Deprecate passing individual tables to `amici_import_petab`

[dweindl]

and replace deprecated petab.Problem.from_files in amici.petab.cli.import_petab._main.

Fixes #2460

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 0% with 13 lines in your changes missing coverage. Please review.

Project coverage is 77.62%. Comparing base (474b473) to head (e6ca959). Report is 1 commits behind head on develop.

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[](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2464?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 #2464 +/- ## =========================================== - Coverage 77.65% 77.62% -0.03% =========================================== Files 324 324 Lines 20927 20933 +6 Branches 1464 1464 =========================================== Hits 16250 16250 - Misses 4674 4680 +6 Partials 3 3 ``` | [Flag](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2464/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/2464/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `73.39% <0.00%> (-0.03%)` | :arrow_down: | | [cpp_python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2464/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `34.08% <0.00%> (-0.01%)` | :arrow_down: | | [petab](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2464/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `36.64% <0.00%> (-0.02%)` | :arrow_down: | | [python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2464/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `72.16% <0.00%> (-0.03%)` | :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](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2464?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/2464?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% <0.00%> (ø)` | |

[dweindl]

Maybe add tests for both calls?

the yaml-based one is used for the benchmark collection, added one for the deprecated call