From 465c2a165939eff2c102db9e6ea35eea2666b9a9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Wed, 8 Mar 2023 19:20:01 -0300
Subject: [PATCH] nauty: update to 2.8.6.

---
 .../nauty/patches/cross-disable-popcnt.patch  |  20 ---
 .../dont-test-popcnt-if-disabled.patch        |  16 ++
 .../nauty-2.8.6-gentreeg-gentourng.patch      | 144 ++++++++++++++++++
 srcpkgs/nauty/template                        |  13 +-
 srcpkgs/nauty/update                          |   3 +-
 5 files changed, 170 insertions(+), 26 deletions(-)
 delete mode 100644 srcpkgs/nauty/patches/cross-disable-popcnt.patch
 create mode 100644 srcpkgs/nauty/patches/dont-test-popcnt-if-disabled.patch
 create mode 100644 srcpkgs/nauty/patches/nauty-2.8.6-gentreeg-gentourng.patch

diff --git a/srcpkgs/nauty/patches/cross-disable-popcnt.patch b/srcpkgs/nauty/patches/cross-disable-popcnt.patch
deleted file mode 100644
index a5b7d59ff4e7..000000000000
--- a/srcpkgs/nauty/patches/cross-disable-popcnt.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Disable popcnt in cross-builds, as we can't run programs to check.
-Note that using `configure --disable-popcnt` is broken.
-
---- a/configure	2021-11-21 20:00:41.599629153 -0300
-+++ b/configure	2021-11-21 20:00:45.891579837 -0300
-@@ -5766,10 +5766,10 @@
- printf %s "checking if popcnt instruction is available and requested... " >&6; }
- if test "$cross_compiling" = yes
- then :
--  { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
--printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;}
--as_fn_error $? "cannot run test program while cross compiling
--See \`config.log' for more details" "$LINENO" 5; }
-+allow_popcnt=0  # { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-+# printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;}
-+# as_fn_error $? "cannot run test program while cross compiling
-+# See \`config.log' for more details" "$LINENO" 5; }
- else $as_nop
-   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
- /* end confdefs.h.  */
diff --git a/srcpkgs/nauty/patches/dont-test-popcnt-if-disabled.patch b/srcpkgs/nauty/patches/dont-test-popcnt-if-disabled.patch
new file mode 100644
index 000000000000..054c1920878e
--- /dev/null
+++ b/srcpkgs/nauty/patches/dont-test-popcnt-if-disabled.patch
@@ -0,0 +1,16 @@
+--- a/configure.ac	2022-11-17 08:33:40.000000000 -0300
++++ b/configure.ac	2023-03-08 19:36:38.120873732 -0300
+@@ -279,12 +279,12 @@
+ AC_CHECK_FUNC(sigprocmask,have_sigprocmask=1,have_sigprocmask=0)
+ AC_SUBST(have_sigprocmask)
+ 
++AS_IF([test "$allow_popcnt" -eq 1],
+ dnl --check if popcnt instruction is available and desired
+ AC_MSG_CHECKING(if popcnt instruction is available and requested)
+ AC_RUN_IFELSE([AC_LANG_PROGRAM([],[[if (__builtin_cpu_supports("popcnt")) return 0; else return 1;]])],
+   popsup=1,popsup=0)
+ 
+-AS_IF([test "$allow_popcnt" -eq 1],
+       [have_hwpopcnt=$popsup
+ test -f /proc/cpuinfo && grep -i popcnt /proc/cpuinfo >/dev/null && have_hwpopcnt=1 
+ test $have_hwpopcnt -eq 0 && sysctl machdep.cpu.features 2>/dev/null | grep -i popcnt >/dev/null && have_hwpopcnt=1
diff --git a/srcpkgs/nauty/patches/nauty-2.8.6-gentreeg-gentourng.patch b/srcpkgs/nauty/patches/nauty-2.8.6-gentreeg-gentourng.patch
new file mode 100644
index 000000000000..322b25326ee0
--- /dev/null
+++ b/srcpkgs/nauty/patches/nauty-2.8.6-gentreeg-gentourng.patch
@@ -0,0 +1,144 @@
+From edb0474a4db8e69f971e4eebe18716309f5a7bb3 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Tue, 17 Jan 2023 19:44:49 -0500
+Subject: [PATCH 1/1] Upstream fixes for gentreeg and gentourng.
+
+https://mailman.anu.edu.au/pipermail/nauty/2023-January/000903.html
+---
+ gentourng.c |  2 +-
+ gentreeg.c  | 95 ++++++++++++++++++++++++++++-------------------------
+ 2 files changed, 51 insertions(+), 46 deletions(-)
+
+diff --git a/gentourng.c b/gentourng.c
+index 634e5e8..5c7ffff 100644
+--- a/gentourng.c
++++ b/gentourng.c
+@@ -1408,7 +1408,7 @@ PLUGIN_INIT
+                 (*outproc)(outfile,g,1);
+             }
+         }
+-        else
