Deprecate old SpikeSorting task

ibllib/pipes/ephys_preprocessing.py

@@ -39,8 +39,8 @@
 from ibllib.plots.snapshot import ReportSnapshot
 from brainbox.behavior.dlc import likelihood_threshold, get_licks, get_pupil_diameter, get_smooth_pupil_diameter
 
-_logger = logging.getLogger("ibllib")
-warnings.warn('`pipes.training_preprocessing` to be removed in favour of dynamic pipeline')
+_logger = logging.getLogger('ibllib')
+warnings.warn('`pipes.ephys_preprocessing` to be removed in favour of dynamic pipeline', DeprecationWarning)
 
 
 #  level 0
@@ -53,7 +53,7 @@ class EphysPulses(tasks.Task):
     io_charge = 30  # this jobs reads raw ap files
     priority = 90  # a lot of jobs depend on this one
     level = 0  # this job doesn't depend on anything
-    force = False  # whether or not to force download of missing data on local server if outputs already exist
+    force = False  # whether to force download of missing data on local server if outputs already exist
     signature = {
         'input_files': [('*ap.meta', 'raw_ephys_data/probe*', True),
                         ('*ap.ch', 'raw_ephys_data/probe*', False),  # not necessary when we have .bin file
@@ -219,7 +219,7 @@ def _run(self, overwrite=False):
 
 class SpikeSorting(tasks.Task):
     """
-    Pykilosort 2.5 pipeline
+    (DEPRECATED) Pykilosort 2.5 pipeline
     """
     gpu = 1
     io_charge = 100  # this jobs reads raw ap files
@@ -238,6 +238,12 @@ class SpikeSorting(tasks.Task):
         'output_files': []  # see setUp method for declaration of inputs
     }
 
+    def __init__(self, *args, **kwargs):
+        warnings.warn('`pipes.ephys_preprocessing.SpikeSorting` to be removed '
+                      'in favour of `pipes.ephys_tasks.SpikeSorting`',
+                      DeprecationWarning)
+        super().__init__(*args, **kwargs)
+
     @staticmethod
     def spike_sorting_signature(pname=None):
         pname = pname if pname is not None else "probe*"

ibllib/tests/test_pipes.py

@@ -795,5 +795,64 @@ def dummy_function(arg1, arg2):
         self.assertEqual(result, ("test1", "test2"))
 
 
+class TestLegacyDeprecations(unittest.TestCase):
+    """Assert removal of old code."""
+
+    def test_remove_legacy_pipeline(self):
+        """Remove old legacy pipeline code.
+
+        The following code is an incomplete list of modules and functions that should be removed:
+
+        - pipes.ephys_preprocessing
+        - pipes.training_preprocessing
+        - io.extractors.biased_trials.extract_all
+        - io.extractors.bpod_trials.extract_all
+        - io.extractors.base.get_session_extractor_type
+        - io.extractors.base.get_pipeline
+        - io.extractors.base._get_pipeline_from_task_type
+        - io.extractors.base._get_task_types_json_config
+        - io.extractors.extractor_types.json
+        - qc.task_extractors.TaskQCExtractor.extract_data
+
+        NB: some tasks in ephys_preprocessing and maybe training_preprocessing may be directly used
+        or subclassed by the dynamic pipeline. The TaskQCExtractor class could be removed entirely.
+        Instead, a function could exist to simply fetch the relevant data from the task's extractor
+        class.  Alos, there may be plenty of iblscripts CI tests to be removed.
+        """
+        self.assertTrue(datetime.today() < datetime(2024, 9, 1), 'remove legacy pipeline')
+
+    def test_remove_legacy_rig_code(self):
+        """Remove old legacy (v7) rig code.
+
+        The following code is an incomplete list of modules and functions that should be removed:
+
+        - pipes.transfer_rig_data
+        - pipes.misc.check_transfer
+        - pipes.misc.transfer_session_folders
+        - pipes.misc.copy_with_check
+        - pipes.misc.backup_session
+        - pipes.misc.transfer_folder
+        - pipes.misc.load_videopc_params
+        - pipes.misc.load_ephyspc_params
+        - pipes.misc.create_basic_transfer_params
+        - pipes.misc.create_videopc_params
+        - pipes.misc.create_ephyspc_params
+        - pipes.misc.rdiff_install
+        - pipes.misc.rsync_paths
+        - pipes.misc.confirm_ephys_remote_folder
+        - pipes.misc.create_ephys_flags
+        - pipes.misc.create_ephys_transfer_done_flag
+        - pipes.misc.create_video_transfer_done_flag
+        - pipes.misc.create_transfer_done_flag
+
+        pipes.misc.backup_session may be worth keeping and utilized by the iblrig code (arguably
+        useful on both rig and local server). The corresponding tests should also be removed.
+
+        In addition some iblscripts.deploy files should be removed, e.g. prepare_ephys_session,
+        prepare_video_session.
+        """
+        self.assertTrue(datetime.today() < datetime(2024, 10, 1), 'remove legacy rig code')
+
+
 if __name__ == '__main__':
     unittest.main(exit=False, verbosity=2)