2.5.84

Significant changes.

1. Based on issue 1877, HyPhy build scripts have been made more robust to incorrectly detecting SIMD features, and an branch for x86 processors supporting AVX (but not AVX2) has been added.
2. Based on issue #1878 (but more broadly), hyphy will now throw an error if dataset validation checks fail. Previosuly, many were treated as warnings (viewable in messages.log with -m option) and opaque actions were taken. These usually resulted in odd behavior or errors later on. Now these errors will be reported at dataset read time. Practically, some of the datasets that used to run, may no longer run. This can be disabled with STRICT_ALIGNMENT_VALIDATION_MODE=0; HyPhy environment variable.
3. Adding constant site ASR reporting for Contrast-FEL
4. Script bug fixes. The first site in any alignment would not be screened by FEL or MEME due to incorrect filtering.
5. Comments and code cleanup.

(LLM generated) HyPhy 2.5.84 Release Notes

This release of HyPhy includes several new features, bug fixes, and performance improvements.

New Features

• Ancestral State Reconstruction (ASR): Improved ancestral state reconstruction for constant sites, providing more accurate and detailed ASR results. A new HBL function
  ancestral.ComputeCompressedSubstitutionConstantSite has been added to handle ASR on constant sites more efficiently. The contrast-fel.bf analysis has been updated to use this new function.
  (2fca8b7)
• Suppress Status Updates: A new SUPPRESS_STATUS_UPDATES option has been added to suppress status line updates, which can be useful when running HyPhy in non-interactive environments.
  (085cab9)

Bug Fixes and Improvements

• NEXUS Parser: The NEXUS parser has been made stricter to better enforce the NEXUS file format. It now reports errors for invalid constructs that were previously ignored or handled with a
  warning. A new strict_alignment_validation_mode environment variable can be used to control the behavior of the parser. (6f3b296)
• FADE Analysis: Fixed a bug in the FADE.bf script where a key was not being accessed correctly. (6f3b296)
• Matrix Multiplication: Fixed a bug in _Matrix::MultElements where the error message for dimension mismatch was not informative. (6f3b296)
• Documentation: Updated author contact information and added Doxygen-style comments to improve code documentation. (6f3b296)

Build System and Performance

• AVX/AVX2 Optimizations: The build system and core numerical libraries have been updated to better utilize AVX and AVX2 instruction sets for improved performance. This includes more
  fine-grained control over AVX/AVX2 features at compile time. (9dca5e1, a9364d2, fe911d6, 1451846, 43c3e94, 15018a7, cb58e94, bb7ab90, 100f546, d6224ad, 32d3970, 65113a4,
  20cf24b, 715eec5, c62c841, 7681935)
• CMake: The CMakeLists.txt file has been updated for more stringent detection of compiler features. (3d1cf17)
• GitHub Actions: The build_and_test.yml workflow has been removed. (2fca8b7)

2.5.83

What's Changed

• 2.5.83 by @spond in #1910

Full Changelog: 2.5.82...2.5.83

2.5.82

What's Changed

• Enhance FEL branch selection documentation by @stevenweaver in #1897
• v2.5.82 by @spond in #1909

Full Changelog: 2.5.81...2.5.82

(🛑) This version was including broken LLM generated source for the builds that rely on SSE to handle matrix operations. This will manifest as failing tests. Version 2.5.83 will revert these changes

2.5.81

What's Changed

• 2.5.81 by @spond in #1907
• Doxygen headers by @spond in #1908

Full Changelog: 2.5.80...2.5.81

2.5.80

What's Changed

• URGENT: Fix HYPHYMPI build error - undeclared identifier 'return_value' by @stevenweaver in #1901
• 2.5.80 by @spond in #1905

Full Changelog: 2.5.79...2.5.80

2.5.79

What's Changed

• Add GitHub Action to automatically update Homebrew formula by @stevenweaver in #1895
• 2.5.79 by @spond in #1896

Full Changelog: 2.5.78...2.5.79

2.5.78

What's Changed

• Fix build on i386 (32-bit x86) by @Jehops in #1892
• 2.5.78 by @spond in #1894

Full Changelog: 2.5.77...2.5.78

2.5.77

What's Changed

• 2.5.77 by @spond in #1891

Full Changelog: 2.5.76...2.5.77

2.5.76

What's Changed

• Develop catchup with master by @spond in #1872
• Code cleanup and refactoring. by @spond in #1881
• Feature/modernize cmake by @spond in #1874
• GCC 9 minimum by @spond in #1882
• Trying to solve an odd compilation issue on silverback by @spond in #1883
• Fixes by @spond in #1884
• Fixing CMake options for WASM by @spond in #1885
• 2.5.76 by @spond in #1886

Full Changelog: 2.5.75...2.5.76

2.5.75

What's Changed

• 2.5.75 by @spond in #1871

Full Changelog: 2.5.74...2.5.75