diff --git a/CHANGELOG.md b/CHANGELOG.md index 22bc0d8..a975bb1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ * The KEGG assets are the `kegg120` release of `toolbox-assets` (was: `kegg118`): the reference model and tables, the taxonomy and the profile HMM libraries of 4246 prokaryotic and 2724 eukaryotic KOs. The baked registry and `data/manifest.json` list them. -## 3.0.0b2 — 2026-11-01 +## 3.0.0b2 (2026-11-01) Second beta toward 3.0. The main changes are RAVEN-format model export, SuppOrth homology input, and a closer match to RAVEN in homology, gap-filling, curation tables and `ftinit`. @@ -201,17 +201,17 @@ Breaking changes: `fill_gaps_kumar_milp` is renamed `fill_gaps_milp`, `omics.hpa * The `docs/` tree and its Read the Docs build are removed; the documentation is on [raven-docs](https://github.com/CompMetEng/raven-docs). The project URLs point to `CompMetEng`, and `data/deeploc` is not part of the source distribution. * Docstrings are corrected for `reporter_metabolites`, `random_sampling`, `remove_no_flux_reactions`, `check_tasks`, `connect_blocked_reactions` and `find_leak_metabolite`. -## 3.0.0b1 — 2026-09-07 +## 3.0.0b1 (2026-09-07) First beta toward 3.0, matching the upcoming MATLAB RAVEN 3.0 beta. * keep `ftinit()` as the only extraction pipeline. -* `analysis.compare_fluxes` replaces `follow_changed` — a `compareFluxes` port, following RAVEN +* `analysis.compare_fluxes` replaces `follow_changed`: a `compareFluxes` port, following RAVEN dropping `followChanged`/`followFluxes`/`mapCompartments`. * `comparison.compare_models` gained EC-code / metabolite-name / equation overlap matrices, folded from `compareRxnsGenesMetsComps`. * New: `curation.rename_model_genes`, ported from `renameModelGenes`. -* New: `curation.get_gene_data`, `download_genome_data`, `process_protein_fasta_file` — the +* New: `curation.get_gene_data`, `download_genome_data`, `process_protein_fasta_file`: the genome-data cluster. * New: `manipulation.replace_metabolite`, ported from `replaceMets`. * New: `gapfilling.find_leak_metabolite`, ported from `findLeakMetabolite`. @@ -227,7 +227,7 @@ First beta toward 3.0, matching the upcoming MATLAB RAVEN 3.0 beta. * `init.ftinit` implements the metabolomics production-bonus (`metabolomics=`, `prod_weight=`). * `init.ftinit` reproducibility parameters renamed: `strict_gap`/`canonical` are now `prove_abs_gap`/`resolve_ties`, with corrected determinism numbers. -* ftINIT task gap-filling now edits the reference model in place instead of copying it — ~23% +* ftINIT task gap-filling now edits the reference model in place instead of copying it, and is ~23% faster on a genome-scale extraction. * Fixed three ftINIT/task-essential bugs: a task-essential boundary default, a checkpoint file-handle leak, and a non-finite tie-break objective. @@ -250,9 +250,9 @@ First beta toward 3.0, matching the upcoming MATLAB RAVEN 3.0 beta. a null genes/reactions/metabolites key as empty. * Parameter defaults measured and unified: BLAST/DIAMOND/HMMER threading, homology `min_align_len`/`evalue`, `get_init_model.allow_excretion`. -* Removed `io.export_model_to_sif` — a mislabeled port of a MATLAB function that never existed. +* Removed `io.export_model_to_sif`: a mislabeled port of a MATLAB function that never existed. -## 0.4.0 — 2026-08-28 +## 0.4.0 (2026-08-28) A `raven-gecko-parity` cross-validation harness closed six MATLAB-parity divergences and brought the YAML writer to byte-parity; ftINIT gained an opt-in deterministic-extraction mode; compartment @@ -266,7 +266,7 @@ placement and gap-filling in `assign_compartments` were fixed for determinism an unreliable indicator-MILP gapfill. * `assign_compartments` reaction placement is now deterministic and score-aligned instead of a solver tie-break (yeast agreement 52.8% → 72.5%). -* `diff_models` compares GPRs as logic (DNF-normalised), not text — operand order no longer +* `diff_models` compares GPRs as logic (DNF-normalised), not text; operand order no longer registers as a difference. * `load_delta_g_csv` now stamps every matched value literally by default, matching `deltaGCSV`. * `confidence.annotate_confidence` runs every applicable scorer in one call; `curation_priority` @@ -285,11 +285,11 @@ placement and gap-filling in `assign_compartments` were fixed for determinism an * BLAST/homology defaults matched to RAVEN and measured: `run_blast.evalue` → `1e-4`, `min_align_len` → `100`; new `review_identity` surfaces near-miss homology candidates. * New `set_exchange_bounds`, RAVEN's `setExchangeBounds` port. -* New cross-language parity testing harness (`tests/parity/`) — exact, set-level, and +* New