Fixed

• Bug in symmetry detection #1101 and rcsb/symmetry#118

Fixed

• Brought back a command line argument for protein comparison tool #1096
• Upgraded the log facade framework to slf4j2 #1094
• Code smell fixes (Sonar issues S2293, S1319) #1095 #1091
• Various small fixes

Removed

• Removed capability of automatic download/caching of PDB archive files in MMTF format, following deprecation
  by RCSB PDB. Code to encode/decode in MMTF format is still in place #1099

Fixed

• Now mmCIF files that have no author fields in atom_site can be read (e.g. from PyMol or ESMAtlas) #775 #1083
• No evaluations of arguments in debug level log statements #1086 #789

Removed

• Minor removal from biojava-core: FileDownloadUtils::copy, replaced by Files::copy

Added

• Class FastaStreamer to read FASTA-formatted files using Java streams

Fixed

• Various minor fixes for code smells
• Some dependency upgrades
• Now using Jakarta as the JAXB implementation #1076
• Fixed SCOP URL #1077

Added

• Some more categories related to entity are now written in mmCIF writer #1063

Fixed

• Not declaring anymore unchecked exceptions in signatures #1062

Fixed

• The jar packages now contain pom.properties files #1057
• Some minor improvements in a few biojava-structure methods #1058

Breaking

• BioJava is now compiled at JDK 11 compatibility level. It will not work anymore under older JREs (e.g. JRE 8).
  This is the main reason for the major version bump.

Added

• Better handling of downloads: file download validation #1024

Fixed

• Upgrade to latest ciftools-java, fixes non-US locale issue #1049
• Issue with some edge cases in CIF parsing #1054
• Minor security issue #1046

Added

• GenBankWriterHelper - method that uses the original locus line rather than creating a new one, preventing loss of information
• GenBankReader - the ability to successfully parse GenBank files with a LOCUS ID containing white space
• GenBankReader - the ability to successfully parse GenBank files missing a LOCUS ID
• Aromaticity calculation in biojava-aa-prop module

Fixed

• GenBankWriter - String Formatter error when key or value of Qualifier has character "%", #886
• GenBankWriter - outputting db_xref feature qualifiers
• GenBankWriter - outputting the accession version and GI ID
• GenBankWriter - outputting feature locations containing joins and partial locations
• GenBankReader - reading locations split over multiple lines
• GenBankReader - set if feature qualifier values require quotes
• Local alignment with linear gap penalty was producing an NPE, #1036
• New default server for PDB files. Note that from Aug 2023 older versions of BioJava will not be able to fetch PDB files unless PDB.FILE.SERVER system property is used to override the default server
• Dependency upgrades
• Some bug and security fixes

Fixed

• Null handling in a few places related to loading PDB, CIF, mmtf files (issue introduced in 6.0.0). #1019

Fixed

• Log4j dependency upgraded to 2.17.1 to avoid new vulnerabilities
• Some new tests
• Fixes in tests and docs
• Bugfix in LocalProteinDomainParser #1009