gnu: Add sage.

* gnu/packages/sagemath.scm (sage): New variable.
(conway-polynomials, graphs, polytopes-db): Make packages private.
* gnu/packages/patches/sage-update-eclib.patch,
gnu/packages/patches/sage-update-pari-gp.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register patches.

Change-Id: I1cf647760ea3af2dd01d11eedbf1e847a2175365

gnu/local.mk

@@ -2204,6 +2204,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/rw-igraph-0.10.patch			\
   %D%/packages/patches/rxvt-unicode-fix-cursor-position.patch	\
   %D%/packages/patches/s7-flint-3.patch                      	\
+  %D%/packages/patches/sage-update-eclib.patch               	\
+  %D%/packages/patches/sage-update-pari-gp.patch               	\
   %D%/packages/patches/sajson-for-gemmi-numbers-as-strings.patch	\
   %D%/packages/patches/sajson-build-with-gcc10.patch		\
   %D%/packages/patches/sbc-fix-build-non-x86.patch		\

gnu/packages/patches/sage-update-eclib.patch

@@ -0,0 +1,222 @@
+From 6dfc26b805d2fb0cafa60f0d778db3d68188b724 Mon Sep 17 00:00:00 2001
+From: John Cremona <john.cremona@gmail.com>
+Date: Wed, 13 Nov 2024 14:46:51 +0000
+Subject: [PATCH 1/4] #38960-eclib-upgrade-20241112
+
+---
+ build/pkgs/eclib/SPKG.rst            | 2 +-
+ build/pkgs/eclib/checksums.ini       | 4 ++--
+ build/pkgs/eclib/package-version.txt | 2 +-
+ build/pkgs/eclib/spkg-configure.m4   | 2 +-
+ 4 files changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/build/pkgs/eclib/SPKG.rst b/build/pkgs/eclib/SPKG.rst
+index 5627fdcb57c..ac8b27b3606 100644
+--- a/build/pkgs/eclib/SPKG.rst
++++ b/build/pkgs/eclib/SPKG.rst
+@@ -30,5 +30,5 @@ Upstream Contact
+ -  Author: John Cremona
+ -  Email: john.cremona@gmail.com
+ -  Website:
+-   http://homepages.warwick.ac.uk/staff/J.E.Cremona/mwrank/index.html
++   https://johncremona.github.io/mwrank/index.html
+ -  Repository: https://github.com/JohnCremona/eclib
+diff --git a/build/pkgs/eclib/checksums.ini b/build/pkgs/eclib/checksums.ini
+index fde4faaee15..b046783341d 100644
+--- a/build/pkgs/eclib/checksums.ini
++++ b/build/pkgs/eclib/checksums.ini
+@@ -1,4 +1,4 @@
+ tarball=eclib-VERSION.tar.bz2
+-sha1=3028ac95e1b76699f5f9e871ac706cda363ab842
+-sha256=32d116a3e359b0de4f6486c2bb6188bb8b553c8b833f618cc2596484e8b6145a
++sha1=749e4fda3660006a9459f129148d05ba482daa29
++sha256=30765c27ca1420141f83517897119d0185fea9b31132392170ddae40b060e46f
+ upstream_url=https://github.com/JohnCremona/eclib/releases/download/vVERSION/eclib-VERSION.tar.bz2
+diff --git a/build/pkgs/eclib/package-version.txt b/build/pkgs/eclib/package-version.txt
+index 190b92f716b..353869c3cba 100644
+--- a/build/pkgs/eclib/package-version.txt
++++ b/build/pkgs/eclib/package-version.txt
+@@ -1 +1 @@
+-20231212
++20241112
+diff --git a/build/pkgs/eclib/spkg-configure.m4 b/build/pkgs/eclib/spkg-configure.m4
+index ba5c22fa090..23771dad1bd 100644
+--- a/build/pkgs/eclib/spkg-configure.m4
++++ b/build/pkgs/eclib/spkg-configure.m4
+@@ -1,7 +1,7 @@
+ SAGE_SPKG_CONFIGURE([eclib], [
+   SAGE_SPKG_DEPCHECK([ntl pari flint], [
+     dnl use existing eclib only if the version reported by pkg-config is recent enough
+-    m4_pushdef([SAGE_ECLIB_VER],["20231212"])
++    m4_pushdef([SAGE_ECLIB_VER],["20241112"])
