petsc: set optimized and withHdf5 default to true

Petsc is commonly optimized built with hdf5 support to be used
as a component of other software and project.
See
    1. https://sources.debian.org/src/petsc/3.22.2%2Bdfsg1-1/debian/rules/#L154
    2. https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=petsc

pkgs/by-name/pe/petsc/package.nix

@@ -14,7 +14,7 @@
   mpiCheckPhaseHook,
 
   # Build options
-  petsc-optimized ? false,
+  petsc-optimized ? true,
   petsc-scalar-type ? "real",
   petsc-precision ? "double",
   mpiSupport ? true,
@@ -22,7 +22,7 @@
   withFullDeps ? false, # full External libraries support
 
   # External libraries options
-  withHdf5 ? withFullDeps,
+  withHdf5 ? true,
   withMetis ? withFullDeps,
   withParmetis ? false, # parmetis is unfree and should be enabled manualy
   withPtscotch ? withFullDeps,

pkgs/top-level/all-packages.nix

@@ -17072,14 +17072,6 @@ with pkgs;
 
   ### SCIENCE/PROGRAMMING
 
-  ### SCIENCE/GEOLOGY
-  pflotran = callPackage ../by-name/pf/pflotran/package.nix {
-    petsc = petsc.override {
-      withHdf5 = true;
-      petsc-optimized = true;
-    };
-  };
-
   ### SCIENCE/LOGIC
 
   abella = callPackage ../applications/science/logic/abella {

pkgs/top-level/python-packages.nix

@@ -10347,7 +10347,6 @@ self: super: with self; {
     python3Packages = self;
     withPetsc4py = true;
     withFullDeps = true;
-    petsc-optimized = true;
   });
 
   pex = callPackage ../development/python-modules/pex { };