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Release v1.1.0 (#13)
* Refactor functions * Update databases (HMDB, LIPID MAPS, etc) * Include subgroups to improve annotations (adducts, isotopes, etc) * Improve summary outputs * Update and Improve GUI * Fix FutureWarnings * Add GitHub actions (#9) * Update dependencies (#12) * Update tests * Update examples * Update README
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‎.coveragerc‎

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[run]
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omit = tests/*,setup.py,beamspy/__main__.py,beamspy/qt/form.py,beamspy/gui.py

‎.github/workflows/build-test.yml‎

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name: beamspy
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on: [push, pull_request]
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, windows-latest, macos-latest]
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python-version: [3.7, 3.8]
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env:
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OS: ${{ matrix.os }}
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PYTHON: ${{ matrix.python-version }}
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steps:
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- uses: actions/checkout@v2
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- name: Setup conda - Python ${{ matrix.python-version }}
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uses: s-weigand/setup-conda@v1
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with:
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update-conda: true
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python-version: ${{ matrix.python-version }}
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conda-channels: conda-forge, bioconda
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- name: Install dependencies
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run: |
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python --version
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conda env update --file environment.yml --name base
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- name: Lint with flake8
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run: |
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conda install flake8
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# stop build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest-cov
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run: |
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python setup.py install
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beamspy --help
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conda install pytest codecov pytest-cov -c conda-forge
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pytest --cov ./ --cov-config=.coveragerc --cov-report=xml
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- name: Upload code coverage to codecov
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uses: codecov/codecov-action@v1
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with:
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flags: unittests
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env_vars: OS,PYTHON
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fail_ci_if_error: true
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verbose: true

‎.travis.yml‎

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services:
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- xvfb
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before_install:
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- python --version
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- pip install -U pip
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- pip install -U pytest
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- pip install codecov pytest-cov
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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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- beamspy --help
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- green -vvv --run-coverage
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- pytest --cov=beamspy tests/
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after_script:
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- python -m codecov
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- codecov
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‎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 requirements.txt
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include examples/run.py
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include examples/run.sh
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include tests/*.py
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include tests/test_data/*.*
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include tests/test_results/.gitignore

