Merge branch 'main' into funke-graph

.github/workflows/reusable_pip_test.yml

@@ -51,7 +51,7 @@ jobs:
         with:
           run: |
             python -m pytest --pyargs napari --color=yes --basetemp=.pytest_tmp --config-file=napari-from-github/pyproject.toml
-            python -m pytest --pyargs napari_builtins --color=yes --basetemp=.pytest_tmp --config-file=napari-from-github/pyproject.toml
+            python -m pytest --pyargs finn_builtins --color=yes --basetemp=.pytest_tmp --config-file=napari-from-github/pyproject.toml
 
       - name: Upload test artifacts
         if: failure()

MANIFEST.in

@@ -3,7 +3,7 @@ include *.cff
 graft finn/_vendor
 recursive-include finn *.pyi
 recursive-include finn _tests/*.py
-recursive-include napari_builtins _tests/*.py
+recursive-include finn_builtins _tests/*.py
 recursive-include finn *.pyi
 recursive-include finn *.png *.svg *.qss *.gif *.ico *.icns
 recursive-include finn *.yaml

finn/_qt/qt_viewer.py

@@ -55,7 +55,7 @@
 from finn.utils.naming import CallerFrame
 from finn.utils.notifications import show_info
 from finn.utils.translations import trans
-from napari_builtins.io import imsave_extensions
+from finn_builtins.io import imsave_extensions
 
 from finn._vispy import VispyCanvas, create_vispy_layer  # isort:skip
 

finn/utils/_register.py

@@ -75,7 +75,6 @@ def create_func(cls, name=None, doc=None):
         ],
         return_annotation=cls,
     )
-    breakpoint()
 
     src = template.format(
         name=name,

finn/utils/io.py

@@ -133,7 +133,7 @@ def __getattr__(name: str):
     }:
         warnings.warn(
             trans._(
-                '{name} was moved from finn.utils.io in v0.4.17. Import it from napari_builtins.io instead.',
+                '{name} was moved from finn.utils.io in v0.4.17. Import it from finn_builtins.io instead.',
                 deferred=True,
                 name=name,
             ),
@@ -142,6 +142,6 @@ def __getattr__(name: str):
         )
         import finn_builtins.io
 
-        return getattr(napari_builtins.io, name)
+        return getattr(finn_builtins.io, name)
 
     raise AttributeError(f'module {__name__} has no attribute {name}')

napari_builtins/__init__.py → finn_builtins/__init__.py

@@ -1,6 +1,6 @@
 from importlib.metadata import PackageNotFoundError, version
 
 try:
-    __version__ = version('napari')
+    __version__ = version('finn')
 except PackageNotFoundError:
     __version__ = 'unknown'

napari_builtins/_tests/conftest.py → finn_builtins/_tests/conftest.py

@@ -22,7 +22,7 @@ def mock_npe2_pm():
 def use_builtins(mock_npe2_pm: PluginManager):
     plugin = DynamicPlugin('napari', plugin_manager=mock_npe2_pm)
     mf = PluginManifest.from_file(
-        Path(napari_builtins.__file__).parent / 'builtins.yaml'
+        Path(finn_builtins.__file__).parent / 'builtins.yaml'
     )
     plugin.manifest = mf
     with plugin:

napari_builtins/_tests/test_io.py → finn_builtins/_tests/test_io.py

@@ -12,14 +12,14 @@
 import tifffile
 import zarr
 
-from napari_builtins.io._read import (
+from finn_builtins.io._read import (
     _guess_layer_type_from_column_names,
     _guess_zarr_path,
     csv_to_layer_data,
     magic_imread,
     read_csv,
 )
-from napari_builtins.io._write import write_csv
+from finn_builtins.io._write import write_csv
 
 
 class ImageSpec(NamedTuple):

napari_builtins/_tests/test_ndims_balls.py → finn_builtins/_tests/test_ndims_balls.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from napari_builtins._ndims_balls import (
+from finn_builtins._ndims_balls import (
     labeled_particles2d,
     labeled_particles3d,
 )

napari_builtins/_tests/test_reader.py → finn_builtins/_tests/test_reader.py

@@ -7,7 +7,7 @@
 import pytest
 import tifffile
 
-from napari_builtins.io._write import write_csv
+from finn_builtins.io._write import write_csv
 
 
 @pytest.fixture

napari_builtins/_tests/test_writer.py → finn_builtins/_tests/test_writer.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pytest
 
-from napari_builtins.io import finn_get_reader
+from finn_builtins.io import finn_get_reader
 
 if TYPE_CHECKING:
     from finn import layers

napari_builtins/builtins.yaml → finn_builtins/builtins.yaml

@@ -4,128 +4,128 @@ name: finn
 contributions:
   commands:
     - id: finn.get_reader
-      python_name: napari_builtins.io:napari_get_reader
+      python_name: finn_builtins.io:napari_get_reader
       title: Builtin Reader
 
