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Package maintenance: quality, tests, docstrings, and README#18

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kdw503 merged 10 commits into
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dwk/mng
May 7, 2026
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Package maintenance: quality, tests, docstrings, and README#18
kdw503 merged 10 commits into
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dwk/mng

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@kdw503 kdw503 commented May 7, 2026

Summary

  • Aqua.jl: added quality checks to the test suite
  • Deprecation removal: removed deprecated padsize(blocksize, maxshift) and padsize!
  • ExplicitImports.jl: audited and fixed all import issues
  • Test coverage: expanded tests and fixed source bugs found during testing
  • Docstrings: added docstrings to all exported symbols; wired up Documenter doctests in CI
  • README: added badges (CI, Codecov), installation instructions (incl. HolyLab registry), key-concept overview, usage examples, and API reference table

Test plan

  • CI passes on min and 1 Julia versions
  • Codecov badge resolves after merge
  • README examples match actual output (verified via MCP Julia session)

🤖 Generated with Claude Code

kdw503 and others added 10 commits May 7, 2026 10:01
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…lper

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Make all wildcard imports explicit (CenterIndexedArrays, ImageCore, RegisterCore)
- Remove stale non-public Base imports: unsafe_length, index_shape
- Replace Base.ViewIndex with inlined Union{Real,AbstractArray}
- Remove no-op Base.@_propagate_inbounds_meta
- Replace Base.reindex with explicit unsafe_reindex fallback methods
- Add test_explicit_imports to test suite
- Add ExplicitImports to [extras]/[targets] with compat "1"

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Fix truncatenoise! array-of-arrays method (used undefined `denoms`)
- Fix allocate_mmarrays real-matrix method (wrong MismatchArray type parameter)
- Fix default_aperture_width error message (tuple indexed by tuple)
- Fix computeoverlap (non-broadcasting max, tuple-minus-vector)
- Add Base.length/eltype to ContainerIterator and FirstDimIterator
- Add 121 new tests covering all testable utility functions
- Coverage: 0% → 87.8%

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds docstrings to all 10 previously undocumented exported symbols
(mismatch, set_FFTPROD, DimsLike, WidthLike, assertsamesize,
checksize_maxshift, padranges, padsize, shiftrange, tovec) and the
module itself. Fixes existing docstrings for correctbias!, mismatch0,
nanpad, aperture_grid, allocate_mmarrays, default_aperture_width,
each_point, truncatenoise!, and register_translate (corrects <= vs <,
misleading thresh description, keyword arg notation, missing return
types, and missing overloads). Adds a jldoctest example to
aperture_grid. Wires Documenter.jl into the test suite so doctests run
with Pkg.test().

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
RegisterCore 1.0 renamed indmin_mismatch to argmin_mismatch (breaking).
The compat allowed "0.2, 1", so CI resolved RegisterCore 1.0.1 and failed
to precompile. Update the import and call site, and tighten the lower
bound to "1".

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Base.tail is not part of Julia's public API. Replace all uses with
size(x)[2:end] (in FirstDimIterator) and a local _tail helper (in
unsafe_reindex), both of which rely only on public indexing.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Tokenless uploads are no longer accepted by Codecov. Switch to
codecov-action@v4 and supply the repository secret.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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codecov Bot commented May 7, 2026

Codecov Report

❌ Patch coverage is 59.09091% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.44%. Comparing base (4173c5a) to head (7178d74).
⚠️ Report is 23 commits behind head on master.

Files with missing lines Patch % Lines
src/RegisterMismatchCommon.jl 59.09% 9 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           master      #18       +/-   ##
===========================================
+ Coverage    0.00%   87.44%   +87.44%     
===========================================
  Files           1        1               
  Lines         240      239        -1     
===========================================
+ Hits            0      209      +209     
+ Misses        240       30      -210     

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@kdw503 kdw503 merged commit 9096a83 into master May 7, 2026
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@kdw503 kdw503 deleted the dwk/mng branch May 7, 2026 17:27
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