rgpycrumbs 0.1.3

A dispatcher-based analytical and visualization suite for chemical physics

Table of Contents

• About
  • CLI Design Philosophy
• Usage
  • CLI Tools
    • EON
• Contributing
  • Release notes
• License

About

A pure-python module of helpful scripts / CLIs I have written mostly for quick and dirty parsing / plotting of optimization methods. Loosely grouped. Not typically optimal at all.

Most of these rely heavily on optional dependencies, with the exception of the _aux helpers (pure Python).

CLI Design Philosophy

The library is designed with the following principles in mind:

• Dispatcher-Based Architecture: The top-level rgpycrumbs.cli command acts as a lightweight dispatcher. It does not contain the core logic of the tools itself. Instead, it parses user commands to identify the target script and then invokes it in an isolated subprocess using the uv runner. This provides a unified command-line interface while keeping the tools decoupled.

• Isolated & Reproducible Execution: Each script is a self-contained unit that declares its own dependencies via PEP 723 metadata. The uv runner uses this information to resolve and install the exact required packages into a temporary, cached environment on-demand. This design guarantees reproducibility and completely eliminates the risk of dependency conflicts between different tools in the collection.

• Lightweight Core, On-Demand Dependencies: The installable rgpycrumbs package is minimal, with its only dependency being the click library for the CLI dispatcher. Heavy scientific libraries like matplotlib are not part of the base installation. They are fetched by uv only when a script that needs them is executed, ensuring the user's base Python environment remains clean and lightweight.

• Modular & Extensible Tooling: Each utility is an independent script. This modularity simplifies development, testing, and maintenance, as changes to one tool cannot inadvertently affect another. New tools can be added to the collection without modifying the core dispatcher logic, making the system easily extensible.

Usage

CLI Tools

The general command structure is:

python -m rgpycrumbs.cli [subcommand-group] [script-name] [script-options]

You can see the list of available command groups:

$ python -m rgpycrumbs.cli --help
Usage: rgpycrumbs [OPTIONS] COMMAND [ARGS]...

  A dispatcher that runs self-contained scripts using 'uv'.

Options:
  --help  Show this message and exit.

Commands:
  eon  Dispatches to a script within the 'eon' submodule.

EON

• Plotting NEB Paths (plt-neb)

  This script visualizes the energy profile of Nudged Elastic Band (NEB) calculations over optimization steps.

  To see the help text for this specific script:

  $ python -m rgpycrumbs eon plt-neb --help
  --> Dispatching to: uv run /path/to/rgpycrumbs/eon/plt_neb.py --help
  Usage: plt_neb.py [OPTIONS]
  
    Plots a series of NEB energy paths from .dat files.
  ...
  Options:
    --input-pattern TEXT      Glob pattern for input data files.
    -o, --output-file PATH    Output file name.
    --start INTEGER           Starting file index to plot (inclusive).
    --end INTEGER             Ending file index to plot (exclusive).
    --help                    Show this message and exit.
  

  To plot a specific range of neb_*.dat files and save the output:

  python -m rgpycrumbs eon plt-neb --start 100 --end 150 -o final_path.pdf
  

  To show the plot interactively without saving:

  python -m rgpycrumbs eon plt-neb --start 280
  

• Splitting CON files (con-splitter)

  This script takes a multi-image trajectory file (e.g., from a finished NEB calculation) and splits it into individual frame files, creating an input file for a new calculation.

  To split a trajectory file:

  rgpycrumbs eon con-splitter neb_final_path.con -o initial_images
  

  This will create a directory named initial_images containing ipath_000.con, ipath_001.con, etc., along with an ipath.dat file listing their paths.

Contributing

All contributions are welcome, but for the CLI tools please follow established best practices.

Release notes

Generally this is a hatch project, so:

uvx hatch test
uvx towncrier build --version "v0.0.4"
git tag -a v0.0.4 -m "Version 0.0.4 release"
uvx hatch build

License

MIT. However, this is an academic resource, so please cite as much as possible via:

• The Zenodo DOI for general use.
• The wailord paper for ORCA usage