Merge branch 'master' into core-updates

1 files changed, 28 insertions, 15 deletions

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5e0df6e409..7bb9bc84a3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1692,7 +1692,7 @@ September 2004}")
 (define-public petsc
   (package
     (name "petsc")
-    (version "3.10.4")
+    (version "3.11.2")
     (source
      (origin
       (method url-fetch)
@@ -1700,7 +1700,7 @@ September 2004}")
       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
                           "petsc-lite-" version ".tar.gz"))
       (sha256
-       (base32 "0fk16944zh3473ra198kdkxdn08rq7b6ap838hxy1mh1i0hb488r"))))
+       (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
     (outputs '("out"                    ; libraries and headers
                "examples"))             ; ~30MiB of examples
     (build-system gnu-build-system)
@@ -1845,7 +1845,11 @@ scientific applications modeled by partial differential equations.")
         ``("--with-mpiexec=mpirun"
            ,(string-append "--with-mpi-dir="
                            (assoc-ref %build-inputs "openmpi"))
-           ,@(delete "--with-mpi=0" ,cf)))))
+           ,@(delete "--with-mpi=0" ,cf)))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-before 'configure 'mpi-setup
+             ,%openmpi-setup)))))
     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
 
 (define-public python-petsc4py
@@ -1910,7 +1914,7 @@ savings are consistently > 5x.")
 (define-public slepc
   (package
     (name "slepc")
-    (version "3.10.1")
+    (version "3.11.1")
     (source
      (origin
        (method url-fetch)
@@ -1918,10 +1922,11 @@ savings are consistently > 5x.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
+         "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("python" ,python-2)))
+     `(("python" ,python-2)
+       ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
     (inputs
      `(("arpack" ,arpack-ng)
        ("gfortran" ,gfortran)))
@@ -1933,7 +1938,10 @@ savings are consistently > 5x.")
        `(,(string-append "--with-arpack-dir="
                          (assoc-ref %build-inputs "arpack") "/lib"))
        #:make-flags                     ;honor (parallel-job-count)
-       `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
+       `(,(format #f "MAKE_NP=~a" (parallel-job-count))
+         ,(string-append "PETSCCONFIGDIR="
+                         (assoc-ref %build-inputs "petsc:examples")
+                         "/share/petsc/examples/config"))
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
@@ -2752,7 +2760,7 @@ to BMP, JPEG or PNG image formats.")
 (define-public maxima
   (package
     (name "maxima")
-    (version "5.42.2")
+    (version "5.43.0")
     (source
      (origin
        (method url-fetch)
@@ -2760,7 +2768,7 @@ to BMP, JPEG or PNG image formats.")
                            version "-source/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn"))
+         "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -2794,11 +2802,18 @@ to BMP, JPEG or PNG image formats.")
              (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
                     (coreutils (assoc-ref inputs "coreutils"))
                     (dirname (string-append coreutils "/bin/dirname"))
-                    (head (string-append coreutils "/bin/head")))
+                    (head (string-append coreutils "/bin/head"))
+                    (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
+                    (python (string-append (assoc-ref inputs "python")
+                                           "/bin/python3")))
                (substitute* "src/maxima.in"
                  (("sed ") (string-append sed " "))
                  (("dirname") dirname)
                  (("head") head))
+               (substitute* "doc/info/Makefile.in"
+                 (("/usr/bin/env perl") perl))
+               (substitute* "doc/info/build_html.sh.in"
+                 (("python") python))
                #t)))
          (add-before 'check 'pre-check
            (lambda _
@@ -2830,9 +2845,6 @@ to BMP, JPEG or PNG image formats.")
                  (mkdir-p "share/emacs")
                  (mkdir-p "share/doc")
                  (symlink
-                  (string-append datadir "/emacs/")
-                  (string-append out "/share/emacs/site-lisp"))
-                 (symlink
                   (string-append datadir "/doc/")
                   (string-append out "/share/doc/maxima"))
                  (with-atomic-file-replacement
@@ -2863,7 +2875,7 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "19.03.1")
+    (version "19.05.7")
     (source
      (origin
        (method git-fetch)
@@ -2873,7 +2885,7 @@ point numbers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1qkf4jg86xnn3wk3782ffmfz12axb92dkjagcz3ffzw2wi1rclml"))))
+         "0zaz71fh156b9inrxf86scnix247al5pl9v18cxhjxcm0lanqxdp"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)))
@@ -3553,6 +3565,7 @@ in finite element programs.")
     (inputs
      `(("mpi" ,openmpi)
        ;;Supported only with MPI:
+       ("hdf5" ,hdf5-parallel-openmpi)  ;TODO: have petsc-openmpi propagate?
        ("p4est" ,p4est-openmpi)
        ("petsc" ,petsc-openmpi)
        ("slepc" ,slepc-openmpi)