Merge branch 'release-v072' into 'master'

Release v072

See merge request flu-informatics/label!5

Author: sammysheep

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 All notable changes to this project will be documented in this file. The format is roughly based on [Keep a Changelog], and this project tries to adheres to [Semantic Versioning]. For IRMA vs IRMA-core compatibility, please see the [version matrix](VERSION_MATRIX.md).
 
+
+## [0.7.2] - 2025-08-15
+
+### Added
+
+- The static build of legacy `shogun` in the third-party distribution is now a fat/universal binary for macOS offering native arm64 support.
+
 ## [0.7.1] - 2025-05-21
 
 ### Fixes

LABEL_RES/third_party/MANIFEST.md

@@ -7,7 +7,7 @@
   - License: [GPL v3]
 - [SHOGUN] version 1.1.0 (2.1+ is not compatible)
   - Artifacts: `shogun` (cmdline_static)
-  - Provided architectures: linux/x86_64, linux/aarch64, apple/x86_64 (arm64 via Rosetta2)
+  - Provided architectures: linux/x86_64, linux/aarch64, apple/universal (*[arm64][arm64-mac-build] + intel)
   - Purpose: executes the SVM decision phase.
   - License: [GPL v3]
 - [SAM] version 3.5
@@ -16,9 +16,12 @@
   - Purpose: build HMM profiles, score sequences for evaluation
   - License: [Custom][sam-license] academic/government, not-for-profit, redistributed [with permission]
 
+* Minor modifications to allow compilation of the legacy software.
+
 [GNU Parallel]: https://www.gnu.org/software/parallel/
 [with permission]: copyright_and_licenses/sam3.5/SAM%20Redistribution%20Special%20Permissions.pdf
 [GPL v3]: https://www.gnu.org/licenses/gpl-3.0.txt
 [SHOGUN]: https://github.com/shogun-toolbox/
 [sam-license]: https://users.soe.ucsc.edu/~karplus/projects-compbio-html/sam-lic/obj.0
 [SAM]: https://users.soe.ucsc.edu/~karplus/projects-compbio-html/sam2src/
+[arm64-mac-build]: https://github.com/sammysheep/shogun/releases/tag/v110-mac-arm-build

LABEL_RES/third_party/shogun_Darwin

@@ -115,7 +115,7 @@ We aggregate and provide [builds of 3rd party software](LABEL_RES/third_party/)
   - License: [GPL v3]
 - [SHOGUN] version 1.1.0 (2.1+ is not compatible)
   - Artifacts: `shogun` (cmdline_static)
-  - Provided architectures: linux/x86_64, linux/aarch64, apple/x86_64 (arm64 via Rosetta2)
+  - Provided architectures: linux/x86_64, linux/aarch64, apple/universal (*[arm64][arm64-mac-build] + intel)
   - Purpose: executes the SVM decision phase.
   - License: [GPL v3]
 - [SAM] version 3.5
@@ -127,6 +127,8 @@ We aggregate and provide [builds of 3rd party software](LABEL_RES/third_party/)
 > [!WARNING]
 > Note that [SAM] is redistributed with permission for LABEL but its terms exclude commerical use without a license. If you are a commercial entity, you might need to reach out to the authors to obtain their [custom][sam-license] license.
 
+* Minor modifications to allow compilation of the legacy software.
+
 ## METHOD
 
 Lineage Assignment By Extended Learning (LABEL) uses hidden Markov model (HMM) profiles of clade alignments--or groups of clades--to analyze query sequences and then classify them via machine learning techniques. The HMM scoring step is performed via [SAM]. Prediction is performed hierarchically--usually starting out at a more general level (e.g., a groups of clades) and going to a very specific terminal level (a particular clade). This roughly corresponds to the hierarchical structure of phylogenetic trees and the H5N1 nomenclature system. The prediction phase of LABEL is done via support vector machines (SVM) using the free SHOGUN Machine Learning Toolbox v1.1.0 (multi-class GMNP SVM with polynomial kernel of degree 20, <www.shogun-toolbox.org>).
@@ -174,4 +176,5 @@ Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
 [SHOGUN]: https://github.com/shogun-toolbox/
 [sam-license]: https://users.soe.ucsc.edu/~karplus/projects-compbio-html/sam-lic/obj.0
 [SAM]: https://users.soe.ucsc.edu/~karplus/projects-compbio-html/sam2src/
-[IRMA]: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6
+[IRMA]: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6
+[arm64-mac-build]: https://github.com/sammysheep/shogun/releases/tag/v110-mac-arm-build