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Documentation update (spring cleaning 2026)#323

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cuddandr wants to merge 8 commits intodevelopfrom
spring-cleaning
Open

Documentation update (spring cleaning 2026)#323
cuddandr wants to merge 8 commits intodevelopfrom
spring-cleaning

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@cuddandr cuddandr commented May 5, 2026

A collection of commits aimed at improving the documentation and organization of the repository.

Highlights include:

  • New Sphinx documentation and GitHub Actions deployment
  • Several very old files were removed from the repository with a copy saved to NERSC DUNE CFS space for record keeping
  • Updated drift velocity default value in consts/detector.py to reduce future confusion
  • Improved warning formatting
  • Updated README
  • General spell check pass and fixed typos

The only code change for larnd-sim itself is in consts/detector.py to update the default drift velocity and fix a bug when calculating DRIFT_MAX_TIME.

- Deleted the unit test workflow since it has not been used ever as a
GitHub action.

- Deleted gitattributes since we do not use Git LFS

- Deleted very old example simulation output.

- Removed execute permissions from a pixel response file.

Remove and rename several ipynb files in examples

- Removed several very old python notebook examples from the repository.
These have been saved on Perlmutter in the DUNE CFS space so they can
still be accessed.

- Renamed a couple notebooks to remove the spaces in their filenames.
Updated all the docstrings in pixels_from_track.py to better include all
the types, add cross-reference links, and in general provide more
information about the function.

Fix a few docstring errors in other functions/files so that Sphinx stops
complaining when building docs.

Fix a couple typos in comments.
Overhauled the Sphinx documentation to have better coverage, improved
organization, and new automation.
The default value for V_DRIFT in consts/detector.py is not the same as
the value calculated using the default E_FIELD and TEMPERATURE.

Change V_DRIFT to match to hopefully reduce confusion when looking at
the values in the file.

Add another calculation of DRIFT_MAX_TIME after V_DRIFT is calculated
using the E_FIELD and TEMPERATURE so it is consistent.
Added a custom warnings format so that the `warnings.warn()` line of
code is no longer printed in addition to the message itself.

Colored warnings yellow using ANSI escape sequences.

Added another custom hook when showing warnings to use tqdm.write() so
that the messages will print on their own line during tqdm wrapped
loops.
Edited and updated the README to correct some outdated information, add
new information (e.g. pixel pedestal configuration), and improve the
readability.

Rewrote the Sphinx `getting_started.rst` page to match the new README.
Fixed various spelling errors / typos in code comments, output
messages, and doc-strings.

No code/variables/etc. were modified.
@cuddandr cuddandr requested a review from mjkramer May 5, 2026 19:41
@cuddandr cuddandr self-assigned this May 5, 2026
@cuddandr cuddandr added the documentation Improvements or additions to documentation label May 5, 2026
Quite a few incorrect references in docstrings that were fixed. Nearly
all of them were using an `array` type as the object annotation.
Needs to be :obj:`numpy.ndarray` (or list) for the reference to be
picked up correctly.

Fixed a couple other docstring issues with the Sphinx referencing.
@cuddandr cuddandr force-pushed the spring-cleaning branch from be899b9 to 8090350 Compare May 5, 2026 20:44
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Very nice!!!

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