Merge pull request #3163 from SpikeInterface/prepare_release

Prepare 0.101.0 release
SpikeInterface · Jul 15, 2024 · 7562b24 · 7562b24
2 parents 1f1a82c + de14d02
commit 7562b24
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Showing 15 changed files with 525 additions and 28 deletions.
diff --git a/.github/import_test.py b/.github/import_test.py
@@ -45,7 +45,7 @@
         time_taken_list.append(time_taken)
 
     for time in time_taken_list:
-        import_time_threshold = 2.0  # Most of the times is sub-second but there outliers
+        import_time_threshold = 3.0  # Most of the times is sub-second but there outliers
         if time >= import_time_threshold:
             exceptions.append(
                 f"Importing {import_statement} took: {time:.2f} s. Should be <: {import_time_threshold} s."
@@ -59,7 +59,7 @@
         times_list_str = ", ".join(f"{time:.2f}" for time in time_taken_list)
         markdown_output += f"| `{import_statement}` | {avg_time:.2f} | {std_time:.2f} | {times_list_str} |\n"
 
-        import_time_threshold = 1.0
+        import_time_threshold = 2.0
         if avg_time > import_time_threshold:
             exceptions.append(
                 f"Importing {import_statement} took: {avg_time:.2f} s in average. Should be <: {import_time_threshold} s."

diff --git a/README.md b/README.md
@@ -46,11 +46,13 @@
 [![Twitter](https://img.shields.io/badge/@spikeinterface-%231DA1F2.svg?style=for-the-badge&logo=Twitter&logoColor=white)](https://twitter.com/spikeinterface) [![Mastodon](https://img.shields.io/badge/-@spikeinterface-%232B90D9?style=for-the-badge&logo=mastodon&logoColor=white)](https://fosstodon.org/@spikeinterface)
 
 
-> :warning::warning::warning:
-> **New features under construction!** 🚧🚧🚧: after the 0.100.0 release (and related bug fixes), the next release will contain
-> a major API improvement: the `SortingAnalyzer`. To read more about this, checkout the
-> [enhancement proposal](https://github.com/SpikeInterface/spikeinterface/issues/2282).
-> Please refer to the stable documentation [here](https://spikeinterface.readthedocs.io/en/0.100.4)
+> :rocket::rocket::rocket:
+> **New features!**: after months of development and testing, we are happy to announce that
+> the latest release (0.101.0) includes a major API improvement: the `SortingAnalyzer`!
+> To read more about why we did this, checkout the
+> [SpikeInterface Enhancement Proposal](https://github.com/SpikeInterface/spikeinterface/issues/2282).
+> Please follow this guide to transition from the old API to the new one:
+> [Updating from legacy](https://spikeinterface.readthedocs.io/en/0.101.0/tutorials/waveform_extractor_to_sorting_analyzer.html).
 
 
 SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.
@@ -74,12 +76,14 @@ With SpikeInterface, users can:
 
 ## Documentation
 
-Detailed documentation of the latest PyPI release of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/0.100.1).
+Detailed documentation of the latest PyPI release of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/stable).
 
 Detailed documentation of the development version of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/latest).
 
 Several tutorials to get started can be found in [spiketutorials](https://github.com/SpikeInterface/spiketutorials).
 
+Checkout our YouTube channel for video tutorials: [SpikeInterface YouTube Channel](https://www.youtube.com/@Spikeinterface).
+
 There are also some useful notebooks [on our blog](https://spikeinterface.github.io) that cover advanced benchmarking
 and sorting components.
 
