From 68ab640ead3364cb5d2e7a238b31a839fdbeaa75 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Tue, 20 Oct 2026 14:47:00 +0200
Subject: [PATCH] Use dependency groups for development dependencies

Move development-only dependencies from extras to dependency groups
(`test`, `doc`, `dev`), keep feature extras (`antimony`, `combine`,
`reports`, `sciml`, `vis`) and add an `all` extra.

* `dev` (`test` + `pre-commit`) is the default group for `uv sync`.
* Merge the former `ci` group into `test`, since the test suite
  requires `petabtests` and `benchmark_models_petab`.
* Use pysb from master via `tool.uv.sources`.
* Relax the `Jinja2` pin in `reports`.
* Drop the unused `sphinxcontrib-napoleon`.
* Read the Docs: install via `uv sync --group doc`.
* CI: fetch the BNGL test corpus without syncing the project.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 .github/workflows/ci_tests.yml |  4 +--
 .readthedocs.yaml              | 17 ++++-----
 doc/development.rst            |  2 +-
 pyproject.toml                 | 63 ++++++++++++++++++----------------
 4 files changed, 45 insertions(+), 41 deletions(-)

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
index 44919375..a140c3ab 100644
--- a/.github/workflows/ci_tests.yml
+++ b/.github/workflows/ci_tests.yml
@@ -30,11 +30,11 @@ jobs:
       if: matrix.platform == 'ubuntu-latest'
 
     - name: Fetch BNGL test corpus
-      run: uv run python tests/v1/fetch_bngl_corpus.py
+      run: uv run --no-project python -P tests/v1/fetch_bngl_corpus.py
 
     - name: Unit tests
       run: |
-        uv sync --group ci
+        uv sync --no-default-groups --group test
         uv pip list
         uv run pytest --cov=petab --cov-report=xml --cov-append --durations=10 tests
 
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 51f9841e..132b6768 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -11,11 +11,12 @@ build:
   os: "ubuntu-24.04"
   tools:
     python: "3.12"
-
-python:
-   install:
-   - method: pip
-     path: .
-     extra_requirements:
-        - doc
-        - vis
+  jobs:
+    pre_create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    create_environment:
+      - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+    install:
+      - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --no-default-groups --group doc
diff --git a/doc/development.rst b/doc/development.rst
index 71b44d51..cf829692 100644
--- a/doc/development.rst
+++ b/doc/development.rst
@@ -85,7 +85,7 @@ To build the documentation, run:
 
 .. code-block:: bash
 
-    uv sync --extra doc --extra vis
+    uv sync --group doc
     cd doc
     make html
     # then open `build/html/index.html` in a browser
diff --git a/pyproject.toml b/pyproject.toml
index f1683d93..482c30ac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,48 +33,26 @@ maintainers = [
 ]
 
 [project.optional-dependencies]
-tests = [
-    "antimony>=3.1.0",
-    "copasi-basico>=0.85",
-    "petab_sciml",
-    "pysb",
-    "pytest",
-    "pytest-cov",
-    "scipy",
-]
-quality = [
-    "pre-commit",
-]
-reports = [
-    # https://github.com/spatialaudio/nbsphinx/issues/641
-    "Jinja2==3.1.6",
-]
 antimony = [
     "antimony>=2.14.0",
 ]
 combine = [
     "python-libcombine>=0.2.6",
 ]
-doc = [
-    "sphinx>=3.5.3, !=5.1.0",
-    "sphinxcontrib-napoleon>=0.7",
-    "sphinx-markdown-tables>=0.0.15",
-    "sphinx-rtd-theme>=0.5.1",
-    "m2r2",
-    "myst-nb>=0.14.0",
-    # https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312
-    "ipython>=7.21.0, !=8.7.0",
-    "pysb",
-    "antimony>=2.14.0",
-]
 vis = [
     "matplotlib>=3.6.0",
     "seaborn",
     "scipy"
 ]
+reports = [
+    "Jinja2",
+]
 sciml = [
     "petab_sciml",
 ]
+all = [
+    "petab[antimony,combine,reports,sciml,vis]",
+]
 
 [project.scripts]
 petablint = "petab.petablint:main"
@@ -85,19 +63,44 @@ Repository = "https://github.com/PEtab-dev/libpetab-python"
 Documentation = "https://petab.readthedocs.io/projects/libpetab-python/"
 
 [dependency-groups]
-ci = [
-    "petab[tests,reports,combine,vis]",
+test = [
+    "petab[all]",
+    "antimony>=3.1.0",
+    "copasi-basico>=0.85",
+    "pysb",
+    "pytest",
+    "pytest-cov",
+    "scipy",
     "petabtests @ git+https://github.com/PEtab-dev/petab_test_suite@main",
     "benchmark_models_petab @ git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python",
 ]
+doc = [
+    "petab[antimony,vis]",
+    "sphinx>=3.5.3, !=5.1.0",
+    "sphinx-markdown-tables>=0.0.15",
+    "sphinx-rtd-theme>=0.5.1",
+    "m2r2",
+    "myst-nb>=0.14.0",
+    # https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312
+    "ipython>=7.21.0, !=8.7.0",
+    "pysb",
+]
+dev = [
+    {include-group = "test"},
+    "pre-commit",
+]
 
 [tool.uv]
+default-groups = ["dev"]
 # pysb<1.17 fails to build: its legacy `ez_setup.py` bootstrap downloads
 # setuptools from a defunct pypi.python.org URL.
 constraint-dependencies = ["pysb>=1.17.0"]
 # pysb pins an older sympy than we need; force a newer one.
 override-dependencies = ["sympy>=1.12.1"]
 
+[tool.uv.sources]
+pysb = { git = "https://github.com/pysb/pysb", branch = "master" }
+
 [tool.setuptools.packages.find]
 include = ["petab", "petab.*"]
 namespaces = false