From b1ccb7526d56f78ade0b4ddb2b696f38d2dfce3f Mon Sep 17 00:00:00 2001 From: Michael Dales Date: Fri, 23 Jan 2026 11:46:40 +0000 Subject: [PATCH] Don't rely on virtual env location in docker --- scripts/run.sh | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/scripts/run.sh b/scripts/run.sh index 9c8b6be..71a060a 100755 --- a/scripts/run.sh +++ b/scripts/run.sh @@ -46,6 +46,11 @@ if [ -z "${VIRTUAL_ENV}" ]; then exit 1 fi +PYTHON_BIN=$(command -v python3) +echo "Located Python: ${PYTHON_BIN}" +AOH_CALC_BIN=$(command -v aoh-calc) +echo "Located aoh-calc: ${AOH_CALC_BIN}" + declare -a TAXALIST=("AMPHIBIA" "AVES" "MAMMALIA" "REPTILIA") if [ ! -d "${DATADIR}" ]; then @@ -106,7 +111,7 @@ echo "Generating AoH task list..." python3 ./utils/aoh_generator.py --input "${DATADIR}"/species-info --datadir "${DATADIR}" --output "${DATADIR}"/aohbatch.csv echo "Generating AoHs..." -littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/aohbatch.log -c "${DATADIR}"/aohbatch.csv "${VIRTUAL_ENV}"/bin/aoh-calc +littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/aohbatch.log -c "${DATADIR}"/aohbatch.csv "${AOH_CALC_BIN}" # Calculate predictors from AoHs echo "Generating species richness..." @@ -142,7 +147,7 @@ echo "Generating threat task list..." python3 ./utils/threats_generator.py --input "${DATADIR}"/species-info --datadir "${DATADIR}" --output "${DATADIR}"/threatbatch.csv echo "Generating threat rasters..." -littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/threatbatch.log -c "${DATADIR}"/threatbatch.csv "${VIRTUAL_ENV}"/bin/python3 -- ./threats/threat_processing.py +littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/threatbatch.log -c "${DATADIR}"/threatbatch.csv "${PYTHON_BIN}" -- ./threats/threat_processing.py echo "Summarising threats..." python3 ./threats/threat_summation.py --threat_rasters "${DATADIR}"/threat_rasters --output "${DATADIR}"/threat_results