From 7517763b008c04717967a72f2a6542c41a62fc3d Mon Sep 17 00:00:00 2001
From: olivier <olivier.winter@hotmail.fr>
Date: Fri, 15 Sep 2023 16:36:18 +0100
Subject: [PATCH 1/2] bugfix: listing of collections do not skip repeat
 protocols in acqusition description

---
 ibllib/__init__.py          |  2 +-
 ibllib/io/session_params.py | 26 +++++++++++++++++++++++---
 ibllib/tests/test_io.py     | 10 ++++++++++
 release_notes.md            |  4 +++-
 4 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/ibllib/__init__.py b/ibllib/__init__.py
index a588ec46c..79d4d537a 100644
--- a/ibllib/__init__.py
+++ b/ibllib/__init__.py
@@ -2,7 +2,7 @@
 import logging
 import warnings
 
-__version__ = '2.25.1'
+__version__ = '2.25.2'
 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
diff --git a/ibllib/io/session_params.py b/ibllib/io/session_params.py
index a15802a3f..34e668ced 100644
--- a/ibllib/io/session_params.py
+++ b/ibllib/io/session_params.py
@@ -382,7 +382,7 @@ def get_task_protocol_number(sess_params, task_protocol=None):
         return (next(iter(numbers)) if len(numbers) == 1 else numbers) or None
 
 
-def get_collections(sess_params):
+def get_collections(sess_params, flat=False):
     """
     Find all collections associated with the session.
 
@@ -390,12 +390,17 @@ def get_collections(sess_params):
     ----------
     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
 
     Returns
     -------
     dict[str, str]
         A map of device/sync/task and the corresponding collection name.
 
+    list[str]
+        A flat list of unique collection names.
+
     Notes
     -----
     - Assumes only the following data types contained: list, dict, None, str.
@@ -408,12 +413,27 @@ def iter_dict(d):
                 for d in filter(lambda x: isinstance(x, dict), v):
                     iter_dict(d)
             elif isinstance(v, dict) and 'collection' in v:
-                collection_map[k] = v['collection']
+                print(k)
+                # if the key already exists, append the collection name to the list
+                if k in collection_map:
+                    clist = collection_map[k] if isinstance(collection_map[k], list) else [collection_map[k]]
+                    collection_map[k] = list(set(clist + [v['collection']]))
+                else:
+                    collection_map[k] = v['collection']
             elif isinstance(v, dict):
                 iter_dict(v)
 
     iter_dict(sess_params)
-    return collection_map
+    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
 
 
 def get_video_compressed(sess_params):
diff --git a/ibllib/tests/test_io.py b/ibllib/tests/test_io.py
index 967a88d32..4cb0dba46 100644
--- a/ibllib/tests/test_io.py
+++ b/ibllib/tests/test_io.py
@@ -578,6 +578,16 @@ def test_get_collections(self):
         }
         self.assertCountEqual(expected, collections)
 
+    def test_get_collections_repeat_protocols(self):
+        tasks = dict(tasks=[
+            {'passiveChoiceWorld': {'collection': 'raw_passive_data', 'sync_label': 'bpod'}},
+            {'ephysChoiceWorld': {'collection': 'raw_behavior_data', 'sync_label': 'bpod'}},
+            {'passiveChoiceWorld': {'collection': 'raw_passive_data_bis'}}])
+        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']))
+
 
 class TestRawDaqLoaders(unittest.TestCase):
     """Tests for raw_daq_loaders module"""
diff --git a/release_notes.md b/release_notes.md
index 5262c7b59..7e1552106 100644
--- a/release_notes.md
+++ b/release_notes.md
@@ -8,7 +8,9 @@
 ### bugfixes
 - fix for untrainable, unbiasable don't repolulate if already exists
 ### 2.25.1
-- relax assertion on Neuropixel channel mappings to allow for personal projects 
+- relax assertion on Neuropixel channel mappings to allow for personal projects
+### 2.25.2
+- listing of all collections does not skip repeat task protocols anymore for copy/extraction
 
 ## Release Notes 2.23
 ### Release Notes 2.23.1 2023-06-15

From 7f62b4ce66b6e2d154f77a74034c0a4b96a0fa55 Mon Sep 17 00:00:00 2001
From: olivier <olivier.winter@hotmail.fr>
Date: Thu, 21 Sep 2023 12:58:40 +0100
Subject: [PATCH 2/2] add ibl-neuropixel 0.8.1 requirement

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 3f49398c7..ed29169af 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -23,7 +23,7 @@ sparse
 seaborn>=0.9.0
 tqdm>=4.32.1
 # ibl libraries
-ibl-neuropixel>=0.8.0
+ibl-neuropixel>=0.8.1
 iblutil>=1.7.0
 labcams  # widefield extractor
 ONE-api>=2.2