# First CLI Run

This tutorial walks through a first successful `psma` run from a CSV
file using the command-line interface.

## Goal

By the end of the tutorial you will:

- run the PSMA workflow from the CLI
- write the standard artifact set to disk
- know which arguments are required for a SMILES-based run

## Prerequisites

- the package is installed with its runtime dependencies
- your input file is a CSV
- the CSV contains:
  - an endpoint column
  - a SMILES column

## Example command

```bash
pixi run psma run docs/_data/solubility_NCATS-sol.csv \
  --output-dir .tmp/ncats_sol_cli \
  --y-col low_solubility \
  --label-threshold 0.5 \
  --label-direction ge \
  --similarity-method rdkit_morgan_tanimoto \
  --smiles-col canonical_smiles \
  --split-method random
```

## What the command does

The CLI reads the CSV, validates the required columns for the selected
similarity backend, computes the PSMA surface, and writes the standard
artifacts to `--output-dir`.

## Expected outputs

After a successful run, the output directory should contain:

- `train_coords.csv`
- `test_coords.csv`
- `predictions_test.csv`
- `surface_grid.npz`
- `params.json`
- `metrics.json`

## Next steps

- To understand the output files, see [Output Artifacts](../reference/output-artifacts.md).
- To compare split strategies, see [Choose Random vs Butina](../how-to/choose-random-vs-butina.md).