Merge branch 'main' of https://github.com/mdmelin/project_extraction

Author: mdmelin

projects/_template.py

@@ -41,8 +41,7 @@ class TemplateBpodTrialsExtractor(BaseBpodTrialsExtractor):
     :class:`ibllib.io.extractors.mesoscope.TimelineTrials` for examples).
 
     To associate this extractor to your task protocol, you must add it to the
-    `projects/task_extractor_map.json` file. Additionally you can associate `Alyx procedures`_ (e.g.
-    'Optical stimulation') to the protocol with the `projects/task_type_procedures.json` file.
+    `projects/task_extractor_map.json` file.
 
     .. _Alyx procedures: https://openalyx.internationalbrainlab.org/admin/actions/proceduretype/
 

projects/base.py

@@ -4,7 +4,7 @@
 
 import one.alf.io as alfio
 from ibllib.io.extractors import ephys_fpga
-from neurodsp.utils import sync_timestamps
+from ibldsp.utils import sync_timestamps
 from ibllib.plots import squares, vertical_lines
 from ibllib.pipes import tasks
 

projects/ephys_passive_opto.py

@@ -5,7 +5,7 @@
 import numpy as np
 import ibllib.exceptions as err
 from ibllib.pipes.base_tasks import WidefieldTask
-import neurodsp as dsp
+import ibldsp as dsp
 import logging
 from one.api import ONE
 from ibllib.io.extractors.camera import get_video_length

projects/extractor_types.json

@@ -1,7 +1,7 @@
+import unittest
 import shutil
 
 import numpy as np
-import ibllib.pipes.training_preprocessing as tpp
 from projects import biased_fibrephotometry
 import one.alf.io as alfio
 from one.api import ONE
@@ -10,6 +10,7 @@
 from ci.tests import base
 
 
+@unittest.skip('old pipeline no longer supported')
 class TestBiasedPhotometry(base.IntegrationTest):
 
     def setUp(self) -> None:
@@ -32,6 +33,7 @@ def setUp(self) -> None:
         #     link.symlink_to(ff)
 
     def test_extraction(self):
+        import ibllib.pipes.training_preprocessing as tpp
 
         # Extract the trials (required for photometry extraction)
         self.assertEqual(

projects/krasniak_widefield.py

@@ -1,3 +1,4 @@
+import unittest
 import shutil
 
 import numpy as np
@@ -6,9 +7,8 @@
 from one.api import ONE
 from ci.tests import base
 
-from projects.ephys_passive_opto import EphysPassiveOptoTrials
-
 
+@unittest.skip('old pipeline no longer supported')
 class TestEphysPassiveOptoTrials(base.IntegrationTest):
 
     def setUp(self) -> None:
@@ -21,6 +21,7 @@ def test_ephys_passive_opto(self):
         :return:
         """
         session_path = self.session_path
+        from projects.ephys_passive_opto import EphysPassiveOptoTrials
         task = EphysPassiveOptoTrials(session_path=session_path, one=self.one_offline)
         task.run()
 

projects/task_type_procedures.json

@@ -5,10 +5,8 @@
 from ci.tests import base
 import unittest
 
-from projects.training_bandit import extract_all as training_extract_all
-from projects.ephys_bandit import extract_all as ephys_extract_all
-
 
+@unittest.skip('old pipeline no longer supported')
 class TestTrainingBanditTrials(base.IntegrationTest):
 
     def setUp(self) -> None:
@@ -21,7 +19,7 @@ def test_training_bandit(self):
         Alejandro training bandit task
         :return:
         """
-
+        from projects.training_bandit import extract_all as training_extract_all
         trials, _, _ = training_extract_all(self.session_path, save=False)
         trials_orig = alfio.load_object(self.session_path.joinpath('alf'), object='trials')
 
@@ -32,6 +30,7 @@ def test_training_bandit(self):
         assert np.array_equal(trials['table']['contrastRight'], trials_orig['contrastRight'])
 
 
+@unittest.skip('old pipeline no longer supported')
 class TestEphysBanditTrials(base.IntegrationTest):
 
     @unittest.skip("Skip FTP upload test")
@@ -44,7 +43,7 @@ def test_ephys_bandit(self):
         Alejandro ephys bandit task
         :return:
         """
-
+        from projects.ephys_bandit import extract_all as ephys_extract_all
         trials, _ = ephys_extract_all(self.session_path, save=False)
         trials_orig = alfio.load_object(self.session_path.joinpath('alf'), object='trials')
 

projects/tests/test_biased_fibrephotometry.py

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name            = "project_extraction"
-version         = "0.2.7"
+version         = "0.3.0"
 description     = "Custom extractors for satellite tasks"
 dynamic         = [ "readme" ]
 keywords        = [ "IBL", "neuro-science" ]