Commit 26d4f3c8 authored by Martino Bertoni's avatar Martino Bertoni 🌋

package boilerplate

parent 1de01de9
# http://editorconfig.org
root = true
[*]
indent_style = space
indent_size = 4
trim_trailing_whitespace = true
insert_final_newline = true
charset = utf-8
end_of_line = lf
[*.bat]
indent_style = tab
end_of_line = crlf
[LICENSE]
insert_final_newline = false
[Makefile]
indent_style = tab
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
# pyenv
.python-version
# celery beat schedule file
celerybeat-schedule
# SageMath parsed files
*.sage.py
# dotenv
.env
# virtualenv
.venv
venv/
ENV/
# Spyder project settings
.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mkdocs documentation
/site
# mypy
.mypy_cache/
image: python:3.6
before_script:
- pip install tox
test:
script:
- tox
=======
Credits
=======
Development Lead
----------------
* Miquel Duran Frigola <miquel.duran@irbbarcelona.org>
* Oriol Guitart <oriol.guitart@irbbarcelona.org>
* Martino Bertoni <martino.bertoni@irbbarcelona.org>
* Adria Fernandez <adria.fernandez@irbbarcelona.org>
Contributors
------------
None yet. Why not be the first?
.. highlight:: shell
============
Contributing
============
Contributions are welcome, and they are greatly appreciated! Every little bit
helps, and credit will always be given.
You can contribute in many ways:
Types of Contributions
----------------------
Report Bugs
~~~~~~~~~~~
Report bugs at http://gitlab.sbnb.org/project-specific-repositories/chemical_checker/issues.
If you are reporting a bug, please include:
* Your operating system name and version.
* Any details about your local setup that might be helpful in troubleshooting.
* Detailed steps to reproduce the bug.
Fix Bugs
~~~~~~~~
Look through the GitLab issues for bugs. Anything tagged with "bug" and "help
wanted" is open to whoever wants to implement it.
Implement Features
~~~~~~~~~~~~~~~~~~
Look through the GitLab issues for features. Anything tagged with "enhancement"
and "help wanted" is open to whoever wants to implement it.
Write Documentation
~~~~~~~~~~~~~~~~~~~
chemicalchecker could always use more documentation, whether as part of the
official chemicalchecker docs, in docstrings, or even on the web in blog posts,
articles, and such.
Submit Feedback
~~~~~~~~~~~~~~~
The best way to send feedback is to file an issue at http://gitlab.sbnb.org/project-specific-repositories/chemical_checker/issues.
If you are proposing a feature:
* Explain in detail how it would work.
* Keep the scope as narrow as possible, to make it easier to implement.
* Remember that this is a volunteer-driven project, and that contributions
are welcome :)
Tips
----
To run a subset of tests::
$ py.test tests.test_chemicalchecker
Deploying
---------
A reminder for the maintainers on how to deploy.
Make sure all your changes are committed (including an entry in HISTORY.rst).
Then run::
$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags
=======
History
=======
0.1.0 (2018-11-21)
------------------
* First release.
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Python Package with everything needed to create and query the Chemical Checker.
Copyright (C) 2018 Martino Bertoni
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
include AUTHORS.rst
include CONTRIBUTING.rst
include HISTORY.rst
include LICENSE
include README.rst
recursive-include tests *
recursive-exclude * __pycache__
recursive-exclude * *.py[co]
recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
.PHONY: clean clean-test clean-pyc clean-build docs help
.DEFAULT_GOAL := help
define BROWSER_PYSCRIPT
import os, webbrowser, sys
try:
from urllib import pathname2url
except:
from urllib.request import pathname2url
webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
endef
export BROWSER_PYSCRIPT
define PRINT_HELP_PYSCRIPT
import re, sys
for line in sys.stdin:
match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
if match:
target, help = match.groups()
print("%-20s %s" % (target, help))
endef
export PRINT_HELP_PYSCRIPT
BROWSER := python -c "$$BROWSER_PYSCRIPT"
help:
@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
clean-build: ## remove build artifacts
rm -fr build/
rm -fr dist/
rm -fr .eggs/
find . -name '*.egg-info' -exec rm -fr {} +
find . -name '*.egg' -exec rm -f {} +
clean-pyc: ## remove Python file artifacts
find . -name '*.pyc' -exec rm -f {} +
find . -name '*.pyo' -exec rm -f {} +
find . -name '*~' -exec rm -f {} +
find . -name '__pycache__' -exec rm -fr {} +
clean-test: ## remove test and coverage artifacts
rm -fr .tox/
rm -f .coverage
rm -fr htmlcov/
rm -fr .pytest_cache
lint: ## check style with flake8
flake8 chemicalchecker tests
test: ## run tests quickly with the default Python
py.test
test-all: ## run tests on every Python version with tox
tox
coverage: ## check code coverage quickly with the default Python
coverage run --source chemicalchecker -m pytest
coverage report -m
coverage html
$(BROWSER) htmlcov/index.html
docs: ## generate Sphinx HTML documentation, including API docs
rm -f docs/chemicalchecker.rst
rm -f docs/modules.rst
sphinx-apidoc -o docs/ chemicalchecker
$(MAKE) -C docs clean
$(MAKE) -C docs html
$(BROWSER) docs/_build/html/index.html
servedocs: docs ## compile the docs watching for changes
watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
release: dist ## package and upload a release
twine upload dist/*
dist: clean ## builds source and wheel package
python setup.py sdist
python setup.py bdist_wheel
ls -l dist
install: clean ## install the package to the active Python's site-packages
python setup.py install
===============
chemicalchecker
===============
Python Package with everything needed to create and query the Chemical Checker.
