Subject: [bug#53065] [PATCH] gnu: dealii: Update to 9.3.2.

From: Felix Gruber <[email-masked]>
Date: Fri, 7 Jan 2022 07:39:05 +0000

* gnu/packages/maths.scm (dealii): Update to 9.3.2.
  [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and
  dealii-fix-sundials.patch.
  [inputs]: Use simplified format.
  [native-inputs]: Use simplified format.
* gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch:
  New file.
* gnu/packages/patches/dealii-fix-sundials.patch: New file.
* gnu/local.mk: Add new patch files.
---
 gnu/local.mk                                  |  4 +-
 gnu/packages/maths.scm                        | 24 ++++----
 ...lii-fix-compiliation-with-boost-1.78.patch | 40 +++++++++++++
 .../patches/dealii-fix-sundials.patch         | 60 +++++++++++++++++++
 4 files changed, 115 insertions(+), 13 deletions(-)
 create mode 100644 gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch
 create mode 100644 gnu/packages/patches/dealii-fix-sundials.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 31354e413f..be5268b9e8 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -31,7 +31,7 @@
 # Copyright © 2020 R Veera Kumar <[email-masked]>
 # Copyright © 2020 Nicolò Balzarotti <[email-masked]>
 # Copyright © 2020 Michael Rohleder <[email-masked]>
-# Copyright © 2020, 2021 Felix Gruber <[email-masked]>
+# Copyright © 2020, 2021, 2022 Felix Gruber <[email-masked]>
 # Copyright © 2020 Ryan Prior <[email-masked]>
 # Copyright © 2020 Jan Wielkiewicz <[email-masked]>
 # Copyright © 2020, 2021 Brice Waegeneire <[email-masked]>
@@ -987,6 +987,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/dbus-c++-gcc-compat.patch		\
   %D%/packages/patches/dbus-c++-threading-mutex.patch		\
   %D%/packages/patches/dbxfs-remove-sentry-sdk.patch		\
+  %D%/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch	\
+  %D%/packages/patches/dealii-fix-sundials.patch		\
   %D%/packages/patches/debops-constants-for-external-program-names.patch \
   %D%/packages/patches/debops-debops-defaults-fall-back-to-less.patch \
   %D%/packages/patches/dee-vapi.patch			\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b0944f307b..f4dba92c11 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -34,7 +34,7 @@
 ;;; Copyright © 2019 Steve Sprang <[email-masked]>
 ;;; Copyright © 2019 Robert Smith <[email-masked]>
 ;;; Copyright © 2020 Jakub Kądziołka <[email-masked]>
-;;; Copyright © 2020, 2021 Felix Gruber <[email-masked]>
+;;; Copyright © 2020–2022 Felix Gruber <[email-masked]>
 ;;; Copyright © 2020 R Veera Kumar <[email-masked]>
 ;;; Copyright © 2020 Vincent Legoll <[email-masked]>
 ;;; Copyright © 2020 Nicolò Balzarotti <[email-masked]>
@@ -5268,14 +5268,16 @@ A unique design feature of Trilinos is its focus on packages.")
 (define-public dealii
   (package
     (name "dealii")
-    (version "9.3.1")
+    (version "9.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/dealii/dealii/releases/"
                            "download/v" version "/dealii-" version ".tar.gz"))
        (sha256
-        (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
+        (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak"))
+       (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch"
+                                "dealii-fix-sundials.patch"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -5286,16 +5288,14 @@ A unique design feature of Trilinos is its focus on packages.")
     (outputs '("out" "doc"))
     (native-inputs
      ;; Required to build the documentation.
-     `(("dot" ,graphviz)
-       ("doxygen" ,doxygen)
-       ("perl" ,perl)))
+      (list graphviz doxygen perl))
     (inputs
-     `(("arpack" ,arpack-ng)
-       ("blas" ,openblas)
-       ("gfortran" ,gfortran)
-       ("lapack" ,lapack)
-       ("muparser" ,muparser)
-       ("zlib" ,zlib)))
+      (list arpack-ng
+            openblas
+            gfortran
+            lapack
+            muparser
+            zlib))
     (propagated-inputs
      ;; Some scripts are installed into share/deal.II/scripts that require
      ;; perl and python, but they are not executable (and some are missing the
diff --git a/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch b/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch
new file mode 100644
index 0000000000..1937aa9afc
--- /dev/null
+++ b/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch
@@ -0,0 +1,40 @@
+From cbef761731627cece2a6f0276b87dacabbdc8a72 Mon Sep 17 00:00:00 2001
+From: David Wells <[email-masked]>
+Date: Tue, 4 Jan 2022 12:46:30 -0500
+Subject: [PATCH] Fix compilation with boost 1.78.
