PyPNM Cleanup Script

The PyPNM Cleanup Script is a shell utility located in the tools/ directory. It provides a structured way to clean up logs, Python cache files, build artifacts, generated output, internal .data folders related to PNM processing, and Docker artifacts.

Use this tool to reset analysis directories and keep the repository free of stale or generated files.

Features

• Clean specific categories of build and runtime artifacts or perform a full cleanup.
• Support for scoped operations (for example, Python caches only, or PNM data only).
• Can be run from any root directory (defaults to the current directory).
• Uses simple, repeatable patterns for targeted or full cleanup flows.

Directories and Options

The table below summarizes which directories are affected by each option. All paths are resolved relative to the chosen ROOT_DIR.

Option	Description	Directories removed (if present)
--logs	Clean application logs (truncate file, keep inode).	logs/pypnm.log
--python	Clean Python cache artifacts.	**/__pycache__/, **/*.pyc, .pytest_cache/
--build	Clean build and packaging outputs.	build/, dist/, *.egg-info
--pnm	Clean PNM working data and databases.	.data/pnm/, .data/db/
--archive	Clean archive artifacts only.	.data/archive/
--excel	Clean Excel/CSV exports.	.data/xlsx/, .data/csv/
--json	Clean JSON exports.	.data/json/
--plot-data	Clean plotting data and archive artifacts.	.data/png/, .data/csv/, .data/archive/
--msg-rsp	Clean message-response artifacts.	.data/msg_rsp/
--output	Clean high-level output files.	output/
--issues	Clean support bundles (preserves issues/ directory).	issues/ contents
--remove-issues	Remove the entire issues/ directory.	issues/
--settings-backup	Remove system.bak.*.json backups.	src/pypnm/settings/system.bak.*.json
--docker	Clean Docker artifacts.	running containers, stopped containers, unused images, build cache, unused volumes, unused networks
--all	Run every cleanup operation listed above.	All of the above, including destructive Docker cleanup

Usage

./tools/maintenance/clean.sh [OPTIONS] [ROOT_DIR]

• OPTIONS: One or more of the flags listed in the table above. Combine them to target multiple areas (for example, --python --build).

• ROOT_DIR: Optional path that serves as the root of the cleanup operation.
  If omitted, the script uses the current working directory.

Examples

Clean everything under the current directory:

./tools/maintenance/clean.sh --all

This includes destructive Docker cleanup. When Docker artifacts exist, --all now:

1. stops running containers
2. removes containers
3. prunes unused images
4. prunes build cache
5. prunes unused volumes
6. prunes unused networks

Use --all only when you intentionally want a full local reset.

Clean only Python caches and build artifacts:

./tools/maintenance/clean.sh --python --build

Clean PNM data and plot-related data from a specific project root:

./tools/maintenance/clean.sh --pnm --plot-data ~/Projects/PyPNM

Clean message-response artifacts only:

./tools/maintenance/clean.sh --msg-rsp

Clean only Docker artifacts:

./tools/maintenance/clean.sh --docker

Notes

• The script uses set -euo pipefail to fail fast on errors or undefined variables.
• Deletion is performed via a small helper that checks for path existence before removal.
• All directories are interpreted relative to ROOT_DIR, which allows you to point the script at different clones or sandboxes.
• --docker and --all use the Docker cleanup helper under tools/maintenance/docker-cleanup.sh.
• Destructive Docker cleanup can stop and remove running containers. Do not use it on a host with containers you intend to keep running.