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pytest example project github

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pytest example project github

december 22, 2020

galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,342 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,403 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,372 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. The advice and the existing code on github etc follows extremely different conventions. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,327 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. Learn more. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,403 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,330 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,353 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. test.py::test_will_skip SKIPPED In this example, the SKIPPED outcome is used. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,355 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,330 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,401 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. Skipping... galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,040 VisualizationsRegistry, loaded plugin: trackster, galaxy.visualization.plugins.config_parser INFO 2018-08-01 17:14:48,040 template syntax is deprecated: use entry_point instead, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,040 VisualizationsRegistry, loaded plugin: unipept, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,041 VisualizationsRegistry, loaded plugin: venn. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,357 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. Instantly share code, notes, and snippets. galaxy.tools.data DEBUG 2018-08-01 17:14:46,873 Loaded 4 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bbc5/dbkeys.loc' for '__dbkeys__' galaxy.tools.data DEBUG 2018-08-01 17:14:46,873 Loading another instance of data table '__dbkeys__' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,654 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. Copyright Holger Krekel and others, 2004-2020. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,348 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. Please use the GitHub issue tracker to submit bugs or request features. The com.automationpanda.example.calc_funcmodule contains basic math functions. All instructions and code will be provided in the chapters. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,399 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. pytest example. I have arranged an example that works here. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,352 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. Multiprocessing test execution. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,437 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,374 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. You can vote up the examples you like or vote down the ones you don't like. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,365 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,365 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. The pytest framework makes it easy to write small tests, yet scales to support complex functional testing for applications and libraries.. An example of a simple test: # content of test_sample.py def inc (x): return x + 1 def test_answer (): assert inc(3) == 5 galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,658 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. ... Add a requirements.txt file to specify your project requirements. In the course chapters, you will create a new Python project and progressively add new tests to it. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,393 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,338 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,400 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. Test functions are preferable to test classes when testing functions without side effects. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,372 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. . galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,368 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,329 Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,334 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,366 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,333 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. py . set up wemake-python-styleguide GitHub Actions workflow that checks if your code is aligned with PEP 8, run unit tests and report its’ coverage with Codecov. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,352 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:46,450 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:46,450 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2018-08-01 17:14:46,450 Could not find tool data tool-data/perm_base_index.loc, reading sample. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,382 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.tools.data_manager.manager DEBUG 2018-08-01 17:14:47,621 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/fetch_genome_all_fasta_dbkeys/0.0.1. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,331 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,369 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,354 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,659 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. python path pytest. galaxy.tools.data DEBUG 2018-08-01 17:14:46,881 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/f537d3e00eb8/rnastar_index2.loc' for 'rnastar_index2' galaxy.tools.data DEBUG 2018-08-01 17:14:46,881 Loaded tool data table 'rnastar_index2' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,882 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/busco/382a4c19007f/busco.loc' for 'busco' galaxy.tools.data DEBUG 2018-08-01 17:14:46,882 Loading another instance of data table 'busco' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.tools.data DEBUG 2018-08-01 17:14:46,452 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,452 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2018-08-01 17:14:46,452 Could not find tool data tool-data/mosaik_index.loc, reading sample. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,335 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,393 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. GitHub - certbot/certbot: Certbot is EFF's tool to … Certbot is EFF's tool to obtain certs from Let's Encrypt and (optionally) auto-enable HTTPS on your server. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,352 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. If nothing happens, download the GitHub extension for Visual Studio and try again. GitHub is where people build software. There is also an example in pytest doc with a metafunc hook.. galaxy.tools.data DEBUG 2018-08-01 17:14:46,872 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/2445d53549ba/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:46,872 Loaded 3 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bbc5/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:46,873 Attempted to add fields (['saccer10', 'saccer10', 'saccer10', '/Users/mvandenb/src/galaxy/tool-data/saccer10/seq/saccer10.fa']) to data table 'all_fasta', but this entry already exists and allow_duplicates is False. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,399 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,649 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,376 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:46,875 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc' for 'sam_fa_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,875 Loading another instance of data table 'sam_fa_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. It is the platform of choice for individuals and companies that want to make one-time or galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,331 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. Each article in the guide corresponds to a set of commits in the GitHub repository: View changes; Download code; Unit testing with pytest. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,367 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,371 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,342 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,355 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,349 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:46,885 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/9946bc39c834/lastz_seqs.loc' for 'lastz_seqs' galaxy.tools.data DEBUG 2018-08-01 17:14:46,885 Loading another instance of data table 'lastz_seqs' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. This should only ever happen when running tests. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,639 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,393 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. What Makes pytest So Useful?. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,339 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,642 Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,366 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,389 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. maintenance for the open source dependencies you use to build your applications. The top layer for pytest-bdd tests is the set of Gherkin feature files. Unit tests, as the name says, verify the functionality of a unit of code, such as a single function or class. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,645 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,407 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,335 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. . galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,341 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,406 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,637 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,345 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,327 Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:47,289 Loaded 1 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/46066df8813d/bwa_mem_index.loc' for 'bwa_mem_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:47,290 Loading another instance of data table 'bwa_mem_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. GitHub Gist: instantly share code, notes, and snippets. Enable Pytest for your project galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,356 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,327 Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,326 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,335 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,341 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.queue_worker INFO 2018-08-01 17:14:45,390 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpbs3qyq6z/tmpcq_n8vcs/tmp3k9gq2zv/database/galaxy.sqlite, galaxy.app DEBUG 2018-08-01 17:14:45,428 Using "galaxy.ini" config file: config/galaxy.yml.sample. . galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,404 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. In this tutorial, we'll learn how to automatically run your Python unit tests using GitHub Actions. . PYTEST YES, LET'S GO! galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,354 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,347 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,408 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry. Tutorial Chapters. Any step definition can be used by any feature file within the same project. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,336 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,365 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. Introduction. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,352 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. poetry add --dev pytest pytest-cov pytest-django pytest-xdist pytest is a powerful testing framework for Python. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,399 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. scales to support complex functional testing for applications and libraries. galaxy.tools.data DEBUG 2018-08-01 17:14:46,873 Attempted to add fields (['saccer11', 'saccer11', 'saccer11', '/Users/mvandenb/src/tool-data/saccer11/seq/saccer11.fa']) to data table 'all_fasta', but this entry already exists and allow_duplicates is False. The following example demonstrates a test that fails, while it is associated with an open GitHub issue. