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

Release v0.1.0

.coveragerc

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

.github/workflows/build-test.yml

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

.gitignore

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+# 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/
+debug.py
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/source/images/alignment.graffle
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+venv-py3/
+ENV/
+
+# PyCharm
+# User-specific stuff:
+.idea/
+
+# vscode
+.vscode
+
+# R-lanaguage
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+#macOS
+*.DS_Store
+
+*~
+

.readthedocs.yml

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

MANIFEST.in

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+include README.rst
+include LICENSE
+include requirements.txt
+include examples/*.*
+include tests/*.py
+include tests/data/*.*
+include tests/results/*.*

README.rst

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+AMIMSpy
+=======
+|Build Status| |Build Status (AppVeyor)| |codecov| |License| |RTD doc| |Git|
+
+Python package for processing acoustic mist ionization mass spectrometry-based metabolomics and lipidomics data
+
+- **Documentation:** https://amimspy.readthedocs.io/en/latest
+- **Source:** https://github.com/computational-metabolomics/amimspy
+- **Bug reports:** https://github.com/computational-metabolomics/amimspy/issues
+
+
+Installation
+------------
+See the `Installation page <https://amimspy.readthedocs.io/en/latest/installation.html>`__ of
+the `online documentation <https://amimspy.readthedocs.io/en/latest/>`__.
+
+
+Bug reports
+-----------
+Please report any bugs that you find `here <https://github.com/computational-metabolomics/amimspy/issues>`_.
+Or fork the repository on `GitHub <https://github.com/computational-metabolomics/amimspy/>`_
+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`.
+
+
+Credits
+-------
+
+**Developers and contributers**
+ - Matthew Smith ([email protected]) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/>`__
+ - Ralf J. M. Weber ([email protected]) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/staff/profiles/biosciences/weber-ralf.aspx>`__
+
+**AMIMSpy acknowledges support from the following funders:**
+ - BBSRC and Waters Corporation for an iCASE PhD studentship.
+
+
+License
+--------
+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
+
+
+.. |Build Status| image:: https://github.com/computational-metabolomics/amimspy/workflows/amimspy/badge.svg
+   :target: https://github.com/computational-metabolomics/amimspy/actions
+
+.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/amimspy.svg?logo=appveyor&style=flat-square&maxAge=600
+   :target: https://ci.appveyor.com/project/RJMW/amimspy/branch/master
+
+.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
+   :target: https://github.com/computational-metabolomics/amimspy
+
+.. |License| image:: https://img.shields.io/badge/License-GPLv3-blue.svg
+   :target: https://www.gnu.org/licenses/gpl-3.0.html
+
+.. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=3600
+   :target: https://amimspy.readthedocs.io/en/latest/
+
+.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/amimspy/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/computational-metabolomics/amimspy

amimspy/__init__.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright © 2020-2021 Matthew Smith, Ralf Weber
+#
+# This file is part of AMIMSpy.
+#
+# AMIMSpy 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.
+#
+# AMIMSpy 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 AMIMSpy.  If not, see <https://www.gnu.org/licenses/>.
+#
+
+__author__ = 'Matthew Smith ([email protected]), Ralf Weber ([email protected])'
+__credits__ = 'Matthew Smith ([email protected]), Ralf Weber ([email protected])'
+__version__ = '0.1.0'
+__license__ = 'GPLv3'