Updated the run_test.sh script
kaguillera
parent
303d1472ed
commit
f4206abc4b
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@ -69,7 +69,7 @@ jobs:
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- "$RENV_PATHS_ROOT"
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- "$TRAVIS_BUILD_DIR/renv/library"
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script:
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- bash tests/scripts/run_tests.sh
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- bash tests/scripts/run_tests.sh all test
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- stage: deploy
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name: Python 3.7 on Xenial Linux Docker
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os: linux
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@ -3,55 +3,168 @@
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echo Setting up for testing...
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# Uncomment the section below if neccessary to remove old files when testing locally
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# echo deleting old data...
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# rm -rf data/raw/*
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# rm -rf data/processed/*
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# rm -rf data/interim/*
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# rm -rf data/external/test*
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clean_old_data() {
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echo deleting old data...
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rm -rf data/processed/*
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rm -rf data/interim/*
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# echo Backing up preprocessing...
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# cp rules/preprocessing.smk bak
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}
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run_periodic_pipeline() {
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echo Running RAPIDS Pipeline periodic segment on testdata...
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snakemake --profile tests/settings/periodic/
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echo Moving produced data from previous pipeline run ...
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mkdir data/processed/features/periodic
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mv data/processed/features/test* data/processed/features/periodic/
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rm -rf data/interim/*
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}
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run_frequency_pipeline() {
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echo Running RAPIDS Pipeline frequency segment on testdata...
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snakemake --profile tests/settings/frequency/
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echo Moving produced data from previous pipeline run...
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mkdir data/processed/features/frequency
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mv data/processed/features/test* data/processed/features/frequency/
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}
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run_periodic_test() {
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echo Running tests on periodic data produced...
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python -m unittest discover tests/scripts/ -v
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echo Re-writing the config file being loaded for testing
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sed -e 's/tests\/settings\/[a-z]*\/testing_config\.yaml/tests\/settings\/periodic\/testing_config\.yaml/' tests/scripts/test_sensor_features.py > test_tmp
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mv test_tmp tests/scripts/test_sensor_features.py
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}
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run_frequency_test() {
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# echo Backing up Testing script...
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# cp tests/scripts/test_sensor_features.py test_bak
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echo Re-writing the config file being loaded for testing
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sed -e 's/tests\/settings\/[a-z]*\/testing_config\.yaml/tests\/settings\/frequency\/testing_config\.yaml/' tests/scripts/test_sensor_features.py > test_tmp
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mv test_tmp tests/scripts/test_sensor_features.py
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echo Running tests on frequency data produced...
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python -m unittest discover tests/scripts/ -v
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}
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display_usage() {
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echo "Usage: run_test.sh [-l] all | periodic | frequency [test]"
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}
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echo Copying files...
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cp -r tests/data/raw/* data/raw
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cp tests/data/external/* data/external
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# Uncomment the section below to backup snakemake file when testing locally
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# echo Backing up preprocessing...
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# cp rules/preprocessing.smk bak
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echo Disabling downloading of dataset...
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sed -e '27,39 s/^/#/' -e 's/rules.download_dataset.output/"data\/raw\/\{pid\}\/\{sensor\}_raw\.csv"/' rules/preprocessing.smk > tmp
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cp tmp rules/preprocessing.smk
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mv tmp rules/preprocessing.smk
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echo Running RAPIDS Pipeline periodic segment on testdata...
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snakemake --profile tests/settings/periodic/
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echo $#
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echo Moving produced data from previous pipeline run ...
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# rm -rf data/raw/*
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mkdir data/processed/features/periodic
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mv data/processed/features/test* data/processed/features/periodic/
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rm -rf data/interim/*
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# rm -rf data/external/test*
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echo Running RAPIDS Pipeline frequnecy segment on testdata...
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snakemake --profile tests/settings/frequency/
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echo Moving produced data from previous pipeline run...
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mkdir data/processed/features/frequency
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mv data/processed/features/test* data/processed/features/frequency/
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echo Running tests on periodic data produced...
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python -m unittest discover tests/scripts/ -v
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echo Backing up Testing script...
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cp tests/scripts/test_sensor_features.py test_bak
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echo Re-writing the config file being loaded for testing
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sed -e 's/tests\/settings\/periodic\/testing_config\.yaml/tests\/settings\/frequency\/testing_config\.yaml/' tests/scripts/test_sensor_features.py > test_tmp
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cp test_tmp tests/scripts/test_sensor_features.py
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echo Running tests on frequency data produced...
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python -m unittest discover tests/scripts/ -v
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if [ $# -eq 1 ]
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then
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if [ $1 == '-l' ] || [ $1 == 'test' ]
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then
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display_usage
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elif [ $1 == 'all' ]
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then
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run_periodic_pipeline
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run_frequency_pipeline
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elif [ $1 == 'periodic' ]
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then
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run_periodic_pipeline
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elif [ $1 == 'frequency' ]
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then
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run_frequency_pipeline
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else
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display_usage
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fi
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elif [ $# -gt 1 ]
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then
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if [ $1 == '-l' ]
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then
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clean_old_data
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if [ $2 == 'all' ]
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then
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run_periodic_pipeline
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run_frequency_pipeline
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if [ $# -gt 2 ] && [ $3 == 'test' ]
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then
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run_periodic_test
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run_frequency_test
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else
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display_usage
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fi
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elif [ $2 == 'periodic' ]
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then
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run_periodic_pipeline
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if [ $# -gt 2 ] && [ $3 == 'test' ]
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then
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run_periodic_test
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else
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display_usage
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fi
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elif [ $2 == 'frequency' ]
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then
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run_frequency_pipeline
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if [ $# -gt 2 ] && [ $3 == 'test' ]
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then
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run_frequency_test
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else
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display_usage
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fi
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else
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display_usage
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fi
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elif [ $1 == 'all' ]
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then
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run_periodic_pipeline
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run_frequency_pipeline
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if [ $2 == 'test' ]
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then
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run_periodic_test
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run_frequency_test
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else
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display_usage
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fi
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elif [ $1 == 'periodic' ]
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then
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run_periodic_pipeline
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if [ $2 == 'test' ]
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then
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run_periodic_test
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else
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display_usage
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fi
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elif [ $1 == 'frequency' ]
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then
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run_frequency_pipeline
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if [ $2 == 'test' ]
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then
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run_frequency_test
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else
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display_usage
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fi
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else
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display_usage
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fi
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else
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display_usage
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fi
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mv bak rules/preprocessing.smk
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# Uncomment to return snakemake back to the original version when testing locally
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# echo Cleaning up...
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# mv bak rules/preprocessing.smk
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@ -2,4 +2,4 @@ directory: ./
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configfile: ./tests/settings/frequency/testing_config.yaml
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snakefile: ./tests/Snakefile
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cores: 1
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forcerun: [join_features_from_providers]
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forcerun: [compute_day_segments, join_features_from_providers]
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@ -2,4 +2,4 @@ directory: ./
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configfile: ./tests/settings/periodic/testing_config.yaml
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snakefile: ./tests/Snakefile
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cores: 1
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forcerun: [join_features_from_providers]
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forcerun: [compute_day_segments, join_features_from_providers]
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