gnu: Remove conkeror.

[jackhill/guix/guix.git] / gnu / packages / maths.scm

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 82abc22..9fb02b7 100644 (file)
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -322,15 +322,15 @@ enough to be used effectively as a scientific calculator.")
 (define-public double-conversion
   (package
     (name "double-conversion")
-    (version "3.0.0")
+    (version "3.1.0")
     (home-page "https://github.com/google/double-conversion")
     (source (origin
-              (method url-fetch)
-              (uri (string-append home-page "/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference (url home-page) (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm"))))
+                "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
     (build-system cmake-build-system)
     (arguments
      '(#:test-target "test"
@@ -1413,9 +1413,9 @@ can solve two kinds of problems:
 
 ;; For a fully featured Octave, users are strongly recommended also to install
 ;; the following packages: less, ghostscript, gnuplot.
-(define-public octave
+(define-public octave-cli
   (package
-    (name "octave")
+    (name "octave-cli")
     (version "4.4.1")
     (source
      (origin
@@ -1497,21 +1497,21 @@ Work may be performed both at the interactive command-line as well as via
 script files.")
     (license license:gpl3+)))
 
-(define-public qtoctave
-  (package (inherit octave)
-    (name "qtoctave")
+(define-public octave
+  (package (inherit octave-cli)
+    (name "octave")
     (source (origin
-              (inherit (package-source octave))))
+              (inherit (package-source octave-cli))))
     (inputs
      `(("qscintilla" ,qscintilla)
        ("qt" ,qtbase)
-       ,@(package-inputs octave)))
+       ,@(package-inputs octave-cli)))
     (native-inputs
      `(("qttools" , qttools) ;for lrelease
        ("texlive" ,texlive) ;for texi2dvi
-       ,@(package-native-inputs octave)))
+       ,@(package-native-inputs octave-cli)))
     (arguments
-     (substitute-keyword-arguments (package-arguments octave)
+     (substitute-keyword-arguments (package-arguments octave-cli)
        ((#:phases phases)
         `(modify-phases ,phases
            (add-before 'configure 'patch-qscintilla-library-name
@@ -1525,6 +1525,9 @@ script files.")
                   "qscintilla2_qt5"))
                #t))))))))
 
+(define-public qtoctave
+  (deprecated-package "qtoctave" octave))
+
 (define-public opencascade-oce
   (package
     (name "opencascade-oce")
@@ -1655,7 +1658,7 @@ September 2004}")
 (define-public petsc
   (package
     (name "petsc")
-    (version "3.9.3")
+    (version "3.10.2")
     (source
      (origin
       (method url-fetch)
@@ -1663,7 +1666,7 @@ September 2004}")
       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
                           "petsc-lite-" version ".tar.gz"))
       (sha256
-       (base32 "1fwkbwv4g7zf2lc8fw865xd0bl9anb6jaczfis5dff7h449gwa48"))))
+       (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
     (outputs '("out"                    ;libraries and headers
                "examples"))             ;~30MiB of examples
     (build-system gnu-build-system)
@@ -1767,16 +1770,18 @@ scientific applications modeled by partial differential equations.")
     (name "petsc-openmpi")
     (inputs
      `(("hdf5" ,hdf5-parallel-openmpi)
+       ("hypre" ,hypre-openmpi)
        ("metis" ,metis)
        ("mumps" ,mumps-openmpi)
        ("openmpi" ,openmpi)
        ("scalapack" ,scalapack)
-       ("scotch" ,pt-scotch)
+       ("scotch" ,pt-scotch32)
        ,@(package-inputs petsc)))
     (arguments
      (substitute-keyword-arguments (package-arguments petsc)
        ((#:configure-flags cf)
-        ``("--with-mpiexec=mpirun"
+        ``("--with-hypre=1"
+           "--with-mpiexec=mpirun"
            "--with-metis=1"
            "--with-mumps=1"
            "--with-scalapack=1"
@@ -1812,14 +1817,14 @@ scientific applications modeled by partial differential equations.")
 (define-public python-petsc4py
   (package
     (name "python-petsc4py")
-    (version "3.9.1")
+    (version "3.10.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "petsc4py" version))
         (sha256
           (base32
-            "1f8zd1ac9irsgkyqmzq30d9kl10fy1nh6zk312dhs43g449fkkhc"))))
+            "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1871,7 +1876,7 @@ savings are consistently > 5x.")
 (define-public slepc
   (package
     (name "slepc")
-    (version "3.9.2")
+    (version "3.10.1")
     (source
      (origin
        (method url-fetch)
@@ -1879,7 +1884,7 @@ savings are consistently > 5x.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0gmhdqac8zm3jx43h935z7bflazjnpvqxjv4jh5za2y1z2rqax94"))))
+         "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))
@@ -1978,14 +1983,14 @@ arising after the discretization of partial differential equations.")
 (define-public python-slepc4py
   (package
     (name "python-slepc4py")
-    (version "3.9.0")
+    (version "3.10.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "slepc4py" version))
         (sha256
           (base32
-            "02xr0vndgibgkz3rgprqk05n3mk5mpgqw550sr4681vcsgz4zvb7"))))
+            "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -2600,15 +2605,16 @@ YACC = bison -pscotchyy -y -b y
            (replace
             'build
             (lambda _
-              (and
-               (zero? (system* "make"
-                               (format #f "-j~a" (parallel-job-count))
-                               "ptscotch" "ptesmumps"))
-               ;; Install the serial metis compatibility library
-               (zero? (system* "make" "-C" "libscotchmetis" "install")))))
-           (replace
-            'check
-            (lambda _ (zero? (system* "make" "ptcheck"))))))))
+              (invoke "make" (format #f "-j~a" (parallel-job-count))
+                      "ptscotch" "ptesmumps")
+
+              ;; Install the serial metis compatibility library
+              (invoke "make" "-C" "libscotchmetis" "install")))
+           (add-before 'check 'mpi-setup
+            ,%openmpi-setup)
+           (replace 'check
+             (lambda _
+               (invoke "make" "ptcheck")))))))
     (synopsis "Programs and libraries for graph algorithms (with MPI)")))
 