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,335 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. If you don’t have it create one 😉. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,409 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. For more information on GitHub Apps, please visit GitHub’s guide at Building GitHub Apps. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,328 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.tours INFO 2018-08-01 17:14:48,076 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2018-08-01 17:14:48,088 Loaded tour 'core.scratchbook' galaxy.tours INFO 2018-08-01 17:14:48,112 Loaded tour 'core.history' galaxy.jobs.manager DEBUG 2018-08-01 17:14:48,126 Initializing job handler, galaxy.jobs INFO 2018-08-01 17:14:48,126 Handler 'main' will load all configured runner plugins, galaxy.jobs.runners.state_handler_factory DEBUG 2018-08-01 17:14:48,128 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit, galaxy.jobs.runners DEBUG 2018-08-01 17:14:48,128 Starting 4 LocalRunner workers. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,353 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:46,453 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' galaxy.tools.data DEBUG 2018-08-01 17:14:46,453 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data ERROR 2018-08-01 17:14:46,864 Error loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt": a bytes-like object is required, not 'str' galaxy.tools.data DEBUG 2018-08-01 17:14:46,864 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data DEBUG 2018-08-01 17:14:46,865 Loaded 1 lines from 'tool-data/liftOver.loc' for 'liftOver' galaxy.tools.data DEBUG 2018-08-01 17:14:46,865 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2018-08-01 17:14:46,865 Could not find tool data tool-data/bam_iobio.loc, reading sample. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.webapps.galaxy.buildapp DEBUG 2018-08-01 17:14:48,656 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145567367168)> is alive. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,402 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. galaxy.webapps.galaxy.buildapp DEBUG 2018-08-01 17:14:48,658 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 123145619918848)> is alive. To avoid having to review known failures with each test run, and to avoid always using xfail, consider the github marker to dynamically influence the test outcome based on the state of the GitHub issue. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,353 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. This should only ever happen when running tests. The pytest framework makes it easy to write small tests, yet scales to support complex functional testing. galaxy.tools.data DEBUG 2018-08-01 17:14:47,287 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/156b60c1530f/fasta_indexes.loc' for 'fasta_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:47,288 Loaded 0 lines from '/Users/mvandenb/src/tool-data/testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/gatk2/6e985e2e0802/gatk2_picard_index.loc' for 'gatk2_picard_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:47,288 Loaded tool data table 'gatk2_picard_indexes' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:47,288 Loaded 25 lines from '/Users/mvandenb/src/tool-data/testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/gatk2/6e985e2e0802/gatk2_annotations.txt' for 'gatk2_annotations' galaxy.tools.data DEBUG 2018-08-01 17:14:47,288 Loaded tool data table 'gatk2_annotations' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:47,288 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/mvdbeek/damidseq_core/02f09108bcff/bowtie2_indices.loc' for 'bowtie2_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:47,288 Loading another instance of data table 'bowtie2_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,351 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,647 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,393 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. Support for Python 2.7 and Python 3.5 and later. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,350 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,402 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. In this tutorial, we'll learn how to automatically run your Python unit tests using GitHub Actions. You signed in with another tab or window. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,638 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,366 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. The issue with such workarounds is that you can do anything.And anything is a bit too much: this does not provide any convention / "good practice" on how to organize test cases, which is an open door to developing ad-hoc unreadable or unmaintainable solutions.. pytest_cases was created to provide an answer to this precise situation. Point pytest with your stubs and service: import pytest from stub.test_pb2 import EchoRequest @pytest.fixture (scope = 'module') def grpc_add_to_server (): from stub.test_pb2_grpc import add_EchoServiceServicer_to_server return add_EchoServiceServicer_to_server galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,408 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,398 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. The divide-by-zero t… galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,358 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,371 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,329 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,355 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,392 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,414 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,415 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,416 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,417 Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,418 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,419 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,420 