gnu: perl-pdl: Update to 2.100.

* gnu/packages/patches/pdl-2.100-reproducibility.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add reference to it.
* gnu/packages/perl-maths.scm (perl-pdl): New variable.

Change-Id: Ie2a025209cb2ae40a57341c6bf3bd693391ef9e4

3 files changed, 123 insertions, 0 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index e6ece8cc48..db011f4777 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1996,6 +1996,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/password-store-tree-compat.patch		\
   %D%/packages/patches/pciutils-hurd64.patch			\
   %D%/packages/patches/pdl-2.019-glut-bitmap-fonts.patch	\
+  %D%/packages/patches/pdl-2.100-reproducibility.patch	\
   %D%/packages/patches/petri-foo-0.1.87-fix-recent-file-not-exist.patch			\
   %D%/packages/patches/plasma-framework-fix-KF5PlasmaMacros.cmake.patch \
   %D%/packages/patches/plasp-fix-normalization.patch \
diff --git a/gnu/packages/patches/pdl-2.100-reproducibility.patch b/gnu/packages/patches/pdl-2.100-reproducibility.patch
new file mode 100644
index 0000000000..999f372479
--- /dev/null
+++ b/gnu/packages/patches/pdl-2.100-reproducibility.patch
@@ -0,0 +1,66 @@
+From efa96da9de3a7cdc104fab92b20e3bf07a9faf98 Mon Sep 17 00:00:00 2001
+From: Danny Milosavljevic <dannym@friendly-machines.com>
+Date: Mon, 5 May 2025 21:46:16 +0200
+Subject: [PATCH] Make doc generator reproducible.
+
+Fixes <https://github.com/PDLPorters/pdl/issues/541>.
+---
+ lib/PDL/Doc.pm | 18 ++++++++++++------
+ 1 file changed, 12 insertions(+), 6 deletions(-)
+
+diff --git a/lib/PDL/Doc.pm b/lib/PDL/Doc.pm
+index 106cd8704..50f132dad 100644
+--- a/lib/PDL/Doc.pm
++++ b/lib/PDL/Doc.pm
+@@ -495,15 +495,17 @@ sub savedb {
+   my $hash = $this->ensuredb;
+   open my $fh, '>', $this->{Outfile} or barf "can't write to symdb $this->{Outfile}: $!";
+   binmode $fh;
+-  while (my ($name,$mods_hash) = each %$hash) {
++  for my $name (sort keys %$hash) {
++    my $mods_hash = $hash->{$name};
+     next if 0 == scalar(%$mods_hash);
+-    while (my ($module,$val) = each %$mods_hash) {
++    for my $module (sort keys %$mods_hash) {
++      my $val = $mods_hash->{$module};
+       my $fi = $val->{File};
+       $val->{File} = abs2rel($fi, dirname($this->{Outfile}))
+         #store paths to *.pm files relative to pdldoc.db
+         if file_name_is_absolute($fi) && -f $fi;
+       delete $val->{Dbfile}; # no need to store Dbfile
+-      my $txt = join(chr(0),$name,$module,%$val);
++      my $txt = join(chr(0),$name,$module,map +($_=>$val->{$_}), sort keys %$val);
+       print $fh pack("S",length($txt)).$txt;
+     }
+   }
+@@ -679,7 +681,8 @@ sub scan {
+   my $hash = $this->{SYMS} ||= {};
+   my $n = 0;
+   $_->{File} = $file2, $n++ for values %{ $parser->{SYMHASH} };
+-  while (my ($key,$val) = each %{ $parser->{SYMHASH} }) {
++  for my $key (sort keys %{ $parser->{SYMHASH} }) {
++    my $val = $hash->{$key};
+     #set up the 3-layer hash/database structure: $hash->{funcname}->{PDL::SomeModule} = $val
+     if (defined($val->{Module})) {
+ 	$hash->{$key}{$val->{Module}} = $val;
+@@ -741,7 +744,10 @@ sub scantree {
+     $ntot += my $n = $this->scan($File::Find::name,$verbose);
+     print "\t$n functions\n";
+   };
+-  File::Find::find($sub,$dir);
++  File::Find::find({
++    wanted => $sub,
++    preprocess => sub { sort @_ }
++  }, $dir);
+   print "\nfound $ntot functions\n";
+   $ntot;
+ }
+@@ -881,7 +887,7 @@ own code.
+  print $pdldoc->gethash->{zeroes}->{PDL::Core}->{Ref};
+ 
+  # Get info for all the functions whose examples use zeroes
+- my @entries = $pdldoc->search('zeroes','Example',1);
++ my @entries = $pdldoc->search('zeroes','Example',1,1);
+ 
+  # All the functions that use zeroes in their example:
+  print "Functions that use 'zeroes' in their examples include:\n";
diff --git a/gnu/packages/perl-maths.scm b/gnu/packages/perl-maths.scm
index 2ea29a13a9..5a87bc70b8 100644
--- a/gnu/packages/perl-maths.scm
+++ b/gnu/packages/perl-maths.scm
@@ -20,7 +20,9 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix gexp)
+  #:use-module (guix utils)
   #:use-module (guix build-system perl)
   #:use-module (gnu packages)
   #:use-module (gnu packages gcc)
@@ -163,3 +165,57 @@ using a list of (X, Y) pairs.")
     (description "This package provides a library and simple REPL for the
 Perl Data Language.")
     (license license:perl-license)))
+
+;; The project has split out several packages.
+(define-public perl-pdl
+  (package
+    (inherit perl-pdl-2.019)
+    (version "2.100")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/PDLPorters/pdl.git")
+             (commit version)))
+       (sha256
+        (base32 "0nkvjb4l8r2l2piz0s9jifpm0kr6g7fy9krky130s82vq8bz19sc"))
+       (patches
+        (search-patches "pdl-2.100-reproducibility.patch"))))
+    (build-system perl-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+         (add-after 'unpack 'patch-includes
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "lib/PDL/Core/Dev.pm"
+              ;; This would cause an underflow (1 - 120 < 0)--so prevent it.
+              (("utime [$]mtime - 120, [$]mtime - 120, [$]pmfile; # so is out of date")
+               "utime $mtime - 1, $mtime - 1, $pmfile; # so is out of date")))))))
+    (inputs (list gd gsl mesa glu))
+    (native-inputs (list perl-capture-tiny ; for a test
+                         perl-devel-checklib
+                         perl-extutils-depends
+                         perl-extutils-f77
+                         gfortran
+                         perl-file-which
+                         perl-pod-parser
+                         perl-test-deep
+                         perl-test-exception
+                         perl-test-warn
+                         perl-text-balanced)) ; our perl is too old, so...
+    (propagated-inputs (list perl-file-map
+                             perl-file-which
+                             perl-inline
+                             perl-inline-c
+                             perl-list-moreutils
+                             perl-opengl
+                             perl-pgplot
+                             perl-pod-parser
+                             perl-sys-sigaction
+                             perl-termreadkey))
+    (home-page "https://metacpan.org/release/PDL")
+    (synopsis "Perl Data Language")
+    (description "This package provides a library and simple REPL for the
+Perl Data Language.")
+    (license license:perl-license)))