General utility scripts for Quetzal projects
Project description
Quetzal-CRUMBS
General utility scripts for the Quetzal framework projects
# Usage in bash
Sampling parameters in prior distribution:
Sampling integers (eg population size): N=$(python3 -m crumbs.sample "uniform_integer" 10 1000)
Sampling double (eg probability): p=$(python3 -m crumbs.sample "uniform_real" 0.0001 0.1)
Sampling coordinate in a landscape (geotiff): latlon=($(python3 -m crumbs.sample "uniform_latlon" "suitability.tif" | tr -d '[],'))
- get latitude with
${latlon[0]}
- get longitude with
${latlon[1]}
To visualize the parameter space:
What parameters lead to simulation that failed?
ids=$(python3 -m crumbs.get_simulations_ID "output.db", "quetzal_EGG_1", failed=True)
What parameters lead to successful simulations?
ids=$(python3 -m crumbs.get_simulations_ID "output.db", "quetzal_EGG_1", failed=False)
for i in ids
do
s=$(python3 -m crumbs.sample "uniform_real" 0.00025 0.0000025)
python3 -m crumbs.simulate_sequences \
--database "output.db" \
--table "quetzal_EGG_1" \
--rowid $i\
--sequence_size 1041 \
--scale_tree $s \
--output "pods/phylip/EGG1_pod_"$i".phyl"
python3 -m crumbs.phylip2arlequin \
--input "pods/phylip/EGG1_pod_"$i".phyl" \
--imap "imap.txt" \
--output "pods/arlequin/EGG1_pod_"$i".arp"
if [ $i -eq 1 ]; then
./arlsumstat3522_64bit "pods/arlequin/EGG1_pod_"$i".arp" outSS 0 1 run_silent
else
./arlsumstat3522_64bit "pods/arlequin/EGG1_pod_"$i".arp" outSS 1 0 run_silent
fi
rm "pods/arlequin/EGG1_pod_"$i".res" -r
Updating the package
From https://circleci.com/blog/publishing-a-python-package/ :
- Create a
feature
branch, make updates to it. - Test the feature
- Bump the version in
setup.cfg
- Bump the version of the
whl
file in.circleci/config.yml
- Update the ChangeLog
- Push to GitHub
When you have a successful build on https://app.circleci.com/pipelines/github/Becheler/quetzal-CRUMBS:
- create a Pull Request (PR) to the develop branch
- Merge the PR if it looks good.
- When that build succeeds, create a PR to the main branch, review it, and merge.
- Go get a beer and bless this new version with some luuuv.
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