open-gira comes with a few small utilities for data processing and file management.

Removing intermediate files

You can remove intermediate files by running the clean rule.

snakemake --cores 1 -R clean

Geoparquet -> Geopackage

As standard we use the .geoparquet format to store vector data on disk. Unfortunately common GIS software such as QGIS may not yet support this file format. To convert file(s) to geopackage, use:

python workflow/scripts/pq_to_gpkg.py <path_to_geoparquet_1> <path_to_geoparquet_2> <...>

This will write .gpkg files beside their source .geoparquet.

Unpickling interactive plots

matplotlib plots can be interactive (zoom, pan, etc.), but not as static images. Some rules produce pickled plot files. To view these, use:

python workflow/scripts/unpickle_plot.py <path_to_pickled_plot>

Archiving results

The bash script archive_results.sh can be used to back up analysis results. Here's an example usage:

./archive_results.sh results/ /mnt/backup/open-gira

This will create a timestamped folder in path of the second argument, e.g. /mnt/backup/open-gira/2023-07-24T101756+0100, containing an archive of results (excluding input files downloaded from the internet) and a README describing the state of the repository at the time of archive creation.