Fix plugin things by moving to non-flat directory struture

brainglobe · Aug 29, 2023 · 32f5e75 · 32f5e75
1 parent f18f840
commit 32f5e75
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Showing 65 changed files with 26 additions and 34 deletions.
diff --git a/.github/workflows/plugin_preview.yml b/.github/workflows/plugin_preview.yml
@@ -3,8 +3,6 @@ name: napari hub Preview Page # we use this name to find your preview page artif
 
 on:
   pull_request:
-    branches:
-      - '**'
 
 jobs:
   preview-page:
@@ -13,7 +11,7 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: napari hub Preview Page Builder
         uses: chanzuckerberg/[email protected]

diff --git a/.github/workflows/test_include_guard.yaml b/.github/workflows/test_include_guard.yaml
@@ -5,7 +5,8 @@ name: Test Tensorflow include guards
 on:
   pull_request:
   push:
-    branches: [main]
+    branches:
+      - main
 
 jobs:
   tensorflow_guards:
@@ -32,6 +33,7 @@ jobs:
           fail-on-error: true
           script: |
             import cellfinder.core
+            import cellfinder.napari
 
       - name: Uninstall tensorflow
         run: python -m pip uninstall -y tensorflow

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,6 +1,7 @@
 include .napari/config.yml
 include LICENSE
 include README.md
+include requirements.txt
 include CF-CORE-README.md
 include CF-NAPARI-README.md
 
@@ -10,6 +11,7 @@ exclude CORE_CHANGELOG.md
 exclude tox.ini
 
 graft cellfinder
+include cellfinder/napari.yaml
 
 prune benchmarks
 prune examples

diff --git a/examples/show_detection_sample.py b/examples/show_detection_sample.py
@@ -14,7 +14,7 @@
 viewer = napari.Viewer()
 # Open plugin
 viewer.window.add_plugin_dock_widget(
-    plugin_name="cellfinder-napari", widget_name="Cell detection"
+    plugin_name="cellfinder", widget_name="Cell detection"
 )
 # Add sample data layers
 for layer in load_sample():

diff --git a/pyproject.toml b/pyproject.toml
@@ -65,8 +65,8 @@ dev = [
     "tox",
 ]
 
-[project.entry-points.'napari.manifest']
-cellfinder-napari = "cellfinder.napari:napari.yaml"
+[project.entry-points."napari.manifest"]
+cellfinder = "cellfinder:napari.yaml"
 
 [project.scripts]
 cellfinder_download = "cellfinder.core.download.cli:main"
@@ -95,7 +95,9 @@ known-first-party = ["cellfinder"]
 
 [tool.setuptools]
 include-package-data = true
-py-modules = ["cellfinder"]
+
+[tool.setuptools.package-data]
+cellfinder = ["*.yaml", "*.png"]
 
 [tool.setuptools_scm]
 

