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AMICI-dev / AMICI

Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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Use `petab.v1` #2471

Closed dweindl closed 3 months ago

dweindl commented 3 months ago

Make amici ready for using libpetab's petab.v1 package instead of the previous, now deprecated imports.

Move tests/petab to tests/petab_ to avoid import issues (tests.petab namespace package vs actual petab package)

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 77.61%. Comparing base (9fe31b6) to head (b56235a). Report is 33 commits behind head on develop.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471/graphs/tree.svg?width=650&height=150&src=pr&token=1bt9lbspzk&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev)](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) ```diff @@ Coverage Diff @@ ## develop #2471 +/- ## =========================================== + Coverage 76.20% 77.61% +1.40% =========================================== Files 319 324 +5 Lines 20772 20933 +161 Branches 1462 1464 +2 =========================================== + Hits 15830 16247 +417 + Misses 4938 4683 -255 + Partials 4 3 -1 ``` | [Flag](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | Coverage Δ | | |---|---|---| | [cpp](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `73.37% <ø> (-0.02%)` | :arrow_down: | | [cpp_python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `34.08% <ø> (ø)` | | | [petab](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `36.64% <ø> (?)` | | | [python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `72.15% <ø> (-0.01%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files with missing lines](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | Coverage Δ | | |---|---|---| | [python/sdist/amici/petab/cli/import\_petab.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fcli%2Fimport_petab.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL2NsaS9pbXBvcnRfcGV0YWIucHk=) | `0.00% <ø> (ø)` | | | [python/sdist/amici/petab/conditions.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fconditions.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL2NvbmRpdGlvbnMucHk=) | `97.43% <ø> (+23.93%)` | :arrow_up: | | [python/sdist/amici/petab/import\_helpers.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fimport_helpers.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL2ltcG9ydF9oZWxwZXJzLnB5) | `86.15% <ø> (+7.69%)` | :arrow_up: | | [python/sdist/amici/petab/parameter\_mapping.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fparameter_mapping.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3BhcmFtZXRlcl9tYXBwaW5nLnB5) | `81.15% <ø> (+28.27%)` | :arrow_up: | | [python/sdist/amici/petab/petab\_import.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fpetab_import.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3BldGFiX2ltcG9ydC5weQ==) | `66.66% <ø> (ø)` | | | [python/sdist/amici/petab/petab\_problem.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fpetab_problem.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3BldGFiX3Byb2JsZW0ucHk=) | `87.69% <ø> (+87.69%)` | :arrow_up: | | [python/sdist/amici/petab/pysb\_import.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fpysb_import.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3B5c2JfaW1wb3J0LnB5) | `51.85% <ø> (+46.29%)` | :arrow_up: | | [python/sdist/amici/petab/sbml\_import.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fsbml_import.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3NibWxfaW1wb3J0LnB5) | `54.28% <ø> (+27.14%)` | :arrow_up: | | [python/sdist/amici/petab/simulations.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fsimulations.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3NpbXVsYXRpb25zLnB5) | `92.85% <ø> (+22.44%)` | :arrow_up: | | [python/sdist/amici/petab/simulator.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpetab%2Fsimulator.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3BldGFiL3NpbXVsYXRvci5weQ==) | `100.00% <ø> (+100.00%)` | :arrow_up: | | ... and [5 more](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | | ... and [8 files with indirect coverage changes](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2471/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev)