AutoTST Updates

.github/workflows/cont_int.yml

@@ -0,0 +1,89 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+    types: [opened, synchronize, reopened, ready_for_review]
+  schedule:
+    - cron: '0 0 * * *'
+
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Checkout RMG-Py
+        uses: actions/checkout@v3
+        with:
+          repository: ReactionMechanismGenerator/RMG-Py
+          path: RMG-Py
+          ref: main
+          fetch-depth: 1
+
+      - name: Checkout RMG-database
+        uses: actions/checkout@v3
+        with:
+          repository: ReactionMechanismGenerator/RMG-database
+          path: RMG-database
+          ref: main
+          fetch-depth: 1
+
+      - name: Set up AutoTST
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: environment.yml
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: tst_env
+          use-mamba: true
+
+      - name: Update Environment
+        run: |
+          mamba env update -f environment.yml
+
+      - name: Add AUTOTST to ENV
+        run: |
+          export AUTOTST=$(pwd)
+          export PYTHONPATH=$PYTHONPATH:$AUTOTST
+          echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV
+          echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
+          echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
+          echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
+
+      - name: Install RMG-Py
+        run: |
+          cd RMG-Py
+          mamba env create -f environment.yml
+          cd ..
+
+      - name: Cythonize RMG-Py
+        run: |
+          cd RMG-Py
+          conda activate rmg_env
+          make
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
+          echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV
+          echo "export rmgpy_path=$(pwd)" >> $GITHUB_ENV
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> ~/.bashrc
+          echo "PATH=$(pwd):$PATH" >> ~/.bashrc
+          echo "export rmgpy_path=$(pwd)" >> ~/.bashrc
+
+      - name: Unittest
+        run: |
+          source ~/.bashrc
+          conda activate tst_env
+          make unittests
+

.gitignore

@@ -33,6 +33,6 @@
 *.symm
 *.ase
 *.com
-*.log
+
 *.ts
 *.kinetics

autotst/calculator/gaussian.py

@@ -35,9 +35,9 @@
 import cclib.io
 
 import autotst
-from ..reaction import Reaction, TS
-from ..species import Species, Conformer
-from ..geometry import Torsion
+from autotst.reaction import Reaction, TS
+from autotst.species import Species, Conformer
+from autotst.geometry import Torsion
 
 import ase
 import ase.calculators.gaussian
@@ -179,7 +179,8 @@ def get_rotor_calc(self,
             addsec=[addsec[:-1]])
 
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        if 'force' in ase_gaussian.parameters:
+            del ase_gaussian.parameters['force']
         return ase_gaussian
 
     def get_conformer_calc(self):
@@ -232,7 +233,8 @@ 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']
+        if 'force' in ase_gaussian.parameters:
+            del ase_gaussian.parameters['force']
         return ase_gaussian
 
     def get_shell_calc(self):
@@ -293,7 +295,8 @@ def get_shell_calc(self):
             addsec=[combos]
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        if 'force' in ase_gaussian.parameters:
+            del ase_gaussian.parameters['force']
 
         return ase_gaussian
 
@@ -353,7 +356,9 @@ def get_center_calc(self):
             addsec=[addsec[:-1]]
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+
+        if 'force' in ase_gaussian.parameters:
+            del ase_gaussian.parameters['force']
 
         return ase_gaussian
 
@@ -399,7 +404,8 @@ 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']
+        if 'force' in ase_gaussian.parameters:
+            del ase_gaussian.parameters['force']
 
         return ase_gaussian
 
@@ -444,7 +450,8 @@ def get_irc_calc(self):
             multiplicity=self.conformer.rmg_molecule.multiplicity
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        if 'force' in ase_gaussian.parameters:
+            del ase_gaussian.parameters['force']
 
