Merge branch 'main' into config-2d-table

pymmcore-plus · Nov 17, 2024 · fa2ec62 · fa2ec62
2 parents 39afe83 + 1cda2b7
commit fa2ec62
Show file tree

Hide file tree

Showing 116 changed files with 3,875 additions and 1,246 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -31,30 +31,25 @@ jobs:
       fail-fast: false
       matrix:
         platform: [macos-13, windows-latest]
-        python-version: ["3.8", "3.11"]
-        backend: [pyside2, pyqt5]
-        include:
-          - platform: macos-13
-            python-version: "3.10"
-            backend: pyside6
-          - platform: macos-13
-            python-version: "3.11"
-            backend: pyqt6
+        python-version: ["3.10", "3.12"]
+        backend: [pyside6, pyqt6]
+        exclude:
           - platform: windows-latest
             python-version: "3.10"
             backend: pyside6
-          - platform: windows-latest
-            python-version: "3.11"
-            backend: pyqt6
-          - platform: windows-latest
+        include:
+          - platform: macos-13
             python-version: "3.9"
             backend: pyside2
           - platform: windows-latest
             python-version: "3.9"
-            backend: pyqt5
-        exclude:
-          - python-version: "3.11"
             backend: pyside2
+          - platform: windows-latest
+            python-version: "3.11"
+            backend: pyqt5
+          # - platform: windows-latest
+          #   python-version: "3.13"
+          #   backend: pyqt6
 
     steps:
       - uses: actions/checkout@v4
@@ -63,6 +58,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
 
       - name: Install dependencies
         run: |

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -5,18 +5,17 @@ name: --pre Test
 
 on:
   schedule:
-    - cron: '0 */12 * * *'  # every 12 hours
+    - cron: "0 */12 * * *" # every 12 hours
   workflow_dispatch:
 
 jobs:
-
   test:
     name: ${{ matrix.platform }} (${{ matrix.python-version }})
     runs-on: ${{ matrix.platform }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ["3.11"]
         platform: [macos-13, windows-latest]
         backend: [pyside2, pyqt5]
 
@@ -55,7 +54,7 @@ jobs:
           PLATFORM: ${{ matrix.platform }}
           PYTHON: ${{ matrix.python }}
           RUN_ID: ${{ github.run_id }}
-          TITLE: '[test-bot] pip install --pre is failing'
+          TITLE: "[test-bot] pip install --pre is failing"
         with:
           filename: .github/TEST_FAIL_TEMPLATE.md
           update_existing: true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,27 +5,27 @@ ci:
 
 repos:
   - repo: https://github.com/crate-ci/typos
-    rev: v1.22.9
+    rev: v1.27.0
     hooks:
       - id: typos
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.7.2
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.18
+    rev: v0.22
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v1.13.0
     hooks:
       - id: mypy
         files: "^src/"
         additional_dependencies:
           - pymmcore-plus >=0.11.0
-          - useq-schema >=0.4.7
+          - useq-schema >=0.5.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,56 @@
 # Changelog
 
