[WIP PATCH 0/5] Add SageMath

+++ b/gnu/local.mk

+  %D%/packages/patches/linbox-fix-pkgconfig.patch		\

+++ b/gnu/packages/algebra.scm

+                "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))

+              (patches (search-patches "linbox-fix-pkgconfig.patch"))))

+    (propagated-inputs

+++ b/gnu/packages/patches/linbox-fix-pkgconfig.patch

+Backported from:

+

+From 426eb97ba762c7663884f57ead0909f2aa3cd6a5 Mon Sep 17 00:00:00 2001

+From: Cyril Bouvier <cyril.bouvier@lirmm.fr>

+Date: Thu, 17 Jan 2019 16:32:19 +0100

+Subject: [PATCH] Remove @LINBOXSAGE_LIBS@ from linbox.pc.in

+

+---

+ linbox.pc.in | 2 +-

+ 1 file changed, 1 insertion(+), 1 deletion(-)

+

+diff --git a/linbox.pc.in b/linbox.pc.in

+index 278f127e4..c6b8091eb 100644

+--- a/linbox.pc.in

++++ b/linbox.pc.in

+@@ -9,6 +9,6 @@ Description: Exact Linear Algebra library

+ URL: http://github.com/linbox-team/linbox

+ Version: @VERSION@

+ Requires: fflas-ffpack >= 2.4.0, givaro >= 4.1.0

+-Libs: -L${libdir} -llinbox @LINBOXSAGE_LIBS@ @NTL_LIBS@ @MPFR_LIBS@ @FPLLL_LIBS@ @IML_LIBS@ @FLINT_LIBS@ @OCL_LIBS@

++Libs: -L${libdir} -llinbox @NTL_LIBS@ @MPFR_LIBS@ @FPLLL_LIBS@ @IML_LIBS@ @FLINT_LIBS@ @OCL_LIBS@

+ Cflags: @DEFAULT_CFLAGS@ -DDISABLE_COMMENTATOR -I${includedir} @NTL_CFLAGS@ @MPFR_CFLAGS@ @FPLLL_CFLAGS@  @IML_CFLAGS@ @FLINT_CFLAGS@ 

+ \-------------------------------------------------------

+++ b/gnu/packages/sagemath.scm

+++ b/gnu/local.mk

+  %D%/packages/patches/ecl-16-format-directive-limit.patch	\

+  %D%/packages/patches/ecl-16-ignore-stderr-write-error.patch	\

+  %D%/packages/patches/ecl-16-libffi.patch			\

+++ b/gnu/packages/patches/ecl-16-format-directive-limit.patch

+Patch backported by Sage.

+

+Fix from upstream that happens to work around

+https://trac.sagemath.org/ticket/23011

+diff --git a/src/lsp/format.lsp b/src/lsp/format.lsp

+index 77ca799..53b887c 100644

+--- a/src/lsp/format.lsp

++++ b/src/lsp/format.lsp

+@@ -307,11 +307,13 @@

+                   :start (format-directive-start struct)

+                   :end (format-directive-end struct))))

+ 

++(defconstant +format-directive-limit+ (1+ (char-code #\~)))

++

+ #+formatter

+ (defparameter *format-directive-expanders*

+-  (make-array char-code-limit :initial-element nil))

++  (make-array +format-directive-limit+ :initial-element nil))

+ (defparameter *format-directive-interpreters*

+-  (make-array char-code-limit :initial-element nil))

++  (make-array +format-directive-limit+ :initial-element nil))

+ 

+ (defparameter *default-format-error-control-string* nil)

+ (defparameter *default-format-error-offset* nil)

+@@ -550,24 +552,24 @@

+            (write-string directive stream)

+            (interpret-directive-list stream (cdr directives) orig-args args))

+           (#-ecl format-directive #+ecl vector

++           (multiple-value-bind

++                 (new-directives new-args)

++               (let* ((code (char-code (format-directive-character directive)))

++                      (function

++                        (and (< code +format-directive-limit+)

++                             (svref *format-directive-interpreters* code)))

++                      (*default-format-error-offset*

++                        (1- (format-directive-end directive))))

++                 (unless function

++                   (error 'format-error

++                          :complaint "Unknown format directive."))

+                  (multiple-value-bind

+                        (new-directives new-args)

+-                     (let ((function

+-                            (svref *format-directive-interpreters*

+-                                   (char-code (format-directive-character

+-                                               directive))))

+-                           (*default-format-error-offset*

+-                            (1- (format-directive-end directive))))

+-                       (unless function

+-                         (error 'format-error

+-                                :complaint "Unknown format directive."))

