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CI: don't cache amici; pytest ignore amici_models; passenv BNGPATH #1523

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Nov 27, 2024
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CI: don't cache amici; pytest ignore amici_models; passenv BNGPATH #1523

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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@ jobs:

- name: Run tests
timeout-minutes: 35
run: tox -e petab
run: tox -e petab && tox e -e petab -- pip uninstall -y amici
env:
CC: clang
CXX: clang++
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1 change: 1 addition & 0 deletions pytest.ini
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Expand Up @@ -2,3 +2,4 @@
addopts = "--doctest-modules"
filterwarnings =
ignore:.*inspect.getargspec\(\) is deprecated.*:DeprecationWarning
norecursedirs = amici_models
10 changes: 7 additions & 3 deletions tox.ini
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Expand Up @@ -29,7 +29,7 @@ envlist =
# Base-environment

[testenv]
passenv = AMICI_PARALLEL_COMPILE,CC,CXX,MPLBACKEND
passenv = AMICI_PARALLEL_COMPILE,CC,CXX,MPLBACKEND,BNGPATH

# Sub-environments
# inherit settings defined in the base
Expand Down Expand Up @@ -75,10 +75,14 @@ description =
Test basic functionality on Windows

[testenv:petab]
extras = test,amici,petab,pyswarm,roadrunner
extras = test,petab,pyswarm,roadrunner
deps =
git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master\#subdirectory=src/python
git+https://github.com/AMICI-dev/amici.git@develop\#egg=amici&subdirectory=python/sdist
# always install amici from develop branch, avoid caching
# to skip re-installation, run `tox -e petab --override testenv:petab.commands_pre=`
commands_pre =
python3 -m pip uninstall -y amici
python3 -m pip install git+https://github.com/AMICI-dev/amici.git@develop\#egg=amici&subdirectory=python/sdist
commands =
python3 -m pip install git+https://github.com/PEtab-dev/petab_test_suite@main
python3 -m pip install git+https://github.com/pysb/pysb@master
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