diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 851602b3556e..ed989be6f710 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -10,7 +10,6 @@
   bison,
   mpi, # generic mpi dependency
   mpiCheckPhaseHook,
-  python3,
   python3Packages,
 
   # Build options
@@ -78,7 +77,6 @@ let
   petscPackages = lib.makeScope newScope (self: {
     inherit
       mpi
-      python3
       python3Packages
       # global override options
       mpiSupport
@@ -111,20 +109,20 @@ let
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "petsc";
-  version = "3.23.5";
+  version = "3.23.6";
 
   src = fetchzip {
     url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${finalAttrs.version}.tar.gz";
-    hash = "sha256-pfGb/9GlKsZJpdEU6lOr61a8AE5NR9MlZ0mHJ/j+eDs=";
+    hash = "sha256-sKXLYtOw6xom7c7ARpOY4dcsV5zR5KgbYrt1bnHF/Io=";
   };
 
   strictDeps = true;
 
   nativeBuildInputs = [
-    python3
     gfortran
     pkg-config
     bison
+    python3Packages.python
   ]
   ++ lib.optional mpiSupport mpi
   ++ lib.optionals pythonSupport [
@@ -154,7 +152,7 @@ stdenv.mkDerivation (finalAttrs: {
 
   patches = [
     (replaceVars ./fix-petsc4py-install-prefix.patch {
-      PYTHON_SITEPACKAGES = python3.sitePackages;
+      PYTHON_SITEPACKAGES = python3Packages.python.sitePackages;
     })
   ];
 
@@ -181,13 +179,7 @@ stdenv.mkDerivation (finalAttrs: {
     "--with-cxx=${lib.getDev mpi}/bin/mpicxx"
     "--with-fc=${lib.getDev mpi}/bin/mpif90"
   ]
-  ++ lib.optionals (!debug) [
-    "--with-debugging=0"
-    "COPTFLAGS=-O3"
-    "FOPTFLAGS=-O3"
-    "CXXOPTFLAGS=-O3"
-    "CXXFLAGS=-O3"
-  ]
+  ++ lib.optional (!debug) "--with-debugging=0"
   ++ lib.optional (!fortranSupport) "--with-fortran-bindings=0"
   ++ lib.optional pythonSupport "--with-petsc4py=1"
   ++ lib.optional withMetis "--with-metis=1"
diff --git a/pkgs/by-name/pf/pflotran/package.nix b/pkgs/by-name/pf/pflotran/package.nix
index b67c0955c1b0..037df5e99e81 100644
--- a/pkgs/by-name/pf/pflotran/package.nix
+++ b/pkgs/by-name/pf/pflotran/package.nix
@@ -11,7 +11,7 @@
   parmetis,
   hdf5-fortran-mpi,
   mpiCheckPhaseHook,
-  python3,
+  python312Packages,
 }:
 
 let
@@ -31,6 +31,7 @@ let
       {
         withMetis = true;
         withParmetis = true;
+        python3Packages = python312Packages;
       };
 in
 stdenv.mkDerivation (finalAttrs: {
diff --git a/pkgs/by-name/sl/slepc/package.nix b/pkgs/by-name/sl/slepc/package.nix
index b44717b8b520..8e9e73833b67 100644
--- a/pkgs/by-name/sl/slepc/package.nix
+++ b/pkgs/by-name/sl/slepc/package.nix
@@ -2,7 +2,6 @@
   lib,
   stdenv,
   fetchFromGitLab,
-  python3,
   python3Packages,
   arpack-mpi,
   petsc,
@@ -29,7 +28,7 @@ stdenv.mkDerivation (finalAttrs: {
     # Fix slepc4py install prefix
     substituteInPlace config/packages/slepc4py.py \
       --replace-fail "slepc.prefixdir,'lib'" \
-      "slepc.prefixdir,'${python3.sitePackages}'"
+      "slepc.prefixdir,'${python3Packages.python.sitePackages}'"
 
     patchShebangs lib/slepc/bin
   '';
@@ -43,7 +42,7 @@ stdenv.mkDerivation (finalAttrs: {
   '';
 
   nativeBuildInputs = [
-    python3
+    python3Packages.python
   ]
   ++ lib.optionals pythonSupport [
     python3Packages.setuptools
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 14b42edaaa55..acfab6557f9e 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -11589,7 +11589,6 @@ self: super: with self; {
 
   petsc4py = toPythonModule (
     pkgs.petsc.override {
-      python3 = python;
       python3Packages = self;
       pythonSupport = true;
     }
@@ -16826,7 +16825,6 @@ self: super: with self; {
   slepc4py = toPythonModule (
     pkgs.slepc.override {
       pythonSupport = true;
-      python3 = self.python;
       python3Packages = self;
       petsc = petsc4py;
     }