diff --git a/docs/conversion_examples_gallery/recording/spikegadgets.rst b/docs/conversion_examples_gallery/recording/spikegadgets.rst index abe831fe4..f62ae0b62 100644 --- a/docs/conversion_examples_gallery/recording/spikegadgets.rst +++ b/docs/conversion_examples_gallery/recording/spikegadgets.rst @@ -4,27 +4,27 @@ Spikegadgets data conversion Convert spikegadgets data to NWB using :py:class:`~nwb_conversion_tools.datainterfaces.ecephys.spikegadgets.spikegadgetsdatainterface.SpikeGadgetsRecordingInterface`. .. code-block:: python + # TODO - re-enable '' lines when SI >0.94 is released + from datetime import datetime + from dateutil import tz + from pathlib import Path + from nwb_conversion_tools import SpikeGadgetsRecordingInterface - >>> from datetime import datetime - >>> from dateutil import tz - >>> from pathlib import Path - >>> from nwb_conversion_tools import SpikeGadgetsRecordingInterface - >>> - >>> # For this interface we need to pass the specific path to the files. - >>> file_path = f"{ECEPHY_DATA_PATH}/spikegadgets/20210225_em8_minirec2_ac.rec" - >>> # Change the file_path to the location in your system - >>> interface = SpikeGadgetsRecordingInterface(file_path=file_path, verbose=False) - >>> - >>> # Extract what metadata we can from the source files - >>> metadata = interface.get_metadata() - >>> # For data provenance we add the time zone information to the conversion - >>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=tz.gettz("US/Pacific")).isoformat() - >>> metadata["NWBFile"] = dict(session_start_time=session_start_time) - >>> - >>> # Choose a path for saving the nwb file and run the conversion - >>> nwbfile_path = f"{path_to_save_nwbfile}" - >>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata) - >>> - >>> # If the conversion was successful this should evaluate to ``True`` as the file was created. - >>> Path(nwbfile_path).is_file() + # For this interface we need to pass the specific path to the files. + file_path = f"{ECEPHY_DATA_PATH}/spikegadgets/20210225_em8_minirec2_ac.rec" + # Change the file_path to the location in your system + interface = SpikeGadgetsRecordingInterface(file_path=file_path, verbose=False) + + # Extract what metadata we can from the source files + metadata = interface.get_metadata() + # For data provenance we add the time zone information to the conversion + session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=tz.gettz("US/Pacific")).isoformat() + metadata["NWBFile"] = dict(session_start_time=session_start_time) + + # Choose a path for saving the nwb file and run the conversion + nwbfile_path = f"{path_to_save_nwbfile}" + interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata) + + # If the conversion was successful this should evaluate to ``True`` as the file was created. + Path(nwbfile_path).is_file() True diff --git a/requirements-full.txt b/requirements-full.txt index de2a55033..e0c8594f6 100644 --- a/requirements-full.txt +++ b/requirements-full.txt @@ -15,9 +15,9 @@ psutil==5.8.0 lxml==4.9.1 opencv-python==4.5.1.48 spikeextractors==0.9.10 -spikeinterface @ git+https://github.com/Spikeinterface/spikeinterface.git@d26f991ca05c3af2fec2b4fbce8004ca9e9cd9f1 +spikeinterface>=0.94.0 neo==0.10.2 -roiextractors @ git+https://github.com/catalystneuro/roiextractors.git@1d50cbeb15c317eecca73f4dcb16bca1bb1ff9f6 +roiextractors==0.4.17 pyintan==0.3.0 pyopenephys==1.1.2 sonpy>=1.7.1 diff --git a/requirements-minimal.txt b/requirements-minimal.txt index 613cc76e3..e525895e3 100644 --- a/requirements-minimal.txt +++ b/requirements-minimal.txt @@ -8,11 +8,11 @@ natsort>=7.1.1 PyYAML>=5.4 jsonschema>=3.2.0 psutil>=5.8.0 -dandi==0.39.6 # 0.39.5 already uses schema v0.7.x +dandi==0.39.6 spikeextractors>=0.9.10 -spikeinterface>=0.93.0 +spikeinterface>=0.94.0 neo>=0.9.0 -roiextractors @ git+https://github.com/catalystneuro/roiextractors.git@1d50cbeb15c317eecca73f4dcb16bca1bb1ff9f6 +roiextractors==0.4.17 lxml>=4.6.5 scipy>=1.4.1 click # must be unspecified version to handle platform/pyVersion