# Command Line Interface

This page summarizes all ursa command line functions. With the exception of `ursa initialize`, which expected to be invoked in the directory containing a project directory, all commands are to be invoked within a project directory.

Most commands depend on the output of other commands. The Snakefile documents the order in which commands are typically executed.

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*   - Command
    - Description
*   - [`ursa analyze exposure`](#ursa.analyze.exposure.main)
    - Conduct exposure analysis (experimental).
*   - [`ursa analyze sensitivity --method <method>`](#ursa.analyze.sensitivity.main)
    - Conduct sensitivity analysis (experimental). The only method currently supported is `linear-regression`.
*   - [`ursa clean files`](#ursa.clean.files.main)
    - Clean up files after running simulations is done and quality control is complete.
*   - [`ursa compile dclaw`](#ursa.compile.dclaw.main)
    - Compile [D-Claw](https://doi.org/10.5066/P13GUXUT) and place D-Claw related files in `<project>/assets/compile/dclaw`.
*   - [`ursa export plots`](#ursa.export.plots.main)
    - Compiles and compresses debris-flow simulation index plots into an archive.
*   - [`ursa export shapefile`](#ursa.export.shapefile.main)
    - Export vector outputs to shapefile format and compress into a zip file including a readme.
*   - [`ursa export sciencebase`](#ursa.export.sciencebase.main)
    - Export results to the standard format for a ScienceBase Child item.
*   - [`ursa initialize <name>`](#ursa.initialize.project.main)
    - Initialize project `<name>`. Optionally include `--clean` to have ursa clean up the files at the end of the workflow.
*   - [`ursa plot experiment`](#ursa.plot.experiment.main)
    - Generate all standard results plots.
*   - [`ursa plot benchmark`](#ursa.plot.benchmark.main)
    - Generate plots synthesizing runtime and other run benchmarks.
*   - [`ursa plot sensitivity --method <method>`](#ursa.plot.sensitivity.main)
    - Generates plots of sensitivity analysis. Requires that [`ursa analyze sensitivity  --method <method>`](#ursa.analyze.sensitivity.main) was already run.
*   - [`ursa plot runs`](#ursa.plot.runs.main)
    - Generates plots of depth, arrival time, and momentum flux for each run.
*   - [`ursa postprocess run --run <run-number>`](#ursa.postprocess.run.main)
    - Postprocess run number `<run-number>`.
*   - [`ursa postprocess experiment`](#ursa.postprocess.experiment.main)
    - Postprocess the entire experiment.
*   - [`ursa preprocess evt`](#ursa.preprocess.evt.main)
    - Preprocess vegetation data (default is EVT 230).
*   - [`ursa preprocess topo`](#ursa.preprocess.topo.main)
    - Preprocess topography data (default is 10-m National Elevation Dataset).
*   - [`ursa preprocess region`](#ursa.preprocess.region.main)
    - Preprocess region data (default is HUC12s).
*   - [`ursa preprocess streams`](#ursa.preprocess.streams.main)
    - Preprocess stream data (default is National Hydrologic Dataset)
*   - [`ursa preprocess buildings`](#ursa.preprocess.buildings.main)
    - Preprocess building data (default is from OpenStreetMap).
*   - [`ursa preprocess roads`](#ursa.preprocess.roads.main)
    - Preprocess road data (default is from OpenStreetMap).
*   - [`ursa preprocess basemap`](#ursa.preprocess.basemap.main)
    - Preprocess basemap (default is USGS Topo tiles).
*   - [`ursa preprocess soil`](#ursa.preprocess.soil.main)
    - Preprocess soil data for kf factor (default is STATSGO hosted by USGS ScienceBase).
*   - [`ursa preprocess retainmenst`](#ursa.preprocess.retainments.main)
    - Preprocess retainments (default is from USGS ScienceBase).
*   - [`ursa preprocess recurrences`](#ursa.preprocess.recurrences.main)
    - Preprocess Atlas 14 rainfall information into rainfall recurrence intervals.
*   - [`ursa qc all`](#ursa.qc.all.main)
    - Run all quality control commands.
*   - [`ursa qc courant`](#ursa.qc.courant.main)
    - Quality control all D-Claw simulations based on the maximum observed courant number.
*   - [`ursa qc passfail`](#ursa.qc.passfail.main)
    - Quality control the number of D-Claw simulations that completed successfully.
*   - [`ursa qc timing`](#ursa.qc.timing.main)
    - Generate synthesis commas separated value files describing runtime.
*   - [`ursa qc version`](#ursa.qc.version.main)
    - Identify the version of ursa used and print it to a time-stamped file.
*   - [`ursa reset snakefile`](#ursa.reset.snakefile.main)
    - Resetting the project snakefile to the most up-to-date snakefile in the ursa library.
*   - [`ursa run all`](#ursa.run.all.main)
    - Run the entire ursa workflow.
*   - [`ursa run dclaw --run <run-number> --sim <simulation-number>`](#ursa.run.dclaw.main)
    - Run a specific D-Claw simulation.
*   - [`ursa run wildcat`](#ursa.run.wildcat.main)
    - Run wildcat.
*   - [`ursa run until-wildcat`](#ursa.run.until_wildcat.main)
    - Run ursa workflow until (inclusive) the wildcat stage.
*   - [`ursa setup extent`](#ursa.setup.extent.main)
    - Identify the considered extent and generate key files documenting the location of the project.
*   - [`ursa setup source`](#ursa.setup.source.main)
    - Use the output of wildcat, or other hazard assessment method to determine the locations within delineated basins above which debris-flow material will be placed by `ursa setup dclaw`.  
*   - [`ursa setup experiment`](#ursa.setup.experiment.main)
    - Generate the file structure containing a directory for each run.
*   - [`ursa setup dclaw --run <run-number>`](#ursa.setup.dclaw_run.main)
    - Set up an individual D-Claw run, including breaking it up into simulations by region and generating input files.
*   - [`ursa upload sciencebase`](#ursa.upload.sciencebase.main)
    - Upload exported child item to ScienceBase (requires authentication). Alternatively, add ``ursa upload sciencebase --update_parent_only`` to only update parent metadata.
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