npe2 migration

.github/workflows/deploy.yml

@@ -19,12 +19,12 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine
+          pip install -U setuptools setuptools_scm wheel twine build
       - name: Build and publish
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
         run: |
           git tag
-          python setup.py sdist bdist_wheel
+          python -m build .
           twine upload dist/*

LICENSE.md → LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2021 Jonas Windhager
+Copyright (c) 2021 University of Zurich
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1,6 +1,6 @@
 include CHANGELOG.md
 include CONTRIBUTING.md
-include LICENSE.md
+include LICENSE
 include README.md
 include requirements.txt
 

README.md

@@ -1,20 +1,11 @@
 # napari-imc
 
-<a href="https://pypi.org/project/napari-imc/">
-    <img src="https://img.shields.io/pypi/v/napari-imc" alt="PyPI" />
-</a>
-<a href="https://github.com/BodenmillerGroup/napari-imc/blob/main/LICENSE.md">
-    <img src="https://img.shields.io/pypi/l/napari-imc" alt="License" />
-</a>
-<a href="https://www.python.org/">
-    <img src="https://img.shields.io/pypi/pyversions/napari-imc" alt="Python" />
-</a>
-<a href="https://github.com/BodenmillerGroup/napari-imc/issues">
-    <img src="https://img.shields.io/github/issues/BodenmillerGroup/napari-imc" alt="Issues" />
-</a>
-<a href="https://github.com/BodenmillerGroup/napari-imc/pulls">
-    <img src="https://img.shields.io/github/issues-pr/BodenmillerGroup/napari-imc" alt="Pull requests" />
-</a>
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-imc)](https://napari-hub.org/plugins/napari-imc)
+[![PyPI](https://img.shields.io/pypi/v/napari-imc.svg?color=green)](https://pypi.org/project/napari-imc)
+[![License](https://img.shields.io/pypi/l/napari-imc.svg?color=green)](https://github.com/BodenmillerGroup/napari-imc/raw/main/LICENSE)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-imc.svg?color=green)](https://python.org)
+[![Issues](https://img.shields.io/github/issues/BodenmillerGroup/napari-imc)](https://github.com/BodenmillerGroup/napari-imc/issues)
+[![Pull requests](https://img.shields.io/github/issues-pr/BodenmillerGroup/napari-imc)](https://github.com/BodenmillerGroup/napari-imc/pulls)
 
 Imaging Mass Cytometry (IMC) file type support for napari
 

napari_imc/__init__.py

@@ -1,14 +1,9 @@
+from ._reader import napari_get_reader
+from .imc_widget import IMCWidget
+
 try:
     from ._version import version as __version__
 except ImportError:
     __version__ = "unknown"
 
-from .imc_widget import IMCWidget
-from ._reader import napari_get_reader
-from ._dock_widget import napari_experimental_provide_dock_widget
-
-__all__ = [
-    "IMCWidget",
-    "napari_get_reader",
-    "napari_experimental_provide_dock_widget",
-]
+__all__ = ["IMCWidget", "napari_get_reader"]

napari_imc/_reader.py

@@ -1,12 +1,11 @@
-from napari import Viewer
-from napari_plugin_engine import napari_hook_implementation
 from typing import Optional
 
-from .imc_widget import IMCWidget
+from napari.viewer import Viewer
+
 from .imc_controller import IMCController
+from .imc_widget import IMCWidget
 
 
-@napari_hook_implementation
 def napari_get_reader(path):
     if isinstance(path, list):
         if any(not IMCController.is_imc_file(p) for p in path):
@@ -46,15 +45,10 @@ def _get_viewer() -> Optional[Viewer]:
 
 def _get_imc_widget(viewer: Viewer) -> IMCWidget:
     # TODO https://github.com/napari/napari/issues/2203
-    dock_widget = viewer.window._dock_widgets.get(IMCWidget.FULL_NAME)
+    dock_widget = viewer.window._dock_widgets.get("Imaging Mass Cytometry")
     if dock_widget is not None:
         imc_widget = dock_widget.widget()
     else:
         imc_widget = IMCWidget(napari_viewer=viewer)
-        viewer.window.add_dock_widget(
-            imc_widget,
-            name=IMCWidget.FULL_NAME,
-            area=IMCWidget.AREA,
-            allowed_areas=IMCWidget.ALLOWED_AREAS,
-        )
+        viewer.window.add_dock_widget(imc_widget, name="Imaging Mass Cytometry")
     return imc_widget

napari_imc/imc_controller.py

@@ -1,16 +1,16 @@
-import numpy as np
+from pathlib import Path
+from typing import TYPE_CHECKING, Any, List, Optional, Sequence, Tuple, Type, Union
 
