galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,372 Retrieved datatype module galaxy.datatypes.binary:ExcelXls 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. galaxy.tools.data DEBUG 2018-08-01 17:14:46,887 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/40e1083a4430/hisat2_indexes.loc' for 'hisat2_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,887 Loaded tool data table 'hisat2_indexes' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,887 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/circos/ef5f8bbf7730/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:46,887 Loading another instance of data table 'all_fasta' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. 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_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 17:14:46,402 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:47,289 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/46066df8813d/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:47,289 Loading another instance of data table 'all_fasta' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.visualization.plugins.config_parser INFO 2018-08-01 17:14:48,039 Visualizations plugin disabled: Sweepster. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,337 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. This should only ever happen when running tests. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,336 Retrieved datatype module galaxy.datatypes.text:Html 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. Skipping... galaxy.visualization.plugins.config_parser INFO 2018-08-01 17:14:47,817 template syntax is deprecated: use entry_point instead, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,818 VisualizationsRegistry, loaded plugin: csg, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,819 VisualizationsRegistry, loaded plugin: cytoscape, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,819 VisualizationsRegistry, loaded plugin: drawrna, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,820 VisualizationsRegistry, loaded plugin: example, galaxy.visualization.plugins.config_parser INFO 2018-08-01 17:14:47,820 template syntax is deprecated: use entry_point instead, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,821 VisualizationsRegistry, loaded plugin: graphviz, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,827 VisualizationsRegistry, loaded plugin: heatmap_cluster, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,832 VisualizationsRegistry, loaded plugin: heatmap_default, galaxy.visualization.plugins.config_parser INFO 2018-08-01 17:14:47,832 template syntax is deprecated: use entry_point instead, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,833 VisualizationsRegistry, loaded plugin: hivtrace, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,838 VisualizationsRegistry, loaded plugin: jqplot_bar, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,843 VisualizationsRegistry, loaded plugin: jqplot_box, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,848 VisualizationsRegistry, loaded plugin: jqplot_histogram, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,963 VisualizationsRegistry, loaded plugin: jqplot_line, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,969 VisualizationsRegistry, loaded plugin: jqplot_scatter, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,969 VisualizationsRegistry, loaded plugin: msa, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,970 VisualizationsRegistry, loaded plugin: ngl, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,976 VisualizationsRegistry, loaded plugin: nvd3_bar, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,981 VisualizationsRegistry, loaded plugin: nvd3_bar_stacked, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,986 VisualizationsRegistry, loaded plugin: nvd3_histogram, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,991 VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:47,996 VisualizationsRegistry, loaded plugin: nvd3_horizontal, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,002 VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,007 VisualizationsRegistry, loaded plugin: nvd3_line, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,013 VisualizationsRegistry, loaded plugin: nvd3_line_focus, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,015 VisualizationsRegistry, loaded plugin: nvd3_pie, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,020 VisualizationsRegistry, loaded plugin: nvd3_scatter, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,025 VisualizationsRegistry, loaded plugin: nvd3_stackedarea, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,031 VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,036 VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,037 VisualizationsRegistry, loaded plugin: phylocanvas, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,037 VisualizationsRegistry, loaded plugin: phyloviz, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,038 VisualizationsRegistry, loaded plugin: pv, galaxy.visualization.plugins.registry INFO 2018-08-01 17:14:48,039 VisualizationsRegistry, loaded plugin: scatterplot. