Package: planemo
Command-line utilities to assist in developingGalaxyandCommon Workflow Languageartifacts -
including tools, workflows, and training materials.Free software: MIT LicenseDocumentation:https://planemo.readthedocs.io.Code:https://github.com/galaxyproject/planemoQuick StartObtainingFor a traditional Python installation of Planemo, first set up a virtualenv
forplanemo(this example creates a new one in.venv) containing
Python 3.7 or newer and then install withpip. Planemo must be installed
with pip 7.0 or newer.$ virtualenv .venv; . .venv/bin/activate
$ pip install "pip>=7" # Upgrade pip if needed.
$ pip install planemoFor information on updating Planemo, installing the latest development release,
or installing Planemo viaBioconda- checkout theinstallationdocumentation.Planemo is also available as avirtual appliancebundled
with a preconfigured Galaxy server and set up forGalaxyandCommon Workflow Languagetool development.
You can choose from open virtualization format (OVA, .ova) orDockerappliances.Basics - GalaxyThis quick start will assume you have a directory with one or more Galaxy
tool XML files. If no such directory is available, one can be quickly created for
demonstratingplanemoas followsproject_init--template=demomytools; cd mytools.Planemo can check tool XML files for common problems and best
practices using thelintcommand(also aliased asl).$ planemo lintLike manyplanemocommands - by default this will search the
current directory and use all tool files it finds. It can be explicitly
passed a path to tool files or a directory of tool files.$ planemo l randomlines.xmlThelintcommand takes in additional options related to
reporting levels, exit code, etc. These options are described
in thedocsor (like with all commands) can be accessed by passing--helpto it.$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATHOnce tools are syntactically correct - it is time to test. Thetestcommandcan be used to test a tool or a directory of tools.$ planemo test --galaxy_root=../galaxy randomlines.xmlIf no--galaxy_rootis defined, Planemo will download and configure
a disposable Galaxy instance for testing.Planemo will create a HTML output report in the current directory namedtool_test_output.html(override with--test_output). See anexampleof such a report for Tophat.Once tools have been linted and tested - the tools can be viewed in a
Galaxy interface using theserve(s)command.$ planemo serveLiketest,serverequires a Galaxy root and one can be
explicitly specified with--galaxy_rootor installed dynamically
with--install_galaxy.For more information on building Galaxy tools in general please check outBuilding Galaxy Tools Using Planemo.For more information on developing Galaxy workflows with Planemo checkoutbest practices for Galaxy Workflowsand the description of Planemo’stest format. For information on developing Galaxy training materials
checkout thecontributing documentationon training.galaxyproject.org.Basics - Common Workflow LanguageThis quick start will assume you have a directory with one or moreCommon Workflow
LanguageYAML files. If no such directory is available, one can be quickly created for
demonstratingplanemoas followsplanemo project_init--template=seqtk_complete_cwlmytools; cd mytools.Planemo can check tools YAML files for common problems and best
practices using thelintcommand(also aliased asl).$ planemo lintLike manyplanemocommands - by default this will search the
current directory and use all tool files it finds. It can be explicitly
passed a path to tool files or a directory of tool files.$ planemo l seqtk_seq.cwlThelintcommand takes in additional options related to
reporting levels, exit code, etc. These options are described
in thedocsor (like with all commands) can be accessed by passing--helpto it.$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATHOnce tools are syntactically correct - it is time to test. Thetestcommandcan be used to test a CWL tool, workflow, or a directories thereof.$ planemo test --engine cwltool seqtk_seq.cwlPlanemo will create a HTML output report in the current directory namedtool_test_output.html. Check out the fileseqtk_seq_tests.ymlfor
an example of Planemo test for a CWL tool. A test consists of any number of
jobs (with input descriptions) and corresponding output assertions.Checkout theCommmon Workflow User Guidefor more information on developing
CWL tools in general andBuilding Common Workflow Language Toolsfor more
information on using Planemo to develop CWL tools.Tool ShedPlanemo can help you publish tools to the Galaxy Tool Shed.
Check outPublishing to the Tool Shedfor more information.CondaPlanemo can help develop tools and Conda packages in unison.
Check out theGalaxyorCWLversion of the “Dependencies and Conda” tutorial
for more information.Docker and ContainersPlanemo can help develop tools that run in “Best Practice” containers for
scientific workflows. Check out theGalaxyorCWLversion of the “Dependencies and Containers” tutorial for more information.History0.75.21 (2024-02-01)Add option to pass extra arguments todocker run(thanks to@bernt-matthias).Pull Request 1428Fix workflow_edit (thanks to@mvdbeek).Pull Request 1427Update to black 2024 stable style (thanks to@nsoranzo).Pull Request
14250.75.20 (2024-01-30)Fix use ofpackage_nameattribute onCondaTargetobjects (thanks to@nsoranzo).Pull Request 1424Don’t crash autoupdate on non-PEP440-compliant tool versions (thanks to@nsoranzo).Pull Request 1422Add now mandatory readthedocs config files (thanks to@nsoranzo).Pull
Request 1419Update action versions (thanks to@nsoranzo).Pull Request 14160.75.19 (2023-12-06)Update upper bound for galaxy packages to < 23.2 (thanks to@bernt-matthias).Pull Request 1388Fix workflow download when using instance id (thanks to@mvdbeek).Pull
Request 1412Remove introduction header from training init (thanks to@hexylena).Pull Request 14100.75.18 (2023-11-16)Pretty-print workflow and use correct version of linked workflow inworkflow_test_init(thanks to@mvdbeek).Pull Request 1408Fix running workflow tests when there are multiple tests (thanks to@mvdbeek).Pull Request 1407Fix matching of tool ids to autoupdate (thanks to@nsoranzo).Pull
Request 14060.75.17 (2023-11-01)Implement running tests against existing invocation (thanks to@mvdbeek).Pull Request 1401Fix test result download (thanks to@mvdbeek).Pull Request 14020.75.16 (2023-11-01)No changes0.75.15 (2023-10-29)Change info message for markdown readme in repo
(thanks to@bernt-matthias).Pull Request 1398Make test reports more resilient to failing invocations (thanks to@mvdbeek).Pull Request 1400Fix zenodo test, drop explicit datatype mapping (thanks to@mvdbeek).Pull Request 1399Fix linting rule selection (thanks to@bernt-matthias).Pull Request
