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Correct the comments and docstrings that seven known issues name - #356

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fix/c21-comment
Oct 25, 2026
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fix/c21-comment

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Follow-up to #355. It corrects the comments, docstrings and one manual formula that seven entries of KNOWN_ISSUES.md name, and deletes those entries. No code behaviour changes; C21 stays open.

  • K1: the comment above test_reduced_vector_fields names KNOWN_ISSUES.md for C21, not CHANGELOG.md.
  • K11: the comment above train_manifold_network states only the present constraint of the AdamOptimizerWithDecay test.
  • K22: the comment in symplectic_attention.jl cites test/layers/…, the real path of the test.
  • K25: the docstrings of LinearSymplecticTransformer and SymplecticTransformer give the gradient layers of one transformer unit as the chain builds them.
  • K26: the SymplecticAutoencoder docstring says that decoder_init_q = true makes the first decoder layer q-type.
  • K27: the UnknownDecoder docstring names n_decoder_blocks and links UnknownEncoder.
  • K18: the tensor-sampling formula in the DataLoader manual has + 1 in its upper bound.

Pre-PR verification

Fixed: none needed. Two nits in the CHANGELOG bullet were corrected before the commit.

Unresolved: none.

Pre-existing, adjacent (not changed here):

  • In the docstrings of LinearSymplecticTransformer and SymplecticTransformer, the n_sympnet bullet says "the number of sympnet layers in the transformer" (the chain has 2·L·n_sympnet), and the init_upper bullet says it selects the type of "the first layer" (the first layer is always the q attention layer; init_upper selects the first gradient layer after each attention layer).
  • The SymplecticTransformer docstring mentions a sequence length that the constructor does not take.

Checked and clean:

  • Full HTML docs build (docs/make.jl): exit 0, rendered completely, 0 unresolved references, no missing docstrings. The new text and the UnknownEncoder link appear in the rendered pages.
  • The new transformer sentence matches the chain for n_sympnet = 1, 2, 3 and init_upper = true, false, for both transformers.
  • The tensor-sampling bound input_time_steps − seq_length − prediction_window + 1 matches number_of_start_positions in four configurations on the manual's example data.
  • decoder_init_q = true gives a GradientLayerQ as the first decoder layer; the third field of UnknownDecoder is n_decoder_blocks.
  • No file:line citation became wrong, and no file still names a removed known-issue ID.

Not checked: type piracy, type stability and allocations, because the diff changes no executable line. Doctests were not run: makedocs runs with doctest = false, and no doctest block changed.

🤖 Generated with Claude Code

…22, K25, K26 and K27 name

Comment, docstring and manual text only; no code behaviour changes.

Co-Authored-By: Claude Sonnet 5.5 <[email protected]>
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  • docs/src/data_loader/data_loader.md
📝 Summary

Summary by CodeRabbit

  • Documentation

    • Clarified the tensor-sampling time-index range, including its final valid starting index.
    • Updated architecture documentation to better describe decoder settings and the ordering and types of layers in symplectic models.
    • Corrected references in documentation and comments.
  • Bug Fixes

    • Recorded the closure of known issues K1, K11, K18, K22, K25, K26, and K27. Known issue C21 remains open.
  • Behavior

    • No application behavior changed.

This change corrects documentation and comments, removes seven resolved entries from KNOWN_ISSUES.md, and records their status in CHANGELOG.md. The edits do not change implementation behavior.

Changes: Documentation corrections and issue cleanup

Layer / File(s) Summary
Correct formulas, descriptions, and references
docs/src/data_loader/data_loader.md, src/architectures/*, src/layers/symplectic_attention.jl, test/optimizers/adam_with_learning_rate_decay.jl, test/reduced_system/reduced_system.jl
The DataLoader formula now includes the final valid start index. Architecture descriptions and comment references were corrected, and outdated optimizer-result claims were removed.
Update known-issue records
KNOWN_ISSUES.md, CHANGELOG.md
The known-issues list removes K1, K11, K18, K22, and K25–K27. The changelog records these closures and notes that C21 remains open.

Priority: Low

Estimated code review effort: 2 (Simple) | ~10 minutes

Change: Other

Possibly related PRs

Merge Risk: Low · up to 2f9a5

Correct the user-facing sampling formula before merging; runtime behavior is unaffected.

Pre-merge checks: Passed 5
Check name Status Explanation
Title check Passed The title clearly summarizes the main changes to comments and docstrings associated with seven known issues. It is concise and related to the changeset.
Description check Passed The description accurately explains the documentation corrections, manual formula update, removal of seven known issues, verification performed, and unchanged behavior.
Docstring Coverage Passed No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
Linked Issues check Passed Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check Passed Check skipped because no linked issues were found for this pull request.
Full details: Docstring Coverage

Explanation

No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0 files. (9 skipped: 9 unsupported.)

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Reviewing files that changed from the base of the PR and between 29b45fe and 2f9a50e.

Files selected for processing: 10
  • CHANGELOG.md
  • KNOWN_ISSUES.md
  • docs/src/data_loader/data_loader.md
  • src/architectures/autoencoder.jl
  • src/architectures/linear_symplectic_transformer.jl
  • src/architectures/symplectic_autoencoder.jl
  • src/architectures/symplectic_transformer.jl
  • src/layers/symplectic_attention.jl
  • test/optimizers/adam_with_learning_rate_decay.jl
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  • KNOWN_ISSUES.md

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Comment thread docs/src/data_loader/data_loader.md Outdated
@michakraus
michakraus enabled auto-merge October 25, 2026 13:38
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codecov Bot commented Oct 25, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.06%. Comparing base (29b45fe) to head (b40df1e).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #356   +/-   ##
=======================================
  Coverage   92.06%   92.06%           
=======================================
  Files          51       51           
  Lines        1109     1109           
=======================================
  Hits         1021     1021           
  Misses         88       88           

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@michakraus
michakraus merged commit a664f5c into main Oct 25, 2026
14 of 17 checks passed
@michakraus
michakraus deleted the fix/c21-comment branch October 25, 2026 14:03
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