Cleaning run artifacts

A PyRETIS run leaves a number of generated files and directories behind – log files, the regenerated out.toml / out.rst, restart files, the NNN ensemble directories, the report directory, the infinite-swapping worker* / load directories, Python byte-code caches, and so on. The pyretis clean sub-command removes them so a run (or example) directory can be reset to its committed inputs:

pyretis clean              # clean the current directory
pyretis clean some/dir     # clean another directory
pyretis clean --dry-run    # list what would be removed, delete nothing

pyretis clean deletes immediately; use --dry-run (or -n) first if you want to preview the list.

What is removed

The removed set is the union of a small built-in default and an optional per-directory configuration file. The built-in defaults cover the artifacts every run can leave behind:

  • files: *.pyc, *.pyo, infswap.toml, restart.toml*;

  • directories: __pycache__, load, worker*.

Reference outputs that are committed in some examples (for instance the NNN ensemble directories or an out.toml golden file) are not in the defaults; a directory removes those through its own configuration so a committed input is never deleted by accident. Anything below a results directory is always preserved.

Per-directory configuration

Drop a clean.toml next to the files to extend (or replace) the defaults:

[clean]
use_defaults = true        # apply the built-in defaults (default: true)
find_files = ["out.toml*", "*.log"]   # extra file-name globs (recursive)
find_dirs  = ["report"]               # extra directory names (recursive)
rm_paths   = ["0*", "lammps/system.data"]  # root-relative rm -rf globs
keep       = ["load/0", "load/1"]     # never delete these (or ancestors)

  • find_files – file-name globs deleted wherever they occur in the tree (like find . -name PATTERN -delete).

  • find_dirs – directory names deleted recursively wherever they occur.

  • rm_paths – root-relative paths or globs removed with rm -rf semantics.

  • keep – paths that must survive; a kept path, anything inside it, and its ancestor directories are never removed. Use this to protect committed inputs that would otherwise match (for example the committed load/0 .. load/7 initial paths of the validation suite).

  • use_defaults = false disables the built-in defaults so the file is the complete, explicit recipe.

This replaces the per-example Makefile clean targets used in earlier PyRETIS versions.