+## [v0.8.0](https://github.com/pymmcore-plus/pymmcore-widgets/tree/v0.8.0) (2024-10-04)
+
+[Full Changelog](https://github.com/pymmcore-plus/pymmcore-widgets/compare/v0.7.2...v0.8.0)
+
+**Implemented enhancements:**
+
+- feat: add HCSWizard to MDAWIdget [\#362](https://github.com/pymmcore-plus/pymmcore-widgets/pull/362) ([fdrgsp](https://github.com/fdrgsp))
+- feat: add High Content Screening wizard [\#360](https://github.com/pymmcore-plus/pymmcore-widgets/pull/360) ([fdrgsp](https://github.com/fdrgsp))
+- feat: reload prior config file on HCW rejection [\#359](https://github.com/pymmcore-plus/pymmcore-widgets/pull/359) ([gselzer](https://github.com/gselzer))
+- feat: plate navigator for HCS calibration testing [\#356](https://github.com/pymmcore-plus/pymmcore-widgets/pull/356) ([fdrgsp](https://github.com/fdrgsp))
+- feat: plate calibration widget [\#355](https://github.com/pymmcore-plus/pymmcore-widgets/pull/355) ([tlambert03](https://github.com/tlambert03))
+- feat: reusable single-well calibration widget for plate calibration widget [\#353](https://github.com/pymmcore-plus/pymmcore-widgets/pull/353) ([fdrgsp](https://github.com/fdrgsp))
+- feat: Refactor GridPlanWidget [\#351](https://github.com/pymmcore-plus/pymmcore-widgets/pull/351) ([gselzer](https://github.com/gselzer))
+- feat: add restrict well area [\#319](https://github.com/pymmcore-plus/pymmcore-widgets/pull/319) ([fdrgsp](https://github.com/fdrgsp))
+- feat: add useq.WellPlanPlan widget with well selection [\#318](https://github.com/pymmcore-plus/pymmcore-widgets/pull/318) ([tlambert03](https://github.com/tlambert03))
+- feat: add overlap checkbox [\#317](https://github.com/pymmcore-plus/pymmcore-widgets/pull/317) ([fdrgsp](https://github.com/fdrgsp))
+- feat: add minimal Points plan view [\#316](https://github.com/pymmcore-plus/pymmcore-widgets/pull/316) ([tlambert03](https://github.com/tlambert03))
+- feat: Points plan selector [\#315](https://github.com/pymmcore-plus/pymmcore-widgets/pull/315) ([tlambert03](https://github.com/tlambert03))
+- feat: multi point plan useq widgets [\#314](https://github.com/pymmcore-plus/pymmcore-widgets/pull/314) ([tlambert03](https://github.com/tlambert03))
+- feat: add select all for hub devices [\#310](https://github.com/pymmcore-plus/pymmcore-widgets/pull/310) ([tlambert03](https://github.com/tlambert03))
+
+**Fixed bugs:**
+
+- fix: fix splitting logic and deduplicate code in Groups Presets Widgets [\#365](https://github.com/pymmcore-plus/pymmcore-widgets/pull/365) ([tlambert03](https://github.com/tlambert03))
+- fix: disable Autofocus checkbox when using HCSWizard [\#364](https://github.com/pymmcore-plus/pymmcore-widgets/pull/364) ([fdrgsp](https://github.com/fdrgsp))
+- fix: enable ct axis order [\#361](https://github.com/pymmcore-plus/pymmcore-widgets/pull/361) ([fdrgsp](https://github.com/fdrgsp))
+- fix: fix valueChanged signals on PropertyWidget [\#352](https://github.com/pymmcore-plus/pymmcore-widgets/pull/352) ([tlambert03](https://github.com/tlambert03))
+- fix: Only allow YAML save/load when YAML available [\#347](https://github.com/pymmcore-plus/pymmcore-widgets/pull/347) ([gselzer](https://github.com/gselzer))
+- fix: Align spin boxes and labels in GridPlan [\#345](https://github.com/pymmcore-plus/pymmcore-widgets/pull/345) ([gselzer](https://github.com/gselzer))
+- fix: update the GroupPresetTableWidget policy [\#330](https://github.com/pymmcore-plus/pymmcore-widgets/pull/330) ([fdrgsp](https://github.com/fdrgsp))
+- fix: make name editable EditGroupWidget [\#328](https://github.com/pymmcore-plus/pymmcore-widgets/pull/328) ([fdrgsp](https://github.com/fdrgsp))
+- fix: WellPlateWidget initial drawing [\#327](https://github.com/pymmcore-plus/pymmcore-widgets/pull/327) ([fdrgsp](https://github.com/fdrgsp))
+- fix: fix bug in config wizard where core state bleeds into model [\#309](https://github.com/pymmcore-plus/pymmcore-widgets/pull/309) ([tlambert03](https://github.com/tlambert03))
+
+**Merged pull requests:**
+
+- build: pin useq-schema to 0.5.0 [\#367](https://github.com/pymmcore-plus/pymmcore-widgets/pull/367) ([tlambert03](https://github.com/tlambert03))
+- refactor: full repo reorganization [\#366](https://github.com/pymmcore-plus/pymmcore-widgets/pull/366) ([tlambert03](https://github.com/tlambert03))
+- ci\(pre-commit.ci\): autoupdate [\#358](https://github.com/pymmcore-plus/pymmcore-widgets/pull/358) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- ci\(pre-commit.ci\): autoupdate [\#357](https://github.com/pymmcore-plus/pymmcore-widgets/pull/357) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- refactor: more grid plan cleanup [\#354](https://github.com/pymmcore-plus/pymmcore-widgets/pull/354) ([tlambert03](https://github.com/tlambert03))
+- refactor: split run mda in mda widget [\#350](https://github.com/pymmcore-plus/pymmcore-widgets/pull/350) ([wl-stepp](https://github.com/wl-stepp))
+- style: clarify save/load buttons in MDAWidget [\#346](https://github.com/pymmcore-plus/pymmcore-widgets/pull/346) ([gselzer](https://github.com/gselzer))
+- style: unfill radio buttions in GridPlanWidget [\#344](https://github.com/pymmcore-plus/pymmcore-widgets/pull/344) ([gselzer](https://github.com/gselzer))
+- style: Manually compute sizeHint\(\) [\#343](https://github.com/pymmcore-plus/pymmcore-widgets/pull/343) ([gselzer](https://github.com/gselzer))
+- style: fix pixel affine table [\#341](https://github.com/pymmcore-plus/pymmcore-widgets/pull/341) ([tlambert03](https://github.com/tlambert03))
+- refactor: refactor stage widget [\#334](https://github.com/pymmcore-plus/pymmcore-widgets/pull/334) ([tlambert03](https://github.com/tlambert03))
+- refactor: remove old MDA widget [\#313](https://github.com/pymmcore-plus/pymmcore-widgets/pull/313) ([tlambert03](https://github.com/tlambert03))
+- refactor: pydantic2 syntax [\#311](https://github.com/pymmcore-plus/pymmcore-widgets/pull/311) ([tlambert03](https://github.com/tlambert03))
+- ci\(pre-commit.ci\): autoupdate [\#306](https://github.com/pymmcore-plus/pymmcore-widgets/pull/306) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+
 ## [v0.7.2](https://github.com/pymmcore-plus/pymmcore-widgets/tree/v0.7.2) (2024-06-13)
 
