Breaking changes
The PdbParser
no longer accepts a strictMode
boolean parameter. The parser is always robust and effectively interprets the provided data.
What's Changed
- build: bump nexus-staging-maven-plugin from 1.6.7 to 1.6.13 by @dependabot in #7
- build: bump slf4j-api from 1.7.36 to 2.0.0 by @dependabot in #8
- build: bump sortpom-maven-plugin from 2.12.0 to 3.2.0 by @dependabot in #9
- build: bump jackson-databind from 2.13.2 to 2.13.3 by @dependabot in #10
- build: bump maven-gpg-plugin from 1.5 to 3.0.1 by @dependabot in #15
- build: bump maven-source-plugin from 3.2.0 to 3.2.1 by @dependabot in #14
- build: bump jackson-annotations from 2.13.2 to 2.13.3 by @dependabot in #16
- build: bump value from 2.9.0 to 2.9.1 by @dependabot in #13
- build: bump versions-maven-plugin from 2.8.1 to 2.11.0 by @dependabot in #12
- feat: replace BioJava dependency by @tzok in #17
- build: bump maven-compiler-plugin from 3.8.1 to 3.10.1 by @dependabot in #24
- build: bump maven-dependency-plugin from 3.1.2 to 3.3.0 by @dependabot in #25
- build: bump maven-javadoc-plugin from 3.2.0 to 3.4.1 by @dependabot in #23
- build: bump actions/checkout from 2 to 3 by @dependabot in #22
- build: bump actions/setup-java from 1 to 3 by @dependabot in #20
- build: bump logback-classic from 1.2.11 to 1.4.0 by @dependabot in #21
- build: bump jackson-annotations from 2.13.3 to 2.13.4 by @dependabot in #28
- build: bump jackson-databind from 2.13.3 to 2.13.4 by @dependabot in #27
- build: bump value from 2.9.1 to 2.9.2 by @dependabot in #30
- build: bump versions-maven-plugin from 2.11.0 to 2.12.0 by @dependabot in #29
- feat: add spotless plugin by @tzok in #31
- feat: make bpseq class more robust by @tzok in #32
- Fix git history by @tzok in #34
- build: bump logback-classic from 1.4.0 to 1.4.1 by @dependabot in #36
- build: bump batik-svggen from 1.14 to 1.15 by @dependabot in #39
- build: bump batik-codec from 1.14 to 1.15 by @dependabot in #38
- build: bump spotless-maven-plugin from 2.25.0 to 2.27.0 by @dependabot in #40
- build: bump slf4j-api from 2.0.0 to 2.0.2 by @dependabot in #41
- build: bump batik-anim from 1.14 to 1.15 by @dependabot in #42
- build: bump batik-transcoder from 1.14 to 1.15 by @dependabot in #43
- build: bump batik-awt-util from 1.14 to 1.15 by @dependabot in #44
- build: bump batik-util from 1.14 to 1.15 by @dependabot in #45
- build: bump batik-bridge from 1.14 to 1.15 by @dependabot in #46
- build: bump batik-gvt from 1.14 to 1.15 by @dependabot in #47
- feat: remove isolated base pairs from dot-bracket by @tzok in #48
- fix: usage of modified residues in base pair parsing by @tzok in #49
- feat: release 3.1.1, remove isolated base pairs from dot-bracket (#48), fix usage of modified residues in base pair parsing (#49) by @tzok in #50
- build: bump jackson-databind from 2.13.4 to 2.13.4.1 by @dependabot in #58
- release: 3.1.2 by @tzok in #62
- release: 3.1.3 by @tzok in #64
- release: 3.1.4 by @tzok in #85
- release: 3.1.5 by @tzok in #94
- release: 3.1.6 by @tzok in #102
- release: 3.1.7 by @tzok in #103
- release: 3.1.8 by @tzok in #106
- release: 3.1.9 by @tzok in #115
- build: bump spotless-maven-plugin from 2.35.0 to 2.36.0 by @dependabot in #116
- build: bump jackson-databind from 2.14.2 to 2.15.0 by @dependabot in #118
- build: bump jackson-annotations from 2.14.2 to 2.15.0 by @dependabot in #117
- build: bump logback-classic from 1.4.6 to 1.4.7 by @dependabot in #119