+     PKG_CHECK_MODULES([ECLIB], [eclib >= SAGE_ECLIB_VER], [
+       AC_CACHE_CHECK([for mwrank version == SAGE_ECLIB_VER], [ac_cv_path_MWRANK], [
+         AC_PATH_PROGS_FEATURE_CHECK([MWRANK], [mwrank], [
+
+From d38cb48c67c7565572064fd29748c1e8da3b3271 Mon Sep 17 00:00:00 2001
+From: John Cremona <john.cremona@gmail.com>
+Date: Tue, 19 Nov 2024 13:51:49 +0000
+Subject: [PATCH 2/4] #38960 fix eclib interface after upgrade
+
+---
+ src/sage/libs/eclib/__init__.pxd | 4 ++--
+ src/sage/libs/eclib/mat.pyx      | 4 ++--
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/sage/libs/eclib/__init__.pxd b/src/sage/libs/eclib/__init__.pxd
+index d44d4fba865..84d1fc92275 100644
+--- a/src/sage/libs/eclib/__init__.pxd
++++ b/src/sage/libs/eclib/__init__.pxd
+@@ -55,7 +55,7 @@ cdef extern from "eclib/matrix.h":
+     cdef cppclass mat:
+         mat()
+         mat(mat m)
+-        scalar* get_entries()
++        vector[scalar] get_entries()
+         scalar sub(long, long)
+         long nrows()
+         long ncols()
+@@ -67,7 +67,7 @@ cdef extern from "eclib/smatrix.h":
+     cdef cppclass smat:
+         smat()
+         smat(smat m)
+-        scalar* get_entries()
++        vector[scalar] get_entries()
+         scalar sub(long, long)
+         long nrows()
+         long ncols()
+diff --git a/src/sage/libs/eclib/mat.pyx b/src/sage/libs/eclib/mat.pyx
+index bfdeb6ae5c1..e7abe369b2b 100644
+--- a/src/sage/libs/eclib/mat.pyx
++++ b/src/sage/libs/eclib/mat.pyx
+@@ -10,7 +10,7 @@ from sage.rings.integer_ring import ZZ
+ from sage.matrix.matrix_integer_sparse cimport Matrix_integer_sparse
+ from sage.matrix.matrix_integer_dense cimport Matrix_integer_dense
+ from sage.rings.integer cimport Integer
+-
++from libcpp.vector cimport vector
+ 
+ cdef class Matrix:
+     """
+@@ -213,7 +213,7 @@ cdef class Matrix:
+         """
+         cdef long n = self.nrows()
+         cdef long i, j, k
+-        cdef scalar* v = <scalar*> self.M.get_entries()   # coercion needed to deal with const
++        cdef vector[scalar] v = <vector[scalar]> self.M.get_entries()   # coercion needed to deal with const
+ 
+         cdef Matrix_integer_dense Td
+         cdef Matrix_integer_sparse Ts
+
+From 4f2cb3f7a943aefd05d4baf7b5845a6fc3dba779 Mon Sep 17 00:00:00 2001
+From: John Cremona <john.cremona@gmail.com>
+Date: Wed, 4 Dec 2024 08:35:58 +0000
+Subject: [PATCH 3/4] #38960 simplify eclib interface
+
+---
+ src/sage/libs/eclib/__init__.pxd |  2 --
+ src/sage/libs/eclib/mat.pyx      | 18 +++++++-----------
+ 2 files changed, 7 insertions(+), 13 deletions(-)
+
+diff --git a/src/sage/libs/eclib/__init__.pxd b/src/sage/libs/eclib/__init__.pxd
+index 84d1fc92275..2673af0613f 100644
+--- a/src/sage/libs/eclib/__init__.pxd
++++ b/src/sage/libs/eclib/__init__.pxd
+@@ -55,7 +55,6 @@ cdef extern from "eclib/matrix.h":
+     cdef cppclass mat:
+         mat()
+         mat(mat m)
+-        vector[scalar] get_entries()
+         scalar sub(long, long)
+         long nrows()
+         long ncols()
+@@ -67,7 +66,6 @@ cdef extern from "eclib/smatrix.h":
+     cdef cppclass smat:
+         smat()
+         smat(smat m)
+-        vector[scalar] get_entries()
+         scalar sub(long, long)
+         long nrows()
