HOTFIX 2.28.1 (#714)

add trainingPhaseChoiceWorld to extractor type
* typo in EphysPostDLC init
* Fix patch_settings for iblrigv8 (#713)
* Fix patch_settings for iblrigv8
* Increase coverage
* Update release notes

---------

Co-authored-by: juhuntenburg <[email protected]>
Co-authored-by: Florian Rau <[email protected]>
Co-authored-by: Gaelle <[email protected]>
Co-authored-by: GaelleChapuis <[email protected]>
Co-authored-by: Mayo Faulkner <[email protected]>

ibllib/__init__.py

@@ -2,7 +2,7 @@
 import logging
 import warnings
 
-__version__ = '2.28'
+__version__ = '2.28.1'
 warnings.filterwarnings('always', category=DeprecationWarning, module='ibllib')
 
 # if this becomes a full-blown library we should let the logging configuration to the discretion of the dev

ibllib/io/extractors/extractor_types.json

@@ -17,5 +17,6 @@
  "_habituationChoiceWorld": "habituation",
  "_trainingChoiceWorld": "training",
  "ephysMockChoiceWorld": "mock_ephys",
- "ephys_certification": "sync_ephys"
+ "ephys_certification": "sync_ephys",
+ "trainingPhaseChoiceWorld": "training"
 }

ibllib/io/raw_data_loaders.py

@@ -736,16 +736,6 @@ def _groom_wheel_data_ge5(data, label='file ', path=''):
     return data
 
 
-def save_bool(save, dataset_type):
-    if isinstance(save, bool):
-        out = save
-    elif isinstance(save, list):
-        out = (dataset_type in save) or (Path(dataset_type).stem in save)
-    if out:
-        _logger.debug('extracting' + dataset_type)
-    return out
-
-
 def sync_trials_robust(t0, t1, diff_threshold=0.001, drift_threshold_ppm=200, max_shift=5,
                        return_index=False):
     """
@@ -945,7 +935,7 @@ def patch_settings(session_path, collection='raw_behavior_data',
     if not settings:
         raise IOError('Settings file not found')
 
-    filename = PureWindowsPath(settings['SETTINGS_FILE_PATH']).name
+    filename = PureWindowsPath(settings.get('SETTINGS_FILE_PATH', '_iblrig_taskSettings.raw.json')).name
     file_path = Path(session_path).joinpath(collection, filename)
 
     if subject:
@@ -955,7 +945,8 @@ def patch_settings(session_path, collection='raw_behavior_data',
         for k in settings.keys():
             if isinstance(settings[k], str):
                 settings[k] = settings[k].replace(f'\\Subjects\\{old_subject}', f'\\Subjects\\{subject}')
-        settings['SESSION_NAME'] = '\\'.join([subject, *settings['SESSION_NAME'].split('\\')[1:]])
+        if 'SESSION_NAME' in settings:
+            settings['SESSION_NAME'] = '\\'.join([subject, *settings['SESSION_NAME'].split('\\')[1:]])
         settings.pop('PYBPOD_SUBJECT_EXTRA', None)  # Get rid of Alyx subject info
 
     if date:
@@ -970,6 +961,10 @@ def patch_settings(session_path, collection='raw_behavior_data',
                     f'\\{settings["SUBJECT_NAME"]}\\{date}'
                 )
         settings['SESSION_DATETIME'] = date + settings['SESSION_DATETIME'][10:]
+        if 'SESSION_END_TIME' in settings:
+            settings['SESSION_END_TIME'] = date + settings['SESSION_END_TIME'][10:]
+        if 'SESSION_START_TIME' in settings:
+            settings['SESSION_START_TIME'] = date + settings['SESSION_START_TIME'][10:]
 
     if number:
         # Patch session number

ibllib/io/session_params.py

@@ -30,6 +30,7 @@
 from copy import deepcopy
 
 from one.converters import ConversionMixin
+from iblutil.util import flatten
 from packaging import version
 
 import ibllib.pipes.misc as misc
@@ -391,15 +392,15 @@ def get_collections(sess_params, flat=False):
     sess_params : dict
         The loaded experiment description map.
     flat : bool (False)
-        If True, return a flat list of unique collections, otherwise return a map of device/sync/task
+        If True, return a flat set of collections, otherwise return a map of device/sync/task
 
     Returns
     -------
     dict[str, str]
         A map of device/sync/task and the corresponding collection name.
 
