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Release 0.26.0 #2473

Merged
merged 12 commits into from
Jul 2, 2024
Merged

Release 0.26.0 #2473

merged 12 commits into from
Jul 2, 2024

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dweindl
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@dweindl dweindl commented Jul 1, 2024 •
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dweindl and others added 8 commits June 16, 2024 20:22
@dweindl
Update valgrind suppressions
043d13a
@dweindl
Require sympy>=1.12.1 for numpy>=2.0 compatibility (AMICI-dev#2462)
9e31013 
So far, sympy was restricted to 1.11 via pysb, but sympy 1.11 is incompatible with numpy>=2.0
@dweindl
Update AMICI papers (AMICI-dev#2466)
474b473
@dweindl
Add deprecation policy (AMICI-dev#2465)
f54abe6 
Add deprecation policy

As suggested in AMICI-dev#2458.
@dweindl
Deprecate passing individual tables to amici_import_petab (AMICI-de…
538fd59 
…v#2464)

Deprecated passing individual tables to `amici_import_petab`

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

Fixes AMICI-dev#2460
@dweindl
GHA: sympy>=1.12.1
3cfb8e7
@dweindl
Doc: fix formatting (AMICI-dev#2470)
e1ab9fb
@dweindl
CMake: Set SUNDIALS_ROOT (AMICI-dev#2468)
f8ce650 
Set SUNDIALS_ROOT to ensure we are finding the sundials CMake config from the vendored library and not any other installation.

Fixes AMICI-dev#2467.
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codecov bot commented Jul 1, 2024 •
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Codecov Report

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

Project coverage is 77.81%. Comparing base (88a5454) to head (3882d94).
Report is 32 commits behind head on master.

Files with missing lines Patch % Lines
python/sdist/amici/petab/cli/import_petab.py 0.00% 13 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           master    #2473       +/-   ##
===========================================
+ Coverage   36.66%   77.81%   +41.14%     
===========================================
  Files         103      324      +221     
  Lines       14881    20933     +6052     
  Branches     1388     1464       +76     
===========================================
+ Hits         5456    16288    +10832     
+ Misses       9116     4642     -4474     
+ Partials      309        3      -306
Flag Coverage Δ
cpp 76.20% <0.00%> (?)
cpp_python 34.08% <0.00%> (?)
petab 36.64% <0.00%> (-0.02%) ⬇️
python 72.35% <0.00%> (?)

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

Files with missing lines Coverage Δ
python/sdist/amici/petab/conditions.py 97.43% <ø> (ø)
python/sdist/amici/petab/import_helpers.py 86.15% <ø> (ø)
python/sdist/amici/petab/parameter_mapping.py 81.15% <ø> (+5.75%) ⬆️
python/sdist/amici/petab/petab_import.py 66.66% <ø> (ø)
python/sdist/amici/petab/petab_problem.py 87.69% <ø> (ø)
python/sdist/amici/petab/pysb_import.py 51.85% <ø> (ø)
python/sdist/amici/petab/sbml_import.py 54.28% <ø> (ø)
python/sdist/amici/petab/simulations.py 92.85% <ø> (+1.02%) ⬆️
python/sdist/amici/petab/simulator.py 100.00% <ø> (ø)
python/sdist/amici/petab/util.py 86.66% <ø> (ø)
... and 5 more

... and 287 files with indirect coverage changes

@dweindl dweindl self-assigned this Jul 1, 2024
dweindl and others added 4 commits July 1, 2024 11:17
@dweindl
Update reference list (AMICI-dev#2472)
65a1138 
* Update reference list

* BaltussenJon2024

* issue link

* ..
@dweindl
Doc: Update installation under conda (AMICI-dev#2474)
9fe31b6 
* anaconda -> conda (to include miniconda)
* not recommended
* Include installation hint from AMICI-dev#2404. Closes AMICI-dev#2402.
@dweindl
Use petab.v1 (AMICI-dev#2471)
6fe648e 
Make amici ready for using libpetab's `petab.v1` package instead of the previous, now deprecated imports.

Move tests/petab to tests/petab_ to avoid import issues (tests.petab namespace package vs actual petab package)
@dweindl
Bump version number, update changelog
3882d94
@dweindl dweindl marked this pull request as ready for review July 2, 2024 10:10
@dweindl dweindl requested a review from a team as a code owner July 2, 2024 10:10
@dweindl dweindl merged commit b958cce into AMICI-dev:master Jul 2, 2024
26 of 27 checks passed
@dweindl dweindl deleted the release_0.26.0 branch July 2, 2024 13:13
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@FFroehlich FFroehlich FFroehlich approved these changes

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@dweindl @FFroehlich