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Commit da03b949 authored by payno's avatar payno
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format files to black style

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doc/conf.py
View file @ da03b949
......@@ -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
View file @ da03b949
......@@ -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