Release 1.9.0

Release 1.9.0 supports some performance improvements, correcting several bugs, AI code based cleanup and a dependency on a custom branch of trinity, PASA, and EVM which have some reimplementation speedup. BUSCO data files are now associated with a github release link rather than osf.io for more reliable download.

Some OSX based bug fixes for releases and conda are applied to upstream tools. This version is tagged and release for general use and any associated followup performance testing will be addressed in a 1.9.1 release.

The general best practice is running from container images attached to this github https://github.com/nextgenusfs/funannotate/pkgs/container/funannotate

An associated nextflow pipeline also supports automation of multiple genomes and rnaseq incorporation from public SRA retrieval or local datasets https://github.com/stajichlab/nf_funannotate1

What's Changed

• update MEROPS release filename is now 'meropsscan.lib' per issue #1054 by @hyphaltip in #1057
• Fix the file name for masking in the tutorial by @tayabsoomro in #1116
• Fix syntax errors in setupDB.py download function by @hyphaltip with @Copilot in #1142
• Remove unreachable socket.error exception handler by @hyphaltip with @Copilot in #1143
• fix bug #1138 by replacing how url requests are made by @hyphaltip in #1141
• remove use of pkg_version which is deprecated, bug #1139 by @hyphaltip in #1140
• add packaging as a required module tho should be part of python distro by @hyphaltip in #1144
• change to use computed EVM path to script variable by @hyphaltip in #1146
• Bugfix1148 db canurl by @hyphaltip in #1150
• fix dbCAN URL to new server address by @hyphaltip in #1157
• make these change from master branched instead for bug #1160 by @hyphaltip in #1162
• Add translationtable support by @hyphaltip in #1158
• Eggnog geneprod issue by @hyphaltip in #1163
• add Gzip support for .xml files by @hyphaltip in #1164
• Stoptrain after trinity by @hyphaltip in #1165
• Auto skip genemark by @hyphaltip in #1166
• Auto skip genemark by @hyphaltip in #1168
• Wrap Augustus rerun extraction in timeout-safe error handling by @hyphaltip in #1170
• fallback to running BUSCO if too few transcripts by @hyphaltip in #1172
• Fix two deadlocks in the BUSCO step that hang funannotate predict by @atiweb in #1173
• fix update step when importing from gbk file by @hyphaltip in #1174
• check: flag an incompatible EvidenceModeler (EVM 2.x) up front by @atiweb in #1177
• Keep the execute bit on bundled aux_scripts after install (#1129) by @atiweb in #1176
• Fix setup crash when a database's metadata record is missing (#1171) by @atiweb in #1175
• Fix/trinity butterfly cpu pool by @hyphaltip in #1182
• fix: correct operator-precedence bug in bamthreads calculation by @hyphaltip in #1181
• fix: use full args.cpus for Trinity-GG Butterfly assembly pool by @hyphaltip in #1180
• Modernize GitHub Actions workflows for Node 20 deprecation and release-tag propagation by @hyphaltip with @Copilot in #1167
• Remove extra backticks by @peterjc in #1183
• Funannotate from BioConda currently works with Python 3.11 too by @peterjc in #1185
• Fix Dockerfile conda env: remove invalid cargo and perl-perl4-corelibs packages by @hyphaltip with @Copilot in #1188
• Split Docker conda resolution into staged solves and harden failure visibility in extra install steps by @hyphaltip with @Copilot in #1189
• Align Docker PASA checks with installed PASAHOME layout by @hyphaltip with @Copilot in #1194
• 1.9.0 test release by @hyphaltip in #1195
• Fix bugs found in library.py code review by @hyphaltip in #1192
• upgrade to glibc >= 2.39 via setting trixie as debian build by @hyphaltip in #1197
• Fix sign job failure in container publish workflow by handling multiline tag outputs safely by @hyphaltip with @Copilot in #1198
• ci: fix sign job syntax error and update actions to Node 24 by @hyphaltip with @Copilot in #1200
• Fix Dockerfile2 base image resolution in GitHub Actions build by @hyphaltip with @Copilot in #1201
• ci: sign funannotate container images by digest instead of tag by @hyphaltip with @Copilot in #1203
• Remove defunct singularity-deploy workflow by @hyphaltip with @Copilot in #1204
• Setting up container retention policy for cleanup by @hyphaltip with @Copilot in #1205
• Add DeepTMHMM transmembrane parsing with test coverage by @hyphaltip in #1206
• train.py: truncate PASA MySQL database name when it exceeds 64 bytes by @hyphaltip in #1208
• Bug pasa mysql dbname toolong by @hyphaltip in #1209
• Fix minimap2 SAM->GFF3 conversion: coordinates from CIGAR (bam2gff3, bam2ExonsHints) by @hyphaltip in #1210
• Mirror BUSCO odb9 lineage tarballs to a GitHub release by @hyphaltip in #1211
• setup: fix HTTP 308 in setup -u; mirror repeats/outgroups to db-mirror release by @hyphaltip in #1214
• [1.9] setup: fix HTTP 308 in setup -u; mirror repeats/outgroups to db-mirror release by @hyphaltip in #1215
• Fix #1179, #1212, #1207, #1196, #1213 by @hyphaltip in #1216
• [1.9] Fix #1212, #1207, #1196, #1213 by @hyphaltip in #1217
• Merge master into release/1.9 by @hyphaltip in #1218
• release: version tags must match version.py; fix publish_release.yml by @hyphaltip in #1220
• ci: run release workflows only for v* tags by @hyphaltip in #1219
• Merge master into release/1.9 (#1219) by @hyphaltip in #1221
• predict: always set AUGUSTUS_BASE (crash with renamed Augustus config dir) by @hyphaltip in #1222
• annotate: set --table default for --genbank/--gff input by @hyphaltip in #1223
• install_scripts: pin PASA v2.6.1-rc.4 and Trinity v2.16.2_rust; drop the Trinity macOS workaround by @hyphaltip in #1227

New Contributors

• @tayabsoomro made their first contribution in #1116
• @atiweb made their first contribution in #1173
• @peterjc made their first contribution in #1183

Full Changelog: v1.8.17...v1.9.0