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6-1-1
This is bug fix release 6.1.1. This release fixes some issues identified in antiSMASH 6.1.0: * Duplicate CDS detection had false positives in unrelated CDS features. * Some long CDS locus tags had spaces inserted when reading via biopython, causing failures on reloading antiSMASH results. Spaces are now stripped from locus tags. * Unpinned python dependencies were causing some issues for some users. These dependencies are now all pinned. * Output zip files were created with owner-only read permissions by default. This has changed to owner, group, and others having read permissions on the zip file. Some code de-duplication was also included. Detailed changes since 6.1.0: Kai Blin (2): secmet: Reduce the risk of crc32 collisions in duplicate CDS location detection main: Make sure the output zipfile has sane permissions Simon Shaw (4): secmet: remove unnecessary code for finding child CDS features for new regions secmet: handle biopython introducing spaces into locus tags chore: pin dependencies -
6-1-0
antiSMASH 6.1.0 Introduces a new visualisation for NRPS/PKS modules along with new NRPS/PKS domains. Updates reference databases for clustercompare's MIBiG comparison, and Pfam detection modules. Also includes a number of fixes and other small improvements Detailed changes since 6.0.0: Kai Blin (6): nrps_pks_domains: Also detect thiocysteine lyase domains as described in doi:10.1038/s41467-021-25798-8 secmet: Allow None for the Feature.overlaps_with() check chore: Don't create dummy CDSes with the exact same location in the modules tests secmet: ensure that we don't add two CDSes with the exact same location secmet: Fix locus tag duplicates even if the conflicting CDSes only overlap with a gene feature of the same name outputs/html: Honour output_basename in the HTML page title Simon Shaw (97): download_databases: fix database dir not propagating to prepare_data lanthipeptides: deconflict prepeptide feature name sactipeptides: deconflict prepeptide feature name thiopeptides: deconflict prepeptide feature name lassopeptides: lassopeptides: deconflict prepeptide feature name clusterblast: fix crash on sideloaded regions with no CDS chore: pin biopython version to avoid incompatibility secmet: move frameshift function to secmet.locations secmet: fix translation generation of frameshifted CDSes common.gff_parser: keep all features found in GFF inputs chore: handle deprecations in jinja2 >= 3.0 html: embed mask SVGs in CSS to avoid CORS on local files common.record_processing: catch bad qualifier warnings early pfam2go: update Pfam GO mapping common.pfamdb: make logging messages consistent download_databases: update Pfam latest to 34.0 clusterblast: adjust tests to handle newer diamond versions html: shrink javascript data size html: allow body detail divs to have scroll bars if necessary html: add structure for visualisation-only submodules html: use collapsers for Pfam/Tigrfam/GO details in sidepanel html: update antismash.js to 0.10.0 html: expand pfam drawing to cover all HMMer results html: default generic domain view to expanded mode nrps_pks_domains: include DH2 as a modification domain nrps_pks_domains: annotate subtypes on ModularDomain where possible nrps_pks_domains: add carnitine-AT domain nrps_pks_domains: add accessor for module components nrps_pks_domains: merge additional modules in split-CDS modules when relevant nrps_pks_domains: include more domains in modules when relevant nrps_pks_domains: don't register modules containing only a single domain nrps_pks_domains: add SH domains in module/double carrier protein handling nrps_pks_domains: add a public method to get CSS and abbreviations for domains nrps_pks_domains: fix ModularDomain being modified post-creation by nrps_pks nrps_pks_domains: include TIGR01720 as a special domain in modules cluster_compare: use a minimal and updatable database for integration tests nrps_pks: add candidate kind to layer nrps_pks: make result schema version public nrps_pks: use starter/final module status instead of specific domains html: add modular domain 'bubble' visualiser secmet: add members for area product category/categories hmm_detection: pass product category to created protoclusters chore: change 'will_handle()' to also take categories hmm_detection: fix linaridin category and add description html: allow fallback to rule category for CSS if no CSS for product rrefinder: use product categories to test if a cluster is a RiPP sideloader: add string functions for result types sideloader: pass full record through to result generation sideloader: require all sideloaded areas to have at least one CDS config: add an action for splitting comma separated lists in args sideloader: add options for creating