GNU logs - #56729, boring messages

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Subject: [bug#56729] [RFC PATCH 00/10] Add sagemath.
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Hello Guix!

This series adds SageMath. Everything compiles just fine and even the
Jupyter notebook interface works, but there is still much work to do. So
far, I have only added the minimal set of inputs required for the build
to succeed. Tests and documentations are still missing.

vicvbcun (10):
  gnu: edge-addition-planarity-suite: Update to 3.0.2.0.
  gnu: gap: Update to 4.11.1.
  gnu: Remove ecl-16.
  gnu: cliquer: Update to 1.22.
  gnu: lcalc: Update to 2.0.5.
  gnu: ntl: Update to 11.5.1.
  gnu: eclib: Update to 20220621.
  gnu: Add python-memory-allocator.
  gnu: Add python-pplpy.
  gnu: Add sagemath.

 gnu/local.mk                                  |   4 -
 gnu/packages/algebra.scm                      |  19 +-
 gnu/packages/graph.scm                        |   4 +-
 .../patches/lcalc-default-parameters-1.patch  |  26 --
 .../patches/lcalc-default-parameters-2.patch  |  58 ----
 gnu/packages/patches/lcalc-lcommon-h.patch    |  13 -
 .../patches/lcalc-using-namespace-std.patch   |  43 ---
 gnu/packages/sagemath.scm                     | 267 ++++++++++++------
 8 files changed, 194 insertions(+), 240 deletions(-)
 delete mode 100644 gnu/packages/patches/lcalc-default-parameters-1.patch
 delete mode 100644 gnu/packages/patches/lcalc-default-parameters-2.patch
 delete mode 100644 gnu/packages/patches/lcalc-lcommon-h.patch
 delete mode 100644 gnu/packages/patches/lcalc-using-namespace-std.patch


base-commit: f6904c0b19c2fcca41bbf1400c738bd833fec9a8
-- 
2.37.0

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To: vicvbcun <guix@HIDDEN>
Subject: bug#56729: Acknowledgement ([RFC PATCH 00/10] Add sagemath.)
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Date: Sat, 23 Jul 2022 20:48:02 +0000

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Subject: [bug#56729] [RFC PATCH 01/10] gnu: edge-addition-planarity-suite: Update to 3.0.2.0.
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* gnu/packages/graph.scm (edge-addition-planarity-suite): Update to 3.0.2.0.
---
 gnu/packages/graph.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 9aadab45e6..109ba68675 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -537,7 +537,7 @@ (define-public python-leidenalg
 (define-public edge-addition-planarity-suite
   (package
     (name "edge-addition-planarity-suite")
-    (version "3.0.0.5")
+    (version "3.0.2.0")
     (source
      (origin
        (method git-fetch)
@@ -548,7 +548,7 @@ (define-public edge-addition-planarity-suite
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
+         "1c7bnxgiz28mqsq3a3msznmjq629w0qqjynm2rqnnjn2qpc22h3i"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake libtool))
-- 
2.37.0

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Subject: [bug#56729] [RFC PATCH 02/10] gnu: gap: Update to 4.11.1.
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* gnu/packages/algebra.scm (gap): Update to 4.11.1.
[install]: install missing config.h header
---
 gnu/packages/algebra.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 95fbdb5e36..b236313129 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1209,17 +1209,17 @@ (define-public xtensor-benchmark
 (define-public gap
   (package
     (name "gap")
-    (version "4.11.0")
+    (version "4.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://files.gap-system.org/gap-"
                            (version-major+minor version)
-                           "/tar.bz2/gap-"
+                           "/tar.gz/gap-"
                            version
-                           ".tar.bz2"))
+                           ".tar.gz"))
        (sha256
-        (base32 "00l6hvy4iggnlrib4vp805sxdm3j7n3hzpv5zs9hbiiavh80l1xz"))
+        (base32 "01535s81h254zcs84zi95xqmhvvn6fn9qss8761myxc2gpdcadb6"))
        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
        (snippet
         '(begin
@@ -1316,6 +1316,7 @@ (define-public gap
                ;; Install the headers and library, which are needed by Sage.
                (invoke "make" "install-headers")
                (invoke "make" "install-libgap")
+               (install-file "gen/config.h" (string-append out "/include/gap"))
                ;; Remove information on the build directory from sysinfo.gap.
                (substitute* "sysinfo.gap"
                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
-- 
2.37.0

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* gnu/packages/sagemath.scm (ecl-16): Delete variable.
---
 gnu/packages/sagemath.scm | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 7f76f8912b..75720f31a5 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -174,27 +174,6 @@ (define-public libhomfly
     (license license:public-domain)
     (home-page "https://github.com/miguelmarco/libhomfly")))
 
-;; 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+)))
-
 (define-public pynac
   (package
     (name "pynac")
-- 
2.37.0

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* gnu/packages/algebra.scm (eclib): Update to 20220621.
---
 gnu/packages/algebra.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 85e8e77d83..13aaec1af5 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1593,16 +1593,16 @@ (define-public m4rie
 (define-public eclib
   (package
     (name "eclib")
-    (version "20190909")
+    (version "20220621")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/JohnCremona/eclib/")
-                    (commit (string-append "v" version))))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
+                "07wbkzmn6w0hrv2vim7f0il7k59ccc66x5vnn623xkmhfw32b3nz"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake libtool))
-- 
2.37.0

