theme itself.  Builtin themes are using these templates by
-# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
-# 'searchbox.html']``.
+# default: ``["localtoc.html", "relations.html", "sourcelink.html",
+# "searchbox.html"]``.
 #
 # html_sidebars = {}
 
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = project + 'doc'
+htmlhelp_basename = project + "doc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
 
 latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
+    # The paper size ("letterpaper" or "a4paper").
+    # "papersize": "letterpaper",
     #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
+    # The font size ("10pt", "11pt" or "12pt").
+    # "pointsize": "10pt",
     #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
     # Latex figure (float) alignment
-    #
     # 'figure_align': 'htbp',
-
+    #
+    # Additional stuff for the LaTeX preamble.
     # Need to manually declare what the delta symbol (Δ) corresponds to.
     "preamble": """
 \DeclareUnicodeCharacter{394}{$\Delta$}
@@ -234,19 +234,21 @@ def setup(app):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, project + '.tex', project + ' Documentation',
-     meta["author"], 'manual'),
+    (
+        master_doc,
+        project + ".tex",
+        project + " Documentation",
+        meta["author"],
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, project, project + ' Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, project, project + " Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -255,9 +257,15 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, project, project + ' Documentation',
-     author, project, meta["description"],
-     'Miscellaneous'),
+    (
+        master_doc,
+        project,
+        project + " Documentation",
+        author,
+        project,
+        meta["description"],
+        "Miscellaneous",
+    ),
 ]
 
 
@@ -269,14 +277,14 @@ def setup(app):
 # The unique identifier of the text. This can be a ISBN number
 # or the project homepage.
 #
-# epub_identifier = ''
+# epub_identifier = ""
 
 # A unique identification for the text.
 #
-# epub_uid = ''
+# epub_uid = ""
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------

diff --git a/docs/source/user-guide.rst b/docs/source/user-guide.rst
@@ -2,4 +2,4 @@ FISSA User Guide
 ================
 
 .. include:: ../../README.rst
-    :start-line: 19
+    :start-line: 21