arbitrary subregions around CDSes by name main: auto-import analysis modules genefinding: move from 'detection' namespace to 'support' main: automatically detect, import, and use detection modules main: split --list-plugins into sections based on detection stage main: remove unreachable returns and raises chore: handle pylint 'consider-using-with' message where possible chore: consistently use 'from ... import ...' style chore: remove unused imports and context handlers clusterblast: clean up test file read logic hmm_detection: remove code for python < 3.5 from tests hmm_detection: add missing docstrings for categories common.hmm_rule_parser: fix accidental concatenation in test strings cluster_compare: fix ineffective order scaling test html: fix variable name shadowing import name secmet: remove shadowed import in region secmet: add missing docstring to AntismashDomain subtype handling chore: style pass for misc pylint 2.10 messages chore: update pinned pylint version to 2.10.2 html,common.layers: fix circular import full_hmmer: fix missing typing in data rebuild script chore: satisfy flake8 whitespace nrps_pks_domains: remove code duplication in tests cassis: break circular dependency on config constants chore: update mypy to 0.910 chore: bump version to 6.1.0 chore: add a github action for comparing pull requests chore: use more permissive mode for linting action domain_identification: prevent cross-CDS modules forming when interrupted html: update antismash.js to 0.10.1 html: fix crash when regions contain no protoclusters html: add test for records without protoclusters nrps_pks: fix non-colinear CDS ordering when cross-CDS modules are involved nrps_pks: fix polymer formation duplicating monomers from cross-CDS modules nrps_pks: don't include chained CDS features in domain-docking count limit html: truncate cross-CDS modules in bubble view when not fully in candidate html: update antismash.js to 0.11.0 html: fix hybrid region CSS sactipeptides: remove unused genbank in tests lanthipeptides: avoid duplication of found CDS features sactipeptides: avoid duplication of found CDS features thiopeptides: avoid duplication of found CDS features lassopeptides: avoid duplication of found CDS features cluster_compare: change data sources in MIBiG DB building cluster_compare: fix MIBiG DB generation for 'Other' subclass cluster_compare: don't include post-detection gene functions in databases download_databases: update clustercompare database version -
6-0-1
This is the bugfix release 6.0.1. This release fixes three issues identified in antiSMASH 6.0.0: * The download_database script didn't propagate the database dir to the prepare_data step. * When using sideloading, subregions not containing any CDSes would crash clusterblast. * In regions containing multiple RiPP protoclusters, if two of the RiPP modules decided that a specific ORF was a potential prepeptide, this would trigger a name conflict for the newly created prepeptide annotation feature. This release also works around the newly released Biopython 1.79 changing the way WGS master record sequences are annotated and breaking our WGS master record detection. 6.0.x releases will keep using Biopython 1.78. Detailed changes: Kai Blin (1): chore: bump version to 6.0.1 Simon Shaw (7): download_databases: fix database dir not propagating to prepare_data lanthipeptides: deconflict prepeptide feature name sactipeptides: deconflict prepeptide feature name thiopeptides: deconflict prepeptide feature name lassopeptides: lassopeptides: deconflict prepeptide feature name clusterblast: fix crash on sideloaded regions with no CDS chore: pin biopython version to avoid incompatibility -
6-0-0
antiSMASH 6.0.0 The antiSMASH team is happy to announce the stable release of antiSMASH 6.0.0. antiSMASH 6.0.0 increases the number of detected BGC types to 71, adds a new cluster comparison algorithm, a TIGRFam detection module, and many other smaller changes. For details, see the [antiSMASH 6 paper](https://doi.org/10.1093/nar/gkab335). Detailed changes: Alexander Kloosterman (3): common.hmmer: allow for disabling cut-tc in searches common.pfamdb: make logging message generic rrefinder: add RREfinder module Kai Blin (48): nrps_pks_domains: Fix off-by-one errors in featute/motif translation calculations nrps/pks: Don't crash in orderfinder if there's no complete module main: More control over output filenames chore: bump antiSMASH version to 6.0.0alpha1 clusterblast: Properly detect magic value used during Docker lite image build chore: Use the most current base image for the docker dev image config: Bump version number in config file to allow for concurrent as5/6 installs common: Relax legal identifier rules to support '2OG-FeII_Oxy' as a profile name common/hmm_rule_parser: