Merge pull request #3457 from SpikeInterface/prepare_release

alejoe91 · web-flow · commit 7725cb237b75 · 2024-10-04T10:51:43.000+02:00
Prepare release 0.101.2
diff --git a/doc/development/development.rst b/doc/development/development.rst
@@ -192,6 +192,7 @@ Miscelleaneous Stylistic Conventions
 #. Avoid using abbreviations in variable names (e.g. use :code:`recording` instead of :code:`rec`). It is especially important to avoid single letter variables.
 #. Use index as singular and indices for plural following the NumPy convention. Avoid idx or indexes. Plus, id and ids are reserved for identifiers (i.e. channel_ids)
 #. We use file_path and folder_path (instead of file_name and folder_name) for clarity.
+#. For the titles of documentation pages, only capitalize the first letter of the first word and classes or software packages. For example, "How to use a SortingAnalyzer in SpikeInterface".
 #. For creating headers to divide sections of code we use the following convention (see issue `#3019 <https://github.com/SpikeInterface/spikeinterface/issues/3019>`_):
 
 
diff --git a/doc/how_to/combine_recordings.rst b/doc/how_to/combine_recordings.rst
@@ -1,4 +1,4 @@
-Combine Recordings in SpikeInterface
+Combine recordings in SpikeInterface
 ====================================
 
 In this tutorial we will walk through combining multiple recording objects. Sometimes this occurs due to hardware
diff --git a/doc/how_to/load_matlab_data.rst b/doc/how_to/load_matlab_data.rst
@@ -1,4 +1,4 @@
-Export MATLAB Data to Binary & Load in SpikeInterface
+Export MATLAB data to binary & load in SpikeInterface
 ========================================================
 
 In this tutorial, we will walk through the process of exporting data from MATLAB in a binary format and subsequently loading it using SpikeInterface in Python.
diff --git a/doc/how_to/load_your_data_into_sorting.rst b/doc/how_to/load_your_data_into_sorting.rst
@@ -1,5 +1,5 @@
-Load Your Own Data into a Sorting
-=================================
+Load your own data into a Sorting object
+========================================
 
 Why make a :code:`Sorting`?
 
diff --git a/doc/how_to/process_by_channel_group.rst b/doc/how_to/process_by_channel_group.rst
@@ -1,4 +1,4 @@
-Process a Recording by Channel Group
+Process a recording by channel group
 ====================================
 
 In this tutorial, we will walk through how to preprocess and sort a recording
diff --git a/doc/how_to/viewers.rst b/doc/how_to/viewers.rst
@@ -1,4 +1,4 @@
-Visualize Data
+Visualize data
 ==============
 
 There are several ways to plot signals (raw, preprocessed) and spikes.
diff --git a/doc/releases/0.101.2.rst b/doc/releases/0.101.2.rst
@@ -0,0 +1,66 @@
+.. _release0.101.2:
+
+SpikeInterface 0.101.2 release notes
+------------------------------------
+
+4th October 2024
+
+Minor release with bug fixes
+
+core:
+
+* Fix `random_spikes_selection()` (#3456)
+* Expose `backend_options` at the analyzer level to set `storage_options` and `saving_options` (#3446)
+* Avoid warnings in `SortingAnalyzer` (#3455)
+* Fix `reset_global_job_kwargs` (#3452)
+* Allow to save recordingless analyzer as (#3443)
+* Fix compute analyzer pipeline with tmp recording (#3433)
+* Fix bug in saving zarr recordings (#3432)
+* Set `run_info` to `None` for `load_waveforms` (#3430)
+* Fix integer overflow in parallel computing (#3426)
+* Refactor `pandas` save load and `convert_dtypes` (#3412)
+* Add spike-train based lazy `SortingGenerator` (#2227)
+
+
+extractors:
+
+* Improve IBL recording extractors by PID (#3449)
+
+sorters:
+
+* Get default encoding for `Popen` (#3439)
+
+postprocessing:
+
+* Add `max_threads_per_process` and `mp_context` to pca by channel computation and PCA metrics (#3434)
+
+widgets:
+
+* Fix metrics widgets for convert_dtypes (#3417)
+* Fix plot motion for multi-segment (#3414)
+
+motion correction:
+
+* Auto-cast recording to float prior to interpolation (#3415)
+
+documentation:
+
+* Add docstring for `generate_unit_locations`  (#3418)
+* Add `get_channel_locations` to the base recording API (#3403)
+
+continuous integration:
+
+* Enable testing arm64 Mac architecture in the CI (#3422)
+* Add kachery_zone secret (#3416)
+
+testing:
+
+* Relax causal filter tests (#3445)
+
+Contributors:
+
+* @alejoe91
+* @h-mayorquin
+* @jiumao2
+* @samuelgarcia
+* @zm711
diff --git a/doc/whatisnew.rst b/doc/whatisnew.rst
@@ -8,6 +8,7 @@ Release notes
 .. toctree::
   :maxdepth: 1
 