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* gnu/packages/algebra.scm (ntl): Update to 11.5.1.
---
 gnu/packages/algebra.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index b236313129..85e8e77d83 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -540,14 +540,14 @@ (define-public python-flint
 (define-public ntl
   (package
    (name "ntl")
-   (version "11.4.4")
+   (version "11.5.1")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://shoup.net/ntl/ntl-"
                                 version ".tar.gz"))
             (sha256
              (base32
-              "1nr1h27j2gdz6badzz9lk2pknxhdijqdxqhd3haryh0sw616wzwx"))
+              "12ka3hym4skg63mp8vgkin79svbpdk2m6i41yvmcdjq62g1hc391"))
             (modules '((guix build utils)))
             (snippet
              '(begin
-- 
2.37.0

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Subject: [bug#56729] [RFC PATCH 09/10] gnu: Add python-pplpy.
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* gnu/packages/sagemath.scm (python-pplpy): New variable.
---
 gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 2e9de70e4a..335d98d9f4 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -36,6 +36,7 @@ (define-module (gnu packages sagemath)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages image)
   #:use-module (gnu packages lisp)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
@@ -373,3 +374,29 @@ (define-public python-memory-allocator
     (synopsis "An extension class to allocate memory easily with cython")
     (description "An extension class to allocate memory easily with cython")
     (license license:gpl3)))
+
+(define-public python-pplpy
+  (package
+    (name "python-pplpy")
+    (version "0.8.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pplpy" version))
+              (sha256
+               (base32
+                "1gfq5czkqxl395k06s77zij3xv7maiwagjvzmrpraxhsmvsd02sh"))))
+    (build-system python-build-system)
+    (inputs (list gmp
+                  mpc
+                  mpfr
+                  pari-gp
+                  ppl
+                  python-cysignals
+                  python-gmpy2))
+    (native-inputs (list python-cython))
+    (home-page "https://gitlab.com/videlec/pplpy")
+    (synopsis "Python PPL wrapper")
+    (description
+     "This Python module pplpy provides a wrapper to the C++ Parma Polyhedra
+Library (PPL).")
+    (license license:gpl3)))
-- 
2.37.0

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* gnu/packages/sagemath.scm (python-memory-allocator): New variable.
---
 gnu/packages/sagemath.scm | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 1237ff8e04..2e9de70e4a 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -356,3 +356,20 @@ (define-public ratpoints
 a given height bound on a hyperelliptic curve in a very efficient way,
 by using an optimized quadratic sieve algorithm.")
     (license license:gpl2+)))
+
+(define-public python-memory-allocator
+  (package
+    (name "python-memory-allocator")
+    (version "0.1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "memory_allocator" version))
+              (sha256
+               (base32
+                "0qiijpv8zr7c5rjy64i4q3rb8qhn6v4yms5mza4p86y0w4m5r00k"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-cython))
+    (home-page "https://github.com/sagemath/memory_allocator")
+    (synopsis "An extension class to allocate memory easily with cython")
+    (description "An extension class to allocate memory easily with cython")
+    (license license:gpl3)))
-- 
2.37.0