Detect all rule keywords in is_a_rule_keyword() check common/hmm_rule_parser: Add CATEGORY keyword to allow classifying protoclusters by MIBiG category hmm_detection: Ensure rule categories are valid hmm_detection: Add prodigiosin rule to pick up Serratia-style prodigiosin clusters html: Allow downloading region SVGs nrps_pks_domains: Allow downloading NRPS/PKS domain SVG html: Allow downloading Pfam domain SVGs html: Allow downloading the record overview SVGs tigrfam: Add new TIGRFam detection module html: Show PFAM and TIGR domain hits in gene details chore: update .gitignores hmm_detection: Use new alias system to simplify PKS rules hmm_detection: Add rule for non-alpha poly-amino acid (NAPAA) clusters hmm_detection: Add cluster rule for pyrrolidines hmm_detection: Rename TfuA-related to thioamitides hmm_detection: Rename 'fused' to 'guanidinotides' hmm_detection: Also try to identify clusters based on RREFinder profiles hmm_detection: LAPs can also contain an E1 type enzyme hmm_detection: TIGR03678 is the patellamide-style precursor, a cyanobactin hmm_detection: Rename 'bacteriocin' type to 'RiPP-like' hmm_detection: change LAP rule to avoid false positives in cyanobactin hmm_detection: our old 'head_to_tail' type is covered by 'sactipeptide' now hmm_detection: Add detection rule new ranthipeptide cluster type hmm_detection: Move some LAP-related profiles from RiPP-like to LAP html: Lipolanthines are sort of lanthipeptides, so colour them like that hmm_detection: detect lanthipeptide class already at cluster detection stage hmm_detection: Detect redox cofactors like PQQ and mycofactocin hmm_detection: Change glycocins to CATEGORY RiPP rrefinder: Update list of RiPP products secmet: ds-DNA is also a valid molecule type common: Give a better error message when non-JSON inputs are passed to --reuse-results hmm_detection: TIGR03793 detects proteusin precursors, move to the appropriate rule hmm_detection: Avoid false positive ranthipeptide calls on thiopeptides hmm_detection: Add detection rule for epipeptides hmm_detection: Add rule for cyclic lactone autoinducers hmm_detection: Add rule to detect spliceotide clusters hmm_detection: Allow filtering supported cluster types by category rrefinder: Dynamically get list of RiPP products from rule parser hmm_detection: Drop a dubious part of the NRPS rule for causing false positives chore: bump version to 6.0.0 Simon Shaw (86): html: add an option to start the overview in compact mode clusterblast,download_databases: update clusterblast to antiSMASH-DB v3 clusterblast: catch older formats of clusterblast database chore: pin mypy version for consistent type checking download_databases: remove unnecessary typing ignore chore: remove all obsolete or typing related unused-import ignores chore: convert all comment type hints to python 3.7 style hints common.hmmer: convert hit dict to dataclass genefinding: fix options test with no checks chore: style pass chore: upgrade pylint version common.logs: handle newer pytest changing caplog behaviour chore: handle biopython's removal of Alphabet in 1.78 and update chore: bump minimum python version to 3.7 clusterfinder: remove module and references to it secmet: remove probabilities from PfamDomains, Regions and Subregions download_databases: remove Pfam27 as a downloaded database clusterblast: fix SVG drawing for inputs with '.' accessions clusterblast: add test for docker runtime mount processing config: fix incorrect executables arg placeholder chore: update mypy to a py3.8 compatible version chore: fix implied removal of 'no cover' pragma for coverage common.hmmer: fix incorrect end coordinate adjustment common.test: add a record id option for DummyRecord common.pfamdb: add gathering cutoffs from profiles common.hmmer: filter overlapping hits by default common.hmmer: make HmmerResults regeneration consistent with ModuleResults html: remove unused and redundant cog_annotations.txt html: add Pfam visualisation secmet: change AntismashDomain to be a generic subclassable feature secmet: add passthrough for domain arg for AntismashDomain secmet: order the results of get_unique_protoclusters() secmet: add sideload variants of protoclusters and subregions secmet: exclude sideloaded detection rules from candidates html: pass a full region instance rather than parts html: make 'unknown' an actual CSS class html: handle sideloaded CDS collections differently config: add an arg action for comma separated paths sideloader: add module for importing external annotations common.hmm_rule_parser: annotate outside protoclusters if in subregions html: update antismash.js to 0.7.0 common.hmmer: remove unnecessarily specific logging secmet: handle biopython inserting spaces in long domain names secmet: remove the option to set