From d4bb0cef583bfb902859a7d1f51518fc3b631610 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 17 Oct 2024 13:22:11 +0200 Subject: [PATCH] Fix pysb branch (#2548) Previous branch no longer exists. Now on master (https://github.com/pysb/pysb/commit/8be8263d32e33bff6c4e92c927f4ba85590dc20f). --- .github/workflows/test_petab_test_suite.yml | 2 +- python/sdist/amici/petab/util.py | 2 +- scripts/installAmiciSource.sh | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml index c16b40bc30..7e86a70d66 100644 --- a/.github/workflows/test_petab_test_suite.yml +++ b/.github/workflows/test_petab_test_suite.yml @@ -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 diff --git a/python/sdist/amici/petab/util.py b/python/sdist/amici/petab/util.py index 5392dcdb86..48e6ed7786 100644 --- a/python/sdist/amici/petab/util.py +++ b/python/sdist/amici/petab/util.py @@ -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 diff --git a/scripts/installAmiciSource.sh b/scripts/installAmiciSource.sh index 6769ebc100..c930696380 100755 --- a/scripts/installAmiciSource.sh +++ b/scripts/installAmiciSource.sh @@ -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