++        else if (!connec || maxn != 2)
+         {
+             makeleveldata();
+ 
+diff --git a/gentreeg.c b/gentreeg.c
+index 946d5f8..15bf87b 100644
+--- a/gentreeg.c
++++ b/gentreeg.c
+@@ -1,4 +1,4 @@
+-/* gentree version 1.3; Brendan McKay Oct 2022 */
++/* gentree version 1.4; Brendan McKay Dec 2022 */
+ /* This program is a wrapper for the program FreeTrees.c written
+  * by Gang Li & Frank Ruskey.  See below for their original
+  * comments. */
+@@ -32,49 +32,54 @@ Counts for n=1..45:
+  1: 1
+  2: 1
+  3: 1
+- 4: 1
+- 5: 2
+- 6: 3
+- 7: 6
+- 8: 11
+- 9: 23
+-10: 47
+-11: 106
+-12: 235
+-13: 551
+-14: 1301
+-15: 3159
+-16: 7741
+-17: 19320
+-18: 48629
+-19: 123867
+-20: 317955
+-21: 823065
+-22: 2144505
+-23: 5623756
+-24: 14828074
+-25: 39299897
+-26: 104636890
+-27: 279793450
+-28: 751065460
+-29: 2023443032
+-30: 5469566585
+-31: 14830871802
+-32: 40330829030
+-33: 109972410221
+-34: 300628862480
+-35: 823779631721
+-36: 2262366343746
+-37: 6226306037178
+-38: 17169677490714
+-39: 47436313524262
+-40: 131290543779126
+-41: 363990257783343
+-42: 1010748076717151
+-43: 2810986483493475
+-44: 7828986221515605
+-45: 21835027912963086
+-********************************/
++ 4: 2
++ 5: 3
++ 6: 6
++ 7: 11
++ 8: 23
++ 9: 47
++10: 106
++11: 235
++12: 551
++13: 1301
++14: 3159
++15: 7741
++16: 19320
++17: 48629
++18: 123867
++19: 317955
++20: 823065
++21: 2144505
++22: 5623756
++23: 14828074
++24: 39299897
++25: 104636890
++26: 279793450
++27: 751065460
++28: 2023443032
++29: 5469566585
++30: 14830871802
++31: 40330829030
++32: 109972410221
++33: 300628862480
++34: 823779631721
++35: 2262366343746
++36: 6226306037178
++37: 17169677490714
++38: 47436313524262
++39: 131290543779126
++40: 363990257783343
++41: 1010748076717151
++42: 2810986483493475
++43: 7828986221515605
++44: 21835027912963086
++45: 60978390985918906
++46: 170508699155987862
++47: 477355090753926460
++48: 1337946100045842285
++49: 3754194185716399992
++50: 10545233702911509534
++*******************************/
+ 
+ /* Comments on original program by original authors */
+ /*==============================================================*/
+@@ -676,7 +681,7 @@ PLUGIN_INIT
+         }
+         else if (nv == 2)
+         {
+-            if (res == 0 && maxdeg >= 1 && mindiam <= 1 && maxdiam >= 2)
++            if (res == 0 && maxdeg >= 1 && mindiam <= 1 && maxdiam >= 1)
+             {
+                 par[1] = 0;
+                 par[2] = 1;
+-- 
+2.38.2
+
diff --git a/srcpkgs/nauty/template b/srcpkgs/nauty/template
index 02945690a861..8be5d050920b 100644
--- a/srcpkgs/nauty/template
+++ b/srcpkgs/nauty/template
@@ -1,17 +1,18 @@
 # Template file for 'nauty'
 pkgname=nauty
-version=2.7r4
+version=2.8.6
 revision=1
 build_style=gnu-configure
 make_install_args="includedir=/usr/include/nauty
  pkgconfigexecdir=/usr/lib/pkgconfig"
+hostmakedepends="automake"
 short_desc="Compute the automorphism groups of graphs and digraphs"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="Apache-2.0"
 homepage="https://pallini.di.uniroma1.it/"
-changelog="https://pallini.di.uniroma1.it/changes24-27.txt"
-distfiles="https://pallini.di.uniroma1.it/nauty${version/./}.tar.gz"
-checksum=b810c85a6fe299f3b4c9f24aaf929cac7f9546c2f35c20e1dd0adbc7408848a6
+changelog="https://pallini.di.uniroma1.it/changes24-28.txt"
+distfiles="https://pallini.di.uniroma1.it/nauty${version//./_}.tar.gz"
+checksum=f2ce98225ca8330f5bce35f7d707b629247e09dda15fc479dc00e726fee5e6fa
 
 build_options="native_build"
 
@@ -19,6 +20,10 @@ if [ -z "$build_option_native_build" ]; then
 	configure_args="--enable-generic --disable-popcnt"
 fi
 
+pre_configure() {
+	autoreconf -fi
+}
+
 nauty-devel_package() {
 	depends="${sourcepkg}>=${version}_${revision} ${makedepends}"
 	short_desc+=" - development files"
diff --git a/srcpkgs/nauty/update b/srcpkgs/nauty/update
index e18d2ec9c984..8c136a991451 100644
--- a/srcpkgs/nauty/update
+++ b/srcpkgs/nauty/update
@@ -1,2 +1 @@
-version=${version/./}
-ignore="*b?"
+pattern='\b\Qnauty\E-?\K[\d._]+(?=\.tar)\b'