 (define-public pt-scotch32
@@ -2622,15 +2628,15 @@ YACC = bison -pscotchyy -y -b y
         `(modify-phases ,scotch32-phases
            (replace 'build
              (lambda _
-               (and
-                (zero? (system* "make"
-                                (format #f "-j~a" (parallel-job-count))
-                                "ptscotch" "ptesmumps"))
-                ;; Install the serial metis compatibility library
-                (zero? (system* "make" "-C" "libscotchmetis" "install")))))
+               (invoke "make" (format #f "-j~a" (parallel-job-count))
+                       "ptscotch" "ptesmumps")
+               ;; Install the serial metis compatibility library
+               (invoke "make" "-C" "libscotchmetis" "install")))
+           (add-before 'check 'mpi-setup
+            ,%openmpi-setup)
            (replace 'check
              (lambda _
-               (zero? (system* "make" "ptcheck"))))))))
+               (invoke "make" "ptcheck")))))))
     (synopsis
      "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
 
@@ -2749,7 +2755,7 @@ to BMP, JPEG or PNG image formats.")
 (define-public maxima
   (package
     (name "maxima")
-    (version "5.42.0")
+    (version "5.42.1")
     (source
      (origin
        (method url-fetch)
@@ -2757,7 +2763,7 @@ to BMP, JPEG or PNG image formats.")
                            version "-source/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0d5pdihvcbwb7r4i4qs5qqgsz46hxlq33qj8is053llrgn9ylpyn"))
+         "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg"))
        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -2848,16 +2854,17 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "18.10.1")
+    (version "18.11.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/wxMaxima-developers/" name
-                           "/archive/Version-" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/wxMaxima-developers/wxmaxima.git")
+             (commit (string-append "Version-" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0c2blq65r0am509p3rjqpwqk6vl5r2yg1p9nh2jczf80vhi3ldas"))))
+         "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)))
@@ -2971,7 +2978,7 @@ parts of it.")
 (define-public openblas
   (package
     (name "openblas")
-    (version "0.3.2")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
@@ -2980,7 +2987,7 @@ parts of it.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq"))))
+         "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -3576,7 +3583,7 @@ in finite element programs.")
      `(("unzip" ,unzip)))
     (inputs
      `(("hdf5" ,hdf5)
-       ("octave" ,octave)
+       ("octave" ,octave-cli)
        ("python" ,python-2) ; print syntax
        ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
        ("zlib" ,zlib)))
@@ -3700,7 +3707,13 @@ set.")
      `(("doc++" ,doc++)
        ("netpbm" ,netpbm)
        ("perl" ,perl)                   ;needed to run 'ppmquant' during tests
-       ("texlive" ,texlive)             ;full package required for fonts
+       ("texlive" ,(texlive-union (list texlive-generic-xypic
+                                        texlive-fonts-xypic
+                                        texlive-latex-hyperref
+                                        texlive-latex-oberdiek
+                                        texlive-generic-ifxetex
+                                        texlive-latex-url
+                                        texlive-bibtex)))
        ("ghostscript" ,ghostscript)))
     (inputs
      `(("blas" ,openblas)
@@ -3717,6 +3730,12 @@ set.")
                            "--with-blas")
        #:phases
        (modify-phases %standard-phases
+         (add-before 'build 'set-HOME
+           (lambda _
