pychemstation 0.10.7.dev1__tar.gz → 0.10.8.dev2__tar.gz

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.7.dev1
+Version: 0.10.8.dev2
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
 Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/pychemstation/control/controllers/comm.py

@@ -173,5 +173,5 @@ class CommunicationController(ABCCommunicationController):
                         data_dirs[i] = "C:" + data_dir
                 return method_dir, sequence_dir, data_dirs
         raise ValueError(
-                f"One of the method: {method_dir}, sequence: {sequence_dir} or data directories: {data_dirs} could not be found, please provide your own."
-            )
+            f"One of the method: {method_dir}, sequence: {sequence_dir} or data directories: {data_dirs} could not be found, please provide your own."
+        )

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/pychemstation/control/controllers/data_aq/method.py

@@ -445,7 +445,7 @@ class MethodController(RunController):
             i = 0
             while folder.is_err() and i < 10:
                 folder = self._fuzzy_match_most_recent_folder(self.data_files[-1], None)
-                i+=1
+                i += 1
             if folder.is_ok():
                 self.data_files[-1] = folder.ok_value
             else:

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/pychemstation/control/controllers/data_aq/sequence.py

@@ -338,8 +338,10 @@ class SequenceController(RunController):
                         and set(most_recent_folder._data_files) == child_dirs
                     ):
                         most_recent_folder.child_dirs = [
-                            os.path.join(most_recent_folder.dir, f) for f in child_dirs
+                            os.path.join(most_recent_folder.dir, f) if not os.path.isdir(f) else f for f in child_dirs
                         ]
+                        for d in most_recent_folder.child_dirs:
+                            assert os.path.isdir(d)
                     else:
                         potential_folders: List[str] = sorted(
                             list(
@@ -427,6 +429,8 @@ class SequenceController(RunController):
                 ).ok_value
             )
         parent_dir = self.data_files[-1]
+        if len(parent_dir._data_files) != len(parent_dir.child_dirs) or len(parent_dir.child_dirs) == 0:
+            parent_dir = self._fuzzy_match_most_recent_folder(most_recent_folder=parent_dir, child_dirs=None)
         spectra = self.get_data()
         reports = []
         for i, child_dir in enumerate(parent_dir.child_dirs):

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/pychemstation/utils/sequence_types.py

@@ -78,10 +78,11 @@ class SequenceTable:
         for self_row, other_row in zip(self.rows, other.rows):
             equal &= self_row.vial_location == other_row.vial_location
             equal &= self_row.data_file == other_row.data_file
-            equal &= (
-                os.path.split(os.path.normpath(self_row.method))[-1]
-                == os.path.split(os.path.normpath(other_row.method))[-1]
-            )
+            if self_row.method and other_row.method:
+                equal &= (
+                    os.path.split(os.path.normpath(self_row.method))[-1]
+                    == os.path.split(os.path.normpath(other_row.method))[-1]
+                )
             equal &= self_row.num_inj == other_row.num_inj
             equal &= self_row.inj_vol == other_row.inj_vol
             equal &= self_row.inj_source == other_row.inj_source

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pychemstation"
-version = "0.10.7.dev1"
+version = "0.10.8.dev2"
 description = "Library to interact with Chemstation software, primarily used in Hein lab"
 authors = [{ name = "lucyhao", email = "hao.lucyy@gmail.com" }]
 requires-python = ">=3.10"

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/tests/comm/test_dirs.py

@@ -28,6 +28,5 @@ class TestComm(unittest.TestCase):
             self.assertTrue(os.path.isdir(data_dir))
 
 
-
 if __name__ == "__main__":
     unittest.main()

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/tests/constants.py

@@ -101,9 +101,9 @@ def set_up_utils(
     comm_dir = room(num)
     if not offline:
         if not os.path.exists(comm_dir):
-                raise FileNotFoundError(
-                    f"{comm_dir} does not exist on your system. If you would like to run tests, please change this path."
-                )
+            raise FileNotFoundError(
+                f"{comm_dir} does not exist on your system. If you would like to run tests, please change this path."
+            )
 
     controller = HPLCController(
         offline=offline,

{pychemstation-0.10.7.dev1 → pychemstation-0.10.8.dev2}/tests/run/test_run_sequence.py

@@ -42,12 +42,12 @@ class TestSequence(unittest.TestCase):
         self.hplc_controller.preprun()
         self.hplc_controller.run_sequence(stall_while_running=False)
         time_left, done = self.hplc_controller.check_sequence_complete()
-        self.assertIsNotNone(
-            self.hplc_controller.sequence_controller.data_files[-1].dir
-        )
-        self.assertIsNotNone(
-            self.hplc_controller.sequence_controller.data_files[-1].child_dirs[0]
-        )
+        sequence_dir = self.hplc_controller.sequence_controller.data_files[-1].dir
+        child_dir = self.hplc_controller.sequence_controller.data_files[-1].child_dirs[0]
+        self.assertIsNotNone(sequence_dir)
+        self.assertIsNotNone(child_dir)
+        self.assertTrue(os.path.isdir(sequence_dir))
+        self.assertTrue(os.path.isdir(child_dir))
         while not done:
             time.sleep(time_left / 2)
             time_left, done = self.hplc_controller.check_sequence_complete()
@@ -62,6 +62,18 @@ class TestSequence(unittest.TestCase):
     def test_run_sequence_stall(self):
         self.hplc_controller.preprun()
         self.hplc_controller.run_sequence(stall_while_running=True)
+        time_left, done = self.hplc_controller.check_sequence_complete()
+        self.assertTrue(done)
+        self.assertTrue(time_left )
+        sequence_dir = self.hplc_controller.sequence_controller.data_files[-1].dir
+        child_dir = self.hplc_controller.sequence_controller.data_files[-1].child_dirs[0]
+        self.assertIsNotNone(sequence_dir)
+        self.assertIsNotNone(child_dir)
+        self.assertTrue(os.path.isdir(sequence_dir))
+        self.assertTrue(os.path.isdir(child_dir))
+        while not done:
+            time.sleep(time_left / 2)
+            time_left, done = self.hplc_controller.check_sequence_complete()
         _ = self.hplc_controller.get_last_run_sequence_data()
         uv = self.hplc_controller.get_last_run_sequence_data(read_uv=True)
         reports = self.hplc_controller.get_last_run_sequence_reports()