Add GitHub actions

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+omit = tests/*,setup.py,msnpy/__main__.py

.github/workflows/build-test.yml

@@ -0,0 +1,60 @@
+name: msnpy
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.7]
+
+    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
+          msnpy --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

README.rst

@@ -1,17 +1,17 @@
 MSnPy
 ======
-|Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |binder|
+|Version| |Py versions| |Git| |Bioconda| |Build Status| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |binder|
 
 Python package to process and annotate MSn fragmentation data
 
-- **Documentation:** https://msnpy.readthedocs.io/en/latest
+- **Documentation:** https://computational-metabolomics.github.io/msnpy
 - **Source:** https://github.com/computational-metabolomics/msnpy
 - **Bug reports:** https://github.com/computational-metabolomics/msnpy/issues
 
 Installation
 ------------
-See the `Installation page <https://msnpy.readthedocs.io/en/latest/introduction.html#installation>`__ of
-the `online documentation <https://msnpy.readthedocs.io/en/latest>`__.
+See the `Installation page <https://computational-metabolomics.github.io/msnpy/introduction.html#installation>`__ of
+the `online documentation <https://computational-metabolomics.github.io/msnpy/>`__.
 
 
 Command line
@@ -31,17 +31,17 @@ will help you to make the PR if you are new to `git`.
 
 Developers & Contributors
 -------------------------
- - Ralf J. M. Weber ([email protected]) - `University of Birmingham (UK) <https://www.birmingham.ac.uk/schools/biosciences/staff/profile.aspx?ReferenceId=156564&Name=dr-ralf-weber>`__
- - Thomas N. Lawson (more) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`__
+ - Ralf J. M. Weber ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
+ - Thomas N. Lawson ([email protected]) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
 
 
 License
 -------
 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/msnpy/blob/master/LICENSE>`_)
 
 
-.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/msnpy.svg?style=flat&maxAge=3600&label=Travis-CI
-   :target: https://travis-ci.com/computational-metabolomics/msnpy
+.. |Build Status| image:: https://github.com/computational-metabolomics/msnpy/workflows/msnpy/badge.svg
+   :target: https://github.com/computational-metabolomics/msnpy/actions
 
 .. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/msnpy.svg?style=flat&maxAge=3600&label=AppVeyor
    :target: https://ci.appveyor.com/project/RJMW/msnpy/branch/master

msnpy/convert.py

@@ -260,7 +260,7 @@ def peaklist2msp(pls, out_pth, msp_type='massbank', polarity='positive', msnpy_a
             if dt.shape[0] == 0:
                 continue
 
-            if not include_ms1 and (re.search('.*Full ms .*', pl.ID) and ms_level == 1):
+            if not include_ms1 and re.search('.*Full ms .*', pl.ID):
                 continue
             if 'convert_id' in pl.metadata:
                 convert_id = pl.metadata['convert_id']