Funannotate

Bug fix release.

- fix FASTA splitter in iprscan local 83ceee5e4119b296aa6c2c33e796747d592dea54
- pin docker and pip installs to biopython<1.80; so we try to avoid any of the other deprecated or breaking code
- update to support EVM v1 or v2; back-port training data from funannotate2 (for testing)
- run signalp6 if in PATH
- fix pandas compatibility >v2
- add config-window parameter to protein2genome script

Bug fix release

- Trying hard to support `augustus v3.5`
- fix sorting by length 896
- update dbCAN Cazyme filtering 890
- fixes for parsing eggnog mapper 868 892
- signalp6 fixes 822
- and many others

Bug fix release

- fix to internal BUSCO code to support Augustus v3.4 742 IanDMedeiros
- several fixes to `funannotate update` 727 740
- several patches to Docker build

Bug fix release

- support for signalp v6 parsing 650 716
- improve protein2genome performance 652 654
- add `--tmpdir` options to most scripts (defaults to `/tmp`), ie use if have access to SSD to improve speed
- upgrade `eggnog-mapper` to newer version, use in memory if enough is available to improve speed
- fix version check 655
- fix for abnormal contig identifiers 672
- fix for EVM contig memory parsing 646
- add `-m,--mito-pass-thru` to `funannotate annotate` to add back mitochondrial genome, mitochondrial contigs should be removed prior to running funannotate as uses different genetic code
- antismash6 support 692
- update download urls to https from ftp
- fix for EVM if last line of GFF3 is blank 709
- simplify runSuprocess functions 707 710 mglubber
- move temporary files for check for soft masking to output folder 722
- conda augustus is apparently broken, fix in docker722 724, so need to install augustus a different way (ie apt-get on Debian)
- add missing help menu options 714
- fix for `funannotate update` compare annotations function 727
- add `--ml_model` to `funannotate compare` to control ML model selection in `iqtree`, default is to run modelfinder which is very slow.

* fix for EvidenceModeler partitioning -- on rare cases genes/contigs were not getting partitioned correctly
* fix logic for PASA training of glimmer/snap 591
* fix logic for pre-trained datasets in `funannotate predict` 597
* re-organize tbl2asn and provide single threaded backup if failure 599 and fix log error 621
* remove perl script generating AGP file --> now python. which removes bioperl as dependency 617
* fix cds-transcripts coordinates (not used for any other processing) but on partial transcripts they were incorrect 614
* fix bug in EVM filtering if no genes to remove 620
* update eggnog parser to support versions >2.1.2 566
* fix tmpdir error in `funannotate clean` 594
* python2 is no longer supported.

Bug fix release
* bug fix for eggnog mapper v2 parsing, occasionally some records have more than 1 OG in the "best_OG" field -- this is probably a bug in emapper.py, but funannotate will now ignore those entries as there is no way to tell which is actually the best OG.
* make fasta2agp accept more IUPAC characters 532
* fix for diamond >v2.0.8 (yet another change in the database info format resulted in error).
* remove support for python 2