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* gnu/packages/sagemath.scm (lcalc): Update to 2.0.5.
* gnu/packages/patches/lcalc-default-parameters-1.patch,
gnu/packages/patches/lcalc-default-parameters-2.patch,
gnu/packages/patches/lcalc-lcommon-h.patch,
gnu/packages/patches/lcalc-using-namespace-std.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove here.
---
 gnu/local.mk                                  |  4 --
 .../patches/lcalc-default-parameters-1.patch  | 26 -------
 .../patches/lcalc-default-parameters-2.patch  | 58 ---------------
 gnu/packages/patches/lcalc-lcommon-h.patch    | 13 ----
 .../patches/lcalc-using-namespace-std.patch   | 43 -----------
 gnu/packages/sagemath.scm                     | 71 ++++++-------------
 6 files changed, 20 insertions(+), 195 deletions(-)
 delete mode 100644 gnu/packages/patches/lcalc-default-parameters-1.patch
 delete mode 100644 gnu/packages/patches/lcalc-default-parameters-2.patch
 delete mode 100644 gnu/packages/patches/lcalc-lcommon-h.patch
 delete mode 100644 gnu/packages/patches/lcalc-using-namespace-std.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 07e3497d10..84c88ea905 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1371,10 +1371,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/kodi-set-libcurl-ssl-parameters.patch		\
   %D%/packages/patches/kodi-skip-test-449.patch		\
   %D%/packages/patches/laby-make-install.patch			\
-  %D%/packages/patches/lcalc-default-parameters-1.patch		\
-  %D%/packages/patches/lcalc-default-parameters-2.patch		\
-  %D%/packages/patches/lcalc-lcommon-h.patch    		\
-  %D%/packages/patches/lcalc-using-namespace-std.patch 		\
   %D%/packages/patches/ldns-drill-examples.patch		\
   %D%/packages/patches/leela-zero-gtest.patch			\
   %D%/packages/patches/less-hurd-path-max.patch			\
diff --git a/gnu/packages/patches/lcalc-default-parameters-1.patch b/gnu/packages/patches/lcalc-default-parameters-1.patch
deleted file mode 100644
index 19b0776320..0000000000
--- a/gnu/packages/patches/lcalc-default-parameters-1.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Patch taken from the Sage packaging system.
-
-diff -Naur lcalc-1.23-vanilla/include/Ldirichlet_series.h lcalc-1.23-fixed-gcc.4.9/include/Ldirichlet_series.h
---- lcalc-1.23-vanilla/include/Ldirichlet_series.h	2012-08-08 23:21:55.000000000 +0200
-+++ lcalc-1.23-fixed-gcc.4.9/include/Ldirichlet_series.h	2014-04-21 14:37:59.027464849 +0200
-@@ -43,7 +43,7 @@
-  //XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
- template <class ttype>
- Complex L_function <ttype>::
--dirichlet_series(Complex s, long long N=-1)
-+dirichlet_series(Complex s, long long N)
- {
-     Complex z=0.;
-     long long m,n;
-diff -Naur lcalc-1.23-vanilla/include/L.h lcalc-1.23-fixed-gcc.4.9/include/L.h
---- lcalc-1.23-vanilla/include/L.h	2012-08-08 23:21:55.000000000 +0200
-+++ lcalc-1.23-fixed-gcc.4.9/include/L.h	2014-04-21 14:32:04.003467348 +0200
-@@ -491,7 +491,7 @@
- 
-     //#include "Ldirichlet_series.h" //for computing Dirichlet series
-     Complex partial_dirichlet_series(Complex s, long long N1, long long N2);
--    Complex dirichlet_series(Complex s, long long N);
-+    Complex dirichlet_series(Complex s, long long N=-1LL);
- 
-     //#include "Ltaylor_series.h" //for computing taylor series for Dirichlet series
-     //void compute_taylor_series(int N, int K, Complex s_0, Complex *series);
diff --git a/gnu/packages/patches/lcalc-default-parameters-2.patch b/gnu/packages/patches/lcalc-default-parameters-2.patch
deleted file mode 100644
index 1d881ee0c4..0000000000
--- a/gnu/packages/patches/lcalc-default-parameters-2.patch
+++ /dev/null
@@ -1,58 +0,0 @@
-Patch taken from the Sage packaging system.
-
---- lcalc-1.23/include/Lgamma.h	2012-08-08 23:21:55.000000000 +0200
-+++ lcalc-1.23/include/Lgamma.h	2014-05-18 21:15:27.786889718 +0200
-@@ -77,7 +77,7 @@
- //n=0 should just give log_GAMMA(z)... thus making log_GAMMA
- //code obsolete. But leave log_GAMMA intact anyways.
- template <class ttype>
--precise(ttype) log_GAMMA (ttype z,int n=0)
-+precise(ttype) log_GAMMA (ttype z,int n)
- {
-     int M;
-     precise(ttype) log_G,r,r2,y;
-@@ -230,7 +230,7 @@
- //value exp_w which holds exp(-w)
- //computes G(z,w), so there's an extra w^(-z) factor.
- template <class ttype>
--Complex inc_GAMMA (ttype z,ttype w, const char *method="temme", ttype exp_w = 0, bool recycle=false)
-+Complex inc_GAMMA (ttype z,ttype w, const char *method, ttype exp_w, bool recycle)
- {
- 
-     Complex G;
-@@ -334,7 +334,7 @@
- 
- 
- template <class ttype>
--ttype cfrac_GAMMA (ttype z,ttype w, ttype exp_w=0, bool recycle=false)  //computes G(z,w) via continued fraction
-+ttype cfrac_GAMMA (ttype z,ttype w, ttype exp_w, bool recycle)  //computes G(z,w) via continued fraction
- {
- 
-         ttype G;
-@@ -424,7 +424,7 @@
- }
- 
- template <class ttype>
--ttype asympt_GAMMA (ttype z,ttype w, ttype exp_w = 0, bool recycle=false)  //computes G(z,w) via asymptotic series
-+ttype asympt_GAMMA (ttype z,ttype w, ttype exp_w, bool recycle)  //computes G(z,w) via asymptotic series
- {
- 
-         if(my_verbose>3) cout << "called asympt_GAMMA("<<z<<","<<w<<")"<< endl;
-@@ -446,7 +446,7 @@
- 
- 
- template <class ttype>
--ttype comp_inc_GAMMA (ttype z,ttype w,ttype exp_w = 0, bool recycle=false)  //computes g(z,w)
-+ttype comp_inc_GAMMA (ttype z,ttype w,ttype exp_w, bool recycle)  //computes g(z,w)
- {
- 
-     ttype g;
-@@ -604,7 +604,7 @@
- }
- 
- template <class ttype>
--Complex gamma_sum(Complex s, int what_type, ttype *coeff, int N, Double g, Complex l, Double Q, Long Period, Complex delta=1, const char *method="temme")
-+Complex gamma_sum(Complex s, int what_type, ttype *coeff, int N, Double g, Complex l, Double Q, Long Period, Complex delta, const char *method)
- {
-     Complex SUM=0;
- 
diff --git a/gnu/packages/patches/lcalc-lcommon-h.patch b/gnu/packages/patches/lcalc-lcommon-h.patch
deleted file mode 100644
index 897956de64..0000000000
--- a/gnu/packages/patches/lcalc-lcommon-h.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Patch taken from the Sage packaging system.
-
---- src/include/Lcommon.h	2010-01-31 15:16:45.000000000 +0000
-+++ src/include/Lcommon.h	2011-03-08 21:19:11.849443238 +0000
-@@ -25,7 +25,7 @@
- #ifdef USE_MPFR
- inline double lcalc_to_double(const double& x) { return x; }
- #endif
--//inline double lcalc_to_double(const long double& x) { return x; }
-+inline double lcalc_to_double(const long double& x) { return x; }
- inline double lcalc_to_double(const int& x) { return x; }
- inline double lcalc_to_double(const long long& x) { return x; }
- inline double lcalc_to_double(const short& x) { return x; }
diff --git a/gnu/packages/patches/lcalc-using-namespace-std.patch b/gnu/packages/patches/lcalc-using-namespace-std.patch
deleted file mode 100644
index 6e0075fdc8..0000000000
--- a/gnu/packages/patches/lcalc-using-namespace-std.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-Patch taken from the Sage packaging system.
-
-diff --git a/include/Lcommon.h b/include/Lcommon.h
-index 1b3be43..bf40532 100644
---- a/include/Lcommon.h
-+++ b/include/Lcommon.h
-@@ -48,7 +48,7 @@ const bool outputSeries=true;	  // Whether to output the coefficients or just th
- 
- // Loop i from m to n
- // Useful in tidying up most for loops
--#define loop(i,m,n) for(typeof(m) i=(m); i!=(n); i++)
-+#define loop(i,m,n) for(auto i=(m); i!=(n); i++)
- 
- // A class for calculations involving polynomials of small degree
- // Not efficient enough for huge polynomials
-diff --git a/include/Lcommon_ld.h b/include/Lcommon_ld.h
-index 86ae4df..33c560c 100644
---- a/include/Lcommon_ld.h
-+++ b/include/Lcommon_ld.h
-@@ -53,7 +53,7 @@ const bool outputSeries=true;	  // Whether to output the coefficients or just th
- 
- // Loop i from m to n
- // Useful in tidying up most for loops
--#define loop(i,m,n) for(typeof(m) i=(m); i!=(n); i++)
-+#define loop(i,m,n) for(auto i=(m); i!=(n); i++)
- 
- // A class for calculations involving polynomials of small degree
- // Not efficient enough for huge polynomials
-diff --git a/include/Lglobals.h b/include/Lglobals.h
-index 60002e4..ca2606c 100644
---- a/include/Lglobals.h
-+++ b/include/Lglobals.h
-@@ -24,9 +24,9 @@
- #ifndef Lglobals_H
- #define Lglobals_H
- 
-+#include <valarray>
- using namespace std;
- 
--#include <valarray>
- #ifdef USE_MPFR
-     #include "Lgmpfrxx.h"
-     typedef mpfr_class Double;
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index b29620a946..1237ff8e04 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -38,6 +38,7 @@ (define-module (gnu packages sagemath)
   #:use-module (gnu packages lisp)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages popt)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz))
 
