Update references to the moved repository

.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/<ProblemID>/v1/` (`problem.yaml`, `model.xml`, `conditions.tsv`,
     `measurements.tsv`, `observables.tsv`, `parameters.tsv`, `simulations.tsv`, `visualizations.tsv`);

.github/workflows/gh-pages.yml

@@ -3,7 +3,7 @@ name: Deploy to Pages
 on:
   push:
     branches:
-        - master
+        - main
         - pages
   workflow_dispatch:
 

.github/workflows/simulate.yml

@@ -2,7 +2,7 @@ name: Simulate
 on:
   push:
     branches:
-      - master
+      - main
   workflow_dispatch:
   merge_group:
   schedule:

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).

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

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.

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"

src/python/benchmark_models_petab/_site/templates/index.html.j2

@@ -337,7 +337,7 @@ footer {
         <p class="lead">
           Parameter estimation problems with published models and experimental
           data in the <a href="https://petab.readthedocs.io">PEtab</a> format,
-          from the <a href="{{ repo_url }}">Benchmark-Models-PEtab</a>
+          from the <a href="{{ repo_url }}">petab-benchmark-problems</a>
           collection.
         </p>
       </div>
@@ -383,7 +383,7 @@ footer {
 </main>
 <footer>
 <div class="wrap">
-  <a href="{{ repo_url }}">Benchmark-Models-PEtab on GitHub</a> ·
+  <a href="{{ repo_url }}">petab-benchmark-problems on GitHub</a> ·
   <a href="https://petab.readthedocs.io">PEtab documentation</a> ·
   <a href="{{ contributing_url }}">Contribute a problem</a>
 </div>

src/python/pyproject.toml

@@ -16,7 +16,7 @@ maintainers = [
 authors = [
     { name = "The Benchmark-Models-PEtab contributors" }
 ]
-urls = { "Homepage" = "https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab" }
+urls = { "Homepage" = "https://github.com/PEtab-dev/petab-benchmark-problems" }
 dependencies = [
     "petab>=0.4.0",
     "pydantic>=2",