diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9fe56251..d8082da2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -86,12 +86,12 @@ jobs: - uses: actions/checkout@v5 # RAVEN is GPL and this package is MIT, so its files are never vendored # here -- the cross-language checks read them from a checkout instead. - # develop3 is the branch raven-docs documents and raven-toolbox tracks. + # develop is the RAVEN branch raven-docs documents and raven-toolbox tracks. - name: Check out MATLAB RAVEN uses: actions/checkout@v5 with: - repository: SysBioChalmers/RAVEN - ref: develop3 + repository: CompMetEng/RAVEN + ref: develop path: .raven - uses: actions/setup-python@v6 with: diff --git a/.github/workflows/parity-nightly.yml b/.github/workflows/parity-nightly.yml index 09a5ff2d..c9e4e4fb 100644 --- a/.github/workflows/parity-nightly.yml +++ b/.github/workflows/parity-nightly.yml @@ -33,7 +33,7 @@ jobs: name: genome-scale parity # Forks do not have the secrets, and a scheduled run there would fail every # night for no reason. - if: github.repository == 'SysBioChalmers/raven-toolbox' + if: github.repository == 'CompMetEng/raven-toolbox' runs-on: ubuntu-latest # Measured against the classic INIT MILP this job used to check (now # ftINIT's run_ftinit, bounded to time_limit=600s -- see @@ -51,8 +51,8 @@ jobs: - name: Check out MATLAB RAVEN uses: actions/checkout@v5 with: - repository: SysBioChalmers/RAVEN - ref: develop3 + repository: CompMetEng/RAVEN + ref: develop path: .raven - uses: actions/setup-python@v6 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 1b000ab4..78a25284 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -115,7 +115,7 @@ jobs: # Trusted Publishing: PyPI verifies this workflow's OIDC identity, so no # long-lived token is stored in the repo. Requires a one-time publisher on # PyPI for raven-toolbox with: - # owner: SysBioChalmers repo: raven-toolbox + # owner: CompMetEng repo: raven-toolbox # workflow: release.yml environment: pypi environment: pypi permissions: diff --git a/CHANGELOG.md b/CHANGELOG.md index 4b884fb9..220d2dba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,8 @@ # Changelog Milestones in the raven-toolbox port. For function-level status see -[docs/raven_migration.md](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/docs/reference/migration.md); for open work see -[docs/todo.md](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/docs/reference/todo.md). +[docs/raven_migration.md](https://github.com/CompMetEng/raven-toolbox/blob/develop/docs/reference/migration.md); for open work see +[docs/todo.md](https://github.com/CompMetEng/raven-toolbox/blob/develop/docs/reference/todo.md). ## 3.0.0b1 — 2026-09-07 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6097bb64..b449e9b9 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -49,7 +49,7 @@ automatically; that side is documented in Publishing the results, and the versioning model behind the releases, is a shared convention rather than a raven-toolbox concern, and is documented in -[raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity/blob/develop/docs/publishing_artefacts.md). +[raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/publishing_artefacts.md). ## Rebuilding the KEGG artefacts diff --git a/IMPROVEMENTS.md b/IMPROVEMENTS.md index ae2a1021..f158b8d7 100644 --- a/IMPROVEMENTS.md +++ b/IMPROVEMENTS.md @@ -5,7 +5,7 @@ made smarter/faster, or where a logical gap in RAVEN's feature set is worth fill change — with enough detail that it can **also be back-ported to MATLAB RAVEN** later. > **Implemented improvements** — and the ones worth carrying upstream into MATLAB RAVEN — now live -> in [matlab_raven_backports.md](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/docs/reference/matlab_raven_backports.md), +> in [matlab_raven_backports.md](https://github.com/CompMetEng/raven-toolbox/blob/develop/docs/reference/matlab_raven_backports.md), > the MATLAB ↔ raven-toolbox **differences** record (both directions: improvements to back-port, and > functionality MATLAB has that raven-toolbox deliberately doesn't). **This file** keeps only the > design decisions behind what was ported *differently* or *not at all*, and the improvements still @@ -92,7 +92,7 @@ several places — and ask before re-adding (see process note: argue pros/cons f ### removeReactions — not ported (orphan cleanup kept coupled) `remove_metabolites` / `remove_genes` are ported -([manipulation/remove.py](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/src/raven_toolbox/manipulation/remove.py)). +([manipulation/remove.py](https://github.com/CompMetEng/raven-toolbox/blob/develop/src/raven_toolbox/manipulation/remove.py)). `removeReactions` was **not** ported: with orphan cleanup kept coupled (decision: don't separate metabolites from genes), it is identical to `cobra.Model.remove_reactions(remove_orphans=...)`. Separable orphan-met vs orphan-gene cleanup (**R1**, ❌ rejected) was considered then dropped — keep @@ -127,7 +127,7 @@ OR-of-AND-complex (DNF) form (`findPotentialErrors`). **Decision (raven-toolbox) only.** cobra auto-normalizes a GPR on assignment (`"(G1 AND G2) OR G3"` is stored as `"(G1 and G2) or G3"`), so the normalization half is redundant. The non-DNF lint has no cobra equivalent and was ported as `find_non_dnf_grrules`/`is_dnf` -([utils/gpr.py](https://github.com/SysBioChalmers/raven-toolbox/blob/develop/src/raven_toolbox/utils/gpr.py)). +([utils/gpr.py](https://github.com/CompMetEng/raven-toolbox/blob/develop/src/raven_toolbox/utils/gpr.py)). ### readYAMLmodel — no separate legacy parser needed diff --git a/README.md b/README.md index 0924e7e2..eb763dad 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ # raven-toolbox -[![CI](https://github.com/SysBioChalmers/raven-toolbox/actions/workflows/ci.yml/badge.svg)](https://github.com/SysBioChalmers/raven-toolbox/actions/workflows/ci.yml) +[![CI](https://github.com/CompMetEng/raven-toolbox/actions/workflows/ci.yml/badge.svg)](https://github.com/CompMetEng/raven-toolbox/actions/workflows/ci.yml) [![PyPI](https://img.shields.io/pypi/v/raven-toolbox.svg)](https://pypi.org/project/raven-toolbox/) **Reconstruction, Analysis and Visualisation of Metabolic Networks — in Python.** `raven-toolbox` is the Python counterpart of the -[RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) (MATLAB). It builds on +[RAVEN Toolbox](https://github.com/CompMetEng/RAVEN) (MATLAB). It builds on [**cobrapy**](https://github.com/opencobra/cobrapy) for everything cobrapy already does well — simulation, standard analyses, SBML I/O, model manipulation — and adds the functionality that is unique to RAVEN: @@ -41,7 +41,7 @@ COBRA ecosystem. ## Status **raven-toolbox 3.0.0b1** is out — the first beta toward 3.0, tracking the upcoming MATLAB -RAVEN 3.0 beta ([release notes](https://github.com/SysBioChalmers/raven-toolbox/releases/tag/v3.0.0b1), +RAVEN 3.0 beta ([release notes](https://github.com/CompMetEng/raven-toolbox/releases/tag/v3.0.0b1), [changelog](CHANGELOG.md)). It has been validated against MATLAB RAVEN on **Human-GEM** (5 Hart2015 cell-line models, Jaccard 0.975–0.980 — see [the Human-GEM validation study](https://github.com/edkerk/raven-docs/blob/main/docs/parameter-tuning/studies/humangem-validation.md) @@ -75,7 +75,7 @@ pip install --pre raven-toolbox To work against the unreleased code on `develop` instead, install from git: ```bash -git clone https://github.com/SysBioChalmers/raven-toolbox +git clone https://github.com/CompMetEng/raven-toolbox cd raven-toolbox pip install -e ".