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GitHub / biojava/biojava-legacy issues and pull requests

#84 - Update guava dependency version to 33.5.0-jre

Pull Request - State: closed - Opened by heuermh 4 months ago

#83 - Update guava dependency version to 33.4.0-jre

Pull Request - State: closed - Opened by heuermh about 1 year ago

#83 - Update guava dependency version to 33.4.0-jre

Pull Request - State: closed - Opened by heuermh about 1 year ago

#82 - Update actions/cache to v4

Pull Request - State: closed - Opened by heuermh about 1 year ago

#82 - Update actions/cache to v4

Pull Request - State: closed - Opened by heuermh about 1 year ago

#81 - Fix deploy snapshot Github Action failures

Issue - State: open - Opened by heuermh over 1 year ago

#80 - Update guava dependency version to 33.3.0-jre

Pull Request - State: closed - Opened by heuermh over 1 year ago

#80 - Update guava dependency version to 33.3.0-jre

Pull Request - State: closed - Opened by heuermh over 1 year ago

#79 - Update guava dependency version to 33.1.0-jre

Pull Request - State: closed - Opened by heuermh almost 2 years ago

#79 - Update guava dependency version to 33.1.0-jre

Pull Request - State: closed - Opened by heuermh almost 2 years ago

#78 - Update guava dependency version to 33.0.0-jre

Pull Request - State: closed - Opened by heuermh about 2 years ago

#78 - Update guava dependency version to 33.0.0-jre

Pull Request - State: closed - Opened by heuermh about 2 years ago

#77 - Update guava dependency version to 31.1.3-jre

Pull Request - State: closed - Opened by heuermh about 2 years ago

#75 - Update guava dependency version to 32.0.1-jre

Pull Request - State: closed - Opened by heuermh over 2 years ago

#74 - Update guava dependency version to 31.1-jre

Pull Request - State: closed - Opened by heuermh almost 4 years ago

#73 - Bump xercesImpl from 2.12.1 to 2.12.2

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#72 - Update guava dependency version to 31.0.1-jre

Pull Request - State: closed - Opened by heuermh about 4 years ago

#71 - Migrate CI from Travis to Github Actions

Pull Request - State: closed - Opened by heuermh over 4 years ago - 6 comments

#70 - Migrate CI from Travis to Github Actions

Issue - State: closed - Opened by heuermh over 4 years ago

#69 - Add line number to error reporting

Pull Request - State: closed - Opened by heuermh over 4 years ago

#68 - Update dependency versions

Pull Request - State: closed - Opened by heuermh almost 5 years ago

#67 - Updates to sequencing module

Pull Request - State: closed - Opened by heuermh about 5 years ago

#66 - Fix maven-enforcer-plugin version

Pull Request - State: closed - Opened by heuermh over 5 years ago

#65 - Update maven plugin dependency versions

Pull Request - State: closed - Opened by heuermh over 5 years ago

#64 - Javadoc target option 1.5 no longer supported under JDK 11+

Issue - State: closed - Opened by heuermh over 5 years ago

#63 - Update maven plugin dependency versions

Issue - State: closed - Opened by heuermh over 5 years ago

#62 - Add module descriptors for javadoc

Issue - State: open - Opened by heuermh over 5 years ago

#61 - Use javadoc configuration for reporting

Pull Request - State: closed - Opened by heuermh over 5 years ago

#60 - Remove use of '_' as identifier

Pull Request - State: closed - Opened by heuermh over 5 years ago

#59 - Javadoc error: '_' used as an identifier in StructureTools

Issue - State: closed - Opened by heuermh over 5 years ago

#58 - Fix broken tests after junit upgrade

Pull Request - State: closed - Opened by heuermh over 5 years ago

#57 - Fix unit test failures in Travis CI builds

Issue - State: closed - Opened by heuermh over 5 years ago

#56 - Bump guava from 24.0-jre to 24.1.1-jre in /sequencing

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago
Labels: dependencies

#55 - Bump junit from 4.10 to 4.13.1

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago
Labels: dependencies

#54 - Release version 1.9.4

Issue - State: closed - Opened by heuermh over 5 years ago

#53 - Bump JDK source and target version to 1.8

Pull Request - State: closed - Opened by heuermh over 5 years ago

#52 - Bump JDK source and target version

Issue - State: closed - Opened by heuermh over 5 years ago

#51 - Bump xercesImpl from 2.4.0 to 2.12.0

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 1 comment
Labels: dependencies

#49 - Configure maven-javadoc-plugin for javadoc 1.8 and later.

Pull Request - State: closed - Opened by heuermh about 7 years ago

#48 - Confirm Genbank parser handles new accession formats.

Pull Request - State: closed - Opened by heuermh about 7 years ago

#47 - Confirm Genbank parser handles new accession formats

Issue - State: closed - Opened by heuermh about 7 years ago

#46 - Update maven-surefire-plugin version to 3.0.0-M1.

Pull Request - State: closed - Opened by heuermh about 7 years ago

#44 - Added getImageReverted method in ABITrace.java

Pull Request - State: open - Opened by el1jaC almost 8 years ago - 2 comments

#43 - Javadoc errors with javac 1.8 or later

Issue - State: closed - Opened by heuermh almost 8 years ago

#42 - Updating guava dependency version to 24.0-jre.

