Install the new interchangeable BLAS system created by Thomas Orgis,
currently supporting Netlib BLAS/LAPACK, OpenBLAS, cblas, lapacke, and
Apple's Accelerate.framework. This system allows the user to select any
BLAS implementation without modifying packages or using package options, by
setting PKGSRC_BLAS_TYPES in mk.conf. See mk/blas.buildlink3.mk for details.
This commit should not alter behavior of existing packages as the system
defaults to Netlib BLAS/LAPACK, which until now has been the only supported
implementation.
Details:
Add new mk/blas.buildlink3.mk for inclusion in dependent packages
Install compatible Netlib math/blas and math/lapack packages
Update math/blas and math/lapack MAINTAINER approved by adam@
OpenBLAS, cblas, and lapacke will follow in separate commits
Update direct dependents to use mk/blas.buildlink3.mk
Perform recursive revbump
1.7.7 2019-12-07 13:41:36-06:00 America/Chicago
* The program bp_chaos_plot has been removed.
* GD is now no longer a dependency, suggestion or requirement.
* #321 - GenBank format fix for un-quoted features, text wrapping
* Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
and a 'private' _sleep() function that mirror those from
Bio::DB::WebDBSeqI, primarily for compliance with potential website
restrictions for the number and frequency of queries (e.g. NCBI eUtils).
* Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
in last release.
1.7.6 2019-08-28 12:37:01+01:00 Europe/London
* The program bp_classify_hits_kingdom has been removed and is
now part of the examples documentation instead.
* GD is now listed as a suggestion instead of a requirement. The
bp_chaos_plot program will now work with the GD module.
* New method Bio::Tree::Statistics::transfer_bootstrap_expectation
to compute Transfer Bootstrap Expectation (TBE) for internal
nodes based on the methods outlined in Lemoine et al, Nature,
2018.
* New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
sequence in the stream faster but not perfect.
1.7.5 2019-02-11 14:57:45+00:00 Europe/London
* The following modules have been removed from the BioPerl
distribution to be part of a separate distribution with
independent development:
Bio::Symbol::*
* The Bio::Seq::SeqWithQuality module, which was deprecated since
2001, was finally removed.
* The deprecated() method has been deprecated. It is recommended
to use Carp::carp to warn.
* The following methods have been deprecated for a long while and
have now been removed:
Bio::Align::AlignI->no_residues
Bio::Align::AlignI->no_sequences
Bio::LocatableSeq->no_gap
Bio::LocatableSeq->no_sequences
Bio::SeqFeature::Generic->slurp_gff_file
Bio::SimpleAlign->no_residues
Bio::SimpleAlign->no_sequences
1.7.4 2019-02-05 16:23:53+00:00 Europe/London
* Fix Bio::Root::Test, and the testuite, to properly check for
internet connection and the NO_NETWORK_TESTING environment
variable. Previously, tests that required internet connection
were not being skipped, causing tests to fail.
1.7.3 2019-01-30 13:30:34+00:00 Europe/London
* The following modules have been removed from the BioPerl
distribution to be part of a separate distribution. They have
been integrated into other module distributions for independent
development:
Bio::Align::Graphics
Bio::AlignIO::nexml
Bio::AlignIO::stockholm
Bio::Assembly::*
Bio::Cluster::*
Bio::ClusterI::*
Bio::ClusterIO::*
Bio::DB::Ace
Bio::DB::BioFetch
Bio::DB::CUTG
Bio::DB::EMBL
Bio::DB::EntrezGene
Bio::DB::Expression::*
Bio::DB::GFF
Bio::DB::GFF::Adaptor::*
Bio::DB::GFF::Aggregator::*
Bio::DB::GFF::Featname
Bio::DB::GFF::Feature
Bio::DB::GFF::Homol
Bio::DB::GFF::RelSegment
Bio::DB::GFF::Segment
Bio::DB::GFF::Typename
Bio::DB::GenBank
Bio::DB::GenPept
Bio::DB::HIV::*
Bio::DB::MeSH
Bio::DB::NCBIHelper
Bio::DB::Query::GenBank
Bio::DB::Query::HIVQuery
Bio::DB::RefSeq
Bio::DB::SeqFeature::*
Bio::DB::SeqVersion::*
Bio::DB::SwissProt