1396Add missingAstronomy,CLIP-seqandMaterials scienceTS
categories (thanks to@bernt-matthias).Pull Request 13970.75.14 (2023-10-19)Fix workflow_lint for json output values (thanks to@mvdbeek).Pull
Request 13950.75.13 (2023-10-18)Add –skip to shed_lint (thanks to@bernt-matthias).Pull Request 1394Remove API key requirement from training_init (thanks to@hexylena).Pull Request 1393Try to fix planemo test workflow when output is collection with identical
name (thanks to@lldelisle).Pull Request 13910.75.12 (2023-09-18)Track subworkflow invocations after main invocation is scheduled (thanks to@mvdbeek).Pull Request 13890.75.11 (2023-09-14)Implement automatic tool generation based on the source code of the tool
(thanks to@Kulivox).Pull Request 1263Support for testing workflows with conditional steps (thanks to@mvdbeek).Pull Request 13870.75.10 (2023-09-01)Add pick_value to distro_tools (thanks to@mvdbeek).Pull Request 1385Allow missing conda_exec (thanks to@mstabrin).Pull Request 1384Fix profile version test (thanks to@bernt-matthias).Pull Request
1383Fix type comparisons (thanks to@bernt-matthias).Pull Request 1382Added a note that docker is required for docker and biocontainers option
(thanks to@paulzierep).Pull Request 1355Optimize disk space usage forplanemo test(thanks to@bernt-matthias).Pull Request 1378Fix for change of base_url in BioBlend 1.2.0 (thanks to@nsoranzo).Pull
Request 13790.75.9 (2023-06-29)Update collection operation tool list (thanks to@mvdbeek).Pull Request
1377Officially support Python 3.10 and 3.11 (thanks to@nsoranzo).Pull
Request 1375Fix links (thanks to@nsoranzo).Pull Request 1374Fixtest_run_gxtool_randomlinestest on Galaxy dev branch (thanks to@nsoranzo).Pull Request 13730.75.8 (2023-06-09)Bump galaxy package requirements to allow for 23.0 (thanks to@bernt-matthias).Pull Request 1372Sanitize and make output names unique (thanks to@mvdbeek).Pull Request 1371Increase bioblend retries for bad networks (thanks to@hexylena).Pull Request 1369Add--biocontainersoption to shed_lint (thanks to@mvdbeek).Pull Request 1370fix regex of orcid + add test (thanks to@lldelisle).Pull Request 1364Dropallow_nonefor finding repository (thanks to@mvdbeek).Pull Request 13580.75.7 (2023-03-01)Drop call toescape_non_unicode_symbols(thanks to@nsoranzo).Pull
Request 13570.75.6 (2023-02-22)Allow running autoupdate against external server (thanks to@mvdbeek).Pull Request 1265Fix extraction of orcid identifiers for .dockstore.yml (thanks to@lldelisle).Pull Request 13500.75.5 (2023-02-10)Bump galaxy packages to 22.05 (thanks to@bernt-matthias).Pull Request
12750.75.4 (2023-02-09)Store datasets by UUID (thanks to@bernt-matthias).Pull Request 1347Fix orcid regex for dockstore_init (thanks to@lldelisle).Pull Request
1348Fix virtualenv dir bookkeeping (thanks to@wm75).Pull Request 1346Deprecate introduction slides folder (thanks to@hexylena).Pull Request
1344Remove note recommending installing dev versions fromplanemo runtutorial
(thanks to@simonbray).Pull Request 1338Rename configuration option removed in tox 4.0 (thanks to@nsoranzo).Pull Request 1337Remove travis-ci.org badge from README.rst (thanks to@SimonWaldherr).Pull Request 13340.75.3 (2022-11-30)Mount test data dir read-only in docker (thanks to@mvdbeek).Pull
Request 1327Add traceback to report template (thanks to@bernt-matthias).Pull
Request 1332Add indent and sort_keys to tool_test_json (thanks to@simonbray).Pull
Request 1330Fixplanemo shed_test(thanks to@mvdbeek).Pull Request 1329Add h5py dependency, required for comparing h5 files (thanks to@mvdbeek).Pull Request 1326Update GitHub action versions (thanks to@nsoranzo).Pull Request 1322Fix “glone” typo in error message (thanks to@bernt-matthias).Pull
Request 1325Type annotation for input staging-related code (thanks to@nsoranzo).Pull Request 1320Add creator dockstore (thanks to@lldelisle).Pull Request 13140.75.2 (2022-11-02)Compare versions, not tool ids to find latest tool ids (thanks to@mvdbeek).Pull Request 1313Fixfor_pathswhen path is directory of tools (thanks to@mvdbeek).Pull Request 1312Fix workflow_lint with list + check elements in collection (thanks to@lldelisle).Pull Request 1310Drop copy_tree workaround for tool sources (thanks to@mvdbeek).Pull
Request 13080.75.1 (2022-10-31)Usepytest.raises()instead of ad-hocassert_raises_regexp()context
manager (thanks to@nsoranzo).Pull Request 1302Add planemo_ci_setup command (thanks to@mvdbeek).Pull Request 1304Don’t fail planemo autoupdate if tool version not found in tool shed (thanks
to@lldelisle).Pull Request 1305workflow_lint: ensure that tool shed tool ids are valid (thanks to@lldelisle).Pull Request 1306Fix recording of virtual_env_dir (thanks to@mvdbeek).Pull Request
13070.75.0 (2022-10-28)Restore running tool tests against directory (thanks to@mvdbeek).Pull
Request 1303Update outdated cuffmerge url (thanks to@martenson).Pull Request
1247Set upstream branch when pushing workflows to GitHub (thanks to@simonbray).Pull Request 1249restore –no_cleanup to set cleanup_job to never (thanks to@bernt-matthias).Pull Request 1255Drop support for Python 3.6 (thanks to@simonbray).Pull Request 1257Replace CoC with link to GalaxyProject’s one (thanks to@nsoranzo).Pull
Request 1259Mains resource selector must be skipped (thanks to@hexylena).Pull
Request 1260Ignore cloudflare 503 status when checking links (thanks to@bernt-matthias).Pull Request 1262Document the use of mandatory macro parameters and add named macro tokens
(thanks to@bernt-matthias).Pull Request 1212Bump galaxy package requirements to 22.01 (thanks to@bernt-matthias).Pull Request 1264Run local galaxy via gravity (thanks to@mvdbeek).Pull Request 1232Lint randomlines.xml file (thanks to@simonbray).Pull Request 1270Check if main requirement isNone(thanks to@bernt-matthias).Pull
Request 1274Planemo type annotation: module planemo.commands.cmd_autoupdate (thanks to@gallardoalba).Pull Request 1278Planemo type annotation: module planemo.cli (thanks to@gallardoalba).Pull Request 1277Planemo type annotation: module cmd_clone (thanks to@gallardoalba).Pull Request 1279Planemo type annotation: module cmd_tool_init (thanks to@gallardoalba).Pull Request 1281Add type annotations toplanemo.autoupdatemodule (thanks to@nsoranzo).Pull Request 1283Planemo type annotation: module cmd_normalize (thanks to@gallardoalba).Pull Request 1280Planemo type annotation: module planemo.conda (thanks to@gallardoalba).Pull Request 1284Add type annotations toplanemo.globandplanemo.virtualenv(thanks
