format files to black style

doc/conf.py

@@ -21,7 +21,7 @@ import os
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 # sys.path.insert(0, os.path.abspath('.'))
-project = u'tomoscan'
+project = u"tomoscan"
 
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -32,42 +32,42 @@ project = u'tomoscan'
 # -- 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 modules names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'nbsphinx',
+    "sphinx.ext.autodoc",
+    "nbsphinx",
 ]
 
 # 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", ".md"]
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'tomoscan'
-copyright = '2016-2020, ESRF'
-author = 'ESRF'
+project = "tomoscan"
+copyright = "2016-2020, ESRF"
+author = "ESRF"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.4'
+version = "0.4"
 # The full version, including alpha/beta/rc tags.
-release = '0.4'
+release = "0.4"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -78,37 +78,37 @@ language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['build', '**.ipynb_checkpoints']
+exclude_patterns = ["build", "**.ipynb_checkpoints"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current modules name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for modules index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -118,22 +118,22 @@ todo_include_todos = False
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'nature'
+html_theme = "nature"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -142,7 +142,7 @@ html_logo = "img/tomoscan.png"
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # 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,
@@ -152,80 +152,77 @@ html_logo = "img/tomoscan.png"
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no modules index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Language to be used for generating the HTML full-text search index.
 # Sphinx supports the following languages:
 #   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
 #   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'
-#html_search_language = 'en'
+# html_search_language = 'en'
 
 # A dictionary with options for the search language support, empty by default.
 # Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
+# html_search_options = {'type': 'default'}
 
 # The name of a javascript file (relative to the configuration directory) that
 # implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
+# html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'tomoscan'
+htmlhelp_basename = "tomoscan"
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
+    # Latex figure (float) alignment
+    #'figure_align': 'htbp',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
@@ -238,41 +235,35 @@ latex_elements = {
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no modules index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- 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, 'tomoscan', 'tomoscan documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "tomoscan", "tomoscan documentation", [author], 1)]
 
-htmlhelp_pages = [
-    (master_doc, 'tomoscan', 'tomoscan documentation',
-     [author], 1)
-]
+htmlhelp_pages = [(master_doc, "tomoscan", "tomoscan documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -281,21 +272,27 @@ htmlhelp_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'tomoscan', 'tomoscan Documentation',
-   author, 'tomoscan', 'utils for getting core information from scan',
-   'Miscellaneous'),
+    (
+        master_doc,
+        "tomoscan",
+        "tomoscan Documentation",
+        author,
+        "tomoscan",
+        "utils for getting core information from scan",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no modules index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
 
 nbsphinx_timeout = 60

setup.py

@@ -41,10 +41,12 @@ logger = logging.getLogger("tomoscan.setup")
 
 
 from distutils.command.build import build as _build
+
 try:
     from setuptools import Command
     from setuptools.command.build_ext import build_ext
     from setuptools.command.sdist import sdist
+
     logger.info("Use setuptools")
 except ImportError:
     try:
@@ -53,11 +55,13 @@ except ImportError:
         from distutils.core import Command
     from distutils.command.build_ext import build_ext
     from distutils.command.sdist import sdist
+
     logger.info("Use distutils")
 
 try:
     import sphinx
     import sphinx.util.console
+
     sphinx.util.console.color_terminal = lambda: False
     from sphinx.setup_command import BuildDoc
 except ImportError:
@@ -67,11 +71,13 @@ except ImportError:
 PROJECT = "tomoscan"
 
 if "LANG" not in os.environ and sys.platform == "darwin" and sys.version_info[0] > 2:
-    print("""WARNING: the LANG environment variable is not defined,
+    print(
+        """WARNING: the LANG environment variable is not defined,
 an utf-8 LANG is mandatory to use setup.py, you may face unexpected UnicodeError.
 export LANG=en_US.utf-8
 export LC_ALL=en_US.utf-8
-""")
+"""
+    )
 
 
 def get_version():
@@ -79,6 +85,7 @@ def get_version():
     dirname = os.path.dirname(os.path.abspath(__file__))
     sys.path.insert(0, dirname)
     import tomoscan.version
+
     sys.path = sys.path[1:]
     return tomoscan.version.strictversion
 
