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@@ -99,3 +99,5 @@ ENV/ | |
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# mypy | ||
.mypy_cache/ | ||
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_version_save.py |
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formats: | ||
requirements_file: docs/requirements.txt | ||
python: | ||
version: 3 |
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language: python | ||
python: | ||
- '3.5' | ||
- '3.6' | ||
notifications: | ||
email: false | ||
env: | ||
matrix: | ||
- TEST="PYTEST" | ||
- TEST="FLAKE8" | ||
install: | ||
# everything else | ||
- travis_retry pip install . | ||
# coverage packages | ||
- travis_retry pip install flake8 | ||
- travis_retry pip install codecov coverage | ||
- pip freeze | ||
script: | ||
- set -ev | ||
- if [ "${TEST}" == "PYTEST" ]; then | ||
coverage run --source=qpformat ./setup.py test; | ||
coverage report -m; | ||
codecov; | ||
else | ||
flake8 qpformat; | ||
flake8 examples; | ||
flake8 tests --ignore E402; | ||
fi; |
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0.1.0 | ||
- initial release |
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include CHANGELOG | ||
include LICENSE | ||
include README.rst | ||
recursive-include examples *.py *.jpg | ||
recursive-include docs *.py *.md *.txt *.rst | ||
recursive-include tests *.py *.md *.zip | ||
prune docs/_build |
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qpformat | ||
======== | ||
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|PyPI Version| |Tests Status| |Coverage Status| |Docs Status| | ||
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**qpformat** is a Python3 library for analyzing spherical objects in quantitative phase imaging. | ||
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Documentation | ||
------------- | ||
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The documentation, including the reference and examples, is available on `readthedocs.io <https://qpformat.readthedocs.io/en/stable/>`__. | ||
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Installation | ||
------------ | ||
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:: | ||
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pip install qpformat | ||
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Testing | ||
------- | ||
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:: | ||
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pip install -e . | ||
python setup.py test | ||
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.. |PyPI Version| image:: http://img.shields.io/pypi/v/qpformat.svg | ||
:target: https://pypi.python.org/pypi/qpformat | ||
.. |Tests Status| image:: http://img.shields.io/travis/RI-imaging/qpformat.svg?label=tests | ||
:target: https://travis-ci.org/RI-imaging/qpformat | ||
.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/RI-imaging/qpformat/master.svg | ||
:target: https://codecov.io/gh/RI-imaging/qpformat | ||
.. |Docs Status| image:: https://readthedocs.org/projects/qpformat/badge/?version=latest | ||
:target: https://readthedocs.org/projects/qpformat/builds/ | ||
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ODTbrain documentation | ||
====================== | ||
To install the requirements for building the documentation, run | ||
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pip install -r requirements.txt | ||
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To compile the documentation, run | ||
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sphinx-build . _build | ||
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#!/usr/bin/env python3 | ||
# -*- coding: utf-8 -*- | ||
# | ||
# qpformat documentation build configuration file, created by | ||
# sphinx-quickstart on Tue Sep 26 17:55:31 2017. | ||
# | ||
# This file is execfile()d with the current directory set to its | ||
# containing dir. | ||
# | ||
# Note that not all possible configuration values are present in this | ||
# autogenerated file. | ||
# | ||
# All configuration values have a default; values that are commented out | ||
# serve to show the default. | ||
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# If extensions (or modules to document with autodoc) are in another directory, | ||
# 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. | ||
# | ||
# import os | ||
# import sys | ||
# sys.path.insert(0, os.path.abspath('.')) | ||
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# Get version number from qpformat._version file | ||
import mock | ||
import os.path as op | ||
import sys | ||
# include parent directory | ||
pdir = op.dirname(op.dirname(op.abspath(__file__))) | ||
sys.path.insert(0, pdir) | ||
# include extenstions | ||
sys.path.append(op.abspath('extensions')) | ||
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# Mock all dependencies | ||
install_requires = ["h5py", "numpy", "scipy", "skimage", | ||
"skimage.restoration"] | ||
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for mod_name in install_requires: | ||
sys.modules[mod_name] = mock.Mock() | ||
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# http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_member_order | ||
# Order class attributes and functions in separate blocks | ||
autodoc_member_order = 'bysource' | ||
autodoc_mock_imports = install_requires | ||
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# Display link to GitHub repo instead of doc on rtfd | ||
rst_prolog = """ | ||
:github_url: https://github.com/RI-imaging/qpformat | ||
""" | ||
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# -- General configuration ------------------------------------------------ | ||
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# If your documentation needs a minimal Sphinx version, state it here. | ||