@@ -292,59 +293,27 @@ (define-public brial
 (define-public lcalc
   (package
     (name "lcalc")
-    (version "1.23")
-    ;; The original home page of the project has disappeared, as well as
-    ;; code hosted by the original author on Google Code. The latter has
-    ;; been copied to gitlab.com/sagemath and purportedly contains patches
-    ;; for a never released version 1.3, that supposedly follows 1.23.
-    ;; We use the tarball as well as the patches hosted inside the sage
-    ;; package system distributed with the sage tarball.
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
-                           "upstream/lcalc/lcalc-1.23.tar.bz2"))
-       (sha256
-        (base32
-         "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
-       (patches (search-patches "lcalc-lcommon-h.patch"
-                                "lcalc-default-parameters-1.patch"
-                                "lcalc-default-parameters-2.patch"
-                                "lcalc-using-namespace-std.patch"))))
+    (version "2.0.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.com/sagemath/lcalc")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1rwyx292y3jbsp88wagn9nhl9z7wsnl2yrs5imxkbxq87pnrj5a7"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ;no tests
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (add-before 'build 'prepare-build
-           (lambda* (#:key outputs #:allow-other-keys)
-             (chdir "src")
-             (let ((out (assoc-ref outputs "out")))
-               (substitute* "Makefile"
-                 (("^INSTALL_DIR= /usr/local")
-                  (string-append "INSTALL_DIR=" out))))
-             #t))
-         (add-before 'install 'make-output-dirs
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (lib (string-append out "/lib"))
-                    (include (string-append out "/include")))
-               (mkdir-p bin)
-               (mkdir-p lib)
-               (mkdir-p include))
-             #t)))))
-    ;; FIXME:
-    ;; We need to add pari-gp and probably pari related patches from the
-    ;; sage project, as well as uncomment the line setting PARI_DEFINE in
-    ;; the Makefile to get the full functionality of this package.
-    ;; For the time being, we hope that sage can be compiled without.
-    (synopsis "C++ library for L-functions")
-    (description "Lcalc computes L-functions, in particular the Riemann
-zeta function and its twists by quadratic characters.")
-    (license license:gpl2+)
-    (home-page "https://gitlab.com/sagemath/sage")))
+     (list #:configure-flags '(list "--with-pari")))
+    (inputs (list pari-gp))
+    (native-inputs (list autoconf automake libtool pkg-config gengetopt))
+    (home-page "https://gitlab.com/sagemath/lcalc")
+    (synopsis "C++ library for with L-functions")
+    (description
+     "Lcalc computes L-functions, in particular the Riemann zeta function and its
+twists by quadratic characters.")
+    (license license:gpl2+)))
 
 (define-public ratpoints
   (package
-- 
2.37.0

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* gnu/packages/sagemath.scm (sagemath): New variable.
---

Notes:
- I'm not sure about native inputs vs. inputs here.
- There is a broken symlink in share/jupyter/kernels/sagemath/doc is
  currently a broken symlink. We should probably remove it and add it
  into the documentation output.
- bin/ is currently full of random stuff, we probably only need a few
  things.

