Install RMGPY ENV

ReactionMechanismGenerator · Jul 31, 2023 · 14347cf · 14347cf
1 parent f5513af
commit 14347cf
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Showing 15 changed files with 7 additions and 188,670 deletions.
diff --git a/.github/workflows/cont_int.yml b/.github/workflows/cont_int.yml
@@ -77,6 +77,8 @@ jobs:
           echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
           echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
           echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
+          export PYTHONPATH=$PYTHONPATH:$(pwd)
+          export PATH=$PATH:$(pwd)
           echo $(pwd)
           make
           cd ..

diff --git a/autotst/common.py b/autotst/common.py
@@ -12,6 +12,8 @@
 
 # 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

diff --git a/autotst/data/base_test.py b/autotst/data/base_test.py
@@ -34,7 +34,7 @@
 import logging
 import numpy as np
 import autotst
-from autotst.common import AUTOTST_PATH
+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
@@ -156,7 +156,7 @@ def setUp(self):
 
         self.settings = {
             "file_path": os.path.join(
-                os.path.join(AUTOTST_PATH, "test", "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}
@@ -178,7 +178,7 @@ def setUp(self):
 
         self.settings = {
             "file_path": os.path.join(
-                os.path.join(AUTOTST_PATH, "database", "H_Abstraction", "TS_training", "TS_groups.py")
+                os.path.join(AUTOTST_DATABASE_PATH, "database", "H_Abstraction", "TS_groups.py")
             ),
             "local_context": {"DistanceData":DistanceData},
             "global_context": {'__builtins__': None}

diff --git a/test/bin/log-files/CC+[O]O_[CH2]C+OO_forward_0.log b/test/bin/log-files/CC+[O]O_[CH2]C+OO_forward_0.log
diff --git a/test/bin/log-files/CC+[O]O_[CH2]C+OO_forward_center_0.log b/test/bin/log-files/CC+[O]O_[CH2]C+OO_forward_center_0.log
diff --git a/test/bin/log-files/CC+[O]O_[CH2]C+OO_forward_shell_0.log b/test/bin/log-files/CC+[O]O_[CH2]C+OO_forward_shell_0.log
diff --git a/test/bin/log-files/CC+[O]O_[CH2]C+OO_reverse_0.log b/test/bin/log-files/CC+[O]O_[CH2]C+OO_reverse_0.log
diff --git a/test/bin/log-files/CC+[O]O_[CH2]C+OO_reverse_center_0.log b/test/bin/log-files/CC+[O]O_[CH2]C+OO_reverse_center_0.log
diff --git a/test/bin/log-files/CC+[O]O_[CH2]C+OO_reverse_shell_0.log b/test/bin/log-files/CC+[O]O_[CH2]C+OO_reverse_shell_0.log
diff --git a/test/bin/log-files/CC_0.log b/test/bin/log-files/CC_0.log
diff --git a/test/bin/log-files/C[CH2]_0.log b/test/bin/log-files/C[CH2]_0.log
diff --git a/test/bin/log-files/C_fod.log b/test/bin/log-files/C_fod.log
diff --git a/test/bin/log-files/OO_0.log b/test/bin/log-files/OO_0.log
diff --git a/test/bin/log-files/[CH3]+CC(F)(F)F_C+[CH2]C(F)(F)F.log b/test/bin/log-files/[CH3]+CC(F)(F)F_C+[CH2]C(F)(F)F.log
diff --git a/test/bin/log-files/[O]O_0.log b/test/bin/log-files/[O]O_0.log