Merge branch 'develop' into fix_mkl

dweindl · May 14, 2024 · ea758bc · ea758bc
2 parents 7780d65 + a63b016
commit ea758bc
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
@@ -13,7 +13,7 @@
 import amici
 import numpy as np
 import sympy as sp
-
+from sympy.abc import _clash
 from . import ExpData, ExpDataPtr, Model, ReturnData, ReturnDataPtr
 
 StrOrExpr = Union[str, sp.Expr]
@@ -497,7 +497,7 @@ def evaluate(expr: StrOrExpr, rdata: ReturnDataView) -> np.array:
     from sympy.utilities.lambdify import lambdify
 
     if isinstance(expr, str):
-        expr = sp.sympify(expr)
+        expr = sp.sympify(expr, locals=_clash)
 
     arg_names = list(sorted(expr.free_symbols, key=lambda x: x.name))
     func = lambdify(arg_names, expr, "numpy")

diff --git a/scripts/installAmiciSource.sh b/scripts/installAmiciSource.sh
@@ -33,7 +33,7 @@ fi
 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 numpy
+python -m pip install --upgrade pip setuptools cmake_build_extension==0.5.1 numpy
 python -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR 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