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Fixes Apptainer bug plus small fixes #2053

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merged 11 commits into from
Oct 2, 2023
+12 −8
Merged

Fixes Apptainer bug plus small fixes #2053

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5fd2627
Allow any integer type.
mhhennig Jun 29, 2023
077a7fe
Fix problem with non-numeric unit IDs.
mhhennig Jun 29, 2023
6c861a4
Allow any integer type.
mhhennig Jun 29, 2023
9b86b48
Fixed docstring
mhhennig Jul 31, 2023
47ff64e
Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …
mhhennig Jul 31, 2023
ac8d061
Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …
mhhennig Aug 6, 2023
8c633ac
Pip install into working directory for containers
mhhennig Sep 29, 2023
5a72604
Merge branch 'main' of github.com:SpikeInterface/spikeinterface
mhhennig Sep 29, 2023
4f2a50d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 29, 2023
d44e99c
Merge branch 'main' into matthias
alejoe91 Oct 2, 2023
5cefdac
Fixes to MDASortingExtractor
alejoe91 Oct 2, 2023
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2 changes: 1 addition & 1 deletion src/spikeinterface/core/base.py
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Expand Up @@ -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
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8 changes: 6 additions & 2 deletions src/spikeinterface/extractors/mdaextractors.py
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Expand Up @@ -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_id_i, unit_id in enumerate(unit_ids):
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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 "biufc":
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labels_list.append(np.ones(times.shape) * unit_id)
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else:
labels_list.append(np.ones(times.shape) * unit_id_i)
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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])
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10 changes: 5 additions & 5 deletions src/spikeinterface/sorters/runsorter.py
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Expand Up @@ -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
Expand All @@ -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
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