Merge pull request #212 from thodkatz/update-dependencies

Update submodules to the latest changes

.gitignore

@@ -8,4 +8,3 @@ tiktorch/__pycache/
 /#wrapper.py#
 /.#wrapper.py#
 .py~
-unet_sample.zip

README.md

@@ -18,7 +18,7 @@ Reasons to install the server component:
 
 We have a how-to for the set up of a tiktorch prediction server (powerful machine with nvidia GPU) to connect to from your client (e.g. ilastik on a laptop): [Installation](#installation).
 
-If you are interested in running Model Zoo networks from Python directly, have a look at [`bioimageio.core`](https://github.com/bioimage-io/core-bioimage-io-python), where we have an [example notebook](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/bioimageio-core-usage.ipynb) to get you started.
+If you are interested in running Model Zoo networks from Python directly, have a look at [`bioimageio.core`](https://github.com/bioimage-io/core-bioimage-io-python), where we have an [example notebook](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_usage.ipynb) to get you started.
 
 
 ## Installation

conda-recipe/meta.yaml

@@ -55,6 +55,7 @@ test:
     - python 3.9.*
     - pytest
     - pytest-grpc
+    - pytest-timeout
     - cpuonly
     - ilastik-pytorch-version-helper-cpu
   imports:

environment.yml

@@ -48,6 +48,7 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-grpc
+  - pytest-timeout
   - bump2version
   - mypy
   - pre_commit

proto/inference.proto

@@ -2,6 +2,7 @@ syntax = "proto3";
 
 service Inference {
   rpc CreateModelSession(CreateModelSessionRequest) returns (ModelSession) {}
+
   rpc CloseModelSession(ModelSession) returns (Empty) {}
 
   rpc CreateDatasetDescription(CreateDatasetDescriptionRequest) returns (DatasetDescription) {}
@@ -56,34 +57,6 @@ message NamedFloats {
 }
 
 
-/* InputShape will always be expected to have `shape` set.
- * For `ShapeType` PARAMETRIZED, also a `stepShape` has to be given.
- * ref: https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/model_spec_latest.md */
-message InputShape {
-  enum ShapeType {
-    EXPLICIT = 0;
-    PARAMETRIZED = 1;
-  }
-
-  ShapeType shapeType = 1;
-  // shape is min, when PARAMETRIZED
-  NamedInts shape = 2;
-  NamedInts stepShape = 4;
-}
-
-message OutputShape {
-  enum ShapeType {
-    EXPLICIT = 0;
-    IMPLICIT = 1;
-  }
-  ShapeType shapeType = 1;
-  NamedInts shape = 2;
-  NamedInts halo = 3;
-  string referenceTensor = 4;
-  NamedFloats scale = 5;
-  NamedFloats offset = 6;
-}
-
 message ModelSession {
   string id = 1;
 }
@@ -136,19 +109,8 @@ message PredictResponse {
 
 message Empty {}
 
-
 service FlightControl {
   rpc Ping(Empty) returns (Empty) {}
   rpc Shutdown(Empty) returns (Empty) {}
 }
 
-message ModelInfo {
-    repeated string deviceIds = 1;
-}
-
-message CreateModelSessionChunkedRequest {
-  oneof data {
-    ModelInfo info = 1;
-    Blob chunk = 2;
-  }
-}

pytest.ini

@@ -1,6 +1,7 @@
 [pytest]
 python_files = test_*.py
 addopts =
+    --timeout 10
     -v
     -s
     --color=yes

setup.py

@@ -27,8 +27,8 @@
     ],
     packages=find_packages(exclude=["tests"]),  # Required
     install_requires=[
-        "bioimageio.spec==0.4.9.post5",
-        "bioimageio.core==0.5.11",
+        "bioimageio.spec==0.5.3.2",
+        "bioimageio.core==0.6.8",
         "grpcio>=1.31",
         "numpy<2",  # pytorch 2.2.2-py3.9_0 for macos is compiled with numpy 1.*
         "protobuf",