git: 93d9572c0a46 - main - science/rdkit: update 2025_09_1 → 2025.09.2

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Mon, 10 Nov 2025 22:56:25 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=93d9572c0a46969bc755a7658217928b5d0ac800

commit 93d9572c0a46969bc755a7658217928b5d0ac800
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-11-10 22:56:12 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-11-10 22:56:21 +0000

    science/rdkit: update 2025_09_1 → 2025.09.2
---
 science/rdkit/Makefile  |  8 ++++++--
 science/rdkit/distinfo  | 38 +++++++++++++++++++-------------------
 science/rdkit/pkg-plist |  1 +
 3 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile
index 9b740c002de8..f02115771af1 100644
--- a/science/rdkit/Makefile
+++ b/science/rdkit/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	rdkit
 DISTVERSIONPREFIX=	Release_
-DISTVERSION=	2025_09_1
+DISTVERSION=	2025_09_2
 CATEGORIES=	science
 MASTER_SITES=	https://github.com/schrodinger/maeparser/archive/:maeparser \
 		https://github.com/schrodinger/coordgenlibs/archive/:coordgen \
@@ -41,7 +41,7 @@ GH_TUPLE+=	ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-a
 
 MAEPARSER_VERSION=	1.3.3
 COORDGEN_VERSION=	3.0.2
-CHEMDRAW_VERSION=	1.0.10
+CHEMDRAW_VERSION=	1.0.11
 RAPIDJSON_VERSION=	1.1.0
 
 CMAKE_ON=	RDK_BUILD_CAIRO_SUPPORT
@@ -121,10 +121,14 @@ pre-build:
 		-e 's|const SizeType length;|SizeType length;|g' \
 		${WRKSRC}/External/rapidjson/rapidjson-1.1.0/include/rapidjson/document.h
 
+post-install:
+	@${RM} -f ${STAGEDIR}${PREFIX}/lib/libexpat.a
+
 post-install-PGSQL-on:
 	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/postgresql/rdkit.so
 
 # many tests fail, see https://github.com/rdkit/rdkit/issues/7779
 # tests as of 2025_09_1: 65% tests passed, 24 tests failed out of 68
+# tests as of 2025_09_2: 63% tests passed, 26 tests failed out of 70
 
 .include <bsd.port.mk>
diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo
index e84d47fcbb7e..2dd40d607202 100644
--- a/science/rdkit/distinfo
+++ b/science/rdkit/distinfo
@@ -1,19 +1,19 @@
-TIMESTAMP = 1761887207
-SHA256 (rdkit-2025.09.1/v1.3.3.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07
-SIZE (rdkit-2025.09.1/v1.3.3.tar.gz) = 39896
-SHA256 (rdkit-2025.09.1/v3.0.2.tar.gz) = f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3
-SIZE (rdkit-2025.09.1/v3.0.2.tar.gz) = 166817
-SHA256 (rdkit-2025.09.1/v1.0.10) = 300680457c92a61ba49b678405906054ab64d3635c49309e37ea2a96c513fa8d
-SIZE (rdkit-2025.09.1/v1.0.10) = 1043718
-SHA256 (rdkit-2025.09.1/v1.1.0.tar.gz) = bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e
-SIZE (rdkit-2025.09.1/v1.1.0.tar.gz) = 1019402
-SHA256 (rdkit-2025.09.1/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6
-SIZE (rdkit-2025.09.1/ComicNeue-Regular.ttf) = 21915
-SHA256 (rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz) = 7fb3510b69af358009e2d0763c1d9665ac34f4c2cd3314cf5210ee3d5a33d501
-SIZE (rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz) = 82885226
-SHA256 (rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
-SIZE (rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
-SHA256 (rdkit-2025.09.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0
-SIZE (rdkit-2025.09.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376
-SHA256 (rdkit-2025.09.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5
-SIZE (rdkit-2025.09.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592
+TIMESTAMP = 1762809861
+SHA256 (rdkit-2025.09.2/v1.3.3.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07
+SIZE (rdkit-2025.09.2/v1.3.3.tar.gz) = 39896
+SHA256 (rdkit-2025.09.2/v3.0.2.tar.gz) = f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3
+SIZE (rdkit-2025.09.2/v3.0.2.tar.gz) = 166817
+SHA256 (rdkit-2025.09.2/v1.0.11) = 405869fc8b3f73395047bc7c54e1da62ef66c08d48bd71af66e47ec9cbe86814
+SIZE (rdkit-2025.09.2/v1.0.11) = 1043261
+SHA256 (rdkit-2025.09.2/v1.1.0.tar.gz) = bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e
+SIZE (rdkit-2025.09.2/v1.1.0.tar.gz) = 1019402
+SHA256 (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6
+SIZE (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 21915
+SHA256 (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = db3254e88ef17cac7bb8480e6da9d1e69dfe180c21774b11637d8a17b5a98fb9
+SIZE (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = 82911180
+SHA256 (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
+SIZE (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
+SHA256 (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0
+SIZE (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376
+SHA256 (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5
+SIZE (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592
diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist
index c4c3acd8b3c9..3cd23f7e900b 100644
--- a/science/rdkit/pkg-plist
+++ b/science/rdkit/pkg-plist
@@ -1200,6 +1200,7 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%%
 %%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/patch/rdkit/Chem/inchi.pyi.diff
 %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/worker.py
 %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__init__.py
 %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__main__.py