+-                       (multiple-value-bind

+-                             (new-directives new-args)

+-                           (funcall function stream directive

+-                                    (cdr directives) orig-args args)

+-                         (values new-directives new-args)))

+-                   (interpret-directive-list stream new-directives

+-                                             orig-args new-args)))))

++                     (funcall function stream directive

++                              (cdr directives) orig-args args)

++                   (values new-directives new-args)))

++             (interpret-directive-list stream new-directives

++                                       orig-args new-args)))))

+       args))

+ 

+ 

+@@ -639,11 +641,12 @@

+        (values `(write-string ,directive stream)

+                more-directives))

+       (format-directive

+-       (let ((expander

+-              (aref *format-directive-expanders*

+-                    (char-code (format-directive-character directive))))

+-             (*default-format-error-offset*

+-              (1- (format-directive-end directive))))

++       (let* ((code (char-code (format-directive-character directive)))

++              (expander

++                (and (< code +format-directive-limit+)

++                     (svref *format-directive-expanders* code)))

++              (*default-format-error-offset*

++                (1- (format-directive-end directive))))

+          (if expander

+              (funcall expander directive more-directives)

+              (error 'format-error

+++ b/gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch

+Patch adapted from Sage.

+diff -Naur ecl-16.1.2.orig/src/c/file.d ecl-16.1.2/src/c/file.d

+--- ecl-16.1.2.orig/src/c/file.d	2016-05-11 13:10:51.867673867 +1200

++++ ecl-16.1.2/src/c/file.d	2016-05-11 14:44:48.121907307 +1200

+@@ -3354,8 +3354,10 @@

+   ecl_disable_interrupts();

+   do {

+     out = fwrite(c, sizeof(char), n, IO_STREAM_FILE(strm));

+-  } while (out < n && restartable_io_error(strm, "fwrite"));

+-  ecl_enable_interrupts();

++  /* Ignore write errors to stderr to avoid an infinite loop */

++  } while (out < n && (IO_STREAM_FILE(strm) != stderr) && restartable_io_error(strm, "fwrite"));

++

++  ecl_enable_interrupts();

+   return out;

+ }

+ 

+++ b/gnu/packages/patches/ecl-16-libffi.patch

+Patch adapted from Sage. Allows building ECL on libffi 3.3.

+diff --git a/src/c/ffi.d b/src/c/ffi.d

+index 8861303e..8a959c23 100644

+--- a/src/c/ffi.d

++++ b/src/c/ffi.d

+@@ -133,8 +133,8 @@ static struct {

+ #elif defined(X86_WIN64)

+   {@':win64', FFI_WIN64},

+ #elif defined(X86_ANY) || defined(X86) || defined(X86_64)

+-  {@':cdecl', FFI_SYSV},

+-  {@':sysv', FFI_SYSV},

++  {@':cdecl', FFI_UNIX64},

++  {@':sysv', FFI_UNIX64},

+   {@':unix64', FFI_UNIX64},

+ #endif

+ };

+++ b/gnu/packages/sagemath.scm

+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>

+  #:use-module (gnu packages lisp)

+;; Sage 9.1 doesn't build with ECL 20.  This won't be necessary once 9.2 is

+;; released.  See https://trac.sagemath.org/ticket/22191

+(define-public ecl-16

+  (package

+    (inherit ecl)

+    (version "16.1.3")

+    (source

+     (origin

+       (method url-fetch)

+       (uri (string-append

+             "https://common-lisp.net/project/ecl/static/files/release/ecl"

+             "-" version ".tgz"))

+       (sha256

+        (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))

+       (patches (search-patches

+                  "ecl-16-libffi.patch"

+                  "ecl-16-ignore-stderr-write-error.patch"

+                  "ecl-16-format-directive-limit.patch"))))

+    ;; Current ECL uses LGPL 2.1+

+    (license license:lgpl2.0+)))

+

+++ b/gnu/packages/sagemath.scm

+                  (string-append "INSTALL_DIR=" out))))

+++ b/gnu/packages/sagemath.scm

+  #:use-module (gnu packages assembly)

+  #:use-module (gnu packages cmake)

+  #:use-module (gnu packages commencement)

+  #:use-module (gnu packages gd)

+  #:use-module (gnu packages gettext)

+  #:use-module (gnu packages graph)

+  #:use-module (gnu packages libffi)

+  #:use-module (gnu packages m4)

+  #:use-module (gnu packages maths)

+  #:use-module (gnu packages ncurses)

