head	1.2;
access;
symbols
	pkgsrc-2026Q2:1.1.0.12
	pkgsrc-2026Q2-base:1.1
	pkgsrc-2026Q1:1.1.0.10
	pkgsrc-2026Q1-base:1.1
	pkgsrc-2025Q4:1.1.0.8
	pkgsrc-2025Q4-base:1.1
	pkgsrc-2025Q3:1.1.0.6
	pkgsrc-2025Q3-base:1.1
	pkgsrc-2025Q2:1.1.0.4
	pkgsrc-2025Q2-base:1.1
	pkgsrc-2025Q1:1.1.0.2
	pkgsrc-2025Q1-base:1.1;
locks; strict;
comment	@# @;


1.2
date	2026.06.22.13.20.21;	author pin;	state Exp;
branches;
next	1.1;
commitid	azrVcawRuwbZqNKG;

1.1
date	2025.01.31.15.49.47;	author wiz;	state Exp;
branches;
next	;
commitid	EuSLylPkbaPCyEHF;


desc
@@


1.2
log
@biology/openbabel: update to 3.2.0

This release reflects the latest stable version, including multiple feature enhancements and many, many bug fixes. It is backwards compatible with 3.0 and 3.1.

We anticipate more bug-fix releases over the course of 2026 and appreciate the many contributions and reports from everyone.
Major Features and Fixes

    Many memory and crash bugs fixed, thanks to OSS-Fuzz (Google) for infrastructure, including Cisco TALOS, Trail of Bits, ADA Logics, and Claude Mythos for bug reports. At the moment, all reported bugs are fixed.
    L-BFGS optimizer added to OBForceField (internal LBFGS.h); gen3d and conformer search now use L-BFGS by default (with CG fallback when Eigen is unavailable). @@ghutchis (#2933)
    New macrocycle ring builder with Dale codes for cycloalkanes with n > 24, plus a post-pass crown builder for unmatched rings up to n ≤ 24. Substantially improves initial 3D geometry for macrocycles. @@ghutchis (#2923)
    Distance-geometry improvements: faster, vectorized implementation ensuring stereochemistry is preserved @@ghutchis (#2896, #2897)
    KET format (Ketcher JSON) read/write, including aromatic-bond preservation and alias expansion for clean round-trip. @@romanbsd (#2909)
    ChemicalJSON (.cjson) format support — Avogadro's native format — with rich metadata: total charge & spin multiplicity, NMR and electronic spectra, conformer energies, unit-cell vectors, and space-group info. @@ghutchis (#2486, #2491, #2516, #2640, #2654)
    InChI bumped to 1.07.5; library version now reported in the format description. @@e-kwsm @@ghutchis (#2857, #2947)
    Python 2 dropped; Python 3.13 supported (distutils removed). @@e-kwsm @@chrisjonesBSU (#2924, #2809) Integrated PyPI binary wheels @@njzjz #2925
    CMake 4 compatibility, FindPython refactor, Eigen 2 dropped, Eigen3::Eigen imported target adopted. @@PPN-SD @@e-kwsm (#2784, #2753, #2858)
    OBRandomMT: new std::mt19937_64-based PRNG wrapper (opt-in via USE_RANDOMMT, default on); OB_RANDOM_SEED environment variable documented for reproducibility. @@e-kwsm (#2241)

New Features and Improvements

    WLN (Wiswesser Line Notation) reader additions. @@baoilleach @@michaelblakey (#2510)
    PDBQT: Meeko-compatible VDW radii @@bmp192529 (#2798); data-block output @@dkoes (#2796); implicit H assignment on read @@fredrikw (#2553); partial-charge column alignment fix @@flatstik (#2601).
    PDB: segment-name parsing/retention @@dkoes (#2637); more robust reading @@dkoes (#2395).
    Tinker: custom atom-class read @@mquevill (#2355); multi-word titles and optional comment line @@mquevill (#2354).
    ORCA: retain all conformers on read @@ghutchis (#2922); ORCA 5 vibration header handled @@ghutchis (#2521).
    xtb: handle "Gaussian"-style vibration output (Raman = 0.0). @@ghutchis (#2653)
    Turbomole: write $lattice block when a unit cell is present. @@e-kwsm (#2823)
    CIF: atomic coordinates are no longer wrapped into the unit cell by default. @@ghutchis (#2629)
    COF: new version-numbering scheme (old files still readable). @@pbecherer (#2840)
    CML/CMLR: support conversion to CMLR @@romanbsd (#2694); dangling-reference fix in the reaction writer @@romanbsd (#2926).
    STL: bond visualization, improved color export, -s scale option, modernized source. @@TheRealSami (#2814)
    FASTA: actually connect atoms on conversion @@fredrikw (#2371); retain chains/residues @@ghutchis (#2734).
    Ruby SWIG wrapper: reactions @@romanbsd (#2748) and tautomers @@romanbsd (#2943) now supported.
    obrms: parameter docs added to help text and man page; length-of-RMSDs sanity check @@e-kwsm (#2942); improvements @@dkoes (#2608).
    obabel: --separate no longer breaks on EOL when reading from stdin. @@matterhorn103 (#2721)
    CorrectForPH now respects perceived chains. @@fredrikw (#2648)
    C++ syntax: OBAtom::GetNbrs() and range-based for loops @@timvdm (#2635); override annotations @@e-kwsm (#2175); noexcept for deprecated throw() @@e-kwsm (#2859); OB_DEPRECATED macros @@e-kwsm (#2002).