CDS sec_met qualifier to None common.serialiser: convert result JSON before truncating existing file chore: change 'make clean' to be more generic with diamond databases clusterblast: move diamond db checks to common.subprocessing.diamond secmet: add a contains method to CDSCollection html: add per-module custom JS data exporting cluster_compare: add new cluster comparison module html: update antismash.js to 0.8.0 html: update javascript to 0.8.1 common.hmmer: fix documentation on build_hits sideloader: fix incomplete help for command line arg rrefinder: fix naming duplications for features rrefinder: fix hits duplicating in overlapping protoclusters common.hmm_rule_parser: fix an incorrect type common.hmm_rule_parser: fix incorrect behaviour with 'not' tigerfam: account for docker-mounted database dirs cluster_compare: account for docker-mounted database dirs html: update javascript to 0.8.2 subprocessing: fix broken f-string in diamond errors download_databases: update to clusterblast database with fungi common.hmm_rule_parser: fix negative score test/check common.hmm_rule_parser: make naming test more obvious when failing common.hmm_rule_parser: add ability to create and use aliases common.hmm_rule_parser: remove inferiors on overlap, not just contains common.json: add support to JS datatypes for multi-CDS modules secmet: fix sorting in multi-CDS modules secmet: add extra tests for multi-CDS modules secmet: restrict multi-CDS Modules to having matching strands secmet: add a protein location fetch per parent for modules html: update antismash.js to 0.9.0 nrps_pks_domains: detect modules involving multiple CDS features secmet: improve reporting for non-integer codon_start qualifiers common.serialiser: include summary of record areas in JSON html: silence FutureWarnings for pyScss genefinding: handle unspecified genefinding error more cleanly secmet: recognise lower-case DNA as valid record type common.record_processing: avoid crashes when inputs contain formatters sideload: improve error messages for invalid/unsuitable JSON chore: add dev wiki link to CONTRIBUTING.md chore: fix out of date minimum python version in CONTRIBUTING.md chore: remove aS5 specific numbering from Dockerfile custom_typing: include missing __iter__ prototype common.record_processing: handle bug in macOS py3.8+ pickling config -
5-2-0
This is release 5.2.0 of antiSMASH. Highlights are: * added detection for lanthidine clusters * improved detection of thioamide-NRP clusters * updates the default PFAM database to 32.0, with matching GO term update * updates the clusterblast database to the antiSMASH-DB version 3 * PKS candidate clusters with products determined by non-colinear gene ordering now record and show the order used * a new command line option `--html-start-compact`, which defaults the HTML overview to the compact view **NOTE:** As the antiSMASH-DB links have changed slightly to be more future proof, the clusterblast database format has also changed slightly to take advantage of that. It is necessary to update the clusterblast database at the same time as updating to 5.2 from previous versions. This can be done by running the command `download-databases` when antiSMASH is installed in your environment (or `antismash/download-databases.py` in the source directory). There is also a direct download of the database tarball available [here](https://dl.secondarymetabolites.org/releases/clusterblast/clusterblast_20201012.tar.xz). Detailed changes: Kai Blin (11): nrps_pks_domains: Also detect SMART PKS_PP domain as ACP main: Bump the antiSMASH version logging line to INFO level chore: Bump version to 5.2.0 common: Fix the java version detection when _JAVA_OPTIONS are set config: fix alternative fasttree executable spelling hmm_detection: Improve thioamide-NRP rules to pick up more clusters detection: Add detection rule for lanthidines chore: Pin Biopython to 1.76, as 1.77 refuses to work with still support Python 3.5 nrps_pks_domains: Fix off-by-one errors in featute/motif translation calculations nrps/pks: Don't crash in orderfinder if there's no complete module main: More control over output filenames Simon Shaw (40): secmet: fix region genbank outputs not adjusting locations in qualifiers nrps_pks_domains: allow AT and CP without KS to be complete module nrps_pks_domains: only allow condensationless modules to be complete if first in a CDS common.record_processing: include record id in error message html: remove duplicate mod-kr CSS rule secmet: handle genbank conversions introducing spaces into aSDomains *peptides: import joblib directly for future scikit-learn versions secmet: replace minimock usage with unittest lassopeptides: replace minimock usage with unittest active_site_finder: replace minimock usage with unittest