+             ;; FIXME: texlive-union does not find the built
+             ;; metafonts, so it tries to generate them in HOME.
+             (setenv "HOME" "/tmp")
+             #t))
          (add-before 'configure 'chdir-src
            (lambda _ (chdir "src")))
          (replace 'configure
@@ -3731,7 +3750,7 @@ set.")
                                           configure-flags)))))))
          (add-after 'build 'build-docs
            (lambda _
-             (zero? (system* "make" "-Cdocs" "pdf" "html"))))
+             (invoke "make" "-Cdocs" "pdf" "html")))
          (replace 'check
            (lambda _
              (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
@@ -3946,15 +3965,16 @@ as equations, scalars, vectors, and matrices.")
 (define-public z3
   (package
     (name "z3")
-    (version "4.5.0")
+    (version "4.8.1")
+    (home-page "https://github.com/Z3Prover/z3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/Z3Prover/z3/archive/z3-"
-                    version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference (url home-page)
+                                  (commit (string-append "z3-" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
+                "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -3965,6 +3985,12 @@ as equations, scalars, vectors, and matrices.")
                             "/lib/python2.7/site-packages"))
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'fix-compatability
+           ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
+           (lambda _
+             (substitute* "src/util/mpz.cpp"
+               (("#include <immintrin.h>") ""))
+             #t))
          (add-before 'configure 'bootstrap
            (lambda _
              (zero?
@@ -3983,7 +4009,6 @@ as equations, scalars, vectors, and matrices.")
     (synopsis "Theorem prover")
     (description "Z3 is a theorem prover and @dfn{satisfiability modulo
 theories} (SMT) solver.  It provides a C/C++ API, as well as Python bindings.")
-    (home-page "https://github.com/Z3Prover/z3")
     (license license:expat)))
 
 (define-public cubicle
@@ -4049,13 +4074,14 @@ exclusion algorithms are typical examples of such systems.")
     (name "elemental")
     (version "0.87.7")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/elemental/Elemental/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/elemental/Elemental.git")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
+                "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
     (build-system cmake-build-system)
     (home-page "http://libelemental.org")
     (native-inputs
@@ -4079,8 +4105,8 @@ exclusion algorithms are typical examples of such systems.")
                            "-DCMAKE_INSTALL_LIBDIR=lib"
                            "-DGFORTRAN_LIB=gfortran")
        #:phases (modify-phases %standard-phases
-                 (add-before 'check 'mpi-setup
-                   ,%openmpi-setup)
+                  (add-before 'check 'mpi-setup
+                    ,%openmpi-setup)
                   (add-before 'check 'setup-tests
                     (lambda _
                       ;; Parallelism is done at the MPI layer.
@@ -4091,7 +4117,7 @@ exclusion algorithms are typical examples of such systems.")
                       ;; Tests are installed, with no easy configuration
                       ;; switch to prevent this, so delete them.
                       (delete-file-recursively
-                       (string-append (assoc-ref outputs "out") "/bin"))
+                        (string-append (assoc-ref outputs "out") "/bin"))
                       #t)))))
     (synopsis "Dense and sparse-direct linear algebra and optimization")
     (description "Elemental is a modern C++ library for distributed-memory