Bio::DB::TFBS::*
Bio::DB::Taxonomy::entrez
Bio::DB::Taxonomy::sqlite
Bio::DB::Universal
Bio::Draw::Pictogram
Bio::Factory::MapFactoryI
Bio::Index::Hmmer
Bio::Index::Stockholm
Bio::LiveSeq::*
Bio::Map::*
Bio::MapIO::*
Bio::MolEvol::CodonModel
Bio::Nexml::Factory
Bio::NexmlIO
Bio::Perl
Bio::Phenotype::*
Bio::PhyloNetwork::*
Bio::PopGen::*
Bio::Restriction::*
Bio::Root::Build
Bio::Search::HSP::HMMERHSP
Bio::Search::HSP::HmmpfamHSP
Bio::Search::Hit::HMMERHit
Bio::Search::Hit::HmmpfamHit
Bio::Search::Hit::hmmer3Hit
Bio::Search::Result::HMMERResult
Bio::Search::Result::HmmpfamResult
Bio::Search::Result::hmmer3Result
Bio::SearchDist
Bio::SearchIO::hmmer
Bio::SearchIO::hmmer2
Bio::SearchIO::hmmer3
Bio::SearchIO::hmmer_pull
Bio::SeqEvolution::*
Bio::SeqFeature::SiRNA::*
Bio::SeqIO::abi
Bio::SeqIO::agave
Bio::SeqIO::alf
Bio::SeqIO::chadoxml
Bio::SeqIO::chaos
Bio::SeqIO::chaosxml
Bio::SeqIO::ctf
Bio::SeqIO::entrezgene
Bio::SeqIO::excel
Bio::SeqIO::exp
Bio::SeqIO::flybase_chadoxml
Bio::SeqIO::lasergene
Bio::SeqIO::nexml
Bio::SeqIO::pln
Bio::SeqIO::strider
Bio::SeqIO::ztr
Bio::Structure::*
Bio::Taxonomy::*
Bio::Tools::AlignFactory
Bio::Tools::Analysis::* (except SimpleAnalysisBase)
Bio::Tools::Gel
Bio::Tools::HMMER::*
Bio::Tools::Hmmpfam
Bio::Tools::Phylo::Gumby
Bio::Tools::Protparam
Bio::Tools::Run::RemoteBlast
Bio::Tools::SiRNA::*
Bio::Tools::dpAlign
Bio::Tools::pSW
Bio::Tree::AlleleNode
Bio::Tree::Draw::Cladogram
Bio::TreeIO::nexml
Bio::TreeIO::svggraph
Bio::Variation::*
* The following modules are new in the BioPerl distribution. They
have been previously released in the BioPerl-Run distribution.
This will enable smaller distributions that provide a
Bio::Tool::Run interface, to be only dependent on the BioPerl
distribution instead of the whole (very large) BioPerl-Run:
Bio::Tools::Run::Analysis
Bio::Tools::Run::AnalysisFactory
Bio::Tools::Run::Phylo::PhyloBase
Bio::Tools::Run::WrapperBase
Bio::Tools::Run::WrapperBase::CommandExts
* The following programs have been removed:
bp_biofetch_genbank_proxy
bp_blast2tree
bp_bulk_load_gff
bp_composite_LD
bp_das_server
bp_download_query_genbank
bp_fast_load_gff
bp_flanks
bp_genbank2gff
bp_generate_histogram
bp_heterogeneity_test
bp_hivq
bp_hmmer_to_table
bp_load_gff
bp_meta_gff
bp_netinstall
bp_parse_hmmsearch
bp_process_wormbase
bp_query_entrez_taxa
bp_remote_blast
bp_seqfeature_delete
bp_seqfeature_gff3
bp_seqfeature_load
* Because of the move of so many modules and programs into
separate distributions, the following modules are no longer
prerequisites:
Ace
Ace::Sequence::Homol
Algorithm::Munkres
Apache::DBI
Archive::Tar
Array::Compare
Bio::ASN1::EntrezGene
Bio::Expression::Contact
Bio::Expression::DataSet
Bio::Expression::Platform
Bio::Expression::Sample
Bio::Ext::Align
Bio::GMOD::CMap::Utils
Bio::Phylo::Factory
Bio::Phylo::Forest::Tree
Bio::Phylo::IO
Bio::Phylo::Matrices
Bio::Phylo::Matrices::Datum
Bio::Phylo::Matrices::Matrix
Bio::SeqFeature::Annotated
Bio::SeqIO::staden::read
Bio::Tools::Run::Alignment::Clustalw
Bio::Tools::Run::Ensembl
Bio::Tools::Run::Phylo::Molphy::ProtML
Bio::Tools::Run::Phylo::Phylip::Neighbor
Bio::Tools::Run::Phylo::Phylip::ProtDist
Bio::Tools::Run::Phylo::Phylip::ProtPars
Bio::Tools::Run::Samtools
CGI
CPAN
Cache::FileCache
Config
Convert::Binary::C
DBD::Pg
DBD::SQLite
Data::Stag::XMLWriter
Encode
English
ExtUtils::Install
ExtUtils::Manifest
File::Glob
GD::Simple
Getopt::Std
Graph::Undirected
GraphViz
HTML::HeadParser
HTML::TableExtract
LWP
LWP::Simple
MIME::Base64
Memoize
PostScript::TextBlock
SVG
SVG::Graph
SVG::Graph::Data
SVG::Graph::Data::Node
SVG::Graph::Data::Tree
Sort::Naturally
Spreadsheet::ParseExcel
Term::ReadLine
Text::NSP::Measures::2D::Fisher2::twotailed
Text::ParseWords
Time::Local
Tree::DAG_Node
URI::Escape
WWW::Mechanize
XML::Simple
* The following is a new prerequisite:
Test::RequiresInternet
* The deobfuscator has been removed.