Bug Fixes

    Stereo leak in SMILES parser @@ghutchis (#2908); tautomer assertion / code bugs.
    Canonical-label generation now has a 5-second timeout to avoid hangs on pathological inputs. @@ghutchis (#2921)
    CDXML: clear ImplicitHydrogens between fragments (fixes segfault, #2696) @@fredrikw (#2697); implicit-H handling generally improved (#2416) @@StashOfCode (#2400).
    CDJSON: implicit-valence handling on read; "l" field deserialization; "h" field respected. @@gregmagdits (#2769)
    libxml2 ≥ 2.12.7 compatibility. @@merkys (#2702)
    InChI: memory leaks @@romanbsd (#2706, #2772) and crashes @@romanbsd (#2717, #2747) fixed; crash converting some bad CML → InChI fixed.
    CML parsing crash on specific inputs. @@romanbsd (#2705)
    AOFORCE parser memory issues. @@tyler92 (#2749)
    SSSR/RingSearch: ring-pruning bug @@fredrikw (#2684); ring iteration with no rings @@dkoes (#2295).
    pybel: missing atom properties @@dkoes (#2293); pybel.draw file-write check; removed _png2 requirement for coordinate generation.
    SMILES: H-suppression bug when specifying output atom order. @@baoilleach (#2287)
    SMILES crashes from malformed input. @@tyler92 (#2746)
    obthermo crash from pointgroup code. @@dspoel (#2285)
    GRO format: first residue index 0 no longer crashes. @@DStarEpoch (#2598)
    VASP and Turbomole format fixes. @@e-kwsm (#2563)
    obminimize help text and docs. (#2519)
    CopySubstructure segfault with option 2. @@baoilleach (#2449)
    Bond perception of ring nitrogens @@dkoes (Nbondfix branch); azete bond order @@dkoes (#2379); ammonium XYZ parsing @@dkoes (#2380).
    MDL v3000 coordinate rounding (%.4f 2D, %.6f 3D). @@ghutchis (#2929)
    Uninitialized arrays / infinite-loop fixes. @@Crivella (#2850, #2851)
    Big-endian / s390x portability fixes. @@pranavkaruvally (#2816)
    PQR debug output cleanup. @@crabby-rathbun (#2854)
    Examples build fix for GCC / libstdc++ 8.3. @@jcbollinger (#2235)
    Misc undefined-behavior and memory leak fixes. @@jcbollinger (#2224, #2227, #2228), @@afonari (#2220, #2225, #2226, #2232, #2233)
    Initialize allocated memory to zero. @@afonari (#2248)
    OBMol::NumHvyAtoms() const + OBResidue::GetNumHvyAtoms(). (#2300, #2299)

Security and Fuzz Hardening

    CVE-2022 (Cisco TALOS): 14 CVEs across MOL2 (CVE-2022-43607), CSR, GRO, PQS, MSI, ORCA, Gaussian, and MOPAC formats — including 5 translationVectors[] OOB writes. @@ghutchis (#2883, #2884, #2885, #2886, #2887)
    CVE-2026 batch: CIF transform3d::DescribeAsString OOB read, MOL2 SetFormalCharge NULL deref, CDXML NULL deref. @@VedantMadane (#2862)
    CVE-2025: GAMESS use-after-free (CVE-2025-10994), zipstream overlapping memcpy (CVE-2025-10995), SMILES heap-buffer-overflow (CVE-2025-10996), ChemKin (CVE-2025-10997/10998), CACAO (CVE-2025-10999), PQS (CVE-2025-11000). @@ghutchis (#2913)
    OSS-Fuzz / Trail of Bits / ADA Logics / Claude Mythos / TALOS: dozens of fixes across MCDL, ChemDraw CDX, Chemkin, abinit, cacao, Gaussian (incl. z-matrix and cube), Molpro, POV-Ray, Tinker, SMARTS, MDL V3000, SDF, CIF, and the SMILES canonicalizer (OOM on hypervalent / high-permutation molecules). @@ghutchis (#2891, #2910, #2916–#2918, #2921, #2928, #2937, #2938, #2939, #2944, #2948, #2949, #2950, #2954)
    Hardening: stack-smashing recursion in FindRings converted to an iterative loop; bond-loop and atom-count bounds checks; charge bounds (±999); rejection of recursive SMARTS (( depth > 1000; bound on heavy atoms (MCDL > 200); guards on tokenize/vs access; rejection of elements > 118; std::unique_ptr adoption to fix leaks/use-after-free.
    MCDL hardening (Arthur Chan / ADA Logics report). @@ghutchis (#2883)
    SECURITY policy and fuzz regression tests added. @@ghutchis (#2882)
    New fuzz harnesses: three new harnesses by @@DavidKorczynski (#2874), plus fuzz_convert by @@tyler92 (#2737). Initial OSS-Fuzz integration by @@catenacyber (#2342).

