upgrade gsl to version 2.7

[dimpase]

One API change in GSL 2.7 causes trouble in Sage, see

• https://groups.google.com/g/sage-devel/c/yQ67Wy0gp58/m/jr6f7xtcBQAJ

Some distros, e.g. Gentoo, now have GSL 2.7 as the default.

Depends on #32607

CC: @orlitzky @sagetrac-tmonteil

Component: packages: standard

Keywords: upgrade, gsl

Author: Lorenz Panny, John Palmieri, Matthias Koeppe

Branch/Commit: bb8b92d

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/32587

[yyyyx4]

Branch: public/32587

[yyyyx4]

comment:1

Here's an attempt. It seemed to build successfully, but I haven't run any tests so far.

---

New commits:

e4a133f

update GSL to 2.7

[yyyyx4]

Commit: e4a133f

[yyyyx4]

Author: Lorenz Panny

[yyyyx4]

comment:2

I just ran make ptestlong with this branch on a fresh Debian 11; all tests passed.

[mkoeppe]

comment:3

Do the changes to the library also work with an older GSL?

[yyyyx4]

comment:4

They should: The new code simply uses the macros provided by GSL itself (in gsl_complex.h) to work with the gsl_complex struct, and those macros haven't changed (they are only #ifdef'd to something else). That said, I haven't tested it.

[mkoeppe]

comment:5

In this case, I would recommend the following. Split this ticket into two:

• one ticket for updating the library so that it can work with system GSL 2.7.
  Because this ticket will not include a change to packages, the patchbot will run on it.
• a follow-up ticket that does the upgrade of the package.

With each of the tickets, we can run portability testing on GH Actions (https://doc.sagemath.org/html/en/developer/portability_testing.html) to make sure that it still works with system GSL on all supported platforms. If necessary, we may need to adjust build/pkgs/gsl/spkg-configure.m4. Currently we accept all GSL >= 2.4.

[yyyyx4]

Dependencies: #32607

[yyyyx4]

comment:7

Alright, all the code changes are now in #32607.

Remaining diff in this branch (after #32607): sagemath/sagetrac-mirror@6633bc4...e4a133f

[dimpase]

comment:8

I'm a bit confused, as Sage with system's GLS 2.7 (as on Gentoo Linux) appears to work without
any changes in the source.

[orlitzky]

comment:9

Replying to @dimpase:

I'm a bit confused, as Sage with system's GLS 2.7 (as on Gentoo Linux) appears to work without
any changes in the source.

Probably the USE=deprecated that is on by default.

[jhpalmieri]

comment:10

From #31621: can we also make the following changes?

• change gsl's spkg-install.in as follows:

diff --git a/build/pkgs/gsl/spkg-install.in b/build/pkgs/gsl/spkg-install.in
index 179b78963a..ef156a7a5c 100644
--- a/build/pkgs/gsl/spkg-install.in
+++ b/build/pkgs/gsl/spkg-install.in
@@ -1,5 +1,5 @@
 cd src
 
-sdh_configure LIBS="`pkg-config --libs-only-l cblas` -lm"
+sdh_configure LIBS="`pkg-config --libs-only-l cblas` -lm" LDFLAGS="$LDFLAGS `pkg-config --libs-only-L cblas`"
 sdh_make
 sdh_make_install

As it stands, on OSX + homebrew, ./configure --with-system-gsl=no fails when building gsl with the error

configure: error: in `/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta1/local/var/tmp/sage/build/gsl-2.6/src':
configure: error: C compiler cannot create executables

and the config.log file says ld: library not found for -lopenblas.

• Also, I think pkgconf should be an order-only dependency for gsl:

diff --git a/build/pkgs/gsl/dependencies b/build/pkgs/gsl/dependencies
index 052eb4373d..576809127c 100644
--- a/build/pkgs/gsl/dependencies
+++ b/build/pkgs/gsl/dependencies
@@ -1,4 +1,4 @@
-$(BLAS)
+$(BLAS) | pkgconf
 
 ----------
 All lines of this file are ignored except the first.

since the package installation scripts use pkg-config.

[yyyyx4]

comment:11

Replying to @jhpalmieri:

From #31621: can we also make the following changes?

Feel free to modify this branch as you please. I don't think I'm familiar enough with Sage's build system to dive any deeper into this...

[dimpase]

comment:12

comment:10 actually gives you diffs you can apply (click on "Unified")

I am travelling and probably won't get around to do this before tomorrow

[sagetrac-git]

Changed commit from e4a133f to e7e2f3f

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

f6f3223	update GSL to 2.7
e7e2f3f	trac 32587: add pkgconf as order-only dependency for gsl,

[jhpalmieri]

comment:14

Here are my proposed changes. (Dima actually proposed the change to spkg-install.in, to give credit where it's due.)

[yyyyx4]

Changed author from Lorenz Panny to Lorenz Panny, John Palmieri

[slel]

Changed keywords from none to upgrade, gsl

[sagetrac-git]

Changed commit from e7e2f3f to 35c1b5f

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

35c1b5f

build/pkgs/gsl/spkg-install.in: Also pass CPPFLAGS, CFLAGS to configure

[mkoeppe]

comment:19

... as suggested in #31621 comment:58

[dimpase]

Reviewer: Dima Pasechnik

[dimpase]

comment:20

lgtm

[vbraun]

comment:21

Merge conflict

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

bb8b92d

Merge tag '9.5.beta5' into public/32587

[sagetrac-git]

Changed commit from 35c1b5f to bb8b92d

[yyyyx4]

Changed author from Lorenz Panny, John Palmieri to Lorenz Panny, John Palmieri, Matthias Koeppe

[yyyyx4]

comment:23

Trivial merge.

[vbraun]

Changed branch from public/32587 to bb8b92d