making $PACKAGES_DIR a local variable and adding warnings about shared...

making $PACKAGES_DIR a local variable and adding warnings about shared variable names at the pipeline level

.gitlab-ci.yml

 
 variables:
-  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
-  PACKAGES_DIR2: "$CI_PROJECT_DIR/packages/"
+  # NOTE, MAKE SURE ANY PIPELINE-LEVEL VARIABLES ARE UNIQUE TO THIS PIPELINE
+  # WHEN CALLED FROM A MULTI-PIPELINE TRIGGER, VARIABLES WITH SHARED NAMES WILL BE OVERWRITTEN
+
   OUTPUT_DIR: "$CI_PROJECT_DIR/outputs/"
 #  OUTPUT_DIR: "/storage/app/EWS_prod/regions/EastAfrica/workspace/"
   TEST_WORKSPACE_DIR: "/storage/app/EWS_prod/regions/EastAfrica/test_workspace/"
@@ -39,9 +40,10 @@ stages:
 .before_script:
   before_script:
 
+      - PACKAGES_DIR="$CI_PROJECT_DIR/packages/"
       - echo "project dir - " $CI_PROJECT_DIR
       - echo "output dir - " $OUTPUT_DIR
-      - echo "packages dir - " $PACKAGES_DIR2
+      - echo "packages dir - " $PACKAGES_DIR
       - echo "pip dir - " $PIP_CACHE_DIR
       - echo "full-fat run date - " $FULL_FAT_RUN_DATE
       - echo "custom full-fat run date - " $CUSTOM_RUN_DATE
@@ -49,31 +51,30 @@ stages:
       - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
       - pip install coverage
       - python3 -V  # Print out python version for debugging
-      - mkdir -p $PACKAGES_DIR2
+      - mkdir -p $PACKAGES_DIR
       - mkdir -p $OUTPUT_DIR
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-source-generation.git" $PACKAGES_DIR2/source_gen
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_plotting.git" $PACKAGES_DIR2/plotting
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/flagdir.git" $PACKAGES_DIR2/flagdir
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-epimodel.git" $PACKAGES_DIR2/epimodel
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-advisory-builder.git" $PACKAGES_DIR2/advisory_builder
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_environmental_suitability_v2.git" $PACKAGES_DIR2/environmental_suitability
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-postprocessing.git" $PACKAGES_DIR2/post_processing
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-met-processing.git" $PACKAGES_DIR2/met_processing
-      - flagdir=$PACKAGES_DIR2/flagdir
-      - epimodel=$PACKAGES_DIR2/epimodel
-      - advisory=$PACKAGES_DIR2/advisory_builder
-      - met_processing=$PACKAGES_DIR2/met_processing
-      - met_processor=$PACKAGES_DIR2/environmental_suitability
-      - met_processor_temp=$PACKAGES_DIR2/environmental_suitability/environmental_suitability
-      - plotting=$PACKAGES_DIR2/plotting
-      - post_processing=$PACKAGES_DIR2/post_processing
-      - source_gen=$PACKAGES_DIR2/source_gen
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-source-generation.git" $PACKAGES_DIR/source_gen
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_plotting.git" $PACKAGES_DIR/plotting
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/flagdir.git" $PACKAGES_DIR/flagdir
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-epimodel.git" $PACKAGES_DIR/epimodel
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-advisory-builder.git" $PACKAGES_DIR/advisory_builder
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_environmental_suitability_v2.git" $PACKAGES_DIR/environmental_suitability
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-postprocessing.git" $PACKAGES_DIR/post_processing
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-met-processing.git" $PACKAGES_DIR/met_processing
+      - flagdir=$PACKAGES_DIR/flagdir
+      - epimodel=$PACKAGES_DIR/epimodel
+      - advisory=$PACKAGES_DIR/advisory_builder
+      - met_processing=$PACKAGES_DIR/met_processing
+      - met_processor=$PACKAGES_DIR/environmental_suitability
+      - plotting=$PACKAGES_DIR/plotting
+      - post_processing=$PACKAGES_DIR/post_processing
+      - source_gen=$PACKAGES_DIR/source_gen
       - coordinator=$CI_PROJECT_DIR/coordinator
       - coordinator_tests=$CI_PROJECT_DIR/tests
       - export PYTHONPATH=$PYTHONPATH:$met_processor_temp:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
       - echo "pythonpath - " $PYTHONPATH
 
-      - ls $PACKAGES_DIR2
+      - ls $PACKAGES_DIR
 
 half_fat_tests:
   when: always