+import numpy as np
 from napari import Viewer
 from napari.layers import Image
-from pathlib import Path
-from typing import Any, List, Optional, Sequence, Tuple, Type, TYPE_CHECKING, Union
 
 from .io import McdFileReader, TxtFileReader
 from .io.base import FileReaderBase
 from .models import (
     ChannelModel,
-    IMCFileModel,
     IMCFileAcquisitionModel,
+    IMCFileModel,
     IMCFilePanoramaModel,
 )
 from .models.base import IMCFileTreeItem

napari_imc/imc_widget.py

@@ -1,20 +1,17 @@
+from typing import Optional
+
 from napari import Viewer
 from qtpy.QtCore import (
-    Qt,
     QItemSelection,
     QItemSelectionModel,
     QModelIndex,
     QSortFilterProxyModel,
+    Qt,
 )
 from qtpy.QtWidgets import QSizePolicy, QSplitter, QStackedWidget, QVBoxLayout, QWidget
-from typing import Optional
 
 from .imc_controller import IMCController
-from .models import (
-    IMCFileModel,
-    IMCFileAcquisitionModel,
-    IMCFilePanoramaModel,
-)
+from .models import IMCFileAcquisitionModel, IMCFileModel, IMCFilePanoramaModel
 from .widgets import (
     ChannelControlsWidget,
     ChannelTableModel,
@@ -25,11 +22,6 @@
 
 
 class IMCWidget(QWidget):
-    NAME = "Imaging Mass Cytometry"
-    FULL_NAME = "Imaging Mass Cytometry"
-    AREA = "right"
-    ALLOWED_AREAS = ["left", "right"]
-
     def __init__(self, napari_viewer: Viewer, parent: Optional[QWidget] = None) -> None:
         super(IMCWidget, self).__init__(parent)
         self._controller = IMCController(napari_viewer, self)

napari_imc/io/__init__.py

@@ -2,8 +2,4 @@
 from .mcd import McdFileReader
 from .txt import TxtFileReader
 
-__all__ = [
-    "ImaxtFileReader",
-    "McdFileReader",
-    "TxtFileReader",
-]
+__all__ = ["ImaxtFileReader", "McdFileReader", "TxtFileReader"]

napari_imc/io/base.py

@@ -1,14 +1,10 @@
-import numpy as np
-
 from abc import abstractmethod
 from pathlib import Path
 from typing import List, NamedTuple, Tuple, Union
 
-from ..models import (
-    IMCFileModel,
-    IMCFileAcquisitionModel,
-    IMCFilePanoramaModel,
-)
+import numpy as np
+
+from ..models import IMCFileAcquisitionModel, IMCFileModel, IMCFilePanoramaModel
 from ..models.base import IMCFileTreeItem
 
 

napari_imc/io/imaxt.py

@@ -1,18 +1,14 @@
-import numpy as np
-
-from imageio import imread
 from pathlib import Path
 from typing import List, Optional, Tuple, Union
 
+import numpy as np
+from imageio import imread
+
 from ..io.base import FileReaderBase, ImageDimensions
-from ..models import (
-    IMCFileModel,
-    IMCFileAcquisitionModel,
-    IMCFilePanoramaModel,
-)
+from ..models import IMCFileAcquisitionModel, IMCFileModel, IMCFilePanoramaModel
 
 try:
-    import zarr
+    import zarr  # type: ignore
 except Exception:
     zarr = None
 

napari_imc/io/mcd.py

@@ -1,15 +1,11 @@
-import numpy as np
-
 from pathlib import Path
-from readimc import MCDFile
 from typing import List, Optional, Tuple, Union
 
+import numpy as np
+from readimc import MCDFile
+
 from ..io.base import FileReaderBase, ImageDimensions
-from ..models import (
-    IMCFileModel,
-    IMCFileAcquisitionModel,
-    IMCFilePanoramaModel,
-)
+from ..models import IMCFileAcquisitionModel, IMCFileModel, IMCFilePanoramaModel
 
 
 class McdFileReader(FileReaderBase):

napari_imc/io/txt.py

@@ -1,16 +1,12 @@
-import numpy as np
 import re
-
 from pathlib import Path
-from readimc import TXTFile
 from typing import List, Optional, Tuple, Union
 
