CVS commit: pkgsrc/biology/openbabel

Module Name:	pkgsrc
Committed By:	pin
Date:		Wed Aug  5 09:20:44 UTC 2026

Modified Files:
	pkgsrc/biology/openbabel: Makefile PLIST distinfo

Log Message:
biology/openbabel: update to 3.2.1

This release reflects the latest stable version, including many bug fixes, including some potentially security related.

As noted with our 3.2.0 release, we anticipate further bug-fix releases over the course of 2026 and appreciate the many contributions and reports from everyone.
🪲 Bug Fixes

    Fix tetrazole protonation handling in the pH model by @Jnelen in #2975
    ChemDraw CDX: handle additional aromatic/fractional bond-order codes by @jlkjr in #2979

🔒 Security and Hardening

    Fix CVE-2026-54751: MMD parser uninitialized value use can expose prior atom data by Carmelo Lin @Carmel0
    Update SECURITY.md with GitHub Security Advisory links by @ghutchis in #2968
    Fix several formats with sscanf validation by @ghutchis in #2973
    Fix more fuzz bugs by @ghutchis in #2977
    Fix stack overflow in gaussformat and cube by @ghutchis in #2985
    Fix additional crashes from fuzz testing by @ghutchis in #2986
    Fix more reported crashes by @ghutchis in #2988
    Fix integer overflow issues by @ghutchis in #2989
    Fix more bug / crash reports by @ghutchis in #2990
    Fix more crash / fuzz reports by @ghutchis in #2991

🛠️ Build Changes

    For now, modify build wheels to take an explicit version number by @ghutchis in #2963
    CMake: Don't look for wxWidgets unless the GUI is requested by @berquist in #2964
    refactor: remove MIN and MAX macros by @e-kwsm in #2970
    fix bindings_php build issues by @e-kwsm in #2971
    build(python): write _openbabel.so under build directory instead of source directory by @e-kwsm in #2974
    Fix headers with system InChi by @PPN-SD in #2969
    build(plugin_descriptors): properly set the include directory of InChI by @e-kwsm in #2982
    chore: update downloads badge, from SF to GH [skip ci] by @e-kwsm in #2966
    docs: fix PAPER_TYPE and configure PROJECT_NUMBER by @e-kwsm in #2981
    Parse openbabel-x-y-z tags for version numbers by @ghutchis in #2967


To generate a diff of this commit:
cvs rdiff -u -r1.88 -r1.89 pkgsrc/biology/openbabel/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/openbabel/PLIST
cvs rdiff -u -r1.17 -r1.18 pkgsrc/biology/openbabel/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/openbabel/Makefile
diff -u pkgsrc/biology/openbabel/Makefile:1.88 pkgsrc/biology/openbabel/Makefile:1.89
--- pkgsrc/biology/openbabel/Makefile:1.88	Mon Jun 22 13:20:21 2026
+++ pkgsrc/biology/openbabel/Makefile	Wed Aug  5 09:20:44 2026
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.88 2026/06/22 13:20:21 pin Exp $
+# $NetBSD: Makefile,v 1.89 2026/08/05 09:20:44 pin Exp $
 
-DISTNAME=	openbabel-3.2.0
+DISTNAME=	openbabel-3.2.1
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=openbabel/}
 GITHUB_TAG=	openbabel-${PKGVERSION_NOREV:S/./-/g}

Index: pkgsrc/biology/openbabel/PLIST
diff -u pkgsrc/biology/openbabel/PLIST:1.11 pkgsrc/biology/openbabel/PLIST:1.12
--- pkgsrc/biology/openbabel/PLIST:1.11	Mon Jun 22 13:35:42 2026
+++ pkgsrc/biology/openbabel/PLIST	Wed Aug  5 09:20:44 2026
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.11 2026/06/22 13:35:42 pin Exp $
+@comment $NetBSD: PLIST,v 1.12 2026/08/05 09:20:44 pin Exp $
 bin/obabel
 bin/obconformer
 bin/obdistgen
@@ -117,7 +117,7 @@ lib/cmake/openbabel3/OpenBabel3_EXPORTS-
 lib/cmake/openbabel3/OpenBabel3_EXPORTS.cmake
 lib/libinchi.so
 lib/libinchi.so.1
-lib/libinchi.so.1.07.4
+lib/libinchi.so.1.07.5
 lib/libopenbabel.so
 lib/libopenbabel.so.8
 lib/libopenbabel.so.8.0.0

Index: pkgsrc/biology/openbabel/distinfo
diff -u pkgsrc/biology/openbabel/distinfo:1.17 pkgsrc/biology/openbabel/distinfo:1.18
--- pkgsrc/biology/openbabel/distinfo:1.17	Mon Jun 22 13:20:21 2026
+++ pkgsrc/biology/openbabel/distinfo	Wed Aug  5 09:20:44 2026
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.17 2026/06/22 13:20:21 pin Exp $
+$NetBSD: distinfo,v 1.18 2026/08/05 09:20:44 pin Exp $
 
-BLAKE2s (openbabel-3.2.0.tar.gz) = 5e6cb4f6678823547d520163da22c6afdf32bce4c8555562a332026b0ef705b5
-SHA512 (openbabel-3.2.0.tar.gz) = 0def0b8c6185ec648c41b32c9c2963329f764b57105efe895fa435fd2ee4878b70141b0ac9e80dddbc82e2ca95281955f612a21ba0dd5c0e7ef715061acf8234
-Size (openbabel-3.2.0.tar.gz) = 37815471 bytes
+BLAKE2s (openbabel-3.2.1.tar.gz) = 10eb5f20beaeb7cc2180aa6b05945ba277f7f1f4f3aa05f02dc07bb58a86fb56
+SHA512 (openbabel-3.2.1.tar.gz) = fb4faf636a3d46fa88c57582a4a3ffe188feb2b21bdc6c43a5de5757617caa051709fbac38f15acdb51328055722a9a37f5410551bc75e1a825593fc80a2f83a
+Size (openbabel-3.2.1.tar.gz) = 37835590 bytes
 SHA1 (patch-CMakeLists.txt) = 8344c3e5cf318fb0f117f499837ebcf86370fb9f
 SHA1 (patch-tools_CMakeLists.txt) = e938dc4459e991e8654b69e10207ca925ab1827d