         return ase_gaussian
 

autotst/calculator/gaussian_test.py

@@ -34,10 +34,12 @@
 import cclib.io
 
 import autotst
-from ..reaction import Reaction, TS
-from ..species import Species, Conformer
-from ..geometry import Torsion
-from .gaussian import Gaussian
+from autotst.common import AUTOTST_PATH
+from autotst.reaction import Reaction, TS
+from autotst.species import Species, Conformer
+from autotst.geometry import Torsion
+from autotst.calculator.gaussian import Gaussian
+
 
 import ase
 import ase.calculators.gaussian
@@ -48,7 +50,7 @@
 
 class TestGaussian(unittest.TestCase):
     def setUp(self):
-        os.environ["PATH"] = os.path.expandvars("$AUTOTST/test/bin:") + os.environ["PATH"]
+        os.environ["PATH"] = os.path.join(AUTOTST_PATH, "test/bin") + os.pathsep + os.environ["PATH"]
         rxn = Reaction(label='C+[O]O_[CH3]+OO')
         ts = rxn.ts["forward"][0]
         ts.get_molecules()
@@ -105,11 +107,11 @@ 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"))
-
+        if os.path.exists(os.path.join(AUTOTST_PATH, "calculator/ts")):
+            shutil.rmtree(os.path.join(AUTOTST_PATH, "calculator/ts"))
+        if os.path.exists(os.path.join(AUTOTST_PATH, "calculator/species")):
+            shutil.rmtree(os.path.join(AUTOTST_PATH, "calculator/species"))
+            
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
 

autotst/calculator/orca_test.py

@@ -31,15 +31,17 @@
 import unittest
 import os, shutil
 
-from .orca import Orca
-from ..species import Conformer
+from autotst.common import AUTOTST_PATH
+from autotst.calculator.orca import Orca
+from autotst.species import Conformer
+
+
 
 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=os.path.join(AUTOTST_PATH,"calculator/fod"))
 
     def test_load_conformer_attributes(self):
         charge = 0
@@ -59,21 +61,17 @@ 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")
+        path = os.path.join(AUTOTST_PATH,"test/bin/log-files/C_fod.log")
         self.assertTrue(self.orca.check_normal_termination(path))
 
     def test_read_fod_log(self):
-        path = os.path.expandvars(
-            "$AUTOTST/test/bin/log-files/C_fod.log")
+        path = os.path.join(AUTOTST_PATH,"test/bin/log-files/C_fod.log")
         fod = self.orca.read_fod_log(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"))
+        if os.path.exists(os.path.join(AUTOTST_PATH,"calculator/fod")):
+            shutil.rmtree(os.path.join(AUTOTST_PATH,"calculator/fod"))
 
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

autotst/calculator/statmech_test.py

@@ -29,8 +29,9 @@
 ##########################################################################
 
 import unittest, os, sys, shutil
-from ..reaction import Reaction
-from .statmech import StatMech
+from autotst.common import AUTOTST_PATH
+from autotst.reaction import Reaction
+from autotst.calculator.statmech import StatMech
 import rmgpy.reaction
 import rmgpy.kinetics
 
@@ -40,7 +41,7 @@ def setUp(self):
         self.reaction.get_labeled_reaction()
         self.reaction.generate_reactants_and_products()
 
-        directory = os.path.expandvars("$AUTOTST/test")
+        directory = os.path.join(AUTOTST_PATH, "test")
         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")):
@@ -66,13 +67,13 @@ def setUp(self):
 
     def tearDown(self):
         try:
-            directory = os.path.expandvars("$AUTOTST/test")
+            directory = os.path.join(AUTOTST_PATH, "test")
             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(AUTOTST_PATH):
                 for fi in files:
                     if fi.endswith(".symm"):
                         os.remove(os.path.join(head, fi))

autotst/calculator/vibrational_analysis_test.py

@@ -36,9 +36,10 @@
 import cclib.io
 import rmgpy
 import rmgpy.molecule
-from ..reaction import Reaction, TS
-from ..species import Species, Conformer
-from .vibrational_analysis import percent_change, VibrationalAnalysis
+from autotst.common import AUTOTST_PATH
+from autotst.reaction import Reaction, TS
+from autotst.species import Species, Conformer
+from autotst.calculator.vibrational_analysis import percent_change, VibrationalAnalysis
 
 class VibrationalAnalysisTest(unittest.TestCase):
 
