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
computational-metabolomics · Feb 19, 2021 · d87c1d5 · d87c1d5
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diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,2 @@
+[run]
+omit = tests/*,setup.py,beamspy/__main__.py,beamspy/qt/form.py,beamspy/gui.py
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -0,0 +1,60 @@
+name: beamspy
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-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
+          beamspy --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
diff --git a/.travis.yml b/.travis.yml
@@ -6,17 +6,22 @@ python:
 services:
   - xvfb
 
+before_install:
+  - python --version
+  - pip install -U pip
+  - pip install -U pytest
+  - pip install codecov pytest-cov
+
 install:
-  - pip install coverage
-  - pip install green codecov
   - pip install .
 
 before_script:
   - "export DISPLAY=:99.0"
 
 script:
   - beamspy --help
-  - green -vvv --run-coverage
+  - pytest --cov=beamspy tests/
 
 after_script:
-  - python -m codecov
+  - codecov
+
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,7 +1,8 @@
 include README.rst
 include LICENSE
-include requirements*.txt
-include examples/*.*
+include requirements.txt
+include examples/run.py
+include examples/run.sh
 include tests/*.py
 include tests/test_data/*.*
 include tests/test_results/.gitignore

diff --git a/README.rst b/README.rst
@@ -1,106 +1,113 @@
-BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)
-==================================================================================
-|Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |mybinder|
-
-BEAMSpy (Birmingham mEtabolite Annotation for Mass Spectrometry) is a Python package that includes several automated and
-seamless computational modules that are applied to putatively annotate metabolites detected in untargeted ultra (high)
-performance liquid chromatography-mass spectrometry or untargeted direct infusion mass spectrometry metabolomic assays
-in an automated process. All reported metabolites are annotated to level 3 of the Metabolomics Standards
-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>`_).
-
-The package is highly flexible to suit the diversity of sample types studied and mass spectrometers applied in
-untargeted metabolomics studies. The user can use the standard reference files included in the package or can develop
-their own reference files.
-
-
-- `Documentation (Read the Docs) <https://beamspy.readthedocs.io/en/latest/>`_
-- `Bug reports <https://github.com/computational-metabolomics/beamspy/issues>`_
-
-
-.. _quick_installation:
-
-Quick installation
--------------------
-
-Conda_
-~~~~~~~
-
-1. `Install Miniconda <https://conda.io/docs/user-guide/install>`_.
-2. Run the following commands to install BEAMSpy.
-
-Windows-64, Linux-64 and OSx
-
-::
-
-    $ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
-    $ activate beamspy
-
-Linux-64 and OSx
-
-::
-
-    $ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
-    $ source activate beamspy
-
-
-Usage
-------------------------
-
-Command line interface (CLI)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-::
-
-    $ beamspy --help
-
-Graphical user interface (GUI)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-::
-
-    $ beamspy start-gui
-
-Bug reports
-------------------------
-
-Please report any bugs that you find `here <https://github.com/computational-metabolomics/beamspy/issues>`_.
-Or fork the repository on `GitHub <https://github.com/computational-metabolomics/beamspy/>`_
-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/>`_.
-
-License
-------------------------
-
-Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/beamspy/LICENSE>`_)
-
-.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/beamspy.svg?branch=dev&style=flat&maxAge=3600&label=Travis-CI
-   :target: https://travis-ci.com/computational-metabolomics/beamspy
-
-.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/beamspy.svg?style=flat&maxAge=3600&label=AppVeyor
-   :target: https://ci.appveyor.com/project/RJMW/beamspy
-
-.. |Py versions| image:: https://img.shields.io/pypi/pyversions/beamspy.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/beamspy/
-
-.. |Version| image:: https://img.shields.io/pypi/v/beamspy.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/beamspy/
-
-.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
-   :target: https://github.com/computational-metabolomics/beamspy
-
-.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
-   :target: http://bioconda.github.io/recipes/beamspy/README.html
-
-.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-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://beamspy.readthedocs.io/en/latest/
-