+         long ncols()
+diff --git a/src/sage/libs/eclib/mat.pyx b/src/sage/libs/eclib/mat.pyx
+index e7abe369b2b..5dbb39faa0e 100644
+--- a/src/sage/libs/eclib/mat.pyx
++++ b/src/sage/libs/eclib/mat.pyx
+@@ -10,7 +10,6 @@ from sage.rings.integer_ring import ZZ
+ from sage.matrix.matrix_integer_sparse cimport Matrix_integer_sparse
+ from sage.matrix.matrix_integer_dense cimport Matrix_integer_dense
+ from sage.rings.integer cimport Integer
+-from libcpp.vector cimport vector
+ 
+ cdef class Matrix:
+     """
+@@ -212,8 +211,7 @@ cdef class Matrix:
+             <class 'sage.matrix.matrix_integer_dense.Matrix_integer_dense'>
+         """
+         cdef long n = self.nrows()
+-        cdef long i, j, k
+-        cdef vector[scalar] v = <vector[scalar]> self.M.get_entries()   # coercion needed to deal with const
++        cdef long i, j
+ 
+         cdef Matrix_integer_dense Td
+         cdef Matrix_integer_sparse Ts
+@@ -221,21 +219,19 @@ cdef class Matrix:
+         # Ugly code...
+         if sparse:
+             Ts = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
+-            k = 0
+             for i from 0 <= i < n:
+                 for j from 0 <= j < n:
+-                    if v[k]:
+-                        Ts.set_unsafe(i, j, Integer(v[k]))
+-                    k += 1
++                    Mij = Integer(self.M.sub(i+1,j+1));
++                    if Mij:
++                        Ts.set_unsafe(i, j, Mij)
+             return Ts
+         else:
+             Td = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
+-            k = 0
+             for i from 0 <= i < n:
+                 for j from 0 <= j < n:
+-                    if v[k]:
+-                        Td.set_unsafe(i, j, Integer(v[k]))
+-                    k += 1
++                    Mij = Integer(self.M.sub(i+1,j+1));
++                    if Mij:
++                        Td.set_unsafe(i, j, Mij)
+             return Td
+ 
+ 
+
+From 8754c7052084043209c8332d3d1154c26c25ae91 Mon Sep 17 00:00:00 2001
+From: John Cremona <john.cremona@gmail.com>
+Date: Wed, 4 Dec 2024 09:20:07 +0000
+Subject: [PATCH 4/4] #38960: fix lint issue
+
+---
+ src/sage/libs/eclib/mat.pyx | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/sage/libs/eclib/mat.pyx b/src/sage/libs/eclib/mat.pyx
+index 5dbb39faa0e..989d9d1a70c 100644
+--- a/src/sage/libs/eclib/mat.pyx
++++ b/src/sage/libs/eclib/mat.pyx
+@@ -221,7 +221,7 @@ cdef class Matrix:
+             Ts = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
+             for i from 0 <= i < n:
+                 for j from 0 <= j < n:
+-                    Mij = Integer(self.M.sub(i+1,j+1));
++                    Mij = Integer(self.M.sub(i+1,j+1))
+                     if Mij:
+                         Ts.set_unsafe(i, j, Mij)
+             return Ts
+@@ -229,7 +229,7 @@ cdef class Matrix:
+             Td = MatrixSpace(ZZ, n, sparse=sparse).zero_matrix().__copy__()
+             for i from 0 <= i < n:
+                 for j from 0 <= j < n:
+-                    Mij = Integer(self.M.sub(i+1,j+1));
++                    Mij = Integer(self.M.sub(i+1,j+1))
+                     if Mij:
+                         Td.set_unsafe(i, j, Mij)
+             return Td