t2pks: replace minimock usage with unittest nrps_pks: replace minimock usage with unittest clusterblast: replace minimock usage with unittest cassis: replace minimock usage with unittest antismash.test: remove unnecessary mocking pfam2go: replace minimock usage with unittest nrps_pks: replace minimock usage with unittest cluster_hmmer: replace minimock usage with unittest full_hmmer: replace minimock usage with unittest lanthipeptides: replace minimock usage with unittest thiopeptides: replace minimock usage with unittest antismash.test: replace minimock usage with unittest chore: remove minimock as a test dependency secmet: remove list inheritance from NRPSPKSQualifier secmet: improve error message for invalid translation table qualifiers common: only check relevant parts in RODEO's sklearn version check hmm_detection: find more transAT-PKS clusters pfam2go: update GO mapping download_databases: update to 32.0 for latest Pfam database common.record_processing: conditionally allow long record identifiers clusterfinder: fix subregions being added twice thiopeptides: fix results regeneration for extra ORFs t2pks: only use CDSs completely within the protocluster -
5-1-2
This is release 5.1.2 of antiSMASH. 5.1.2 is mainly a bugfix release, dealing with a number of issues reported since our 5.1.1 release. Highlights are: * Better error messages on invalid inputs * improved compatibility with future sklearn versions * fixes for Bioconda-related issues Detailed changes: Kai Blin (2): common: Fix the java version detection when _JAVA_OPTIONS are set chore: bump version to 5.1.2 Simon Shaw (23): common.record_processing: include record id in error message html: remove duplicate mod-kr CSS rule secmet: handle genbank conversions introducing spaces into aSDomains *peptides: import joblib directly for future scikit-learn versions secmet: replace minimock usage with unittest lassopeptides: replace minimock usage with unittest active_site_finder: replace minimock usage with unittest t2pks: replace minimock usage with unittest nrps_pks: replace minimock usage with unittest clusterblast: replace minimock usage with unittest cassis: replace minimock usage with unittest antismash.test: remove unnecessary mocking pfam2go: replace minimock usage with unittest nrps_pks: replace minimock usage with unittest cluster_hmmer: replace minimock usage with unittest full_hmmer: replace minimock usage with unittest lanthipeptides: replace minimock usage with unittest thiopeptides: replace minimock usage with unittest antismash.test: replace minimock usage with unittest chore: remove minimock as a test dependency secmet: remove list inheritance from NRPSPKSQualifier secmet: improve error message for invalid translation table qualifiers common: only check relevant parts in RODEO's sklearn version check -
5-1-1
This is the bugfix release 5.1.1 This relase fixes some corner cases in the module detection and other minor issues. Detailed changes: Kai Blin (3): nrps_pks_domains: Also detect SMART PKS_PP domain as ACP main: Bump the antiSMASH version logging line to INFO level chore: bump version to 5.1.1 Simon Shaw (3): secmet: fix region genbank outputs not adjusting locations in qualifiers nrps_pks_domains: allow AT and CP without KS to be complete module nrps_pks_domains: only allow condensationless modules to be complete if first in a CDS -
5-1-0
antiSMASH 5.1.0 Introduces NRPS/PKS modules, a new TfuA-related RiPP cluster type, and a new fungal PKS domain. The knownclusterblast database has been updated to the latest MIBiG release (2.0). Detailed changes since 5.0.0: Kai Blin (6): chore: Add config for no-response probot plugin hmm_detection: Adjust Chal_sti_synth_* profile cutoffs to cutoff values given in files detection: Add TfuA-related clusters nrps_pks_domains: Identify fungal non-reducing PKS product template (PT) domains secmet: Python 3.7 no longer escapes : chore: use os.path.realpath to fix path tests on OSX Simon Shaw (96): clusterblast: fix SVG colouring missing when hits have same accession clusterblast: don't exclude self-hits in SVGs for subclusterblast nrps_pks_domains: add a trusted cutoff for Enedyne_KS to match other KSs common.record_processing: include NRPS_PKS qualifier in stripping step common.record_processing: use secmet stripping function after conversion html: update antismash.js to 0.4.2 common.hmmer: remove broken check secmet: restrict protocluster products to same style as ruleset common.record_processing: differentiate between no records found and records too small hmm_detection: improve reuse handling of strictness option html: hide detection rule section when no rule-based clusters present secmet: always pass through a Seq to Record's inner SeqRecord html: make output less horrific for slow loading