‎README.rst‎

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BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)
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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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BEAMSpy (Birmingham mEtabolite Annotation for Mass Spectrometry) is a Python package that includes several automated and
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seamless computational modules that are applied to putatively annotate metabolites detected in untargeted ultra (high)
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performance liquid chromatography-mass spectrometry or untargeted direct infusion mass spectrometry metabolomic assays
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in an automated process. All reported metabolites are annotated to level 3 of the Metabolomics Standards
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Initiative (MSI) reporting standards (Metabolomics. 2007 Sep; 3(3): 211–221. `doi: 10.1007/s11306-007-0082-2 <https://doi.org/10.1007/s11306-007-0082-2>`_).
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The package is highly flexible to suit the diversity of sample types studied and mass spectrometers applied in
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untargeted metabolomics studies. The user can use the standard reference files included in the package or can develop
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their own reference files.
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- `Documentation (Read the Docs) <https://beamspy.readthedocs.io/en/latest/>`_
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- `Bug reports <https://github.com/computational-metabolomics/beamspy/issues>`_
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.. _quick_installation:
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Quick installation
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-------------------
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Conda_
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~~~~~~~
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1. `Install Miniconda <https://conda.io/docs/user-guide/install>`_.
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2. Run the following commands to install BEAMSpy.
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Windows-64, Linux-64 and OSx
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::
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$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
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$ activate beamspy
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Linux-64 and OSx
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::
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$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
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$ source activate beamspy
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Usage
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------------------------
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Command line interface (CLI)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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$ beamspy --help
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Graphical user interface (GUI)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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$ beamspy start-gui
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Bug reports
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------------------------
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Please report any bugs that you find `here <https://github.com/computational-metabolomics/beamspy/issues>`_.
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Or fork the repository on `GitHub <https://github.com/computational-metabolomics/beamspy/>`_
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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/beamspy/LICENSE>`_)
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.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/beamspy.svg?branch=dev&style=flat&maxAge=3600&label=Travis-CI
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:target: https://travis-ci.com/computational-metabolomics/beamspy
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.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/beamspy.svg?style=flat&maxAge=3600&label=AppVeyor
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:target: https://ci.appveyor.com/project/RJMW/beamspy
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.. |Py versions| image:: https://img.shields.io/pypi/pyversions/beamspy.svg?style=flat&maxAge=3600
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:target: https://pypi.python.org/pypi/beamspy/
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.. |Version| image:: https://img.shields.io/pypi/v/beamspy.svg?style=flat&maxAge=3600
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:target: https://pypi.python.org/pypi/beamspy/
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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/beamspy
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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/beamspy/README.html
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.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
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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: https://beamspy.readthedocs.io/en/latest/
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.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/beamspy/branch/master/graph/badge.svg
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:target: https://codecov.io/gh/computational-metabolomics/beamspy
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.. |mybinder| image:: https://mybinder.org/badge_logo.svg
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:target: https://mybinder.org/v2/gh/computational-metabolomics/beamspy/master?filepath=notebooks
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.. _pip: https://pip.pypa.io/
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.. _Conda: http://conda.pydata.org/docs/
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BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)
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==================================================================================
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|Version| |Py versions| |Git| |Bioconda| |Build Status| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |mybinder|
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BEAMSpy (Birmingham mEtabolite Annotation for Mass Spectrometry) is a Python package that includes several automated and
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seamless computational modules that are applied to putatively annotate metabolites detected in untargeted ultra (high)
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performance liquid chromatography-mass spectrometry or untargeted direct infusion mass spectrometry metabolomic assays.
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All reported metabolites are annotated to level 2 or 3 of the Metabolomics Standards
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Initiative (MSI) reporting standards (Metabolomics. 2007 Sep; 3(3): 211–221. `doi: 10.1007/s11306-007-0082-2 <https://doi.org/10.1007/s11306-007-0082-2>`_).
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The package is highly flexible to suit the diversity of sample types studied and mass spectrometers applied in
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untargeted metabolomics studies. The user can use the standard reference files included in the package or can develop
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their own reference files.
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- `Documentation (Read the Docs) <https://beamspy.readthedocs.io/en/latest/>`_
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- `Bug reports <https://github.com/computational-metabolomics/beamspy/issues>`_
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Quick installation
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-------------------
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Conda_
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~~~~~~~
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1. Install `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_. Follow the steps described `here <https://docs.conda.io/projects/conda/en/latest/user-guide/install>`__.
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2. Run the following commands to install BEAMSpy.
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Windows-64, Linux-64 and OSx
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::
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$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
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$ activate beamspy
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Linux-64 and OSx
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::
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$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
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$ source activate beamspy
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Usage
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------------------------
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Command line interface (CLI)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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$ beamspy --help
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Graphical user interface (GUI)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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$ beamspy start-gui
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Bug reports
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------------------------
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Please report any bugs that you find `here <https://github.com/computational-metabolomics/beamspy/issues>`__.
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Or fork the repository on `GitHub <https://github.com/computational-metabolomics/beamspy/>`_
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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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Credits
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-------
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- `Team (University of Birmingham and EMBL-EBI) <https://more.bham.ac.uk/beams/team/>`__
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**Code base**
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- Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/staff/profiles/biosciences/weber-ralf.aspx>`__
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License
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------------------------
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Released under the GNU General Public License v3.0 (see `LICENSE <https://github.com/computational-metabolomics/beamspy/blob/master/LICENSE>`_)
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.. |Build Status| image:: https://github.com/computational-metabolomics/beamspy/workflows/beamspy/badge.svg
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:target: https://github.com/computational-metabolomics/beamspy/actions
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.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/beamspy.svg?style=flat&maxAge=3600&label=AppVeyor
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:target: https://ci.appveyor.com/project/RJMW/beamspy
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.. |Py versions| image:: https://img.shields.io/pypi/pyversions/beamspy.svg?style=flat&maxAge=3600
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:target: https://pypi.python.org/pypi/beamspy/
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.. |Version| image:: https://img.shields.io/pypi/v/beamspy.svg?style=flat&maxAge=3600
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:target: https://pypi.python.org/pypi/beamspy/
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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/beamspy
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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/beamspy/README.html
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.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
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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: https://beamspy.readthedocs.io/en/latest/
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.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/beamspy/branch/master/graph/badge.svg
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:target: https://codecov.io/gh/computational-metabolomics/beamspy
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.. |mybinder| image:: https://mybinder.org/badge_logo.svg
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:target: https://mybinder.org/v2/gh/computational-metabolomics/beamspy/master?filepath=notebooks
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.. _pip: https://pip.pypa.io/
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.. _Conda: https://conda.io/en/latest/

‎appveyor.yml‎

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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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- '%PYTHON%\python.exe -m pip install pytest'
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test_script:
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- '%PYTHON%\python.exe -m green -vvv --run-coverage'
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- '%PYTHON%\python.exe -m pytest'

‎beamspy/__init__.py‎

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__author__ = 'r.j.weber@bham.ac.uk'
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__credits__ = 'r.j.weber@bham.ac.uk'
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__version__ = '1.0.0'
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__version__ = '1.1.0'
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__license__ = 'GPLv3'

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