From 6287120431f275affc8bfcf4df5e2c948b43b748 Mon Sep 17 00:00:00 2001
From: Sebastian Blauth <sebastian.blauth@itwm.fraunhofer.de>
Date: Tue, 4 Jul 2023 08:49:06 +0200
Subject: [PATCH 1/2] PETSc Patch for 3.18

---
 cashocs/_utils/linalg.py | 52 +++++++++++++++++++++++++++++-----------
 1 file changed, 38 insertions(+), 14 deletions(-)

diff --git a/cashocs/_utils/linalg.py b/cashocs/_utils/linalg.py
index 98d25269..e9dc487a 100644
--- a/cashocs/_utils/linalg.py
+++ b/cashocs/_utils/linalg.py
@@ -280,6 +280,40 @@ def define_ksp_options(
     return options
 
 
+def setup_matrix_and_preconditioner(
+    ksp: PETSc.KSP,
+    A: Optional[PETSc.Mat] = None,  # pylint: disable=invalid-name
+    P: Optional[PETSc.Mat] = None,  # pylint: disable=invalid-name
+) -> PETSc.Mat:
+    """Set up the system matrix and preconditioner for a linear solve.
+
+    Args:
+        ksp: The KSP object used to solve the problem.
+        A: The system matrix or `None`.
+        P: The preconditioner matrix or `None`.
+
+    Returns:
+        The system matrix.
+
+    """
+    if A is not None:
+        if P is None:
+            ksp.setOperators(A)
+        else:
+            ksp.setOperators(A, P)
+    else:
+        A = ksp.getOperators()[0]
+        if A.size[0] == -1 and A.size[1] == -1:
+            raise _exceptions.InputError(
+                "cashocs._utils.solve_linear_problem",
+                "ksp",
+                "The KSP object has to be initialized with some Matrix in case A is "
+                "None.",
+            )
+
+    return A
+
+
 def solve_linear_problem(
     A: Optional[PETSc.Mat] = None,  # pylint: disable=invalid-name
     b: Optional[PETSc.Vec] = None,
@@ -318,20 +352,7 @@ def solve_linear_problem(
     comm = _initialize_comm(comm)
     ksp = PETSc.KSP().create(comm=comm)
 
-    if A is not None:
-        if P is None:
-            ksp.setOperators(A)
-        else:
-            ksp.setOperators(A, P)
-    else:
-        A = ksp.getOperators()[0]
-        if A.size[0] == -1 and A.size[1] == -1:
-            raise _exceptions.InputError(
-                "cashocs._utils.solve_linear_problem",
-                "ksp",
-                "The KSP object has to be initialized with some Matrix in case A is "
-                "None.",
-            )
+    A = setup_matrix_and_preconditioner(ksp, A, P)
 
     if b is None:
         return A.getVecs()[0]
@@ -355,6 +376,9 @@ def solve_linear_problem(
     if ksp.getConvergedReason() < 0:
         raise _exceptions.PETScKSPError(ksp.getConvergedReason())
 
+    if hasattr(PETSc, "garbage_cleanup"):
+        PETSc.garbage_cleanup(comm=comm)
+
     if fun is not None:
         fun.vector().apply("")
 

From 9bed654c5eaaab5f4566d547e27bb091d5dea828 Mon Sep 17 00:00:00 2001
From: Sebastian Blauth <sebastian.blauth@itwm.fraunhofer.de>
Date: Tue, 4 Jul 2023 08:50:17 +0200
Subject: [PATCH 2/2] version bump

---
 .zenodo.json                              | 4 ++--
 cashocs/__init__.py                       | 2 +-
 docs/source/_static/version_switcher.json | 4 ++--
 docs/source/conf.py                       | 2 +-
 pyproject.toml                            | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index d21e47ce..b215ad54 100755
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -1,8 +1,8 @@
 {
     "description": "<p>cashocs is a computational, adjoint-based shape optimization and optimal control software.</p>", 
     "license": "GPL-3.0+", 
-    "title": "cashocs v2.0.5",
-    "version": "v2.0.5",
+    "title": "cashocs v2.0.7",
+    "version": "v2.0.7",
     "upload_type": "software", 
     "creators": [
         {
diff --git a/cashocs/__init__.py b/cashocs/__init__.py
index 5b06a477..86d925ce 100755
--- a/cashocs/__init__.py
+++ b/cashocs/__init__.py
@@ -60,7 +60,7 @@
 from cashocs.nonlinear_solvers import newton_solve
 from cashocs.nonlinear_solvers import picard_iteration
 
-__version__ = "2.0.5"
+__version__ = "2.0.7"
 
 __citation__ = """
 @Article{Blauth2021cashocs,
diff --git a/docs/source/_static/version_switcher.json b/docs/source/_static/version_switcher.json
index 02a9d5c1..dc106f60 100755
--- a/docs/source/_static/version_switcher.json
+++ b/docs/source/_static/version_switcher.json
@@ -6,8 +6,8 @@
     },
     {
         "name": "2.0 (stable)",
-        "version": "2.0.5",
-        "url": "https://cashocs.readthedocs.io/en/v2.0.5/"
+        "version": "2.0.7",
+        "url": "https://cashocs.readthedocs.io/en/v2.0.7/"
     },    
     {
         "name": "1.8",
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 86073198..8d4df84f 100755
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -28,7 +28,7 @@
 author = "Sebastian Blauth"
 
 # The full version, including alpha/beta/rc tags
-release = "2.0.5"
+release = "2.0.7"
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/pyproject.toml b/pyproject.toml
index 4a189ac6..a58621c0 100755
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cashocs"
-version = "2.0.5"
+version = "2.0.7"
 description = "Computational Adjoint-Based Shape Optimization and Optimal Control Software"
 readme = "README.rst"
 requires-python = ">=3.8"