feat(io.yaml): factor model_from_yaml_data out of read_yaml_model + back-port docs / known-issues / localization / scripts#11

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edkerk merged 29 commits into

developfrom

feature/quality-and-matlab-docs

May 30, 2026

Commits on May 29, 2026

Project scaffold: pyproject + package skeleton + README + LICENSE
edkerk
committed
Add GitHub Actions CI and the maintainer-scripts README
edkerk
committed
Add the foundation utilities: GPR, balance, parse, sort, validate
edkerk
committed
Add the model-manipulation layer (add, remove, transport, merge, etc.)
edkerk
committed
Add binary + data resolvers for external tools and published artefacts
edkerk
committed
Add YAML and SIF model I/O
edkerk
committed
Add Excel export and the Standard-GEM git-layout export
edkerk
committed
Add BLAST and DIAMOND wrappers for protein-homology searches
edkerk
committed
Add the homology-based draft model builder (getModelFromHomology port)
edkerk
committed
Add KEGG download, dump parser and taxonomy parser
edkerk
committed
Add KEGG HMM-library build and HMM-based KO assignment
edkerk
committed
Add KEGG species-model assembly (per-organism reconstruction)
edkerk
committed
Add KEGG artefact-build scripts and HMM-cutoff calibration docs
edkerk
committed
Add metabolic-task parsing and the check_tasks validator
edkerk
committed
Add connectivity gap-filling (MILP) against template models
edkerk
committed
Add the tINIT (INIT) MILP and its supporting machinery
edkerk
committed
Add the ftINIT pipeline and task-aware gap-filling
edkerk
committed
Add Human-GEM validation, parameter studies and cross-solver tests
edkerk
committed
Add HPA omics ingestion (proteomics + RNA-seq)
edkerk
committed
Add FSEOF, reporter metabolites and flux sampling
edkerk
committed
Add N-model comparison (presence + Jaccard + optional task check)
edkerk
committed
Add subcellular-localisation prediction (MILP) with pluggable predictors
edkerk
committed
Add the yeast-GEM localization benchmark (real-data validation)
edkerk
committed
Add the documentation index, RAVEN migration map and CHANGELOG
edkerk
committed
Add known-issues catalogue with closed sweep A–F regression notes
edkerk
committed
Add the consolidated MATLAB RAVEN back-port proposals doc
edkerk
committed
feat(io.yaml): factor model_from_yaml_data out of read_yaml_model
edkerk
committed
fix(io.yaml): drop metaData/version/_yaml_sections from doc['notes']
edkerk
committed

Commits on May 30, 2026

Merge remote-tracking branch 'origin/develop' into feature/quality-and-matlab-docs
edkerk
committed

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feat(io.yaml): factor model_from_yaml_data out of read_yaml_model + back-port docs / known-issues / localization / scripts#11

feat(io.yaml): factor model_from_yaml_data out of read_yaml_model + back-port docs / known-issues / localization / scripts#11
edkerk merged 29 commits into
developfrom
feature/quality-and-matlab-docs

Commits on May 29, 2026

Project scaffold: pyproject + package skeleton + README + LICENSE

Add GitHub Actions CI and the maintainer-scripts README

Add the foundation utilities: GPR, balance, parse, sort, validate

Add the model-manipulation layer (add, remove, transport, merge, etc.)

Add binary + data resolvers for external tools and published artefacts

Add YAML and SIF model I/O

Add Excel export and the Standard-GEM git-layout export

Add BLAST and DIAMOND wrappers for protein-homology searches

Add the homology-based draft model builder (getModelFromHomology port)

Add KEGG download, dump parser and taxonomy parser

Add KEGG HMM-library build and HMM-based KO assignment

Add KEGG species-model assembly (per-organism reconstruction)

Add KEGG artefact-build scripts and HMM-cutoff calibration docs

Add metabolic-task parsing and the check_tasks validator

Add connectivity gap-filling (MILP) against template models

Add the tINIT (INIT) MILP and its supporting machinery

Add the ftINIT pipeline and task-aware gap-filling

Add Human-GEM validation, parameter studies and cross-solver tests

Add HPA omics ingestion (proteomics + RNA-seq)

Add FSEOF, reporter metabolites and flux sampling

Add N-model comparison (presence + Jaccard + optional task check)

Add subcellular-localisation prediction (MILP) with pluggable predictors

Add the yeast-GEM localization benchmark (real-data validation)

Add the documentation index, RAVEN migration map and CHANGELOG

Add known-issues catalogue with closed sweep A–F regression notes

Add the consolidated MATLAB RAVEN back-port proposals doc

feat(io.yaml): factor model_from_yaml_data out of read_yaml_model

fix(io.yaml): drop metaData/version/_yaml_sections from doc['notes']

Commits on May 30, 2026

Merge remote-tracking branch 'origin/develop' into feature/quality-and-matlab-docs