Try seg and upload artefacts

.github/workflows/run-algos.yml

@@ -61,4 +61,20 @@ jobs:
         export PIPELINE_NAME="$(basename "${{ matrix.algo }}")"
         
         bash run.sh algos/${PIPELINE_NAME}
-        
+
+    - name: Reconstruct and evaluate
+      run: |
+        #sudo apt-get update
+        #sudo apt-get install python3.10 python3.10-venv python-is-python3 -y
+        #pip install osfclient argparse numpy scikit-learn scikit-image scipy
+        export PATH=$PATH:/home/runnerx/.local/bin
+
+        export PIPELINE_NAME="$(basename "${{ matrix.algo }}")"
+        
+        bash run.sh algos/${PIPELINE_NAME}
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: Segmentation files
+          path: |
+            output/${PIPELINE_NAME}/output.tar.gz

algos/ads_2/main.sh

@@ -23,3 +23,31 @@ pip uninstall h5py
 pip install h5py==2.10.0
 
 py.test --cov AxonDeepSeg/ --cov-report term-missing
+
+# Run on images
+
+git clone https://github.com/axondeepseg/data_ci.git data
+
+cd data
+
+# SEM
+
+cd sem
+
+axondeepseg -t SEM -i image.png
+
+cd ..
+
+# TEM
+
+cd tem
+
+axondeepseg -t TEM -i image.png
+
+cd ..
+
+# Compress
+
+cd ..
+
+tar -zcvf /seg_ci/output.tar.gz data

algos/ads_3/main.sh

@@ -16,3 +16,31 @@ source activate ads_v3
 pip install -e .
 
 py.test --cov AxonDeepSeg/ --cov-report term-missing 
+
+# Run on images
+
+git clone https://github.com/axondeepseg/data_ci.git data
+
+cd data
+
+# SEM
+
+cd sem
+
+axondeepseg -t SEM -i image.png
+
+cd ..
+
+# TEM
+
+cd tem
+
+axondeepseg -t TEM -i image.png
+
+cd ..
+
+# Compress
+
+cd ..
+
+tar -zcvf /seg_ci/output.tar.gz data

algos/ads_4/main.sh

@@ -16,3 +16,31 @@ source activate ads_v4
 pip install -e .
 
 py.test --cov AxonDeepSeg/ --cov-report term-missing 
+
+# Run on images
+
+git clone https://github.com/axondeepseg/data_ci.git data
+
+cd data
+
+# SEM
+
+cd sem
+
+axondeepseg -t SEM --no-patch -i image.png
+
+cd ..
+
+# TEM
+
+cd tem
+
+axondeepseg -t TEM --no-patch -i image.png
+
+cd ..
+
+# Compress
+
+cd ..
+
+tar -zcvf /seg_ci/output.tar.gz data

algos/ads_5/main.sh

@@ -20,3 +20,31 @@ source /home/jovyan/.bashrc
 source ads_conda/bin/activate ads_conda/envs/venv_ads/
 
 py.test --cov AxonDeepSeg/ --cov-report term-missing
+
+# Run on images
+
+git clone https://github.com/axondeepseg/data_ci.git data
+
+cd data
+
+# SEM
+
+cd sem
+
+axondeepseg -i image.png
+
+cd ..
+
+# TEM
+
+cd tem
+
+axondeepseg -i image.png
+
+cd ..
+
+# Compress
+
+cd ..
+
+tar -zcvf /seg_ci/output.tar.gz data