diff --git a/cellfinder/__init__.py → src/cellfinder/__init__.py b/cellfinder/__init__.py → src/cellfinder/__init__.py
diff --git a/cellfinder/core/__init__.py → src/cellfinder/core/__init__.py b/cellfinder/core/__init__.py → src/cellfinder/core/__init__.py
diff --git a/cellfinder/core/classify/__init__.py → src/cellfinder/core/classify/__init__.py b/cellfinder/core/classify/__init__.py → src/cellfinder/core/classify/__init__.py
diff --git a/cellfinder/core/classify/augment.py → src/cellfinder/core/classify/augment.py b/cellfinder/core/classify/augment.py → src/cellfinder/core/classify/augment.py
diff --git a/cellfinder/core/classify/classify.py → src/cellfinder/core/classify/classify.py b/cellfinder/core/classify/classify.py → src/cellfinder/core/classify/classify.py
diff --git a/cellfinder/core/classify/cube_generator.py → ...ellfinder/core/classify/cube_generator.py b/cellfinder/core/classify/cube_generator.py → ...ellfinder/core/classify/cube_generator.py
diff --git a/cellfinder/core/classify/resnet.py → src/cellfinder/core/classify/resnet.py b/cellfinder/core/classify/resnet.py → src/cellfinder/core/classify/resnet.py
diff --git a/cellfinder/core/classify/tools.py → src/cellfinder/core/classify/tools.py b/cellfinder/core/classify/tools.py → src/cellfinder/core/classify/tools.py
diff --git a/cellfinder/core/config/__init__.py → src/cellfinder/core/config/__init__.py b/cellfinder/core/config/__init__.py → src/cellfinder/core/config/__init__.py
diff --git a/cellfinder/core/config/cellfinder.conf → src/cellfinder/core/config/cellfinder.conf b/cellfinder/core/config/cellfinder.conf → src/cellfinder/core/config/cellfinder.conf
diff --git a/cellfinder/core/detect/__init__.py → src/cellfinder/core/detect/__init__.py b/cellfinder/core/detect/__init__.py → src/cellfinder/core/detect/__init__.py
diff --git a/cellfinder/core/detect/detect.py → src/cellfinder/core/detect/detect.py b/cellfinder/core/detect/detect.py → src/cellfinder/core/detect/detect.py
diff --git a/cellfinder/core/detect/filters/__init__.py → ...ellfinder/core/detect/filters/__init__.py b/cellfinder/core/detect/filters/__init__.py → ...ellfinder/core/detect/filters/__init__.py
diff --git a/...der/core/detect/filters/plane/__init__.py → ...der/core/detect/filters/plane/__init__.py b/...der/core/detect/filters/plane/__init__.py → ...der/core/detect/filters/plane/__init__.py
diff --git a/.../detect/filters/plane/classical_filter.py → .../detect/filters/plane/classical_filter.py b/.../detect/filters/plane/classical_filter.py → .../detect/filters/plane/classical_filter.py
diff --git a/...core/detect/filters/plane/plane_filter.py → ...core/detect/filters/plane/plane_filter.py b/...core/detect/filters/plane/plane_filter.py → ...core/detect/filters/plane/plane_filter.py
diff --git a/.../core/detect/filters/plane/tile_walker.py → .../core/detect/filters/plane/tile_walker.py b/.../core/detect/filters/plane/tile_walker.py → .../core/detect/filters/plane/tile_walker.py
diff --git a/...nder/core/detect/filters/setup_filters.py → ...nder/core/detect/filters/setup_filters.py b/...nder/core/detect/filters/setup_filters.py → ...nder/core/detect/filters/setup_filters.py
diff --git a/...er/core/detect/filters/volume/__init__.py → ...er/core/detect/filters/volume/__init__.py b/...er/core/detect/filters/volume/__init__.py → ...er/core/detect/filters/volume/__init__.py
diff --git a/...core/detect/filters/volume/ball_filter.py → ...core/detect/filters/volume/ball_filter.py b/...core/detect/filters/volume/ball_filter.py → ...core/detect/filters/volume/ball_filter.py
diff --git a/...ect/filters/volume/structure_detection.py → ...ect/filters/volume/structure_detection.py b/...ect/filters/volume/structure_detection.py → ...ect/filters/volume/structure_detection.py
