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AMICI-dev / AMICI

Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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Release 0.29.0 #2597

Closed dweindl closed 1 day ago

socket-security[bot] commented 4 days ago

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

Package New capabilities Transitives Size Publisher
pypi/beartype@0.19.0 environment, eval, filesystem, shell, unsafe Transitive: network +70 677 MB leycec
pypi/diffrax@0.6.0 eval Transitive: environment, filesystem, network, shell, unsafe +6 1.98 MB patrick-kidger
pypi/equinox@0.11.9 environment, eval, filesystem Transitive: shell, unsafe +2 1.17 MB patrick-kidger
pypi/interpax@0.3.3 environment, eval, filesystem, shell 0 258 kB f0uriest
pypi/jax@0.4.35 environment, eval, filesystem, network, shell, unsafe 0 8 MB Jake.Vanderplas, gnecula, google_opensource, ...6 more
pypi/jaxlib@0.4.35 environment, eval, network, shell, unsafe 0 364 MB Jake.Vanderplas, gnecula, google_opensource, ...6 more
pypi/jaxtyping@0.2.36 None 0 0 B
pypi/optimistix@0.0.9 eval Transitive: environment, filesystem, shell, unsafe +2 827 kB patrick-kidger

View full report↗︎

codecov[bot] commented 4 days ago

Codecov Report

Attention: Patch coverage is 32.21289% with 242 lines in your changes missing coverage. Please review.

Project coverage is 36.95%. Comparing base (c3bbdd9) to head (593b800). Report is 20 commits behind head on master.

Files with missing lines Patch % Lines
src/hdf5.cpp 0.00% 118 Missing :warning:
python/sdist/amici/jax/petab.py 28.57% 50 Missing :warning:
python/sdist/amici/jax/model.py 45.34% 47 Missing :warning:
python/sdist/amici/petab/parameter_mapping.py 46.66% 8 Missing :warning:
python/sdist/amici/__init__.py 66.66% 5 Missing :warning:
python/tests/conftest.py 37.50% 5 Missing :warning:
python/sdist/amici/jaxcodeprinter.py 76.92% 3 Missing :warning:
python/sdist/amici/__main__.py 0.00% 2 Missing :warning:
python/sdist/amici/de_export.py 92.00% 2 Missing :warning:
src/solver_cvodes.cpp 0.00% 2 Missing :warning:

:exclamation: There is a different number of reports uploaded between BASE (c3bbdd9) and HEAD (593b800). Click for more details.

HEAD has 13 uploads less than BASE | Flag | BASE (c3bbdd9) | HEAD (593b800) | |------|------|------| |petab|2|1| |python|6|0| |cpp_python|3|0| |cpp|3|0|
Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597/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/2597?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) ```diff @@ Coverage Diff @@ ## master #2597 +/- ## =========================================== - Coverage 77.83% 36.95% -40.88% =========================================== Files 325 108 -217 Lines 21852 15346 -6506 Branches 1456 1403 -53 =========================================== - Hits 17008 5671 -11337 - Misses 4833 9361 +4528 - Partials 11 314 +303 ``` | [Flag](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597/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/2597/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `?` | | | [cpp_python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `?` | | | [petab](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `36.95% <32.21%> (-0.21%)` | :arrow_down: | | [python](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | `?` | | 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/2597?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 | | |---|---|---| | [include/amici/rdata.h](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree&filepath=include%2Famici%2Frdata.h&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-aW5jbHVkZS9hbWljaS9yZGF0YS5o) | `66.66% <ø> (-33.34%)` | :arrow_down: | | [include/amici/solver.h](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree&filepath=include%2Famici%2Fsolver.h&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-aW5jbHVkZS9hbWljaS9zb2x2ZXIuaA==) | `59.37% <ø> (-34.75%)` | :arrow_down: | | [python/sdist/amici/jax/\_\_init\_\_.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fjax%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL2pheC9fX2luaXRfXy5weQ==) | `100.00% <100.00%> (ø)` | | | [python/sdist/amici/petab/conditions.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?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=) | `97.45% <100.00%> (+0.02%)` | :arrow_up: | | [python/sdist/amici/petab/import\_helpers.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?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) | `85.93% <ø> (ø)` | | | [python/sdist/amici/petab/petab\_import.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?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/pysb\_import.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fpysb_import.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL3B5c2JfaW1wb3J0LnB5) | `58.22% <100.00%> (-36.08%)` | :arrow_down: | | [src/solver.cpp](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree&filepath=src%2Fsolver.cpp&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-c3JjL3NvbHZlci5jcHA=) | `31.85% <ø> (-46.65%)` | :arrow_down: | | [python/sdist/amici/\_\_main\_\_.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2F__main__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL19fbWFpbl9fLnB5) | `0.00% <0.00%> (ø)` | | | [python/sdist/amici/de\_export.py](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree&filepath=python%2Fsdist%2Famici%2Fde_export.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev#diff-cHl0aG9uL3NkaXN0L2FtaWNpL2RlX2V4cG9ydC5weQ==) | `82.81% <92.00%> (-13.33%)` | :arrow_down: | | ... and [8 more](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev) | | ... and [285 files with indirect coverage changes](https://app.codecov.io/gh/AMICI-dev/AMICI/pull/2597/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=AMICI-dev)