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[bug#49500] gnu: dealii: Update to 9.3.0 and clean up.

Message ID yn2vRALFbprdnXhnek1v2WTocaA1kdm_OSya3Uy3JaCk8v9XD4or7fgTsyY9F0WV817AZ79kkP1rFGMWrUt8X3qjiqniS9ys-M2MrrgwwL4=@apatience.com
State Accepted
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Series [bug#49500] gnu: dealii: Update to 9.3.0 and clean up. | expand


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Commit Message

Paul A. Patience July 9, 2021, 10:53 p.m. UTC
This revised patch removes perl and python from the inputs,
because if they were included it would have had to be in propagated
inputs because the scripts they are required for are not
Anyway, see the comment in the patch for more info.

Best regards,
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From 30429d0b48cf61d0ebfaf6fac96ae9c67755a072 Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Fri, 9 Jul 2021 18:48:19 -0400
Subject: [PATCH] gnu: dealii: Update to 9.3.0 and clean up.

The cleanup notably:

* Builds and installs the documentation into a separate doc output (in
the process moving around some files erroneously installed into the root
directory); and
* Removes unnecessary inputs and moves some inputs into
propagated-inputs (the candidates of which were determined with a search
for "include.*LIBNAME" in include/deal.II).

* gnu/packages/maths.scm (dealii): Reword comments.
[version]: Update to 9.3.0.
[outputs]: New field including doc output.
[native-inputs]: New field.
[inputs]: Sort them. Remove p4est (deal.II interfaces with it only when
MPI is enabled). Move boost, suitesparse and tbb to...
[propagated-inputs]: ...here. New field including hdf5, which is
actually supported in deal.II without MPI.
[arguments]<#:tests?>: New argument. The tests were not being run before
<#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag.
[-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md,
README.md, detailed.log and summary.log files from being installed in
the root directory (though note that the logs are removed in the new
remove-build-logs phase).
[-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory
from being installed in the root directory.
[-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been
<#:phases>{remove-build-logs}: New phase.
[home-page]: Add trailing slash.
(dealii-openmpi): Use package/inherit.
[inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer
interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi,
p4est-openmpi, petsc-openmpi and slepc-openmpi to...
[propagated-inputs]: ...here. New field.
[arguments]<#:configure-flags>: Rename cf variable to flags.
<#:phases>{mpi-setup}: Remove phase which is unused because the tests
are disabled.
 gnu/packages/maths.scm | 95 +++++++++++++++++++++++++++---------------
 1 file changed, 62 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b8e9a31be7..9e40b681c1 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4436,40 +4436,75 @@  revised simplex and the branch-and-bound methods.")
 (define-public dealii
     (name "dealii")
-    (version "9.2.0")
+    (version "9.3.0")
        (method url-fetch)
        (uri (string-append "https://github.com/dealii/dealii/releases/"
                            "download/v" version "/dealii-" version ".tar.gz"))
-        (base32
-         "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh"))
+        (base32 "0cdr74l4ymdjcmxgm5lzq16h10pzggnx9gg3z9yq5khhfnlcgy5f"))
        (modules '((guix build utils)))
-        ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
+           ;; Remove bundled boost, muparser, TBB and UMFPACK.
            (delete-file-recursively "bundled")
     (build-system cmake-build-system)
+    (outputs '("out" "doc"))
+    (native-inputs
+     ;; Required to build the documentation.
+     `(("dot" ,graphviz)
+       ("doxygen" ,doxygen)
+       ("perl" ,perl)))
-     `(("tbb" ,tbb)
-       ("zlib" ,zlib)
-       ("boost" ,boost)
-       ("p4est" ,p4est)
+     `(("arpack" ,arpack-ng)
        ("blas" ,openblas)
+       ("gfortran" ,gfortran)
        ("lapack" ,lapack)
-       ("arpack" ,arpack-ng)
        ("muparser" ,muparser)
-       ("gfortran" ,gfortran)
-       ("suitesparse" ,suitesparse)))   ;for UMFPACK
+       ("zlib" ,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
+     ;; shebang line) and therefore must be explicitly passed to the
+     ;; interpreter.
+     ;; Anyway, they are meant to be used at build time, so rather than adding
+     ;; the interpreters here, any package depending on them should just add
+     ;; the requisite interpreter to its native inputs.
+     `(("boost" ,boost)
+       ("hdf5" ,hdf5)
+       ("suitesparse" ,suitesparse)     ; For UMFPACK.
+       ("tbb" ,tbb)))
-     `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
+     `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
+       ;; The tests take too long and must be explicitly enabled with "make
+       ;; setup_tests".
+       ;; See https://www.dealii.org/developer/developers/testsuite.html.
+       ;; (They can also be run for an already installed deal.II.)
+       #:tests? #f
-       ;; Work around a bug in libsuitesparseconfig linking
-       ;; see https://github.com/dealii/dealii/issues/4745
-    (home-page "https://www.dealii.org")
+       (let ((doc (string-append (assoc-ref %outputs "doc")
+                                 "/share/doc/" ,name "-" ,version)))
+           ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
+           ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
+           ;; Don't compile the examples because the source and CMakeLists.txt
+           ;; are installed anyway, allowing users to do so for themselves.
+           ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'remove-build-logs
+           ;; These build logs leak the name of the build directory by storing
+           ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((doc (string-append (assoc-ref outputs "doc")
+                                       "/share/doc/" ,name "-" ,version)))
+               (for-each delete-file (map (lambda (f) (string-append doc "/" f))
+                                          '("detailed.log" "summary.log"))))
+             #t)))))
+    (home-page "https://www.dealii.org/")
     (synopsis "Finite element library")
      "Deal.II is a C++ program library targeted at the computational solution
@@ -4480,30 +4515,24 @@  in finite element programs.")
     (license license:lgpl2.1+)))
 (define-public dealii-openmpi
-  (package (inherit dealii)
+  (package/inherit dealii
     (name "dealii-openmpi")
-     `(("mpi" ,openmpi)
-       ;;Supported only with MPI:
-       ("hdf5" ,hdf5-parallel-openmpi)  ;TODO: have petsc-openmpi propagate?
+     `(("arpack" ,arpack-ng-openmpi)
+       ("metis" ,metis)
+       ("scalapack" ,scalapack)
+       ,@(alist-delete "arpack" (package-inputs dealii))))
+    (propagated-inputs
+     `(("hdf5" ,hdf5-parallel-openmpi)
+       ("mpi" ,openmpi)
        ("p4est" ,p4est-openmpi)
        ("petsc" ,petsc-openmpi)
        ("slepc" ,slepc-openmpi)
-       ("metis" ,metis)               ;for MUMPS
-       ("scalapack" ,scalapack)       ;for MUMPS
-       ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
-       ("arpack" ,arpack-ng-openmpi)
-       ,@(fold alist-delete (package-inputs dealii)
-               '("p4est" "arpack"))))
+       ,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
      (substitute-keyword-arguments (package-arguments dealii)
-       ((#:configure-flags cf)
-        `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
-               ,cf))
-       ((#:phases phases '%standard-phases)
-        `(modify-phases ,phases
-           (add-before 'check 'mpi-setup
-             ,%openmpi-setup)))))
+       ((#:configure-flags flags)
+        `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
     (synopsis "Finite element library (with MPI support)")))
 (define-public flann