diff --git a/.github/workflows/run-algos.yml b/.github/workflows/run-algos.yml index 3a0182c..0a31105 100644 --- a/.github/workflows/run-algos.yml +++ b/.github/workflows/run-algos.yml @@ -61,4 +61,20 @@ jobs: export PIPELINE_NAME="$(basename "${{ matrix.algo }}")" bash run.sh algos/${PIPELINE_NAME} - \ No newline at end of file + + - name: Reconstruct and evaluate + run: | + #sudo apt-get update + #sudo apt-get install python3.10 python3.10-venv python-is-python3 -y + #pip install osfclient argparse numpy scikit-learn scikit-image scipy + export PATH=$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 \ No newline at end of file diff --git a/algos/ads_2/main.sh b/algos/ads_2/main.sh index 9e1b0d2..2e83ce2 100644 --- a/algos/ads_2/main.sh +++ b/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 diff --git a/algos/ads_3/main.sh b/algos/ads_3/main.sh index 92d0e85..974ada1 100644 --- a/algos/ads_3/main.sh +++ b/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 \ No newline at end of file diff --git a/algos/ads_4/main.sh b/algos/ads_4/main.sh index aa310f5..a940e05 100644 --- a/algos/ads_4/main.sh +++ b/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 \ No newline at end of file diff --git a/algos/ads_5/main.sh b/algos/ads_5/main.sh index 6541827..66289f4 100644 --- a/algos/ads_5/main.sh +++ b/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 \ No newline at end of file