Update GitHub actions and configs

.github/workflows/build-test.yml

@@ -9,10 +9,8 @@ jobs:
 
     strategy:
       matrix:
-        # os: [ubuntu-latest, windows-latest, macos-latest]
-        # python-version: [3.7, 3.8]
-        os: [windows-latest]
-        python-version: ['3.9', '3.10']
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10']
 
     env:
       OS: ${{ matrix.os }}
@@ -32,7 +30,7 @@ jobs:
         run: |
 
           python --version
-          conda env update --file environment.yml --name base
+          conda env update --file environment.yml --name __setup_conda
 
       - name: Lint with flake8
         run: |
@@ -47,17 +45,18 @@ jobs:
 
       - name: Test with pytest-cov
         run: |
-
-          python setup.py install
-          beamspy --help
-
           conda install pytest codecov pytest-cov -c conda-forge
+
+          python -m pip install --no-deps -e .
+          beamspy --help
+
           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
+      - name: Upload code coverage to codecov
+        uses: codecov/codecov-action@v1
+        if: matrix.os == 'ubuntu-latest'
+        with:
+          flags: unittests
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          verbose: true

README.rst

@@ -1,6 +1,6 @@
 BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)
 ==================================================================================
-|Version| |Py versions| |Git| |Bioconda| |Build Status| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |mybinder|
+|Version| |Py versions| |Git| |Bioconda| |Build Status| |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)
@@ -82,9 +82,6 @@ Released under the GNU General Public License v3.0 (see `LICENSE <https://github
 .. |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/
 

environment.yml

@@ -3,15 +3,14 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
- - numpy
- - scipy
- - requests
- - networkx
- - pandas
- - matplotlib
- - seaborn
- - pyteomics
- - biopython
- - pyside2
- - tqdm
-
+  - numpy
+  - scipy
+  - requests
+  - networkx<=2.5
+  - pandas<=1.5.3
+  - matplotlib
+  - seaborn
+  - pyteomics<=4.4.1
+  - biopython<=1.78
+  - pyside2
+  - tqdm

requirements.txt

@@ -1,11 +1,9 @@
 numpy
 scipy
 requests
-networkx
-pandas
+networkx<=2.5
+pandas<=1.5.3
 matplotlib
 seaborn
-pyteomics
-biopython
-pyside2
-tqdm
+pyteomics<=4.4.1
+biopython<=1.78

setup.py

@@ -21,14 +21,15 @@ def main():
         platforms=["Windows, UNIX"],
         keywords=["Metabolomics", "Mass spectrometry", "Liquid-Chromatography Mass Spectrometry", "Metabolite Annotation"],
         packages=setuptools.find_packages(),
-        python_requires=">=3.7",
+        python_requires=">=3.8",
         test_suite="tests.suite",
         install_requires=install_requires,
         include_package_data=True,
         classifiers=[
             "Programming Language :: Python :: 3",
-            "Programming Language :: Python :: 3.7",
             "Programming Language :: Python :: 3.8",
+            "Programming Language :: Python :: 3.9",
+            "Programming Language :: Python :: 3.10",
             "Topic :: Scientific/Engineering :: Bio-Informatics",
             "Topic :: Scientific/Engineering :: Chemistry",
             "Topic :: Utilities",