Write output to logs and notebooks subfolders

.gitlab-ci.yml

@@ -115,7 +115,7 @@ create-conda-environment:
     - GIT_REV=$(git rev-parse --short HEAD)
     - export OUTPUT_DIR=${DATAPKG_OUTPUT_DIR}/${CI_PROJECT_NAME}/${CI_COMMIT_REF_SLUG}/${CI_JOB_NAME}/${GIT_REV}
     - if [[ -d ${OUTPUT_DIR} ]] ; then echo "OUTPUT_DIR '${OUTPUT_DIR}' already exists!" ; exit -1 ; fi
-    - mkdir -p "${OUTPUT_DIR}"
+    - mkdir -p "${OUTPUT_DIR}" "${OUTPUT_DIR}/logs" "${OUTPUT_DIR}/notebooks"
     - echo "export OUTPUT_DIR=${OUTPUT_DIR}" | tee -a env.sh
 
 .sbatch: &sbatch
@@ -127,7 +127,7 @@ create-conda-environment:
       [email protected]
       --mail-type=ALL
       --chdir=`pwd`
-      --output=${OUTPUT_DIR}/sbatch-${CI_JOB_ID}-%N-%A-%a.log
+      --output=${OUTPUT_DIR}/logs/sbatch-${CI_JOB_ID}-%N-%A-%a.log
       --export=ALL
       --wait
       ${SBATCH_ARGS}

scripts/qsub.sh

@@ -63,7 +63,7 @@ if [[ -n ${INTERACTIVE} ]] ; then
 else
     python ${SLURM_SUBMIT_DIR}/scripts/execute_notebook.py \
         -i ./notebooks/${NOTEBOOK_NAME}.ipynb \
-        -o "${OUTPUT_DIR}/${NOTEBOOK_NAME}${EXTENSION}.html"
+        -o "${OUTPUT_DIR}/notebooks/${NOTEBOOK_NAME}${EXTENSION}.html"
 fi
 
 # Alternatively, we can use the CLI