* The emacs bioperl minor mode is no longer distributed as part of the
perl module distributions. See
https://github.com/bioperl/emacs-bioperl-mode
1.73 2018-09-24 21:31:26-05:00 America/Chicago
* Fix regex warnings for Perl 5.28.
* New module 'Bio::SeqIO::entrezgene' imported from the BioPerl
distribution. This means Bio-ASN1-Entrezgene now "Enhances"
BioPerl's Bio::SeqIO instead of being a hard dependency of
BioPerl.
Construct and analyze projection matrix models from a demography study
of marked individuals classified by age or stage. The package covers
methods described in Matrix Population Models by Caswell (2001) and
Quantitative Conservation Biology by Morris and Doak (2002).
Minor enhancements since 0.45
0.46.2 is available, but has serious regressions.
Reverted to bundled htslib 1.4.1, since kallisto source contains modified
htslib files that are incompatible with the current 1.10.2 package.
Numerous enhancements and bug fixes since 1.9, including:
Elimited refernce file size limits
SAM header API
On-the-fly indexing
Improved Amazon S3 interface
This package contains a patch for recent libcurl not in the upstream release
Changelog:
Version 0.14.16:
GChemPaint:
* Do not show buttons for non yet implemented tools.
Version 0.14.15:
GCCV library:
* Don't use the abs() function on unsigned numbers.
Other:
* Updated appdata files.
Version 0.14.14:
Mozilla plugin:
* Fix build.
Version 0.14.13:
GChemPaint:
* Optional use of Lasem to display maths.
* Fix rendering with gtk+ >= 3.20.
* Fix crash with atom charges larger than 1.
* Fix crash when deleting a bond outside a molecule. [#48256]
Gnumeric plugin:
* Add monoisotopicmass function in gnumeric and more.
Databases:
* Update names for elements 113, 115, 117 and 118.
Version 0.14.12:
GChemPaint:
* Enhanced Chemdraw formats support. [sr #108952]
* Optional use of Lasem to display maths.
* Fix rendering with gtk+ >= 3.20.
GChemCalc:
* Don't crash on "Ac" string. [#47366]
Version 0.14.11:
GChemPaint:
* Fix an infinite loop condition in retrosyntheses alignment.
* Don't crash when importing an invalid string. [Redhat bug #1285154]
* Fix drawing when zoomed.
* Fix various runtime errors.
* Fix crash when creating a reaction with no product.
* Enhanced Chemdraw formats support.
* Fix embedding of a whole molecule inside brackets. [#47224]
GChemTable:
* Don't crash when showing an already existing chart.
[Redhat bug #1302135]
GCrystal:
* Fix build with gcc-6. [Redhat bug #1307546]
GCrystal and GChem3D:
* Don't crash when rendering to memory (images and print). [#47169]
Other:
* Added keywords to desktop files.
* Updated appdata files.
Version 0.14.10:
GChemPaint:
* Fix an object bounds issue.
Mozilla plugin:
* Supports the npapi-sdk package as requirement.
Other:
* Fixed typos in appdata files.
Version 0.14.9:
GChemPaint:
* Ensure that the document size is always updated. [#43091]
3d viewer and GCrystal:
* Fix rotation. [#42977] (patch from Toni Andjelkovic)
All applications:
* Add appdata files.
Version 0.14.8
GChemPaint:
* Fix drawing with Gtk+ >= 3.10.
Version 0.14.7
GCrystal:
* Fix crash in dialogs with recent Gtk+.
Mozilla plugin:
* Fix crashers for 2D and 3D molecules.
Version 0.14.6
3d viewer:
* Avoid empty entries in recent list.
CGchemPaint:
* Restore .mol files support.
* Fix CML import (also affected 3d viewer and >GCrystal).
* Fix BMP export.
GCrystal:
* Fix test order in lines code. [#41261]
GSpectrum:
* Fix access to uninitialized data.
* Don' double free a string.
GOffice component:
* Don't crash when editing after saving a GChemPaint object.