@@ -92,32 +99,35 @@ def get_readme():
     return long_description
 
 
-classifiers = ["Development Status :: 4 - Beta",
-               "Environment :: Console",
-               "Environment :: MacOS X",
-               "Environment :: Win32 (MS Windows)",
-               "Intended Audience :: Education",
-               "Intended Audience :: Science/Research",
-               "License :: OSI Approved :: MIT License",
-               "Natural Language :: English",
-               "Operating System :: MacOS",
-               "Operating System :: Microsoft :: Windows",
-               "Operating System :: POSIX",
-               "Programming Language :: Cython",
-               "Programming Language :: Python :: 3.5",
-               "Programming Language :: Python :: 3.6",
-               "Programming Language :: Python :: 3.7",
-               "Programming Language :: Python :: Implementation :: CPython",
-               "Topic :: Scientific/Engineering :: Physics",
-               "Topic :: Software Development :: Libraries :: Python Modules",
-               ]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Environment :: MacOS X",
+    "Environment :: Win32 (MS Windows)",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Programming Language :: Cython",
+    "Programming Language :: Python :: 3.5",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
 
 ########
 # Test #
 ########
 
+
 class PyTest(Command):
     """Command to start tests running the script: run_tests.py"""
+
     user_options = []
 
     description = "Execute the unittests"
@@ -130,7 +140,8 @@ class PyTest(Command):
 
     def run(self):
         import subprocess
-        errno = subprocess.call([sys.executable, 'run_tests.py'])
+
+        errno = subprocess.call([sys.executable, "run_tests.py"])
         if errno != 0:
             raise SystemExit(errno)
 
@@ -140,8 +151,10 @@ class PyTest(Command):
 # ################### #
 
 if sphinx is None:
+
     class SphinxExpectedCommand(Command):
         """Command to inform that sphinx is missing"""
+
         user_options = []
 
         def initialize_options(self):
@@ -152,11 +165,13 @@ if sphinx is None:
 
         def run(self):
             raise RuntimeError(
-                'Sphinx is required to build or test the documentation.\n'
-                'Please install Sphinx (http://www.sphinx-doc.org).')
+                "Sphinx is required to build or test the documentation.\n"
+                "Please install Sphinx (http://www.sphinx-doc.org)."
+            )
 
 
 if sphinx is not None:
+
     class BuildDocCommand(BuildDoc):
         """Command to build documentation using sphinx.
 
@@ -168,17 +183,18 @@ if sphinx is not None:
             # code so that the documentation is built on this and not a
             # previously installed version
 
-            build = self.get_finalized_command('build')
+            build = self.get_finalized_command("build")
             sys.path.insert(0, os.path.abspath(build.build_lib))
 
             # Build the Users Guide in HTML and TeX format
-            for builder in ['html', 'latex']:
+            for builder in ["html", "latex"]:
                 self.builder = builder
                 self.builder_target_dir = os.path.join(self.build_dir, builder)
                 self.mkpath(self.builder_target_dir)
                 BuildDoc.run(self)
             sys.path.pop(0)
 
+
 else:
     BuildDocCommand = SphinxExpectedCommand
 
@@ -187,7 +203,8 @@ else:
 # numpy.distutils Configuration #
 # ############################# #
 
-def configuration(parent_package='', top_path=None):
+
+def configuration(parent_package="", top_path=None):
     """Recursive construction of package info to be used in setup().
 
     See http://docs.scipy.org/doc/numpy/reference/distutils.html#numpy.distutils.misc_util.Configuration
@@ -197,16 +214,19 @@ def configuration(parent_package='', top_path=None):
     except ImportError:
         raise ImportError(
             "To install this package, you must install numpy first\n"
-            "(See https://pypi.python.org/pypi/numpy)")
+            "(See https://pypi.python.org/pypi/numpy)"
+        )
     config = Configuration(None, parent_package, top_path)
     config.set_options(
         ignore_setup_xxx_py=True,
         assume_default_configuration=True,
         delegate_options_to_subpackages=True,
-        quiet=True)
+        quiet=True,
+    )
     config.add_subpackage(PROJECT)
     return config
 