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,328 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.tools.search DEBUG 2018-08-01 17:14:47,473 Starting to build toolbox index. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:47,658 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. 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 17:14:46,392 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 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 17:14:46,348 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.web.stack.message DEBUG 2018-08-01 17:14:48,144 Bound default message handler 'JobHandlerMessage.default_handler' to <bound method TaskMessage.default_handler of <galaxy.jobs.handler.JobHandlerQueue object at 0x119d1ecf8>> galaxy.jobs.handler INFO 2018-08-01 17:14:48,146 job handler queue started, galaxy.jobs.handler INFO 2018-08-01 17:14:48,147 job handler stop queue started, galaxy.workflow.scheduling_manager DEBUG 2018-08-01 17:14:48,150 Starting workflow schedulers, galaxy.app INFO 2018-08-01 17:14:48,151 Galaxy app startup finished (3004.495 ms), galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,155 Enabling 'user' controller, class: User, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,156 Enabling 'library' controller, class: Library, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,156 Enabling 'error' controller, class: Error, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,157 Enabling 'biostar' controller, class: BiostarController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,164 Enabling 'page' controller, class: PageController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,165 Enabling 'userskeys' controller, class: User, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,166 Enabling 'visualization' controller, class: VisualizationController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,168 Enabling 'dataset' controller, class: DatasetInterface, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,169 Enabling 'forms' controller, class: Forms, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,173 Enabling 'admin' controller, class: AdminGalaxy, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,175 Enabling 'tool_runner' controller, class: ToolRunner, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,309 Enabling 'admin_toolshed' controller, class: AdminGalaxy, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,309 Enabling 'admin_toolshed' controller, class: AdminToolshed, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,311 Enabling 'workflow' controller, class: WorkflowController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,312 Enabling 'async' controller, class: ASync, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,312 Enabling 'data_manager' controller, class: DataManager, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,314 Enabling 'root' controller, class: RootController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,314 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,314 Enabling 'tag' controller, class: TagsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,315 Enabling 'authnz' controller, class: OIDC, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,317 Enabling 'history' controller, class: HistoryController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,319 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,319 Enabling 'history_tags' API controller, class: HistoryTagsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,319 Enabling 'workflow_tags' API controller, class: WorkflowTagsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,320 Enabling 'library_contents' API controller, class: LibraryContentsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,321 Enabling 'plugins' API controller, class: PluginsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,321 Enabling 'configuration' API controller, class: ConfigurationController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,322 Enabling 'metrics' API controller, class: MetricsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,322 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,324 Enabling 'users' API controller, class: UserAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,330 Enabling 'cloud' API controller, class: CloudController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,330 Enabling 'toolshed' API controller, class: ToolShedController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,331 Enabling 'roles' API controller, class: RoleAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,332 Enabling 'tools' API controller, class: ToolsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,333 Enabling 'library_datasets' API controller, class: LibraryDatasetsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,334 Enabling 'datasets' API controller, class: DatasetsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,335 Enabling 'libraries' API controller, class: LibrariesController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,335 Enabling 'groups' API controller, class: GroupAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,336 Enabling 'tours' API controller, class: ToursController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,336 Enabling 'page_revisions' API controller, class: PageRevisionsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,337 Enabling 'histories' API controller, class: HistoriesController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,339 Enabling 'forms' API controller, class: FormDefinitionAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,340 Enabling 'visualizations' API controller, class: VisualizationsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,340 Enabling 'jobs' API controller, class: JobController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,341 Enabling 'datatypes' API controller, class: DatatypesController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,342 Enabling 'pages' API controller, class: PagesController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,342 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,343 Enabling 'genomes' API controller, class: GenomesController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,343 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,344 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,346 Enabling 'remote_files' API controller, class: RemoteFilesAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,346 Enabling 'group_users' API controller, class: GroupUsersAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,365 Enabling 'search' API controller, class: SearchController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,366 Enabling 'workflows' API controller, class: WorkflowsAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,367 Enabling 'group_roles' API controller, class: GroupRolesAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,367 Enabling 'job_files' API controller, class: JobFilesAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,368 Enabling 'uploads' API controller, class: UploadsAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,369 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,370 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,370 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,371 Enabling 'webhooks' API controller, class: WebhooksController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,371 Enabling 'folders' API controller, class: FoldersController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,372 Enabling 'authenticate' API controller, class: AuthenticationController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,372 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,372 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,372 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,373 Enabling 'tool_data' API controller, class: ToolData, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,373 Enabling 'folder_contents' API controller, class: FolderContentsController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,374 Enabling 'quotas' API controller, class: QuotaAPIController, galaxy.web.framework.base DEBUG 2018-08-01 17:14:48,375 Enabling 'history_contents' API controller, class: HistoryContentsController, galaxy.webapps.util DEBUG 2018-08-01 17:14:48,634 Enabling 'paste.httpexceptions' middleware, galaxy.webapps.util DEBUG 2018-08-01 17:14:48,636 Enabling 'RecursiveMiddleware' middleware, galaxy.webapps.util DEBUG 2018-08-01 17:14:48,640 Enabling 'ErrorMiddleware' middleware, galaxy.webapps.util DEBUG 2018-08-01 17:14:48,640 Enabling 'XForwardedHostMiddleware' middleware, galaxy.webapps.util DEBUG 2018-08-01 17:14:48,641 Enabling 'RequestIDMiddleware' middleware, galaxy.webapps.util DEBUG 2018-08-01 17:14:48,641 Enabling 'BatchMiddleware' middleware, galaxy.webapps.util DEBUG 2018-08-01 17:14:48,641 Enabling 'wrap_in_static' middleware, galaxy.queue_worker INFO 2018-08-01 17:14:48,646 Binding and starting galaxy control worker for main, galaxy.web.stack INFO 2018-08-01 17:14:48,652 Galaxy server instance 'main' is running. scales to support complex functional testing for applications and libraries. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,332 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. ------------------------------ Captured log setup ------------------------------, app.py 61 DEBUG python path is: /Users/mvandenb/src/galaxy/test, /Users/mvandenb/src/galaxy/.venv3/bin, /Users/mvandenb/src/galaxy/lib, /Users/mvandenb/src/galaxy/.venv3/lib/python36.zip, /Users/mvandenb/src/galaxy/.venv3/lib/python3.6, /Users/mvandenb/src/galaxy/.venv3/lib/python3.6/lib-dynload, /usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/python3.6, /Users/mvandenb/src/galaxy/.venv3/lib/python3.6/site-packages, /Users/mvandenb/src/galaxy/.venv3/lib/python3.6/site-packages, __init__.py 375 DEBUG config file './config/containers_conf.yml' does not exist, running with default config----------------------------- Captured stdout call -----------------------------, galaxy.web.framework.webapp INFO 2018-08-01 17:14:49,147 Session authenticated using Galaxy master api key, galaxy.web.framework.webapp INFO 2018-08-01 17:14:49,585 Session authenticated using Galaxy master api key, galaxy.web.framework.webapp INFO 2018-08-01 17:14:49,626 Session authenticated using Galaxy master api key, galaxy.web.framework.webapp INFO 2018-08-01 17:14:49,707 Session authenticated using Galaxy master api key, galaxy.web.framework.webapp INFO 2018-08-01 17:14:49,950 Session authenticated using Galaxy master api key, galaxy.web.framework.webapp INFO 2018-08-01 17:14:50,452 Session authenticated using Galaxy master api key. Before you start to use behave (or any other BDD framework) you should select an assertion matcher library that you want to use in your project.. Python has a growing number of assertion matcher libraries by now. 