Release prep/fix package size

[junniest]

This PR is to reduce the final package size of the crate. It moves small data files used in doctests into the examples/data directory and updates paths to the files. Additionally, it simplifies the PhyloInfoBuilder class by removing the redundant sequence_file method, as this one file path is the only necessary attribute to create a valid PhyloInfo.

[Copilot]

Pull Request Overview

This PR reduces the crate’s final package size by moving small test data into examples/data and cleaning up the builder API.

• Moves all small data files used in doctests into examples/data and updates paths accordingly
• Removes the redundant sequence_file setter method from PhyloInfoBuilder
• Updates Cargo.toml to exclude the old data directory and other non-shipped folders

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
phylo/src/phylo_info/phyloinfo_builder.rs	Updated doctest paths to examples/data and removed sequence_file setter
phylo/src/phylo_info/mod.rs	Updated example paths in docs to examples/data
phylo/src/optimisers/topo_optimiser.rs	Updated example path for K80 data
phylo/src/io/mod.rs	Updated all doctest paths for sequence/tree I/O
phylo/examples/data/*	Added moved data files
phylo/Cargo.toml	Adjusted exclude patterns to drop data/, add benches/ and target/
README.md	Updated sample code path for K80.fasta example

Comments suppressed due to low confidence (3)

phylo/src/phylo_info/phyloinfo_builder.rs:59

• Removing the sequence_file setter method breaks the existing builder API; consider deprecating it first or bumping the crate's major version under semantic versioning.

        PhyloInfoBuilder {

phylo/src/io/mod.rs:109

• [nitpick] Example doctest writes output into the source-tracked examples/data directory; it may be better to use std::env::temp_dir() or a dedicated temporary path to avoid choking version control or write-permission issues.

/// let output_path = PathBuf::from("./examples/data/doctest_tmp_output.fasta");

phylo/Cargo.toml:15

• [nitpick] The exclude list includes benches/ and target/, but these directories may not exist in the crate root; consider verifying or removing unused patterns to simplify the manifest.

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.65%. Comparing base (c9c73d6) to head (e72bff7).
Report is 7 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #70      +/-   ##
===========================================
+ Coverage    96.26%   96.65%   +0.38%     
===========================================
  Files           27       30       +3     
  Lines         3991     4240     +249     
===========================================
+ Hits          3842     4098     +256     
+ Misses         149      142       -7     

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