Merge pull request #397 from Dana-Farber-AIOS/dev-onnx

Merge dev_onnx into dev_graph
Dana-Farber-AIOS · Dec 6, 2023 · 44eca15 · 44eca15
2 parents 453e085 + 711f735
commit 44eca15
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diff --git a/.github/workflows/publish-to-docker-hub.yml b/.github/workflows/publish-to-docker-hub.yml
@@ -27,9 +27,10 @@ jobs:
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2.7.0
+        uses: docker/build-push-action@v4 
         with:
           context: .
+          platforms: linux/amd64,linux/arm64  
           push: true
           tags: |
             pathml/pathml:latest

diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml
@@ -40,7 +40,10 @@ jobs:
         auto-activate-base: false
         activate-environment: pathml
         environment-file: environment.yml
-        mamba-version: "*"
+        # mamba-version: "*"
+        miniforge-version: latest
+        use-mamba: true
+        channels: conda-forge
         python-version: ${{ matrix.python-version }}
     - name: Debugging
       run: |

diff --git a/docs/readthedocs-requirements.txt b/docs/readthedocs-requirements.txt
@@ -4,4 +4,4 @@ nbsphinx-link==1.3.0
 sphinx-rtd-theme==1.3.0
 sphinx-autoapi==3.0.0
 ipython==8.10.0
-sphinx-copybutton==0.5.2
+sphinx-copybutton==0.5.2
diff --git a/environment.yml b/environment.yml
@@ -34,4 +34,4 @@ dependencies:
         - loguru==0.5.3
         - pandas==1.5.2 # orig no req
         - torch-geometric==2.3.1
-        - jpype1
+        - jpype1
diff --git a/examples/InferenceOnnx_tutorial.ipynb b/examples/InferenceOnnx_tutorial.ipynb
diff --git a/pathml/__init__.py b/pathml/__init__.py
@@ -1,10 +1,10 @@
 """
-Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine
+Copyright 2023, Dana-Farber Cancer Institute and Weill Cornell Medicine
 License: GNU GPL 2.0
 """
 
 from . import datasets as ds
-from . import ml
+from . import inference, ml
 from . import preprocessing as pp
 from ._logging import PathMLLogger
 from ._version import __version__

diff --git a/pathml/inference/__init__.py b/pathml/inference/__init__.py
@@ -0,0 +1,14 @@
+"""
+Copyright 2023, Dana-Farber Cancer Institute and Weill Cornell Medicine
+License: GNU GPL 2.0
+"""
+
+from .inference import (
+    HaloAIInference,
+    Inference,
+    InferenceBase,
+    RemoteTestHoverNet,
+    check_onnx_clean,
+    convert_pytorch_onnx,
+    remove_initializer_from_input,
+)