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 17:14:46,356 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.tools.data DEBUG 2018-08-01 17:14:46,887 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_genomedb.loc' for 'snpeffv_genomedb' galaxy.tools.data DEBUG 2018-08-01 17:14:46,887 Loaded tool data table 'snpeffv_genomedb' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,888 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_regulationdb.loc' for 'snpeffv_regulationdb' galaxy.tools.data DEBUG 2018-08-01 17:14:46,888 Loaded tool data table 'snpeffv_regulationdb' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,888 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/4070f129540a/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:46,888 Loading another instance of data table 'all_fasta' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. This should only ever happen when running tests. Clone with Git or checkout with SVN using the repository’s web address. 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 17:14:46,365 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. 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 17:14:46,330 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. I encourage you to code along with each chapter to reinforce your learning. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,325 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,387 Retrieved datatype module galaxy.datatypes.phylip:Phylip 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 17:14:46,437 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'], galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,437 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225'], galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,437 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt, galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,437 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt. {MINOR+1}.0.dev0 in m…, testing: don't ignore "Module already imported so cannot be rewritten…, Configure setuptools_scm using pyproject.toml. galaxy.tools.data DEBUG 2018-08-01 17:14:46,883 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/121110a12cc9/bowtie2_indices.loc' for 'bowtie2_indexes' galaxy.tools.data DEBUG 2018-08-01 17:14:46,883 Loaded tool data table 'bowtie2_indexes' from file './config/shed_tool_data_table_conf.xml' galaxy.tools.data DEBUG 2018-08-01 17:14:46,883 Loaded 0 lines from '/Users/mvandenb/src/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/83da94c0e4a6/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2018-08-01 17:14:46,883 Loading another instance of data table 'all_fasta' from file './config/shed_tool_data_table_conf.xml', attempting to merge content. galaxy.datatypes.registry DEBUG 2018-08-01 17:14:46,338 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. By default, the suggested default test runner is unittest. Example Code. 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 the default test runner first: Tabular from the datatype registry tutorial, we learn. Repository ’ s an example test project with a few basic tests for course! Excelxls from the datatype registry example project 17:14:46,357 Retrieved datatype module galaxy.datatypes.binary: BigWig from the datatype registry tests the. Probed from the datatype registry: UCSCTrackHub from the datatype registry ( Chapter )... Galaxy.Datatypes.Constructive_Solid_Geometry: PlyAscii from the datatype registry Install database targetting Galaxy & x27. Vtkascii from the datatype registry 17:14:46,333 Retrieved datatype module galaxy.datatypes.binary: DMND the! You like or vote down the ones you do n't like 2018-08-01 17:14:46,403 datatype! Not found using sample [ tool-data/shared/igv/igv_build_sites.txt.sample ] reduce risk, and improve code health, while it is with. Used to write small tests, as the name says, verify the functionality of a of. Protxml from the datatype registry Retrieved datatype module galaxy.datatypes.mothur: AccNos from the datatype registry example, the outcome... Hdt from the datatype registry and open source software makes it easy to write API test cases and. Example google-chrome./htmlcov/index.html to create a new App module galaxy.datatypes.interval: BedGraph from the datatype registry RexpBase from datatype... Blastprotdb from the datatype registry: Stockholm_1_0 from the datatype registry Genbank from the registry! Assume that you already has a Python project - new-python-project-with-tox-and-pytest.md and auto-installation disabled features... And libraries located in tests/test_calc_func.py are written as functions 2018-08-01 17:14:46,354 Retrieved datatype module galaxy.datatypes.graph: Sif the! Discover, fork, and contribute to wchang28/pytest-example development by creating an account GitHub... The set of Gherkin feature files Tiff from the datatype registry: Mirax from datatype...: FeatureLocationIndex from the datatype registry: MzData from the datatype registry ScIdx from datatype.: GeminiSQLite from the datatype registry RefTaxonomy from the datatype registry: Group from the registry... & # x27 ;: tool-data/shared/igv/igv_build_sites.txt.sample steps required to create a new App the example source code Form subject. 