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Fixes for scripts #38

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Merged
mdales merged 1 commit into from
Sep 24, 2025
Merged

Fixes for scripts #38

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6 changes: 3 additions & 3 deletions scripts/run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,7 @@ fi
# Get species data per taxa from IUCN data
for TAXA in "${TAXAS[@]}"
do
if [ ! -f "${DATADIR}"/overrides.csv ]; then
if [ -f "${DATADIR}"/overrides.csv ]; then
python3 ./prepare_species/extract_species_psql.py --class "${TAXA}" \
--output "${DATADIR}"/species-info/"${TAXA}"/ \
--projection "EPSG:4326" \
Expand All @@ -259,7 +259,7 @@ python3 ./utils/persistencegenerator.py --datadir "${DATADIR}" \
--scenarios "${SCENARIOS[@]}"

# Calculate all the AoHs
littlejohn -j 700 -o "${DATADIR}"/aohbatch.log -c "${DATADIR}"/aohbatch.csv aoh-calc -- --force-habitat
littlejohn -j 30 -o "${DATADIR}"/aohbatch.log -c "${DATADIR}"/aohbatch.csv "${VIRTUAL_ENV}"/bin/aoh-calc -- --force-habitat

# Generate validation summaries
aoh-collate-data --aoh_results "${DATADIR}"/aohs/current/ --output "${DATADIR}"/aohs/current.csv
Expand All @@ -277,7 +277,7 @@ aoh-endemism --aohs_folder "${DATADIR}"/aohs/current/ \
--output "${DATADIR}"/predictors/endemism.tif

# Calculate the per species Delta P values
littlejohn -j 200 -o "${DATADIR}"/persistencebatch.log -c "${DATADIR}"/persistencebatch.csv "${VIRTUAL_ENV}"/bin/python3 -- ./deltap/global_code_residents_pixel.py
littlejohn -j 30 -o "${DATADIR}"/persistencebatch.log -c "${DATADIR}"/persistencebatch.csv "${VIRTUAL_ENV}"/bin/python3 -- ./deltap/global_code_residents_pixel.py

for SCENARIO in "${SCENARIOS[@]}"
do
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