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  • Hooft001-master-patch-88968
  • ipresto_refactor
  • master default protected
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Created with Raphaël 2.2.015Feb18Aug10212May317Mar1410221Jan24Nov22191211106Oct30Mar257Feb331Jan272423918Dec171611106325Nov128628Oct2524232127Sep20428Aug21201925Jul24232221191816121110985432128Jun27262423212018171312117654329May2827242221171310976326Apr252423222119181716151211109843230Mar29272625Merge branch 'Hooft001-master-patch-88968' into 'master'mastermasterUpdate README.mdHooft001-master…Hooft001-master-patch-88968Update output messageUpdate usageadd back --use_domtabs to circumvent lack of hmmer in test envsuccesfully test querying with presto-top and add existing lda_model to test_subclusters to do soUpdate Readme according to refactoring.Merge branch 'ipresto_refactor' into 'master'Merge branch 'ipresto_refactor' of https://git.wur.nl/bioinformatics/iPRESTO into ipresto_refactoripresto_refactoripresto_refactorimprove documentationprevent overriding gbks_path_filediscover stats about annotated subcluster motifsupdates to training multiple lda modelsCorrect typoAdd use_domtabs to all ipresto.py tests so hmmscan is not attempted in test environmentAdd domtables for test bgcs so hmmscan doesnt have to be run in test envSpecify gensim version to 3.8.3Replace build stage with before_script in .gitlab-ci.yml fileAdd valid python image in .gitlab-ci.yml fileUpdate .gitlab-ci.yml fileInit basic .gitlab-ci.yml fileAllow testing for alpha and beta values of lda modelTry out different parametersUnify remove_infr_doms functionsturn off sorting topics in lda vis so topic numbers correspondadd outfolder parameter to run_lda_from_existing to reflect changes in previous commitsave corpusremove bgcs_and_modules output, add modules_w_info when querying and making new model so wirte_bgc_mod_fasta gets correct input alwayscorrect to use --visualise_subclusters properly - if statement was wrong way aroundlintingadd step 5. visualise subclusters, add verbose to arrowerkeep plots from crashing when there are no matches + lintinginclude presto_toplintinglinting, moving presto_stat functionality to ipresto.py and query_statistical_modules.pytest subclusters to test the --stat_subclusters flaglintinginclude running PRESTO-STAT for predetermined subclusters (to use with --stat_subclusters) + testsadd prints for general steps, lintingtemporarily remove CI pipeline while runners are not set up