trying to get full integrations test working via runner

.gitlab-ci.yml

@@ -54,7 +54,24 @@ stages:
 
 .full_fat_before_script:
   before_script:
-      - CI_PYTHON_PATH="cakebar"
+      - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
+      - pip install coverage
+      - pwd
+      - CODE_DIR="/storage/app/EWS_prod/code/"
+      - flagdir=$CODE_DIR/flagdir
+      - epimodel=$CODE_DIR/epimodel
+      - advisory=$CODE_DIR/advisory_builder
+      - met_processing=$CODE_DIR/met_extractor_v2/met_data_extraction
+      - met_processor=$CODE_DIR/environmental_suitability/environmental_suitability
+      - plotting=$CODE_DIR/plotting/plotting
+      - post_processing=$CODE_DIR/post_processing/ews_postprocessing
+      - source_gen=$CODE_DIR/source_gen
+      - coordinator=$CODE_DIR/coordinator
+      - coordinator_tests=$CODE_DIR/tests
+      - export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
+
+      - echo $PYTHONPATH
+      - CI_PYTHON_PATH=$PYTHONPATH
 
 half_fat_tests:
   when: manual
@@ -110,4 +127,7 @@ manual_job:
     - export PYTHONPATH="$CI_PYTHON_PATH"
     - echo $PYTHONPATH
     - echo "this is a manual job"
+    - full_test_deposition.py --config /storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json \
+      --outdir /storage/app/EWS_prod/regions/EastAfrica/workspace/ \
+      --email_cred /storage/app/EWS_prod/envs/credentials/Cred_gmail.json