 gnu/packages/sagemath.scm | 106 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 335d98d9f4..f84440db93 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@HIDDEN>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@HIDDEN>
 ;;; Copyright © 2021 Efraim Flashner <efraim@HIDDEN>
+;;; Copyright © 2022 vicvbcun <guix@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,6 +26,7 @@ (define-module (gnu packages sagemath)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (guix utils)
@@ -34,6 +36,8 @@ (define-module (gnu packages sagemath)
   #:use-module (gnu packages bdw-gc)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages gd)
+  #:use-module (gnu packages graph)
   #:use-module (gnu packages image)
   #:use-module (gnu packages lisp)
   #:use-module (gnu packages maths)
@@ -41,6 +45,7 @@ (define-module (gnu packages sagemath)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz))
 
 
@@ -400,3 +405,104 @@ (define-public python-pplpy
      "This Python module pplpy provides a wrapper to the C++ Parma Polyhedra
 Library (PPL).")
     (license license:gpl3)))
+
+(define-public sagemath
+  (package
+    (name "sagemath")
+    (version "9.6")
+    (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
+                "0k91l3aid09hy94ps2r6acg22bxgsprxnh1b92hma3z1mn0ii3s1"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:tests? #f                  ; may take a long time, I'm scared
+           #:use-setuptools? #f
+           #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'prepare-build
+                          (lambda _
+                            (setenv "SAGE_NUM_THREADS"
+                                    (number->string (parallel-job-count)))
+                            (setenv "SAGE_VENV" #$output)
+                            (chdir "src")))
+                        (add-after 'install 'fix-logo-symlinks
+                          ;; these symlinks point to /tmp/guix-build-... so we
+                          ;; need to recreate them
+                          (lambda _
+                            (for-each
+                             (lambda (file)
+                               (let
+                                   ((source (string-append "sage/ext_data/notebook-ipython/" file))
+                                    (target (string-append #$output "/share/jupyter/kernels/sagemath/" file)))
+                                 (delete-file target)
+                                 (copy-file source target)))
+                             '("logo.svg" "logo-64x64.png"))))
+                        (add-after 'install 'delete-nbextensions
+                          ;; broken symlink to threejs-sage which we
+                          ;; don't even package
+                          (lambda _
+                            (delete-file-recursively (string-append #$output "/share/jupyter/nbextensions"))))
+                        (add-after 'install 'install-bin
+                          ;; so far, we have only installed the
+                          ;; library part of sage
+                          (lambda _
+                            ;; this copies way to much
+                            (copy-recursively "bin" (string-append #$output "/bin")))))))
+    (inputs (list arb
+                  boost
+                  brial
+                  cliquer
+                  ecl
+                  eclib
+                  edge-addition-planarity-suite
+                  flint
+                  gap
+                  gd
+                  giac
+                  givaro
+                  glpk
+                  gmp
+                  gmp-ecm
+                  gsl
+                  iml
+                  lcalc
+                  libbraiding
+                  libhomfly
+                  linbox
+                  m4ri
+                  m4rie
+                  mpc
+                  mpfi
+                  ntl
+                  openblas
+                  pari-gp
+                  python-cypari2
+                  python-gmpy2
+                  python-jinja2
+                  python-jupyter-core
+                  python-memory-allocator
+                  python-numpy
+                  python-pkgconfig
+                  python-pplpy
+                  python-setuptools
+                  python-wheel
+                  rw
+                  singular
+                  symmetrica
+                  zlib
+                  zn-poly))
+    (native-inputs (list pkg-config python-cython))
+    (home-page "https://www.sagemath.org")
+    (synopsis "Python-based computer algebra system")
+    (description
+     "SageMath is a free open-source mathematics software system licensed under the
+GPL. It builds on top of many existing open-source packages: NumPy, SciPy,
+matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined
+power through a common, Python-based language or directly via interfaces or
+wrappers.")
+    (license license:gpl3)))
-- 
2.37.0

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Switch to an autotoolized fork.

* gnu/packages/sagemath.scm (cliquer): Update to 1.22.
---
 gnu/packages/sagemath.scm | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 75720f31a5..b29620a946 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -101,19 +101,18 @@ (define-public python-gmpy2
 (define-public cliquer
   (package
     (name "cliquer")
-    (version "1.21")
-    ;; The original source package is available from the home page and
-    ;; has not seen any release since 2010; it comes with only a Makefile
-    ;; without an "install" target. Instead, there is an autotoolized
-    ;; tarball available from the Sage project.
-    (source
-     (origin
-       (method url-fetch)
-       (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
-       (sha256
-        (base32
-         "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
+    (version "1.22")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dimpase/autocliquer")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "00gcmrhi2fjn8b246w5a3b0pl7p6haxy5wjvd9kcqib1xanz59z4"))))
     (build-system gnu-build-system)
+    (native-inputs (list autoconf automake libtool))
     (synopsis "C routines for finding cliques in weighted graphs")
     (description "Cliquer is a set of reentrant C routines for finding
 cliques in a weighted or unweighted graph.  It uses an exact
@@ -122,7 +121,7 @@ (define-public cliquer
 search to maximal cliques, store cliques in memory and call a user-defined
 function for every found clique.")
     (license license:gpl2+)
-    (home-page "https://users.aalto.fi/~pat/cliquer.html")))
+    (home-page "https://github.com/dimpase/autocliquer")))
 
 (define-public libbraiding
   (package
-- 
2.37.0

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Hello!

vicvbcun <guix@HIDDEN> skribis:

> This series adds SageMath. Everything compiles just fine and even the
> Jupyter notebook interface works, but there is still much work to do. So
> far, I have only added the minimal set of inputs required for the build
> to succeed. Tests and documentations are still missing.