Mozilla plugin:
* Fix supported mime-types list. (see Debian bug #716961)
Other:
* Fix build on FreeBSD (Koop Mast). [#41256]
Version 0.14.5
GChemPaint:
* Make adding template work again.
Version 0.14.4
GChemPaint:
* Do not use a NULL atom properties. [#40194]
Version 0.14.3
GChemPaint:
* Really close the window on delete event.
* Don't crash when aligning ungrouped objects.
GChemTable:
* Fix crash when using masses in a graph.
* Fix graph behavior after edition.
All:
* Make sure to not create a C++ locale from a NULL string.
Version 0.14.2
GChemPaint:
* Fix crash when loading some molecules (was introduced in 0.14.1).
Version 0.14.1
GChemPaint:
* Do not allow a mesomery destruction when inside a reaction.
* Fix molecule deletion inside a mesomery.
* Fix reactant deletion inside a reaction.
* Don't crash when a mesomery inside a reaction is destroyed.
* Check molecule consistency when loading, avoids a stack overflow.
* Enhanced representaion of chiral molecules imported from CML and other
formats.
* Fix crash when deleting a cyclic bond.
GCrystal:
* Fix row selection operations order in grids.
Version 0.14.0
GChemPaint:
* Fix reaction construction.
* Fix non bonding electron pairs.
Version 0.13.99
GChemPaint:
* Fix squiggle bonds period.
* Allow brackets around a mesomery.
* Allow a mesomery inside a reaction.
* Fixed some meomory access issues.
* Fixed crash when loading a group.
* Fixed mesomery construction.
* Fixed crash when ungrouping.
Version 0.13.98
GChemPaint:
* Don't freeze after an aborted molecules merge.
* Initialize the bond order for the Newman projection tool.
* Don't crash when adding brackets around a fragment.
* Fix undoing a molecule partial flip.
* Fix bracket stoichiometry index position after a transform.
* Fix explicit lone pairs count evaluation.
Version 0.13.92
GChemCalc
* Updated the documentation.
GChemPaint:
* Fix View::BuildSVG() and View::BuildEPS() which were missing the
trailing 0.
* Fix misleading error message while saving.
* Fix loading of arrows inside a group. [#27032]
GCrystal:
* Apply element change to all slected atoms.
* Updated the documentation.
GSpectrum:
* Add "Response factor" as supported unit.
* Fixed widgets spacing.
* Updated the documentation.
GChemTable:
* Updated the documentation.
Version 0.13.91
3d viewer:
* Show all menu items when a molecule is loaded from the command line.
* Updated user documentation.
GChemPaint:
* Don't crash on startup.
All:
* Fix localization issues.
* Fixed modal message boxes behavior.
Version 0.13.90
3d viewer:
* Fix import from pdb files. [#36582]
GCrystal:
* Fix infinite loop condition. [#36583]
* Fix atomic radius change issue.
GChemTable:
* Fix languages translation.
Version 0.13.7
GChemPaint:
* Fixed crash when selecting the alignment item inside a mechanism
step. [#35626]
GCrystal:
* Fixed loading CIF files using uptodate space groups descriptions.
Other:
* License is now GPL version 3 (except for the OpenBabel related code).
* Fix build on big endian machines (Dan Horak). [#36175]
* Updated API documentation.
Version 0.13.6
GChemPaint:
* fixed text position serialization. [#34947]
* add some support for Newman projections.
* accept some multisteps reactions.
Goffice component:
* Add support for 3D molecular structures.
Other:
* Fixed pixmaps installation directory. [#35272]
* fixed build with ->l,--no-undefined. [patch #7677]
Version 0.13.5
3d viewer:
* Import from InChI or SMILES.
* Export to GChemPaint and GChemCalc.
* Generates InChI, InChiKey and SMILES.
* Add access to databases.
GChemPaint:
* Brackets inside a molecule accept a stoichiometry coefficient.
GCrystal:
* Use multiple selection in atoms and lines dialogs.
GSpectrum:
* Allow markup in combo boxes and axes titles.
Goffice component:
* Add support for crystal structures.
Other:
* Fixed one more OpenGL related crasher.
Version 0.13.4
All:
* Ported to Gtk+-3.0.
GCrystal:
* Use the new GcrGrid item in atoms, lines and cleavages dialogs.
* Make these and size dialogs instant apply.
GChemTable:
* Use a more complete tip window for elements.
Version 0.13.3
GChemPaint:
* Fixed build with gcc-4.6. [#32363]
* Allow colored atomic symbols on a per-document basis.
* Brackets tool now working, not perfectly though.
Other:
* Don't use POLLRDHUP when not defined. [#32768]
* Split libgcu so that libgcu itself never calls gtk+ directly.
Version 0.13.2
GChemPaint:
* Do not allow document changes using keyboard while
dragging the mouse. [#31812]
* Don't add new molecules when undoing a mechanism arrow deletion.
