Prepare 0.13.0 release (#255)

Author: alejoe91

docs/source/index.rst

@@ -56,3 +56,4 @@ This is a web app internally using Panel, useful when the data is remote
    views
    developers
    credits
+   release_notes

docs/source/release_notes.rst

@@ -0,0 +1,324 @@
+.. _release_notes:
+
+Release Notes
+=============
+
+.. _release0.13.0:
+
+0.13.0
+------
+
+*Release date: March 23rd, 2026*
+
+New views
+~~~~~~~~~
+
+* **EventView** (PR #218): new view showing aligned spike rasters and PSTHs around events; events can be passed to ``run_mainwindow`` as a plain dict or as a ``spikeinterface.BaseEvent`` object
+* **AmplitudeScalingsView** (PR #230): new view showing amplitude scaling factors
+* **MainChannelTemplate view** (PR #233): shows the main channel waveform template
+
+Curation
+~~~~~~~~
+
+* Renamed ``CurationModel`` to ``Curation`` to align with the updated SpikeInterface API (PR #252)
+* Added ``curation_callback`` and ``set_external_curation`` for programmatic curation control (PR #241)
+* Validate curation data and support curation format v1/v2 (PR #211)
+* Remove default ``num_chan`` (sparsity) column from unit list; add a "clear" label shortcut (PR #244)
+* Fixed ``include_deleted`` behavior and unit order in merge list (PR #245)
+* Added "remove from merge list" to unit list right-click context menu (PR #232)
+
+Trace and scatter views
+~~~~~~~~~~~~~~~~~~~~~~~
+
+* **Valid periods regions in scatter plots** (PR #254): shaded valid-period regions on scatter views (e.g. amplitude, ISI); can be disabled in settings
+* **Event navigation in Trace/TraceMap views** (PR #218): previous/next event buttons with event-type selector; event overlays on trace and trace map views
+* Fixed binning and limits in ``basescatterview`` (PRs #235, #246)
+* Fixed ``tracemapview`` for multi-shank probes (PR #248)
+* Selectively update y-range only when unit or time changes (PR #248)
+
+UX improvements
+~~~~~~~~~~~~~~~
+
+* **Focus mode** (PR #227): toggle to focus the display on a single unit
+* **Waveform display mode** is now a persistent setting (PR #238)
+* ``user_main_settings`` parameter exposed so callers can pre-configure GUI settings programmatically (PR #243)
+* Fixed relative spike rate plot (PR #212)
+* Allow ``nan`` metric values in MetricsView (PR #217)
+* Make ``template_metrics`` dependency optional (PR #247)
+
+Backend and architecture
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+* **Plugin architecture** (PR #219): full plugin system with ``get_all_possible_views()``; plugin documentation page added
+* ``skip_extensions`` parameter now passed through to the CLI entry point (PR #216)
+* Allow remote S3 paths for loading (PR #214)
+* ``external_data`` support in controller: pass arbitrary external data into the GUI (PR #231)
+* Panel backend: multi-thread/multi-process server support (PR #240); fix color-by-visibility (PR #250)
+* Removed pandas dependency
+* Renamed ``crosscorrelogramview`` → ``correlogramview``
+* Added codespell CI workflow (PR #215)
+
+
+.. _release0.12.0:
+
+0.12.0
+------
+
+*Release date: November 13, 2025*
+
+New views
+~~~~~~~~~
+
+* **Unit splitting**: full splitting workflow in ``ScatterViews``, ``CurationView``, and ``CorrelogramsView``; lasso-select spikes, confirm or get notified on failure
+* **Metrics view**: new view displaying quality/template metrics for selected units (Qt and Panel backends)
+* **Binned spikes view**: new ``BinnedSpikesView`` showing spike rate over time
+
+Curation
+~~~~~~~~
+
+* **Curation format v2**: updated curation format with validation; raises error on invalid curation dict
+* **Auto-merge presets**: added SpikeInterface automerge presets including ``similarity``
+* **Curation file CLI arg**: load a pre-existing curation file with ``--curation-file``
+* **Exit dialog**: warning shown if the user has unsaved curation when closing
+
+UX improvements
+~~~~~~~~~~~~~~~
+
+* **User settings**: save and restore default settings via a config folder
