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Merge pull request #1 from computational-metabolomics/Release-v0.1.0
Release v0.1.0
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‎.coveragerc

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[run]
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omit = tests/*,setup.py,amimspy/__main__.py

‎.github/workflows/build-test.yml

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name: amimspy
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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, 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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amimspy --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

‎.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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debug.py
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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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docs/source/images/alignment.graffle
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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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venv-py3/
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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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# vscode
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.vscode
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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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‎.readthedocs.yml

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# .readthedocs.yml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/source/conf.py
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# Optionally build your docs in additional formats such as PDF and ePub
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formats: all
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conda:
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environment: environment.yml
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python:
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version: 3.7
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install:
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- method: pip
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path: .

‎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/data/*.*
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include tests/results/*.*

‎README.rst

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AMIMSpy
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=======
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|Build Status| |Build Status (AppVeyor)| |codecov| |License| |RTD doc| |Git|
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Python package for processing acoustic mist ionization mass spectrometry-based metabolomics and lipidomics data
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- **Documentation:** https://amimspy.readthedocs.io/en/latest
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- **Source:** https://github.com/computational-metabolomics/amimspy
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- **Bug reports:** https://github.com/computational-metabolomics/amimspy/issues
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Installation
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------------
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See the `Installation page <https://amimspy.readthedocs.io/en/latest/installation.html>`__ of
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the `online documentation <https://amimspy.readthedocs.io/en/latest/>`__.
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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/amimspy/issues>`_.
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Or fork the repository on `GitHub <https://github.com/computational-metabolomics/amimspy/>`_
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and create a pull request (PR). We welcome all contributions, and we
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will help you to make the PR if you are new to `git`.
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Credits
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-------
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**Developers and contributers**
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- Matthew Smith ([email protected]) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/>`__
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- Ralf J. M. Weber ([email protected]) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/staff/profiles/biosciences/weber-ralf.aspx>`__
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**AMIMSpy acknowledges support from the following funders:**
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- BBSRC and Waters Corporation for an iCASE PhD studentship.
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License
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--------
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AMIMSpy is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/amimspy/blob/master/LICENSE>`_ for licensing information). Copyright © 2020 Matthew Smith, Ralf Weber
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.. |Build Status| image:: https://github.com/computational-metabolomics/amimspy/workflows/amimspy/badge.svg
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:target: https://github.com/computational-metabolomics/amimspy/actions
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.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/amimspy.svg?logo=appveyor&style=flat-square&maxAge=600
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:target: https://ci.appveyor.com/project/RJMW/amimspy/branch/master
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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/amimspy
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.. |License| image:: https://img.shields.io/badge/License-GPLv3-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://amimspy.readthedocs.io/en/latest/
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.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/amimspy/branch/master/graph/badge.svg
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:target: https://codecov.io/gh/computational-metabolomics/amimspy

‎amimspy/__init__.py

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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#
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# Copyright © 2020-2021 Matthew Smith, Ralf Weber
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#
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# This file is part of AMIMSpy.
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#
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# AMIMSpy 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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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# AMIMSpy is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with AMIMSpy. If not, see <https://www.gnu.org/licenses/>.
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#
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__author__ = 'Matthew Smith ([email protected]), Ralf Weber ([email protected])'
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__credits__ = 'Matthew Smith ([email protected]), Ralf Weber ([email protected])'
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__version__ = '0.1.0'
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__license__ = 'GPLv3'

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