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Merge pull request #5 from computational-metabolomics/dev
Add and merge developments
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‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*,cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# dotenv
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.env
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# virtualenv
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.venv
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venv/
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ENV/
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# PyCharm
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# User-specific stuff:
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.idea/
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# R-lanaguage
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# History files
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.Rhistory
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.Rapp.history
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# Session Data files
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.RData
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#macOS
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*.DS_Store
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*~
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‎.travis.yml‎

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dist: xenial
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language: python
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python:
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- "3.7"
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services:
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- xvfb
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install:
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- pip install coverage
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- pip install green codecov
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- pip install .
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before_script:
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- "export DISPLAY=:99.0"
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script:
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- beams --help
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- green -vvv --run-coverage
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after_script:
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- python -m codecov

‎LICENSE‎

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state the exclusion of warranty; and each file should have at least
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the "copyright" line and a pointer to where the full notice is found.
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<one line to give the program's name and a brief idea of what it does.>
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Copyright (C) <year> <name of author>
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{one line to give the program's name and a brief idea of what it does.}
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Copyright (C) {year} {name of author}
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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If the program does terminal interaction, make it output a short
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notice like this when it starts in an interactive mode:
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<program> Copyright (C) <year> <name of author>
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{project} Copyright (C) {year} {fullname}
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This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
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This is free software, and you are welcome to redistribute it
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under certain conditions; type `show c' for details.

‎MANIFEST.in‎

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include README.rst
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include LICENSE
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include requirements*.txt
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include examples/*.*
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include tests/*.py
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include tests/test_data/*.*
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include tests/test_results/.gitignore
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include beams/data/*.txt
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include beams/data/databases/*.sql.gz
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include beams/data/databases/databases.txt

‎README.md‎

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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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|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 to annotate LC-MS and DIMS data.
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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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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, Linux-64 and OSx
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::
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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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Linux-64 and OSx
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::
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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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Usage
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------------------------
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Command line
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~~~~~~~~~~~~~
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::
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$ beams --help
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GUI
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~~~~~~~~~~~~~
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::
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$ beams start-gui
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Bugs
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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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Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/beams/LICENSE>`_)
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.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/beams.svg?branch=dev&style=flat&maxAge=3600&label=Travis-CI
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:target: https://travis-ci.com/computational-metabolomics/beams
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.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/beams.svg?style=flat&maxAge=3600&label=AppVeyor
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:target: https://ci.appveyor.com/project/RJMW/beams
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.. |Py versions| image:: https://img.shields.io/pypi/pyversions/beams.svg?style=flat&maxAge=3600
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:target: https://pypi.python.org/pypi/beams/
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.. |Version| image:: https://img.shields.io/pypi/v/beams.svg?style=flat&maxAge=3600
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:target: https://pypi.python.org/pypi/beams/
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.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
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:target: https://github.com/computational-metabolomics/beams
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.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
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:target: http://bioconda.github.io/recipes/beams/README.html
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.. |License| image:: https://img.shields.io/pypi/l/beams.svg?style=flat&maxAge=3600
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:target: https://www.gnu.org/licenses/gpl-3.0.html
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.. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=3600
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:target: http://beams.readthedocs.io/en/latest/beams/index.html
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.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/beams/branch/master/graph/badge.svg
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:target: https://codecov.io/gh/computational-metabolomics/beams
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.. |mybinder| image:: https://mybinder.org/badge_logo.svg
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:target: https://mybinder.org/v2/gh/computational-metabolomics/beams/master?filepath=notebooks
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.. |documentation| raw:: html
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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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<a href="https://github.com/computational-metabolomics/beams/tree/dev/beams" target="_blank">Source</a>
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.. |bug reports| raw:: html
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<a href="https://github.com/computational-metabolomics/beams/issues" target="_blank">Bug reports</a>
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.. |conda_install| raw:: html
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<a href="https://conda.io/docs/user-guide/install" target="_blank">here</a>
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.. |miniconda| raw:: html
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<a href="http://conda.pydata.org/miniconda.html" target="_blank">Miniconda</a>
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.. _pip: https://pip.pypa.io/
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.. _Conda: http://conda.pydata.org/docs/
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‎appveyor.yml‎

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environment:
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matrix:
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- PYTHON: "C:\\Python37"
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build_script:
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- '%PYTHON%\python.exe -m pip install .'
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before_test:
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- '%PYTHON%\python.exe -m pip install coverage green'
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test_script:
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- '%PYTHON%\python.exe -m green -vvv --run-coverage'

‎beams/__init__.py‎

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__author__ = '[email protected], [email protected]'
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__credits__ = '[email protected], [email protected]'
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__version__ = '0.1.0'
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__license__ = 'GPLv3'

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