Update Dependencies

[arrjon]

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Codecov Report

❌ Patch coverage is 76.92308% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.18%. Comparing base (47d494e) to head (5f2b297).

Files with missing lines	Patch %	Lines
pyabc/petab/amici.py	75.00%	3 Missing ⚠️
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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #664      +/-   ##
==========================================
- Coverage   79.93%   79.18%   -0.76%     
==========================================
  Files         141      141              
  Lines        8325     8327       +2     
  Branches     1110     1110              
==========================================
- Hits         6655     6594      -61     
- Misses       1298     1363      +65     
+ Partials      372      370       -2     

Flag	Coverage Δ
base	59.31% <7.69%> (-0.12%)	⬇️
external-R	36.82% <7.69%> (+0.13%)	⬆️
external-other-simulators	31.43% <7.69%> (-4.01%)	⬇️
migrate	25.35% <7.69%> (-0.01%)	⬇️
petab	35.49% <76.92%> (+0.05%)	⬆️
visualization	52.63% <7.69%> (-0.16%)	⬇️

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[Copilot]

Pull request overview

This PR updates pyABC’s dependency/tooling stack (notably Python and AMICI), adjusts CI/tox configuration accordingly, and updates tests/docs to match new APIs and formatting expectations.

Changes:

• Drop Python 3.10 support (package metadata + CI matrix) and align linting/tooling targets to Python 3.11+.
• Update AMICI/PEtab integration to AMICI ≥ 1.0 APIs and adjust PEtab tests/examples accordingly.
• Restructure external (R/Julia) test coverage by moving rpy2-related storage tests into dedicated external tox envs and updating CI provisioning (setup-r / Julia/PyCall).

Reviewed changes

Copilot reviewed 25 out of 26 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
tox.ini	Removes R from base env; expands external env commands; adds floating git deps for PEtab suite.
pyproject.toml	Raises minimum Python to 3.11 and updates dependency constraints (incl. AMICI ≥ 1.0).
pyabc/petab/amici.py	Migrates AMICI integration to new import paths/APIs and updates solver settings handling.
test/petab/test_petab.py	Updates AMICI PEtab import + solver creation calls for AMICI 1.0+.
test/petab/test_petab_suite.py	Updates PEtab suite execution to new AMICI API functions.
test/external/test_rpy2_storage.py	Adds external-only rpy2 storage test coverage for History sum-stats.
test/external/test_rpy2_bytesstorage.py	Adds external-only bytes storage coverage for rpy2 DataFrames.
test/base/test_storage.py	Removes rpy2-specific assertions from base storage tests.
test/base/test_bytesstorage.py	Removes rpy2-related bytesstorage cases from base tests.
test/base/test_integrated_model.py	Minor comment edit (contains a new typo).
CHANGELOG.rst	Adds 0.12.18 release notes (Python 3.10 drop, AMICI 1.0 support).
.github/workflows/ci.yml	Updates CI matrix; adds setup-r for external envs; tweaks Julia setup behavior; updates coverage upload step.
.github/workflows/deploy.yml	Updates checkout/python setup action versions for release deploy.
.github/workflows/install_deps.sh	Removes R installation path and simplifies AMICI deps install.
.pre-commit-config.yaml	Moves default pre-commit Python to 3.13.
doc/sampler.rst	Whitespace cleanup.
doc/examples/*.ipynb	Mostly quote/format normalization; updates AMICI API usage in PEtab notebooks.
pyabc/version.py	Bumps version to 0.12.18.

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