[dev]" ``` @@ -123,12 +123,12 @@ site is generated from the docstrings here at build time, so a docstring edit reaches the site without anything being copied across. Contributor and maintainer notes are in [CONTRIBUTING.md](CONTRIBUTING.md); the roadmap, the backlog and the MATLAB parity record are in -[raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity). +[raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity). ## Relationship to MATLAB RAVEN `raven-toolbox` is an independent Python reimplementation of the -[RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN), released under the permissive +[RAVEN Toolbox](https://github.com/CompMetEng/RAVEN), released under the permissive **MIT** license. If you use it in scientific work, please cite the RAVEN 2 paper: > Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, diff --git a/data/manifest.schema.json b/data/manifest.schema.json index a426492a..c5ac7d91 100644 --- a/data/manifest.schema.json +++ b/data/manifest.schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://github.com/SysBioChalmers/raven-toolbox/manifest.schema.json", + "$id": "https://github.com/CompMetEng/raven-toolbox/manifest.schema.json", "title": "RAVEN data/binary manifest", "description": "Language-agnostic registry of downloadable raven-toolbox / RAVEN data artefacts and external binary bundles. Consumed by the Python resolvers (raven_toolbox.data / raven_toolbox.binaries) and by MATLAB RAVEN. Every file carries a SHA256 so consumers verify integrity after download.", "type": "object", diff --git a/pyproject.toml b/pyproject.toml index 98b79e31..98814005 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,10 +61,10 @@ excel = [ raven-toolbox-binaries = "raven_toolbox.binaries_cli:main" [project.urls] -Homepage = "https://github.com/SysBioChalmers/raven-toolbox" -Source = "https://github.com/SysBioChalmers/raven-toolbox" -Issues = "https://github.com/SysBioChalmers/raven-toolbox/issues" -"RAVEN MATLAB" = "https://github.com/SysBioChalmers/RAVEN" +Homepage = "https://github.com/CompMetEng/raven-toolbox" +Source = "https://github.com/CompMetEng/raven-toolbox" +Issues = "https://github.com/CompMetEng/raven-toolbox/issues" +"RAVEN MATLAB" = "https://github.com/CompMetEng/RAVEN" [tool.hatch.build.targets.wheel] packages = ["src/raven_toolbox"] diff --git a/scripts/README.md b/scripts/README.md index 6cb8fc58..75ab5034 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -4,7 +4,7 @@ Release-time tooling. Not part of the installed package — run them from a chec with raven-toolbox installed (`pip install -e .`). End users never need these. The full publish workflow (build → upload → manifest → sync) is documented in -[artefact_hosting.md](https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/artefact_hosting.md) +[artefact_hosting.md](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/artefact_hosting.md) (raven-gecko-parity). The localisation/DeepLoc benchmark scripts (`benchmark_deeploc*.py`, @@ -12,15 +12,15 @@ The localisation/DeepLoc benchmark scripts (`benchmark_deeploc*.py`, `build_carvefungi_yeast_model.py`, `compare_localization_sources.py`, `extract_compartment_structure.py`, `finetune_localization_yeast.py`, `benchmark_replicate_yeast_gem.py`) expect their input/output data under `data/deeploc/`, -which lives in [raven-gecko-parity](https://github.com/SysBioChalmers/raven-gecko-parity/tree/develop/data/deeploc) — +which lives in [raven-gecko-parity](https://github.com/CompMetEng/raven-gecko-parity/tree/develop/data/deeploc) — fetch it there first. The write-ups that use these scripts are in -[raven-gecko-parity/docs/localization/](https://github.com/SysBioChalmers/raven-gecko-parity/tree/develop/docs/localization). +[raven-gecko-parity/docs/localization/](https://github.com/CompMetEng/raven-gecko-parity/tree/develop/docs/localization). ## `build_binary_bundles.py` Build the per-platform binary ZIPs (BLAST+/DIAMOND/HMMER) from RAVEN's vetted `software/` binaries (pinned commits) into `dist/binaries/`, with checksums and -provenance. See [maintaining_binaries.md](https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md) +provenance. See [maintaining_binaries.md](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md) (raven-gecko-parity). ```bash @@ -43,7 +43,7 @@ python scripts/publish_to_raven_data.py --dry-run release --tag manifest-v1 data Build the publishable KEGG artefact set from an arranged KEGG dump (see `download_kegg_dump`): the gzipped-YAML reference model, the gzipped-TSV tables, and (with `--hmms`) the per-domain pressed HMM libraries. Output is laid out ready -to upload as release assets. See [maintaining_kegg_data.md](https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_kegg_data.md) +to upload as release assets. See [maintaining_kegg_data.md](https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_kegg_data.md) (raven-gecko-parity). ```bash diff --git a/src/raven_toolbox/analysis/differential_sampling.py b/src/raven_toolbox/analysis/differential_sampling.py index a3bf5585..f5b65e4f 100644 --- a/src/raven_toolbox/analysis/differential_sampling.py +++ b/src/raven_toolbox/analysis/differential_sampling.py @@ -10,7 +10,7 @@ changed, or they moved in opposite directions. ``analyzeSampling.m`` calls ``getFluxZ.m`` directly and cannot be usefully -ported without it (SysBioChalmers/raven-gecko-parity#41), so both are ported +ported without it (CompMetEng/raven-gecko-parity#41), so both are ported together here. Sample orientation is *samples × reactions* (rows are samples, columns are diff --git a/src/raven_toolbox/binaries.py b/src/raven_toolbox/binaries.py index 24a0c8b6..2238bc5b 100644 --- a/src/raven_toolbox/binaries.py +++ b/src/raven_toolbox/binaries.py @@ -8,7 +8,7 @@ → FileNotFoundError with install guidance So a pre-installed/conda binary always wins; the bundled ZIP is the zero-setup -fallback. See https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md +fallback. See https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md for how the release ZIPs and the registry are produced and updated. """ from __future__ import annotations @@ -26,7 +26,7 @@ # Keyed by *bundle*; one bundle can provide several executables (e.g. "blast" -> # blastp + makeblastdb). Baked snapshot of data/manifest.json's `binaries` block — # regenerate from the manifest with `python scripts/make_registry_snippet.py sync` -# (never hand-edit). See https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md. +# (never hand-edit). See https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md. # bundle -> {version, provides:[exe...], platforms:{"-": {url, sha256}}} _REGISTRY: dict = { "blast": { diff --git a/src/raven_toolbox/binaries_cli.py b/src/raven_toolbox/binaries_cli.py index 98850cf5..1d97aacd 100644 --- a/src/raven_toolbox/binaries_cli.py +++ b/src/raven_toolbox/binaries_cli.py @@ -13,7 +13,7 @@ unless ``--force-download`` is given. Tools with no bundle for this OS/arch (e.g. MAFFT/CD-HIT on native Windows) are reported as unavailable with a conda/WSL2 hint — see -https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md. +https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md. """ from __future__ import annotations @@ -82,7 +82,7 @@ def main(argv: list[str] | None = None) -> int: f"{', '.join(r.executable for r in unavailable)}.\n" "Install them via conda (`conda install -c bioconda `) or, on " "native Windows for HMMER/MAFFT/CD-HIT, run inside WSL2 (see " - "https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/maintaining_binaries.md)." + "https://github.com/CompMetEng/raven-gecko-parity/blob/develop/docs/maintaining_binaries.md)." ) if errors: print(f"\n{len(errors)} download(s) failed:") diff --git a/src/raven_toolbox/confidence.py b/src/raven_toolbox/confidence.py index 5880d2aa..ffad5432 100644 --- a/src/raven_toolbox/confidence.py +++ b/src/raven_toolbox/confidence.py @@ -31,7 +31,7 @@ "non-growth associated maintenance reaction", and a name regex must never silence a chemistry check. The design and the measured yeast-GEM distributions are in the `confidence tracking study -`_ on raven-gecko-parity; the +`_ on raven-gecko-parity; the facet set above is closed. Wire it in by calling :func:`score_localization_confidence` on an :class:`~raven_toolbox.localization.AssignmentProposal`, :func:`score_equation_confidence` and :func:`score_gene_association_confidence` on any model, and :func:`mark_curated` when a curator firmly diff --git a/src/raven_toolbox/localization/certify.py b/src/raven_toolbox/localization/certify.py index 4fbb2deb..1074f6a0 100644 --- a/src/raven_toolbox/localization/certify.py +++ b/src/raven_toolbox/localization/certify.py @@ -25,7 +25,7 @@ that cannot grow is never reported as if it could. See the `compartment-assignment redesign -`_ on raven-gecko-parity for the design rationale. +`_ on raven-gecko-parity for the design rationale. """ from __future__ import annotations @@ -473,7 +473,7 @@ def _enrich_multilocalization(model, proposal, scores, sc, conditions, default_c The scalable, ghost-free replacement for the in-MILP ``aF``/``aR`` machinery (see `multi-localisation design - `_): propose, for each placed reaction, a second + `_): propose, for each placed reaction, a second compartment its gene has DeepLoc evidence for (score ``>= threshold``); materialise every candidate as a duplicate; then keep only those a **loopless FVA** shows can carry flux ``>= eps`` in a biomass-supporting solution. A dead duplicate (which would harvest a compartment's score for free) @@ -581,7 +581,7 @@ def assign_compartments( Placement is decided by a flux-free score MILP, and functionality is a separate, materialised-FBA-verified repair (see the module docstring and the `compartment-assignment redesign - `_ on raven-gecko-parity). Notable parameters: + `_ on raven-gecko-parity). Notable parameters: ``transport_cost`` Accepted for signature compatibility but **not used**: the placement master is flux-free and diff --git a/src/raven_toolbox/localization/curation.py b/src/raven_toolbox/localization/curation.py index 57508628..b03dbaa1 100644 --- a/src/raven_toolbox/localization/curation.py +++ b/src/raven_toolbox/localization/curation.py @@ -5,7 +5,7 @@ thousands of calls and review only the highest-value few percent. It is a post-processor — no new solve except an optional gated essentiality FBA — combining several cheap signals that each flag a *distinct* way a placement can be wrong. See the `curation-priority signals study -`_ on raven-gecko-parity for the full catalogue; +`_ on raven-gecko-parity for the full catalogue; this ships the recommended first composite: * **override** — the reaction was placed *against* its gene's top DeepLoc compartment, and that top diff --git a/src/raven_toolbox/localization/scores.py b/src/raven_toolbox/localization/scores.py index c421d4af..9f10fba7 100644 --- a/src/raven_toolbox/localization/scores.py +++ b/src/raven_toolbox/localization/scores.py @@ -184,7 +184,7 @@ def load_deeploc(path: str | Path, *, compartment ids (post-``compartment_map``). **Only the mitochondrial split (`m`/`mm`) is supported by the evidence** (matrix-vs-membrane AUC ~0.92); DeepLoc does *not* separate ER lumen from membrane, so do not add `er`/`erm`. See the `DeepLoc yeast-GEM benchmark - `_ on raven-gecko-parity. + `_ on raven-gecko-parity. ``keep_raw_confidence=True`` attaches the per-gene *pre-normalisation* top probability to :attr:`LocalizationScores.raw_confidence` (normalisation otherwise forces every top to 1.0). It @@ -195,7 +195,7 @@ def load_deeploc(path: str | Path, *, a 0.40 one), so leaving them un-normalised lets a downstream