[PATCH 0/2] Update GNU Scientific Library

[PATCH 0/2] Update GNU Scientific Library

[Efraim Flashner]

GSL has an update to 2.0. As part of the update we no longer need the two
patches that modified the source, and the tests for i686-linux passed when
I tried `guix build gsl -s i686-linux`, so I added a patch to re-enable them.
I haven't written such a complex commit message so I wanted to make sure I got
everything correct.

Efraim Flashner (2):
  gnu: gsl: Update to 2.0.
  gnu: gsl: Enable tests.

 gnu-system.am                                    |  2 -
 gnu/packages/maths.scm                           | 21 ++----
 gnu/packages/patches/gsl-poly-test-fix-pt1.patch | 84 ------------------------
 gnu/packages/patches/gsl-poly-test-fix-pt2.patch | 27 --------
 4 files changed, 4 insertions(+), 130 deletions(-)
 delete mode 100644 gnu/packages/patches/gsl-poly-test-fix-pt1.patch
 delete mode 100644 gnu/packages/patches/gsl-poly-test-fix-pt2.patch

-- 
2.6.2

[PATCH 1/2] gnu: gsl: Update to 2.0.

[Efraim Flashner]

* gnu/packages/maths.scm (gsl): Update to 2.0.
  [source]: Remove patches.
* gnu/packages/patches/gsl-poly-test-fix-pt1.patch: Remove file.
* gnu/packages/patches/gsl-poly-test-fix-pt2.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch.
---
 gnu-system.am                                    |  2 -
 gnu/packages/maths.scm                           |  6 +-
 gnu/packages/patches/gsl-poly-test-fix-pt1.patch | 84 ------------------------
 gnu/packages/patches/gsl-poly-test-fix-pt2.patch | 27 --------
 4 files changed, 2 insertions(+), 117 deletions(-)
 delete mode 100644 gnu/packages/patches/gsl-poly-test-fix-pt1.patch
 delete mode 100644 gnu/packages/patches/gsl-poly-test-fix-pt2.patch

