Fix bioimageio apps

bioimage-io · May 6, 2024 · 8728d46 · 8728d46
1 parent 2bcb2eb
commit 8728d46
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Showing 19 changed files with 5 additions and 3 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,2 +1,4 @@
 include environments/*
-recursive-include apps
+recursive-include bioimageio/apps
+global-exclude *.pyc
+global-exclude *__pycache__*
diff --git a/apps/cellpose/README.md → bioimageio/apps/cellpose/README.md b/apps/cellpose/README.md → bioimageio/apps/cellpose/README.md
diff --git a/apps/cellpose/cellpose-predict/1/model.py → ...apps/cellpose/cellpose-predict/1/model.py b/apps/cellpose/cellpose-predict/1/model.py → ...apps/cellpose/cellpose-predict/1/model.py
diff --git a/...llpose/cellpose-predict/1/pyodide_test.py → ...llpose/cellpose-predict/1/pyodide_test.py b/...llpose/cellpose-predict/1/pyodide_test.py → ...llpose/cellpose-predict/1/pyodide_test.py
diff --git a/apps/cellpose/cellpose-predict/config.pbtxt → ...ps/cellpose/cellpose-predict/config.pbtxt b/apps/cellpose/cellpose-predict/config.pbtxt → ...ps/cellpose/cellpose-predict/config.pbtxt
diff --git a/...lpose-train/1/build_bioimageio_package.py → ...lpose-train/1/build_bioimageio_package.py b/...lpose-train/1/build_bioimageio_package.py → ...lpose-train/1/build_bioimageio_package.py
diff --git a/.../cellpose-train/1/interactive_cellpose.py → .../cellpose-train/1/interactive_cellpose.py b/.../cellpose-train/1/interactive_cellpose.py → .../cellpose-train/1/interactive_cellpose.py
diff --git a/apps/cellpose/cellpose-train/1/model.py → ...o/apps/cellpose/cellpose-train/1/model.py b/apps/cellpose/cellpose-train/1/model.py → ...o/apps/cellpose/cellpose-train/1/model.py
diff --git a/apps/cellpose/cellpose-train/1/predict.py → ...apps/cellpose/cellpose-train/1/predict.py b/apps/cellpose/cellpose-train/1/predict.py → ...apps/cellpose/cellpose-train/1/predict.py
diff --git a/...e/cellpose-train/1/test_cellpose_train.py → ...e/cellpose-train/1/test_cellpose_train.py b/...e/cellpose-train/1/test_cellpose_train.py → ...e/cellpose-train/1/test_cellpose_train.py
diff --git a/.../cellpose/cellpose-train/1/test_native.py → .../cellpose/cellpose-train/1/test_native.py b/.../cellpose/cellpose-train/1/test_native.py → .../cellpose/cellpose-train/1/test_native.py
diff --git a/.../cellpose/cellpose-train/1/test_triton.py → .../cellpose/cellpose-train/1/test_triton.py b/.../cellpose/cellpose-train/1/test_triton.py → .../cellpose/cellpose-train/1/test_triton.py
diff --git a/apps/cellpose/cellpose-train/config.pbtxt → ...apps/cellpose/cellpose-train/config.pbtxt b/apps/cellpose/cellpose-train/config.pbtxt → ...apps/cellpose/cellpose-train/config.pbtxt
diff --git a/apps/cellpose/main.py → bioimageio/apps/cellpose/main.py b/apps/cellpose/main.py → bioimageio/apps/cellpose/main.py
diff --git a/apps/cellpose/manifest.yaml → bioimageio/apps/cellpose/manifest.yaml b/apps/cellpose/manifest.yaml → bioimageio/apps/cellpose/manifest.yaml
diff --git a/apps/imagej/main.py → bioimageio/apps/imagej/main.py b/apps/imagej/main.py → bioimageio/apps/imagej/main.py
diff --git a/apps/imagej/manifest.yaml → bioimageio/apps/imagej/manifest.yaml b/apps/imagej/manifest.yaml → bioimageio/apps/imagej/manifest.yaml
diff --git a/apps/imagej/run_imagej.py → bioimageio/apps/imagej/run_imagej.py b/apps/imagej/run_imagej.py → bioimageio/apps/imagej/run_imagej.py
diff --git a/bioimageio/engine/app_loader.py b/bioimageio/engine/app_loader.py
@@ -24,7 +24,7 @@ async def run(self, server):
         if self.runtime == AppRuntime.python:
             assert self.entrypoint
 
-            file_path = Path(__file__).parent.parent.parent / "apps" / self.id / self.entrypoint
+            file_path = Path(__file__).parent.parent.parent / "bioimageio/apps" / self.id / self.entrypoint
             module_name = 'bioimageio.engine.apps.' + self.id.replace('-', '_')
             spec = importlib.util.spec_from_file_location(module_name, file_path)
             module = importlib.util.module_from_spec(spec)
@@ -37,7 +37,7 @@ async def run(self, server):
 
 def load_apps():
     current_dir = Path(__file__).parent
-    apps_dir = current_dir.parent.parent / "apps"
+    apps_dir = current_dir.parent.parent / "bioimageio/apps"
     # list folders under apps_dir
     apps = {}
     for app_dir in apps_dir.iterdir():