Pull Request - State: closed - Opened by heuermh almost 8 years ago

#41 - Added getImageReverted method in ABITrace.java

Pull Request - State: closed - Opened by el1jaC almost 8 years ago - 4 comments

#40 - ABITrace method getImageReverted to represent RC of trace.

Issue - State: open - Opened by el1jaC almost 8 years ago - 7 comments

#39 - ABITrace support for quality score

Pull Request - State: closed - Opened by gwaldon almost 9 years ago - 1 comment

#37 - `mvn package` fails some tests

Issue - State: closed - Opened by dariober about 9 years ago - 3 comments

#36 - FetchURL attempts to access retired NBCI LocusLink service

Issue - State: closed - Opened by heuermh over 9 years ago

#35 - Release biojava-legacy version 1.9.3

Issue - State: closed - Opened by heuermh over 9 years ago - 1 comment

#34 - Use HTTPS to access NCBI Entrez and QBLAST

Pull Request - State: closed - Opened by heuermh over 9 years ago

#33 - Fix minor style issue with variable names

Pull Request - State: closed - Opened by heuermh almost 10 years ago

#32 - Editing of ChunkedSymbolList plus tests.

Pull Request - State: closed - Opened by gwaldon almost 10 years ago - 2 comments

#31 - Deploy version 1.9.2 javadocs and update wiki

Issue - State: closed - Opened by heuermh almost 10 years ago - 3 comments

#30 - Update FASTQ I/O API examples in the cookbook documentation

Issue - State: open - Opened by heuermh almost 10 years ago - 1 comment

#29 - Style fixes and unit tests for Edit properties change

Pull Request - State: closed - Opened by heuermh about 10 years ago - 2 comments

#28 - adding Fastq.convertTo(FastqVariant) and supporting methods

Pull Request - State: closed - Opened by heuermh over 10 years ago - 3 comments

#27 - Release version 1.9.2 to Maven Central repository

Issue - State: closed - Opened by heuermh almost 11 years ago - 1 comment

#26 - Cherry-pick commits from pull request #23

Pull Request - State: closed - Opened by heuermh almost 11 years ago - 1 comment

#25 - Change BLAST URL per http://www.ncbi.nlm.nih.gov/news/05-22-2014-BLAST-U...

Pull Request - State: closed - Opened by heuermh about 11 years ago - 1 comment

#23 - GenbankFormat changes to allow reading of Ensembl Genbank files

Pull Request - State: closed - Opened by brianrepko over 11 years ago - 6 comments

#21 - Update guava dependency version to 18.0

Issue - State: closed - Opened by heuermh over 11 years ago - 2 comments

#20 - Adding static Fastq.builder() method

Pull Request - State: closed - Opened by heuermh over 11 years ago

#19 - make SubstitutionMatrix serializable

Pull Request - State: closed - Opened by heuermh over 11 years ago

#18 - adding getQuery and getSubject as gapped sequence methods to AlignmentPair

Pull Request - State: closed - Opened by heuermh over 11 years ago

#17 - update guava to version 17.0, refactor methods that accept InputSupplier...

Pull Request - State: closed - Opened by heuermh over 11 years ago

#16 - Adding KEYS file with developer code signing keys

Pull Request - State: closed - Opened by heuermh over 11 years ago

#15 - Preparation for release to Maven Central repository, version 1.9.0 release

Pull Request - State: closed - Opened by heuermh over 11 years ago

#14 - Host biojava-legacy release jars from Maven Central

Issue - State: closed - Opened by heuermh over 11 years ago - 4 comments

#13 - adding static factory method getSubstitutionMatrix(FiniteAlphabet, Buffe...

Pull Request - State: closed - Opened by heuermh over 11 years ago - 1 comment

#11 - Update maven-surefire-plugin dependency to version 2.17 and other update...

Pull Request - State: closed - Opened by heuermh almost 12 years ago

#10 - updating guava dependency version to 15.0

Pull Request - State: closed - Opened by heuermh over 12 years ago

#9 - Prepare for 1.8.4 release

Pull Request - State: closed - Opened by heuermh over 12 years ago

#8 - Changing note value to "text" type because hsqldb 2.3.0 tries to store i...

Pull Request - State: closed - Opened by rylarson over 12 years ago

#7 - Prepare for 1.8.3 release

Pull Request - State: closed - Opened by heuermh over 12 years ago

#6 - fixed a bug that caused a wrong offset when parsing SCF files

Pull Request - State: closed - Opened by brandstaetter almost 13 years ago

#5 - updating distribution management config

Pull Request - State: closed - Opened by andreasprlic almost 13 years ago

#4 - updating distribution management config

Pull Request - State: closed - Opened by andreasprlic almost 13 years ago

#3 - Update maven plugin dependency versions

Pull Request - State: closed - Opened by heuermh almost 13 years ago

#2 - Minor updates to fastq package in sequencing module

Pull Request - State: closed - Opened by heuermh almost 13 years ago

#1 - fixing possible exception when reading SCF files

Pull Request - State: closed - Opened by brandstaetter almost 13 years ago