gnu/packages/sagemath.scm

@@ -26,18 +26,24 @@
   #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix gexp)
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bdw-gc)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages gd)
+  #:use-module (gnu packages graph)
   #:use-module (gnu packages image)
-  #:use-module (gnu packages maths)
   #:use-module (gnu packages lisp)
+  #:use-module (gnu packages m4)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
@@ -45,7 +51,6 @@
   #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz))
 
-
 (define-public brial
   (package
     (name "brial")
@@ -285,7 +290,7 @@ libraries GMO, MPFR and MPC.")
 Polyhedra Library (PPL).")
     (license license:gpl3+)))
 
-(define-public conway-polynomials
+(define conway-polynomials
   (package
     (name "conway-polynomials")
     (version "0.10")
@@ -306,7 +311,7 @@ polynomials.  The aim of this package is to make them available through a
 generic Python interface.")
     (license license:gpl3+)))
 
-(define-public polytopes-db
+(define polytopes-db
   (package
     (name "polytopes-db")
     (version "20170220")
@@ -328,7 +333,7 @@ to be used by SageMath.")
     ;; Debian says GPLv2+.
     (license license:gpl2+)))
 
-(define-public graphs
+(define graphs
   (package
     (name "graphs")
     (version "20210214")
@@ -351,3 +356,167 @@ to be used by SageMath.")
 database.")
     ;; Debian says GPLv2+.
     (license license:gpl2+)))
+
+(define-public sage
+  (package
+    (name "sage")
+    (version "10.6.beta6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/sagemath/sage")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0w2v5c4k2khlpglaj9sq1vbs7q03ib3d46pgr6k4n3mclhsy2idk"))
+              (patches (search-patches "sage-update-eclib.patch"
+                                       "sage-update-pari-gp.patch"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+      (list autoconf automake m4 pkg-config ; for ./bootstrap
+            python-cython-3
+            python-cysignals
+            python-memory-allocator
+            python-pkgconfig
+            python-jinja2
+            python-setuptools
+            python-wheel))
+    (propagated-inputs
+      (list ;; required to make the sage script start
+            python-ipython
+            python-ipywidgets
+            python-traitlets
+            ;; required for the Jupyter notebook
+            python-jupyter-client
+            python-notebook))
+    (inputs
+      (list boost
+            brial
+            cliquer
+            conway-polynomials
+            coreutils
+            ecl
+            eclib
+            edge-addition-planarity-suite
+            fflas-ffpack
+            flint
+            fontconfig
+            freetype
+            gap
+            gd
+            giac
+            givaro
+            glpk
+            gmp
+            gmp-ecm
+            graphs
+            gsl
+            ijg-libjpeg
+            iml
+            lcalc
+            libbraiding
+            libhomfly
+            linbox
+            libpng
+            m4ri
+            m4rie
+            maxima-ecl
+            mpc
+            mpfi
+            mpfr
+            ntl
+            openblas
+            pari-gp
+            polytopes-db
+            python
+            python-cypari2
+            python-fpylll
+            python-gmpy2
+            python-numpy
+            python-pplpy
+            rw
+            sed
+            singular
+            symmetrica))
+    (arguments
+      (list
+        #:tests? #f ; Tests can be run using "make ptestlong", but it is
+                    ; expected that some of them fail.
+        #:phases
+        #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-source
+            (lambda _
+              (let ((ecl #$(this-package-input "ecl"))
+                    (ecm #$(this-package-input "gmp-ecm"))