diff --git a/...ect/filters/volume/structure_splitting.py → ...ect/filters/volume/structure_splitting.py b/...ect/filters/volume/structure_splitting.py → ...ect/filters/volume/structure_splitting.py
diff --git a/...re/detect/filters/volume/volume_filter.py → ...re/detect/filters/volume/volume_filter.py b/...re/detect/filters/volume/volume_filter.py → ...re/detect/filters/volume/volume_filter.py
diff --git a/cellfinder/core/download/__init__.py → src/cellfinder/core/download/__init__.py b/cellfinder/core/download/__init__.py → src/cellfinder/core/download/__init__.py
diff --git a/cellfinder/core/download/cli.py → src/cellfinder/core/download/cli.py b/cellfinder/core/download/cli.py → src/cellfinder/core/download/cli.py
diff --git a/cellfinder/core/download/download.py → src/cellfinder/core/download/download.py b/cellfinder/core/download/download.py → src/cellfinder/core/download/download.py
diff --git a/cellfinder/core/download/models.py → src/cellfinder/core/download/models.py b/cellfinder/core/download/models.py → src/cellfinder/core/download/models.py
diff --git a/cellfinder/core/main.py → src/cellfinder/core/main.py b/cellfinder/core/main.py → src/cellfinder/core/main.py
diff --git a/cellfinder/core/tools/IO.py → src/cellfinder/core/tools/IO.py b/cellfinder/core/tools/IO.py → src/cellfinder/core/tools/IO.py
diff --git a/cellfinder/core/tools/__init__.py → src/cellfinder/core/tools/__init__.py b/cellfinder/core/tools/__init__.py → src/cellfinder/core/tools/__init__.py
diff --git a/cellfinder/core/tools/array_operations.py → ...cellfinder/core/tools/array_operations.py b/cellfinder/core/tools/array_operations.py → ...cellfinder/core/tools/array_operations.py
diff --git a/cellfinder/core/tools/geometry.py → src/cellfinder/core/tools/geometry.py b/cellfinder/core/tools/geometry.py → src/cellfinder/core/tools/geometry.py
diff --git a/cellfinder/core/tools/image_processing.py → ...cellfinder/core/tools/image_processing.py b/cellfinder/core/tools/image_processing.py → ...cellfinder/core/tools/image_processing.py
diff --git a/cellfinder/core/tools/prep.py → src/cellfinder/core/tools/prep.py b/cellfinder/core/tools/prep.py → src/cellfinder/core/tools/prep.py
diff --git a/cellfinder/core/tools/source_files.py → src/cellfinder/core/tools/source_files.py b/cellfinder/core/tools/source_files.py → src/cellfinder/core/tools/source_files.py
diff --git a/cellfinder/core/tools/system.py → src/cellfinder/core/tools/system.py b/cellfinder/core/tools/system.py → src/cellfinder/core/tools/system.py
diff --git a/cellfinder/core/tools/tf.py → src/cellfinder/core/tools/tf.py b/cellfinder/core/tools/tf.py → src/cellfinder/core/tools/tf.py
diff --git a/cellfinder/core/tools/tiff.py → src/cellfinder/core/tools/tiff.py b/cellfinder/core/tools/tiff.py → src/cellfinder/core/tools/tiff.py
diff --git a/cellfinder/core/tools/tools.py → src/cellfinder/core/tools/tools.py b/cellfinder/core/tools/tools.py → src/cellfinder/core/tools/tools.py
diff --git a/cellfinder/core/train/__init__.py → src/cellfinder/core/train/__init__.py b/cellfinder/core/train/__init__.py → src/cellfinder/core/train/__init__.py
diff --git a/cellfinder/core/train/train_yml.py → src/cellfinder/core/train/train_yml.py b/cellfinder/core/train/train_yml.py → src/cellfinder/core/train/train_yml.py
diff --git a/cellfinder/core/types.py → src/cellfinder/core/types.py b/cellfinder/core/types.py → src/cellfinder/core/types.py
diff --git a/cellfinder/napari.yaml → src/cellfinder/napari.yaml b/cellfinder/napari.yaml → src/cellfinder/napari.yaml
@@ -1,32 +1,32 @@
-name: cellfinder-napari
+name: cellfinder
 schema_version: 0.1.0
 contributions:
   commands:
-  - id: cellfinder-napari.detect_widget
+  - id: cellfinder.detect_widget
     title: Create Cell detection
     python_name: cellfinder.napari.detect:detect_widget
 