* Free software: GNU General Public License v3
* Documentation: http://gitlab.sbnb.org/project-specific-repositories/chemical_checker/wikis/home
Features
--------
* TODO
Unit-testing
----
Got to your chemicalchecker package directory
To run all tests::
$ pytest
To run a subset of tests::
$ pytest tests.test_chemicalchecker
Deploying
---------
A reminder for the maintainers on how to deploy.
Make sure all your changes are committed (including an entry in HISTORY.rst).
Then run::
$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags
# -*- coding: utf-8 -*-
"""Top-level package for chemicalchecker."""
__author__ = """SBNB"""
__email__ = 'sbnb@irbbarcelona.org'
__version__ = '0.1.0'
# -*- coding: utf-8 -*-
"""Main module."""
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = python -msphinx
SPHINXPROJ = chemicalchecker
SOURCEDIR = .
BUILDDIR = _build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.. include:: ../AUTHORS.rst
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# chemicalchecker documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 9 13:47:02 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.
# 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('..'))
import chemicalchecker
# -- General configuration ---------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# 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 ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
# Add any paths that contain templates here, relative to this directory.
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'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'chemicalchecker'
copyright = u"2018, SBNB"
author = u"SBNB"
# 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 = chemicalchecker.__version__
# The full version, including alpha/beta/rc tags.
release = chemicalchecker.__version__
# 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
# 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']
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
# -- Options for HTML output -------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'alabaster'
# 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 = {}
# 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']
# -- Options for HTMLHelp output ---------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'chemicalcheckerdoc'
# -- 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',
}
# 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, 'chemicalchecker.tex',
u'chemicalchecker Documentation',
u'SBNB', '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, 'chemicalchecker',
u'chemicalchecker Documentation',
[author], 1)
]
# -- Options for Texinfo output ----------------------------------------
# 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, 'chemicalchecker',
u'chemicalchecker Documentation',
author,
'chemicalchecker',
'One line description of project.',
'Miscellaneous'),
]
.. include:: ../CONTRIBUTING.rst
.. include:: ../HISTORY.rst
Welcome to chemicalchecker's documentation!
======================================
.. toctree::
:maxdepth: 2
:caption: Contents:
readme
installation
usage
modules
contributing
authors
history
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
.. highlight:: shell
============
Installation
============
Stable release
--------------
To install chemicalchecker, run this command in your terminal:
.. code-block:: console
$ pip install chemicalchecker
This is the preferred method to install chemicalchecker, as it will always install the most recent stable release.
If you don't have `pip`_ installed, this `Python installation guide`_ can guide
you through the process.
.. _pip: https://pip.pypa.io
.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
@ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=python -msphinx
)
set SOURCEDIR=.
set BUILDDIR=_build
set SPHINXPROJ=chemicalchecker
if "%1" == "" goto help
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The Sphinx module was not found. Make sure you have Sphinx installed,
echo.then set the SPHINXBUILD environment variable to point to the full
echo.path of the 'sphinx-build' executable. Alternatively you may add the
echo.Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
goto end
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
:end
popd
.. include:: ../README.rst
=====
Usage
=====
To use chemicalchecker in a project::
import chemicalchecker
#!/bin/bash
PACKAGE_NAME=$1
FULL_VERSION=$2
MINOR_VERSION=${FULL_VERSION%.*}
MAJOR_VERSION=${FULL_VERSION%.*.*}
cd docs
make html
cd ..
#init_devpi.sh
devpi upload --with-docs
devpi test ${PACKAGE_NAME}==$FULL_VERSION
devpi push ${PACKAGE_NAME}==$FULL_VERSION root/dev
pip==18.1
bumpversion==0.5.3
wheel==0.32.1
watchdog==0.9.0
flake8==3.5.0
tox==3.5.2
coverage==4.5.1
Sphinx==1.8.1
twine==1.12.1
pytest==3.8.2
pytest-runner==4.2
[bumpversion]
current_version = 0.1.0
commit = True
tag = True
[bumpversion:file:setup.py]
search = version='{current_version}'
replace = version='{new_version}'
[bumpversion:file:chemicalchecker/__init__.py]
search = __version__ = '{current_version}'
replace = __version__ = '{new_version}'