diff --git a/gnu-system.am b/gnu-system.am
index 3b7e62c..2a1ecf3 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -486,8 +486,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/grep-CVE-2015-1345.patch			\
   gnu/packages/patches/grub-gets-undeclared.patch		\
   gnu/packages/patches/grub-freetype.patch			\
-  gnu/packages/patches/gsl-poly-test-fix-pt1.patch		\
-  gnu/packages/patches/gsl-poly-test-fix-pt2.patch		\
   gnu/packages/patches/guile-1.8-cpp-4.5.patch			\
   gnu/packages/patches/guile-arm-fixes.patch			\
   gnu/packages/patches/guile-default-utf8.patch			\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b4b930d..1aba362 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -149,7 +149,7 @@ semiconductors.")
 (define-public gsl
   (package
     (name "gsl")
-    (version "1.16")
+    (version "2.0")
     (source
      (origin
       (method url-fetch)
@@ -157,9 +157,7 @@ semiconductors.")
                           version ".tar.gz"))
       (sha256
        (base32
-        "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))
-      (patches (map search-patch '("gsl-poly-test-fix-pt1.patch"
-                                   "gsl-poly-test-fix-pt2.patch")))))
+        "0bfahlsgil0695104a44c3c8vjkyvxmg3s92371fddcrj6qz0qg3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f
diff --git a/gnu/packages/patches/gsl-poly-test-fix-pt1.patch b/gnu/packages/patches/gsl-poly-test-fix-pt1.patch
deleted file mode 100644
index 3d1ed42..0000000
--- a/gnu/packages/patches/gsl-poly-test-fix-pt1.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-From 9cc12d0377dd634b1b97954d076b715f982853b7 Mon Sep 17 00:00:00 2001
-From: Patrick Alken <alken@colorado.edu>
-Date: Fri, 4 Apr 2014 13:36:16 -0600
-Subject: [PATCH] bug fix in sorting of complex numbers (bug #39055)
-
----
- poly/test.c | 49 ++++++++++++++++++++++++++++++-------------------
- 1 file changed, 30 insertions(+), 19 deletions(-)
-
-diff --git a/poly/test.c b/poly/test.c
-index 9c147f6..d090802 100644
---- a/poly/test.c
-+++ b/poly/test.c
-@@ -25,11 +25,21 @@
- #include <gsl/gsl_poly.h>
- #include <gsl/gsl_heapsort.h>
- 
-+/* sort by Re(z) then by Im(z) */
- static int
- cmp_cplx(const double *a, const double *b)
- {
--	double t = (a[0] * a[0] + a[1] * a[1]) - (b[0] * b[0] + b[1] * b[1]);
--	return t < 0.0 ? -1 : t > 0.0 ? 1 : 0;
-+  double r = a[0] - b[0];
-+
-+  if (r == 0.0)
-+    {
-+      double t = a[1] - b[1];
-+	    return t < 0.0 ? -1 : t > 0.0 ? 1 : 0;
-+    }
-+  else if (r < 0.0)
-+    return -1;
-+  else
-+    return 1;
- }
- 
- int
-@@ -534,25 +544,26 @@ main (void)
-        Problem reported by Munagala Ramanath (bug #39055)
-     */
- 
--    double a[16] = { 32, -48, -8, 28, -8, 16, -16, 12, -16, 6, 10, -17, 10, 2, -4, 1 };
-+    double a[16] = { 32, -48, -8, 28, -8, 16, -16, 12,
-+                    -16, 6, 10, -17, 10, 2, -4, 1 };
-     double z[16*2];
- 
--    double expected[16*20] = {
--	   1.0000000000000000,  0.00000000000000000,
--	   1.0000000000000000,  0.00000000000000000,
--	  -1.0000000000000000,  0.00000000000000000,
--	 -0.65893856175240950,  0.83459757287426684,
--	 -0.65893856175240950, -0.83459757287426684,
--	-0.070891117403341281,  -1.1359249087587791,
--	-0.070891117403341281,   1.1359249087587791,
--	   1.1142366961812986, -0.48083981203389980,
--	   1.1142366961812986,  0.48083981203389980,
--	  -1.3066982484920768,  0.00000000000000000,
--	  0.57284747839410854,   1.1987808988289705,
--	  0.57284747839410854,  -1.1987808988289705,
--	  -1.6078107423472359,  0.00000000000000000,
--	   2.0000000000000000,  0.00000000000000000,
--	   2.0000000000000000,  0.00000000000000000 };
-+    double expected[16*2] = {
-+     -1.6078107423472359,    0.00000000000000000,
-+     -1.3066982484920768,    0.00000000000000000,
-+     -1.0000000000000000,    0.00000000000000000,
-+     -0.65893856175240950,  -0.83459757287426684,
-+     -0.65893856175240950,   0.83459757287426684,
-+     -0.070891117403341281, -1.1359249087587791,
-+     -0.070891117403341281,  1.1359249087587791,
-+      0.57284747839410854,  -1.1987808988289705,
-+      0.57284747839410854,   1.1987808988289705,
-+      1.0000000000000000,    0.00000000000000000,
-+      1.0000000000000000,    0.00000000000000000,
-+      1.1142366961812986,   -0.48083981203389980,
-+      1.1142366961812986,    0.48083981203389980,
-+      2.0000000000000000,    0.00000000000000000,
-+      2.0000000000000000,    0.00000000000000000 };
- 
-     int i;
- 
--- 
-2.4.3
-
diff --git a/gnu/packages/patches/gsl-poly-test-fix-pt2.patch b/gnu/packages/patches/gsl-poly-test-fix-pt2.patch
deleted file mode 100644
index 0e6fcf1..0000000
--- a/gnu/packages/patches/gsl-poly-test-fix-pt2.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-From 0466df8660a7b6ddf2e082a1ec38bc6ea25a3c5c Mon Sep 17 00:00:00 2001
-From: Patrick Alken <alken@colorado.edu>
-Date: Mon, 7 Apr 2014 10:59:58 -0600
-Subject: [PATCH] change error test for 15th degree polynomial (bug #39055)
-
----
- poly/test.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/poly/test.c b/poly/test.c
-index d090802..f6a7e3f 100644
---- a/poly/test.c
-+++ b/poly/test.c
-@@ -579,8 +579,8 @@ main (void)
- 
-     for (i = 0; i<15; i++)
-       {
--        gsl_test_abs (z[2*i], expected[2*i], 1e-7, "z%d.real, 15th-order polynomial", i);
--        gsl_test_abs (z[2*i+1], expected[2*i+1], 1e-7, "z%d.imag, 15th-order polynomial", i);
-+        gsl_test_rel (z[2*i], expected[2*i], 1e-7, "z%d.real, 15th-order polynomial", i);
-+        gsl_test_rel (z[2*i+1], expected[2*i+1], 1e-7, "z%d.imag, 15th-order polynomial", i);
-       }
-   }
- 
--- 
-2.4.3
-
-- 
2.6.2

[PATCH 2/2] gnu: gsl: Enable tests.

