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name: cli-and-configuration description: "Use pymatgen command-line tools and persistent configuration safely, including pmg subcommands, POTCAR setup, Materials Project keys, FEFF helpers, and redacted environment probes." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

CLI and Configuration

Use this sub-skill when a task is about pmg, pmg config, pmg analyze, pmg query, pmg plot, pmg structure, pmg view, pmg diff, pmg potcar, get_environment, FEFF plotting console scripts, .pmgrc.yaml, PMG_CONFIG_FILE, PMG_MAPI_KEY, PMG_VASP_PSP_DIR, PMG_POTCAR_CHECKS, PMG_DEFAULT_FUNCTIONAL, or PMG_CP2K_DATA_DIR.

Read First

• Read references/cli-reference.md for exact command flags, file expectations, and safe-versus-mutating command classification.
• Read references/configuration.md before changing .pmgrc.yaml, using PMG_CONFIG_FILE, saving a Materials Project key, configuring POTCAR paths, or generating CP2K data resources.
• Read references/troubleshooting.md when console scripts are missing, config changes are risky, POTCAR resources are unavailable, credentials fail, VASP/FEFF files are absent, plotting is headless, or recursive scans could be dangerous.

Bundled Safe Probes

• Run scripts/pmg_help_probe.py to call only --help for known pymatgen console scripts and pmg subcommands; it does not mutate config, access the network, open GUIs, scan user directories, or touch POTCAR data.
• Run scripts/pymatgen_environment_probe.py for redacted distribution, import, entry-point, and console-script checks; local executable paths are hidden unless the user explicitly asks for private debugging with --reveal-paths.

Safety Policy

• Safe without extra approval: --help checks, redacted import/version checks, and entry-point discovery.
• Ask before running commands that mutate .pmgrc.yaml, create/copy resource files, write POTCAR, save output files, read credentials, access Materials Project, recursively scan calculation directories, open a GUI, or inspect large user directory trees.
• Use pmg plot ... --out_file ... instead of display windows whenever possible, and avoid pmg view on headless systems unless the user confirms visualization support.
• For query semantics and network behavior, route to ../external-data-access/SKILL.md; for VASP/Borg analysis semantics behind pmg analyze, route to ../entries-thermodynamics-and-batteries/SKILL.md; for diffraction, spectra, and plotting interpretation, route to ../spectra-diffraction-and-visualization/SKILL.md; for structure/local-environment interpretation, route to ../structures-local-environments-and-transformations/SKILL.md.