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AMICI-dev / AMICI

Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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Remove deprecated functionality for PEtab import from individual files instead of petab.Problem #2459

Closed dweindl closed 3 months ago

dweindl commented 3 months ago

Since almost two years, it's possible to pass a petab.Problem, which is safer and more convenient. Omitting the parameter table for model import (since there is no option to supply this) is likely to produce unwanted results (see #2458 and #2455 for more details), and therefore, this functionality is best removed.

Closes #2458

After #2392

socket-security[bot] commented 3 months ago

New and removed dependencies detected. Learn more about Socket for GitHub ↗︎

Package New capabilities Transitives Size Publisher

🚮 Removed packages: pypi/oldest-supported-numpy@2023.12.21, pypi/oldest-supported-numpy@2023.12.21

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codecov[bot] commented 3 months ago

Codecov Report

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

Project coverage is 36.66%. Comparing base (6277a5e) to head (3637854). Report is 27 commits behind head on develop.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2459/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/2459?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 #2459 +/- ## ======================================== Coverage 36.66% 36.66% ======================================== Files 103 103 Lines 14881 14881 Branches 1388 1388 ======================================== Hits 5456 5456 Misses 9116 9116 Partials 309 309 ``` | [Flag](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2459/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | Coverage Δ | | |---|---|---| | [petab](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2459/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `36.66% <ø> (ø)` | | 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/2459?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/sbml\_import.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2459?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> (ø)` | |