From ca4cfa5dad769db147c4f5df53ade679eaa68d07 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 9 Nov 2026 12:37:43 +0100 Subject: [PATCH] Update references to the moved repository The repository moved to `PEtab-dev/petab-benchmark-problems` and the default branch changed from `master` to `main`. Update URLs, the GitHub Pages URL, workflow branch triggers, and `GITHUB_REPO` / `GITHUB_DEFAULT_BRANCH` used for generated links. Co-Authored-By: Claude Opus 5.5 --- .github/pull_request_template.md | 4 ++-- .github/workflows/gh-pages.yml | 2 +- .github/workflows/simulate.yml | 2 +- CONTRIBUTING.md | 2 +- INSTALL.md | 6 +++--- README.md | 2 +- src/python/benchmark_models_petab/C.py | 4 ++-- .../benchmark_models_petab/_site/templates/index.html.j2 | 4 ++-- src/python/pyproject.toml | 2 +- 9 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index e5a511ce..ba3e3896 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -11,8 +11,8 @@ - [ ] Experience of fitting / uncertainty analysis (e.g. optimizer used, hyperparameters, reproducibility of best fit) - [ ] Source of nominal parameters (e.g.: taken from the original publication, or from your own fitting) - [ ] The SBML file - - [ ] Annotation with reference to the original publication ([example](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L4-L14)) - - [ ] The model ID and model name attributes in the SBML model file match the problem name ([example](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L3)) + - [ ] Annotation with reference to the original publication ([example](https://github.com/PEtab-dev/petab-benchmark-problems/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L4-L14)) + - [ ] The model ID and model name attributes in the SBML model file match the problem name ([example](https://github.com/PEtab-dev/petab-benchmark-problems/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L3)) - [ ] PEtab files - [ ] Files are placed under `problems//v1/` (`problem.yaml`, `model.xml`, `conditions.tsv`, `measurements.tsv`, `observables.tsv`, `parameters.tsv`, `simulations.tsv`, `visualizations.tsv`); diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 1d25657b..f1aa9ed2 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -3,7 +3,7 @@ name: Deploy to Pages on: push: branches: - - master + - main - pages workflow_dispatch: diff --git a/.github/workflows/simulate.yml b/.github/workflows/simulate.yml index f8346e69..7c46b329 100644 --- a/.github/workflows/simulate.yml +++ b/.github/workflows/simulate.yml @@ -2,7 +2,7 @@ name: Simulate on: push: branches: - - master + - main workflow_dispatch: merge_group: schedule: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 594c32f1..d8dd88a4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -51,5 +51,5 @@ log-transformed. If the same placeholder also receives non-positive numbers or p stay on linear scale, the observable is split, so that each copy's placeholder only receives overrides that can be log-transformed, or none at all. -See [#333](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/issues/333) for +See [#333](https://github.com/PEtab-dev/petab-benchmark-problems/issues/333) for the rationale (option C there). diff --git a/INSTALL.md b/INSTALL.md index 667cb4ee..ee3bfd45 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -6,12 +6,12 @@ There are various ways of installing or downloading the benchmark models: The repository containing the benchmark models can be cloned from GitHub via: - git clone git@github.com:Benchmarking-Initiative/Benchmark-Models-PEtab.git + git clone git@github.com:PEtab-dev/petab-benchmark-problems.git ## Download source files The Benchmark files can be downloaded from GitHub as a -[ZIP file](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/archive/refs/heads/master.zip). +[ZIP file](https://github.com/PEtab-dev/petab-benchmark-problems/archive/refs/heads/main.zip). ## Python package @@ -20,7 +20,7 @@ provides access functionality at [src/python](src/python). It can be installed directly from GitHub via: - pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python + pip install git+https://github.com/PEtab-dev/petab-benchmark-problems.git@main#subdirectory=src/python Alternatively, when the whole repository has been cloned (see above), the python package can be installed via diff --git a/README.md b/README.md index 85729fd5..1d1f1e71 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ as well as the numbers of observables, parameters, measurements, and experimental conditions, and features such as events, preequilibration, and noise and prior distributions. For these details, see the sortable and filterable -[overview tables](https://benchmarking-initiative.github.io/Benchmark-Models-PEtab/). +[overview tables](https://petab-dev.github.io/petab-benchmark-problems/). The following table lists the problems in the collection and the available encodings in PEtab v1 and v2. diff --git a/src/python/benchmark_models_petab/C.py b/src/python/benchmark_models_petab/C.py index e4e54aec..9711b438 100644 --- a/src/python/benchmark_models_petab/C.py +++ b/src/python/benchmark_models_petab/C.py @@ -17,5 +17,5 @@ SIMULATIONS_FILENAME: str = "simulations.tsv" METADATA_FILENAME: str = "metadata.yaml" -GITHUB_REPO: str = "Benchmarking-Initiative/Benchmark-Models-PEtab" -GITHUB_DEFAULT_BRANCH: str = "master" +GITHUB_REPO: str = "PEtab-dev/petab-benchmark-problems" +GITHUB_DEFAULT_BRANCH: str = "main" diff --git a/src/python/benchmark_models_petab/_site/templates/index.html.j2 b/src/python/benchmark_models_petab/_site/templates/index.html.j2 index 278ddd8d..037b9fa6 100644 --- a/src/python/benchmark_models_petab/_site/templates/index.html.j2 +++ b/src/python/benchmark_models_petab/_site/templates/index.html.j2 @@ -337,7 +337,7 @@ footer {

Parameter estimation problems with published models and experimental data in the PEtab format, - from the Benchmark-Models-PEtab + from the petab-benchmark-problems collection.

@@ -383,7 +383,7 @@ footer {