[#32433]
* Removed the Wikipedia tool which was obsolete.
* Reorganized molecule contextual menu with new 3D options
and databases access.
Other:
* OpenBabel support has been moved to a separate process and greatly
enhanced, specially for 3D export from gchempaint.
* A lot of bugs have been fixed.
Version 0.13.1
GSpectrum:
* Loads NUTS files.
* Transforms FID to spectrum.
Version 0.13.0
GChemPaint:
* New "lasso" tool to allow partial selections.
* New "brackets" tool (doesn't work yet).
Other:
* libgcr: new library for GCrystal.
* Fixed all bugs discovered in the 0.12 banch.
* Depends on boost. If you have boost, cmake detects boost and it causes
build failure.
Changelog:
3.1.1
This version primarily reflects fixes for packaging on Linux and FreeBSD
relative to 3.1.0. No features or significant bug fixes were involved.
3.1.0
This version represents additional API and is backwards-compatible with the 3.0 release.
Significant features and fixes
Fixed tautomer code (by timvdm #2171)
New functionality: Support for periodic boundary conditions. See additional option -p for MMCIF format, and write option 'g' for CIF. (by bbucior, #1853)
New functionality: Add distance geometry method (by n-yoshikawa, #1875, by timvdm #2158)
Fixed crashes with new 3D coordinate generation (by timvdm #2149 and ghutchis #2150)
New features and improvements
New file format: Wiswesser Line Notation reader from Roger Sayle (by baoilleach, #2084)
New option: Add the --neutralize operation to convert charged atoms to neutral (by baoilleach, #2109)
Update GAS CONSTANT to 2018 CODATA recommended value (by e-kwsm, #2045)
Support #0 in SMARTS so that asterisks can be matched (by baoilleach, #2079)
Bring back support for lowercase elements and D/T in GetAtomicNum(). (by baoilleach, #2100)
Change docstrings of add/delete hydrogens to better reflect their functionality (by baoilleach, #2110)
Support kekulization of aromatic sulfoxides (by baoilleach, #2121)
Enable casting to StereoBase in the Python bindings (by baoilleach, #2124)
OBBuilder: Add error message for ring/rigid fragments with all zero coords. (by timvdm, #2149)
R script updates (by khoran, #2145)
Be more strict when parsing charges in SMILES (by baoilleach, #2132)
Improve tools/obconformer.cpp (by e-kwsm, #2154)
Bug fixes
Fix CMake error with R and C# bindings (by ghutchis, #2051)
Rename MAESTRO extensions from uppercase to lowercase (by baoilleach, #2053)
Fix file format docstrings that were causing problems with Sphinx or GUI (by baoilleach, #2054)
Fix BUILD_SHARED=OFF (by dkoes, #2056)
Fix import of openbabel (by e-kwsm, #2058)
Update for Open Babel 3 (by e-kwsm, #2060)
Fix maeparser compile error with some Boost configs (by fredrikw, #2076)
Find or build maeparser & coordgen libraries (by ricrogz, #2064)
Fix issue #2095, caused by incorrect application of protonated SMARTS (by au1985, #2102)
Fix issue #1794, UFF atom typing for deuterium (by ghutchis, #2114)
Fix segfault on SMI to InChI conversion when using "-d" (by timvdm, #2115)
Correct the path to the openbabel-python.cpp (by baoilleach, #2119)
Remove fragments with zero coordinates - fixes#2144. (by ghutchis, #2150)
Fix issue #2125 - Zero occupancy in cif file treated as 1.0. (by orex, #2136)
Fix#2071 - obrms parser segmentation fault (by e-kwsm, #2073)
Fix#2098 - OBDistanceGeometry is unavailable to users (by n-yoshikawa, #2105)
Set MAEPARSER_BUILD_SHARED_LIBS (fix#2089) (by e-kwsm, #2155)
Fix the import of Tkinter in Python 3+ (by mrakitin, #2157)
Fix for segault (with regression test) (by dkoes, #2162)
Follow-up with missing spelling fixes from #2163 (by mrakitin, #2166)
Prefer std::fabs resolves build problem on mac-current (by ghutchis, #2168)
Fix distance geometry stereo issues (by timvdm, #2158)
Merge of "Improve OBConversion::WriteString() and WriteFile() initialization" (adalke) #1923 (by baoilleach, #2176)
Fix output format in the cifformat writer (by afonari, #2170)
Development/Build/Install improvements
Avoid using namespace in headers (by e-kwsm, #2055)
Remove babel doc (by e-kwsm, #2057)
Do not hard-code Open Babel major version for include directory (by e-kwsm, #2059)
Patched to build on NetBSD (by voidpin, #2093)
Update download link (by njzjz, #2094)
Fix GitHub ISSUE_TEMPLATE (by RMeli, #2082)
Define OpenBabel3_LIBRARY (by dkoes, #2086)
Initial GitHub action - misspell-fixer (by ghutchis, #2163)
Automated GitHub builds (by ghutchis, #2165)
These packages are susceptible to bugs when confronted with non-ASCII
characters.
