AutoTST Update (Python 3.9)

.github/workflows/ci.yml

@@ -0,0 +1,33 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: '0 6 * * 1'  # Weekly on Monday at 06:00 UTC
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          environment-file: environment.yml
+          activate-environment: tst_env
+          miniforge-version: latest
+
+      - name: Run tests
+        env:
+          PYTHONPATH: ${{ github.workspace }}
+        run: |
+          pytest --verbose --tb=short autotst/
+          rm -rf species ts test/species test/ts

Makefile

@@ -1,6 +1,3 @@
 unittest unittests test-unittest test-unittests:
-	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage  --cover-package=autotst 
-	rm -r species
-	rm -r ts
-	rm -r test/species
-	rm -r test/ts
+	pytest --verbose --tb=short autotst/
+	rm -rf species ts test/species test/ts

README.md

@@ -37,9 +37,7 @@ Now, create the anaconda environment for AutoTST
 
 Modify environment variables. Add AutoTST to the `PYTHONPATH` to ensure that you can access modules from any folder. Modify your ~/.bashrc file by adding the following line:
 
-- `export AUTOTST="your_folder/AutoTST`
-
-- `export PYTHONPATH=$AUTOTST:$PYTHONPATH`
+- `export PYTHONPATH=/path/to/AutoTST:$PYTHONPATH`
 
 To be able to run AutoTST in any conda environment, you can set your path to the following by modifing your ~/.bashrc: 
 

autotst/calculator/gaussian.py

@@ -179,7 +179,7 @@ def get_rotor_calc(self,
             addsec=[addsec[:-1]])
 
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
         return ase_gaussian
 
     def get_conformer_calc(self):
@@ -232,7 +232,7 @@ def get_conformer_calc(self):
             extra=f"opt=(calcfc,maxcycles=900,{self.convergence}) freq IOP(7/33=1,2/16=3) scf=(maxcycle=900)",
             multiplicity=self.conformer.rmg_molecule.multiplicity)
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
         return ase_gaussian
 
     def get_shell_calc(self):
@@ -293,7 +293,7 @@ def get_shell_calc(self):
             addsec=[combos]
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 
@@ -353,7 +353,7 @@ def get_center_calc(self):
             addsec=[addsec[:-1]]
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 
@@ -399,7 +399,7 @@ def get_overall_calc(self):
             extra="opt=(ts,calcfc,noeigentest,maxcycles=900) freq scf=(maxcycle=900) IOP(7/33=1,2/16=3)",
             multiplicity=self.conformer.rmg_molecule.multiplicity)
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 
@@ -444,7 +444,7 @@ def get_irc_calc(self):
             multiplicity=self.conformer.rmg_molecule.multiplicity
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 

autotst/calculator/gaussian_test.py

@@ -38,6 +38,7 @@
 from ..species import Species, Conformer
 from ..geometry import Torsion
 from .gaussian import Gaussian
+from ..utils.paths import project_root, test_bin_dir
 
 import ase
 import ase.calculators.gaussian
@@ -48,7 +49,7 @@
 
 class TestGaussian(unittest.TestCase):
     def setUp(self):
-        os.environ["PATH"] = os.path.expandvars("$AUTOTST/test/bin:") + os.environ["PATH"]
+        os.environ["PATH"] = f"{test_bin_dir()}:{os.environ['PATH']}"
         rxn = Reaction(label='C+[O]O_[CH3]+OO')
         ts = rxn.ts["forward"][0]
         ts.get_molecules()
@@ -105,12 +106,14 @@ def test_irc_calc(self):
         self.assertIsInstance(calc_dict,dict)
 
     def tearDown(self):
-        if os.path.exists(os.path.expandvars("$AUTOTST/autotst/calculator/ts")):
-            shutil.rmtree(os.path.expandvars("$AUTOTST/autotst/calculator/ts"))
-        if os.path.exists(os.path.expandvars("$AUTOTST/autotst/calculator/species")):
-            shutil.rmtree(os.path.expandvars("$AUTOTST/autotst/calculator/species"))
+        ts_dir = project_root() / "autotst" / "calculator" / "ts"
+        species_dir = project_root() / "autotst" / "calculator" / "species"
+        if os.path.exists(ts_dir):
+            shutil.rmtree(ts_dir)
+        if os.path.exists(species_dir):
+            shutil.rmtree(species_dir)
 