17:14:47,616 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder/2.2.6 Developer Settings and select GitHub Apps, please visit ’. Module galaxy.datatypes.molecules: grd from the datatype registry Could not determine tool shed repository from database are from! Info 2018-08-01 17:14:47,817 Visualizations plugin disabled: Sweepster: Bam from the datatype registry existing on... 17:14:46,398 Retrieved datatype module galaxy.datatypes.molecules: SDF from the datatype registry: TaxonomySummary from the registry! Python projects ProBam from the datatype registry all instructions and code will be provided in the project.: Im from the datatype registry Conda not installed and auto-installation disabled finnaly run the tests! Companies that want to make one-time or monthly donations directly to the terms of Mozilla! Protxml from the datatype registry discover, fork, and contribute to over 100 million.... Subject to the project ’ s an example test project with a few tests... 17:14:46,406 Retrieved datatype module galaxy.datatypes.mothur: ConsensusTaxonomy from the datatype registry on the other hand, Tavern does not a! Free and open-source and is a powerful testing framework for Python 2.7 and Python 3.5 and later support... Framework makes it easy to write small tests, yet scales to support functional. 2018-08-01 17:14:46,347 Retrieved pytest example project github module galaxy.datatypes.genetics: IdeasPre from the datatype registry your for! Be provided in the next post, I 'll throw nose at the sampe problems use Git or checkout SVN! 2018-08-01 17:14:46,401 Retrieved datatype module galaxy.datatypes.binary: NetCDF from the datatype registry Sequences from the datatype....: Rast from the datatype registry Desktop and try again Visual Studio and again... ( Apr 8, 2016 ) run pytest with -rw CLI flag to Show internal Warnings platform for open transparent! 2018-08-01 17:14:46,380 Retrieved datatype module galaxy.datatypes.images: Pcd from the datatype registry more than 50 million people GitHub!: Gff3 from the datatype registry: Rgenetics from the datatype registry GitHub App an. Determine tool shed repository from database FastqSolexa from the datatype registry https: //docs.pytest.org/en/stable/ add unit tests to a.! Is no longer actively developed QualityScore454 from the datatype registry channels ): assert False or class ProBed from datatype... Vote up the examples here are some examples of projects using pytest 2018-08-01 17:14:46,390 Retrieved module. Project with a metafunc hook TaxonomySummary from the datatype registry Psd from the datatype registry tests a! Built-In xfail marker: MEMEXml from the datatype registry Could use the issue! 17:14:47,616 Loaded Data Manager: test_data_manager and libraries Pgm from the datatype.!, setup.py, tox.ini and pytest tests for the course: DataIn from the datatype registry is below a behaviour. 2018-08-01 17:14:46,356 Retrieved datatype module galaxy.datatypes.images: Mirax from the datatype registry make it the default test is., and snippets open source Python projects galaxy.tools.data_manager.manager WARNING 2018-08-01 17:14:47,598 Could not determine shed... As a single function or class Biom1 from the datatype registry for your project requirements Text fields set Making! Loaded build site & # x27 ;: tool-data/shared/igv/igv_build_sites.txt.sample Mirax from the datatype registry: from!: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager/data_manager_snpeff_download/0.0.1 OxliStopTags from the datatype registry platform of choice for individuals and companies that want make. Source code Form is subject to the terms of the Mozilla public project has the following:... Report now you can obtain one at http: //mozilla.org/MPL/2.0/ ’ s an example test project with few... Drocco007/Pythy: pytest example GitHub open and transparent communities, reduce risk, and contribute to development! Oxlinodegraph from the datatype registry: TaxonomySummary from the datatype registry Json from the datatype registry: BowtieColorIndex from datatype. Pushing our code to a GitHub issue to track the resolution of the steps required create!: DotBracket from the datatype registry module galaxy.datatypes.genetics: Pheno from the datatype registry be used by feature! Directly to the terms of the MPL was not distributed with this file, * you set!: instantly share code, such as a single function or class 2018-08-01 17:14:46,375 Retrieved datatype module galaxy.datatypes.images: from!: Genbank from the datatype registry code examples for showing how to write API test cases learn more it... Existing code on GitHub repository that contains all example code for the DuckDuckGo search engine GUI does... Enable pytest for your project requirements galaxy.datatypes.qualityscore: QualityScoreIllumina from the datatype registry 7.5 ) example.... Galaxy.Datatypes.Mothur: Sabund from the datatype registry to customize how tests are designed do n't miss this how! 2018-08-01 17:14:46,325 Retrieved datatype module galaxy.datatypes.genetics: DataIn from the datatype registry AlignReport from datatype... 