Build Improvements

    CI: CIFuzz GitHub Action @@DavidKorczynski (#2551); CodeQL workflow @@lgtm-migrator (#2546); Dependabot for GitHub Actions @@ghutchis (#2739); cibuildwheel workflow producing relocatable Python wheels for Windows / macOS / Linux / Linux ARM64 @@ghutchis (#2946); Linux ARM64 ASAN+UBSAN test build @@ghutchis (#2898); Python lint with safety policy.
    CMake 4 compatibility end-to-end @@PPN-SD (#2784); replaced deprecated exec_program and other modernization @@e-kwsm (#2507); OpenBabel3Config.cmake retains include info @@e-kwsm (#2802); public/private include-dir hygiene @@pinotree (#2315); Windows config-install location fix @@nicolasfella (#2463); CMake-version bumps for Python @@chrisjonesBSU (#2809).
    FindPython adopted; Python install path/prefix modernized @@e-kwsm (#2753, #2927); per-language *_INSTDIR variables (Python, Java, R, Perl, Ruby, C#, PHP) made configurable @@cygwin-lem (#2289).
    Eigen: drop Eigen 2; find Eigen3 in config mode and link Eigen3::Eigen; ensure HAVE_EIGEN3 is set at configure @@e-kwsm (#2858).
    Dependencies: InChI 1.07.5 @@e-kwsm (#2857); maeparser 1.3.3 @@e-kwsm (#2899); coordgen pinned to v3.0.2-10-gd20e735 @@e-kwsm (#2901), with template-file lookup removed @@bsiegert (#2297).
    Compiler/portability: include <ctime> for GCC 12+/C++17 @@KunhuanLiu (#2844); CMake time-check typo for GCC 12 @@thesamesam (#2493); drop register @@e-kwsm (#2920); drop deprecated <ciso646> @@e-kwsm (#2860); replace std::random_shuffle with std::shuffle @@e-kwsm (#2931); remove deprecated C headers @@e-kwsm (#2388); MSVC2015 back_inserter include @@baoilleach (#2230); Intel build uses IPO and strip at link in Release; big-endian / s390x fixes @@pranavkaruvally (#2816).
    Modernization: SWIG 4.x support and Javadoc/Pydoc bindings @@baoilleach (#2242, #2243); std::unordered_map adoption @@e-kwsm (#2500); always use std::shared_ptr (#2501); remove deprecated std::bind1st/bind2nd/binary_function @@e-kwsm (#2569, #2001, #2464); replace deprecated throw spec with noexcept @@e-kwsm (#2859); IOError → OSError in Python tests @@e-kwsm (#2466).
    Misc.: .gitattributes + EOL renormalization @@e-kwsm (#2489); updated built-in data files @@dkoes (#2328); debug/sanitizer build variants skip slow tests @@ghutchis (#2907); many internal deprecation warnings removed in a final refactor @@ghutchis (#2937).

Contributors

Many thanks to everyone who contributed code, bug reports, and reviews
for 3.2. Full shortlog: git shortlog -sn openbabel-3-1-1..openbabel-3-2-0.
@
text
@$NetBSD$

Remove obsolete variable.

--- tools/CMakeLists.txt.orig	2026-06-22 05:15:09.677983564 +0000
+++ tools/CMakeLists.txt
@@@@ -5,7 +5,7 @@@@ else(MINIMAL_BUILD)
 else(MINIMAL_BUILD)
   find_package(Boost COMPONENTS program_options iostreams)
   if(Boost_FOUND)
-    include_directories(${Boost_INCLUDE_DIRS} ${Boost_INCLUDE_DIR})
+    include_directories(${Boost_INCLUDE_DIRS})
   endif()
 
 
@


1.1
log
@openbabel: fix build
@
text
@d5 1
a5 1
--- tools/CMakeLists.txt.orig	2025-01-31 15:47:10.271879998 +0000
d7 1
a7 1
@@@@ -5,7 +5,7 @@@@ if(MINIMAL_BUILD)
@