This looks great already!  To make sure things don=E2=80=99t stall, we could
apply the patch series piecemeal, starting with the dependencies that
you think are ready, and leaving more time to polish the =E2=80=98sagemath=
=E2=80=99
package.

WDYT?

Regarding SageMath, my understanding is that it bundles lots of things.
In Guix, we=E2=80=99d like to make sure we do not use the bundled packages,
unless we practically can=E2=80=99t avoid it.  To do that, the best option =
is to
remove =E2=80=9Cthird-party=E2=80=9D (or similar) directories right in the =
=E2=80=98snippet=E2=80=99 of
the =E2=80=98sagemath=E2=80=99 package.  Could you give that a try?

Then, as you note, we=E2=80=99d rather run tests to make sure the package w=
orks
as intended.

Cc=E2=80=99ing Andreas, who I think is quite familiar with Sage.

Ludo=E2=80=99.

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Hello,

On 2022-08-01T11:24:31+0200, Ludovic Courtès wrote:
> > This series adds SageMath. Everything compiles just fine and even the
> > Jupyter notebook interface works, but there is still much work to do. So
> > far, I have only added the minimal set of inputs required for the build
> > to succeed. Tests and documentations are still missing.
> 
> This looks great already!  To make sure things don’t stall, we could
> apply the patch series piecemeal, starting with the dependencies that
> you think are ready, and leaving more time to polish the ‘sagemath’
> package.
> 
> WDYT?
Sounds like a good idea. The updates all seem fine to me (except gap)
and other than perhaps a better description for python-memory-allocator
I don't think there is much left to do for the other ones.

As for gap, I took another stab at it and it now builds reproducibly for
me. I also removed all the trailing #t's and changed the phases to use a
gexp.
By the way, the gap definition contains a snippet that deletes many gap
packages over concerns due to missing explicit licenses. However in a
cursory look at the tarball, I can see many LICENSE/COPYING files so
that may have changed.

> Regarding SageMath, my understanding is that it bundles lots of things.
> In Guix, we’d like to make sure we do not use the bundled packages,
> unless we practically can’t avoid it.  To do that, the best option is to
> remove “third-party” (or similar) directories right in the ‘snippet’ of
> the ‘sagemath’ package.  Could you give that a try?
If I understand the Sage build system correctly, missing dependencies
are automatically retrieved and build only when using the provided
Makefile. As is, the package definition builds and installs only the
python library part using setup.py. Thus a missing dependency probably
leads to a runtime error, though I haven't checked this.

> Then, as you note, we’d rather run tests to make sure the package works
> as intended.
I will try to see if I can get tests to work, though probably as
separate "package" like nixpkgs does[0], to avoid rebuilding sagemath so
often :).

As for sagemath itself, I will have a look at what exactly we need in
bin/.

[0]:
https://github.com/NixOS/nixpkgs/blob/master/pkgs/applications/science/math/sage/sage-tests.nix

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Remove logs that are not reproducible.

