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Draft PR for debugging CI failures #1397

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e2a7d1c
comment out scpca data parts for temporary testing
sjspielman Apr 3, 2026
6b3cb52
add debugging step
sjspielman Apr 3, 2026
4746e09
rip out Rhtslib install
sjspielman Apr 3, 2026
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48 changes: 29 additions & 19 deletions .github/workflows/run_doublet-detection.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,18 +41,27 @@ jobs:
- name: Checkout repo
uses: actions/checkout@v4

- name: Download test data in SCE format
env:
# Use all samples for testing unless this is triggered by a PR, in which case only use a subset of samples for faster testing
# A single sample (or combination of samples for multiplexed data) was chosen for each ScPCA project as:
# Unless otherwise stated, the first sample ID in the given project
# For the multiplexed project SCPCP000009, set of samples `SCPCS000133,SCPCS000134,SCPCS000135,SCPCS000136` (this group of samples has 2 associated libraries). Only `SCPCS000133` is specified in the SAMPLES string here.
# For the project SCPCP000011, the sample SCPCS000435 was specifically selected as an edge case sample with <10 cells
SAMPLES: ${{ github.event_name != 'pull_request' && 'all' || 'SCPCS000001,SCPCS000024,SCPCS000050,SCPCS000101,SCPCS000124,SCPCS000133,SCPCS000168,SCPCS000216,SCPCS000246,SCPCS000250,SCPCS000298,SCPCS000435,SCPCS000481,SCPCS000484,SCPCS000490,SCPCS000502,SCPCS000514,SCPCS000616,SCPCS000632,SCPCS000758' }}

- name: Debug R environment
run: |
conda activate openscpca-doublet-detection
./download-data.py --test-data --format SCE --samples ${SAMPLES}
Rscript -e ".libPaths()"
Rscript -e "find.package('xfun')"
Rscript -e "packageVersion('xfun')"
echo "R_LIBS_USER: $R_LIBS_USER"
echo "R_LIBS: $R_LIBS"
echo "R_LIBS_SITE: $R_LIBS_SITE"

# - name: Download test data in SCE format
# env:
# # Use all samples for testing unless this is triggered by a PR, in which case only use a subset of samples for faster testing
# # A single sample (or combination of samples for multiplexed data) was chosen for each ScPCA project as:
# # Unless otherwise stated, the first sample ID in the given project
# # For the multiplexed project SCPCP000009, set of samples `SCPCS000133,SCPCS000134,SCPCS000135,SCPCS000136` (this group of samples has 2 associated libraries). Only `SCPCS000133` is specified in the SAMPLES string here.
# # For the project SCPCP000011, the sample SCPCS000435 was specifically selected as an edge case sample with <10 cells
# SAMPLES: ${{ github.event_name != 'pull_request' && 'all' || 'SCPCS000001,SCPCS000024,SCPCS000050,SCPCS000101,SCPCS000124,SCPCS000133,SCPCS000168,SCPCS000216,SCPCS000246,SCPCS000250,SCPCS000298,SCPCS000435,SCPCS000481,SCPCS000484,SCPCS000490,SCPCS000502,SCPCS000514,SCPCS000616,SCPCS000632,SCPCS000758' }}
#
# run: |
# conda activate openscpca-doublet-detection
# ./download-data.py --test-data --format SCE --samples ${SAMPLES}

- name: Run doublet-detection module on benchmark test data
run: |
Expand All @@ -61,11 +70,12 @@ jobs:
test=1 ./run_doublet-detection-benchmark.sh

# Note that this step uses only R, so we don't need to activate the conda environment
- name: Run doublet-detection module on ScPCA test data
run: |
projects=$(basename -a data/current/SCPCP*)

cd ${MODULE_PATH}
for project in $projects; do
./run_doublet-detection-scpca.sh $project
done
#- name: Run doublet-detection module on ScPCA test data
# run: |
# projects=$(basename -a data/current/SCPCP*)
#
# cd ${MODULE_PATH}
# for project in $projects; do
# ./run_doublet-detection-scpca.sh $project
# done
#
2 changes: 0 additions & 2 deletions analyses/doublet-detection/Dockerfile
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Expand Up @@ -59,8 +59,6 @@ RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc
# Copy the renv.lock file from the host environment to the image
COPY renv.lock renv.lock

# Install Rhtslib first to prevent package installation errors
RUN Rscript -e 'BiocManager::install("Rhtslib")'

# restore from renv.lock file and clean up to reduce image size
RUN Rscript -e 'renv::restore()' \
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