Merge pull request #48 from srnas/gh-actions2

Added GitHub Actions
srnas · Jun 20, 2022 · 528d50a · 528d50a
2 parents db22173 + ce27cbe
commit 528d50a
Show file tree

Hide file tree

Showing 29 changed files with 15,344 additions and 15,318 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,30 @@
+
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  python:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install
+      run: |
+        pip install .
+    - name: Test with pytest
+      run: |
+        pip install pytest pytest-cov
+        pytest -v --cov=barnaba
+        bash <(curl -s https://codecov.io/bash)
diff --git a/setup.py b/setup.py
@@ -12,14 +12,11 @@ def readme():
           'Intended Audience :: Science/Research',
           'Topic :: Scientific/Engineering :: Bio-Informatics',
           'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
-          'Programming Language :: Python :: 2',
-          'Programming Language :: Python :: 2.6',
-          'Programming Language :: Python :: 2.7',
-          'Programming Language :: Python :: 3',
-          'Programming Language :: Python :: 3.3',
-          'Programming Language :: Python :: 3.4',
-          'Programming Language :: Python :: 3.5',
           'Programming Language :: Python :: 3.6',
+          'Programming Language :: Python :: 3.7',
+          'Programming Language :: Python :: 3.8',
+          'Programming Language :: Python :: 3.9',
+          'Programming Language :: Python :: 3.10',
       ],      
       url='https://github.com/srnas/barnaba',
       author='Sandro Bottaro',
@@ -28,8 +25,7 @@ def readme():
       setup_requires = ['setuptools_scm','setuptools_scm_git_archive'],
       packages=find_packages(),
       python_requires='>=2.6',
-      install_requires=['numpy','scipy','mdtraj','future'],
-      test_suite='nose.collector',
+      install_requires=['numpy','scipy','mdtraj','future','sklearn'],
       scripts=['bin/barnaba'],
       zip_safe=False)
 

diff --git a/test/README.md b/test/README.md
@@ -1,11 +1,11 @@
-You can run all the tests using nose
+You can run all the tests using pytest
 
-> pip install nose
+> pip install pytest
 
 and then run all of them from the root directory with the command
 
-> nosetests
+> pytest
 
 a single test can be also performed e.g.
 
-> nosetests test/test_sugar.py
+> pytest test/test_sugar.py
diff --git a/test/reference/ds_motif_00001_C_171_0_0.pdb b/test/reference/ds_motif_00001_C_171_0_0.pdb
diff --git a/test/reference/ds_motif_00002_G_209_0_0.pdb b/test/reference/ds_motif_00002_G_209_0_0.pdb
diff --git a/test/reference/ds_motif_00003_A_354_0_0.pdb b/test/reference/ds_motif_00003_A_354_0_0.pdb
diff --git a/test/reference/ds_motif_00004_U_584_0_0.pdb b/test/reference/ds_motif_00004_U_584_0_0.pdb
diff --git a/test/reference/ds_motif_00005_C_1366_0_0.pdb b/test/reference/ds_motif_00005_C_1366_0_0.pdb
diff --git a/test/reference/ds_motif_00006_U_2688_0_0.pdb b/test/reference/ds_motif_00006_U_2688_0_0.pdb
diff --git a/test/reference/ds_motif_00007_G_74_1_0.pdb b/test/reference/ds_motif_00007_G_74_1_0.pdb
diff --git a/test/reference/enm_14.test.pdb b/test/reference/enm_14.test.pdb
diff --git a/test/reference/ss_motif_00001_C_252_0_0.pdb b/test/reference/ss_motif_00001_C_252_0_0.pdb
diff --git a/test/reference/ss_motif_00002_U_468_0_0.pdb b/test/reference/ss_motif_00002_U_468_0_0.pdb
diff --git a/test/reference/ss_motif_00003_C_576_0_0.pdb b/test/reference/ss_motif_00003_C_576_0_0.pdb
diff --git a/test/reference/ss_motif_00004_G_690_0_0.pdb b/test/reference/ss_motif_00004_G_690_0_0.pdb
diff --git a/test/reference/ss_motif_00005_C_804_0_0.pdb b/test/reference/ss_motif_00005_C_804_0_0.pdb
diff --git a/test/reference/ss_motif_00006_U_1326_0_0.pdb b/test/reference/ss_motif_00006_U_1326_0_0.pdb
diff --git a/test/reference/ss_motif_00007_G_1628_0_0.pdb b/test/reference/ss_motif_00007_G_1628_0_0.pdb
diff --git a/test/reference/ss_motif_00008_C_1862_0_0.pdb b/test/reference/ss_motif_00008_C_1862_0_0.pdb
diff --git a/test/reference/ss_motif_00009_C_2248_0_0.pdb b/test/reference/ss_motif_00009_C_2248_0_0.pdb
diff --git a/test/reference/ss_motif_00010_C_2411_0_0.pdb b/test/reference/ss_motif_00010_C_2411_0_0.pdb
diff --git a/test/reference/ss_motif_00011_C_2629_0_0.pdb b/test/reference/ss_motif_00011_C_2629_0_0.pdb
diff --git a/test/reference/ss_motif_00012_C_2695_0_0.pdb b/test/reference/ss_motif_00012_C_2695_0_0.pdb
diff --git a/test/reference/ss_motif_00013_G_2876_0_0.pdb b/test/reference/ss_motif_00013_G_2876_0_0.pdb
diff --git a/test/reference/ss_motif_00014_C_89_1_0.pdb b/test/reference/ss_motif_00014_C_89_1_0.pdb
diff --git a/test/reference/ss_motif_00015_C_1594_0_0.pdb b/test/reference/ss_motif_00015_C_1594_0_0.pdb
diff --git a/test/reference/ss_motif_00016_U_493_0_0.pdb b/test/reference/ss_motif_00016_U_493_0_0.pdb
diff --git a/test/reference/ss_motif_00017_G_1054_0_0.pdb b/test/reference/ss_motif_00017_G_1054_0_0.pdb
diff --git a/test/reference/ss_motif_00018_C_1793_0_0.pdb b/test/reference/ss_motif_00018_C_1793_0_0.pdb