+
+I bisected (fortunately Boost.Geometry a header-only library so adding the
+include directory sufficed) and
+https://github.com/boostorg/geometry/commit/6eb9e238bcb37e26dc31d16acf826784a2ba30f4
+is where this problem starts for us. See also
+https://github.com/boostorg/geometry/issues/792 - the easiest fix for all such
+issues is to just include the project header `boost/geometry/geometry.hpp`.
+
+In this particular case, if you look at the commit which causes grid_tools.cc
+fails to compile, its because we were relying on some implicit includes. In
+particular, we need the distance header to find the distance between points and
+boxes, but that was previously included in another file.
+
+This patch has been adapted from
+e0e76835519d122fd12b5858e16d08641a641c6a to apply to dealii 9.3.2.
+
+See https://github.com/dealii/dealii/pull/13165.
+---
+ include/deal.II/numerics/rtree.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/deal.II/numerics/rtree.h b/include/deal.II/numerics/rtree.h
+index 1b9d04dacd..1e1bfd2932 100644
+--- a/include/deal.II/numerics/rtree.h
++++ b/include/deal.II/numerics/rtree.h
+@@ -26,6 +26,7 @@
+ #include <deal.II/boost_adaptors/segment.h>
+ 
+ DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
++#include <boost/geometry/algorithms/distance.hpp>
+ #include <boost/geometry/index/rtree.hpp>
+ #include <boost/geometry/strategies/strategies.hpp>
+ DEAL_II_ENABLE_EXTRA_DIAGNOSTICS
+-- 
+2.30.2
+
diff --git a/gnu/packages/patches/dealii-fix-sundials.patch b/gnu/packages/patches/dealii-fix-sundials.patch
new file mode 100644
index 0000000000..7dd5df45da
--- /dev/null
+++ b/gnu/packages/patches/dealii-fix-sundials.patch
@@ -0,0 +1,60 @@
+From af73f368f7f9d4a00df075d1a9f50fc495f8e87a Mon Sep 17 00:00:00 2001
+From: Timo Heister <[email-masked]>
+Date: Sat, 25 Dec 2021 12:30:45 -0500
+Subject: [PATCH] fix sundials compilation
+
+---
+ include/deal.II/sundials/n_vector.templates.h | 11 ++++++-----
+ 1 file changed, 6 insertions(+), 5 deletions(-)
+
+diff --git a/include/deal.II/sundials/n_vector.templates.h b/include/deal.II/sundials/n_vector.templates.h
+index 2b49e3efc9..746f63a03b 100644
+--- a/include/deal.II/sundials/n_vector.templates.h
++++ b/include/deal.II/sundials/n_vector.templates.h
+@@ -253,13 +253,13 @@ namespace SUNDIALS
+       template <
+         typename VectorType,
+         typename std::enable_if_t<!IsBlockVector<VectorType>::value, int> = 0>
+-      MPI_Comm
++      const MPI_Comm &
+       get_communicator(N_Vector v);
+ 
+       template <
+         typename VectorType,
+         typename std::enable_if_t<IsBlockVector<VectorType>::value, int> = 0>
+-      MPI_Comm
++      const MPI_Comm &
+       get_communicator(N_Vector v);
+ 
+       /**
+@@ -481,7 +481,7 @@ SUNDIALS::internal::NVectorOperations::destroy(N_Vector v)
+ 
+ template <typename VectorType,
+           std::enable_if_t<IsBlockVector<VectorType>::value, int>>
+-MPI_Comm
++const MPI_Comm &
+ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ {
+   return unwrap_nvector_const<VectorType>(v)->block(0).get_mpi_communicator();
+@@ -491,7 +491,7 @@ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ 
+ template <typename VectorType,
+           std::enable_if_t<!IsBlockVector<VectorType>::value, int>>
+-MPI_Comm
++const MPI_Comm &
+ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ {
+   return unwrap_nvector_const<VectorType>(v)->get_mpi_communicator();
+@@ -519,7 +519,8 @@ SUNDIALS::internal::NVectorOperations::get_communicator_as_void_ptr(N_Vector v)
+   (void)v;
+   return nullptr;
+ #  else
+-  return get_communicator<VectorType>(v);
++  // We need to cast away const here, as SUNDIALS demands a pure `void *`.
++  return &(const_cast<MPI_Comm &>(get_communicator<VectorType>(v)));
+ #  endif
+ }
+ 
+-- 
+2.30.2
+
-- 
2.30.2