# | ||
# needs_sphinx = '1.0' | ||
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# Add any Sphinx extension module names here, as strings. They can be | ||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom | ||
# ones. | ||
extensions = ['sphinx.ext.autodoc', | ||
'sphinx.ext.autosummary', | ||
'sphinx.ext.intersphinx', | ||
'sphinx.ext.mathjax', | ||
'sphinx.ext.viewcode', | ||
'sphinx.ext.napoleon', | ||
'sphinxcontrib.bibtex', | ||
'fancy_include', | ||
] | ||
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# Add any paths that contain templates here, relative to this directory. | ||
templates_path = ['_templates'] | ||
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# The suffix(es) of source filenames. | ||
# You can specify multiple suffix as a list of string: | ||
# | ||
# source_suffix = ['.rst', '.md'] | ||
source_suffix = '.rst' | ||
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# The master toctree document. | ||
master_doc = 'index' | ||
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# General information about the project. | ||
project = 'qpformat' | ||
copyright = '2017, Paul Müller' | ||
author = 'Paul Müller' | ||
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# 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. | ||
# | ||
# The full version, including alpha/beta/rc tags. | ||
# This gets 'version' | ||
exec(open(op.join(pdir, "qpformat/_version.py")).read()) | ||
release = version #@UndefinedVariable | ||
# The language for content autogenerated by Sphinx. Refer to documentation | ||
# for a list of supported languages. | ||
# | ||
# This is also used if you do content translation via gettext catalogs. | ||
# Usually you set "language" from the command line for these cases. | ||
language = None | ||
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# List of patterns, relative to source directory, that match files and | ||
# directories to ignore when looking for source files. | ||
# This patterns also effect to html_static_path and html_extra_path | ||
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] | ||
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# The name of the Pygments (syntax highlighting) style to use. | ||
pygments_style = 'sphinx' | ||
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# If true, `todo` and `todoList` produce output, else they produce nothing. | ||
todo_include_todos = False | ||
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# -- Options for HTML output ---------------------------------------------- | ||
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# The theme to use for HTML and HTML Help pages. See the documentation for | ||
# a list of builtin themes. | ||
# | ||
html_theme = 'default' | ||
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# 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 = {} | ||
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# 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'] | ||
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# -- Options for HTMLHelp output ------------------------------------------ | ||
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# Output file base name for HTML help builder. | ||
htmlhelp_basename = 'qpformatdoc' | ||
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# -- Options for LaTeX output --------------------------------------------- | ||
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latex_elements = { | ||
# The paper size ('letterpaper' or 'a4paper'). | ||
# | ||
# 'papersize': 'letterpaper', | ||
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# The font size ('10pt', '11pt' or '12pt'). | ||
# | ||
# 'pointsize': '10pt', | ||
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# Additional stuff for the LaTeX preamble. | ||
# | ||
# 'preamble': '', | ||
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# Latex figure (float) alignment | ||
# | ||
# 'figure_align': 'htbp', | ||
} | ||
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# Grouping the document tree into LaTeX files. List of tuples | ||
# (source start file, target name, title, | ||
# author, documentclass [howto, manual, or own class]). | ||
latex_documents = [ | ||
(master_doc, 'qpformat.tex', 'qpformat Documentation', | ||
'Paul Müller', 'manual'), | ||
] | ||
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# -- Options for manual page output --------------------------------------- | ||
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# One entry per manual page. List of tuples | ||
# (source start file, name, description, authors, manual section). | ||
man_pages = [ | ||
(master_doc, 'qpformat', 'qpformat Documentation', | ||
[author], 1) | ||
] | ||
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# -- Options for Texinfo output ------------------------------------------- | ||
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# Grouping the document tree into Texinfo files. List of tuples | ||
# (source start file, target name, title, author, | ||
# dir menu entry, description, category) | ||
texinfo_documents = [ | ||
(master_doc, 'qpformat', 'qpformat Documentation', | ||
author, 'qpformat', 'One line description of project.', | ||
'Miscellaneous'), | ||
] | ||
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# Example configuration for intersphinx: refer to the Python standard library. | ||
intersphinx_mapping = {"python": ('https://docs.python.org/', None), | ||
"numpy": ('http://docs.scipy.org/doc/numpy', None), | ||
"scipy": ('https://docs.scipy.org/doc/scipy/reference/', None), | ||
"skimage": ('http://scikit-image.org/docs/stable/', None), | ||
"qpimage": ('http://qpimage.readthedocs.io/en/stable', None), | ||
} |
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======== | ||
Examples | ||
======== | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
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