use temporary directories

AMICI-dev · Nov 18, 2024 · dc4992e · dc4992e
1 parent 250f9dd
commit dc4992e
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Showing 2 changed files with 29 additions and 26 deletions.
diff --git a/python/sdist/amici/jaxcodeprinter.py b/python/sdist/amici/jaxcodeprinter.py
@@ -2,6 +2,7 @@
 
 import re
 from collections.abc import Iterable
+from logging import warning
 
 import sympy as sp
 from sympy.printing.numpy import NumPyPrinter
@@ -22,6 +23,7 @@ def doprint(self, expr: sp.Expr, assign_to: str | None = None) -> str:
             ) from e
 
     def _print_AmiciSpline(self, expr: sp.Expr) -> str:
+        warning("Spline interpolation is support in JAX is untested")
         # FIXME: untested, where are spline nodes coming from anyways?
         return f'interp1d(time, {self.doprint(expr.args[2:])}, kind="cubic")'
 

diff --git a/python/tests/test_jax.py b/python/tests/test_jax.py
@@ -11,6 +11,7 @@
 from beartype import beartype
 
 from amici.pysb_import import pysb2amici
+from amici.testing import TemporaryDirectoryWinSafe
 from numpy.testing import assert_allclose
 
 pysb = pytest.importorskip("pysb")
@@ -28,17 +29,17 @@ def test_conversion():
     pysb.Rule("conv", a(s="a") >> a(s="b"), pysb.Parameter("kcat", 0.05))
     pysb.Observable("ab", a(s="b"))
 
-    outdir = model.name
-    pysb2amici(model, outdir, verbose=True, observables=["ab"])
+    with TemporaryDirectoryWinSafe(prefix=model.name) as outdir:
+        pysb2amici(model, outdir, verbose=True, observables=["ab"])
 
-    model_module = amici.import_model_module(
-        module_name=model.name, module_path=outdir
-    )
+        model_module = amici.import_model_module(
+            module_name=model.name, module_path=outdir
+        )
 
-    ts = tuple(np.linspace(0, 1, 10))
-    p = jnp.stack((1.0, 0.1), axis=-1)
-    k = tuple()
-    _test_model(model_module, ts, p, k)
+        ts = tuple(np.linspace(0, 1, 10))
+        p = jnp.stack((1.0, 0.1), axis=-1)
+        k = tuple()
+        _test_model(model_module, ts, p, k)
 
 
 @pytest.mark.filterwarnings(
@@ -74,23 +75,23 @@ def test_dimerization():
     pysb.Observable("a_obs", a())
     pysb.Observable("b_obs", b())
 
-    outdir = model.name
-    pysb2amici(
-        model,
-        outdir,
-        verbose=True,
-        observables=["a_obs", "b_obs"],
-        constant_parameters=["ksyn_a", "ksyn_b"],
-    )
-
-    model_module = amici.import_model_module(
-        module_name=model.name, module_path=outdir
-    )
-
-    ts = tuple(np.linspace(0, 1, 10))
-    p = jnp.stack((5, 0.5, 0.5, 0.5), axis=-1)
-    k = (0.5, 5)
-    _test_model(model_module, ts, p, k)
+    with TemporaryDirectoryWinSafe(prefix=model.name) as outdir:
+        pysb2amici(
+            model,
+            outdir,
+            verbose=True,
+            observables=["a_obs", "b_obs"],
+            constant_parameters=["ksyn_a", "ksyn_b"],
+        )
+
+        model_module = amici.import_model_module(
+            module_name=model.name, module_path=outdir
+        )
+
+        ts = tuple(np.linspace(0, 1, 10))
+        p = jnp.stack((5, 0.5, 0.5, 0.5), axis=-1)
+        k = (0.5, 5)
+        _test_model(model_module, ts, p, k)
 
 
 def _test_model(model_module, ts, p, k):