From 5d1d86fba034a9fb1d40646d301de1267908984a Mon Sep 17 00:00:00 2001 From: lb584 <lb584@cam.ac.uk> Date: Mon, 30 Jan 2023 15:44:56 +0000 Subject: [PATCH] experimenting with manual jobs --- .gitlab-ci.yml | 69 ++++++++++++++++++++++++++------------------------ 1 file changed, 36 insertions(+), 33 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 390399d..002ddb1 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -19,40 +19,41 @@ stages: - half-fat - full-fat -prepare_code: - stage: half-fat - image: lb584/ews_coordinator:latest - script: - - python3 -V # Print out python version for debugging - - echo $PACKAGES_DIR - - mkdir $PACKAGES_DIR - - git clone "https://nouser:$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_data_extraction.git" $PACKAGES_DIR/met_extractor_v2 - - ls $PACKAGES_DIR - - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/ - - pip install coverage - - pwd - - flagdir=$PACKAGES_DIR/flagdir - - epimodel=$PACKAGES_DIR/epimodel - - advisory=$PACKAGES_DIR/advisory_builder - - met_processing=$PACKAGES_DIR/met_extractor_v2/met_data_extraction - - met_processor=$PACKAGES_DIR/environmental_suitability/environmental_suitability - - plotting=$PACKAGES_DIR/plotting/plotting - - post_processing=$PACKAGES_DIR/post_processing/ews_postprocessing - - source_gen=$PACKAGES_DIR/source_gen - - coordinator=$CI_PROJECT_DIR/coordinator - - coordinator_tests=$CI_PROJECT_DIR/tests - - export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests +.half_fat_before_script: + before_script: + stage: half-fat + image: lb584/ews_coordinator:latest + script: + - python3 -V # Print out python version for debugging + - echo $PACKAGES_DIR + - mkdir $PACKAGES_DIR + - git clone "https://nouser:$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_data_extraction.git" $PACKAGES_DIR/met_extractor_v2 + - ls $PACKAGES_DIR + - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/ + - pip install coverage + - pwd + - flagdir=$PACKAGES_DIR/flagdir + - epimodel=$PACKAGES_DIR/epimodel + - advisory=$PACKAGES_DIR/advisory_builder + - met_processing=$PACKAGES_DIR/met_extractor_v2/met_data_extraction + - met_processor=$PACKAGES_DIR/environmental_suitability/environmental_suitability + - plotting=$PACKAGES_DIR/plotting/plotting + - post_processing=$PACKAGES_DIR/post_processing/ews_postprocessing + - source_gen=$PACKAGES_DIR/source_gen + - coordinator=$CI_PROJECT_DIR/coordinator + - coordinator_tests=$CI_PROJECT_DIR/tests + - export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests - - echo $PYTHONPATH - - CI_PYTHON_PATH=$PYTHONPATH - - ls ../ + - echo $PYTHONPATH + - CI_PYTHON_PATH=$PYTHONPATH + - ls ../ .full_fat_before_script: before_script: @@ -61,6 +62,7 @@ prepare_code: half_fat_tests: when: manual stage: half-fat + extends: .half_fat_before_script image: lb584/ews_coordinator:latest needs: ["prepare_code"] @@ -87,6 +89,7 @@ half_fat_tests: half_fat_epi_tests: when: manual stage: half-fat + extends: .half_fat_before_script image: lb584/ews_coordinator:latest needs: ["prepare_code"] -- GitLab