to@nsoranzo).Pull Request 1287Dropconda_lintcommand (thanks to@nsoranzo).Pull Request 1288Type annotations for planemo.bioblend, planemo.git, and planemo.cwl.run
(thanks to@adRn-s).Pull Request 1285Add FAQ page to docs (thanks to@simonbray).Pull Request 1271Add type annotations toplanemo.runnableandplanemo.workflow_lint(thanks to@nsoranzo).Pull Request 1291Make–channelsalso affect mulled channels and update/extend howto use
bioconda artifacts (thanks to@bernt-matthias).Pull Request 1227Planemo type annotation: config, context and factory (thanks to@gallardoalba).Pull Request 1292[Training] update templates to use new, more accessible box style (thanks to@shiltemann).Pull Request 1293Pre-create expected output file on disk (thanks to@mvdbeek).Pull
Request 1276Control publish setting in .dockstore.yml, fix first release not appearing
on dockstore (thanks to@mvdbeek).Pull Request 1295Fix disclosure css for summary elements (thanks to@mvdbeek).Pull
Request 1294Enable providing multiple–tool_data_tableoptions (thanks to@mvdbeek).Pull Request 1296Make startup timeout configurable (thanks to@mvdbeek).Pull Request
1298Fix printing planemo test logs (thanks to@mvdbeek).Pull Request 1299Fix workflow test when input is optional but also workflow output (thanks to@mvdbeek).Pull Request 12970.74.11 (2022-06-08)Removing broken link, update it to current doc (thanks to@profgiuseppe).Pull Request 1244Implement nested collection inputs and outputs in workflow_test_initPull
Request 1242More fixes for auto-generating workflow testsPull Request 1241Fix workflow_test_init for collection outputsPull Request 12390.74.10 (2022-05-31)Allow specifying URL and API key with workflow autoupdate and docs
improvements (thanks to@simonbray).Pull Request 1237Pin planemo to last known working major galaxy versionPull Request 1230Drop unused Python dependencies and upgrade syntax to Python 3.6Pull Request 1228Updatebest_practice_search()for changes in galaxy-tool-utilPull Request 1224Make galaxy configcleanup_jobdepend on–no_cleanup(thanks to@bernt-matthias).Pull Request 1226Tool builder: add profile and suffix version
(thanks to@gallardoalba).Pull Request 1222training-init: add the FAQ index page to tutorial folder
(thanks to@shiltemann).Pull Request 1217Adding best practices and assertion checks to workflow_lint
(thanks to@simonbray).Pull Request 1213Updates to workflow autoupdate required for IWC bot
(thanks to@simonbray).Pull Request 1214Add test and fix for failing docker_galaxy engine
(thanks to@simonbray).Pull Request 1215Generate workflow test from invocation id
(thanks to@simonbray).Pull Request 1209Fixed minor typo in documentation
(thanks to@stain).Pull Request 1206Add missing ToolShed categoriesPull Request 1207Use WorkflowId rather than StoredWorkflowId when autoupdating subworkflows
(thanks to@simonbray).Pull Request 1205Always use random id_secret for testing (thanks to@bernt-matthias).Pull Request 1198Add rerun subcommand for rerunning jobs (thanks to@simonbray).Pull Request 11400.74.9 (2021-11-03)Fix rendering of subworkflow steps for workflow testing report (thanks to@simonbray).Pull Request 1200Replace Galaxy interactor galaxy_requests_post with make_post_request from
BioBlend (thanks to@simonbray).Pull Request 12010.74.8 (2021-10-10)Exclude click 8.0.2.Pull Request 1196Add tool version numbers to autoupdate logging (thanks to@simonbray).Pull Request 1188Allow tool autoupdate without conda installation (thanks to@simonbray).Pull Request 1193use correct key execution_problem in template (thanks to@bernt-matthias).Pull Request 11950.74.7 (2021-09-21)Fix documentation to include--download_outputsflag (thanks to@simonbray).Pull Request 1184Select refgenie config based on Galaxy versionPull Request 1187Extend autoupdate subcommand to workflows (thanks to@simonbray).Pull
Request 11510.74.6 (2021-07-23)Add JSON report for planemo run invocations (thanks to@simonbray).Pull
Request 1153Ignore failure to download output datasetsPull Request 1179Allow location to point to url for outputsPull Request 1180Fix –shed_install for gxformat2 workflowsPull Request 11820.74.5 (2021-06-25)Remove iuc from default channelsPull Request 1170Fix parsing of changelog for git releasePull Request 1171Remove legacy commands, egg handlingPull Request 1172Use bioblend’s invoke_workflowPull Request 1173Create more useful output for failed invocationsPull Request 1174Improve dockstore_initPull Request 11770.74.4 (2021-06-01)Relicense under the MIT licensePull Request 1169Revise log levels (thanks to@bernt-matthias).Pull Request 1165Create upload_data subcommand (thanks to@simonbray).Pull Request
1164Create--download_outputsflag for theruncommand
(thanks to@simonbray).Pull Request 1157Make simultaneous file upload configurable for the run and test commands
(thanks to@simonbray).Pull Request 1156Add option to add tags to a history with theruncommand
(thanks to@simonbray).Pull Request 1154ReviseAllurereporting experience for workflows.Pull Request 11520.74.3 (2021-02-25)Load both cat1 versions when testing workflowsPull Request 1146Fix isolated virtualenv not getting activatedPull Request 1145Use bioblend’s make_get_request for authenticated requestPull Request 1144Display live logs when Galaxy is run in backgroundPull Request 11420.74.2 (2021-02-21)Allow testing dir of workflowsPull Request 1095Fix container register for gh workflowPull Request 1135,Pull Request 1133Don’t fail URL linting if blocked by CloudFlarePull Request 11341133`_Allow planemo run to stage exisiting datasets and relative paths (thanks to@simonbray).Pull Request 11280.74.1 (2021-01-03)Fixci_find_toolsandci_find_reposcommands.Pull Request 11270.74.0 (2020-12-30)Allow running Galaxy workflow tests against externally defined workflows.Pull Request 1126,Pull Request 1125,Pull Request 1123Require Pythontabulatepackage for thelist_invocationscommand.Pull Request 11240.73.0 (2020-12-28)Integrate important features fromgxwffor running workflows - including
building up profile commands for creating aliases, allowing referencing workflows
by external IDs, and listing invocations (thanks to@simonbray).Pull Request 1076Documentation for usingplanemo runto execute workflows (thanks to@simonbray).Pull Request 1102Addworkflow_uploadcommand for publishing each workflow of a repository with many
workflows to their own standalone repository.Pull Request 1091Update github commands to authenticate with a token rather than
