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Release 0.21.2 #2287

Merged
merged 15 commits into from
Feb 6, 2024
Merged

Release 0.21.2 #2287

merged 15 commits into from
Feb 6, 2024

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dweindl
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@dweindl dweindl commented Feb 6, 2024

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dweindl and others added 15 commits January 17, 2024 09:47
Use PyPI [trusted publishing](https://docs.pypi.org/trusted-publishers/) instead of username/password.
Avoids
```
.tox\unit\lib\site-packages\pandas\__init__.py:249: in <module>
    warnings.warn(
E   DeprecationWarning:
E   Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
E   (to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
E   but was not found to be installed on your system.
E   If this would cause problems for you,
E   please provide us feedback at pandas-dev/pandas#54466
```
* Update valgrind suppressions

* ..

* ..
* Fix Solver copyctor issues with swig4.2

Closes AMICI-dev#2275
* GHA: update actions to use Node.js 20

Fixes this warnings:
> Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/checkout@v3, actions/upload-artifact@v3

Closes AMICI-dev#2277

* unique artifact names

* [email protected]
Fix `IndexError: tuple index out of range` when calling `amici.ExpData` without any argument.
> PRs made from forks to the upstream public repos will support tokenless (e.g. contributors to OS projects do not need the upstream repo's Codecov token)
Some formatting changed with clang17.
Re-run clang-format and cmake-format.
…ev#2281)

* Fix invalid type error when loading antimony model from file

`pathlib.Path` -> `str`

* More informative exceptions
The second argument never was optional.
Not sure whether there would be any good default value.
@dweindl dweindl requested a review from a team as a code owner February 6, 2024 13:00
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New dependencies detected. Learn more about Socket for GitHub ↗︎

Package New capabilities Transitives Size Publisher
pypi/[email protected] environment, filesystem, shell Transitive: eval, network, unsafe +275 1.41 GB svenevs

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codecov bot commented Feb 6, 2024

Codecov Report

Attention: 23 lines in your changes are missing coverage. Please review.

Comparison is base (ec4ee25) 77.21% compared to head (5e64ed4) 77.93%.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2287      +/-   ##
==========================================
+ Coverage   77.21%   77.93%   +0.72%     
==========================================
  Files          94      318     +224     
  Lines       15089    20511    +5422     
  Branches        0     1436    +1436     
==========================================
+ Hits        11651    15986    +4335     
- Misses       3438     4522    +1084     
- Partials        0        3       +3     
Flag Coverage Δ
cpp 76.35% <90.17%> (+2.25%) ⬆️
cpp_python 33.99% <17.67%> (-3.37%) ⬇️
petab 36.40% <35.22%> (-17.61%) ⬇️
python 72.49% <90.12%> (-4.49%) ⬇️
sbmlsuite ∅ <ø> (∅)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
include/amici/abstract_model.h 100.00% <ø> (+100.00%) ⬆️
include/amici/backwardproblem.h 100.00% <ø> (ø)
include/amici/misc.h 79.59% <100.00%> (+15.59%) ⬆️
include/amici/model.h 73.68% <ø> (+12.57%) ⬆️
include/amici/model_ode.h 100.00% <ø> (ø)
include/amici/rdata.h 100.00% <ø> (+4.76%) ⬆️
include/amici/serialization.h 96.61% <100.00%> (ø)
include/amici/simulation_parameters.h 100.00% <ø> (+33.33%) ⬆️
include/amici/solver.h 100.00% <ø> (+18.75%) ⬆️
include/amici/solver_cvodes.h 100.00% <ø> (ø)
... and 20 more

... and 241 files with indirect coverage changes

@dweindl dweindl merged commit fa7c0bd into AMICI-dev:master Feb 6, 2024
34 checks passed
@dweindl dweindl deleted the release_0.21.2 branch February 6, 2024 17:40
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2 participants