Merge branch 'main' of github.com:SpikeInterface/spikeinterface into refactor_GTStudy

Author: samuelgarcia

.github/scripts/determine_testing_environment.py

@@ -31,6 +31,7 @@
 sortingcomponents_changed = False
 generation_changed = False
 stream_extractors_changed = False
+github_actions_changed = False
 
 
 for changed_file in changed_files_in_the_pull_request_paths:
@@ -78,9 +79,12 @@
             sorters_internal_changed = True
         else:
             sorters_changed = True
+    elif ".github" in changed_file.parts:
+        if "workflows" in changed_file.parts:
+            github_actions_changed = True
 
 
-run_everything = core_changed or pyproject_toml_changed or neobaseextractor_changed
+run_everything = core_changed or pyproject_toml_changed or neobaseextractor_changed or github_actions_changed
 run_generation_tests = run_everything or generation_changed
 run_extractor_tests = run_everything or extractors_changed or plexon2_changed
 run_preprocessing_tests = run_everything or preprocessing_changed
@@ -96,7 +100,7 @@
 run_sorters_test = run_everything or sorters_changed
 run_internal_sorters_test = run_everything or run_sortingcomponents_tests or sorters_internal_changed
 
-run_streaming_extractors_test = stream_extractors_changed
+run_streaming_extractors_test = stream_extractors_changed or github_actions_changed
 
 install_plexon_dependencies = plexon2_changed
 

.github/workflows/all-tests.yml

@@ -12,6 +12,7 @@ on:
 env:
   KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }}
   KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }}
+  KACHERY_ZONE: ${{ secrets.KACHERY_ZONE }}
 
 concurrency:  # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -25,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.12"]  # Lower and higher versions we support
-        os: [macos-13, windows-latest, ubuntu-latest]
+        os: [macos-latest, windows-latest, ubuntu-latest]
     steps:
       - uses: actions/checkout@v4
       - name: Setup Python ${{ matrix.python-version }}

.github/workflows/full-test-with-codecov.yml

@@ -8,6 +8,7 @@ on:
 env:
   KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }}
   KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }}
+  KACHERY_ZONE: ${{ secrets.KACHERY_ZONE }}
 
 jobs:
   full-tests-with-codecov:

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>`_):
 
 

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

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.

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`?
 

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

doc/how_to/viewers.rst

@@ -1,4 +1,4 @@
-Visualize Data
+Visualize data
 ==============
 
 There are several ways to plot signals (raw, preprocessed) and spikes.

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