+
 # ############## #
 # Compiler flags #
 # ############## #
@@ -229,6 +249,7 @@ class Build(_build):
         logger.warning(msg, key, content)
         return None
 
+
 ################################################################################
 # Debian source tree
 ################################################################################
@@ -249,6 +270,7 @@ class sdist_debian(sdist):
     @staticmethod
     def get_debian_name():
         import tomoscan.version
+
         name = "%s_%s" % (PROJECT, tomoscan.version.debianversion)
         return name
 
@@ -263,7 +285,7 @@ class sdist_debian(sdist):
         for root, _, files in os.walk(search_root):
             for afile in files:
                 if os.path.splitext(afile)[1].lower() == ".pyx":
-                    base_file = os.path.join(root, afile)[len(search_root) + 1:-4]
+                    base_file = os.path.join(root, afile)[len(search_root) + 1 : -4]
                     self.filelist.exclude_pattern(pattern=base_file + ".c")
                     self.filelist.exclude_pattern(pattern=base_file + ".cpp")
                     self.filelist.exclude_pattern(pattern=base_file + ".html")
@@ -293,6 +315,7 @@ class sdist_debian(sdist):
 # setup #
 # ##### #
 
+
 def get_project_configuration(dry_run):
     """Returns project arguments for setup"""
     install_requires = [
@@ -302,28 +325,24 @@ def get_project_configuration(dry_run):
         "lxml",
     ]
 
-    setup_requires = ["setuptools",]
+    setup_requires = [
+        "setuptools",
+    ]
 
     # extras requirements: target 'full' to install all dependencies at once
-    full_requires = [
-
-    ]
+    full_requires = []
 
     extras_require = {
-        'full': full_requires,
+        "full": full_requires,
     }
 
-    package_data = {
-    }
+    package_data = {}
 
-    entry_points = {
-    }
+    entry_points = {}
 
     cmdclass = dict(
-        build=Build,
-        test=PyTest,
-        build_doc=BuildDocCommand,
-        debian_src=sdist_debian)
+        build=Build, test=PyTest, build_doc=BuildDocCommand, debian_src=sdist_debian
+    )
 
     if dry_run:
         # DRY_RUN implies actions which do not require NumPy
@@ -336,23 +355,23 @@ def get_project_configuration(dry_run):
         config = configuration()
         setup_kwargs = config.todict()
 
-
-    setup_kwargs.update(name=PROJECT,
-                        version=get_version(),
-                        url="https://gitlab.esrf.fr/tomotools/tomoscan.git",
-                        author="data analysis unit",
-                        author_email="henri.payno@esrf.fr",
-                        classifiers=classifiers,
-                        description="utilitary to access tomography data at esrf",
-                        long_description=get_readme(),
-                        install_requires=install_requires,
-                        setup_requires=setup_requires,
-                        extras_require=extras_require,
-                        cmdclass=cmdclass,
-                        package_data=package_data,
-                        zip_safe=False,
-                        entry_points=entry_points,
-                        )
+    setup_kwargs.update(
+        name=PROJECT,
+        version=get_version(),
+        url="https://gitlab.esrf.fr/tomotools/tomoscan.git",
+        author="data analysis unit",
+        author_email="henri.payno@esrf.fr",
+        classifiers=classifiers,
+        description="utilitary to access tomography data at esrf",
+        long_description=get_readme(),
+        install_requires=install_requires,
+        setup_requires=setup_requires,
+        extras_require=extras_require,
+        cmdclass=cmdclass,
+        package_data=package_data,
+        zip_safe=False,
+        entry_points=entry_points,
+    )
     return setup_kwargs
 
 
@@ -364,24 +383,31 @@ def setup_package():
     """
 
     # Check if action requires build/install
-    dry_run = len(sys.argv) == 1 or (len(sys.argv) >= 2 and (
-        '--help' in sys.argv[1:] or
-        sys.argv[1] in ('--help-commands', 'egg_info', '--version',
-                        'clean', '--name')))
+    dry_run = len(sys.argv) == 1 or (
+        len(sys.argv) >= 2
+        and (