username/password (thanks to@simonbray).Pull Request 1083Document “advanced” tool test debugging (thanks to@bernt-matthias).Pull Request 1108Various fixes for workflow commands - includingworkflow_convert,workflow_lint,workflow_job_init, andworkflow_test_init(thanks to@simonbray).Pull Request 1101,Pull Request 1118,Pull Request 1121,Pull Request 1116,Pull Request 1064Allow outputting test results asAllureframework results.Pull Request 1115Fixrun_tests.shinvocationPull Request 1099Tiny typo in debugging output (thanks to@abretaud).Pull Request 1066Fix typo in ‘planemo test’ help text for –skip_venv (thanks to@peterjc).Pull Request 1068Fixes for CLI whenexternal_galaxyis used as the engine (thanks to@simonbray).Pull Request 1072Updating base image to 20.05 for training topics
(thanks to@bedroesb).Pull Request 1074Changes to update_test_data testing mode (thanks to@simonbray).Pull Request 1079Fix docker options when fillingjob_conf.xmltemplate.Pull Request 1086Explicit tests for Galaxy 20.09.Pull Request 1093Minor fix forci_find_reposcommand.Pull Request 1094Fix a couple ofCheetahurls in Galaxy tool documentation (thanks to@martenson).Pull Request 1096Fix doc link from a redirect loop to a section (thanks to@martenson).Pull Request 1110Clarifytutorial.mdusage of citations (thanks to@blankenberg).Pull Request 1114FixZeroDivisionErrorwhen no tests are executed (thanks to@simonbray).Pull Request 11200.72.0 (2020-08-04)More documentation/support around running workflows including new command
to initialize workflow jobsworkflow_init_job.Pull Request 1052Workflow tests and documentation for tagging inputs.Pull Request 1058Various documentation improvements.Pull Request 1061,Pull Request 1062Add mypy type checking.Pull Request 1060Progress decoupling Planemo’s core from click & CLI interactions.Pull Request 1059Tests for workflow testing script.Pull Request 8210.71.0 (2020-08-03)Drop Python 2 support.Pull Request 1026Rev Galaxy dependencies - including bumping bioblend to 0.14.0, galaxy-tool-util,
and unpinning cwltool (last of these thanks to thanks to@TMiguelT).Pull Request 1038,Pull Request 1034Workflow linting, best practices, and tooling to assist in following them.Pull Request 1028,Pull Request 1049,Pull Request 1051Pull Request 1044Substantial rewrites to Galaxy workflow input staging - including allow nested
collection and composite inputs to Galaxy forrunandtest.Pull Request 900,Pull Request 1029Remove assorted older, likely unused commands.Pull Request 1043Update installation.rst (thanks to@mblue9).Pull Request 1032Automatic PyPI upload on tag using GitHub Actions.Pull Request 994Fix quay repository presence check for single target builds.Pull Request 993More fine grained options for--shed_install(thanks to@AndreasSko).Pull Request 1001Change default Python version for Galaxy (thanks to@bernt-matthias).Pull Request 1021Sort tests by id when merging (thanks to@bernt-matthias).Pull Request 1022Add--group_toolsoption toci_find_tools(thanks to@bernt-matthias).Pull Request 1008Add shared data library path to the data upload box for training material
(thanks to@shiltemann).Pull Request 1013Add support for tool versions to tutorial template generator (thanks to@shiltemann).Pull Request 1041Only copy test files if they don’t exist.Pull Request 1037Improvements to loading stock tools for workflow testing and serving (
add new stock tools to list and check subworkflows).Pull Request 1031Fix link for composite data type docs (thanks to@bernt-matthias).Pull Request 1020Do not usegi._make_url()internal BioBlend method.Switch CWL examples to usehttps://schema.org/version/latest/schema.rdf(thanks to@mr-c).Pull Request 1015Fix docs not to claim Galaxy can’t run on Python 3.Pull Request 1023Improved abstractions around target Galaxy instance.Pull Request 1046Add empty refgenie config for tests (thanks to@blankenberg).Pull Request 1025Substantial reworking of testing infrastructure.Pull Request 1024,Pull Request 1003,Pull Request 1011,Pull Request 1006,Pull Request 1040,Pull Request 1036,Pull Request 10420.70.0 (2020-01-29)Temporarily add galaxy-util requirementPull Request 991Make symlinks in tool tree work for planemo testPull Request 988Reduce use ofshell=Truein subprocessesPull Request 989Drop planemo database seed optionPull Request 985Don’t executeuntar_to()subprocesses through the shellPull Request  984Allow setting database_connection for planemo test runsPull Request 986Fix copy-paste mistakesPull Request 983Add planemo list_repos commandPull Request 982Make container_register build files with headers and include base_imagePull Request 980Replace deprecated galaxy-lib requirement with galaxy-tool-utilPull  Request 978Close all opened files (thanks to@bernt-matthias).Pull Request 979Build single requirement container, log if requirement not in best-practice channelsPull Request 977Use tojson jinja2 filter instead of json.dumpsPull Request 975Add merge_test_reports commandPull Request 974Implement github workflow and fix profile commands if psql unavailablePull Request 976Fix planemo lint –biocontainers if no build number in containerPull Request 972Update a training command (thanks to@hexylena).Pull Request 973Allow passing through GALAXY_VIRTUAL_ENV variable to venv setupPull Request 971Correct help text (thanks to@hexylena).Pull Request 970Remove unneeded html5lib requirementPull Request 9680.62.1 (2019-10-14)Init & update submodules when installing and creating packages. Stop
distributing eggs (thanks to@nsoranzo).1ab85300.62.0 (2019-10-11)Useunicodify()on exceptions and subprocess outputs (thanks to@nsoranzo)Pull Request 944Do not overrideNonewith empty string (thanks to@ic4f).Pull Request
950Update Docker template for training material generation (thanks to@bedroesb).Pull Request 958Add support for suite of repos with different owners (thanks to@nsoranzo).Pull Request 959Link for collection details updated in the docs (thanks to@martin-raden).Pull Request 963Move most tests to Python 3.7, drop Python 3.4 (thanks to@nsoranzo).Pull Request 964Remove confusing warningPull Request 9660.61.0 (2019-07-08)Training - fix empty repeat + some formatting (thanks to@bebatut).Pull
Request 926Training - add bibliography to tutorial template (thanks to@shiltemann).Pull Request 938Training - support new class definition for input in workflow step (thanks to@bebatut).Pull Request 943Various tool tutorial fixes ahead of GCC 2019 (thanks to@nsoranzo).Pull Request 940Return validation error if doi is empty (thanks to@nsoranzo).Pull Request 9370.60.0 (2019-05-31)Return validation error if doi is emptyPull Request 937Add junit as test reporter (thanks to@selten).Pull Request 935Update galaxy.xsd for new python 3 compatibility attribute (thanks to@martenson).Pull Request
