git: 24b277649925 - main - science/gemmi: add patch to fix the testcase in science/py-gemmi

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=24b2776499252f342001b8f6cb75919d02a65a4a

commit 24b2776499252f342001b8f6cb75919d02a65a4a
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-09-23 06:00:21 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-09-23 07:25:54 +0000

    science/gemmi: add patch to fix the testcase in science/py-gemmi
---
 science/gemmi/Makefile                                     |  1 +
 ...h-include_gemmi_third__party_tao_pegtl_parse__error.hpp | 14 ++++++++++++++
 2 files changed, 15 insertions(+)

diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile
index ffbf674a0ed3..7d34b5902244 100644
--- a/science/gemmi/Makefile
+++ b/science/gemmi/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	gemmi
 DISTVERSIONPREFIX=	v
 DISTVERSION=	0.7.5
+PORTREVISION=	1
 CATEGORIES=	science # chemistry
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/gemmi/files/patch-include_gemmi_third__party_tao_pegtl_parse__error.hpp b/science/gemmi/files/patch-include_gemmi_third__party_tao_pegtl_parse__error.hpp
new file mode 100644
index 000000000000..e405380a2513
--- /dev/null
+++ b/science/gemmi/files/patch-include_gemmi_third__party_tao_pegtl_parse__error.hpp
@@ -0,0 +1,14 @@
+-- fix for the bug in the Gemmi project: https://github.com/project-gemmi/gemmi/issues/384#issuecomment-5789847575
+-- this bug causes one testcase to fail due to duplicate C++ typeinfo objects
+
+--- include/gemmi/third_party/tao/pegtl/parse_error.hpp.orig	2026-03-02 03:06:09 UTC
++++ include/gemmi/third_party/tao/pegtl/parse_error.hpp
+@@ -14,7 +14,7 @@ namespace tao
+ {
+    namespace TAO_PEGTL_NAMESPACE
+    {
+-      struct parse_error
++      struct __attribute__((visibility("default"))) parse_error
+          : public std::runtime_error
+       {
+          parse_error( const std::string& msg, std::vector< position >&& in_positions )