assignment weight confident genes more heavily; the default ``True`` preserves the RAVEN ``parseScores`` convention and keeps multi-source scales comparable. See the `DeepLoc normalisation benchmark - `_ on raven-gecko-parity. + `_ on raven-gecko-parity. """ raw = pd.read_csv(path) wide = _wide_mapped(raw, id_column=None, compartment_map=compartment_map, source=str(path)) diff --git a/src/raven_toolbox/localization/transport_evidence.py b/src/raven_toolbox/localization/transport_evidence.py index a844bcd3..a87274b7 100644 --- a/src/raven_toolbox/localization/transport_evidence.py +++ b/src/raven_toolbox/localization/transport_evidence.py @@ -18,7 +18,7 @@ :func:`annotate_transporters` takes a pre-computed table instead. Substrate matching is *coarse-first* (family → coarse class), with a finer per-substrate ChEBI layer available via ``ontology``. See the `evidence-aware transport scoring design -`_ on raven-gecko-parity for the full design. +`_ on raven-gecko-parity for the full design. """ from __future__ import annotations diff --git a/src/raven_toolbox/localization/transporter_tables.py b/src/raven_toolbox/localization/transporter_tables.py index bb9e0645..5c7017a3 100644 --- a/src/raven_toolbox/localization/transporter_tables.py +++ b/src/raven_toolbox/localization/transporter_tables.py @@ -2,7 +2,7 @@ These small hand-maintained tables are the "coarse-first" substrate layer of the evidence-aware transport scoring (see the `design -`_ on raven-gecko-parity). They serve two consumers: +`_ on raven-gecko-parity). They serve two consumers: * ``scripts/build_transporter_data.py`` reads :data:`PFAM_TRANSPORTERS` to know **which** Pfam HMMs to fetch (from InterPro) into the bundled transporter HMM database. diff --git a/src/raven_toolbox/localization/triage.py b/src/raven_toolbox/localization/triage.py index 19fd4d69..7bd14267 100644 --- a/src/raven_toolbox/localization/triage.py +++ b/src/raven_toolbox/localization/triage.py @@ -21,7 +21,7 @@ Impact (essentiality / flux) and pathway-level aggregation are v2/v3; this is the cheap, no-solver core. See the `DeepLoc yeast-GEM benchmark -`_ on raven-gecko-parity for where the thresholds come from. +`_ on raven-gecko-parity for where the thresholds come from. """ from __future__ import annotations @@ -38,7 +38,7 @@ #: Per-compartment reliability of a DeepLoc 2.1 organelle call, finetuned on the slow (ProtT5) #: yeast-GEM run (organelle-collapsed accuracy; `localisation finetuning -#: `_ on raven-gecko-parity, +#: `_ on raven-gecko-parity, #: regenerate with ``scripts/finetune_localization_yeast.py``). ``mm`` inherits ``m`` because the #: mitochondrial split is the one validated routing (AUC ~0.93); the other organelle membranes and #: ``ce``/``lp`` stay 0 — DeepLoc cannot reach them reliably. Yeast/DeepLoc-specific — override via diff --git a/tests/parity/README.md b/tests/parity/README.md index 7d35a085..123d60dc 100644 --- a/tests/parity/README.md +++ b/tests/parity/README.md @@ -60,7 +60,7 @@ Two sources, with different trade-offs: `RAVEN_ROOT` points at one: ```bash - git clone --depth 1 -b develop3 https://github.com/SysBioChalmers/RAVEN + git clone --depth 1 -b develop https://github.com/CompMetEng/RAVEN RAVEN_ROOT=$PWD/RAVEN pytest -m parity ``` diff --git a/tests/parity/conftest.py b/tests/parity/conftest.py index 4f925073..53b70778 100644 --- a/tests/parity/conftest.py +++ b/tests/parity/conftest.py @@ -29,8 +29,8 @@ def raven_root() -> Path: if not root: pytest.skip( "RAVEN_ROOT is not set. Clone RAVEN and point at it to run the " - "cross-language checks: git clone --depth 1 -b develop3 " - "https://github.com/SysBioChalmers/RAVEN && RAVEN_ROOT=$PWD/RAVEN " + "cross-language checks: git clone --depth 1 -b develop " + "https://github.com/CompMetEng/RAVEN && RAVEN_ROOT=$PWD/RAVEN " "pytest -m parity" ) path = Path(root)