     - id: finn.write_image
-      python_name: napari_builtins.io:napari_write_image
+      python_name: finn_builtins.io:napari_write_image
       title: napari built-in image writer
     - id: finn.write_labels
-      python_name: napari_builtins.io:napari_write_labels
+      python_name: finn_builtins.io:napari_write_labels
       title: napari built-in label field writer
     - id: finn.write_points
-      python_name: napari_builtins.io:napari_write_points
+      python_name: finn_builtins.io:napari_write_points
       title: napari built-in points writer
     - id: finn.write_shapes
-      python_name: napari_builtins.io:napari_write_shapes
+      python_name: finn_builtins.io:napari_write_shapes
       title: napari built-in shapes writer
     - id: finn.write_directory
-      python_name: napari_builtins.io:write_layer_data_with_plugins
+      python_name: finn_builtins.io:write_layer_data_with_plugins
       title: napari built-in save to folder
 
     # samples
     - id: finn.data.astronaut
       title: Generate astronaut sample
-      python_name: napari_builtins._skimage_data:astronaut
+      python_name: finn_builtins._skimage_data:astronaut
     - id: finn.data.binary_blobs
       title: Generate binary_blobs sample
-      python_name: napari_builtins._skimage_data:binary_blobs
+      python_name: finn_builtins._skimage_data:binary_blobs
     - id: finn.data.binary_blobs_3D
       title: Generate binary_blobs_3D sample
-      python_name: napari_builtins._skimage_data:binary_blobs_3D
+      python_name: finn_builtins._skimage_data:binary_blobs_3D
     - id: finn.data.brain
       title: Generate brain sample
-      python_name: napari_builtins._skimage_data:brain
+      python_name: finn_builtins._skimage_data:brain
     - id: finn.data.brick
       title: Generate brick sample
-      python_name: napari_builtins._skimage_data:brick
+      python_name: finn_builtins._skimage_data:brick
     - id: finn.data.camera
       title: Generate camera sample
-      python_name: napari_builtins._skimage_data:camera
+      python_name: finn_builtins._skimage_data:camera
     - id: finn.data.cat
       title: Generate cat sample
-      python_name: napari_builtins._skimage_data:cat
+      python_name: finn_builtins._skimage_data:cat
     - id: finn.data.cell
       title: Generate cell sample
-      python_name: napari_builtins._skimage_data:cell
+      python_name: finn_builtins._skimage_data:cell
     - id: finn.data.cells3d
       title: Generate cells3d sample
-      python_name: napari_builtins._skimage_data:cells3d
+      python_name: finn_builtins._skimage_data:cells3d
     - id: finn.data.checkerboard
       title: Generate checkerboard sample
-      python_name: napari_builtins._skimage_data:checkerboard
+      python_name: finn_builtins._skimage_data:checkerboard
     - id: finn.data.clock
       title: Generate clock sample
-      python_name: napari_builtins._skimage_data:clock
+      python_name: finn_builtins._skimage_data:clock
     - id: finn.data.coffee
       title: Generate coffee sample
-      python_name: napari_builtins._skimage_data:coffee
+      python_name: finn_builtins._skimage_data:coffee
     - id: finn.data.coins
       title: Generate coins sample
-      python_name: napari_builtins._skimage_data:coins
+      python_name: finn_builtins._skimage_data:coins
     - id: finn.data.colorwheel
       title: Generate colorwheel sample
-      python_name: napari_builtins._skimage_data:colorwheel
+      python_name: finn_builtins._skimage_data:colorwheel
     - id: finn.data.eagle
       title: Generate eagle sample
-      python_name: napari_builtins._skimage_data:eagle
+      python_name: finn_builtins._skimage_data:eagle
     - id: finn.data.grass
       title: Generate grass sample
-      python_name: napari_builtins._skimage_data:grass
+      python_name: finn_builtins._skimage_data:grass
     - id: finn.data.gravel
       title: Generate gravel sample
-      python_name: napari_builtins._skimage_data:gravel
+      python_name: finn_builtins._skimage_data:gravel
     - id: finn.data.horse
       title: Generate horse sample
-      python_name: napari_builtins._skimage_data:horse
+      python_name: finn_builtins._skimage_data:horse
     - id: finn.data.hubble_deep_field
       title: Generate hubble_deep_field sample
-      python_name: napari_builtins._skimage_data:hubble_deep_field
+      python_name: finn_builtins._skimage_data:hubble_deep_field
     - id: finn.data.human_mitosis
       title: Generate human_mitosis sample
-      python_name: napari_builtins._skimage_data:human_mitosis
+      python_name: finn_builtins._skimage_data:human_mitosis
     - id: finn.data.immunohistochemistry
       title: Generate immunohistochemistry sample
-      python_name: napari_builtins._skimage_data:immunohistochemistry
+      python_name: finn_builtins._skimage_data:immunohistochemistry
     - id: finn.data.kidney
       title: Generate kidney sample
-      python_name: napari_builtins._skimage_data:kidney
+      python_name: finn_builtins._skimage_data:kidney
     - id: finn.data.lfw_subset
       title: Generate lfw_subset sample
-      python_name: napari_builtins._skimage_data:lfw_subset
+      python_name: finn_builtins._skimage_data:lfw_subset
     - id: finn.data.lily
       title: Generate lily sample
-      python_name: napari_builtins._skimage_data:lily
+      python_name: finn_builtins._skimage_data:lily
     - id: finn.data.microaneurysms
       title: Generate microaneurysms sample
-      python_name: napari_builtins._skimage_data:microaneurysms
+      python_name: finn_builtins._skimage_data:microaneurysms
     - id: finn.data.moon
       title: Generate moon sample
-      python_name: napari_builtins._skimage_data:moon
+      python_name: finn_builtins._skimage_data:moon
     - id: finn.data.page
       title: Generate page sample
-      python_name: napari_builtins._skimage_data:page
+      python_name: finn_builtins._skimage_data:page
     - id: finn.data.retina
       title: Generate retina sample
-      python_name: napari_builtins._skimage_data:retina
+      python_name: finn_builtins._skimage_data:retina
     - id: finn.data.rocket
       title: Generate rocket sample
-      python_name: napari_builtins._skimage_data:rocket
+      python_name: finn_builtins._skimage_data:rocket
     - id: finn.data.shepp_logan_phantom
       title: Generate shepp_logan_phantom sample
-      python_name: napari_builtins._skimage_data:shepp_logan_phantom
+      python_name: finn_builtins._skimage_data:shepp_logan_phantom
     - id: finn.data.skin
       title: Generate skin sample
-      python_name: napari_builtins._skimage_data:skin
+      python_name: finn_builtins._skimage_data:skin
     - id: finn.data.text
       title: Generate text sample
-      python_name: napari_builtins._skimage_data:text
+      python_name: finn_builtins._skimage_data:text
     - id: finn.data.balls_2d
       title: Generate 2d_balls sample
-      python_name: napari_builtins._ndims_balls:labeled_particles2d
+      python_name: finn_builtins._ndims_balls:labeled_particles2d
     - id: finn.data.balls_3d
       title: Generate 3d_balls sample
-      python_name: napari_builtins._ndims_balls:labeled_particles3d
+      python_name: finn_builtins._ndims_balls:labeled_particles3d
 
