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Fix pysb branch #2548

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merged 1 commit into from
Oct 17, 2024
Merged

Fix pysb branch #2548

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2 changes: 1 addition & 1 deletion .github/workflows/test_petab_test_suite.yml
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Expand Up @@ -79,7 +79,7 @@ jobs:
source ./venv/bin/activate \
&& python3 -m pip uninstall -y petab \
&& python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
&& python3 -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching \
&& python3 -m pip install git+https://github.com/pysb/pysb@master \
&& python3 -m pip install sympy>=1.12.1


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2 changes: 1 addition & 1 deletion python/sdist/amici/petab/util.py
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Expand Up @@ -71,7 +71,7 @@ def get_states_in_condition_table(
raise NotImplementedError(
"Requires https://github.com/pysb/pysb/pull/570. "
"To use this functionality, update pysb via "
"`pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching`"
"`pip install git+https://github.com/pysb/pysb@master`"
)

# expose model components as variables so we can evaluate patterns
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2 changes: 1 addition & 1 deletion scripts/installAmiciSource.sh
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Expand Up @@ -34,7 +34,7 @@ export PYTHON_EXECUTABLE="${AMICI_PATH}/venv/bin/python"

python -m pip install --upgrade pip wheel
python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy petab
python -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments
python -m pip install git+https://github.com/pysb/pysb@master # for SPM with compartments
AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" \
python -m pip install --verbose -e "${AMICI_PATH}/python/sdist[petab,test,vis]" --no-build-isolation
deactivate
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