* gnu/packages/algebra.scm (gap): Update to 4.11.1.
[source]<snippet>: Remove trailing #t.
[arguments]<#:phases>: Remove trailing #t, use gexps.
[install]: Install missing config.h header.
---
 gnu/packages/algebra.scm | 181 +++++++++++++++++++--------------------
 1 file changed, 90 insertions(+), 91 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 95fbdb5e36..c3b1c7fc3b 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1209,17 +1209,17 @@ (define-public xtensor-benchmark
 (define-public gap
   (package
     (name "gap")
-    (version "4.11.0")
+    (version "4.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://files.gap-system.org/gap-"
                            (version-major+minor version)
-                           "/tar.bz2/gap-"
+                           "/tar.gz/gap-"
                            version
-                           ".tar.bz2"))
+                           ".tar.gz"))
        (sha256
-        (base32 "00l6hvy4iggnlrib4vp805sxdm3j7n3hzpv5zs9hbiiavh80l1xz"))
+        (base32 "01535s81h254zcs84zi95xqmhvvn6fn9qss8761myxc2gpdcadb6"))
        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
        (snippet
         '(begin
@@ -1235,97 +1235,96 @@ (define-public gap
            ;; given by their names up to version numbers.
            (with-directory-excursion "pkg"
              (for-each delete-file-recursively
-               (lset-difference
-                 (lambda (all keep) (string-prefix? keep all))
-                 (scandir ".")
-                 '("." ".."
-                   ;; Necessary packages.
-                   "GAPDoc-"
-                   "primgrp-"
-                   "SmallGrp-"   ; artistic2.0
-                   "transgrp"    ; artistic2.0 for data,
-                                 ; gpl2 or gpl3 for code
-                   ;; Recommended package.
-                   "io-"         ; gpl3+
-                   ;; Optional packages, searched for at start,
-                   ;; and their depedencies.
-                   "alnuth-"
-                   "autpgrp-"
-                   "crisp-"      ; bsd-2
-                   "ctbllib"     ; gpl3+, clarified in the next release;
-                                 ; see
-                                 ; http://www.math.rwth-aachen.de/~Thomas.Breuer/ctbllib/README.md
-                   "FactInt-"
-                   "fga"
-                   "irredsol-"   ; bsd-2
-                   "laguna-"
-                   "polenta-"
-                   "polycyclic-"
-                   "radiroot-"
-                   "resclasses-"
-                   "sophus-"
-                   "tomlib-"
-                   "utils-"))))
-           #t))))
+                       (lset-difference
+                        (lambda (all keep) (string-prefix? keep all))
+                        (scandir ".")
+                        '("." ".."
+                          ;; Necessary packages.
+                          "GAPDoc-"
+                          "primgrp-"
+                          "SmallGrp-"   ; artistic2.0
+                          "transgrp"    ; artistic2.0 for data,
+                                        ; gpl2 or gpl3 for code
+                          ;; Recommended package.
+                          "io-"   ; gpl3+
+                          ;; Optional packages, searched for at start,
+                          ;; and their depedencies.
+                          "alnuth-"
+                          "autpgrp-"
+                          "crisp-"     ; bsd-2
+                          "ctbllib"    ; gpl3+, clarified in the next release;
+                                        ; see
+                                        ; http://www.math.rwth-aachen.de/~Thomas.Breuer/ctbllib/README.md
+                          "FactInt-"
+                          "fga"
+                          "irredsol-"   ; bsd-2
+                          "laguna-"
+                          "polenta-"
+                          "polycyclic-"
+                          "radiroot-"
+                          "resclasses-"
+                          "sophus-"
+                          "tomlib-"
+                          "utils-"))))))))
     (build-system gnu-build-system)
     (inputs
      (list gmp readline zlib))
     (arguments
-     `(#:modules ((ice-9 ftw)
-                  (srfi srfi-26)
-                  (guix build gnu-build-system)
-                  (guix build utils))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'build 'build-packages
-           ;; Compile all packages that have not been deleted by the
-           ;; code snippet above.
-           (lambda _
-             (setenv "CONFIG_SHELL" (which "bash"))
-             (with-directory-excursion "pkg"
-               (invoke "../bin/BuildPackages.sh")
-             #t)))
-         (add-after 'build-packages 'build-doc
-           ;; The documentation is bundled, but we create it from source.
-           (lambda _
-             (with-directory-excursion "doc"
-               (invoke "./make_doc"))
-             #t))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (prog (string-append bin "/gap"))
-                    (prog-real (string-append bin "/.gap-real"))
-                    (share (string-append out "/share/gap")))
-               ;; Install only the gap binary; the gac compiler is left
-               ;; for maybe later. "Wrap" it in a shell script that calls
-               ;; the binary with the correct parameter.
-               ;; The make target install-bin is supposed to do that, but
-               ;; is not currently working.
-               (mkdir-p bin)
-               (copy-file "gap" prog-real)
-               (call-with-output-file prog
-                 (lambda (port)
-                   (format port
-                           "#!~a~%exec ~a -l ~a \"$@\"~%"
-                           (which "bash")
-                           prog-real
-                           share)))
-               (chmod prog #o755)
-               ;; Install the headers and library, which are needed by Sage.
-               (invoke "make" "install-headers")
-               (invoke "make" "install-libgap")
-               ;; Remove information on the build directory from sysinfo.gap.
-               (substitute* "sysinfo.gap"
-                 (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
-                 (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
-                 (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
-               (invoke "make" "install-gaproot")
-               ;; Copy the directory of compiled packages; the make target
-               ;; install-pkg is currently empty.
-               (copy-recursively "pkg" (string-append share "/pkg")))
-             #t)))))
+     (list #:modules '((ice-9 ftw)
+                       (srfi srfi-26)
+                       (guix build gnu-build-system)
+                       (guix build utils))
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'build 'build-packages
+                 ;; Compile all packages that have not been deleted by the
+                 ;; code snippet above.
+                 (lambda _
+                   (setenv "CONFIG_SHELL" (which "bash"))
+                   (with-directory-excursion "pkg"
+                     (invoke "../bin/BuildPackages.sh"))))
+               (add-after 'build-packages 'build-doc
+                 ;; The documentation is bundled, but we create it from source.
+                 (lambda _
+                   (with-directory-excursion "doc"
+                     (invoke "./make_doc"))))
+               (replace 'install
+                 (lambda _
+                   (let* ((bin (string-append #$output "/bin"))
+                          (prog (string-append bin "/gap"))
+                          (prog-real (string-append bin "/.gap-real"))
+                          (share (string-append #$output "/share/gap")))
+                     ;; Install only the gap binary; the gac compiler is left
+                     ;; for maybe later. "Wrap" it in a shell script that calls
+                     ;; the binary with the correct parameter.
+                     ;; The make target install-bin is supposed to do that, but
+                     ;; is not currently working.
+                     (mkdir-p bin)
+                     (copy-file "gap" prog-real)
+                     (call-with-output-file prog
+                       (lambda (port)
+                         (format port
+                                 "#!~a~%exec ~a -l ~a \"$@\"~%"
+                                 (which "bash")
+                                 prog-real
+                                 share)))
+                     (chmod prog #o755)
+                     ;; Install the headers and library, which are needed by Sage.
+                     (invoke "make" "install-headers")
+                     (invoke "make" "install-libgap")
+                     (install-file "gen/config.h" (string-append #$output "/include/gap"))
+                     ;; Remove information on the build directory from sysinfo.gap.
+                     (substitute* "sysinfo.gap"
+                       (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
+                       (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
+                       (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
+                     (invoke "make" "install-gaproot")
+                     ;; Copy the directory of compiled packages; the make target
+                     ;; install-pkg is currently empty.
+                     (copy-recursively "pkg" (string-append share "/pkg"))
+                     ;; these log files are not reproducible
+                     (delete-file (string-append share "/pkg/io-4.7.0/config.log"))
+                     (delete-file-recursively (string-append share "/pkg/log"))))))))
     (home-page "https://www.gap-system.org/")
     (synopsis
      "System for computational group theory")

base-commit: f6904c0b19c2fcca41bbf1400c738bd833fec9a8
prerequisite-patch-id: 73510fd06d7520fe1f53a6d654ad79bfb197731a
-- 
2.37.0

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On 2022-07-23T21:59:07+0200, vicvbcun wrote:
> Everything compiles just fine and even the Jupyter notebook interface
> works, [...]
Well, I spoke to soon. As it turns out, the `sage' command I invoked to
test things a bit wound up using the sage installed by pacman, so no
wonder it worked perfectly. Nonetheless, I got some things working in a
guix shell container (so hopefully this wont happen again) with the help
of wrap-program and a few more dependencies.