See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=94182.
It takes some time to analyze and fix these individually, therefore they
are only marked as "needs work".
/usr/bin/chmod -R g-w /home/pbulk/build/biology/canu/work
chmod: WARNING: can't change /home/pbulk/build/biology/canu/work/.gcc/bin/cc
chmod: WARNING: can't change /home/pbulk/build/biology/canu/work/.gcc/bin/g++
Just good that serious pkgsrc builds are run as an unprivileged user,
with no chance of bricking the whole operating system.
pkglint -r --network --only "migrate"
As a side-effect of migrating the homepages, pkglint also fixed a few
indentations in unrelated lines. These and the new homepages have been
checked manually.
pkglint --only "https instead of http" -r -F
With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.
This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.
Upstream changelog
==================
Open Babel 3.0.0
@ghutchis ghutchis released this on 10 Oct - 29 commits to master since this release
This release represents a major update and is strongly recommended for all users.
It also removes deprecated components and breaks the API in a few places. For information on migrating from the previous version, please see:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#migrating-to-3-0
We intend to move to semi-annual releases in Spring and Fall, with bug fix releases as needed.
A sample of major new features:
Code for handling implicit hydrogens and kekulization has been entirely replaced. As well as being accurate, the new approach is much faster.
Speed of reading and writing SMILES has been improved by more than 50-fold.
Removal of the old 'babel' binary in favor of the newer 'obabel' command-line tool.
New improved fragment-based 3D coordinate generation code as part of Google Summer of code 2018/2019. Significantly faster and more accurate: https://doi.org/10.1186/s13321-019-0372-5
(Please cite J. Cheminf. (2019) v11, article 49 if you use the new 3D coordinate generation.)
New API for handling reactions stored as molecules (e.g. Reaction InChI, etc.)
New API for copying part of an OBMol as a substructure
Support for Maestro file format, contributed by Patrick Lorton of Schrodinger
There are an incredible number of improvements, minor features and many bug fixes.
For a full list of changes and to download source packages (and eventually binaries)
https://open-babel.readthedocs.io/en/latest/ReleaseNotes/ob300.htmlhttps://github.com/openbabel/openbabel/releases
Thanks to a cast of many for this release, particularly including Noel O'Boyle;
aandi, adalke (Andrew Dalke), adamjstewart (Adam J. Stewart), afonari (Alexandr Fonari), artoria2e5 (Mingye Wang), baoilleach (Noel O'Boyle), barrymoo (Barry Moore), bbucior (Ben Bucior), boryszef (Borys Szefczyk), camannguyen (An Nguyen), cmanion (Charles A. Manion), cowsandmilk (David Hall), cstein (Casper Steinmann), derekharmon (Derek Harmon), djhogan (Daniel Hogan), dkoes (David Koes), e-kwsm (Eisuke Kawashima), eloyfelix (Eloy Felix), fredrikw (Fredrik Wallner), ghutchis (Geoff Hutchison), hille721 (Christoph Hille), hseara (Hector Martinez-Seara), jasonychuang (Jason Huang), jeffjanes (Jeff Janes), johnmay (John Mayfield), katrinleinweber (Katrin Leinweber), keipertk (Kristopher Keipert), kyle-roberts-arzeda, langner (Karol M. Langner), lorton (Pat Lorton), mcs07 (Matt Swain), merkys (Andrius Merkys), mkrykunov, mmghahremanpour (Mohammad Ghahremanpour), mwojcikowski (Maciej Wojcikowski), n-yoshikawa (Naruki Yoshikawa), nakatamaho (Nakata Maho), nsoranzo (Nicola Soranzo), oititov (Titov Oleg), orex (Kirill Okhotnikov), pbecherer (Paul Becherer), peawagon (Jen), philthiel (Philipp Thiel), psavery (Patrick Avery), rmeli (Rocco Meli), serval2412 (Julien Nabet), sunoru, susilehtola (Susi Lehtola), tgaudin (Theophile Gaudin), theavey (Thomas Heavey), timvdm (Tim Vandermeersch), torcolvin (Tor Colvin), wojdyr (Marcin Wojdyr), xomachine (Dmitriy Fomichev), yishutu (Yi-Shu Tu)
Open Babel 2.4.0 (2016-9-21)
This release represents a major update and should be a stable upgrade, strongly recommended for all users.