931Documentation: add a little warning for <param … multiple=”true”> (thanks to@bernt-matthias).Pull Request 9300.59.0 (2019-05-09)Add ability to test data manager tools (thanks to@mvdbeek).Pull Request 912Update Training for new requirement definition (thanks to@bebatut).Pull Request 913Drop amqp workaround (thanks to@mvdbeek).Pull Request 917Useyaml.safe_load()instead of deprecatedload()(thanks to@nsoranzo).Pull Request 921Allow convertingtool_test_report.jsonto xunit (thanks to@mvdbeek).Pull Request 918Fix error if testcase.data.job does not exist (thanks to@mvdbeek).Pull Request 924Fix deprecatedgetchildren()(thanks to@nsoranzo).Pull Request 9250.58.2 (2019-03-01)Fix display of tool ids in planemo html report (thanks to@mvdbeek).Pull Request 908Single quotes for file names (thanks to@bernt-matthias).Pull Request
909Fix doc linting (thanks to@mvdbeek).Pull Request 910Update TS categories (thanks to@nsoranzo).07dc6e0Close tag in doc help, to help with copy&paste (thanks to@blankenberg).Pull Request 914Update the tool XSD file (thanks to@bgruening).Pull Request 9150.58.1 (2019-01-03)Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to@nsoranzo).Pull Request 906Fix command run byplanemo test –skip_venv(thanks to@nsoranzo).Pull Request 9070.58.0 (2019-01-01)Remove deprecatedsudo: falsefrom .travis.yml (thanks to@nsoranzo).Pull Request 902Do not skip Galaxy client build forplanemo serve. Install Galaxy when the
directory specified with--galaxy_rootdoes not exist or is empty. (thanks
to@nsoranzo).Pull Request 895,Issue 8450.57.1 (2018-11-23)Fix username validation for shed linting (thanks to@martenson).Pull Request 899,Issue 8980.57.0 (2018-11-19)Allowworkflow_convertto convert a native.gaworkflows to format 2 (yaml).Pull Request 896New command (workflow_edit) to open workflow in a synchronized graphical editor.Pull Request 894Conda tutorial fixes (thanks to@nsoranzo).Pull Request 876Enable--conda_use_localoption forplanemo test(thanks to@nsoranzo).Pull Request 876When testing, skip workflow outputs that do not have alabelset (thanks to@bgruening).Pull Request 893Add__repr__forTestCaseto improve debugging Planemo
(thanks to@bgruening).Pull Request 892Increase IO polling interval over time (thanks to@martenson).Pull Request 891Sync galaxy xsd and fix tests (thanks to@mvdbeek).Pull Request 889Linting fix forW605(thanks to@martenson).Pull Request 888Add icon for repeat parameters in training (thanks to@bebatut).Pull Request 8870.56.0 (2018-10-30)Allow selection of Python version when starting managed Galaxy
(thanks to@mvdbeek).Pull Request 874Change the channel priority of conda (again). (thanks to@bgruening).Pull Request 867Some small english corrections (thanks to@hexylena).Pull Request 868Print the list of excluded paths when runningci_find_repos(thanks to@nsoranzo).Pull Request 877Improved XSD lint reporting.Pull Request 871Fix Planemo writing a file calledgx_venv_None.Pull Request 870Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to@nsoranzo).Pull Request 864Fix to make workflow testing more robust.Pull Request 8820.55.0 (2018-09-12)Add commands to create Galaxy training materials (thanks to@bebatut).Pull Request 861Fixplanemo testwhen TEMP env variable contain spaces (thanks to@nsoranzo).Pull Request 851Support testing a completely remote galaxy instance (thanks to@hexylena).Pull Request 856Allow naming history from command line (thanks to@hexylena).Pull Request 860Sync galaxy.xsd from galaxy repo (thanks to@nsoranzo).Pull Request 866Fix ServeTestCase.test_shed_serve test (thanks to@nsoranzo).bad810a0.54.0 (2018-06-06)Better support for testings against different versions of Galaxy efficiently and robustly.Pull Request 849New database version (thanks to@bgruening).Pull Request 847Hyperlink DOIs against preferred resolver (thanks to@katrinleinweber).Pull Request 850Tests for collection inputs to workflows.Pull Request 843Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust.b12b117More tutorial testing, tutorial updates.016b923,324c776,2002b49More isolatedtest_shed_upload.pytests.72d2ca7Add filetype support for workflow test inputs (thanks to@bgruening).Pull Request 842Add--no_shed_installoption, to prevent shed installs as part of workflow testing.Pull Request 841Small docs fix (thanks to@hexylena).Pull Request 8480.53.0 (2018-05-22)Make Planemo testing easier for CWL tools and workflows in various ways and update
tutorials to reflect these simplifications.Pull Request 837Test and fix running workflow tests against externally managed Galaxy servers.Pull Request 833,Pull Request 836Allow using URIs for inputs of workflow test.Pull Request 840Slide Galaxy testing window to include 18.05 and drop 17.09.Pull Request 8380.52.0 (2018-05-20)Allow optional disabling of Galaxy single user mode.Pull Request 835Fix for path pasting options during workflow testing.Pull Request 8340.51.0 (2018-05-19)Fix essentially allCondaandBioContainersrelated functionality to allow parity betweenCWLand existing Galaxy functionality - fixes and enhances many commands includinglint,conda_install,conda_env,test,run, andmull.Pull Request 828Add two new tutorials forCondaandContainerdevelopment with CWL tools that mirrors the existing tutorials for Galaxy tools - including new
CWL exercises, answers, and example project templates.347c622Improve the CWL generated by thetool_initcommand to properly deal withSoftwareRequirements and generate more idiomatic CWL.Pull Request 820,a5c72e3Add new engine type (--enginetoil) for testing and runningCWLtools (requires
manually installingToilwithpip install toilin Planemo’s environment).Pull Request 831Adddocumentationfor the Galaxy Workflow andCWLtest format files (includes information on configuring
various test engines).Pull Request 832Better default logging config for CWL development.Pull Request 830Various fixes for theconda_searchcommand.Pull Request 826Fix test coverage configuration.Pull Request 822Reorganize .travis.yml for clarity.Pull Request 829More isolated, robust unit tests that usegit.Pull Request 827,Pull Request 818Fix default list of best-practice Conda channels.Pull Request 825Refactor tests to speed up quick tests - fewer buggy URLs fetched in “quick” mode.Pull Request 823Fix upload configuration of workflow testing to default (overrideable) external Galaxies
to not use path pasting.Pull Request 816Fix test number parsing for workflow tests.Pull Request 8170.50.1 (2018-05-11)Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container--engine.0.50.0 (2018-05-10)Fixes and small CLI tweaks to get the Docker Galaxy container working as an--enginefor the
