git: b0f5256f17a1 - main - science/rdkit: update 2023_09_3 → 2023_09_5

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Tue, 13 Feb 2024 16:44:23 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=b0f5256f17a15e6b91d7cec952e80b4d567fc5d3

commit b0f5256f17a15e6b91d7cec952e80b4d567fc5d3
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-02-13 16:42:03 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-02-13 16:44:08 +0000

    science/rdkit: update 2023_09_3 → 2023_09_5
    
    Reported by:    portscout
---
 science/rdkit/Makefile  |  8 ++++----
 science/rdkit/distinfo  | 14 +++++++-------
 science/rdkit/pkg-plist |  6 ++++++
 3 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile
index ffa181a74888..f64903afc7b5 100644
--- a/science/rdkit/Makefile
+++ b/science/rdkit/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	rdkit
 DISTVERSIONPREFIX=	Release_
-DISTVERSION=	2023_09_3
-PORTREVISION=	1
+DISTVERSION=	2023_09_5
 CATEGORIES=	science
 MASTER_SITES=	https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font
 DISTFILES=	Comic_Neue.zip:font
@@ -15,8 +14,6 @@ LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
 BROKEN_i386=	non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp', see https://github.com/rdkit/rdkit/issues/4934
-BROKEN_FreeBSD_14=	fails to compile as clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652
-BROKEN_FreeBSD_15=	fails to compile as clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=272652
 
 BUILD_DEPENDS=	catch>0:devel/catch \
 		flex:textproc/flex \
@@ -37,6 +34,9 @@ CMAKE_OFF=	RDK_INSTALL_INTREE RDK_USE_FLEXBISON \
 		RDK_BUILD_CPP_TESTS
 CMAKE_ARGS=	-DCATCH_DIR=${LOCALBASE}/include/catch2
 
+CFLAGS+=	-D_GNU_SOURCE
+CXXFLAGS+=	-D_GNU_SOURCE
+
 DATADIR=	${PREFIX}/share/RDKit
 DOCSDIR=	${PREFIX}/share/doc/RDKit
 
diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo
index ea87061de483..64fcb3758191 100644
--- a/science/rdkit/distinfo
+++ b/science/rdkit/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1701933126
-SHA256 (rdkit-2023.09.3/Comic_Neue.zip) = b90d32da89882e5eea971682a83efa0feac9e5d9db1e43070c9eea7a87f96ff5
-SIZE (rdkit-2023.09.3/Comic_Neue.zip) = 180686
-SHA256 (rdkit-2023.09.3/rdkit-rdkit-Release_2023_09_3_GH0.tar.gz) = 8e8bb732ca2dc9481940bbf5dfa1127f0f014f80b73a1faa3c56761acb899748
-SIZE (rdkit-2023.09.3/rdkit-rdkit-Release_2023_09_3_GH0.tar.gz) = 80177185
-SHA256 (rdkit-2023.09.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
-SIZE (rdkit-2023.09.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
+TIMESTAMP = 1707816112
+SHA256 (rdkit-2023.09.5/Comic_Neue.zip) = ee69c0c8f7ae7777cea33d9df1437815b0c79b12bd5d9ec7ca2877983bb6b980
+SIZE (rdkit-2023.09.5/Comic_Neue.zip) = 180682
+SHA256 (rdkit-2023.09.5/rdkit-rdkit-Release_2023_09_5_GH0.tar.gz) = 0b1ddf2bf822879e0863caf8efb794154e0a424108f2c1333ac94381c01fd688
+SIZE (rdkit-2023.09.5/rdkit-rdkit-Release_2023_09_5_GH0.tar.gz) = 80229877
+SHA256 (rdkit-2023.09.5/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
+SIZE (rdkit-2023.09.5/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist
index 296cc3c4db44..d0d492982c90 100644
--- a/science/rdkit/pkg-plist
+++ b/science/rdkit/pkg-plist
@@ -1181,6 +1181,12 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%DATADIR%%/Scripts/PythonFormat.py
 %%PYTHON%%%%DATADIR%%/Scripts/README.md
 %%PYTHON%%%%DATADIR%%/Scripts/create_deb_packages.sh
+%%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__init__.py
+%%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__main__.py
+%%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/worker.py
+%%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__init__.py
+%%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__main__.py
+%%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/clang_worker.py
 %%PYTHON%%%%DATADIR%%/Scripts/test.sh
 %%DATADIR%%/license.txt
 %%PGSQL%%share/postgresql/extension/rdkit--3.8--4.0.sql