pyqt scatter widget (#270)

* simplify conditional * basic pyqt graph * mouse actions test * editable rois added * working gradient widget * discret data works with lut widget * discrete widget prototype * discrete color widget works * Rectangular selection implemented * complex shapes columns saved with names * translocation of ROIs works * shortcuts implemented * highlight sensitivity linked to zoom * display discrete values by name * fixed histogram notches * fixed sensitivity issues with debouncing timer * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * main fix for merge * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename dialog * tests - part 1 * tests part 2 * pyqtgraph added to the setup * notebook - update_01 * changed initialization logic * init modified - v2 * logger trim * axis naming fixed * scatter export connects with the main viewer * saving implemented * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * allow annotation overwriting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * style fix * allow annotation overwriting - part2 * overwrite warning * pyqt5 in cfg * cfg test * test cfg 2 * status updates added * corrections for scatterwidget init * plot widget tests updated * fixtures fixed * export tests * PEP8 name changes * PEP8 vs mouse events war resolved. Mice won. * notebooks - part_1 * notebooks - part_2 * workaround mouse bug windows and macOS * fix paths icons * adding pytest-mock to test install requirements * small fixes * remove points border * changes to the notebooks based on the review * index * initial_pos initialized * control of auto range changed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * improved comments for tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pyqtgraph dropped from docs and readthedocs * fixed finding view widget by number * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated changelog * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix position line placement * Explicitly asking to install napari * unification of notebooks starting parts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix data update * updated notebooks --------- Co-authored-by: Wouter-Michiel Vierdag <[email protected]> Co-authored-by: Wouter-Michiel Vierdag <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Luca Marconato <[email protected]>
scverse · Dec 17, 2024 · a5191c7 · a5191c7
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,6 +34,25 @@ and this project adheres to [Semantic Versioning][].
 - Bug when changing channel for a multichannel image #301 #302
 - Bug when plotting catgorical annotations on points #304
 
+## [0.5.3] - 2024-08-
+
+### Added
+
+- New Scatter Widget based on PyQtGraph, replacing the previous Matplotlib-based widget.
+  - New Features:
+    - Separate color controls for continuous and discrete data:
+      - Continuous: Histogram of values, LUT adjustment, contrast control.
+      - Discrete: Scrollable legend, class color modification.
+    - Pseudohistogram plot for single-axis data.
+    - Highlight nearby data points under the cursor with dynamic status display.
+    - Expanded ROI annotations (lasso and rectangle tools)
+    - Multiple disjointed ROIs with modifiable options.
+    - Annotation name dialog for saving annotations.
+
+### Updated
+
+Documentation: Notebooks updated with the new Scatter Widget information and screenshots.
+
 ## [0.5.2] - 2024-08-16
 
 ### Minor

diff --git a/docs/index.md b/docs/index.md
@@ -23,4 +23,5 @@ cli.md
 notebooks/nanostring_analysis
 notebooks/mibitof_analysis
 notebooks/scatterwidget
+notebooks/scatterwidget_annotation
 ```
diff --git a/docs/notebooks/mibitof_analysis.ipynb b/docs/notebooks/mibitof_analysis.ipynb
diff --git a/docs/notebooks/nanostring_analysis.ipynb b/docs/notebooks/nanostring_analysis.ipynb
diff --git a/docs/notebooks/scatterwidget.ipynb b/docs/notebooks/scatterwidget.ipynb
diff --git a/docs/notebooks/scatterwidget_annotation.ipynb b/docs/notebooks/scatterwidget_annotation.ipynb
diff --git a/docs/notebooks/spatialdata.ipynb b/docs/notebooks/spatialdata.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -34,6 +34,7 @@ exclude = [
     "__pycache__",
     "build",
     "docs/_build",
+    "docs/notebooks",
     "dist",
     "setup.py",
 ]

diff --git a/setup.cfg b/setup.cfg
@@ -48,6 +48,7 @@ install_requires =
     packaging
     pandas
     pillow
+    pyqtgraph
     qtpy
     scanpy
     scipy
@@ -69,6 +70,7 @@ test =
     loguru
     pytest
     pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+    pytest-mock # https://pytest-mock.readthedocs.io/en/latest/
     pytest-qt  # https://pytest-qt.readthedocs.io/en/latest/
     pre-commit>=2.9.0