cross-language parity testing harness (`tests/parity/`): exact, set-level, and statistical comparison tiers against real MATLAB RAVEN output. * Fixed a downloaded binary bundle leaving its non-primary executables non-executable. -## 0.3.0 — 2026-07-16 +## 0.3.0 (2026-07-16) Compartment localisation and per-reaction confidence tracking, new gap-filling and flux-sampling algorithms, ftINIT brought to parity with RAVEN, and KEGG artefact hosting @@ -303,23 +303,23 @@ moved to the dedicated `raven-data` repository. * Fixed `get_elemental_balance` crashing on an unparseable polymer formula (now `unknown`). * Fixed `score_localization_confidence` vetoing reactions it simply couldn't measure. * Fixed gap-fill materialising on the wrong compartment metabolite in `assign_compartments`. -* New `localization.transport_evidence` — per-gene transporter evidence lowers a metabolite's +* New `localization.transport_evidence`: per-gene transporter evidence lowers a metabolite's transport cost in the assignment MILPs. * `assign_compartments`/`apply_assignment`/`AssignmentProposal` consolidated into raven-toolbox from the standalone `assignCompartments` repo. * Benchmarked the compartment-assignment MILP against CarveFungi's own carve-MILP and against - RAVEN's `predictLocalization` — more accurate and deterministic on both. -* New `triage_localization` — flags genes/reactions whose localisation call is shakiest, each + RAVEN's `predictLocalization`, more accurate and deterministic on both. +* New `triage_localization`: flags genes/reactions whose localisation call is shakiest, each with a plain-English reason. * Retuned `DEEPLOC_COMPARTMENT_TRUST` and the `min_confidence`/`membrane_threshold` gates from real yeast validation data. -* Cross-species DeepLoc benchmarks (yeast, *Arabidopsis*, *Chlamydomonas*, Human-GEM) — DeepLoc +* Cross-species DeepLoc benchmarks (yeast, *Arabidopsis*, *Chlamydomonas*, Human-GEM): DeepLoc 2.1 generalises across kingdoms. * `load_deeploc` gained `normalise=False` for raw calibrated probabilities (accuracy-neutral for assignment). * New `combine_scores` (weighted-sum consensus across localisation predictors) and `min_confidence=`/`membrane_split=` loader gates. -* New `prepare_deeploc_input`, `fetch_protein_sequences`, `write_fasta` — writes a +* New `prepare_deeploc_input`, `fetch_protein_sequences`, `write_fasta`: writes a DeepLoc-ready protein FASTA for a model's genes. * New localisation loaders: `load_mulocdeep`, `load_compartments`, `load_uniprot`, `fetch_uniprot_localization`. Removed `load_wolfpsort`. @@ -337,18 +337,18 @@ moved to the dedicated `raven-data` repository. * CI now runs on macOS and Windows in addition to Linux. * Docstring rendering fixes for `set_gam` and `add_sbo_terms` (no API change). -## 0.2.0 — 2026-06-14 +## 0.2.0 (2026-06-14) Project rename plus KEGG-reconstruction and CI improvements. * Project renamed `raven-python` → `raven-toolbox`; import package is now `raven_toolbox`. * `get_kegg_model_from_sequences` uses `hmmsearch` instead of `hmmscan`. * `get_kegg_model_for_organism_from_artefacts` auto-resolves its taxonomy artefact. -* Test data no longer ships real KEGG records — generated at runtime instead. +* Test data no longer ships real KEGG records; they are generated at runtime instead. * Removed the unimplemented `visualization` stub and its extra. * CI updated to Node 24 / `actions/checkout@v5` / `actions/setup-python@v6`. -## 0.1.0 — 2026-06-10 +## 0.1.0 (2026-06-10) First release with published, downloadable KEGG artefacts, plus a cobra-aligned hardening pass. @@ -362,7 +362,7 @@ First release with published, downloadable KEGG artefacts, plus a cobra-aligned `connect_blocked_reactions` non-positive-penalty guard, SHA256 cache re-verification, and fixes for a handful of latent edge-case crashes, each with a regression test. -## 0.1.0a1 — 2026-05-30 +## 0.1.0a1 (2026-05-30) First alpha release. Covers the functional scope of RAVEN built on cobrapy: de-novo reconstruction (KEGG / homology), context-specific modeling (tINIT / ftINIT), metabolic-task diff --git a/src/raven_toolbox/manifest.py b/src/raven_toolbox/manifest.py index 8f27e67..3821b8f 100644 --- a/src/raven_toolbox/manifest.py +++ b/src/raven_toolbox/manifest.py @@ -15,7 +15,7 @@ Usage:: from raven_toolbox import manifest - manifest.load_into_registries("https://github.com/CompMetEng/toolbox-assets/releases/download/manifest-v1/manifest.json") + manifest.load_into_registries("https://github.com/CompMetEng/toolbox-assets/releases/download/manifest-v5/manifest.json") or set ``RAVEN_PYTHON_MANIFEST`` (a path or URL) and the resolvers load it lazily on first use::