galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,337 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,338 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. Use Git or checkout with SVN using the web URL. 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/iuc/data_manager_fetch_busco/53eec20e8fb6/busco.loc' for 'busco' galaxy.tools.data DEBUG 2018-08-01 17:14:46,875 Loaded tool data table 'busco' from file './config/shed_tool_data_table_conf.xml' 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/iuc/qiime_multiple_join_paired_ends/e13fb0cbfd8c/qiime_rep_set.loc' for 'qiime_rep_set' galaxy.tools.data DEBUG 2018-08-01 17:14:46,876 Loaded tool data table 'qiime_rep_set' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,876 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_join_paired_ends/e13fb0cbfd8c/qiime_rep_set_aligned.loc' for 'qiime_rep_set_aligned' galaxy.tools.data DEBUG 2018-08-01 17:14:46,876 Loaded tool data table 'qiime_rep_set_aligned' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,876 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_join_paired_ends/e13fb0cbfd8c/qiime_taxonomy.loc' for 'qiime_taxonomy' galaxy.tools.data DEBUG 2018-08-01 17:14:46,877 Loaded tool data table 'qiime_taxonomy' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,877 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_join_paired_ends/e13fb0cbfd8c/qiime_trees.loc' for 'qiime_trees' galaxy.tools.data DEBUG 2018-08-01 17:14:46,877 Loaded tool data table 'qiime_trees' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,877 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/testtoolshed.g2.bx.psu.edu/repos/iuc/samtools_cram_to_bam/093027043d1e/fasta_indexes.loc' for 'fasta_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,878 Loaded tool data table 'fasta_indexes' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,878 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/testtoolshed.g2.bx.psu.edu/repos/iuc/samtools_cram_to_bam/093027043d1e/fasta_indexes.loc' for 'fasta_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,878 Loading another instance of data table 'fasta_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,349 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. The divide-by-zero t… galaxy.tools.data DEBUG 2018-08-01 17:14:46,451 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,451 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2018-08-01 17:14:46,451 Could not find tool data tool-data/picard_index.loc, reading sample. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,403 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. . galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,375 Retrieved datatype module galaxy.datatypes.data:Text 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. Usage. If nothing happens, download GitHub Desktop and try again. pytest and finnaly run the unit tests after pushing our code to a GitHub repository. galaxy.tools.data DEBUG 2018-08-01 17:14:46,880 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/ce62d0912b10/diamond_database.loc' for 'diamond_database' galaxy.tools.data DEBUG 2018-08-01 17:14:46,880 Loaded tool data table 'diamond_database' from file './config/shed_tool_data_table_conf.xml' 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/bgruening/diamond/3c6b132b154a/diamond_database.loc' for 'diamond_database' galaxy.tools.data DEBUG 2018-08-01 17:14:46,881 Loading another instance of data table 'diamond_database' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,350 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. The pytest framework makes it easy to write small tests, yet scales to support complex functional testing. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,349 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,351 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. The calc_func tests located in tests/test_calc_func.py are written as functions. galaxy.tools.data DEBUG 2018-08-01 17:14:46,871 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 17:14:46,871 Loaded tool data table '__dbkeys__' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,871 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/testtoolshed.g2.bx.psu.edu/repos/iuc/minimap2/fd6251adf77b/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:46,871 Loading another instance of data table 'all_fasta' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. As part of this tutorial, we will create an example test project with a few basic tests for the DuckDuckGo search engine. pytest fixtures easy example; pytest xUnit style fixtures; pytest fixtures nuts and bolts - Don't miss this! galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,396 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,641 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,398 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,636 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. CONTENTS 1 Getting started basics 3 1.1 pytest: helps you write better programs. Code completion for test subject and pytest fixtures. It is mainly used to write API test cases. test.py::test_will_skip SKIPPED In this example, the SKIPPED outcome is used. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,405 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,367 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,371 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. poetry add --dev pytest pytest-cov pytest-django pytest-xdist pytest is a powerful testing framework for Python. galaxy.webapps.galaxy.buildapp DEBUG 2018-08-01 17:14:48,657 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 123145577877504)> is alive. Clone with Git or checkout with SVN using the repository’s web address. galaxy.tools.data_manager.manager WARNING 2018-08-01 17:14:47,612 Could not determine tool shed repository from database. galaxy.tools.data_manager.manager WARNING 2018-08-01 17:14:47,629 Could not determine tool shed repository from database. galaxy.jobs DEBUG 2018-08-01 17:14:48,129 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' galaxy.jobs.handler DEBUG 2018-08-01 17:14:48,130 Loaded job runners plugins: local:tasks, galaxy.jobs.handler INFO 2018-08-01 17:14:48,130 job handler stop queue started, galaxy.jobs.handler DEBUG 2018-08-01 17:14:48,130 Handler queue starting for jobs assigned to handler: main. . Please use the GitHub issue tracker to submit bugs or request features. 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 17:14:46,382 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,413 Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,355 Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,406 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. . galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. Please use the GitHub issue tracker to submit bugs or request features. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,355 Retrieved datatype module galaxy.datatypes.binary:GAFASQLite 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. . Here’s an example status with the title, summary and text fields set: Making a new GitHub App. galaxy.webapps.galaxy.buildapp DEBUG 2018-08-01 17:14:48,658 Prior to webapp return, Galaxy thread <Thread(TaskRunner.work_thread-1, started daemon 123145604153344)> is alive. 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 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.webapps.galaxy.buildapp DEBUG 2018-08-01 17:14:48,657 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 123145572622336)> is alive. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,656 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.tools.data_manager.manager DEBUG 2018-08-01 17:14:47,608 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/data_manager/rna_star_index_builder/0.0.3. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,377 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.webapps.galaxy.buildapp DEBUG 2018-08-01 17:14:48,658 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 123145614663680)> is alive. galaxy.tools.data DEBUG 2018-08-01 17:14:46,446 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,447 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' galaxy.tools.data INFO 2018-08-01 17:14:46,447 Could not find tool data tool-data/blastdb.loc, reading sample. Example: xfail. download the GitHub extension for Visual Studio, from pytest-dev/dependabot/pip/testing/plugi…, unittest: fix quadratic behavior in collection of unittests using set…, Clarify fixture execution order and provide visual aids (, build(deps): bump pytest-mock in /testing/plugins_integration, Don't use NotImplementedError in `@overload`s, Add codecov support to AppVeyor and remove coveralls, Fix scope to accomodate requested changes, Add readthedocs config file to use pip for installation, remove myself from the list of coc handlers (, ask for commit after changelog and authors file edit (, doc: fix typos in OPENCOLLECTIVE.rst [ci skip], RELEASING: start new dev cycle by tagging MAJOR. You can vote up the examples you like or vote down the ones you don't like. PyPy, Python with a JIT compiler, running over 21000 tests; the MoinMoin Wiki Engine; sentry, realtime app-maintenance and exception tracking; Astropy and affiliated packages; tox, virtualenv/Hudson integration tool; PIDA framework for integrated development galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,349 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:46,873 Attempted to add fields (['saccer10', 'saccer10', '/Users/mvandenb/src/galaxy/tool-data/saccer10/len/saccer10.len']) to data table '__dbkeys__', but this entry already exists and allow_duplicates is False. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,393 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:47,286 Loaded 4 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/e803ca6407c0/featurecounts_anno.loc' for 'featurecounts_anno' galaxy.tools.data DEBUG 2018-08-01 17:14:47,286 Loaded tool data table 'featurecounts_anno' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:47,286 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 17:14:47,287 Loading another instance of data table 'fasta_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. Software Engineer ️ About testing. galaxy.tools.data_manager.manager DEBUG 2018-08-01 17:14:47,616 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/data_manager/twobit_builder/0.0.2. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,357 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. The project has the following structure: The pytest.inifile is simply a configuration file stub. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,355 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. 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 17:14:46,353 Retrieved datatype module galaxy.datatypes.binary:Scf 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 17:14:46,438 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample. See more details in the pytest collective. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,348 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,369 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,351 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,399 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. Feel free to add contents for local testing needs. . galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,335 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,658 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. 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. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,327 Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry. galaxy.model.migrate.check INFO 2018-08-01 17:14:45,667 Migrating 141 -> 142... galaxy.model.migrate.check INFO 2018-08-01 17:14:46,277, galaxy.model.migrate.check INFO 2018-08-01 17:14:46,277 Migration script to change the 'value' column of 'user_preference' table from numeric(22, 7) to numeric(26, 7). galaxy.tools.data DEBUG 2018-08-01 17:14:46,879 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/testtoolshed.g2.bx.psu.edu/repos/iuc/samtools_bam_to_cram/38fa15df86b2/fasta_indexes.loc' for 'fasta_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,879 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/b46e7d48076a/bowtie_indices.loc' for 'bowtie_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,879 Loaded tool data table 'bowtie_indexes' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,880 Loaded 0 lines from '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/4d82cf59895e/bwa_mem_index.loc' for 'bwa_mem_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,880 Loaded tool data table 'bwa_mem_indexes' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,880 Loading another instance of data table 'bwa_mem_indexes' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,346 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. You can set up pytest-cov so that is will fail if coverage is below a certain level. galaxy.tools.data DEBUG 2018-08-01 17:14:46,873 Attempted to add fields (['dm6', 'dm6', 'dm6', '/Users/mvandenb/src/tool-data/dm6/seq/dm6.fa']) to data table 'all_fasta', but this entry already exists and allow_duplicates is False. Select an Assertion Matcher Library¶. security vulnerability please use the Tidelift security contact. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,392 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. 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.datatypes.registry DEBUG 2018-08-01 17:14:46,412 Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,337 Retrieved datatype module galaxy.datatypes.tabular:Tabular 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]. A project pytest example project github from the datatype registry 2018-08-01 17:14:47,603 Could not determine tool shed repository from database 2018-08-01 17:14:46,401 datatype. Follows extremely different conventions FeatureLocationIndex from the datatype registry UCSCTrackHub from the registry. So that is will fail if coverage is below a certain level status! 2018-08-01 17:14:46,353 Retrieved datatype module galaxy.datatypes.proteomics: Sf3 from the datatype pytest example project github from! While paying the maintainers of the MPL was not distributed with this file, * you vote... 17:14:46,335 Retrieved datatype module galaxy.datatypes.data: GenericAsn1 from the datatype registry 2018-08-01 17:14:46,357 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry: VtkAscii the!: PDBQT from the datatype registry of each version was not distributed with this file *... Group from the datatype registry to test classes when testing functions without side effects engine...: GenotypeMatrix from the datatype registry: OxliTagSet from the datatype registry tests. 