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Remove deprecated petab.* aliases for petab.v1 - #538
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Accessing `petab.<name>` or importing `petab.<module>` has been deprecated in favor of `petab.v1` since 0.4.0. Remove the `__getattr__` fallback and the `sys.modules` aliases. The only top-level names left are `petab.v1`, `petab.v2`, `petab.ENV_NUM_THREADS` and `petab.__version__`. Everything else now raises `AttributeError` or `ModuleNotFoundError`. As a side effect, `import petab` no longer imports `petab.v1`. Removing the eager `petab.v1` import exposed a circular import between `petab.versions` and `petab.v1.yaml`. Fix it by importing `petab.v1` lazily in `get_major_version`. Also: * import `ENV_NUM_THREADS` in `petab.v1.parameter_mapping` from `petab` instead of defining it again * update tests, docstring cross-references, messages, README and the visualization notebook to use `petab.v1` * remove `test_problem_with_sbml_model`, which only differed from `test_get_condition_specific_models` by using the deprecated alias * add a changelog section for the unreleased 0.10.0 Generated with AI assistance. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #538 +/- ##
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- Coverage 76.77% 76.67% -0.10%
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Files 67 67
Lines 7547 7516 -31
Branches 1346 1339 -7
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- Hits 5794 5763 -31
- Misses 1259 1262 +3
+ Partials 494 491 -3 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Accessing
petab.<name>or importingpetab.<module>has been deprecated in favor ofpetab.v1since 0.4.0 (July 2024). This removes the__getattr__fallback and thesys.modulesaliases frompetab/__init__.py. The only top-level names left arepetab.v1,petab.v2,petab.ENV_NUM_THREADSandpetab.__version__. Everything else now raisesAttributeErrororModuleNotFoundError. As a side effect,import petabno longer importspetab.v1.This is a breaking change for code that still uses the old paths. The fix is to replace
import petabwithimport petab.v1 as petabandfrom petab.<module> import ...withfrom petab.v1.<module> import ....Other changes:
petab.versionsandpetab.v1.yamlthat the old eagerpetab.v1import had been hiding.petab.v1.parameter_mappingnow importsENV_NUM_THREADSfrompetabinstead of defining it again.petab.v1.test_problem_with_sbml_model, which only differed fromtest_get_condition_specific_modelsby using the deprecated alias.Requires Benchmarking-Initiative/Benchmark-Models-PEtab#330: CI installs
benchmark_models_petabfrom master, which still importspetab.yaml.tests/v1/test_priors.pyfails until that PR is merged.🤖 Drafted with AI assistance (Claude Code)