Skip to content

Don't rely on virtual env location in docker #20

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mdales merged 1 commit into from
Jan 23, 2026
Merged

Don't rely on virtual env location in docker #20

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 7 additions & 2 deletions scripts/run.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 "${DATADIR}" ]; then
Expand Down Expand Up @@ -106,7 +111,7 @@ echo "Generating AoH task list..."
python3 ./utils/aoh_generator.py --input "${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..."
Expand Down Expand Up @@ -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