@@ -48,7 +49,7 @@ def setUp(self):
         self.ts = self.reaction.ts["forward"][0]
         self.ts.get_molecules()
 
-        directory = os.path.expandvars("$AUTOTST/test")
+        directory = os.path.join(AUTOTST_PATH,"test")
         if not os.path.exists(os.path.join(directory, "ts", self.reaction.label, "conformers")):
             os.makedirs(os.path.join(directory, "ts", self.reaction.label, "conformers"))
         if not os.path.exists(os.path.join(directory, "ts", self.reaction.label, self.reaction.label + ".log")):
@@ -140,11 +141,11 @@ def test_validate(self):
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
     try:
-        directory = os.path.expandvars("$AUTOTST/test")
+        directory = os.path.join(AUTOTST_PATH, "test")
         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(AUTOTST_PATH):
             for fi in files:
                 if fi.endswith(".symm"):
                     os.remove(os.path.join(head, fi))

autotst/common.py

@@ -0,0 +1,22 @@
+"""
+
+This module contains common functions that are used throughout AutoTST
+Therefore, it should not import any other AutoTST modules to avoid circular imports
+
+"""
+
+import os
+
+import rmgpy
+
+
+# Absolute path to the AutoTST directory
+AUTOTST_PATH = os.path.dirname(os.path.abspath(__file__))
+# Absolute path to the AutoTST database directory - One directory above AUTOTST_PATH
+AUTOTST_DATABASE_PATH = os.path.abspath(os.path.join(AUTOTST_PATH, os.pardir))
+# Abolsute path to RMG-Py directory
+RMG_PY_PATH = os.path.abspath(os.path.dirname(os.path.dirname(rmgpy.__file__)))
+# Absolute path to the RMG-database directory
+RMG_DATABASE_PATH = os.path.abspath(os.path.dirname(os.path.dirname(rmgpy.settings['database.directory'])))
+
+VERSION = "1.0.0"

autotst/data/base_test.py

@@ -34,8 +34,9 @@
 import logging
 import numpy as np
 import autotst
-from ..reaction import Reaction
-from .base import QMData, DistanceData, TransitionStates, TransitionStateDepository, TSGroups
+from autotst.common import AUTOTST_PATH, AUTOTST_DATABASE_PATH
+from autotst.reaction import Reaction
+from autotst.data.base import QMData, DistanceData, TransitionStates, TransitionStateDepository, TSGroups
 import rmgpy
 import rmgpy.data.rmg
 
@@ -61,7 +62,7 @@ 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"))
+        self.qmdata.get_qmdata(os.path.join(AUTOTST_PATH, "test", "bin", "log-files", "CC+[O]O_[CH2]C+OO_forward_0.log"))
 
         self.assertEqual(self.qmdata.ground_state_degeneracy, 2)
         self.assertAlmostEqual(self.qmdata.molecular_mass[0], 126.1, places=1)
@@ -155,7 +156,7 @@ def setUp(self):
 
         self.settings = {
             "file_path": os.path.join(
-                os.path.expandvars("$AUTOTST"), "database", "H_Abstraction", "TS_training", "reactions.py"
+                os.path.join(AUTOTST_DATABASE_PATH, "database", "H_Abstraction", "TS_training", "reactions.py")
             ),
             "local_context": {"DistanceData":DistanceData},
             "global_context": {'__builtins__': None}
@@ -177,7 +178,7 @@ def setUp(self):
 
         self.settings = {
             "file_path": os.path.join(
-                os.path.expandvars("$AUTOTST"), "database", "H_Abstraction", "TS_groups.py"
+                os.path.join(AUTOTST_DATABASE_PATH, "database", "H_Abstraction", "TS_groups.py")
             ),
             "local_context": {"DistanceData":DistanceData},
             "global_context": {'__builtins__': None}