From 2ebc149a4fbe29beffc7e0bfd4be36e703180e82 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 26 Nov 2024 08:30:36 +0100
Subject: [PATCH 1/2] Bump codecov/codecov-action from 4 to 5 (#2595)

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v4...v5)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/test_benchmark_collection_models.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
index 201ae88da8..e68ec1518b 100644
--- a/.github/workflows/test_benchmark_collection_models.yml
+++ b/.github/workflows/test_benchmark_collection_models.yml
@@ -74,7 +74,7 @@ jobs:
 
     - name: Codecov Python
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage_py.xml

From b210b01dbee96153a920533783f16cb9df412823 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Tue, 26 Nov 2024 12:55:41 +0100
Subject: [PATCH 2/2] Update valgrind suppressions / skip (#2600)

Update valgrind suppressions

Skip JAX tests under valgrind
---
 .github/workflows/test_valgrind.yml | 4 ++++
 python/tests/test_jax.py            | 4 +++-
 python/tests/valgrind-python.supp   | 9 +++++++++
 3 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
index b3f893647f..ef5ef9ba95 100644
--- a/.github/workflows/test_valgrind.yml
+++ b/.github/workflows/test_valgrind.yml
@@ -89,5 +89,9 @@ jobs:
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
+    - name: Remove jax
+      # avoid valgrind errors due to jax et al.
+      run: venv/bin/pip uninstall -y jax
+
     - name: Python tests / Valgrind
       run: scripts/run-valgrind-py.sh
diff --git a/python/tests/test_jax.py b/python/tests/test_jax.py
index d124a6e1be..40dbb27e47 100644
--- a/python/tests/test_jax.py
+++ b/python/tests/test_jax.py
@@ -11,7 +11,7 @@
 from beartype import beartype
 
 from amici.pysb_import import pysb2amici
-from amici.testing import TemporaryDirectoryWinSafe
+from amici.testing import TemporaryDirectoryWinSafe, skip_on_valgrind
 from numpy.testing import assert_allclose
 
 pysb = pytest.importorskip("pysb")
@@ -19,6 +19,7 @@
 jax.config.update("jax_enable_x64", True)
 
 
+@skip_on_valgrind
 def test_conversion():
     pysb.SelfExporter.cleanup()  # reset pysb
     pysb.SelfExporter.do_export = True
@@ -42,6 +43,7 @@ def test_conversion():
         _test_model(model_module, ts, p, k)
 
 
+@skip_on_valgrind
 @pytest.mark.filterwarnings(
     "ignore:Model does not contain any initial conditions"
 )
diff --git a/python/tests/valgrind-python.supp b/python/tests/valgrind-python.supp
index 16c92e3d1f..93fd8614de 100644
--- a/python/tests/valgrind-python.supp
+++ b/python/tests/valgrind-python.supp
@@ -985,3 +985,12 @@
    fun:_PyTuple_Resize
    ...
 }
+
+{
+   Python
+   Memcheck:Cond
+   fun:PyObject_RichCompareBool
+   fun:tuplerichcompare
+   fun:do_richcompare
+   ...
+}