-    list[str]
-        A flat list of unique collection names.
+    set[str]
+        A set of unique collection names.
 
     Notes
     -----
@@ -423,16 +424,7 @@ def iter_dict(d):
                 iter_dict(v)
 
     iter_dict(sess_params)
-    if flat:
-        cflat = []
-        for k, v in collection_map.items():
-            if isinstance(v, list):
-                cflat.extend(v)
-            else:
-                cflat.append(v)
-        return list(set(cflat))
-    else:
-        return collection_map
+    return set(flatten(collection_map.values())) if flat else collection_map
 
 
 def get_video_compressed(sess_params):

ibllib/pipes/video_tasks.py

@@ -467,7 +467,7 @@ class EphysPostDLC(base_tasks.VideoTask):
     level = 3
     force = True
 
-    def __int__(self, *args, **kwargs):
+    def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.trials_collection = kwargs.get('trials_collection', 'alf')
 

ibllib/tests/test_io.py

@@ -166,11 +166,15 @@ def test_load_encoder_trial_info(self):
         self.session = Path(__file__).parent.joinpath('extractors', 'data', 'session_biased_ge5')
         data = raw.load_encoder_trial_info(self.session)
         self.assertTrue(data is not None)
+        self.assertIsNone(raw.load_encoder_trial_info(self.session.with_name('empty')))
+        self.assertIsNone(raw.load_encoder_trial_info(None))
 
     def test_load_camera_ssv_times(self):
         session = Path(__file__).parent.joinpath('extractors', 'data', 'session_ephys')
         with self.assertRaises(ValueError):
             raw.load_camera_ssv_times(session, 'tail')
+        with self.assertRaises(FileNotFoundError):
+            raw.load_camera_ssv_times(session.with_name('foobar'), 'body')
         bonsai, camera = raw.load_camera_ssv_times(session, 'body')
         self.assertTrue(bonsai.size == camera.size == 6001)
         self.assertEqual(bonsai.dtype.str, '<M8[ns]')
@@ -297,6 +301,18 @@ def test_load_camera_frameData(self):
         self.assertTrue(fd.dtypes.to_dict() == parsed_dtypes)
         self.assertTrue(all([x == np.int64 for x in fd_raw.dtypes]))
 
+    def test_load_settings(self):
+        main_path = Path(__file__).parent.joinpath('extractors', 'data')
+        self.training_ge5 = main_path / 'session_training_ge5'
+        settings = raw.load_settings(self.training_ge5)
+        self.assertIsInstance(settings, dict)
+        self.assertEqual(144, len(settings))
+        with self.assertLogs(raw._logger, level=20):
+            self.assertIsNone(raw.load_settings(None))
+        # Should return None when path empty
+        with self.assertLogs(raw._logger, level=20):
+            self.assertIsNone(raw.load_settings(self.training_ge5, 'raw_task_data_00'))
+
     def tearDown(self):
         self.tempfile.close()
         os.unlink(self.tempfile.name)
@@ -588,7 +604,7 @@ def test_get_collections_repeat_protocols(self):
         collections = session_params.get_collections(tasks)
         self.assertEqual(set(collections['passiveChoiceWorld']), set(['raw_passive_data_bis', 'raw_passive_data']))
         collections = session_params.get_collections(tasks, flat=True)
-        self.assertEqual(set(collections), set(['raw_passive_data_bis', 'raw_passive_data', 'raw_behavior_data']))
+        self.assertEqual(collections, {'raw_passive_data_bis', 'raw_passive_data', 'raw_behavior_data'})
 
 
 class TestRawDaqLoaders(unittest.TestCase):

release_notes.md

@@ -9,6 +9,10 @@
 ### other
 - Change behavior qc to pass if number of trials > 400 (from start) can be found for which easy trial performance > 0.9
 
+#### 2.28.1
+- Typo in ibllib.pipes.video_tasks.EphysPostDLC class
+- ibllib.io.raw_data_loaders.patch_settings works with iblrigv8 settings files
+
 ## Release Notes 2.27
 
 ### features