Merge branch 'main' into arkane_match

Author: calvinp0

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

arc/job/adapter.py

@@ -662,6 +662,32 @@ def determine_run_time(self):
         else:
             self.run_time = None
 
+    @staticmethod
+    def _rotate_csv_if_needed(csv_path: str, max_lines: int = 10000, line_count: Optional[int] = None) -> None:
+        """
+        Rotate a CSV file if it reaches or exceeds ``max_lines`` lines (including the header).
+        The archived file is renamed with a timestamp suffix in the same directory.
+        A fresh file (with headers) will be created by the caller as needed.
+
+        Args:
+            csv_path (str): The path to the CSV file.
+            max_lines (int): The maximum number of lines before rotation is triggered.
+            line_count (int, optional): Pre-computed line count to avoid re-reading the file.
+        """
+        if not os.path.isfile(csv_path):
+            return
+        if line_count is None:
+            with open(csv_path, 'r') as f:
+                line_count = sum(1 for _ in f)
+        if line_count >= max_lines:
+            local_time = datetime.datetime.now().strftime("%d_%m_%y")
+            base, ext = os.path.splitext(csv_path)
+            archive_path = f"{base}.old.{local_time}{ext}"
+            try:
+                os.rename(csv_path, archive_path)
+            except FileNotFoundError:
+                pass  # Another process already rotated the file.
+
     def _set_job_number(self):
         """
         Used as the entry number in the database, as well as the job name on the server.
@@ -686,12 +712,16 @@ def _set_job_number(self):
                 writer.writerow(row)
         with open(csv_path, 'r') as f:
             reader = csv.reader(f, dialect='excel')
+            line_count = 0
             job_num = 0
             for _ in reader:
+                line_count += 1
                 job_num += 1
                 if job_num == 100000:
                     job_num = 0
             self.job_num = job_num
+        # Rotate after counting to avoid a second full read of the file.
+        self._rotate_csv_if_needed(csv_path, max_lines=10000, line_count=line_count)
         # 2. Set other related attributes job_name and job_server_name.
         self.job_server_name = self.job_server_name or 'a' + str(self.job_num)
         if self.conformer is not None and self.job_name is None:
@@ -728,6 +758,7 @@ def write_completed_job_to_csv_file(self):
                 self.determine_job_status()
             local_arc_path_ = local_arc_path if os.path.isdir(local_arc_path) else ARC_PATH
             csv_path = os.path.join(local_arc_path_, 'completed_jobs.csv')
+            self._rotate_csv_if_needed(csv_path)
             if os.path.isfile(csv_path):
                 # check that this is the updated version
                 with open(csv_path, 'r') as f:

arc/job/adapter_test.py

@@ -6,8 +6,10 @@
 """
 
 import datetime
+import glob
 import math
 import os
+import tempfile
 import time
 import shutil
 import unittest
@@ -17,7 +19,7 @@
 
 from arc.common import ARC_TESTING_PATH
 from arc.imports import settings
-from arc.job.adapter import DataPoint, JobEnum, JobTypeEnum, JobExecutionTypeEnum
+from arc.job.adapter import DataPoint, JobAdapter, JobEnum, JobTypeEnum, JobExecutionTypeEnum
 from arc.job.adapters.gaussian import GaussianAdapter
 from arc.level import Level
 from arc.species import ARCSpecies
@@ -194,28 +196,34 @@ def setUpClass(cls):
                                     species=[ARCSpecies(label='spc1', xyz=['O 0 0 1'])],
                                     testing=True,
                                     )
+        # Copy the PBS time limit fixture into the directory structure the adapter expects.
+        stl_dir = os.path.join(ARC_TESTING_PATH, 'test_JobAdapter_ServerTimeLimit')
+        err_dest = os.path.join(stl_dir, 'calcs', 'Species', 'spc1', 'opt_101')
+        os.makedirs(err_dest, exist_ok=True)
+        shutil.copy(os.path.join(ARC_TESTING_PATH, 'server', 'pbs', 'timelimit', 'err.txt'),
+                    os.path.join(err_dest, 'err.txt'))
         cls.job_5 = GaussianAdapter(execution_type='queue',
-                                    job_name='spc1',
+                                    job_name='opt_101',
                                     job_type='opt',
                                     job_id='123456',
                                     job_num=101,
-                                    job_server_name = 'server3',
+                                    job_server_name='server3',
                                     level=Level(method='cbs-qb3'),
                                     project='test',
-                                    project_directory=os.path.join(ARC_TESTING_PATH, 'test_JobAdapter_ServerTimeLimit'),
+                                    project_directory=stl_dir,
                                     species=[ARCSpecies(label='spc1', xyz=['O 0 0 1'])],
                                     server='server3',
                                     testing=True,
                                     )
         cls.job_6 = GaussianAdapter(execution_type='queue',
-                                    job_name='spc1',
+                                    job_name='opt_101',
                                     job_type='opt',
                                     job_id='123456',
                                     job_num=101,
-                                    job_server_name = 'server1',
+                                    job_server_name='server1',
                                     level=Level(method='cbs-qb3'),
                                     project='test',
-                                    project_directory=os.path.join(ARC_TESTING_PATH, 'test_JobAdapter_ServerTimeLimit'),
+                                    project_directory=stl_dir,
                                     species=[ARCSpecies(label='spc1', xyz=['O 0 0 1'])],
                                     testing=True,
                                     queue='short_queue',
@@ -471,5 +479,62 @@ def tearDownClass(cls):
         shutil.rmtree(os.path.join(ARC_TESTING_PATH, 'test_JobAdapter_ServerTimeLimit'), ignore_errors=True)
 
