Merge pull request #595 from catalystneuro/prepare_for_new_release

Prepare for v0.11.37 release

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

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

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