run, serve, and test commands.0.49.2 (2018-05-09)Various small fixes for new external Galaxy engine type.0.49.1 (2018-05-06)FixPyPIREADME rendering for 0.49.0 release changes.0.49.0 (2018-05-06)Implement external Galaxy engine.Pull Request 781Restructure serve testing code for reuse.Pull Request 795Improve test report handling for JSON generated via galaxy-lib testing
script.Pull Request 799Improve how various branches of Galaxy are tested.Pull Request 800Added documentation forGALAXY_MEMORY_MB(thanks to@bernt-matthias).Pull Request 801Log tool config in verbose logging mode.Pull Request 802Replacerchannel withconda-forge(thanks to@bgruening).Pull Request 805Syncgalaxy.xsdwith latest Galaxy updates (thanks to@nsoranzo).Pull Request 806Userequests.get()when validating http URLs (thanks to@nsoranzo).Pull Request 809Do not consider tools with “deprecated” in the path (thanks to@bgruening).Pull Request 810Automatically load tools shipped with Galaxy when testing, running, or serving
workflows that reference these tools.Pull Request 790Revise README and touch up documentation in general.Pull Request 787Various small changes to testing and test framework.Pull Request 792Various Python 3 fixes.8cfe9e9,41f7df1Fixes for Galaxy 18.0X releases.Pull Request 803,dc443d60.48.0 (2018-02-28)Run all CI tests against Python 3 (thanks to@nsoranzo).Pull Request 768andPull Request 774Python 3 fix - subprocess withuniversal_newlines=True(thanks to@peterjc).Pull Request 764RecordCWLconformance test results using JUnit xml
(thanks to@mr-c).Pull Request 756Restore run test case for simple Galaxy tools.Pull Request 769Enhancements to Galaxy profiles and workflow testing.Pull Request 773Fix resolving & installing shed repositories from workflows fortestandruncommands.Pull Request 776Implement planemo command to convert format 2 workflows into .ga workflows.Pull Request 771Add a native Galaxy workflow (.ga) testing test.Pull Request 770Drop Brew support but add more detailed install instructions.Pull Request 761Clean upCWLconformance test execution.Pull Request 753Assorted smallCWLand deamon serve fixes.Pull Request 7590.47.0 (2017-11-18)Update to the latest Galaxy tool XSD  (thanks to@nsoranzo).Pull Request 747Re-fix problem when shed_update would fail if nothing to update
(thanks to@nsoranzo).Pull Request 747Update instructions for installation via conda (thanks to@nsoranzo) .Pull Request 743Bug fix for MacOSchmoddoesn’t support–recursiveflag.
(thanks to@dfornika).Pull Request 739Bug fix to alsosocket.errorwhen linting URLs
(thanks to@nsoranzo).Pull Request 738Disable broken tests.Pull Request 7450.46.1 (2017-09-26)Rev to latest versions ofbioblendandgalaxy-libfor various fixes
related toCWL.0.46.0 (2017-09-15)Change behavior of--dockerflag, for a few releases it would require
Galaxy use a container for every non-upload tool. This breaks various
conversion tools for instance and so was reverted.Pull Request 733Add ‘Accept’ header when linting doc URLs (thanks to@nsoranzo).Pull Request 725Fix–conda_auto_installhelp (thanks to@nsoranzo).Pull Request 727Incremental progress toward CWL support via Galaxy.Pull Request 729,Pull Request 732Update galaxy-lib to latest version to fix various issues.Pull Request 730Fix lint detected problems with documentation.Pull Request 7310.45.0 (2017-09-06)Update to the latestgalaxy-libfor Conda fixes. (thanks@nsoranzo)
and updatedCWLutilities.Pull Request 716,Pull Request 723UpdateCondachannel order to sync withBioconda(thanks to@nsoranzo).Pull Request 715Experimental support runningCWLworkflows through theCWLfork of Galaxy.Mentionplanemo command--helpin main help
(thanks to@peterjc).Pull Request 709Bugfix handleNonerequirement versions when registering containers
(thanks to@bgruening).Pull Request 704Bugfix for dependencies by pinning ruamel.yaml version
(thanks to@mvdbeek).Pull Request 7200.44.0 (2017-06-22)Fix and improve Galaxy root option specification options.Pull Request 701,8a608e0Updateplanemo mullto use a default action ofbuild-and-testsincebuildno longer cleans up itself.ecc1bc2Add a command to pre-installInvolucro.Pull Request 7020.43.0 (2017-06-22)Remove stdio from generated tools - just use exit_code for everything.91b6fa0Implement some ad-hoc documentation tests.Pull Request 699A large number of small enhancements and fixes for the documentation and
example projects.0.42.1 (2017-06-16)Fix Readme typos (thanks to@manabuishii)904d77aFixcontainer_registerto create pull requests against the newly finalized home of the
multi-package-containers registry repository.9636682Fixuse_global_configanduse_env_varfor options with unspecified defaults.475104c0.42.0 (2017-06-15)Conda/Container documentation and option naming improvements.Pull Request
684Syncgalaxy.xsdwith latest upstream Galaxy updates (thanks to@nsoranzo).Pull Request 687Fixci_find_reposcommand to not filter repos whose only modifications where
in subdirs (thanks to@nsoranzo).Pull Request 688Updatecontainer_registerfor mulled version 2 and repository name changes.Pull Request 689Better pull request messages for thecontainer_registercommand.Pull Request 6900.41.0 (2017-06-05)Fixshed_updatenot fail if there is nothing to update
(thanks to@nsoranzo).Issue 494,Pull Request 680Conda documentation and option naming improvements.Pull Request 683Implementcontainer_registerfor tool repositories.Pull Request 675Fixhubbinary installation for Mac OS X.Pull Request 6820.40.1 (2017-05-03)Fix data manager configuration to not conflict with original Galaxy atgalaxy_root(thanks to@nsoranzo).Pull Request 662Fixfilter_paths()to not partial match paths when filtering shed repositories
(thanks to@nsoranzo).Pull Request 665Fix description when creating.shed.ymlfiles (thanks to@RJMW).Pull Request 6640.40.0 (2017-03-16)Implement instructions and project template for GA4GH Tool Execution
Challenge Phase 1.84c4a73Eliminate Conda hack forcing/tmpas temp directory.b4ae44dRun dependency script tests in isolated directories.32f41c9Fix OS X bug inplanemo runby reworking it to wait using urllib instead of sockets.31292160.39.0 (2017-03-15)Implement documentation and examples for Conda-based dependency development (under
“Advanced” topics).Pull Request 642,Pull Request 643Implement documentation and examples for container-based dependency development (under
“Advanced” topics).0a1abfeImplement aplanemo conda_searchcommand for searching best practice channels
from the command line.Pull Request 642Allow Planemo to work with locally built Conda packages using the--conda_use_localcommand.Pull Request 643,Issue 620Implement anopen(or justo) command to quickly open the last test results
(or any file if supplied).Pull Request 641Linting improvements and fixes due togalaxy-libupdate.