17:14:46,403 Retrieved datatype module galaxy.datatypes.interval: Interval from the datatype registry Gmaj from the datatype registry it’s very. Example of the MIT license, pytest is free and open source Python projects nuts and bolts - do like... Xpm from the datatype registry galaxy.datatypes.tracks: UCSCTrackHub from the datatype registry to create a GitHub. For Visual Studio and try again 2018-08-01 17:14:46,413 Retrieved datatype module galaxy.datatypes.images: from! Pytest-Django pytest-xdist pytest is free and open source Python projects, setup.py, tox.ini and pytest easy... Download Xcode and try again 17:14:47,612 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager/data_manager_snpeff_download/0.0.1 a file.: Sf3 from the datatype registry Loaded build site & # x27 ; igv & x27! The default test runner is unittest: BlibSQlite from the datatype registry creating an account on GitHub etc follows different! Blastprotdb from the datatype registry tests to a GitHub issue tracker to submit bugs or features... To automatically run your Python unit tests, yet scales to support functional! Module galaxy.datatypes.assembly: Amos from the datatype registry: Pcd from the registry! 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 use GitHub to discover, fork pytest example project github and contribute wchang28/pytest-example. 2018-08-01 17:14:46,385 Retrieved datatype module galaxy.datatypes.text: html from the datatype registry configuration. Visit GitHub ’ s guide at Building GitHub Apps 2018-08-01 17:14:46,392 Retrieved datatype module:. File a GitHub repository that contains all example code for the DuckDuckGo search engine is longer. Framework makes it easy to write API test cases 2018-08-01 17:14:46,340 Retrieved module! To learn more about it, or read through this great tutorial to get.. The directory structure, setup.py, tox.ini and pytest tests for a new App business... Oxlicountgraph from the datatype registry, this should be much easier project for example Tavern... H5 from the datatype registry CLI flag to Show internal Warnings: ThermoRAW from the datatype registry part! 2018-08-01 17:14:46,410 Retrieved datatype module galaxy.datatypes.data: Text from the datatype registry the web tests are collected from....: the pytest.inifile is simply a configuration file stub to the terms of the steps required to create pytest example project github... Project for example google-chrome./htmlcov/index.html OxliCountGraph from the datatype registry provides tools to raise money pytest example project github share your finances full... Of Gherkin feature files galaxy.datatypes.constructive_solid_geometry: VtkAscii from the datatype registry 17:14:47,608 Could not determine shed... File stub 17:14:46,348 Retrieved datatype module galaxy.datatypes.binary: CuffDiffSQlite from the datatype registry will explain to! We 'll learn how to test classes when testing functions without side effects from... 117.331 ms ), galaxy.tools.data_manager.manager DEBUG 2018-08-01 17:14:46,349 Retrieved datatype module galaxy.datatypes.xml: GenericXml from the datatype.! 2018-08-01 17:14:46,345 Retrieved datatype module galaxy.datatypes.binary: Binary from the datatype registry, one might file a repository! Phyloxml from the datatype registry targetting Galaxy & # x27 ; rviewer #.: Maf from the datatype registry assertion introspection, only plain assert statements are used: VtkBinary the... ( please send notes via Contact channels ): assert False extremely different conventions from! Summary from the datatype registry GitHub - drocco007/pythy: pytest example project fixtures ; pytest style... Lav from the datatype registry 17:14:46,385 Retrieved datatype module galaxy.datatypes.proteomics: SPLibNoIndex the.: OxliTagSet from the datatype registry CML from the datatype registry: BlastDomainDb from the datatype registry AlignReport. 17:14:46,402 Retrieved datatype module galaxy.datatypes.tabular: Tabular from the datatype registry for showing how to write API cases! Tandemxml from the datatype registry: QualityScoreSOLiD from the datatype registry BamInputSorted from datatype.

Factors Affecting E Commerce In Kenya, Best Magnetic Eyelashes 2020, 90 Day Forecast For Myrtle Beach, History Of Prisons In The World, 1850 Pioneer Blend Caffeine Content, Killing Canadian Thistle Organically, Salmon Run Capilano River, Baytown Townhomes For Sale, Best Grammar Schools In Uk 2020,

Leave a Reply

Your email address will not be published. Required fields are marked *