or missing CSS common.record_processing: fix loss of record annotations with --start or --end main: improve genbank meta-comment annotation common.record_processing,gff_parser: read GFF input only once for features common.record_processing: log error details when present for bad GFFs html: use correct header border colour based on variant config: allow testing error messages from arg parsing config: add an arg action to ensure paths are readable config,*: use path actions where appropriate clusterblast: fix SVGs generating with extra end anchor links nrps_pks_domains: don't create an empty HTML tab, similar to monomers/compounds html: update antismash.js to 0.4.3 __main__: change git version to use source dir, not working dir html: fix header/footer images with overridden sizes html: update antismash.js to 0.4.4 secmet: alter genefunction tool priority html: change resistance gene visualisation to a marker under the gene html: add a symbol based legend macro html: change resistance and TTA legends to use their symbols secmet: add a test for gene function qualifier conversion secmet: track child core location for candidate clusters secmet: allow sorting comparisons of features and locations secmet: prevent orphaning and inconsistent grouping of protoclusters setup.py: fix pytest version to solve coverage issues antismash.test: shift global --check-prereqs unit test to integration chore: silence deprecation warnings within pyScss during testing chore: re-silence Cython warnings silenced by numpy and unsilenced by pytest hmm_detection: log strictness level html: add hmm_detection strictness to overview page secmet: handle biopython/genbank conversions losing spaces in qualifiers secmet: handle bad codon errors in CDS translation secmet: fix outdated docstring secmet: include record ID in text for bad locations html: use a serif font for CDS names html: fix single pixel header tab underline in edge config: don't report 'does not exist' if the target is a directory secmet: fix candidate creation issue with multiple fully-contained non-hybrids chore: clean pickled classifiers and add them to ignore chore: silence mypy errors in externally provided code common.external: add a simplified pickle function for rodeo lanthipeptides: rebuild classifier in prepare_data lassopeptides: rebuild classifier in prepare_data thiopeptides: rebuild classifier in prepare_data sactipeptides: rebuild classifier in prepare_data chore: unpin scikit-learn version lassopeptides: change to standard copyright/license header common.test: bring in more helper classes from secmet common.hmmscan_refinement: allow comparisons and hashing of HMMResult secmet: add missing SubRegion __slots__ secmet: fix cdscollection typing issue secmet: make from_biopython conversion interface consistent secmet: make Record's adding of biopython features consistent secmet: simplify postponed feature logic secmet: add support for explicit int conversion in parse_format secmet: support subtypes in NRPS/PKS domains secmet: enforce Domains having locus tag and protein location html,nrps_pks_domains: move styling and abbreviating domains from javascript to CSS/python common.json: add abbreviations for Aminotran domains common.json: don't colour ACPS domains html: make heights of single feature domain SVGs and all feature SVGs match nrps_pks: remove unnecessary END from SMILES set nrps_pks: fix pks smiles replacement being overeager nrps_pks_domains: remove duplicate add_to_record secmet: add Module feature nrps_pks_domains,nrps_pks: add module identification and visualisation nrps_pks_domains: add PP-binding as a fallback for *CP profiles nrps_pks_domains: show a question mark on HTML modules if unknown substrate nrps_pks: use lower case for smiles to reduce duplication nrps_pks: assign smiles even if only one monomer is present nrps_pks: update SMILES values and format html: reduce size of serif CDS names in NRPS domains tab nrps_pks: display Stachelhaus codes with serif font nrps_pks_domains: fix error message using incorrect count nrps_pks_domains: move DummyHMMResult to common test helpers nrps_pks_domains: consolidate matching of PKS_KS domains to their subtypes nrps_pks: fix error with X monomer substitutions secmet: fix inconsistent sorting in interleaved candidate construction nrps_pks: add SMILES parser/reconstructor nrps_pks: add methylation logic nrps_pks: refactor SMILES generation common.hmmer: catch missing hmmpress before attempts to use it clusterblast: catch missing diamond before attempting to use it antismash.test: ensure check-prereqs fails gracefully chore: bump version to 5.1.0 Zach Charlop-Powers(2): Remove Unused Args from Function Docs Use os.makedirs instead of os.mkdir -
5-0-0
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 -