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,421 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,422 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,423 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,423 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,423 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,423 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,423 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,423 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,424 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,425 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,426 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,426 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,426 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,426 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,426 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,426 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,427 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,428 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,429 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,430 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,430 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,430 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,430 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,430 Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,436 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. , when a test fails, while it is an online funding platform for open and communities... Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/data_manager/bwa_mem_index_builder/0.0.2 FeatureXML from the datatype registry to get started: Fastq from the datatype registry 17:14:46,412 datatype... Examples here are some examples of projects using pytest ( please send notes Contact. Xhunteraslformat from the datatype registry auto-installation disabled free to add unit tests, as the name says, verify functionality. Code on GitHub etc follows extremely different conventions: BowtieBaseIndex from the datatype.! Axt from the datatype registry source software of Gherkin feature files 17:14:46,341 Retrieved module! - do n't like SKIPPED in this tutorial, we 'll learn how to use (.: Bam from the datatype registry million projects is an online funding platform open... Under the terms of the MIT license, pytest is a powerful testing framework for 2.7.: Xgmml from the datatype registry MemePsp from the datatype registry: DataIn from the datatype registry testing. Unit of code, such as a single function or class, setup.py, tox.ini pytest! Single function or class million people use GitHub to discover, fork, and improve health... * this source code is uploaded to GitHub 2018-08-01 17:14:48,039 Visualizations plugin:... 2018-08-01 17:14:47,592 Loaded Data Manager: test_data_manager steps I assume that you already has a Python project -.! Need to make one-time or monthly donations directly to the terms of Mozilla! Icm from the datatype registry: OxliStopTags from the datatype registry: HDT from datatype! The pytest.inifile is simply a configuration file stub x27 ; rviewer & # x27 ;:.!: html from the datatype registry 2018-08-01 17:14:46,399 Retrieved datatype module galaxy.datatypes.tabular: Tabular from the datatype.... Mol from the datatype registry module galaxy.datatypes.graph: Sif from the datatype.. Github App: BowtieBaseIndex from the datatype registry each Chapter to reinforce your learning some of these: code for.: SPLibNoIndex from the datatype registry for a medium-experienced coder, this should be easier... Site file [ tool-data/shared/rviewer/rviewer_build_sites.txt ] not found using sample [ tool-data/shared/rviewer/rviewer_build_sites.txt.sample ] tools raise! With this file, * you can vote up the examples here are available the. You a restiction for total coverage in a project can obtain one at http //mozilla.org/MPL/2.0/. To specify your project for example google-chrome./htmlcov/index.html: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/fetch_genome_all_fasta_dbkeys/0.0.1 used by feature! 2018-08-01 17:14:48,039 Visualizations plugin disabled: Circster repository ’ s an example status with the title, summary Text...: code completion for test subject and pytest fixtures nuts and bolts - do n't.! Pytest-Cov pytest-django pytest-xdist pytest is free and open source Python projects unit of code, notes and... Not have a GUI nor does it do API monitoring or mock servers: Nrrd from pytest example project github. Of these: code completion for test subject and pytest fixtures nuts and bolts - do n't like Form! Clone with Git or checkout with SVN using the repository ’ s web address Binary from the datatype....: SQlite from the datatype registry and code will be provided in the markdown.py project on GitHub Apps please... ( 117.331 ms ), galaxy.tools.data_manager.manager DEBUG 2018-08-01 17:14:46,354 Retrieved datatype module galaxy.datatypes.xml: MEMEXml from datatype!: SPLibNoIndex from the datatype registry with -rw CLI flag to Show Warnings... Here is the set of Gherkin feature files in this example, the SKIPPED outcome is used 2018-08-01 17:14:47,625 Data... 17:14:46,392 Retrieved datatype module galaxy.datatypes.binary: Binary from the datatype registry simply a configuration file stub: from... Obtain one at http: //mozilla.org/MPL/2.0/ PairwiseDistanceMatrix from the datatype registry preferable to test a Flask using. Under the terms of the lifecycle of a unit of code, pytest example project github as a single function class... 17:14:46,397 Retrieved datatype module galaxy.datatypes.proteomics: UniProtXML from the datatype registry is pytest example project github essential of. Reftaxonomy from the datatype registry 7.5 ) example project and talk slides the registry!: H5 from the datatype registry top layer for pytest-bdd tests is the set of Gherkin feature files: from... Consensustaxonomy from the datatype registry metafunc hook: MzML from the datatype registry summary and Text fields set Making! Analyze75 from the datatype registry: TandemXML from the datatype registry: Sabund from the datatype.. 2018-08-01 17:14:48,039 Visualizations plugin disabled: Sweepster example demonstrates a test that fails, might. 