+* **Waveform improvements**: option to plot sample waveforms; x/y scalebars; improved geometry mode with ``allow_long_zone``; separate auto-move and auto-zoom settings
+* **Custom layout**: JSON layout support via ``--layout`` CLI argument; refactored greedy layout algorithm
+* **Busy indicator**: context manager for busy indicator during long operations (traces, merges, compute)
+* **Recording times**: ``main_setting`` option to use recording times
+
+Backend and architecture
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+* **Only load required extensions**: skip analyzer extensions not needed by the displayed views
+* **Performance (Panel/web)**: caching correlograms, pre-initializing probe view ranges, faster unit list refresh, skip unrequested views
+* **ReadTheDocs**: added full documentation deployment
+
+Bug fixes
+~~~~~~~~~
+
+* ``nanmin``/``nanmax`` for spike location extrema; channel ordering in probe map; lasso selection and split shortcut; noise levels when analyzer has no noise; spike rate for short recordings; ``return_scaled`` → ``return_in_uV`` API change
+
+
+.. _release0.11.0:
+
+0.11.0
+------
+
+*Release date: June 25, 2025*
+
+Backend and architecture
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+* **Dual-backend architecture**: major refactoring to support both a Qt desktop backend and a Panel/Bokeh web backend from the same codebase
+* **Launcher**: GUI launcher for desktop (Qt) and web (Panel) modes; supports ``analyzer_folders`` dict; prints server address
+* **Layout presets**: 8-zone layout system with configurable presets; GridStack for web layout
+
+UX improvements
+~~~~~~~~~~~~~~~
+
+* **Color modes**: configurable color mode in main settings
+* **Waveform overlap**: show overlapping waveforms with ``Ctrl+O``; ``Alt+Scroll`` to widen narrow waveforms
+* **Exclude deleted units from merge view**: option to hide already-deleted units in ``MergeView``
+* **Probe view**: better automatic ROI when multiple units are selected
+* ``with_traces=False`` **option**: option to not show traces in the main window
+
+Performance and bug fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Faster waveform loading; faster spike amplitude and correlograms; export curation to download JSON
+* Manual unit label fix; ``time_info_updated`` signal to avoid recursive calls
+
+
+.. _release0.10.0:
+
+0.10.0
+------
+
+*Release date: February 12, 2025*
+
+* **Lasso selection in spike amplitude view**: visually select spikes with a lasso tool; enable/disable lasso button
+* ``--recording`` **CLI option**: pass a recording path from the command line
+* ``--recording-base-folder`` **option**: flexible recording path resolution
+* **Unit list improvements**: column drag-and-drop reordering; fix string column sorting
+* ``compute_merge_unit_groups``: now uses the function directly from SpikeInterface
+* **Improved unit tables**: better column display
+
+
+.. _release0.9.1:
+
+0.9.1
+-----
+
+*Release date: October 9, 2024*
+
+* **ProbeGroup support**: handle multi-shank probes via ``ProbeGroup``
+* **Probe view**: second ROI with ``Ctrl``-click to add ROI for units
+* **Similarity view**: ``Ctrl``-click for append mode
+* ``--no-traces`` **CLI option**: start the GUI without loading traces; small trace cache added
+* **Python version**: updated support for Python 3.9+ and 3.11
+* **Bug fixes**: spike list and visible spikes; documentation updates
+
+
+.. _release0.9.0:
+
+0.9.0
+-----
+
+*Release date: July 19, 2024*
+
+New views
+~~~~~~~~~
+
+* **TraceMapView**: new view showing a heatmap of traces on the probe
+* ``WaveformHeatMapView`` **made optional**: avoid accidentally triggering expensive recomputation
+
+Curation
+~~~~~~~~
+
+* **Curation GUI**: full curation interface with merge, delete, label operations, keyboard shortcuts (``d`` delete, ``Space`` toggle visibility, ``m`` merge), and curation export aligned with SpikeInterface curation format
+* **Sortable unit and pair lists**: click column headers to sort; pair list shows merge candidates