 
+class TestRotateCSV(unittest.TestCase):
+    """
+    Contains unit tests for the CSV rotation logic.
+    """
+
+    def _make_csv(self, path, num_lines):
+        """Helper to create a CSV file with a header and ``num_lines - 1`` data rows."""
+        with open(path, 'w') as f:
+            f.write('col1,col2\n')
+            for i in range(num_lines - 1):
+                f.write(f'{i},data\n')
+
+    def test_no_rotation_below_threshold(self):
+        """Test that no rotation occurs when the file is below the threshold."""
+        with tempfile.TemporaryDirectory() as tmp:
+            csv_path = os.path.join(tmp, 'jobs.csv')
+            self._make_csv(csv_path, 10)
+            JobAdapter._rotate_csv_if_needed(csv_path, max_lines=50)
+            self.assertTrue(os.path.isfile(csv_path))
+            self.assertEqual(glob.glob(os.path.join(tmp, 'jobs.old.*.csv')), [])
+
+    def test_rotation_at_threshold(self):
+        """Test that the file is rotated when it reaches the threshold."""
+        with tempfile.TemporaryDirectory() as tmp:
+            csv_path = os.path.join(tmp, 'jobs.csv')
+            self._make_csv(csv_path, 50)
+            JobAdapter._rotate_csv_if_needed(csv_path, max_lines=50)
+            self.assertFalse(os.path.isfile(csv_path))
+            archives = glob.glob(os.path.join(tmp, 'jobs.old.*.csv'))
+            self.assertEqual(len(archives), 1)
+
+    def test_no_error_for_missing_file(self):
+        """Test that rotation is a no-op when the file does not exist."""
+        JobAdapter._rotate_csv_if_needed('/tmp/nonexistent_arc_test.csv')
+
+    def test_multiple_rotations(self):
+        """Test that multiple rotations produce distinct archive files."""
+        with tempfile.TemporaryDirectory() as tmp:
+            csv_path = os.path.join(tmp, 'jobs.csv')
+            # First rotation on "day 1"
+            self._make_csv(csv_path, 50)
+            with patch('arc.job.adapter.datetime') as mock_dt:
+                mock_dt.datetime.now.return_value = datetime.datetime(2026, 1, 15)
+                mock_dt.timedelta = datetime.timedelta
+                JobAdapter._rotate_csv_if_needed(csv_path, max_lines=50)
+            self.assertFalse(os.path.isfile(csv_path))
+            # Second rotation on "day 2"
+            self._make_csv(csv_path, 50)
+            with patch('arc.job.adapter.datetime') as mock_dt:
+                mock_dt.datetime.now.return_value = datetime.datetime(2026, 2, 20)
+                mock_dt.timedelta = datetime.timedelta
+                JobAdapter._rotate_csv_if_needed(csv_path, max_lines=50)
+            self.assertFalse(os.path.isfile(csv_path))
+            archives = glob.glob(os.path.join(tmp, 'jobs.old.*.csv'))
+            self.assertEqual(len(archives), 2)
+
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))