quetzal-crumbs 0.0.15

General utility scripts for Quetzal projects

Quetzal-CRUMBS

General utility scripts for the Quetzal framework projects

Usage in bash

At the present moment the python interfaces are not very stable, and are not really meant to be used directly. I prefer to use Quetzal-CRUMBS in bash scripts when I'm doing ABC-inference or when I'm calibrating my simulations.

Sampling parameters in prior distribution

• Sampling integers (e.g., population size): N=$(python3 -m crumbs.sample "uniform_integer" 10 1000)
• Sampling double (e.g., probability): p=$(python3 -m crumbs.sample "uniform_real" 0.0001 0.1)
• Sampling a coordinate uniformly at random in a geotiff file:
  • latlon=($(python3 -m crumbs.sample "uniform_latlon" "file.tif" | tr -d '[],'))
  • get latitude with ${latlon[0]}
  • get longitude with ${latlon[1]}

Visualizing demographic history:

• If you chose to log the demographic history from Quetzal-EGGS programs (option log-history=history.tif in the EGG configuration file), then you can convert it into an animation using CRUMBS. It is quite handy to check the impact of parameters or suitability on the simulation. The animate function can be called with the following:
  • Default settings (generates an animated gif):
    python3 animate.py --input "animation.tif"
  • Change the output format (detects the mp4 extension and converts accordingly):
    python3 animate.py --input "animation.tif" --output "animation.mp4"
  • Change the colorbar cap value (if none is given then the max value is inferred from the multiband raster):
    python3 animate.py --input "animation.tif" --vmax 100
  • Combination of the previous:
    python3 animate.py --input "animation.tif" --output "animation.mp4" --vmax 100

Updating the package (tip note for the dev)

• 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.

Workflow from https://circleci.com/blog/publishing-a-python-package/.