Note that this release deprecates the babel executable in favor of obabel. A future release will remove babel entirely. For information on the differences, please see the documentation.
New file formats
DALTON output files (read only) and DALTON input files (read/write) (Casper Steinmann)
JSON format used by ChemDoodle (read/write) (Matt Swain)
JSON format used by PubChem (read/write) (Matt Swain)
LPMD's atomic configuration file (read/write) (Joaquin Peralta)
The format used by the CONTFF and POSFF files in MDFF (read/write) (Kirill Okhotnikov)
ORCA output files (read only) and ORCA input files (write only) (Dagmar Lenk)
ORCA-AICCM's extended XYZ format (read/write) (Dagmar Lenk)
Painter format for custom 2D depictions (write only) (Noel O'Boyle)
Siesta output files (read only) (Patrick Avery)
Smiley parser for parsing SMILES according to the OpenSMILES specification (read only) (Tim Vandermeersch)
STL 3D-printing format (write only) (Matt Harvey)
Turbomole AOFORCE output (read only) (Mathias Laurin)
A representation of the VDW surface as a point cloud (write only) (Matt Harvey)
New file format capabilities and options
AutoDock PDBQT: Options to preserve hydrogens and/or atom names (Matt Harvey)
CAR: Improved space group support in .car files (kartlee)
CDXML: Read/write isotopes (Roger Sayle)
CIF: Extract charges (Kirill Okhotnikov)
CIF: Improved support for space-groups and symmetries (Alexandr Fonari)
DL_Poly: Cell information is now read (Kirill Okhotnikov)
Gaussian FCHK: Parse alpha and beta orbitals (Geoff Hutchison)
Gaussian out: Extract true enthalpy of formation, quadrupole, polarizability tensor, electrostatic potential fitting points and potential values, and more (David van der Spoel)
MDL Mol: Read in atom class information by default and optionally write it out (Roger Sayle)
MDL Mol: Support added for ZBO, ZCH and HYD extensions (Matt Swain)
MDL Mol: Implement the MDL valence model on reading (Roger Sayle)
MDL SDF: Option to write out an ASCII depiction as a property (Noel O'Boyle)
mmCIF: Improved mmCIF reading (Patrick Fuller)
mmCIF: Support for atom occupancy and atom_type (Kirill Okhotnikov)
Mol2: Option to read UCSF Dock scores (Maciej Wojcikowski)
MOPAC: Read z-matrix data and parse (and prefer) ESP charges (Geoff Hutchison)
NWChem: Support sequential calculations by optionally overwriting earlier ones (Dmitriy Fomichev)
NWChem: Extract info on MEP(IRC), NEB and quadrupole moments (Dmitriy Fomichev)
PDB: Read/write PDB insertion codes (Steffen Moller)
PNG: Options to crop the margin, and control the background and bond colors (Fredrik Wallner)
PQR: Use a stored atom radius (if present) in preference to the generic element radius (Zhixiong Zhao)
PWSCF: Extend parsing of lattice vectors (David Lonie)
PWSCF: Support newer versions, and the 'alat' term (Patrick Avery)
SVG: Option to avoid addition of hydrogens to fill valence (Lee-Ping)
SVG: Option to draw as ball-and-stick (Jean-Noel Avila)
VASP: Vibration intensities are calculated (Christian Neiss, Mathias Laurin)
VASP: Custom atom element sorting on writing (Kirill Okhotnikov)
Other new features and improvements
2D layout: Improved the choice of which bonds to designate as hash/wedge bonds around a stereo center (Craig James)
3D builder: Use bond length corrections based on bond order from Pyykko and Atsumi (http://dx.doi.org/10.1002/chem.200901472) (Geoff Hutchison)
3D generation: "--gen3d", allow user to specify the desired speed/quality (Geoff Hutchison)
Aromaticity: Improved detection (Geoff Hutchison)
Canonicalisation: Changed behaviour for multi-molecule SMILES. Now each molecule is canonicalized individually and then sorted. (Geoff Hutchison/Tim Vandermeersch)
Charge models: "--print" writes the partial charges to standard output after calculation (Geoff Hutchison)
Conformations: Confab, the systematic conformation generator, has been incorporated into Open Babel (David Hall/Noel O'Boyle)
Conformations: Initial support for ring rotamer sampling (Geoff Hutchison)
Conformer searching: Performance improvement by avoiding gradient calculation and optimising the default parameters (Geoff Hutchison)
EEM charge model: Extend to use additional params from http://dx.doi.org/10.1186/s13321-015-0107-1 (Tomas Racek)
FillUnitCell operation: Improved behavior (Patrick Fuller)