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
 
-
+

autotst/calculator/orca_test.py

@@ -33,13 +33,16 @@
 
 from .orca import Orca
 from ..species import Conformer
+from ..utils.paths import project_root, test_data_dir
 
 class TestOrca(unittest.TestCase):
 
     def setUp(self):
         conf = Conformer(smiles='C')
-        self.orca = Orca(conformer=conf, directory=os.path.expandvars(
-            "$AUTOTST/autotst/calculator/fod"))
+        self.orca = Orca(
+            conformer=conf,
+            directory=str(project_root() / "autotst" / "calculator" / "fod")
+        )
 
     def test_load_conformer_attributes(self):
         charge = 0
@@ -59,21 +62,19 @@ def test_write_fod_input(self):
         self.assertTrue(os.path.exists(os.path.join(self.orca.directory,'C_fod.inp')))
 
     def test_check_normal_termination(self):
-        path = os.path.expandvars(
-            "$AUTOTST/test/bin/log-files/C_fod.log")
-        self.assertTrue(self.orca.check_normal_termination(path))
+        path = test_data_dir() / "C_fod.log"
+        self.assertTrue(self.orca.check_normal_termination(str(path)))
 
     def test_read_fod_log(self):
-        path = os.path.expandvars(
-            "$AUTOTST/test/bin/log-files/C_fod.log")
-        fod = self.orca.read_fod_log(path)
+        path = test_data_dir() / "C_fod.log"
+        fod = self.orca.read_fod_log(str(path))
         self.assertEquals(float(0.000025),fod)
 
     def tearDown(self):
 
-        if os.path.exists(os.path.expandvars("$AUTOTST/autotst/calculator/fod")):
-            shutil.rmtree(os.path.expandvars(
-                "$AUTOTST/autotst/calculator/fod"))
+        fod_dir = project_root() / "autotst" / "calculator" / "fod"
+        if os.path.exists(fod_dir):
+            shutil.rmtree(fod_dir)
 
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

autotst/calculator/statmech_test.py

@@ -31,6 +31,7 @@
 import unittest, os, sys, shutil
 from ..reaction import Reaction
 from .statmech import StatMech
+from ..utils.paths import project_root, test_data_dir, test_dir
 import rmgpy.reaction
 import rmgpy.kinetics
 
@@ -40,12 +41,12 @@ def setUp(self):
         self.reaction.get_labeled_reaction()
         self.reaction.generate_reactants_and_products()
 
-        directory = os.path.expandvars("$AUTOTST/test")
+        directory = test_dir()
         if not os.path.exists(os.path.join(directory, "ts", self.reaction.label)):
             os.makedirs(os.path.join(directory, "ts", self.reaction.label))
         if not os.path.exists(os.path.join(directory, "ts", self.reaction.label, self.reaction.label + ".log")):
             shutil.copy(
-                os.path.join(directory, "bin", "log-files", self.reaction.label + "_forward_0.log"),
+                test_data_dir() / f"{self.reaction.label}_forward_0.log",
                 os.path.join(directory, "ts", self.reaction.label, self.reaction.label + ".log")
             )
 
@@ -55,24 +56,24 @@ def setUp(self):
                     os.makedirs(os.path.join(directory, "species", smiles))
                 if not os.path.exists(os.path.join(directory, "species", smiles, smiles+".log")):
                     shutil.copy(
-                        os.path.join(directory, "bin", "log-files", smiles + "_0.log"),
+                        test_data_dir() / f"{smiles}_0.log",
                         os.path.join(directory, "species", smiles, smiles+".log")
                     )
 
         self.statmech = StatMech(
             reaction = self.reaction,
-            directory = directory
+            directory = str(directory)
         )
 
     def tearDown(self):
         try:
-            directory = os.path.expandvars("$AUTOTST/test")
+            directory = test_dir()
             if os.path.exists(os.path.join(directory, "ts")):
                 shutil.rmtree(os.path.join(directory, "ts"))
             if os.path.exists(os.path.join(directory, "species")):
                 shutil.rmtree(os.path.join(directory, "species"))
 
-            for head, _, files in os.walk(os.path.expandvars("$AUTOTST")):
+            for head, _, files in os.walk(project_root()):
                 for fi in files:
                     if fi.endswith(".symm"):
                         os.remove(os.path.join(head, fi))
@@ -176,4 +177,4 @@ def test_set_results(self):
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
 
-
+

autotst/calculator/vibrational_analysis_test.py

@@ -39,6 +39,7 @@
 from ..reaction import Reaction, TS
 from ..species import Species, Conformer
 from .vibrational_analysis import percent_change, VibrationalAnalysis
+from ..utils.paths import project_root, test_data_dir, test_dir
 
 class VibrationalAnalysisTest(unittest.TestCase):
 
