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Release 0.25.0 #2433

Merged
merged 20 commits into from
May 8, 2024
Merged

Release 0.25.0 #2433

merged 20 commits into from
May 8, 2024

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dweindl
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@dweindl dweindl commented May 7, 2024

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dweindl and others added 17 commits April 22, 2024 09:58
Let's reduce the number of package configuration files...
…`ExpData`. (AMICI-dev#2396)

This avoids shading the `ExpData` class by  `amici.swig_wrappers.ExpData`.
The old implementation prevented using e.g. `isinstance(x, amici.ExpData)`.

This required also:
* Moving some annotation types and `_get_ptr` from `amici.swig_wrappers` to the swig-generated `amici.py`
* Some smaller changes to allow for using `from __future__ import annotations` in `amici.py`

Closes AMICI-dev#2380
NEP 29:

> On Apr 05, 2024 drop support for Python 3.9
* Run pyupgrade for python>=3.10
* Update configuration for recent ruff 


manual changes:
* .pre-commit-config.yam
* pyproject.toml
Deploy releases (actual releases, not only release branches) to Docker Hub.

Closes AMICI-dev#2383
Fix test failures related to switching from macos-12 to macos-14-arm64.

Fixes AMICI-dev#2415.
Remove setup.cfg, originally removed in AMICI-dev#2408, accidentally re-added in AMICI-dev#2391
… root functions (AMICI-dev#2417)

Don't compute things we don't need.

For my test model, this reduces code generation time from 76s to 12s (-83%).
Make it easier to find out where warnings originate from.
... and show numpy version detected by CMake
When using the Python interface, we don't rely on C(++) output anywhere anymore, and thus, we don't need wurlitzer anymore.


Closes AMICI-dev#2409
Previously, in some cases (see AMICI-dev#2426), event assignments to compartments would result in incorrect concentrations because an incorrect post-event volume was used. This is fixed here.

Closes AMICI-dev#2426.
…ts (AMICI-dev#2425)

Event-assignments to compartments weren't supported yet, now they are.

Compartments that are targets of event assignments are now processed as "species", the same way as it is already done for parameters that are targets of event assignments.

Closes AMICI-dev#2424.

---------

Co-authored-by: Fabian Fröhlich <[email protected]>
@dweindl dweindl self-assigned this May 7, 2024
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codecov bot commented May 7, 2024

Codecov Report

Attention: Patch coverage is 80.72289% with 16 lines in your changes are missing coverage. Please review.

Project coverage is 77.82%. Comparing base (29b7ee8) to head (52996d3).

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2433      +/-   ##
==========================================
+ Coverage   77.71%   77.82%   +0.10%     
==========================================
  Files         324      324              
  Lines       20925    20928       +3     
  Branches     1464     1464              
==========================================
+ Hits        16262    16287      +25     
+ Misses       4660     4638      -22     
  Partials        3        3              
Flag Coverage Δ
cpp 76.22% <77.10%> (+2.72%) ⬆️
cpp_python 34.09% <50.60%> (-0.08%) ⬇️
petab 36.65% <51.80%> (-0.10%) ⬇️
python 72.36% <77.10%> (+0.11%) ⬆️

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

Files Coverage Δ
python/sdist/amici/__init__.py 94.44% <100.00%> (ø)
python/sdist/amici/_codegen/cxx_functions.py 95.65% <ø> (ø)
python/sdist/amici/_codegen/model_class.py 100.00% <ø> (ø)
python/sdist/amici/_codegen/template.py 100.00% <ø> (ø)
python/sdist/amici/antimony_import.py 94.11% <100.00%> (ø)
python/sdist/amici/bngl_import.py 100.00% <ø> (ø)
python/sdist/amici/compile.py 68.42% <ø> (ø)
...thon/sdist/amici/conserved_quantities_demartino.py 65.69% <ø> (+0.13%) ⬆️
python/sdist/amici/conserved_quantities_rref.py 96.42% <ø> (ø)
python/sdist/amici/cxxcodeprinter.py 94.11% <100.00%> (ø)
... and 36 more

... and 3 files with indirect coverage changes

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socket-security bot commented May 8, 2024

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

Package New capabilities Transitives Size Publisher
pypi/[email protected] None 0 14.2 MB 0u812, adelhpour, andrewbriand, ...3 more
pypi/[email protected] None 0 14.5 MB 0u812, adelhpour, andrewbriand, ...3 more
pypi/[email protected] environment, eval, filesystem, shell, unsafe 0 15.9 MB Thomas.Caswell, matthew.brett, scopatz, ...1 more
pypi/[email protected] environment 0 43 kB Kyle.Kelley, bgranger, darian, ...5 more
pypi/[email protected] environment, eval, filesystem, network, shell, unsafe 0 67.5 MB ivanov, matthew.brett, mdboom2
pypi/[email protected] environment, eval, filesystem, network, unsafe 0 3.7 MB fredrik
pypi/[email protected] environment, eval, filesystem, network, shell, unsafe 0 62.2 MB MarcoGorelli, datapythonista, jbrockmendel, ...8 more
pypi/[email protected] environment, filesystem, network Transitive: eval, shell, unsafe +169 109 MB Leonardo.Uieda, santisoler
pypi/[email protected] eval, network Transitive: environment, filesystem, shell +2 2.69 MB DanielHavlikGocept, florianpilz, icemac, ...4 more
pypi/[email protected] environment, eval, filesystem, network, shell, unsafe 0 242 MB bgoli, frankbergmann.myopenid.com, smkeating
pypi/[email protected] environment, eval, filesystem, network, shell, unsafe 0 152 MB matthew.brett, pv, rgommers, ...3 more
pypi/[email protected] environment, eval, filesystem Transitive: network, shell, unsafe +159 1.19 GB mwaskom
pypi/[email protected] environment, shell Transitive: eval, filesystem, network, unsafe +53 79.2 MB vaab
pypi/[email protected] None 0 40 kB ericvsmith

View full report↗︎

@dweindl dweindl force-pushed the release_0.25.0 branch 2 times, most recently from e237980 to a0566b0 Compare May 8, 2024 07:02
@dweindl dweindl marked this pull request as ready for review May 8, 2024 08:57
@dweindl dweindl requested a review from a team as a code owner May 8, 2024 08:57
dweindl and others added 3 commits May 8, 2024 11:59
…MICI-dev#2429)

Check whether we are able to handle a given event according to its `useValuesFromTriggerTime` setting. See also AMICI-dev#2427.

Does not affect SBML test suite stats.

Closes AMICI-dev#2427.
@dweindl dweindl merged commit 7487607 into AMICI-dev:master May 8, 2024
33 checks passed
@dweindl dweindl deleted the release_0.25.0 branch May 8, 2024 13:04
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2 participants