Merge pull request #507 from ReactionMechanismGenerator/CI_with_mamba

CI with mamba

.github/workflows/cont_int.yml

@@ -1,11 +1,16 @@
-name: continuous integration
+name: CI
 
 on:
   push:
+    branches:
+      - '*'
   pull_request:
     branches:
       - main
     types: [opened, synchronize, reopened, ready_for_review, review_requested]
+  schedule:
+    - cron: '0 0 * * *'
+
 
 jobs:
   build:
@@ -17,16 +22,21 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up miniconda Python 3.7
+    - name: Setup Mambaforge Python 3.7
       uses: conda-incubator/setup-miniconda@v2
       with:
         environment-file: environment.yml
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
         activate-environment: arc_env
         python-version: 3.7
-        auto-activate-base: false
+        use-mamba: true
+
+    - name: Update environment
+      run: mamba env update -n arc_env -f environment.yml
 
     - name: Install codecov
-      run: conda install -y -c conda-forge codecov
+      run: mamba install -y -c conda-forge codecov
 
     - name: Install dependencies
       run: |
@@ -49,13 +59,14 @@ jobs:
 
     - name: Lint with flake8
       run: |
-        conda install flake8
+        mamba install flake8
+        mamba config --append channels anaconda
         # stop the build if there are Python syntax errors or undefined names
         python -m flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         python -m flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
-    - name: Test with nosetests
+    - name: Test with python unittest
       run: |
         cd ..
         cd RMG-Py

arc/species/conformersTest.py

@@ -1632,7 +1632,7 @@ def test_translate_group(self):
         expected_xyz1 = {'symbols': ('O', 'O', 'C'), 'isotopes': (16, 16, 12),
                          'coords': ((8.749511531958021e-17, 3.469446951953614e-18, 1.405000000524252),
                                     (-1.40486421, -0.01953339, 0.0), (0.0, 0.0, 0.0))}
-        self.assertEqual(new_xyz1, expected_xyz1)
+        self.assertTrue(almost_equal_coords_lists(new_xyz1, expected_xyz1))
 
         xyz2 = converter.str_to_xyz("""Cl      1.47512188   -0.78746253   -0.20393322
 S      -1.45707856   -0.94104506   -0.20275830

arc/species/speciesTest.py

@@ -1733,49 +1733,6 @@ def test_xyz_perception(self):
         mol_graph_1 = MolGraph(symbols=xyz_arb['symbols'], coords=xyz_arb['coords'])
         self.assertEqual(mol_graph_1.get_formula(), 'CH3NO2')
 
-    def test_gcn(self):
-        """
-        Test that ARC can call the GNN to make TS guesses for further optimization.
-        """
-        # create temporary project directory to delete afterwards
-        project_dir = os.path.join(ARC_PATH, 'arc', 'testing', 'gcn_tst')
-
-        r_xyz = """C  -1.3087    0.0068    0.0318
-        C  0.1715   -0.0344    0.0210
-        N  0.9054   -0.9001    0.6395
-        O  2.1683   -0.5483    0.3437
-        N  2.1499    0.5449   -0.4631
-        N  0.9613    0.8655   -0.6660
-        H  -1.6558    0.9505    0.4530
-        H  -1.6934   -0.0680   -0.9854
-        H  -1.6986   -0.8169    0.6255"""
-        reactant = ARCSpecies(label='reactant', smiles='C([C]1=[N]O[N]=[N]1)', xyz=r_xyz)
-
-        p_xyz = """C  -1.0108   -0.0114   -0.0610  
-        C  0.4780    0.0191    0.0139    
-        N  1.2974   -0.9930    0.4693    
-        O  0.6928   -1.9845    0.8337    
-        N  1.7456    1.9701   -0.6976    
-        N  1.1642    1.0763   -0.3716    
-        H  -1.4020    0.9134   -0.4821  
-        H  -1.3327   -0.8499   -0.6803   
-        H  -1.4329   -0.1554    0.9349"""
-        product = ARCSpecies(label='product', smiles='[N-]=[N+]=C(N=O)C', xyz=p_xyz)
-
-        rxn = ARCReaction(label='reactant <=> product', ts_methods=['gcn'], ts_label='TS0')
-        rxn.r_species = [reactant]
-        rxn.p_species = [product]
-        ts_guess = TSGuess(arc_reaction=rxn, method='gcn', project_dir=project_dir)
-        ts_guess.execute_ts_guess_method()
-
-        # verify that the method correctly create TS.xyz
-        ts_path = os.path.join(project_dir, 'calcs', 'TSs', rxn.ts_label, 'GCN', 'TS.xyz')
-        ts_xyz_dict = str_to_xyz(ts_path)
-        self.assertEqual(ts_xyz_dict['symbols'], ('C', 'C', 'N', 'O', 'N', 'N', 'H', 'H', 'H'))
-
-        if os.path.exists(project_dir):
-            shutil.rmtree(project_dir, ignore_errors=True)
-
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

arc/species/zmatTest.py

@@ -1151,7 +1151,9 @@ def test_zmat_to_coords(self):
                                    (-3.871932295381926, -0.9306597576029849, -2.5400987960833166),
                                    (-3.440082669618663, 0.6565731451487455, -1.8462094217817948)]
         expected_ordered_symbols = ['C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'C', 'C', 'O', 'O', 'H', 'H', 'H', 'H', 'H']
-        self.assertEqual(ordered_coords, expected_ordered_coords)
+        for coords1, coords2 in zip(expected_ordered_coords, ordered_coords):
+            for coord1, coord2 in zip(coords1, coords2):
+                self.assertAlmostEqual(coord1, coord2)
         self.assertEqual(ordered_symbols, expected_ordered_symbols)
 
         ordered_symbols = zmat.zmat_to_coords(zmat=zmat1, keep_dummy=True)[1]
@@ -1662,14 +1664,15 @@ def test_remove_1st_atom(self):
 
         coords, symbols = zmat.zmat_to_coords(expected_zmat_3)
         self.assertEqual(symbols, ['C', 'C', 'H', 'H', 'H', 'H', 'H'])
-        self.assertEqual(coords, [(0.0, 0.0, 0.0),
+        for coords1, coords2 in zip(coords, [(0.0, 0.0, 0.0),
                                   (0.0, 0.0, 1.5120487296562577),
                                   (0.0, 1.0243258057118119, -0.3843844758142396),
                                   (-0.8871049813083173, -0.5121760994984771, -0.38436337480993366),
                                   (-2.635365836667347e-08, -1.0243258057118116, 1.8964332054704973),
                                   (-0.8870987970032913, 0.512186345981728, 1.8964193919074686),
-                                  (0.8871050112557137, 0.5121760476286488, 1.8964121044661915)])
-
+                                  (0.8871050112557137, 0.5121760476286488, 1.8964121044661915)]):
+            for coord1, coord2 in zip(coords1, coords2):
+                self.assertAlmostEqual(coord1, coord2)
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))