+                    (maxima #$(this-package-input "maxima-ecl"))
+                    (maxima-version #$(package-version
+                                        (this-package-input "maxima-ecl")))
+                    (singular #$(this-package-input "singular"))
+                    (gap #$(this-package-input "gap"))
+                    (pari-gp #$(this-package-input "pari-gp"))
+                    (python #$(this-package-input "python"))
+                    (coreutils #$(this-package-input "coreutils"))
+                    (sed #$(this-package-input "sed"))
+                    (graphs #$(this-package-input "graphs"))
+                    (polytopes-db #$(this-package-input "polytopes-db")))
+                (substitute* (find-files "build/bin")
+                  (("sage-bootstrap-python") "python"))
+                (substitute* "src/sage/env.py"
+                  (("\"ecl-config\"")
+                   (string-append "\"" ecl "/bin/ecl-config\""))
+                  (("\"ecm\"")
+                   (string-append "\"" ecm "/bin/ecm\""))
+                  (("\"maxima\"")
+                   (string-append "\"" maxima "/bin/maxima\""))
+                  (("\"MAXIMA_FAS\"")
+                   (string-append "\"MAXIMA_FAS\", \"" maxima
+                                  "/lib/maxima/" maxima-version
+                                  "/binary-ecl/maxima.fas\""))
+                  (("\"Singular\"")
+                   (string-append "\"" singular "/bin/Singular\""))
+                  (("var\\('SAGE_GAP_COMMAND', None\\)")
+                   (string-append "var('SAGE_GAP_COMMAND', \""
+                                  gap "/bin/gap\")"))
+                  (("join\\(SAGE_LOCAL, \"lib\", \"gap\"\\)")
+                   (string-append "\"" gap "/lib/gap\""))
+                  (("join\\(SAGE_LOCAL, \"share\", \"gap\"\\)")
+                   (string-append "\"" gap "/share/gap\""))
+                  ;; definition of SAGE_VENV, which ends up in kernel.json
+                  (("os.path.abspath\\(sys.prefix\\)")
+                   (string-append "\"" #$output "\""))
+                  ;; paths of the databases
+                  (("GRAPHS_DATA_DIR\"")
+                   (string-append
+                     "GRAPHS_DATA_DIR\", "
+                     "\"" graphs "/share/graphs\""))
+                  (("POLYTOPE_DATA_DIR\"")
+                   (string-append
+                     "POLYTOPE_DATA_DIR\", "
+                     "\"" polytopes-db "/share/reflexive_polytopes\"")))
+                (substitute* "src/sage/interfaces/gp.py"
+                  (("command=f\"gp")
+                   (string-append "command=f\"" pari-gp "/bin/gp")))
+                (substitute* "src/bin/sage"
+                  (("exec python3")
+                   (string-append "exec " python "/bin/python3"))
+                  (("mkdir")
+                   (string-append coreutils "/bin/mkdir"))
+                  ((" sed ")
+                   (string-append " " sed "/bin/sed "))))))
+          (add-before 'build 'setup
+            (lambda _
+              (setenv "SAGE_NUM_THREADS"
+                      (number->string (parallel-job-count)))
+              (invoke "./bootstrap")
+              (chdir "src")))
+          (delete 'sanity-check)))) ; does not reflect reality
+    (home-page "https://www.sagemath.org/")
+    (synopsis "SageMath computer algebra system")
+    (description
+     "SageMath is a mathematics software built on top of many existing
+packages such as NumPy, SciPy, Matplotlib, Sympy, Maxima, GAP, FLINT,
+R and others. Their combined power may be accessed through a common,
+Python-based language or directly via interfaces or wrappers.")
+    ;; Documentation under cc-by-sa3.0, see COPYING.txt in the distribution.
+    (license license:gpl3)))