+* **Proposed merges**: compute and propose merge groups based on multiple methods/criteria
+
+Backend and architecture
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+* **SortingAnalyzer support**: complete refactor to use the new ``SortingAnalyzer`` API from SpikeInterface (replaces ``WaveformExtractor``)
+* **View dependency on extensions**: views only shown/enabled if the required analyzer extension is computed
+* ``noise_levels`` **optional**: noise display on spike amplitude view is optional if not computed
+
+
+.. _release0.8.0:
+
+0.8.0
+-----
+
+*Release date: March 12, 2024*
+
+* API compatibility update: ``sample_ind`` → ``sample_index``
+* Minor fixes and README/documentation improvements
+
+
+.. _release0.7.0:
+
+0.7.0
+-----
+
+*Release date: July 7, 2023*
+
+* Requires SpikeInterface >= 0.98
+* **Improved channel visibility on unit selection**
+* **More intuitive channel ordering** when using ROI in probe view
+* Removed auto channel visibility triggered by spike list selection
+* API update: ``sample_ind`` → ``sample_index``
+* Documentation improvements
+
+
+.. _release0.6.0:
+
+0.6.0
+-----
+
+*Release date: February 10, 2023*
+
+* **Sparsity from WaveformExtractor**: use sparsity defined in the waveform extractor when available
+* Performance optimizations at startup
+
+
+.. _release0.5.1:
+
+0.5.1
+-----
+
+*Release date: October 21, 2022*
+
+* Migrated packaging from ``setup.py`` to ``pyproject.toml``
+* Anticipate upcoming SpikeInterface API changes
+* Small bug fixes
+
+
+.. _release0.5.0:
+
+0.5.0
+-----
+
+*Release date: September 2, 2022*
+
+* **Compatibility with SpikeInterface 0.95.0**: updates for the SI master refactor
+* **Speed improvements**: faster startup and faster multi-unit selection
+* Correlogram: ``symmetrize=True`` by default
+* Background color change and small fixes
+
+
+.. _release0.4.1:
+
+0.4.1
+-----
+
+*Release date: April 15, 2022*
+
+* API fix: ``localize_unit`` → ``localize_units``
+* Bug fix: ``QColor`` cast issue
+
+
+.. _release0.4.0:
+
+0.4.0
+-----
+
+*Release date: February 4, 2022*
+
+New views
+~~~~~~~~~
+
+* **Spike amplitude view**: new view showing spike amplitudes over time with amplitude histogram
+* **Metrics in unit list**: quality/template metrics displayed as columns in the unit list
+
+Bug fixes
+~~~~~~~~~
+
+* Switched to ``localize_units`` from SpikeInterface
+* Fixed label order in trace view
+* Avoid refreshing channel visibility on spike select
+* Various small fixes
+
+
+.. _release0.3.0:
+
+0.3.0
+-----
+
+*Release date: October 12, 2021*
+
+* **Speed improvements**: removed internal spike ``selected``/``visible`` tracking for faster performance
+* Improved waveform width handling
+* Improved spike list view
+* ProbeView bug fix: ``on_unit_visibility_changed``
+* Code cleanup
+
+
+.. _release0.2.0:
+
+0.2.0
+-----
+
+*Release date: October 7, 2021*
+
+* **Compute button**: trigger waveform/extension computation from within the GUI
+* **Help in dock title bar**: contextual help accessible from view title bars
+* **Speed improvements**: startup speed and probe view refresh speed
+* Configurable sparsity threshold
+* Color and sparsity improvements
+
+
+.. _release0.1.0:
+
+0.1.0
+-----
+
+*Release date: September 22, 2021*
+
+* Initial release

pyproject.toml

@@ -1,12 +1,13 @@
 [project]
 name = "spikeinterface-gui"
-version = '0.12.1'
+version = '0.13.0'
 authors = [
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
+  { name="Chris Halcrow", email="chalcrow@ed.ac.uk" },
 ]
 
-description = "Qt GUI for spikeinterface"
+description = "GUI for SpikeInterface"
 readme = "README.md"
 requires-python = ">=3.10"
 classifiers = [
@@ -46,7 +47,7 @@ sigui = "spikeinterface_gui.main:run_mainwindow_cli"
 [project.optional-dependencies]
 
 desktop = [
-    "PySide6==6.7.3",
+    "PySide6",
     "pyqtgraph",
 ]
 
@@ -57,7 +58,7 @@ web = [
 
 test = [
     "pytest",
-    "PySide6==6.7.3",
+    "PySide6",
 ]
 
 docs = [