- build: bump maven-gpg-plugin from 3.0.1 to 3.1.0 by @dependabot in #120
- build: bump commons-io from 2.11.0 to 2.12.0 by @dependabot in #121
- build: bump jackson-databind from 2.15.0 to 2.15.1 by @dependabot in #122
- build: bump ciftools-java from 5.0.0 to 5.0.1 by @dependabot in #124
- build: bump spotless-maven-plugin from 2.36.0 to 2.37.0 by @dependabot in #126
- build: bump jackson-annotations from 2.15.0 to 2.15.2 by @dependabot in #128
- build: bump jackson-databind from 2.15.1 to 2.15.2 by @dependabot in #129
- build: bump commons-io from 2.12.0 to 2.13.0 by @dependabot in #130
- build: bump logback-classic from 1.4.7 to 1.4.8 by @dependabot in #131
- build: bump com.diffplug.spotless:spotless-maven-plugin from 2.37.0 to 2.38.0 by @dependabot in #132
- build: bump org.apache.commons:commons-lang3 from 3.12.0 to 3.13.0 by @dependabot in #133
- build: bump com.github.ekryd.sortpom:sortpom-maven-plugin from 3.2.1 to 3.3.0 by @dependabot in #134
- build: bump ch.qos.logback:logback-classic from 1.4.8 to 1.4.9 by @dependabot in #135
- build: bump ch.qos.logback:logback-classic from 1.4.9 to 1.4.11 by @dependabot in #136
- build: bump org.apache.xmlgraphics:batik-bridge from 1.16 to 1.17 by @dependabot in #137
- build: bump org.apache.xmlgraphics:batik-transcoder from 1.16 to 1.17 by @dependabot in #138
- build: bump org.apache.xmlgraphics:batik-anim from 1.16 to 1.17 by @dependabot in #140
- build: bump org.apache.xmlgraphics:batik-awt-util from 1.16 to 1.17 by @dependabot in #139
- build: bump org.apache.xmlgraphics:batik-gvt from 1.16 to 1.17 by @dependabot in #141
- build: bump org.apache.xmlgraphics:batik-svggen from 1.16 to 1.17 by @dependabot in #144
- build: bump org.apache.xmlgraphics:fop from 2.8 to 2.9 by @dependabot in #142
- build: bump org.apache.xmlgraphics:batik-util from 1.16 to 1.17 by @dependabot in #146
- build: bump com.diffplug.spotless:spotless-maven-plugin from 2.38.0 to 2.39.0 by @dependabot in #147
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.5.0 to 3.6.0 by @dependabot in #148
- build: bump org.slf4j:slf4j-api from 2.0.7 to 2.0.9 by @dependabot in #149
- build: bump commons-io:commons-io from 2.13.0 to 2.14.0 by @dependabot in #150
- build: bump com.diffplug.spotless:spotless-maven-plugin from 2.39.0 to 2.40.0 by @dependabot in #151
- build: bump org.rcsb:ciftools-java from 5.0.1 to 5.0.2 by @dependabot in #152
- build: bump org.immutables:value from 2.9.3 to 2.10.0 by @dependabot in #153
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.15.2 to 2.15.3 by @dependabot in #155
- build: bump actions/checkout from 3 to 4 by @dependabot in #145
- build: bump org.apache.xmlgraphics:batik-codec from 1.16 to 1.17 by @dependabot in #143
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.15.2 to 2.15.3 by @dependabot in #154
- build: bump org.apache.maven.plugins:maven-dependency-plugin from 3.5.0 to 3.6.1 by @dependabot in #156
- build: bump maven-source-plugin from 3.2.1 to 3.3.0 by @dependabot in #123
- build: bump commons-io:commons-io from 2.14.0 to 2.15.0 by @dependabot in #157
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.6.0 to 3.6.2 by @dependabot in #158
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.15.3 to 2.16.0 by @dependabot in #159
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.15.3 to 2.16.0 by @dependabot in #160