@@ -48,29 +49,28 @@ def setUp(self):
         self.ts = self.reaction.ts["forward"][0]
         self.ts.get_molecules()
 
-        directory = os.path.expandvars("$AUTOTST/test")
+        directory = test_dir()
         if not os.path.exists(os.path.join(directory, "ts", self.reaction.label, "conformers")):
             os.makedirs(os.path.join(directory, "ts", self.reaction.label, "conformers"))
         if not os.path.exists(os.path.join(directory, "ts", self.reaction.label, self.reaction.label + ".log")):
             shutil.copy(
-                os.path.join(directory, "bin", "log-files", self.reaction.label + "_forward_0.log"),
+                test_data_dir() / f"{self.reaction.label}_forward_0.log",
                 os.path.join(directory, "ts", self.reaction.label, "conformers", self.reaction.label + "_forward_0.log")
             )
 
         self.directory = directory
         self.vibrational_analysis = VibrationalAnalysis(
             transitionstate = self.ts,
-            directory = self.directory
+            directory = str(self.directory)
         )
 
         self.reaction2 = Reaction("[CH3]+CC(F)(F)F_C+[CH2]C(F)(F)F")
         self.reaction2.get_labeled_reaction()
         self.ts2 = self.reaction2.ts["forward"][0]
-        log_file = os.path.join(
-            directory, "bin", "log-files", "[CH3]+CC(F)(F)F_C+[CH2]C(F)(F)F.log")
+        log_file = test_data_dir() / "[CH3]+CC(F)(F)F_C+[CH2]C(F)(F)F.log"
         self.vibrational_analysis2 = VibrationalAnalysis(
             transitionstate = self.ts2,
-            log_file = log_file
+            log_file = str(log_file)
         )
 
     def test_get_log_file(self):
@@ -140,14 +140,13 @@ def test_validate(self):
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
     try:
-        directory = os.path.expandvars("$AUTOTST/test")
+        directory = test_dir()
         if os.path.exists(os.path.join(directory, "ts")):
             shutil.rmtree(os.path.join(directory, "ts"))
 
-        for head, _, files in os.walk(os.path.expandvars("$AUTOTST")):
+        for head, _, files in os.walk(project_root()):
             for fi in files:
                 if fi.endswith(".symm"):
                     os.remove(os.path.join(head, fi))
-    except:
+    except Exception:
         None
-

autotst/data/base_test.py

@@ -36,6 +36,7 @@
 import autotst
 from ..reaction import Reaction
 from .base import QMData, DistanceData, TransitionStates, TransitionStateDepository, TSGroups
+from ..utils.paths import database_dir, test_data_dir
 import rmgpy
 import rmgpy.data.rmg
 
@@ -61,7 +62,8 @@ def test_get_qmdata(self):
         A method that is designed to obtain the QM data for a transitionstate or molecule
         Returns a qmdata object
         """
-        self.qmdata.get_qmdata(os.path.expandvars("$AUTOTST/test/bin/log-files/CC+[O]O_[CH2]C+OO_forward_0.log"))
+        log_path = test_data_dir() / "CC+[O]O_[CH2]C+OO_forward_0.log"
+        self.qmdata.get_qmdata(str(log_path))
 
         self.assertEqual(self.qmdata.ground_state_degeneracy, 2)
         self.assertAlmostEqual(self.qmdata.molecular_mass[0], 126.1, places=1)
@@ -154,9 +156,7 @@ def setUp(self):
         self.ts_depository = TransitionStateDepository(label="test")
 
         self.settings = {
-            "file_path": os.path.join(
-                os.path.expandvars("$AUTOTST"), "database", "H_Abstraction", "TS_training", "reactions.py"
-            ),
+            "file_path": str(database_dir() / "H_Abstraction" / "TS_training" / "reactions.py"),
             "local_context": {"DistanceData":DistanceData},
             "global_context": {'__builtins__': None}
         }
@@ -176,9 +176,7 @@ def setUp(self):
         self.ts_groups = TSGroups(label="test")
 
         self.settings = {
-            "file_path": os.path.join(
-                os.path.expandvars("$AUTOTST"), "database", "H_Abstraction", "TS_groups.py"
-            ),
+            "file_path": str(database_dir() / "H_Abstraction" / "TS_groups.py"),
             "local_context": {"DistanceData":DistanceData},
             "global_context": {'__builtins__': None}
         }
@@ -211,4 +209,4 @@ def test_estimate_distances_using_group_additivity(self):
         self.assertAlmostEquals(d23, distance_data.distances["d23"], places=1)
 
 if __name__ == "__main__":
-    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))