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Release 0.13.0 - #1870

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dweindl merged 7 commits into
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release_0.13.0
Oct 5, 2022
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Release 0.13.0#1870
dweindl merged 7 commits into
masterfrom
release_0.13.0

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@dweindl

@dweindl dweindl commented Oct 4, 2022

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dweindl and others added 7 commits September 7, 2022 12:22
Valgrind runs are taking too long again.

* Let's skip some more tests under valgrind. (`python/tests/test_events.py::test_models[events_plus_heavisides]` alone takes ~1.5h)
* Split Valgrind C++ and Python tests into 2 parallel jobs
* Clean up running-under-valgrind test logic, to also work without GHA or setting extra env vars

Valgrind jobs now finish in about 30min instead of 3h.
Got broken #1859 (cc5f7cc#diff-44c38f8a81d42beabd5ab6dfd5db9a33bda06ded71f7cbfa5a47a7a1b8fd824eL3028), so that `AMICI_EXTRACT_CSE=1` had no effect.

That change also broke the use of human-readable lhs symbols in generated code. Also fixed here.

Added tests for both.
* Makes it easier to test that part
* Smaller functions
* ODEModel usable for purposes other than code-generation
* try replacing symlinks

* move more stuff

* move more stuff, fix GHA workflows

* move remaining files

* move init
@dweindl
dweindl requested a review from FFroehlich October 4, 2022 12:30
@codecov

codecov Bot commented Oct 4, 2022

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Codecov Report

Merging #1870 (5c16d59) into master (9c36029) will decrease coverage by 0.59%.
The diff coverage is 77.43%.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1870      +/-   ##
==========================================
- Coverage   76.14%   75.55%   -0.60%     
==========================================
  Files          74       74              
  Lines       12858    12877      +19     
==========================================
- Hits         9791     9729      -62     
- Misses       3067     3148      +81     
Flag Coverage Δ
cpp 72.82% <ø> (-0.03%) ⬇️
petab 59.11% <50.55%> (+0.25%) ⬆️
python 69.04% <54.33%> (+0.50%) ⬆️
sbmlsuite ∅ <ø> (∅)

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

Impacted Files Coverage Δ
include/amici/amici.h 100.00% <ø> (ø)
python/sdist/amici/__main__.py 0.00% <0.00%> (ø)
python/sdist/amici/ode_export.py 91.77% <ø> (ø)
python/sdist/amici/plotting.py 0.00% <0.00%> (ø)
python/sdist/amici/pysb_import.py 94.61% <ø> (ø)
python/sdist/amici/sbml_import.py 81.04% <ø> (ø)
python/sdist/amici/setuptools.py 57.69% <ø> (ø)
python/sdist/amici/swig.py 32.20% <ø> (ø)
python/sdist/amici/swig_wrappers.py 94.91% <ø> (ø)
python/sdist/amici/testing.py 60.00% <ø> (ø)
... and 25 more

@sonarqubecloud

sonarqubecloud Bot commented Oct 4, 2022

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SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 1 Code Smell

0.0% 0.0% Coverage
0.0% 0.0% Duplication

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👍

@dweindl
dweindl merged commit 11a881e into master Oct 5, 2022
@dweindl
dweindl deleted the release_0.13.0 branch October 5, 2022 11:46
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2 participants