 [Full Changelog](https://github.com/pymmcore-plus/pymmcore-widgets/compare/v0.7.1...v0.7.2)

diff --git a/README.md b/README.md
@@ -18,7 +18,6 @@ It forms the basis of [`napari-micromanager`](https://github.com/pymmcore-plus/n
 
 See complete list of available widgets in the [documentation](https://pymmcore-plus.github.io/pymmcore-widgets/#widgets)
 
-
 ## Installation
 
 ```sh
@@ -28,5 +27,5 @@ pip install pymmcore-widgets
 # you must install one yourself, for example:
 pip install PyQt5
 
-# package is tested against PyQt5, PyQt6, PySide2, and PySide6
+# package is tested against PyQt5, PyQt6, PySide2, and PySide6(==6.7)
 ```
diff --git a/docs/getting_started.md b/docs/getting_started.md
@@ -12,7 +12,18 @@ pip install pymmcore-widgets
 
 ### Installing PyQt or PySide
 
-Since [pymmcore-widgets](./index.md) relies on either the [PyQt](https://riverbankcomputing.com/software/pyqt/) or [PySide](https://www.qt.io/qt-for-python) libraries, you also **need** to install one of these packages. You can use any of the available versions of these libraries: [PyQt5](https://pypi.org/project/PyQt5/), [PyQt6](https://pypi.org/project/PyQt6/), [PySide2](https://pypi.org/project/PySide2/) or [PySide6](https://pypi.org/project/PySide6/). For example, to install [PyQt6](https://riverbankcomputing.com/software/pyqt/download), you can use:
+Since [pymmcore-widgets](./index.md) relies on either the
+[PyQt](https://riverbankcomputing.com/software/pyqt/) or
+[PySide](https://www.qt.io/qt-for-python) libraries, you also **need** to
+install one of these packages. You can use any of the available versions of
+these libraries: [PyQt5](https://pypi.org/project/PyQt5/),
+[PyQt6](https://pypi.org/project/PyQt6/),
+[PySide2](https://pypi.org/project/PySide2/) or
+[PySide6](https://pypi.org/project/PySide6/).  We strongly recommend using PyQt6
+if possible.  If you must use a specific backend version and run into problems,
+please open an issue
+
+For example, to install [PyQt6](https://riverbankcomputing.com/software/pyqt/download), you can use:
 
 ```sh
 pip install PyQt6
@@ -21,10 +32,9 @@ pip install PyQt6
 !!! Note
     Widgets are tested on:
 
-    * `macOS & Windows`
-    * `Python 3.8, 3.9 3.10 & 3.11`
-    * `PyQt5 & PyQt6`
-    * `PySide2 & PySide6`
+    * macOS & Windows
+    * Python 3.9 and above
+    * PyQt5, PyQt6, PySide2 & PySide6(==6.7)
 
 ### Installing Micro-Manager
 

diff --git a/examples/grid_plan_widget.py b/examples/grid_plan_widget.py
@@ -15,6 +15,7 @@
 mmc.loadSystemConfiguration()
 
 grid_wdg = GridPlanWidget()
+grid_wdg.valueChanged.connect(print)
 grid_wdg.show()
 
 app.exec_()
diff --git a/examples/hcs_wizard.py b/examples/hcs_wizard.py
@@ -0,0 +1,32 @@
+from contextlib import suppress
+
+import useq
+from pymmcore_plus import CMMCorePlus
+from qtpy.QtWidgets import QApplication
+
+from pymmcore_widgets import StageWidget
+
+with suppress(ImportError):
+    from rich import print
+
+from pymmcore_widgets.hcs import HCSWizard
+
+app = QApplication([])
+mmc = CMMCorePlus.instance()
+mmc.loadSystemConfiguration()
+w = HCSWizard()
+w.show()
+w.accepted.connect(lambda: print(w.value()))
+s = StageWidget("XY", mmcore=mmc)
+s.show()
+
+
+plan = useq.WellPlatePlan(
+    plate=useq.WellPlate.from_str("96-well"),
+    a1_center_xy=(1000, 1500),