@@ -128,3 +132,6 @@ If you find SpikeInterface useful in your research, please cite:
   publisher={eLife Sciences Publications Limited}
 }
 ```
+
+Please also cite other relevant papers for the specific components you use.
+For a ful list of references, please check the [references](https://spikeinterface.readthedocs.io/en/latest/references.html) page.
diff --git a/doc/images/overview.png b/doc/images/overview.png
diff --git a/doc/index.rst b/doc/index.rst
@@ -14,11 +14,13 @@ state-of-the-art spike sorters, post-process and curate the output, compute qual
 
 .. warning::
 
-    a major API improvement: the :code:`SortingAnalyzer`. To read more about this, checkout the
+    Version 0.101.0 introduces a major API improvement: the :code:`SortingAnalyzer`.`
+    To read more about the motivations, checkout the
     `enhancement proposal <https://github.com/SpikeInterface/spikeinterface/issues/2282>`_.
-    Please refer to the `stable documentation <https://spikeinterface.readthedocs.io/en/0.100.4>`_.
-    Learn how to :ref:`update your code here <tutorials/waveform_extractor_to_sorting_analyzer:From WaveformExtractor to SortingAnalyzer>` and read more about the
-    :ref:`SortingAnalyzer here <modules/postprocessing:Postprocessing module>`.
+    Learn how to :ref:`update your code here <tutorials/waveform_extractor_to_sorting_analyzer:From WaveformExtractor to SortingAnalyzer>`
+    and read more about the :code:`SortingAnalyzer`, please refer to the
+    :ref:`core <modules/core:SortingAnalyzer>` and :ref:`postprocessing <modules/postprocessing>` module
+    documentation.
 
 
 

diff --git a/doc/modules/core.rst b/doc/modules/core.rst
@@ -388,7 +388,7 @@ and merging unit groups.
     sorting_analyzer_merge = sorting_analyzer.merge_units([0, 1], [2, 3])
 
 All computed extensions will be automatically propagated or merged when curating. Please refer to the
-:ref:`modules/curation` documentation for more information.
+:ref:`modules/curation:Curation module` documentation for more information.
 
 
 Event

diff --git a/doc/modules/curation.rst b/doc/modules/curation.rst
@@ -1,4 +1,5 @@
 .. _curation:
+
 Curation module
 ===============
 

diff --git a/doc/modules/preprocessing.rst b/doc/modules/preprocessing.rst
@@ -32,7 +32,7 @@ These two preprocessors will not compute anything at instantiation, but the comp
 
     traces = recording_cmr.get_traces(start_frame=100_000, end_frame=200_000)
 
-Some internal sorters (see :ref:`modules/sorters:Intertnal Sorters`) can work directly on these preprocessed objects so there is no need to
+Some internal sorters (see :ref:`modules/sorters:Internal Sorters`) can work directly on these preprocessed objects so there is no need to
 save the object:
 
 .. code-block:: python

diff --git a/doc/modules/sorters.rst b/doc/modules/sorters.rst
@@ -473,8 +473,8 @@ Here is the list of external sorters accessible using the run_sorter wrapper:
 * **HDSort** :code:`run_sorter(sorter_name='hdsort')`
 * **YASS** :code:`run_sorter(sorter_name='yass')`
 
-Intertnal Sorters
------------------
+Internal Sorters
+----------------
 
 Here a list of internal sorter based on `spikeinterface.sortingcomponents`; they are totally
 experimental for now:

diff --git a/doc/modules/widgets.rst b/doc/modules/widgets.rst
@@ -198,7 +198,7 @@ The functions have the following additional arguments:
 
     # sortingview backend
     w_ts = sw.plot_traces(recording=recording, backend="sortingview")
-    w_ss = sw.plot_sorting_summary(waveform_extractor=we, curation=True, backend="sortingview")
+    w_ss = sw.plot_sorting_summary(sorting_analyzer=sorting_analyzer, curation=True, backend="sortingview")
 
 
 **Output:**

diff --git a/doc/releases/0.100.8.rst b/doc/releases/0.100.8.rst
@@ -0,0 +1,16 @@
+.. _release0.100.8:
+
+SpikeInterface 0.100.8 release notes
+------------------------------------
+
+24th June 2024
+
+Minor release with bug fixes
+
+* Remove separate default job_kwarg n_jobs for sorters (#2712)
+* Fix math error in sd_ratio (#2964)
+* Add `whiteningRange` added as Kilosort 2/2.5/3 parameter (#2997)
+* Make sure we check `is_filtered()`` rather than bound method during run basesorter (#3037)
+* Numpy 2.0 cap Fix most egregorious deprecated behavior and cap version (#3032, #3056)
+* Add support for kilosort>=4.0.12 (#3055)
+* Check start_frame/end_frame in BaseRecording.get_traces() (#3059)