Enhancement/alphabet refactor

[junniest]

Refactor alphabets for clarity and fewer memory allocations (alphabets are now always represented as a reference to a static object). Added doctrings to Alphabet methods.

[Copilot]

Pull Request Overview

This PR refactors the alphabet system to use static references (&'static Alphabet) instead of owned Alphabet values, reducing memory allocations and providing clearer semantics. The refactor also adds comprehensive docstrings to all public Alphabet methods.

Key changes:

• Alphabet instances are now accessed via Alphabet::dna() and Alphabet::protein() static methods that return &'static Alphabet
• The QMatrix::alphabet() and EvoModel::alphabet() methods are now static methods (called as Q::alphabet() rather than instance.alphabet())
• The alphabet field has been removed from all QMatrix implementations (DNA and protein models) as it's now accessed statically
• Renamed gap_encoding() to missing_char_encoding() for better semantic clarity
• Updated all test templates to use Q::alphabet() for retrieving the alphabet from generic type parameters
• Added comprehensive docstrings with examples for all public Alphabet methods

Reviewed Changes

Copilot reviewed 26 out of 26 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
phylo/src/alphabets/mod.rs	Core refactor: added static dna() and protein() methods, removed full_set field, renamed methods, added extensive docstrings
phylo/src/alphabets/parsimony_set.rs	Added Eq derive to ParsimonySet for better comparison support
phylo/src/alphabets/tests.rs	Updated tests to use Alphabet::dna() and Alphabet::protein() static methods
phylo/src/alignment/mod.rs	Updated documentation examples to use new static alphabet methods
phylo/src/alignment/sequences.rs	Changed alphabet field type to &'static Alphabet, moved detect_alphabet to module-level function
phylo/src/alignment/tests.rs	Updated tests to use static alphabet methods
phylo/src/substitution_models/mod.rs	Changed QMatrix::alphabet() to static method, updated alphabet comparison in builder to use Q::alphabet(), renamed gap_encoding() to missing_char_encoding()
phylo/src/substitution_models/dna_models/mod.rs	Removed alphabet field from all DNA model structs, implemented static alphabet() method
phylo/src/substitution_models/protein_models/mod.rs	Removed alphabet field from protein model macro, implemented static alphabet() method
phylo/src/substitution_models/tests.rs	Updated test templates to remove alphabet parameters and use Q::alphabet() for generic alphabet access
phylo/src/evolutionary_models/mod.rs	Changed EvoModel::alphabet() to static method with where Self: Sized constraint
phylo/src/tkf_model/tkf91.rs	Updated alphabet comparison to use Q::alphabet()
phylo/src/tkf_model/tkf92.rs	Updated alphabet comparison to use Q::alphabet()
phylo/src/tkf_model/tkf_indel.rs	Updated test code to use Alphabet::dna()
phylo/src/tkf_model/tests.rs	Updated test functions and helpers to use &'static Alphabet and static alphabet methods
phylo/src/pip_model/mod.rs	Changed alphabet() implementation to use Q::alphabet()
phylo/src/pip_model/tests.rs	Updated test templates to use Q::alphabet() instead of alphabet parameters
phylo/src/phylo_info/mod.rs	Replaced alphabet.empty_freqs() with FreqVector::zeros(alphabet.len())
phylo/src/phylo_info/tests.rs	Updated tests to use static alphabet methods
phylo/src/phylo_info/phyloinfo_builder.rs	Changed alphabet parameter type to &'static Alphabet, updated documentation and comparisons
phylo/src/likelihood/tests.rs	Updated test templates to remove alphabet parameters and use Q::alphabet()
phylo/src/parsimony/mod.rs	Updated to pass alphabet reference directly instead of dereferencing
phylo/src/parsimony/scoring/model_scoring.rs	Added EvoModel bound to trait implementations, removed alphabet field, use P::alphabet() statically
phylo/src/parsimony/cost/dollo_parsimony_cost.rs	Updated test to use Alphabet::dna()
phylo/src/optimisers/blen_optimiser_tests.rs	Updated test to use Alphabet::protein()
phylo/src/io/mod.rs	Updated to use Alphabet::protein() for validation

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Test Results

587 tests  +11   586 ✅ +11   26m 43s ⏱️ -21s
  2 suites ± 0     1 💤 ± 0 
  1 files   ± 0     0 ❌ ± 0 

Results for commit 7134607. ± Comparison against base commit 792e96d.

This pull request removes 8 and adds 19 tests. Note that renamed tests count towards both.

alphabets::tests ‑ full_sets
src/alignment/mod.rs - alignment::MASA ‑ from_aligned (line 385)
src/alignment/mod.rs - alignment::MASA ‑ from_aligned_with_ancestral_unchecked (line 466)
src/alignment/mod.rs - alignment::MSA ‑ from_aligned_unchecked (line 264)
src/alignment/mod.rs - alignment::MSA ‑ len (line 201)
src/alignment/mod.rs - alignment::MSA ‑ seq_count (line 229)
src/phylo_info/phyloinfo_builder.rs - phylo_info::phyloinfo_builder::PhyloInfoBuilder<A,AA> ‑ alphabet (line 103)
src/phylo_info/phyloinfo_builder.rs - phylo_info::phyloinfo_builder::PhyloInfoBuilder<A,AA> ‑ build_w_rng (line 130)

alphabets::tests ‑ ambiguous_sets
alphabets::tests ‑ dna_alphabet_display
alphabets::tests ‑ protein_alphabet_display
src/alignment/mod.rs - alignment::MASA ‑ from_aligned (line 384)
src/alignment/mod.rs - alignment::MASA ‑ from_aligned_with_ancestral_unchecked (line 465)
src/alignment/mod.rs - alignment::MSA ‑ from_aligned_unchecked (line 263)
src/alignment/mod.rs - alignment::MSA ‑ len (line 200)
src/alignment/mod.rs - alignment::MSA ‑ seq_count (line 228)
src/alphabets/mod.rs - alphabets::Alphabet ‑ ambiguous (line 112)
src/alphabets/mod.rs - alphabets::Alphabet ‑ char_encoding (line 156)
…

♻️ This comment has been updated with latest results.

[codecov]

Codecov Report

❌ Patch coverage is 92.68293% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.13%. Comparing base (527040d) to head (7134607).
⚠️ Report is 22 commits behind head on develop.

Files with missing lines	Patch %	Lines
phylo/src/alphabets/mod.rs	88.23%	4 Missing ⚠️
phylo/src/pip_model/mod.rs	33.33%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #125      +/-   ##
===========================================
+ Coverage    96.32%   97.13%   +0.80%     
===========================================
  Files           32       45      +13     
  Lines         4355     5656    +1301     
===========================================
+ Hits          4195     5494    +1299     
- Misses         160      162       +2     

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[Copilot]

Pull Request Overview

Copilot reviewed 26 out of 26 changed files in this pull request and generated no new comments.

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