nismod/open-gira
Open-data Global Infrastructure Risk/Resilience Analysis
Overview
Topics:
Latest release: v0.3.1, Last update: 2025-02-25
Linting: linting: failed, Formatting:formatting: failed
Deployment
Step 1: Install Snakemake and Snakedeploy
Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.
When using Mamba, run
mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy
to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via
conda activate snakemake
Step 2: Deploy workflow
With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:
mkdir -p path/to/project-workdir
cd path/to/project-workdir
In all following steps, we will assume that you are inside of that directory. Then run
snakedeploy deploy-workflow https://github.com/nismod/open-gira . --tag v0.3.1
Snakedeploy will create two folders, workflow
and config
. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.
Step 3: Configure workflow
To configure the workflow, adapt config/config.yml
to your needs following the instructions below.
Step 4: Run workflow
The deployment method is controlled using the --software-deployment-method
(short --sdm
) argument.
Snakemake will automatically detect the main Snakefile
in the workflow
subfolder and execute the workflow module that has been defined by the deployment in step 2.
For further options such as cluster and cloud execution, see the docs.
Step 5: Generate report
After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using
snakemake --report report.zip
Configuration
The following section is imported from the workflow’s config/README.md
.
This file.
YAML configuration file. This file contains parameters that are frequently modified prior to an analysis. Refer to it for more information.
A lookup table from a land use classification scheme to a typical surface roughness length. This is used in downscaling wind speeds in tropical-cyclone analyses.
snakemake
profile for running open-gira on the University of Oxford's ARC
cluster.
CSV files, one per asset_type
, describing the relationship between hazard
intensity and damage fraction. These are used for direct damage estimation.
Fairly self-explanatory, contains files containing lists of hazard file URLs to acquire for analyses.
Text files for use by osmium to filter features based on tag. We used these to construct infrastructure networks from OpenStreetMap data.
CSV files containing rehabilitation cost estimates in USD. One file per sector,
each row a unique asset_type
.
JSON files, each containing a single list. The list may contain zero or many
unique string storm IDs. These can be used to subset a parent STORM_SET
, e.g.
IBTrACS may be subset to contain just storms that hit Mexico since 2000, if the
relevant storm IDs are provided. Where the list provided is empty, this is
interpreted as "process every storm in the parent set", i.e. all of IBTrACS.
Linting and formatting
Linting results
/tmp/tmpwfoyhgyf/nismod-open-gira-ef81de1/workflow/Snakefile:82: SyntaxWarning: invalid escape sequence '\d'
COST_OR_FRACTION="cost|fraction",
/tmp/tmpwfoyhgyf/nismod-open-gira-ef81de1/workflow/Snakefile:102: SyntaxWarning: invalid escape sequence '\/'
SAMPLE="\d+",
/tmp/tmpwfoyhgyf/nismod-open-gira-ef81de1/workflow/Snakefile:103: SyntaxWarning: invalid escape sequence '\d'
# may be upper or lower, one 'f' or two
/tmp/tmpwfoyhgyf/nismod-open-gira-ef81de1/workflow/Snakefile:105: SyntaxWarning: invalid escape sequence '\/'
ModuleNotFoundError in file /tmp/tmpwfoyhgyf/nismod-open-gira-ef81de1/workflow/Snakefile, line 20:
No module named 'open_gira'
File "/tmp/tmpwfoyhgyf/nismod-open-gira-ef81de1/workflow/Snakefile", line 20, in <module>
Formatting results
[DEBUG]
<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
<unknown>:1: SyntaxWarning: invalid escape sequence '\/'
<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
<unknown>:1: SyntaxWarning: invalid escape sequence '\/'
[DEBUG] In file "/tmp/tmpwfoyhgyf/nismod-open-gira-ef81de1/workflow/Snakefile": Formatted content is different from original
[INFO] 1 file(s) would be changed 😬
snakefmt version: 0.10.2