Merge pull request #757 from josemduarte/changelogforv5

josemduarte · web-flow · commit ebe3515b0f0f · 2018-03-23T15:51:58.000-07:00
A changelog draft for the 5.0.0 release
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,17 +1,49 @@
 BioJava 5.0.0
 =============
 
-unreleased. Notes are WIP
+This release contains [1,170 commits](https://github.com/biojava/biojava/compare/biojava-4.2.11...biojava-5.0.0) from 19 contributors.
 
+Requires Java 8 or newer.
+
+### New features
+
+#### biojava-alignment
+* New utlity methods for sequence alignment objects (gap, similarity and coverage).
+
+#### biojava-structure
+* The data structures to represent 3D macromolecules now follow the mmCIF data model.
+* [MMTF format](http://mmtf.rcsb.org/) support.
+* Symmetry detection algorithms overhaul: better symmetry detection for tertiary and quaternary structure levels.
+* New method and data structures for the clustering of protein subunits at the sequence and structure levels.
+* New method to align biological assemblies, see `org.biojava.nbio.structure.align.quaternary.QsAlign`.
+* New algorithms for base-pair geometry in nucleic acids.
+* New SuperPosition interface for different 3D-structure superposition algorithms, see `org.biojava.nbio.structure.geometry.SuperPosition`.
+* Geometry-related API now more consistently based on vecmath interfaces.
+
+### Changed
 * For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included
+* Symmetry expansion for bioassembly creation is now by default happening via adding new chains instead of new models. 
+* Make objects serializable for compatibility with big data frameworks (e.g. Spark).
+
+### Breaking API changes
+
+* module biojava-phylo merged into biojava-alignment. The package namespace stays the same (`org.biojava.nbio.phylo`).
+* module biojava-sequencing merged into biojava-genome. Package `org.biojava.nbio.sequencing.io.fastq` is now `org.biojava.nbio.genome.io.fastq`
+* `org.biojava.nbio.structure.Compound` -> `org.biojava.nbio.structure.EntityInfo`
+* `org.biojava.nbio.structure.io.util.FileDownloadUtils` -> `org.biojava.nbio.core.util.FileDownloadUtils`
+* `org.biojava.nbio.structure.symmetry.core.AxisAligner` -> `org.biojava.nbio.structure.symmetry.axis.AxisAligner`
+* `org.biojava.nbio.structure.symmetry.core.Subunits` -> refactored into several classes in `org.biojava.nbio.structure.cluster`: Subunit, SubunitCluster, SubunitClusterer
+* `org.biojava.nbio.structure.align.helper.AlignTools` -> `org.biojava.nbio.structure.align.helper.AlignUtils`
+* All deprecations introduced in 4.0.0 or before were removed.
 
-Breaking API changes
-* org.biojava.nbio.structure.Compound -> org.biojava.nbio.structure.EntityInfo
-* org.biojava.nbio.structure.io.util.FileDownloadUtils -> org.biojava.nbio.core.util.FileDownloadUtils
-* org.biojava.nbio.structure.symmetry.core.AxisAligner -> org.biojava.nbio.structure.symmetry.axis.AxisAligner
-* org.biojava.nbio.structure.symmetry.core.Subunits -> refactored into serveral classes in org.biojava.nbio.structure.cluster: Subunit, SubunitCluster, SubunitClusterer
+### General
 
+* Javadocs improvements across the board.
+* All tests are now Junit4.
+* Updated dependency versions (guava, slf4j, and log4j).
 
+### Bug fixes
+A very long list.
 
 BioJava 4.2.11
 ==============
@@ -163,26 +195,24 @@ release date: March 10th 2016
 
 This release contains over [750](https://github.com/biojava/biojava/compare/6f8d796fee92edbbcd001c33cdae4f15c5480741...biojava-4.2.0) commits from 16 contributors.
 
-### New Features
-
 BioJava 4.2.0 offers many new features, as well several bug-fixes.
 
-General  
-
 -   Requires Java 7
 -   Better logging with SLF4J
 
-Biojava-Core  
+### New Features
+
+#### biojava-core
 
 -   New SearchIO framework including blast xml parser
 
-Biojava-structure  
+#### biojava-structure
 
 -   Secondary structure assignment (DSSP compatible)
 -   Multiple Structure Alignments
     -   New MultipleStructureAlignment datastructure supporting flexible and order-independent alignments
     -   MultipleMC algorithm
-        -   Can use any pairwise StructureAlignment implementation
+        - Can use any pairwise StructureAlignment implementation
     -   serialize and parse multiple structure alignments as XML files, output as Text, FatCat, FASTA, Rotation Matrices, etc.
 -   More complete mmCIF and cif parsing
     -   Parse bonds, sites, charges
@@ -193,20 +223,19 @@ Biojava-structure
 -   Improved chemical component framework, now by default providing full chemical description by using DownloadChemCompProvider
 -   Optimised memory usage of Residue/Atoms
 
-Biojava-structure-gui  
+#### biojava-structure-gui  
 
 -   MultipleAlignmentGUI for visualizing Multiple Structure Alignments with Jmol
 -   SymmetryDisplay for visualizing internal symmetry
 
-Biojava-Phylo  
+#### biojava-phylo  
 
--   Use Forester 1.038
+-   Use `Forester 1.038`
 -   Significant bug fixes
--   use SubstitutionMatrices in the core module (instead of imported Jalview matrices),
--   use Sequence and Compound classes from the alignment module
--   provide some Wrapper methods to communicate with forester,
--   decouple distance matrix calculation from tree constructor,
--   provide methods for common distance matrix calculations and framework for user-defined distances,
+-   use `SubstitutionMatrices` in the core module (instead of imported Jalview matrices)
+-   use `Sequence` and `Compound` classes from the alignment module
+-   provide some Wrapper methods to communicate with forester
+-   decouple distance matrix calculation from tree constructor
+-   provide methods for common distance matrix calculations and framework for user-defined distances
 -   update the forester version to have the correct NJ tree constructor
-    AND
 -   correct some of the tree evaluator statistics.
