Ignore the .h5 files generated by the scripts

[michakraus]

scripts/symplectic_autoencoders/integration.jl writes a 7.9 MiB snapshot_matrix.h5 into the
source tree on every run, and .gitignore did not cover it. The script passes a bare relative name
to h5open, so the file lands in the process working directory — at the repository root when the
script is run from there, or in the script's own directory when run from there. Two anchored rules
cover both, and the six committed network weights under docs/src/tutorials/ stay tracked.

Sub-task T3 of Tasks/Restructure the GeometricMachineLearning test and script trees.md.

Note what this does and does not do: the script still writes the file on every run, and deleting it
is still manual. What changed is that git status no longer reports it.

Pre-PR verification

Fixed

• .gitignore:15 — dropped the trailing full stop from the block's header comment, which the file's other ten header comments do not carry.

Unresolved — none.

Pre-existing, adjacent — none fixed. scripts/symplectic_autoencoders/integration.jl passes a bare relative file name to h5open; changing that is a behaviour decision, and training.jl and plot_waves.jl read the same bare name.

Checked and clean

• Pattern behaviour, with git check-ignore -v: snapshot_matrix.h5 and snapshot_matrix2.h5 at the root match /snapshot_matrix*.h5; scripts/**/*.h5 matches at every depth under scripts/, including directly in it; docs/src/tutorials/sae_parameters.h5 and a hypothetical seventh weight file there are not ignored. git ls-files -c -i --exclude-standard is empty — no tracked file became ignored.
• No workflow under .github/ references .h5.
• Comment tense: both .gitignore comment blocks describe the rules as they are, and carry no history markers.
• Changelog accuracy: the 7.9 MiB figure re-derives exactly (260×4000 Float64 = 8 320 000 B = 7.9346 MiB) from Ñ = 128, n_params = 20, n_time_steps = 200; p_zero = false as committed; the six tracked weight files are exactly those named, and all six are loaded from @setup or @example blocks in the two tutorials. The entry sits under ### Fixed within ## [Unreleased] — 0.8.0, both existing headings.

Not checked

• Type piracy, type instability, allocations, imports, fatou lint, the load test and the test suite: not applicable — the diff contains no Julia source.
• Doctests: not applicable — the diff touches no file under docs/.
• Whether another Julia job was running: ps is blocked in the sandbox. No measured point depended on it.

Verification

integration.jl was run in an isolated process both ways — from the repository root, and with
its own directory as the working directory — each writing 8,322,056 bytes. After each run
git status --short was empty, and git ls-files '*.h5' returned the same six
docs/src/tutorials/ weights before and after the change.

The one counterfactual claim the changelog makes — that a bare *.h5 would leave the six tracked
weights alone but would make git add refuse a seventh — was reproduced in a throwaway repository
rather than reasoned about.

🤖 Generated with Claude Code

[Copilot]

🟢 Approval recommended

No unresolved issues were identified, and tracked tutorial weights remain preserved.

Pull request overview

This pull request prevents generated .h5 snapshot files from appearing as untracked changes while preserving tracked tutorial weights.

Changes:

• Adds scoped ignore rules for generated snapshot files.
• Documents the behavior and scope in the changelog.

File summaries

File	Summary
CHANGELOG.md	Documents the ignore-rule behavior and scope.
.gitignore	Ignores generated HDF5 files in supported locations.

Review details

• Files reviewed: 1/2 changed files
• Comments generated: 0
• Review effort level: Lite

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.40%. Comparing base (2d48e94) to head (128db38).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #265   +/-   ##
=======================================
  Coverage   72.40%   72.40%           
=======================================
  Files          99       99           
  Lines        3606     3606           
=======================================
  Hits         2611     2611           
  Misses        995      995           

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