antiSMASH 5.0.0
The antiSMASH team is happy to announce the stable release of antiSMASH 5.0.0.
antiSMASH 5.0.0 is a large-scale rewrite to migrate to Python 3, and detailed
changes are too numerous to list here. For a high-level overview, see the
[antiSMASH 5 features list](https://docs.antismash.secondarymetabolites.org/antiSMASH5features/)
or see the [antiSMASH 5 paper](http://doi.org/c568).
Detailed changes since 5.0.0rc1:
Kai Blin (18):
args: Print the correct version in the help output.
subprocessing: get rid of trailing newline in diamond version string
subprocessing: Add command to get the blastp release version
main: Print versions of the found CLI tools
subprocessing: Add function to get version of makeblastdb
subprocessing: Allow getting the muscle binary version
subprocessing: Allow getting the prodigal binary version
subprocessing: Allow getting the java binary version
subprocessing: Allow getting the meme/fimo binary versions
subprocessing: Allow getting the hmmpfam2 binary version
subprocessing: Only run hmmpfam2 in multithreading mode when the build supports it
subprocessing: Allow getting the hmmpress binary version
subprocessing: Allow getting the hmmsearch binary version
subprocessing: Allow getting the hmmscan binary version
subprocessing: check if hmmscan supports multithreading via the help output
hmmdetection: Add cluster rule for thioamide-containing NRPs
hmmdetection: Add support for tropodithietic acid like clusters
chore: Bump version to 5.0.0
Simon Shaw (58):
clusterblast: add check for outdated diamond databases
clusterblast: use a mock database for testing general CB
clusterblast: add a constant for data location instead of always regenerating
clusterblast: use a mock database for testing known CB
clusterblast: remove newly redundant case in test code
clusterblast: remove TODO by improving docstring
clusterblast: remove code made obselete by new databases
subprocessing: fix java version testing
secmet: forbid conversion of records with features outside sequence
secmet: use a more meaningful bad location message
common.gff_parser: remove unnecessary arguments
common.record_processing: remove cds uniqueness check, covered by secmet
secmet: add extra test for reverse compound locations
secmet: treat locations that are completely unordered as errors
secmet: reraise errors from location splitting as secmet input errors
secmet: forbid overlapping exons (but allow frameshifts)
common.record_processing: consider GFF reading as part of input parsing
common.record_processing: re-parallelise GFF parsing
secmet: allow reversing of reverse strand exons
secmet: add a function for all feature location validation
secmet: reraise feature conversion errors as secmet input errors
clusterblast: remove unused arguments
clusterblast: style pass
common.hmm_rule_parser: remove unused variables
html: style pass
genefunctions: style pass
secmet: avoid a pylint complaint on comparing len to zero
common.subprocessing: allow execute to function without args being parsed first
config: fix cyclic import for version information
secmet: style pass
cassis: check version of fimo/meme
antismash/test: clean up config building
nrps_pks: fix some pylint issues
chore: silence some overeager pylint issues
hmm_detection: style pass
common.subprocessing: split subprocessing into separate files
config: store executable names deterministically
secmet: remove small exons restriction
common.record_processing: convert some biopython warnings to exceptions
common.record_processing: extract the strict parsing into a separate function
common.record_processing: prevent biopython ignoring unparsable locations
secmet: simplify overlapping exons check to shared stop codons
main: update removal of region genbank files
secmet: deduplicate code
config.executables: don't store names if no path could be found
config.executables: add an alternate name for fasttree
cassis: remove print statements
secmet: change subregion 'anchor' to more generic 'label'
clusterblast: handle single core runs and file splitting
subprocessing: make threading support check for hmmpfam2 more robust
subprocessing: remove caching for hmmpfam2 help
secmet: fix protocluster cores not annotating tool
secmet: change to 1-indexing in region genbanks to match record
common.test.helpers: rework to use more thorough record stripping/regen
secmet: add regeneration for NRPS/PKS qualifier
secmet: add NRPS/PKS qualifier to biopython conversions
nrps_pks_domains: use the correct KS subtypes for CDS classification
nrps_pks_domains: fix glycopeptide NRPS prediction