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Add initial docs for RTD (#3)
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README.rst

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BEAMS - Birmingham mEtabolite Annotation for Mass SpectroMetry
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===============================================================
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================================================================
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|Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |mybinder|
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BEAMS is a Python Package **(Beta version)** to annotate LC-MS and DIMS data. **Stable release coming soon.**
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BEAMS is a Python Package to annotate LC-MS and DIMS data.
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- Documentation (Available soon)
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- |documentation|
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- |source|
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- |bug reports|
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Installation
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--------
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------------------------
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Conda_
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~~~~~~~
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1. Install |miniconda|. Follow the steps described |conda_install|.
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2. Run the following commands to install BEAMS.
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Windows-64
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Windows-64, Linux-64 and OSx
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::
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$ conda create -n beams python=2.7 -y --name beams python=2.7 numpy scipy networkx requests pandas -c conda-forge
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$ conda create -n beams beams -c conda-forge -c bioconda -c computational-metabolomics
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$ activate beams
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$ pip install git+https://github.com/computational-metabolomics/beams.git@dev
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Linux-64 and OSx
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::
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$ conda create -n beams python=2.7 -y --name beams python=2.7 numpy scipy networkx requests pandas pyqt -c conda-forge
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$ conda create -n beams beams -c conda-forge -c bioconda -c computational-metabolomics
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$ source activate beams
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$ pip install git+https://github.com/computational-metabolomics/beams.git@dev
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Usage
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------
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------------------------
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Command line
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~~~~~~~~~~~~~
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$ beams start-gui
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Bugs
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----
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------------------------
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Please report any bugs that you find `here <https://github.com/computational-metabolomics/beams/issues>`_.
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Or fork the repository on `GitHub <https://github.com/computational-metabolomics/beams/>`_
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and create a pull request (PR). We welcome all contributions, and we will help you to make the PR if you are new to `git <https://guides.github.com/activities/hello-world/>`_.
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License
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-------
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------------------------
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Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/beams/LICENSE>`_)
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.. |documentation| raw:: html
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<a href="https://computational-metabolomics.github.io/beams" target="_blank">Documentation</a>
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<a href="http://beams.readthedocs.io/en/latest/beams/index.html" target="_blank">Documentation</a>
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.. |source| raw:: html
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docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

docs/source/beams.rst

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BEAMS package
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==================================
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beams.annotation module
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-----------------------
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.. automodule:: beams.annotation
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:members:
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:undoc-members:
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:show-inheritance:
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beams.auxiliary module
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----------------------
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.. automodule:: beams.auxiliary
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:members:
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:undoc-members:
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:show-inheritance:
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beams.db\_parsers module
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------------------------
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.. automodule:: beams.db_parsers
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:members:
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:undoc-members:
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:show-inheritance:
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beams.grouping module
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---------------------
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.. automodule:: beams.grouping
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:members:
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:undoc-members:
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:show-inheritance:
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beams.gui module
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----------------
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.. automodule:: beams.gui
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:members:
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:undoc-members:
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:show-inheritance:
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beams.in\_out module
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--------------------
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.. automodule:: beams.in_out
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:members:
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:undoc-members:
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:show-inheritance:
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beams.libraries module
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----------------------
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.. automodule:: beams.libraries
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:members:
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:undoc-members:
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:show-inheritance:
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beams.plots module
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------------------
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.. automodule:: beams.plots
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:members:
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:undoc-members:
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:show-inheritance:
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beams.statistics module
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-----------------------
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.. automodule:: beams.statistics
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:members:
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:undoc-members:
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:show-inheritance:
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docs/source/cli.rst

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Command line interface (CLI)
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==================================
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docs/source/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# http://www.sphinx-doc.org/en/master/config
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath('..'))
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# -- Project information -----------------------------------------------------
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project = 'BEAMS'
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copyright = '2019, Ralf Weber'
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author = 'Ralf Weber'
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# The full version, including alpha/beta/rc tags
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release = '0.1.0'
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.doctest',
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'sphinx.ext.viewcode',
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'sphinx.ext.napoleon',
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'sphinx.ext.todo',
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'sphinx.ext.mathjax'
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# The master toctree document.
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master_doc = 'index'
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
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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
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# a list of builtin themes.
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#
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html_theme = 'sphinx_rtd_theme'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']

docs/source/galaxy.rst

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Galaxy tools & workflows
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==================================
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docs/source/gui.rst

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Graphical user interface (GUI)
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==================================
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docs/source/index.rst

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.. BEAMS documentation master file, created by
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sphinx-quickstart on Sun Aug 11 22:50:29 2019.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Welcome to BEAMS's documentation!
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=================================
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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introduction
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quickstart
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cli
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gui
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galaxy
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beams
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

docs/source/introduction.rst

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Introduction
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=============
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