- build: bump org.apache.commons:commons-lang3 from 3.13.0 to 3.14.0 by @dependabot in #162
- build: bump com.diffplug.spotless:spotless-maven-plugin from 2.40.0 to 2.41.0 by @dependabot in #161
- build: bump ch.qos.logback:logback-classic from 1.4.11 to 1.4.12 by @dependabot in #163
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.6.2 to 3.6.3 by @dependabot in #166
- build: bump ch.qos.logback:logback-classic from 1.4.12 to 1.4.14 by @dependabot in #165
- build: bump com.diffplug.spotless:spotless-maven-plugin from 2.41.0 to 2.41.1 by @dependabot in #168
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.16.0 to 2.16.1 by @dependabot in #171
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.16.0 to 2.16.1 by @dependabot in #169
- build: bump org.apache.maven.plugins:maven-compiler-plugin from 3.11.0 to 3.12.1 by @dependabot in #170
- build: bump org.slf4j:slf4j-api from 2.0.9 to 2.0.10 by @dependabot in #172
- build: bump org.apache.commons:commons-exec from 1.3 to 1.4.0 by @dependabot in #173
- build: bump org.slf4j:slf4j-api from 2.0.10 to 2.0.11 by @dependabot in #174
- build: bump com.diffplug.spotless:spotless-maven-plugin from 2.41.1 to 2.42.0 by @dependabot in #175
- build: bump com.diffplug.spotless:spotless-maven-plugin from 2.42.0 to 2.43.0 by @dependabot in #176
- build: bump commons-io:commons-io from 2.15.0 to 2.15.1 by @dependabot in #167
- build: bump actions/setup-java from 3 to 4 by @dependabot in #164
- build: bump org.slf4j:slf4j-api from 2.0.11 to 2.0.12 by @dependabot in #177
- build: bump org.immutables:value from 2.10.0 to 2.10.1 by @dependabot in #179
- build: bump ch.qos.logback:logback-classic from 1.4.14 to 1.5.0 by @dependabot in #178
- build: bump com.github.ekryd.sortpom:sortpom-maven-plugin from 3.3.0 to 3.4.0 by @dependabot in #180
- build: bump ch.qos.logback:logback-classic from 1.5.0 to 1.5.2 by @dependabot in #181
- build: bump ch.qos.logback:logback-classic from 1.5.2 to 1.5.3 by @dependabot in #182
- build: bump com.github.ekryd.sortpom:sortpom-maven-plugin from 3.4.0 to 3.4.1 by @dependabot in #185
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.16.1 to 2.16.2 by @dependabot in #184
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.16.1 to 2.17.0 by @dependabot in #187
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.16.2 to 2.17.0 by @dependabot in #188
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.1.0 to 3.2.0 by @dependabot in #186
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.2.0 to 3.2.1 by @dependabot in #189
- build: bump org.apache.maven.plugins:maven-compiler-plugin from 3.12.1 to 3.13.0 by @dependabot in #191
- build: bump commons-io:commons-io from 2.15.1 to 2.16.0 by @dependabot in #193
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.2.1 to 3.2.2 by @dependabot in #194
- build: bump org.apache.maven.plugins:maven-source-plugin from 3.3.0 to 3.3.1 by @dependabot in #195
- build: bump commons-io:commons-io from 2.16.0 to 2.16.1 by @dependabot in #197
- build: bump ch.qos.logback:logback-classic from 1.5.3 to 1.5.5 by @dependabot in #196
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.2.2 to 3.2.3 by @dependabot in #199
- build: bump org.slf4j:slf4j-api from 2.0.12 to 2.0.13 by @dependabot in #198
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.2.3 to 3.2.4 by @dependabot in #201
- build: bump ch.qos.logback:logback-classic from 1.5.5 to 1.5.6 by @dependabot in #200