Find duplicates: The "--duplicate" option can now return duplicates instead of just removing them (Chris Morley)
GAFF forcefield: Atom types updated to match Wang et al. J. Comp. Chem. 2004, 25, 1157 (Mohammad Ghahremanpour)
New charge model: EQeq crystal charge equilibration method (a speed-optimized crystal-focused charge estimator, http://pubs.acs.org/doi/abs/10.1021/jz3008485) (David Lonie)
New charge model: "fromfile" reads partial charges from a named file (Matt Harvey)
New conversion operation: "changecell", for changing cell dimensions (Kirill Okhotnikov)
New command-line utility: "obthermo", for extracting thermochemistry data from QM calculations (David van der Spoel)
New fingerprint: ECFP (Geoff Hutchison/Noel O'Boyle/Roger Sayle)
OBConversion: Improvements and API changes to deal with a long-standing memory leak (David Koes)
OBAtom::IsHBondAcceptor(): Definition updated to take into account the atom environment (Stefano Forli)
Performance: Faster ring-finding algorithm (Roger Sayle)
Performance: Faster fingerprint similarity calculations if compiled with -DOPTIMIZE_NATIVE=ON (Noel O'Boyle/Jeff Janes)
SMARTS matching: The "-s" option now accepts an integer specifying the number of matches required (Chris Morley)
UFF: Update to use traditional Rappe angle potential (Geoff Hutchison)
Language bindings
Bindings: Support compiling only the bindings against system libopenbabel (Reinis Danne)
Java bindings: Add example Scala program using the Java bindings (Reinis Danne)
New bindings: PHP (Maciej Wojcikowski)
PHP bindings: BaPHPel, a simplified interface (Maciej Wojcikowski)
Python bindings: Add 3D depiction support for Jupyter notebook (Patrick Fuller)
Python bindings, Pybel: calccharges() and convertdbonds() added (Patrick Fuller, Bjorn Gruning)
Python bindings, Pybel: compress output if filename ends with .gz (Maciej Wojcikowski)
Python bindings, Pybel: Residue support (Maciej Wojcikowski)
Development/Build/Install Improvements
Version control: move to git and GitHub from subversion and SourceForge
Continuous integration: Travis for Linux builds and Appveyor for Windows builds (David Lonie and Noel O'Boyle)
Python installer: Improvements to the Python setup.py installer and "pip install openbabel" (David Hall, Matt Swain, Joshua Swamidass)
Compilation speedup: Speed up compilation by combining the tests (Noel O'Boyle)
MacOSX: Support compiling with libc++ on MacOSX (Matt Swain)
Cast of contributors
Alexandr Fonari, Anders Steen Christensen, Andreas Kempe, arkose, Benoit Leblanc, Bjorn Gruning, Casper Steinmann, Chris Morley, Christoph Willing, Craig James, Dagmar Lenk, David Hall, David Koes, David Lonie, David van der Spoel, Dmitriy Fomichev, Fulvio Ciriaco, Fredrik Wallner, Geoff Hutchison, Heiko Becker, Itay Zandbank, Jean-Noel Avila, Jeff Janes, Joaquin Peralta, Joshua Swamidass, Julien Nabet, Karol Langner, Karthik Rajagopalan, Katsuhiko Nishimra, Kevin Horan, Kirill Okhotnikov, Lee-Ping, Matt Harvey, Maciej Wojcikowski, Marcus Hanwell, Mathias Laurin, Matt Swain, Mohamad Mohebifar, Mohammad Ghahremanpour, Noel O'Boyle, Patrick Avery, Patrick Fuller, Paul van Maaren, Peng Bai, Philipp Thiel, Reinis Danne, Roger Sayle, Ronald Cohen, Scott McKechnie, Stefano Forli, Steve Roughley, Steffen Moeller, Tim Vandermeersch, Tomas Racek, Tomas Trnka, Tor Colvin, Torsten Sachse, Yi-Shu Tu, Zhixiong Zhao
Start building FreeGLUT with GLUT compatibility on.
- GLUT's maintainance state is much worse than FreeGLUT's, with no
substanital commits since 2011.
- GLUT can no longer be consider a core component of Mesa or X11.
- Nobody except us seems to be using it...
Other vendors still shipping GLUT:
- GoboLinux, T2 SDE, PLD Linux
Revbump packages using GLUT or freeglut by default.
The biopython license is _very_ similar, but not identical, to many
other open source licenses used throughout pkgsrc. The gratuitous
differences are being addressed by the project through an effort to
relicense all files to the 3-clause BSD license. In the meantime,
Debian has accepted that the current biopython license meets the DFSG
and includes the package in their main distribution. Consequently,
rename the license file and add it to DEFAULT_ACCEPTABLE_LICENSES.
See http://mail-index.netbsd.org/pkgsrc-changes/2019/08/13/msg195804.html.