+  #:use-module (gnu packages networking)

+  #:use-module (gnu packages pcre)

+  #:use-module (gnu packages perl)

+  #:use-module (gnu packages python-xyz)

+  #:use-module (gnu packages readline)

+  #:use-module (gnu packages sqlite)

+  #:use-module (gnu packages tex)

+  #:use-module (gnu packages tls))

+

+(define-public sagemath

+  (package

+    (name "sagemath")

+    (version "9.1")

+    (source

+     (origin

+       (method git-fetch)

+       (uri (git-reference

+              (url "git://git.sagemath.org/sage.git/")

+              (commit version)))

+       (file-name (git-file-name name version))

+       (sha256

+        (base32

+         "1imlqa5mg7xxp6xbzzjnjjpd8k79vlx48zm0qfj7cd4bi0i809pp"))))

+    (build-system python-build-system)

+    (arguments

+     `(#:use-setuptools? #f

+       #:tests? #f

+       #:phases

+       (modify-phases %standard-phases

+         (add-after 'unpack 'prepare

+           (lambda _

+            (setenv "HOME" "/tmp")

+            (setenv "SAGE_ROOT" (getcwd))

+            (setenv "SAGE_LOCAL" (getcwd))

+            (setenv "SAGE_SHARE" (string-append (getcwd) "/share"))

+            (setenv "SAGE_NUM_THREADS" (number->string (parallel-job-count)))

+            (mkdir-p "var/lib/sage/installed")

+            (chdir "src")

+            #t)))))

+    (propagated-inputs

+     `(("python-cypari2" ,python-cypari2)

+       ("python-cysignals" ,python-cysignals)

+       ("python-cython" ,python-cython)

+       ("python-gmpy2" ,python-gmpy2)

+       ("python-jinja2" ,python-jinja2)

+       ("python-numpy" ,python-numpy)

+       ("python-pkgconfig" ,python-pkgconfig)

+       ("python-six" ,python-six)))

+    (inputs

+     `(("arb" ,arb)

+       ("boost" ,boost) ; TODO: Is this needed?

+       ("braiding" ,libbraiding)

+       ("brial" ,brial)

+       ("bzip2" ,bzip2)

+       ("cliquer" ,cliquer)

+       ("ecl" ,ecl-16)

+       ("eclib" ,eclib)

+       ("ecm" ,gmp-ecm)

+       ("ecm:libatomic-ops" ,libatomic-ops)

+       ("flint" ,flint)

+       ("gf2x" ,gf2x)

+       ("gap" ,gap)

+       ("gc" ,libgc)

+       ("gd" ,gd)

+       ("givaro" ,givaro)

+       ("glpk" ,glpk)

+       ("gmp" ,gmp)

+       ("gsl" ,gsl)

+       ("homfly" ,libhomfly)

+       ("iml" ,iml)

+       ("lcalc" ,lcalc)

+       ("libffi" ,libffi)

+       ("libpng" ,libpng)

+       ("linbox" ,linbox)

+       ("lrcalc" ,lrcalc)

+       ("m4ri" ,m4ri)

+       ("m4rie" ,m4rie)

+       ("mpc" ,mpc)

+       ("mpfi" ,mpfi)

+       ("mpfr" ,mpfr)

+       ("ncurses" ,ncurses)

+       ("ntl" ,ntl)

+       ("openssl" ,openssl)

+       ("pari" ,pari-gp)

+       ("pcre" ,pcre)

+       ("planarity" ,edge-addition-planarity-suite)

+       ("ppl" ,ppl)

+       ("pynac" ,pynac)

+       ("rw" ,rw)

+       ("ratpoints" ,ratpoints)

+       ("readline" ,readline)

+       ("singular" ,singular)

+       ("sqlite" ,sqlite)

+       ("symmetrica" ,symmetrica)

+       ("texlive" ,texlive-tiny)

+       ("zeromq" ,zeromq) ; TODO: Is this needed?

+       ("zlib" ,zlib)

+       ("zn-poly" ,zn-poly)))

+    (native-inputs

+     `(("autoconf" ,autoconf)

+       ("automake" ,automake)

+       ("cmake" ,cmake)

+       ("gettext" ,gettext-minimal)

+       ("gfortran" ,gfortran-toolchain)

+       ("m4" ,m4)

+       ("perl" ,perl)

+       ("pkg-config" ,pkg-config)

+       ("yasm" ,yasm)))

+    (home-page "https://www.sagemath.org/")

+    (synopsis "Python-based computer algebra system")

+    (description "TODO")

+    (license license:gpl3)))