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Fix pyinstaller windows #737

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merged 6 commits into from
Apr 11, 2024
Merged

Fix pyinstaller windows #737

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9c5e46f
include tifffile and dlc2nwb explicitly
CodyCBakerPhD Apr 11, 2024
65d2a13
debug and simplify
CodyCBakerPhD Apr 11, 2024
a0f095f
add constraint flags to mamba
CodyCBakerPhD Apr 11, 2024
fe66dd3
try other order
CodyCBakerPhD Apr 11, 2024
55298ef
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 11, 2024
a6ea142
remove extra flags
CodyCBakerPhD Apr 11, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/testing.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ jobs:

- if: steps.cache.outputs.cache-hit != 'true'
name: Create and activate environment
run: mamba env update -n nwb-guide -f ${{ matrix.label }}
run: mamba env update --name nwb-guide --file ${{ matrix.label }}

- name: Use Node.js 20
uses: actions/setup-node@v4
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4 changes: 4 additions & 0 deletions guide_testing_suite.yml
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Expand Up @@ -44,3 +44,7 @@ pipelines:
folder_path: ephy_testing_data/cellexplorer/dataset_4/Peter_MS22_180629_110319_concat_stubbed
CellExplorerSortingInterface:
file_path: ephy_testing_data/cellexplorer/dataset_4/Peter_MS22_180629_110319_concat_stubbed/Peter_MS22_180629_110319_concat_stubbed.spikes.cellinfo.mat

IntanSingleFileRecording:
IntanRecordingInterface:
file_path: ephy_testing_data/intan/intan_rhd_test_1.rhd
4 changes: 4 additions & 0 deletions nwb-guide.spec
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Expand Up @@ -42,6 +42,10 @@ tmp_ret = collect_all('sklearn')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('ci_info')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('tifffile')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('dlc2nwb')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]


block_cipher = None
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8 changes: 2 additions & 6 deletions pyflask/manageNeuroconv/manage_neuroconv.py
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Expand Up @@ -1384,7 +1384,6 @@ def update_recording_properties_from_table_as_json(

recording_extractor = recording_interface.recording_extractor
channel_ids = recording_extractor.get_channel_ids()
stream_prefix = channel_ids[0].split("#")[0] # TODO: see if this generalized across formats

# TODO: uncomment when neuroconv supports contact vectors (probe interface)
# property_names = recording_extractor.get_property_keys()
Expand All @@ -1394,7 +1393,7 @@ def update_recording_properties_from_table_as_json(

for entry_index, entry in enumerate(electrode_table_json):
electrode_properties = dict(entry) # copy
channel_name = electrode_properties.pop("channel_name", None)
# channel_name = electrode_properties.pop("channel_name", None)
for property_name, property_value in electrode_properties.items():
if property_name not in electrode_column_data_types: # Skip data with missing column information
continue
Expand All @@ -1403,13 +1402,10 @@ def update_recording_properties_from_table_as_json(
# property_index = contact_vector_property_names.index(property_name)
# modified_contact_vector[entry_index][property_index] = property_value
else:
ids = (
[stream_prefix + "#" + channel_name] if channel_name else []
) # Correct for minimal metadata (e.g. CellExplorer)
recording_extractor.set_property(
key=property_name,
values=np.array([property_value], dtype=electrode_column_data_types[property_name]),
ids=ids,
ids=[channel_ids[entry_index]], # Assume rows match indices of channel list
)

# TODO: uncomment when neuroconv supports contact vectors (probe interface)
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