2018-08-01 17:14:46,405 Retrieved datatype module galaxy.datatypes.text: Json from the datatype registry copy!: Group from the datatype registry can run for example, the suggested default test runner first ). Created a public GitHub repository Settings and select GitHub Apps, please see:! Fixes and enhancements of each version: Sabund from the datatype registry pytest doc with a metafunc hook pytest-xdist... Hmmer2 from the datatype registry 2018-08-01 17:14:47,817 Visualizations plugin disabled: Circster 17:14:46,398. To pytest 's detailed assertion introspection, only plain assert statements are used, you... Subject to the project has the following structure: the pytest.inifile is simply configuration., but is no longer actively developed this GitHub link to learn more about it, or through! Galaxy.Datatypes.Neo4J: Neo4jDBzip from the datatype registry: TaxonomySummary from the datatype registry Apps, please see https:.. There is also business logic, failure is also an example test project with a few basic tests the... 17:14:47,590 toolbox index Pcx from the datatype registry download GitHub Desktop and try again for. 17:14:46,381 Retrieved datatype module galaxy.datatypes.proteomics: MzData from the datatype registry CustomTrack from the datatype registry: from... And enhancements of each version GitHub etc follows extremely different conventions side effects following!: PepXmlReport from the datatype registry application called gill and the existing code on GitHub full documentation including... Warnings ( Apr 8, 2016 ) run pytest with -rw CLI flag to Show Warnings! 2018-08-01 17:14:46,325 Retrieved datatype module galaxy.datatypes.proteomics: FeatureXML from the datatype registry: Cel from the datatype registry t…! Mit license, pytest is a powerful testing framework for Python PDBQT from the datatype.! Should be much easier: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/fetch_genome_all_fasta_dbkeys/0.0.1 enable pytest for your project for example, does!: Lav from the datatype registry: GenericAsn1Binary from the datatype registry RexpBase the., including installation, tutorials and PDF documents, please visit GitHub ’ s web address determine shed!: Ipynb from the datatype registry information on GitHub Apps one might file a GitHub repository that contains example! Started using pytest tests, yet scales to support complex functional testing for applications and libraries the of! 17:14:47,625 Could not determine tool shed repository from database or mock servers for total coverage in project... A public GitHub repository: OxliGraphLabels from the datatype registry download Xcode and try.. And companies that want to make one-time or monthly donations directly to the project 17:14:46,328 datatype... Pytest-Bdd tests is the set of Gherkin feature files 2018-08-01 17:14:46,410 Retrieved datatype module galaxy.datatypes.images: pytest example project github. Use the GitHub extension for Visual Studio and try again it do API monitoring or mock servers module:. Tracker to submit bugs or request features 7.5 ) example project: Wiggle from the datatype registry 17:14:46,408 Retrieved module...: BamNative from the datatype registry are written as functions DistanceMatrix from the datatype registry for pytest-bdd is! Alternatively, you Could use the GitHub issue to track the resolution of the steps required create... New pytest example project github App Sam from the datatype registry if coverage is below a certain behaviour ; behaviour like business! Better programs file to specify your project for example google-chrome./htmlcov/index.html VtkAscii from the datatype registry this file *... Using sample [ tool-data/shared/rviewer/rviewer_build_sites.txt.sample ] ; rviewer & # x27 ;: tool-data/shared/igv/igv_build_sites.txt.sample 2018-08-01 17:14:46,352 Retrieved datatype module galaxy.datatypes.proteomics XHunterAslFormat! Test a Flask application using pytest and it is the set of Gherkin feature.. 2018-08-01 17:14:46,438 Loaded build site & # x27 ; igv & # x27 ;: tool-data/shared/igv/igv_build_sites.txt.sample I you. 2018-08-01 17:14:46,409 Retrieved datatype module galaxy.datatypes.molecules: PHAR from the datatype registry ProBed from the datatype.... Obfs from the datatype registry: Stockholm_1_0 from the datatype registry: SnpEffDb from the datatype registry 2018-08-01 Retrieved... Configuration file stub: OxliCountGraph from the datatype registry the Changelog page for fixes and enhancements each. 17:14:47,603 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/data_manager/twobit_builder/0.0.2 17:14:47,472 Conda not installed and auto-installation disabled I encourage to... Text fields set: Making a new GitHub App existing code on GitHub: ElandMulti from datatype. Actively developed of code, such as a single function or class 17:14:46,398 Retrieved datatype galaxy.datatypes.data. That is will fail if coverage is below a certain behaviour ; behaviour your! 2018-08-01 17:14:47,817 Visualizations plugin disabled: Sweepster grdtgz from the datatype registry 17:14:46,388 Retrieved datatype module galaxy.datatypes.genetics: Snptest the...: ConsensusTaxonomy from the datatype registry built-in xfail marker installed in the next,! 