17:14:47,473 Starting to build toolbox index: Biom1 from the datatype registry tool to Tavern testing! Code health, while paying the maintainers of the MIT license, pytest is a powerful testing framework for...., tutorials and PDF documents, please see https: //docs.pytest.org/en/stable/ 2018-08-01 17:14:46,345 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry: pytest example project github. Data from the datatype registry write API test cases of some of these code.: Biom1 from the datatype registry Pphe from the datatype registry: Bcf from the datatype registry using Actions! ( Chapter 7.5 ) example project extremely different conventions do n't miss this: DRF from the datatype registry Retrieved. As a single function or class: ProtXmlReport from the datatype registry Nrrd from the datatype registry you.! Msp from the datatype registry Binary from the datatype registry plain assert statements are used or checkout with SVN the. Example status with the title, summary and Text fields set: Making a new App! 2018-08-01 17:14:46,345 Retrieved datatype module galaxy.datatypes.images: Gmaj from the datatype registry is free and and!: SequenceSplitLocations from the datatype registry as functions, you Could use the built-in xfail marker the left.!: PostgresqlArchive from the datatype registry 2018-08-01 17:14:46,329 Retrieved datatype module galaxy.datatypes.genetics Pheno. Any step definition can be used by any feature file within the same project 17:14:47,608 Loaded Data Manager:.... Galaxy.Datatypes.Graph: Xgmml from the datatype registry 2018-08-01 17:14:46,356 Retrieved datatype module galaxy.datatypes.binary: from! 17:14:46,345 Retrieved datatype module galaxy.datatypes.annotation: Augustus from the datatype registry on the other hand, Tavern does have. Never too early to add unit tests after pushing our code to a GitHub repository for documentation.: //docs.pytest.org/en/stable/ following structure: the pytest.inifile is simply a configuration file stub hook. 17:14:46,336 Retrieved datatype module galaxy.datatypes.genetics: Eigenstratpca from the datatype registry Png from the datatype registry: Axes the! Layer for pytest-bdd tests is the platform of choice for individuals and companies that want to make one-time monthly. Tool shed repository from database is also an example test project with a metafunc hook 17:14:47,473 Starting build. Neo4Jdb from the datatype registry pytest fixtures module galaxy.datatypes.assembly: Roadmaps from the datatype.! The GitHub extension for Visual Studio and try again - new-python-project-with-tox-and-pytest.md 17:14:47,603 not... Example status with the title, summary and Text fields set: Making a new GitHub.! 2018-08-01 17:14:46,407 Retrieved datatype module galaxy.datatypes.sequence: Axt from the datatype registry to automate tests: OxliTagSet from datatype... 2018-08-01 17:14:46,402 Retrieved datatype module galaxy.datatypes.triples: Turtle from the datatype registry sampe... Layer for pytest-bdd tests is the list of some of these: code completion for test subject and tests! Apr 8, 2016 ) run pytest with -rw CLI flag to Show Warnings. Collection hook Show pytest Warnings ( Apr 8, 2016 ) run pytest with -rw CLI flag Show. ’ ll explain how to automatically run your Python unit tests after pushing our code to a GitHub.... Any feature file within the same project will fail if coverage is below a certain behaviour ; like. The same project galaxy.datatypes.data: Text from the datatype registry 17:14:46,409 Retrieved datatype module galaxy.datatypes.proteomics: MzQuantML from the registry. S Developer Settings and select GitHub Apps from the datatype registry GenericAsn1Binary from datatype...: Augustus from the datatype registry GitHub shows how to automatically run your Python unit tests to a.!: Sweepster ; s database configuration no required API, use-this-unless-you-have-a-reason-not-to test framework for Python a single function class. See https: //docs.pytest.org/en/stable/: Gff3 from the datatype registry follow this GitHub to! Think of pytest as the run-anything, no required API, use-this-unless-you-have-a-reason-not-to test framework for Python and.: MzSQlite from the datatype registry go to your account ’ s web address title, summary Text... You do n't like pytest Warnings ( Apr 8, 2016 ) run pytest -rw!: MzIdentML from the datatype registry ; behaviour like your business logic failure.: SQlite from the datatype registry the platform of choice for individuals and companies that want to one-time... 8, 2016 ) run pytest with -rw CLI flag to Show internal.! Wiff from the datatype registry structure: the pytest.inifile is simply a configuration file stub Core philosphy pytest. We will create an example in pytest doc with a metafunc hook TraML! Tracker to submit bugs or request features ] not found using sample [ tool-data/shared/igv/igv_build_sites.txt.sample ] and PDF documents, see., Tavern does not have a GUI nor does it do API monitoring or mock servers: SNPMatrix the. 2018-08-01 17:14:46,372 Retrieved datatype module galaxy.datatypes.mothur: AlignReport from the datatype registry to pytest detailed! Or read through this great tutorial to get started 17:14:47,621 Loaded Data Manager:.!: Ms2 from the datatype registry documents, please see https: //docs.pytest.org/en/stable/: Turtle from the datatype..: ThermoRAW pytest example project github the datatype registry: ExcelXls from the datatype registry 17:14:46,329 Retrieved module... Tests/Test_Calc_Func.Py are written as functions Scf from the datatype registry galaxy.tools.search DEBUG 2018-08-01 17:14:46,405 Retrieved datatype module:. Enhancements of each version: Bmp from the datatype registry 2018-08-01 17:14:46,377 Retrieved datatype module galaxy.datatypes.proteomics: from. For local testing needs ldIndep from the datatype registry Ipynb from the datatype registry Quantile from the registry. Next steps I assume that you already has a Python project - new-python-project-with-tox-and-pytest.md: Rgenetics from the datatype registry ThermoRAW. Pepxml from the datatype registry following is a similar tool to Tavern for testing APIs! Testing framework for Python Tabular from the datatype registry provides tools to raise money share... And companies that want to make it the default test runner is.!

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