[Efraim Flashner]

* gnu/packages/maths.scm (gsl): Enable tests for i686-linux.
---
 gnu/packages/maths.scm | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1aba362..4eeb39d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -160,19 +161,7 @@ semiconductors.")
         "0bfahlsgil0695104a44c3c8vjkyvxmg3s92371fddcrj6qz0qg3"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:parallel-tests? #f
-       #:phases
-        (alist-replace
-         'configure
-         (lambda* (#:key target system outputs #:allow-other-keys #:rest args)
-           (let ((configure (assoc-ref %standard-phases 'configure)))
-             ;; disable numerically unstable test on i686, see thread at
-             ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
-             (if (string=? (or target system) "i686-linux")
-                 (substitute* "ode-initval2/Makefile.in"
-                   (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
-             (apply configure args)))
-         %standard-phases)))
+     `(#:parallel-tests? #f))
     (home-page "http://www.gnu.org/software/gsl/")
     (synopsis "Numerical library for C and C++")
     (description
-- 
2.6.2

Re: [PATCH 1/2] gnu: gsl: Update to 2.0.

[Ricardo Wurmus]

Efraim Flashner <efraim@flashner.co.il> writes:

> * gnu/packages/maths.scm (gsl): Update to 2.0.
>   [source]: Remove patches.
> * gnu/packages/patches/gsl-poly-test-fix-pt1.patch: Remove file.
> * gnu/packages/patches/gsl-poly-test-fix-pt2.patch: Remove file.
> * gnu-system.am (dist_patch_DATA): Remove patch.
                                            ^^^^^  “patches” / “them”?

Does the version bump mean that there have been API changes to GSL?  I
wonder if packages depending on GSL still build.

~~ Ricardo

Re: [PATCH 2/2] gnu: gsl: Enable tests.

[Ricardo Wurmus]

Efraim Flashner <efraim@flashner.co.il> writes:

> * gnu/packages/maths.scm (gsl): Enable tests for i686-linux.

I think this should be

  * gnu/packages/maths.scm (gsl)[arguments]: Enable tests for i686-linux.

Looks good otherwise.

~~ Ricardo

Re: [PATCH 1/2] gnu: gsl: Update to 2.0.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 1367 bytes --]

On Sun, 01 Nov 2015 10:06:25 +0100
Ricardo Wurmus <rekado@elephly.net> wrote:

> Efraim Flashner <efraim@flashner.co.il> writes:
> 
> > * gnu/packages/maths.scm (gsl): Update to 2.0.
> >   [source]: Remove patches.
> > * gnu/packages/patches/gsl-poly-test-fix-pt1.patch: Remove file.
> > * gnu/packages/patches/gsl-poly-test-fix-pt2.patch: Remove file.
> > * gnu-system.am (dist_patch_DATA): Remove patch.  
>                                             ^^^^^  “patches” / “them”?
> 
> Does the version bump mean that there have been API changes to GSL?  I
> wonder if packages depending on GSL still build.
> 
> ~~ Ricardo
> 

I tested pspp and it build without any problems

https://lists.gnu.org/archive/html/info-gnu/2015-10/msg00014.html :
"Version 2.0 of the GNU Scientific Library (GSL) is now available. GSL
provides a large collection of routines for numerical computing in C.
The major version number was increased, since a number of internal
workspaces have changed and so existing binaries must be recompiled
against this new library. There are also a small number of API changes
and deprecated functions."

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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Re: [PATCH 1/2] gnu: gsl: Update to 2.0.

[Andreas Enge]

Hello,

just nitpicking on the commit message:

On Sun, Nov 01, 2015 at 10:09:59AM +0200, Efraim Flashner wrote:
> * gnu/packages/patches/gsl-poly-test-fix-pt1.patch: Remove file.
> * gnu/packages/patches/gsl-poly-test-fix-pt2.patch: Remove file.

This is usually:
* gnu/packages/patches/gsl-poly-test-fix-pt1.patch,
  gnu/packages/patches/gsl-poly-test-fix-pt2.patch: Remove files.

I wonder if it should not even be (question to the commit log wizards):
* gnu/packages/patches/{gsl-poly-test-fix-pt1.patch,
  gsl-poly-test-fix-pt2.patch}: Remove files.
?

> * gnu/packages/maths.scm (gsl): Enable tests for i686-linux.

Maybe "Reenable test"? as there is only one and not all of them were
disabled previously?

Andreas