-.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/beamspy/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/computational-metabolomics/beamspy
-
-.. |mybinder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/computational-metabolomics/beamspy/master?filepath=notebooks
-
-.. _pip: https://pip.pypa.io/
-.. _Conda: http://conda.pydata.org/docs/
+BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)
+==================================================================================
+|Version| |Py versions| |Git| |Bioconda| |Build Status| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |mybinder|
+
+BEAMSpy (Birmingham mEtabolite Annotation for Mass Spectrometry) is a Python package that includes several automated and
+seamless computational modules that are applied to putatively annotate metabolites detected in untargeted ultra (high)
+performance liquid chromatography-mass spectrometry or untargeted direct infusion mass spectrometry metabolomic assays.
+All reported metabolites are annotated to level 2 or 3 of the Metabolomics Standards
+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>`_).
+The package is highly flexible to suit the diversity of sample types studied and mass spectrometers applied in
+untargeted metabolomics studies. The user can use the standard reference files included in the package or can develop
+their own reference files.
+
+
+- `Documentation (Read the Docs) <https://beamspy.readthedocs.io/en/latest/>`_
+- `Bug reports <https://github.com/computational-metabolomics/beamspy/issues>`_
+
+
+Quick installation
+-------------------
+
+Conda_
+~~~~~~~
+
+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>`__.
+2. Run the following commands to install BEAMSpy.
+
+Windows-64, Linux-64 and OSx
+
+::
+
+    $ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
+    $ activate beamspy
+
+Linux-64 and OSx
+
+::
+
+    $ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
+    $ source activate beamspy
+
+
+Usage
+------------------------
+
+Command line interface (CLI)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+
+    $ beamspy --help
+
+Graphical user interface (GUI)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+
+    $ beamspy start-gui
+
+
+Bug reports
+------------------------
+
+Please report any bugs that you find `here <https://github.com/computational-metabolomics/beamspy/issues>`__.
+Or fork the repository on `GitHub <https://github.com/computational-metabolomics/beamspy/>`_
+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/>`_.
+
+
+Credits
+-------
+ - `Team (University of Birmingham and EMBL-EBI) <https://more.bham.ac.uk/beams/team/>`__
+
+**Code base**
+ - 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>`__
+
+
+License
+------------------------
+
+Released under the GNU General Public License v3.0 (see `LICENSE <https://github.com/computational-metabolomics/beamspy/blob/master/LICENSE>`_)
+
+.. |Build Status| image:: https://github.com/computational-metabolomics/beamspy/workflows/beamspy/badge.svg
+   :target: https://github.com/computational-metabolomics/beamspy/actions
+
+.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/beamspy.svg?style=flat&maxAge=3600&label=AppVeyor
+   :target: https://ci.appveyor.com/project/RJMW/beamspy
+
+.. |Py versions| image:: https://img.shields.io/pypi/pyversions/beamspy.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/beamspy/
+
+.. |Version| image:: https://img.shields.io/pypi/v/beamspy.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/beamspy/
+
+.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
+   :target: https://github.com/computational-metabolomics/beamspy
+
+.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
+   :target: http://bioconda.github.io/recipes/beamspy/README.html
+
+.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-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://beamspy.readthedocs.io/en/latest/
+
+.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/beamspy/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/computational-metabolomics/beamspy
+
+.. |mybinder| image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/computational-metabolomics/beamspy/master?filepath=notebooks
+
+.. _pip: https://pip.pypa.io/
+.. _Conda: https://conda.io/en/latest/
diff --git a/appveyor.yml b/appveyor.yml
@@ -6,7 +6,7 @@ build_script:
   - '%PYTHON%\python.exe -m pip install .'
 
 before_test:
-  - '%PYTHON%\python.exe -m pip install coverage green'
+  - '%PYTHON%\python.exe -m pip install pytest'
 
 test_script:
-  - '%PYTHON%\python.exe -m green -vvv --run-coverage'
+  - '%PYTHON%\python.exe -m pytest'
diff --git a/beamspy/__init__.py b/beamspy/__init__.py
@@ -1,4 +1,4 @@
 __author__ = 'r.j.weber@bham.ac.uk'
 __credits__ = 'r.j.weber@bham.ac.uk'
-__version__ = '1.0.0'
+__version__ = '1.1.0'
 __license__ = 'GPLv3'