Merge pull request #2053 from SpikeInterface/matthias

Fixes Apptainer bug plus small fixes
SpikeInterface · Oct 2, 2023 · ca48f6b · ca48f6b
2 parents cb16ff8 + 5cefdac
commit ca48f6b
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 8 deletions.
diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
@@ -616,7 +616,7 @@ def dump_to_pickle(
         Parameters
         ----------
         file_path: str
-            Path of the json file
+            Path of the pickle file
         include_properties: bool
             If True, all properties are dumped
         folder_metadata: str, Path, or None

diff --git a/src/spikeinterface/extractors/mdaextractors.py b/src/spikeinterface/extractors/mdaextractors.py
@@ -216,10 +216,14 @@ def write_sorting(sorting, save_path, write_primary_channels=False):
         times_list = []
         labels_list = []
         primary_channels_list = []
-        for unit_id in unit_ids:
+        for unit_index, unit_id in enumerate(unit_ids):
             times = sorting.get_unit_spike_train(unit_id=unit_id)
             times_list.append(times)
-            labels_list.append(np.ones(times.shape) * unit_id)
+            # unit id may not be numeric
+            if unit_id.dtype.kind in "iu":
+                labels_list.append(np.ones(times.shape, dtype=unit_id.dtype) * unit_id)
+            else:
+                labels_list.append(np.ones(times.shape, dtype=int) * unit_index)
             if write_primary_channels:
                 if "max_channel" in sorting.get_unit_property_names(unit_id):
                     primary_channels_list.append([sorting.get_unit_property(unit_id, "max_channel")] * times.shape[0])

diff --git a/src/spikeinterface/sorters/runsorter.py b/src/spikeinterface/sorters/runsorter.py
@@ -514,19 +514,19 @@ def run_sorter_container(
                 res_output = container_client.run_command(cmd)
                 cmd = f"cp -r {si_dev_path_unix} {si_source_folder}"
                 res_output = container_client.run_command(cmd)
-                cmd = f"pip install {si_source_folder}/spikeinterface[full]"
+                cmd = f"pip install --user {si_source_folder}/spikeinterface[full]"
             else:
                 si_source = "remote repository"
-                cmd = "pip install --upgrade --no-input git+https://github.com/SpikeInterface/spikeinterface.git#egg=spikeinterface[full]"
+                cmd = "pip install --user --upgrade --no-input git+https://github.com/SpikeInterface/spikeinterface.git#egg=spikeinterface[full]"
             if verbose:
                 print(f"Installing dev spikeinterface from {si_source}")
             res_output = container_client.run_command(cmd)
-            cmd = "pip install --upgrade --no-input https://github.com/NeuralEnsemble/python-neo/archive/master.zip"
+            cmd = "pip install --user --upgrade --no-input https://github.com/NeuralEnsemble/python-neo/archive/master.zip"
             res_output = container_client.run_command(cmd)
         else:
             if verbose:
                 print(f"Installing spikeinterface=={si_version} in {container_image}")
-            cmd = f"pip install --upgrade --no-input spikeinterface[full]=={si_version}"
+            cmd = f"pip install --user --upgrade --no-input spikeinterface[full]=={si_version}"
             res_output = container_client.run_command(cmd)
     else:
         # TODO version checking
@@ -540,7 +540,7 @@ def run_sorter_container(
     if extra_requirements:
         if verbose:
             print(f"Installing extra requirements: {extra_requirements}")
-        cmd = f"pip install --upgrade --no-input {' '.join(extra_requirements)}"
+        cmd = f"pip install --user --upgrade --no-input {' '.join(extra_requirements)}"
         res_output = container_client.run_command(cmd)
 
     # run sorter on folder