* WARN on test output names not found or not matching.
* INFO correct information about stdio if profile version is found.
* WARN if profile version is incorrect.
* INFO profile version
* Fixassert_commandnot detected as a valid test (fixesIssue 260).Havelint--conda_requirementscheck that at least one actual requirement is found.6638caaAllowconda_installto work with packages as well as just tools.8faf661Add--globaloption to conda_install to install requirements into global Conda setup
instead of using an environment.8faf661Implementplanemo lint--biocontainerthat checks that a tool has an available BioContainer
registered.0a1abfeAdd more options and more documentation to theplanemo mullcommand.0a1abfeHack around a bug in Conda 4.2 that makes it soplanemo mulldoesn’t work out of the box on
Mac OS X.0a1abfeAllow URIs to be used instead of paths for a couple operations.ce0dc4eImplement non-strict CWL parsing option.4c0f100Fixes for changes tocwltooland general CWL-relate functionality.3c95b7b,06bcf19,525de8f,9867e56,9ab4a0dEliminate deprecated XML-based abstraction fromplanemo.tools.04238d3FixMANIFEST.inentry that was migrated to galaxy-lib.ced5ce2Various fixes for the commandconda_env.Pull Request 640Improved command help - both formatting and content.Pull Request 639Implement a--no_dependency_resolutionoption disabling conda dependency
resolver.Pull Request 635,Issue 633Tests for new linting logic.Pull Request 638Fix bug where tool IDs needs to be lowercase for the shed (thanks to@bgruening).Pull Request 649Update seqtk version targetted by intro docs.e343b67Various other Conda usability improvements.Pull Request 6340.38.1 (2017-02-06)Fix bug withshed_lint--urlsintroduced in 0.38.0.84ebc1f0.38.0 (2017-02-06)Trim down the default amount of logging during testing.Pull Request 629,Issue 515Improved log messages during shed operations.08c067cUpdate tool XSD against latest Galaxy.fca4183,03c9658Fix bug whereshed_lint--toolsfor a suite lints the same tools multiple
times.Issue 564,Pull Request 6280.37.0 (2017-01-25)Update to the latestgalaxy-librelease. This means new installs start with
Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes manyCondarelated bugs.Change defaults so that Conda automatically initializes and performs tool installs
by default from within the spawned Galaxy server. The trio of flags--conda_dependency_resolution,--conda_auto_install, and--conda_auto_initare effectively enabled by default now.4595953Use the Galaxy cached dependency manager by default (thanks to@abretaud).Pull Request 612Test Conda dependency resolution for more versions of Galaxy including the forthcoming
release of 17.01.Update to the latest Galaxy tool XSD for various tool linting fixes.32acd68Fix pip ignores forbioconda_scripts(thanks to@nturaga)Pull Request 6140.36.1 (2016-12-12)Fix move error when usingproject_init.Issue 388,Pull Request 610Improved integration testing fortestcommand.Pull Request 609Update CWL links to v1.0 (thanks to@mr-c).Pull Request 6080.36.0 (2016-12-11)Bring in latest tool XSD file from Galaxy (thanks to@peterjc).Pull Request 605PEP8 fixes for various linting problems
(thanks to@peterjc).Pull Request 606Update tool syntax URL to new URL (thanks to@mvdbeek).Pull Request 6020.35.0 (2016-11-14)Native support for building bioconductor tools and recipes
(thanks to@nturaga).Pull Request 570Fixes for running Galaxy via docker-galaxy-stable (thanks to@bgruening).50d3c4aImport order linting fixes (thanks to@bgruening).0.34.1 (2016-10-12)Mimic web browser to validate user help URLs fixingIssue 578(thanks to@peterjc).Pull Request 591Fix for Bioconda recipes depending onconda-forge(thanks to@nsoranzo).Pull Request 5900.34.0 (2016-10-05)Implementmullcommand to build containers for tools based onCondarecipes matching requirement definitions.08cef54Implement--mulled_containersflag ontest,serve, andruncommands to run tools in “mulled” containers. Galaxy will first search
locally cache containers (such as ones built withmull), then search
the mulled namespace ofquay.io, and finally build one on-demand if
needed usinggalaxy-libandInvolucrodeveloped by@thriqon.Implement--conda_requirementsflag onlintcommand to ensure requirements
can be resolved in best practice channels.9da8387Allowconda_installcommand over multiple tool paths.2e4e5fcUpdatepipas part of setting virtual environment inMakefiletarget.19b2ee9Add script to auto-updateBiocondarecipe for Planemo and open a pull request.f0da66f0.33.2 (2016-09-28)Fix HISTORY.rst link problem that prevented correct display of content onPyPI.0.33.1 (2016-09-28)Fixlint--urlsfalse positives by being more restrictive with what is considered a URL
(fixed by@hexylenaafter detailed report from@peterjc).Issue 573,Pull Request 5790.33.0 (2016-09-23)Enable XSD validation of tools by default (restore old behavior withplanemo lint--no_xsd).1ef05d2Implement aconda_lintcommand to lintCondarecipes based
onanaconda-verify.6a6f164Implementcloneandpull_requestcommands to ease PRs
(with documentation fixes from@martenson).e925ba1,ea5324fUpdategalaxy.xsdto allow version_command’s to have an interpreter
attribute.7cca2e4Apply improvement from@nsoranzofor Planemo’s use ofgit diff.6f91719Pull in downstream refactoring oftool_initcode from@nturaga’sBioconductorwork.ccdd2d5Update to latestTool Factorycode fromtools-iuc.ca88b0cSmall code cleanups.b6d8294,d6da3a8Fixup docs inplanemo.xml.validation.Allow skipping newly requiredlxmldependency insetup.py.34538de0.32.0 (2016-09-16)Enhanceplanemo lint--xsdto use a fairly complete and newly official XSD