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.17.0 to 2.17.1 by @dependabot in #203
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.17.0 to 2.17.1 by @dependabot in #202
- feat: make cif parser more robust by @tzok in #204
- build: bump dependabot/fetch-metadata from 1 to 2 by @dependabot in #192
- build: bump org.rcsb:ciftools-java from 5.0.2 to 6.0.0 by @dependabot in #190
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.6.3 to 3.7.0 by @dependabot in #206
- build: bump org.sonatype.plugins:nexus-staging-maven-plugin from 1.6.13 to 1.7.0 by @dependabot in #207
- build: bump org.apache.maven.plugins:maven-dependency-plugin from 3.6.1 to 3.7.0 by @dependabot in #208
- build: bump org.apache.maven.plugins:maven-dependency-plugin from 3.7.0 to 3.7.1 by @dependabot in #209
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.17.1 to 2.17.2 by @dependabot in #210
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.17.1 to 2.17.2 by @dependabot in #211
- build: bump org.apache.commons:commons-lang3 from 3.14.0 to 3.15.0 by @dependabot in #212
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.7.0 to 3.8.0 by @dependabot in #213
- build: bump org.slf4j:slf4j-api from 2.0.13 to 2.0.16 by @dependabot in #216
- build: bump org.apache.commons:commons-lang3 from 3.15.0 to 3.16.0 by @dependabot in #215
- build: bump ch.qos.logback:logback-classic from 1.5.6 to 1.5.7 by @dependabot in #217
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.2.4 to 3.2.5 by @dependabot in #218
- build: bump org.apache.maven.plugins:maven-dependency-plugin from 3.7.1 to 3.8.0 by @dependabot in #219
- build: bump org.apache.commons:commons-lang3 from 3.16.0 to 3.17.0 by @dependabot in #220
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.8.0 to 3.10.0 by @dependabot in #221
- build: bump ch.qos.logback:logback-classic from 1.5.7 to 1.5.8 by @dependabot in #222
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.2.5 to 3.2.6 by @dependabot in #223
- build: bump commons-io:commons-io from 2.16.1 to 2.17.0 by @dependabot in #224
- build: bump com.fasterxml.jackson.core:jackson-annotations from 2.17.2 to 2.18.0 by @dependabot in #226
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.17.2 to 2.18.0 by @dependabot in #225
- build: bump org.apache.maven.plugins:maven-gpg-plugin from 3.2.6 to 3.2.7 by @dependabot in #227
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.10.0 to 3.10.1 by @dependabot in #228
- build: bump org.apache.xmlgraphics:batik-bridge from 1.17 to 1.18 by @dependabot in #230
- build: bump org.apache.xmlgraphics:batik-util from 1.17 to 1.18 by @dependabot in #231
- build: bump org.apache.xmlgraphics:fop from 2.9 to 2.10 by @dependabot in #229
- build: bump org.apache.xmlgraphics:batik-awt-util from 1.17 to 1.18 by @dependabot in #233
- build: bump org.apache.xmlgraphics:batik-codec from 1.17 to 1.18 by @dependabot in #232
- build: bump org.apache.xmlgraphics:batik-gvt from 1.17 to 1.18 by @dependabot in #235
- build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.10.1 to 3.11.1 by @dependabot in #237
- build: bump com.fasterxml.jackson.core:jackson-databind from 2.18.0 to 2.18.1 by @dependabot in #238
- feat: make all immutables serializable by @tzok in #239
- build: bump ch.qos.logback:logback-classic from 1.5.8 to 1.5.12 by @dependabot in #240
- feat: make PDB parser more robust by @tzok in #241
Full Changelog: 3.1.0...3.2.0