ci: updating actions for bfio (#549)

PolusAI · Jul 12, 2024 · 70b4583 · 70b4583
1 parent 887eff2
commit 70b4583
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diff --git a/.github/workflows/find-all-tools.yml b/.github/workflows/find-all-tools.yml
@@ -20,17 +20,25 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          repository: 'polusai/image-tools'
+          repository: 'PolusAI/image-tools'
           ref: 'master'
       - name: Find tools
         id: set-matrix
         run: |
           # List of directories to ignore
-          ignored_dirs="polus-python-template ftl-label .venv"
+          ignored_dirs="polus-python-template .venv"
 
           # TODO: Remove these after merging PR #547
           # List of tools that are broken for known reasons
-          broken_tools="binary-operations basic-flatfield-estimation microjson-to-ome cell-border-segmentation precompute-slide vector-to-label"
+          broken_tools="binary-operations precompute-slide microjson-to-ome region-segmentation-eval basic-flatfield-estimation ftl-label cell-border-segmentation"
+          # Reasons:
+            # - binary-operations: Not fully updated to new tool standards
+            # - precompute-slide (Najib): Single failing test: 1023_1024_Segmentation_Zarr
+            # - microjson-to-ome (Hamdah): AttributeError: type object 'SerializerConfig' has no attribute '__slots__'
+            # - region-segmentation-eval: Installation error with numba.
+            # - basic-flatfield-estimation: Jax installation error.
+            # - ftl-label: Requires Rust installation. Also, has not been updated to new tool standards.
+            # - cell-border-segmentation (Hamdah): keras.models.load_model() is getting incorrect model format error.
 
           # Initialize variables
           ignored_dirs="$ignored_dirs $broken_tools"

diff --git a/clustering/k-means-clustering-tool/pyproject.toml b/clustering/k-means-clustering-tool/pyproject.toml
@@ -17,6 +17,7 @@ typer = "^0.7.0"
 nyxus = "^0.5.0"
 vaex = "^4.7.0"
 scikit_learn="^1.0.2"
+numpy = "<2.0.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

diff --git a/features/feature-segmentation-eval-tool/.bumpversion.cfg b/features/feature-segmentation-eval-tool/.bumpversion.cfg
diff --git a/features/feature-segmentation-eval-tool/Dockerfile b/features/feature-segmentation-eval-tool/Dockerfile
diff --git a/features/feature-segmentation-eval-tool/README.md b/features/feature-segmentation-eval-tool/README.md
diff --git a/features/feature-segmentation-eval-tool/VERSION b/features/feature-segmentation-eval-tool/VERSION
diff --git a/features/feature-segmentation-eval-tool/build-docker.sh b/features/feature-segmentation-eval-tool/build-docker.sh
diff --git a/features/feature-segmentation-eval-tool/featuresegmentationeval.cwl b/features/feature-segmentation-eval-tool/featuresegmentationeval.cwl
diff --git a/features/feature-segmentation-eval-tool/ict.yaml b/features/feature-segmentation-eval-tool/ict.yaml
diff --git a/features/feature-segmentation-eval-tool/plugin.json b/features/feature-segmentation-eval-tool/plugin.json
diff --git a/features/feature-segmentation-eval-tool/pyproject.toml b/features/feature-segmentation-eval-tool/pyproject.toml