I will try to post something that actually works a bit soon.

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Hello,

Am Mon, Aug 01, 2022 at 11:24:31AM +0200 schrieb Ludovic Courtès:
> > This series adds SageMath. Everything compiles just fine and even the
> > Jupyter notebook interface works, but there is still much work to do. So
> > far, I have only added the minimal set of inputs required for the build
> > to succeed. Tests and documentations are still missing.
> This looks great already!  To make sure things don’t stall, we could
> apply the patch series piecemeal, starting with the dependencies that
> you think are ready, and leaving more time to polish the ‘sagemath’
> package.

thanks for letting me know, I will start by having a look at the patches
doing version updates.

Concerning sagemath itself, below is my very old version of an attempt at
packaging the library. Some things look reassuringly similar, my handling
of the number of cores is less nice, but I do delete the bundled packages.

Maybe you could copy useful parts into your recipe?

As for tests, indeed we should drop them for the time being until we have
a working sage package.

Thanks for these efforts!

Andreas



(define-public sage
  (package
    (name "sage")
    (version "8.7")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-"
                    version ".tar.gz"))
              (sha256
               (base32
                "04l7i29vvxbd276z7hq6lj00ij42iy05pj7x765f0wswjiz0jlax"))
              (modules '((guix build utils)))
              (snippet '(begin (delete-file-recursively "upstream")
                               (delete-file-recursively ".git")
                               #t))))
    (build-system python-build-system)
    (native-inputs
     `(("cython" ,python-cython)
       ("pkg-config" ,pkg-config)
       ("python-cysignals" ,python-cysignals)
       ("python-pkgconfig" ,python-pkgconfig)
       ("python-jinja2" ,python-jinja2)))
    (inputs
     `(("arb" ,arb)
       ("boost" ,boost)
       ("brial" ,brial)
       ("cliquer" ,cliquer)
       ("ecl" ,ecl)
       ("eclib" ,eclib)
       ("gmp-ecm" ,gmp-ecm)
       ("edge-addition-planarity-suite" ,edge-addition-planarity-suite)
       ("fflas-ffpack" ,fflas-ffpack-2.3.2)
       ("flint" ,flint)
       ("gap" ,gap)
       ("gd" ,gd)
       ("gf2x" ,gf2x)
       ("givaro" ,givaro-4.0.4)
       ("glpk" ,glpk)
       ("gmp" ,gmp)
       ("gsl" ,gsl)
       ("iml" ,iml)
       ("lcalc" ,lcalc)
       ("libbraiding" ,libbraiding)
       ("libgc" ,libgc)
       ("libhomfly" ,libhomfly)
       ("linbox" ,linbox-1.5.2)
       ("lrcalc" ,lrcalc)
       ("m4ri" ,m4ri)
       ("m4rie" ,m4rie)
       ("mpc" ,mpc)
       ("mpfr" ,mpfi)
       ("ntl" ,ntl)
       ("pari-gp" ,pari-gp)
       ("ppl" ,ppl)
       ("pynac" ,pynac)
       ("python-cypari2" ,python-cypari2)
       ("python-gmpy2" ,python-gmpy2)
       ("python-numpy" ,python-numpy)
       ("python-six" ,python-six)
       ("ratpoints" ,ratpoints)
       ("readline" ,readline)
       ("rw" ,rw)
       ("singular" ,singular)
       ("symmetrica" ,symmetrica)
       ("zlib" ,zlib)
       ("zn-poly" ,zn-poly)))
    (arguments
     `(#:tests? #f ; a test since this phase fails with an error in setup.py
       #:use-setuptools? #f ; otherwise setup.py complains about
                            ; --single-version-externally-managed
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'setup
           (lambda _
             (setenv "SAGE_ROOT" (getcwd))
             (setenv "SAGE_LOCAL" (getcwd))
             (setenv "SAGE_SHARE" (string-append (getcwd) "/share"))
             (setenv "PATH" (string-append (getcwd) "/build/bin:"
                            (getcwd) "/src/bin:"
                            (getenv "PATH")))
             (setenv "SAGE_NUM_THREADS" "32") ; arbitrary number, 32 cores
                                              ; on bayfront
             (mkdir-p "var/lib/sage/installed")
             (mkdir-p (string-append (getcwd)
                                     "/share/sage/ext/notebook-ipython"))
             (chdir "src")
             #t))
         (add-after 'install 'save-space
           ;; The Nix package deletes a directory with over 100MB, which
           ;; apparently is not needed. Let us do the same.
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (python (assoc-ref inputs "python"))
                    (python-version
                      ((@@ (guix build python-build-system)
                           get-python-version) python))
                    (site (string-append out "/lib/python"
                                         python-version
                                         "/site-packages"))
                    (directory (string-append site "/sage/cython_debug")))
               (delete-file-recursively directory))
             #t)))))
    (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, bundled packages under various
    ;; other licenses, see COPYING.txt in the distribution
    (license license:gpl3)
    (home-page "https://www.sagemath.org/")))

Last modified: Mon, 8 Aug 2022 14:45:01 UTC

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Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.