-  - id: cellfinder-napari.training_widget
+  - id: cellfinder.training_widget
     title: Create Train network
     python_name: cellfinder.napari.train:training_widget
 
-  - id: cellfinder-napari.CurationWidget
+  - id: cellfinder.CurationWidget
     title: Create Curation
     python_name: cellfinder.napari.curation:CurationWidget
 
-  - id: cellfinder-napari.SampleData
+  - id: cellfinder.SampleData
     title: Sample data
     python_name: cellfinder.napari.sample_data:load_sample
 
   widgets:
-  - command: cellfinder-napari.detect_widget
+  - command: cellfinder.detect_widget
     display_name: Cell detection
-  - command: cellfinder-napari.training_widget
+  - command: cellfinder.training_widget
     display_name: Train network
-  - command: cellfinder-napari.CurationWidget
+  - command: cellfinder.CurationWidget
     display_name: Curation
 
   sample_data:
   - key: sample
     display_name: Sample data
-    command: cellfinder-napari.SampleData
+    command: cellfinder.SampleData
diff --git a/cellfinder/napari/__init__.py → src/cellfinder/napari/__init__.py b/cellfinder/napari/__init__.py → src/cellfinder/napari/__init__.py
diff --git a/cellfinder/napari/curation.py → src/cellfinder/napari/curation.py b/cellfinder/napari/curation.py → src/cellfinder/napari/curation.py
diff --git a/cellfinder/napari/detect/__init__.py → src/cellfinder/napari/detect/__init__.py b/cellfinder/napari/detect/__init__.py → src/cellfinder/napari/detect/__init__.py
diff --git a/cellfinder/napari/detect/detect.py → src/cellfinder/napari/detect/detect.py b/cellfinder/napari/detect/detect.py → src/cellfinder/napari/detect/detect.py
diff --git a/...finder/napari/detect/detect_containers.py → ...finder/napari/detect/detect_containers.py b/...finder/napari/detect/detect_containers.py → ...finder/napari/detect/detect_containers.py
diff --git a/cellfinder/napari/detect/thread_worker.py → ...cellfinder/napari/detect/thread_worker.py b/cellfinder/napari/detect/thread_worker.py → ...cellfinder/napari/detect/thread_worker.py
diff --git a/cellfinder/napari/images/brainglobe.png → src/cellfinder/napari/images/brainglobe.png b/cellfinder/napari/images/brainglobe.png → src/cellfinder/napari/images/brainglobe.png
diff --git a/cellfinder/napari/input_container.py → src/cellfinder/napari/input_container.py b/cellfinder/napari/input_container.py → src/cellfinder/napari/input_container.py
diff --git a/cellfinder/napari/sample_data.py → src/cellfinder/napari/sample_data.py b/cellfinder/napari/sample_data.py → src/cellfinder/napari/sample_data.py
diff --git a/cellfinder/napari/train/__init__.py → src/cellfinder/napari/train/__init__.py b/cellfinder/napari/train/__init__.py → src/cellfinder/napari/train/__init__.py
diff --git a/cellfinder/napari/train/train.py → src/cellfinder/napari/train/train.py b/cellfinder/napari/train/train.py → src/cellfinder/napari/train/train.py
diff --git a/cellfinder/napari/train/train_containers.py → ...llfinder/napari/train/train_containers.py b/cellfinder/napari/train/train_containers.py → ...llfinder/napari/train/train_containers.py
diff --git a/cellfinder/napari/utils.py → src/cellfinder/napari/utils.py b/cellfinder/napari/utils.py → src/cellfinder/napari/utils.py
diff --git a/tests/napari/test_curation.py b/tests/napari/test_curation.py
@@ -19,7 +19,7 @@ def curation_widget(make_napari_viewer):
     """
     viewer = make_napari_viewer()
     _, widget = viewer.window.add_plugin_dock_widget(
-        plugin_name="cellfinder-napari", widget_name="Curation"
+        plugin_name="cellfinder", widget_name="Curation"
     )
     return widget
 
@@ -103,7 +103,7 @@ def valid_curation_widget(make_napari_viewer) -> CurationWidget:
 
     num_dw = len(viewer.window._dock_widgets)
     _, curation_widget = viewer.window.add_plugin_dock_widget(
-        plugin_name="cellfinder-napari", widget_name="Curation"
+        plugin_name="cellfinder", widget_name="Curation"
     )
     assert len(viewer.window._dock_widgets) == num_dw + 1
 

diff --git a/tests/napari/test_detection.py b/tests/napari/test_detection.py
@@ -21,7 +21,7 @@ def get_detect_widget(make_napari_viewer):
     for layer in load_sample():
         viewer.add_layer(napari.layers.Image(layer[0], **layer[1]))
     _, widget = viewer.window.add_plugin_dock_widget(
-        plugin_name="cellfinder-napari", widget_name="Cell detection"
+        plugin_name="cellfinder", widget_name="Cell detection"
     )
     return widget
 

diff --git a/tests/napari/test_training.py b/tests/napari/test_training.py
@@ -17,7 +17,7 @@ def get_training_widget(make_napari_viewer):
     viewer = make_napari_viewer()
     widget = training_widget()
     _, widget = viewer.window.add_plugin_dock_widget(
-        plugin_name="cellfinder-napari", widget_name="Train network"
+        plugin_name="cellfinder", widget_name="Train network"
     )
     viewer.window.add_dock_widget(widget)
     return widget

diff --git a/tox.ini b/tox.ini
@@ -15,27 +15,15 @@ commands = python -m pytest -v --color=yes
 deps =
     pytest
     pytest-cov
-
-[testenv:core]
-description = Run core tests
-commands = python -m pytest -v --color=yes tests/core
-deps =
     pytest-lazy-fixture
     pytest-mock
     pytest-timeout
-passenv =
-    NUMBA_DISABLE_JIT
-
-[testenv:napari]
-description = Run napari plugin tests
-commands = pytest -v --color=yes --cov=cellfinder --cov-report=xml tests/napari
-deps =
     # Even though napari is a requirement for cellfinder-napari, we have to
     # ensure it is installed with the default Qt backend here.
-    qtpy
     napari[all]
     pytest-qt
 passenv =
+    NUMBA_DISABLE_JIT
     CI
     GITHUB_ACTIONS
     DISPLAY