+  releases/0.101.2.rst
   releases/0.101.1.rst
   releases/0.101.0.rst
   releases/0.100.8.rst
@@ -44,6 +45,11 @@ Release notes
   releases/0.9.1.rst
 
 
+Version 0.101.2
+===============
+
+* Minor release with bug fixes
+
 Version 0.101.1
 ===============
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -124,16 +124,16 @@ test_core = [
 
     # for github test : probeinterface and neo from master
     # for release we need pypi, so this need to be commented
-     "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-     "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 test_extractors = [
     # Functions to download data in neo test suite
     "pooch>=1.8.2",
     "datalad>=1.0.2",
-     "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-     "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 test_preprocessing = [
@@ -173,8 +173,8 @@ test = [
 
     # for github test : probeinterface and neo from master
     # for release we need pypi, so this need to be commented
-     "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-     "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 docs = [
diff --git a/src/spikeinterface/__init__.py b/src/spikeinterface/__init__.py
@@ -30,5 +30,5 @@
 # This flag must be set to False for release
 # This avoids using versioning that contains ".dev0" (and this is a better choice)
 # This is mainly useful when using run_sorter in a container and spikeinterface install
-DEV_MODE = True
-# DEV_MODE = False
+# DEV_MODE = True
+DEV_MODE = False
diff --git a/src/spikeinterface/core/sortinganalyzer.py b/src/spikeinterface/core/sortinganalyzer.py
@@ -2245,9 +2245,15 @@ def _save_data(self):
                 elif HAS_PANDAS and isinstance(ext_data, pd.DataFrame):
                     df_group = extension_group.create_group(ext_data_name)
                     # first we save the index
-                    df_group.create_dataset(name="index", data=ext_data.index.to_numpy())
+                    indices = ext_data.index.to_numpy()
+                    if indices.dtype.kind == "O":
+                        indices = indices.astype(str)
+                    df_group.create_dataset(name="index", data=indices)
                     for col in ext_data.columns:
-                        df_group.create_dataset(name=col, data=ext_data[col].to_numpy())
+                        col_data = ext_data[col].to_numpy()
+                        if col_data.dtype.kind == "O":
+                            col_data = col_data.astype(str)
+                        df_group.create_dataset(name=col, data=col_data)
                     df_group.attrs["dataframe"] = True
                 else:
                     # any object

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-Combine Recordings in SpikeInterface`
	`1`	`+Combine recordings in SpikeInterface`
`2`	`2`	`====================================`
`3`	`3`
`4`	`4`	`In this tutorial we will walk through combining multiple recording objects. Sometimes this occurs due to hardware`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-Export MATLAB Data to Binary & Load in SpikeInterface`
	`1`	`+Export MATLAB data to binary & load in SpikeInterface`
`2`	`2`	`========================================================`
`3`	`3`
`4`	`4`	`In this tutorial, we will walk through the process of exporting data from MATLAB in a binary format and subsequently loading it using SpikeInterface in Python.`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-Process a Recording by Channel Group`
	`1`	`+Process a recording by channel group`
`2`	`2`	`====================================`
`3`	`3`
`4`	`4`	`In this tutorial, we will walk through how to preprocess and sort a recording`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-Visualize Data`
	`1`	`+Visualize data`
`2`	`2`	`==============`
`3`	`3`
`4`	`4`	`There are several ways to plot signals (raw, preprocessed) and spikes.`