Snakemake - GRASS GIS interface

Create reproducible and scaleable GRASS workflows

Author:	Michel Wortmannn wortmann@pik-potsdam.de
Version:	v0.1

Requirements

• GRASS >= 7.8
• Snakemake
• Python >= 3.5 (Snakemake requirement)
• tested with Bash

Installation

Latest release:

$ pip install snakemake_grass

Latest development version:

$ git clone git@github.com:mwort/snakemake_grass.git
$ pip install -e ./snakemake_grass/

Rationale

Snakemake is a great way to create reproducible, scaleable and portable computational workflows based on input and output file tracking (Perkel 2019). This presents a challenge for the database approach of GRASS. This Python module provides an interface between the two.

Docs and examples

API documentation

Here is a quick example Snakefile with one wildcard/template rule and two target rules:

from snakemake_grass import GrassLocation, input_to_map, output_to_map

grass_ll = GrassLocation('grassdb', 'lonlat', epsg=4326)

rule new_raster:
    output: grass_ll.raster('new_raster')
    shell: grass_ll('r.mapcalc', exp='new_raster=1')

rule raster_template:
    input: rules.new_raster.output
    output: grass_ll.raster('raster{i}@raster{i}')
    shell:
        grass_ll('r.mapcalc', mapset=output_to_map(),
                 exp='raster{wildcards.i}={wildcards.i}')

rule merged_raster:
    input: grass_ll.rasters('raster{i}@raster{i}', i=range(6))
    output: grass_ll.raster('merged_raster')
    shell:
        grass_ll('r.series', input=[input_to_map(i) for i in range(6)],
                 method='count', output=output_to_map())

Run the last rule on 3 CPUs and create a graph of the workflow:

$ snakemake -j 3 merged_raster
$ snakemake --dag merged_raster | dot -T png -o dag.png

Instead of running r.mapcalc/r.series, it may be more common to actually run entire Bash/Python script but any one command will work. For more examples, see tests/Snakefile.

Tests

Tests are provided in a tests/Snakefile:Snakefile and are run in the tests/ directory like this, e.g. on 3 CPUs:

$ snakemake -j 3 all
$ snakemake clean