Great! Thanks, Andreas, for performing the release and getting it to work on Maven Central! And to all the other contributors, of course!
On Fri, Jan 30, 2015 at 9:59 PM, Andreas Prlic <[email protected]> wrote: > BioJava 4.0.0 has been released and is available from Maven Central as > well as from http://biojava.org/wiki/BioJava:Download. > > BioJava 4.0.0 is a major release, with many new features as well as core > API changes. In accordance with semantic versioning nomenclature, the jump > to 4.x.x indicates that existing applications may need to be modified (e.g. > due to the removal of deprecated methods). In most cases there should be a > clearly documented replacement method. See below for details on how to > upgrade. > > This release contains over 500 commits from 17 authors: > > @andreasprlic @benjamintboyle @christiam @dmyersturnbull @Elinow > @emckee2006 @jgrzebyta @josemduarte @kevinwu1 @pibizza @heuermh @paolopavan > @parit @pwrose @sbliven @sroughley @willishf > > *New Features:* > > - General > - Consistent error logging. SLF4J is used for logging and provides > adaptors for all major logging implementations. (many contributors, > including @benjamintboyle and @josemduarte) > - Improved handling of exceptions (@dmyersturnbull) > - Removed deprecated methods > - Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and > @sbliven) > - Updated dependencies where applicable > - Available on Maven Central (@andreasprlic and @heuermh) > - biojava3-core > - Improved Genbank parser, including support for feature records, > qualifiers, and nested locations. (@paolopavan and @jgrzebyta) > - biojava3-structure > - Better support for crystallographic information, including > crystallographic operators, unit cells, and protein-protein interfaces. > (@josemduarte) > - Better organization of downloaded structure files (set using the > PDB_DIR and PDB_CACHE_DIR environmental variables) (@sbliven) > - Better command-line tools for structure alignment (@sbliven) > - New algorithm for symmetry detection in biological assemblies > (@pwrose) > - New algorithm for fast contact calculation, both intra-chain and > inter-chain (@josemduarte) > - Support for Accessible Surface Area (ASA) calculation through and > implementation of the Shrake & Rupley algorithm, both single-thread and > parallel (memory permitting) (@josemduarte) > - Support for large structures (memory permitting) and > multi-character chain IDs. > - Default to mmCIF file format, as recommended by the wwPDB > > This version is compatible with Java 6, 7, and 8. > > *Upgrading* > > Since we renamed all package names to be consistent across the whole > project, there will be import errors when upgrading to this version. These > can automatically get resolved using IDEs such as Eclipse or IntelliJ by > selecting the *Optimize Import* menu item. > > *About BioJava:* > > BioJava is a mature open-source project that provides a framework for > processing of biological data. BioJava contains powerful analysis and > statistical routines, tools for parsing common file formats, and packages > for manipulating sequences and 3D structures. It enables rapid > bioinformatics application development in the Java programming language. > > Happy BioJava-ing, > > Andreas > > _______________________________________________ > biojava-dev mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/biojava-dev >
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