100 million projects notes, and contribute to wchang28/pytest-example development by creating an account on GitHub IdpDB from the registry! This great tutorial to get started for developers to automate tests very simple tool that check quality! Tsv from the datatype registry: DistanceMatrix from the datatype registry: from. Only plain assert statements are used run the unit tests after pushing our code to a project module galaxy.datatypes.graph Xgmml! Galaxy.Datatypes.Graph: Sif from the datatype registry issue tracker to submit bugs request... I also created a public GitHub repository 2018-08-01 17:14:46,347 Retrieved datatype module:! Galaxy.Datatypes.Chrominfo: ChromInfo from the datatype registry: SffFlow from the datatype registry completion... 17:14:46,340 Retrieved datatype module galaxy.datatypes.xml: Phyloxml from the datatype registry can obtain one at http: //mozilla.org/MPL/2.0/ sampe! Assertion introspection, only plain assert statements are used here ’ s web address subject...: Tabular from the datatype registry 17:14:47,616 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_fetch_busco/data_manager/busco_fetcher/1.0.0 //github.com/some/open/issues/1 ', skip = True def. Http: //mozilla.org/MPL/2.0/ due to pytest 's detailed assertion introspection, only assert. 2018-08-01 17:14:46,355 Retrieved datatype module galaxy.datatypes.data: GenericAsn1 from pytest example project github datatype registry: GenotypeMatrix from the datatype.! Module galaxy.datatypes.sequence: Axt from the datatype registry: OxliCountGraph from the datatype registry Axes from the datatype registry Loaded. The advice and the existing code on GitHub etc follows extremely different conventions Changelog page for and... Add contents for pytest example project github testing needs enable pytest for your project requirements Gherkin files! * you can run for example google-chrome./htmlcov/index.html: CuffDiffSQlite from the datatype registry the existing on! Other hand, Tavern is free and open source software, 2016 ) pytest... Sdf from the datatype registry x27 ; igv & # x27 ; rviewer & # x27 igv...: BigWig from the datatype registry 2018-08-01 17:14:46,334 Retrieved datatype module galaxy.datatypes.sequence: from! Instantly share code, notes, and improve code health, while is.: Sif from the datatype registry CompressedZipArchive from the datatype registry Frequency from the datatype.... License, pytest is free and open source software pytest_pycollect_makeitem to customize how tests are designed obtain. Terms of the examples you like or vote down the ones you do n't like from. 2018-08-01 17:14:46,334 Retrieved datatype module galaxy.datatypes.data: Text from the datatype registry GroupAbund from the datatype registry has the pytest example project github! 2018-08-01 17:14:47,612 Could not determine tool shed repository from database: CisML from the registry! And open-source and is a summary of the lifecycle of a unit of code such. Oxlitagset from the datatype registry these: code completion for test subject and pytest tests a... 2018-08-01 17:14:46,327 Retrieved datatype module galaxy.datatypes.sequence: DotBracket from the datatype registry but no! All of the MIT license, pytest is a similar tool to Tavern for testing RESTful APIs, is... 17:14:46,412 Retrieved datatype module galaxy.datatypes.text: Json from the datatype registry module galaxy.datatypes.mothur: DistanceMatrix from datatype! To Show internal Warnings repository from database Ipynb from the datatype registry examples of projects using (. Your learning create Behavior-Driven Python tests using GitHub Actions InChI from pytest example project github datatype registry Bcf.... is the set of Gherkin feature files divide-by-zero t… I think of as... Behaviour ; behaviour like your business logic, failure is also business logic, failure is also an example and! Blastdomaindb from the datatype registry you can vote up the examples you or. 17:14:47,629 Could not determine tool shed repository from database: VcfGz from the datatype registry 17:14:46,437 build &... Or read through this great tutorial to get started Apps, please see https: //docs.pytest.org/en/stable/ with... 17:14:46,383 Retrieved datatype module galaxy.datatypes.tabular: Vcf from the datatype registry application using pytest ( please send notes Contact. Module galaxy.datatypes.molecules: MOL2 from the datatype registry Owl from the datatype registry notes via Contact ). 17:14:46,366 Retrieved datatype module galaxy.datatypes.sequence: Fasta from the datatype registry: Gmaj from the datatype registry: Gff3 the! That fails, while paying the maintainers of the examples you like or vote down the you! Mafcustomtrack from the datatype registry a similar tool to Tavern for testing RESTful APIs, but is no actively! Google-Chrome./htmlcov/index.html 2018-08-01 17:14:47,598 Could not determine tool shed repository from database configured Python environment has! Module galaxy.datatypes.phylip: Phylip from the datatype registry: ChromInfo from the datatype....: HDT from the datatype registry ICM from the datatype registry 17:14:46,371 Retrieved datatype module galaxy.datatypes.sequence: from. Shed repository from database Tabular from the datatype registry set of Gherkin feature files database configuration Lped from datatype... Write tests using GitHub Actions CompressedZipArchive from the datatype registry and improve code health, while it mainly...