+    rotation=0.3,
+    selected_wells=slice(0, 8, 2),
+)
+w.setValue(plan)
+
+app.exec()
diff --git a/examples/mda_widget.py b/examples/mda_widget.py
@@ -3,12 +3,17 @@
 It is fully connected to the CMMCorePlus object, and has a "run" button.
 """
 
+from contextlib import suppress
+
 import useq
 from pymmcore_plus import CMMCorePlus
 from qtpy.QtWidgets import QApplication
 
 from pymmcore_widgets import MDAWidget
 
+with suppress(ImportError):
+    from rich import print
+
 app = QApplication([])
 
 CMMCorePlus.instance().loadSystemConfiguration()

diff --git a/examples/stage_widget.py b/examples/stage_widget.py
@@ -15,23 +15,18 @@
 mmc.loadSystemConfiguration()
 
 wdg = QWidget()
-wdg.setLayout(QHBoxLayout())
-
-stage_dev_list = list(mmc.getLoadedDevicesOfType(DeviceType.XYStage))
-stage_dev_list.extend(iter(mmc.getLoadedDevicesOfType(DeviceType.Stage)))
-
-for stage_dev in stage_dev_list:
-    if mmc.getDeviceType(stage_dev) is DeviceType.XYStage:
-        bx = QGroupBox("XY Control")
-        bx.setLayout(QHBoxLayout())
-        bx.layout().addWidget(StageWidget(device=stage_dev))
-        wdg.layout().addWidget(bx)
-    if mmc.getDeviceType(stage_dev) is DeviceType.Stage:
-        bx = QGroupBox("Z Control")
-        bx.setLayout(QHBoxLayout())
-        bx.layout().addWidget(StageWidget(device=stage_dev))
-        wdg.layout().addWidget(bx)
+wdg_layout = QHBoxLayout(wdg)
+
+stages = list(mmc.getLoadedDevicesOfType(DeviceType.XYStage))
+stages.extend(mmc.getLoadedDevicesOfType(DeviceType.Stage))
+for stage in stages:
+    lbl = "Z" if mmc.getDeviceType(stage) == DeviceType.Stage else "XY"
+    bx = QGroupBox(f"{lbl} Control")
+    bx_layout = QHBoxLayout(bx)
+    bx_layout.setContentsMargins(0, 0, 0, 0)
+    bx_layout.addWidget(StageWidget(device=stage, position_label_below=True))
+    wdg_layout.addWidget(bx)
 
-wdg.show()
 
-app.exec_()
+wdg.show()
+app.exec()
diff --git a/examples/temp/plate_calibration_widget.py b/examples/temp/plate_calibration_widget.py
@@ -0,0 +1,26 @@
+import useq
+from pymmcore_plus import CMMCorePlus
+from qtpy.QtWidgets import QApplication
+
+from pymmcore_widgets import StageWidget
+from pymmcore_widgets.hcs._plate_calibration_widget import PlateCalibrationWidget
+
+mmc = CMMCorePlus.instance()
+mmc.loadSystemConfiguration()
+
+app = QApplication([])
+
+s = StageWidget("XY")
+s.show()
+
+plan = useq.WellPlatePlan(
+    plate=useq.WellPlate.from_str("96-well"),
+    a1_center_xy=(1000, 1500),
+    rotation=0.3,
+)
+
+wdg = PlateCalibrationWidget(mmcore=mmc)
+wdg.setValue(plan)
+wdg.show()
+
+app.exec()
diff --git a/examples/temp/well_calibration_widget.py b/examples/temp/well_calibration_widget.py
@@ -0,0 +1,26 @@
+from pymmcore_plus import CMMCorePlus
+from qtpy.QtWidgets import QApplication
+
+from pymmcore_widgets import StageWidget
+from pymmcore_widgets.hcs._well_calibration_widget import WellCalibrationWidget
+
+mmc = CMMCorePlus.instance()
+mmc.loadSystemConfiguration()
+
+app = QApplication([])
+
+s = StageWidget("XY")
+s.show()
+c = WellCalibrationWidget(mmcore=mmc)
+
+
+@c.calibrationChanged.connect
+def _on_calibration_changed(calibrated: bool) -> None:
+    if calibrated:
+        print("Calibration changed! New center:", c.wellCenter())
+
+
+c.setCircularWell(True)
+c.show()
+
+app.exec()