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@tzok tzok released this 22 Nov 10:03
· 12 commits to master since this release
5af729d

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