   readers:
     - command: finn.get_reader

napari_builtins/io/__init__.py → finn_builtins/io/__init__.py

@@ -1,12 +1,12 @@
-from napari_builtins.io._read import (
+from finn_builtins.io._read import (
     csv_to_layer_data,
     imread,
     magic_imread,
     napari_get_reader,
     read_csv,
     read_zarr_dataset,
 )
-from napari_builtins.io._write import (
+from finn_builtins.io._write import (
     imsave_extensions,
     napari_write_image,
     napari_write_labels,

pyproject.toml

@@ -176,7 +176,7 @@ build = [
 finn = "finn.utils._testsupport"
 
 [project.entry-points."finn.manifest"]
-napari_builtins = "napari_builtins:builtins.yaml"
+finn_builtins = "finn_builtins:builtins.yaml"
 
 [tool.setuptools]
 zip-safe = false
@@ -192,7 +192,7 @@ namespaces = false
 "*" = [
     "*.pyi",
 ]
-napari_builtins = [
+finn_builtins = [
     "builtins.yaml",
 ]
 
@@ -338,7 +338,7 @@ console_output_style = "count"
 minversion = "8"
 # log_cli_level = "INFO"
 xfail_strict = true
-testpaths = ["finn", "napari_builtins"]
+testpaths = ["finn", "finn_builtins"]
 
 
 # NOTE: only put things that will never change in here.
@@ -416,7 +416,7 @@ module = [
   '*.experimental.*',
   '*._vendor.*',
   '*.benchmarks.*',
-  'napari_builtins.*'
+  'finn_builtins.*'
 ]
 ignore_errors = true
 
@@ -782,15 +782,15 @@ omit = [
 ]
 source = [
     "finn",
-    "napari_builtins",
+    "finn_builtins",
 ]
 
 [tool.coverage.paths]
 source = [
     "finn/",
 ]
 builtins = [
-    "napari_builtins/",
+    "finn_builtins/",
 ]
 
 [tool.importlinter]