Merge pull request #504 from ReactionMechanismGenerator/job

Job adapters

.github/workflows/cont_int.yml

@@ -41,20 +41,22 @@ jobs:
     - name: Install dependencies
       run: |
         export PYTHONPATH=$PYTHONPATH:$(pwd)
+        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
         conda activate arc_env
         cd ..
         git clone https://github.com/ReactionMechanismGenerator/RMG-Py
         cd RMG-Py
         export PYTHONPATH=$PYTHONPATH:$(pwd)
+        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
         make
         cd ..
         git clone https://github.com/ReactionMechanismGenerator/RMG-database
         cd ARC
-        conda deactivate
-        make gcn-cpu
-        cd ..
-        echo $(pwd)
+        source ~/.bashrc
+        make install-all
+        source ~/.bashrc
         conda activate arc_env
+        echo $PYTHONPATH
         conda list
 
     - name: Lint with flake8
@@ -68,11 +70,8 @@ jobs:
 
     - name: Test with python unittest
       run: |
-        cd ..
-        cd RMG-Py
-        export PYTHONPATH=$PYTHONPATH:$(pwd)
-        cd ..
-        cd ARC
+        source ~/.bashrc
         conda activate arc_env
+        echo $PYTHONPATH
         make test
         codecov --token=f259713a-7f1d-4e9c-b140-bb3bb371d3ef

Makefile

@@ -9,12 +9,21 @@
 test test-unittests:
 	python3 -m unittest discover -p *Test.py -v
 
-gcn:
+install-all:
+	bash devtools/install_all.sh
+
+install-autotst:
+	bash devtools/install_autotst.sh
+
+install-gcn:
 	bash devtools/install_gcn.sh
 
-gcn-cpu:
+install-gcn-cpu:
 	bash devtools/install_gcn_cpu.sh
 
+install-kinbot:
+	bash devtools/install_kinbot.sh
+
 clean:
 	find -type d -name __pycache__ -exec rm -rf {} +
 	rm -rf testing

arc/__init__.py

@@ -1,6 +1,7 @@
 import arc.exceptions
 import arc.main
 from arc.main import ARC
+import arc.checks
 import arc.common
 import arc.imports
 import arc.level

arc/checks/__init__.py

@@ -0,0 +1,2 @@
+import arc.checks.ts
+import arc.checks.common

arc/checks/common.py

@@ -0,0 +1,43 @@
+"""
+A module with common functionalities used for checking the quality of calculations,
+contains helper functions for Scheduler.
+"""
+
+import datetime
+
+from typing import List, Optional
+
+
+def sum_time_delta(timedelta_list: List[datetime.timedelta]) -> datetime.timedelta:
+    """
+    A helper function for summing datetime.timedelta objects.
+
+    Args:
+        timedelta_list (list): Time delta's to sum.
+
+    Returns:
+        datetime.timedelta: The timedelta sum.
+    """
+    result = datetime.timedelta(0)
+    for timedelta in timedelta_list:
+        if type(timedelta) == type(result):
+            result += timedelta
+    return result
+
+
+def get_i_from_job_name(job_name: str) -> Optional[int]:
+    """
+    Get the conformer or tsg index from the job name.
+
+    Args:
+        job_name (str): The job name, e.g., 'conformer12' or 'tsg5'.
+
+    Returns:
+        Optional[int]: The corresponding conformer or tsg index.
+    """
+    i = None
+    if 'conformer' in job_name:
+        i = int(job_name[9:])
+    elif 'tsg' in job_name:
+        i = int(job_name[3:])
+    return i

arc/checks/commonTest.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+
+"""
+This module contains unit tests for the arc.checks.common module
+"""
+
+import datetime
+import unittest
+
+import arc.checks.common as common
+
+
+class TestChecks(unittest.TestCase):
+    """
+    Contains unit tests for the check module.
+    """
+    def test_sum_time_delta(self):
+        """Test the sum_time_delta() function"""
+        dt1 = datetime.timedelta(days=0, minutes=0, seconds=0)
+        dt2 = datetime.timedelta(days=0, minutes=0, seconds=0)
+        dt3 = datetime.timedelta(days=0, minutes=1, seconds=15)
+        dt4 = datetime.timedelta(days=10, minutes=1, seconds=15, microseconds=300)
+        fake_dt5 = None
+        fake_dt6 = 'fake'
+        fake_dt7 = 18.52
+        self.assertEqual(common.sum_time_delta([]), datetime.timedelta(days=0, minutes=0, seconds=0))
+        self.assertEqual(common.sum_time_delta([dt1]), datetime.timedelta(days=0, minutes=0, seconds=0))
+        self.assertEqual(common.sum_time_delta([dt1, dt2]), datetime.timedelta(days=0, minutes=0, seconds=0))
+        self.assertEqual(common.sum_time_delta([dt1, dt3]), datetime.timedelta(days=0, minutes=1, seconds=15))
+        self.assertEqual(common.sum_time_delta([dt3, dt4]), datetime.timedelta(days=10, minutes=2, seconds=30, microseconds=300))
+        self.assertEqual(common.sum_time_delta([dt3, fake_dt5, fake_dt6, fake_dt7]),
+                         datetime.timedelta(days=0, minutes=1, seconds=15))
+
+    def test_get_i_from_job_name(self):
+        """Test the get_i_from_job_name() function"""
+        self.assertIsNone(common.get_i_from_job_name(''))
+        self.assertIsNone(common.get_i_from_job_name('some_job_name'))
+        self.assertEqual(common.get_i_from_job_name('conformer3'), 3)
+        self.assertEqual(common.get_i_from_job_name('conformer33'), 33)
+        self.assertEqual(common.get_i_from_job_name('conformer3355'), 3355)
+        self.assertEqual(common.get_i_from_job_name('tsg2'), 2)
+
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))