Merge branch 'hotfix/2.2.1' into develop

Author: oliche

ibllib/pipes/misc.py

@@ -3,6 +3,7 @@
 import shutil
 from pathlib import Path
 import re
+from typing import Union, List
 
 import iblutil.io.params as params
 from one.alf.spec import is_uuid_string, is_session_path
@@ -346,6 +347,23 @@ def confirm_ephys_remote_folder(
         check_create_raw_session_flag(remote_session_path)
 
 
+def probe_labels_from_session_path(session_path: Union[str, Path]) -> List[str]:
+    """
+    Finds ephys probes according to the metadata spikeglx files. Only returns first subfolder
+    name under raw_ephys_data folder, ie. raw_ephys_data/probe00/copy_of_probe00 won't be returned
+    :param session_path:
+    :return: list of strings
+    """
+    plabels = []
+    raw_ephys_folder = session_path.joinpath('raw_ephys_data')
+    for meta_file in raw_ephys_folder.rglob('*.ap.meta'):
+        if meta_file.parents[1] != raw_ephys_folder:
+            continue
+        plabels.append(meta_file.parts[-2])
+    plabels.sort()
+    return plabels
+
+
 def create_alyx_probe_insertions(
     session_path: str,
     force: bool = False,
@@ -363,24 +381,15 @@ def create_alyx_probe_insertions(
         pmodel = "3B2" if probe_model == "3B" else probe_model
     else:
         pmodel = model
-    raw_ephys_data_path = Path(session_path) / "raw_ephys_data"
-    if labels is None:
-        probe_labels = [
-            x.name
-            for x in Path(raw_ephys_data_path).glob("*")
-            if x.is_dir() and ("00" in x.name or "01" in x.name)
-        ]
-    else:
-        probe_labels = labels
-
+    labels = labels or probe_labels_from_session_path(session_path)
     # create the qc fields in the json field
     qc_dict = {}
     qc_dict.update({"qc": "NOT_SET"})
     qc_dict.update({"extended_qc": {}})
 
     # create the dictionary
     insertions = []
-    for plabel in probe_labels:
+    for plabel in labels:
         insdict = {"session": eid, "name": plabel, "model": pmodel, "json": qc_dict}
         # search for the corresponding insertion in Alyx
         alyx_insertion = one.alyx.get(f'/insertions?&session={eid}&name={plabel}', clobber=True)

ibllib/tests/test_pipes.py

@@ -301,6 +301,22 @@ def test_create_alyx_probe_insertions(self):
         one.alyx.rest("insertions", "delete", id=alyx_insertion[0]["id"])
         one.alyx.rest("insertions", "delete", id=alyx_insertion[1]["id"])
 
+    def test_probe_names_from_session_path(self):
+        pnames = ['probe01', 'probe03', 'just_a_probe']
+
+        with tempfile.TemporaryDirectory() as tdir:
+            session_path = Path(tdir).joinpath('Algernon', '2021-02-12', '001')
+            raw_ephys_path = session_path.joinpath('raw_ephys_data')
+            raw_ephys_path.mkdir(parents=True, exist_ok=True)
+            raw_ephys_path.joinpath("_spikeglx_ephysData_g0_t0.nidq.meta").touch()
+            for pname in pnames:
+                probe_path = raw_ephys_path.joinpath(pname)
+                probe_path.mkdir()
+                probe_path.joinpath('_spikeglx_ephysData_g0_t0.imec0.ap.meta').touch()
+                probe_path.joinpath('nested_folder').mkdir()
+                probe_path.joinpath('nested_folder', 'toto.ap.meta').touch()
+            assert set(misc.probe_labels_from_session_path(session_path)) == set(pnames)
+
     def test_rename_session(self):
         self._inputs = ('foo', '2020-02-02', '002')
         with mock.patch('builtins.input', self._input_side_effect):

release_notes.md

@@ -1,9 +1,14 @@
-## Develop
+## Release Notes 2.2
+### Release Notes 2.2.0 2021-11-02
+- allows more than 2 probes in ephys computer probe creation
+
+### Release Notes 2.2.0 2021-10-29
 - brainbox.io.one load_spike_sorting fast: merge channel info in clusters
 - brainbox.io.one generic function to interpolate channels after alignment
 - dsp: spike detection by voltage thresholding and cadzow filtering docs
 - ibllib.io.spikeglx: get geometry from metadata
 - RawEphysQC outputs basic detection spike rates
+- ibllib.atlas.regions: add new mapping cosmos and revise Beryl
 
 ## Release Notes 2.1
 ### Release Notes 2.1.0 2021-10-05

setup.py

@@ -24,7 +24,7 @@
 
 setup(
     name='ibllib',
-    version='2.1.3',
+    version='2.2.1',
     python_requires='>={}.{}'.format(*REQUIRED_PYTHON),
     description='IBL libraries',
     license="MIT",