+import numpy as np
+from readimc import TXTFile
+
 from ..io.base import FileReaderBase, ImageDimensions
-from ..models import (
-    IMCFileModel,
-    IMCFileAcquisitionModel,
-    IMCFilePanoramaModel,
-)
+from ..models import IMCFileAcquisitionModel, IMCFileModel, IMCFilePanoramaModel
 
 
 class TxtFileReader(FileReaderBase):

napari_imc/models/channel.py

@@ -1,4 +1,4 @@
-from typing import Dict, List, Optional, Tuple, TYPE_CHECKING
+from typing import TYPE_CHECKING, Dict, List, Optional, Tuple
 
 from napari.layers import Image
 from napari.utils import Colormap

napari_imc/models/imc_file_acquisition.py

@@ -1,4 +1,4 @@
-from typing import Any, List, Optional, Sequence, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, List, Optional, Sequence
 
 from .base import IMCFileTreeItem, ModelBase
 

napari_imc/models/imc_file_panorama.py

@@ -1,5 +1,6 @@
+from typing import TYPE_CHECKING, Any, List, Optional
+
 from napari.layers import Image
-from typing import Any, List, Optional, TYPE_CHECKING
 
 from .base import IMCFileTreeItem, ModelBase
 

napari_imc/napari.yaml

@@ -0,0 +1,17 @@
+name: napari-imc
+schema_version: 0.1.0
+contributions:
+  commands:
+  - id: napari-imc.IMCWidget
+    title: Create Imaging Mass Cytometry
+    python_name: napari_imc:IMCWidget
+  - id: napari-imc.get_reader
+    title: Read Imaging Mass Cytometry (IMC) files using readimc
+    python_name: napari_imc:napari_get_reader
+  readers:
+  - command: napari-imc.get_reader
+    filename_patterns: ["*.mcd", "*.txt"]
+    accepts_directories: false
+  widgets:
+  - command: napari-imc.IMCWidget
+    display_name: Imaging Mass Cytometry

napari_imc/widgets/_color_picker.py

@@ -1,7 +1,8 @@
-from qtpy.QtCore import Qt, QObject, Signal
+from typing import Optional
+
+from qtpy.QtCore import QObject, Qt, Signal
 from qtpy.QtGui import QColor, qGray
 from qtpy.QtWidgets import QColorDialog, QMenu, QPushButton, QWidget, QWidgetAction
-from typing import Optional
 
 
 class ColorPicker(QPushButton):

napari_imc/widgets/channel_controls_widget.py

@@ -1,10 +1,11 @@
+from typing import TYPE_CHECKING, Optional, Tuple
+
 from napari.layers.base.base import Blending
 from napari.layers.image.image import Interpolation
 from qtpy.QtCore import Qt
 from qtpy.QtGui import QColor
 from qtpy.QtWidgets import QComboBox, QFormLayout, QSlider, QWidget
 from superqt import QDoubleRangeSlider
-from typing import Optional, Tuple, TYPE_CHECKING
 
 from ._color_picker import ColorPicker
 

napari_imc/widgets/channel_table_model.py

@@ -1,6 +1,7 @@
 from contextlib import contextmanager
-from qtpy.QtCore import Qt, QAbstractTableModel, QModelIndex, QObject
-from typing import Any, Optional, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, Optional
+
+from qtpy.QtCore import QAbstractTableModel, QModelIndex, QObject, Qt
 
 if TYPE_CHECKING:
     from ..imc_controller import IMCController

napari_imc/widgets/channel_table_view.py

@@ -1,6 +1,7 @@
+from typing import Optional
+
 from qtpy.QtCore import QModelIndex
 from qtpy.QtWidgets import QTableView, QWidget
-from typing import Optional
 
 
 class ChannelTableView(QTableView):

napari_imc/widgets/imc_file_tree_model.py

@@ -1,6 +1,7 @@
 from contextlib import contextmanager
-from qtpy.QtCore import Qt, QAbstractItemModel, QModelIndex, QObject
-from typing import Any, Optional, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, Optional
+
+from qtpy.QtCore import QAbstractItemModel, QModelIndex, QObject, Qt
 
 from ..models.base import IMCFileTreeItem
 

napari_imc/widgets/imc_file_tree_view.py

@@ -1,7 +1,8 @@
-from qtpy.QtCore import Qt, QModelIndex, QObject, QPoint, Signal
-from qtpy.QtWidgets import QMenu, QStyle, QTreeView, QWidget
 from typing import Optional
 
+from qtpy.QtCore import QModelIndex, QObject, QPoint, Qt, Signal
+from qtpy.QtWidgets import QMenu, QStyle, QTreeView, QWidget
+
 from ..models import IMCFileModel
 
 

requirements.txt

@@ -2,7 +2,8 @@
 # Requirements of your napari plugin should be listed in setup.cfg
 # See also: https://caremad.io/posts/2013/07/setup-vs-requirement/
 
-napari[all]
-flake8
-black
 -e .
+black
+flake8
+isort
+napari[all]