definition.Pull Request 566Migrate and update documentation related to tool XML macros and handling
multiple outputs from the Galaxy wiki (with help from@bgruening,@mvdbeek,
and@nsoranzo).Pull Request 559Documentation fixes (thanks to@ramezrawas).Pull Request 561Do not fail URL linting in case of too many requests (thanks to@nsoranzo).Pull Request 5650.31.0 (2016-09-06)Implement new commands toci_find_reposandci_find_toolsto ease
CI scripting.Pull Request 5550.30.2 (2016-09-01)Fix another problem withCondaprefix handling when using--conda_dependency_resolution.f7b6c7e0.30.1 (2016-09-01)Fix a problem withCondaprefix handling when using--conda_dependency_resolution.f7b6c7eFix for quote problem inupdate_planemo_recipe.bash.6c03de8Fix to restore linting oftests/directory and fix import order throughout
module.ef4b9f40.30.0 (2016-09-01)Update to the latestgalaxy-librelease and changeCondasemantics to match
recent updates to Galaxy. For the most robustCondausage - use planemo 0.30+
with Galaxy 16.07 or master.07d94bdImplement the--conda_auto_initflag forconda_install.ca19910Allow the environment variablePLANEMO_CONDA_PREFIXto set a default
for--conda_prefix.24008abFixup documentation regarding installs andConda.ce44e87Fix and lint Python module import order throughout project.Pull Request 550Usecprather than symlink to$DOWNLOAD_CACHEin thedependency_scriptcommand (thanks to@peterjc).c2204b3Fixes for the Homebrew recipe updater.c262b6d0.29.1 (2016-08-19)Improved handling of Python 2.7 specific dependencies.0.29.0 (2016-08-19)Look for sha256sum checksums during shed_lint (thanks to@peterjc).Pull Request 539An assortment fixes and enhancements to thedependency_scriptcommand
(thanks to@peterjc).Pull Request 541,Pull Request 545Fix shed_build to respect exclude: in .shed.yml (thanks to@nsoranzo).Pull Request 540Fix linting of tool URLs (thanks to@nsoranzo).Pull Request 5460.28.0 (2016-08-17)Fixes forbioblendv0.8.0 (thanks to@nsoranzo).9fdf490Enable shed repo type update (thanks to@nsoranzo).3ceaa40Create suite repositories with repository_suite_definition type by default
(thanks to@nsoranzo).057f4f0Includeshed_lintin script run bytravis_init(thanks to@peterjc).Pull Request 528Minor polish to thetravis_initcommand (thanks to@peterjc).Pull Request 512Updatepipand setuptools on TravisCI; fix travis_init (thanks to@peterjc).Pull Request 521Shorten command one line descriptions for main help (thanks to@peterjc).Pull Request 510Useplanemo test--no_cache_galaxyunder TravisCI (thanks to@peterjc).Pull Request 513Improve and fix docs ahead of GCC 2016 (thanks to@martenson).Pull Request 498,725b232Add description ofexpect_num_outputsto planemo FAQ.a066afbRevise planemo tools docs to be more explicit about collection identifiers.a811e65Add more docs on existing dynamic tool output features.Pull Request 526Fix serve command doc (thanks to@nsoranzo).8c088c6Fixmake lint-readme(RST link errors) (thanks to@peterjc).Pull Request 525Add union bedgraph example to project templates (for GCC demo example).d53bcd6Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as
shed categories (thanks to@bgruening,@gregvonkuster, and@nsoranzo).e890ab5,08bb354,e2398fbRemove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to
Paul Stewart@pstew).Pull Request 5070.27.0 (2016-06-22)Use ephemeris to handle syncing shed tools for workflow actions.1c6cfbbMore planemo testing enhancements for testing artifacts that aren’t
Galaxy tools.Pull Request 491Implementdocker_galaxyengine type.eb039c0,Issue 15Enhance profiles to be Dockerized Galaxy-aware.Pull Request 488Add linter for DOI type citation - thanks to@mvdbeek.Pull Request 4840.26.0 (2016-05-20)ImplementEngineandRunnableabstractions - Planemo now has
beta support for testing Galaxy workflows andCWLtools with Galaxy and
anyCWLartifact withcwltool.Pull Request 454,7be1bf5Fix missing command_line in test output json.e38c436More explicit Galaxyjob_conf.xmlhandling, fixes bugs caused bygalaxy_roothaving existing and incompatiblejob_conf.xmlfiles
and makes it possible to specify defaults with fixed server name.c4dfd55Introduce profile commands (profile_create,profile_delete, andprofile_list) and profile improvements (automatic postgres database
creation support).Pull Request 480,a87899bRework Galaxy test reporting to use structured data instead of XUnit
data.4d29bf1Refactor Galaxy configuration toward support for running Galaxy in
docker-galaxy-stable.Pull Request 4790.25.1 (2016-05-11)Tweak dependencies to try to fixcwltoolrelated issues - such
asIssue 475.0.25.0 (2016-05-11)Implement Galaxy “profiles” - the ability to configure
perisistent, named environments forserveandtest.5d08b67Greatly improvedservecommand - maketest-dataavailable as an FTP folder, (on 16.07) automatically log
in an admin user, and many more options (such as those
required for “profiles” and a--daemonmode).Two fixes to ensure more consistent, dependabletestoutput.Pull Request 472,f3c6917Add code and documentation for linting (lint) and
building (tool_init)CWLtools.a4e6958,b0b867e,4cd571cIf needed forCondaworkaround, shortenconfig_directorypath (thanks to@mvdbeek).efc5f30Fix--no_cache_galaxyoption (thanks to Gildas Le
Corguillé).d8f2038Target draft 3 ofCWLinstead of draft 2.775bf49Fixcwltooldependency version - upstream changes broke
compatibility.65b999dAdd documentation section and slides about recent Galaxy
tool framework changes (with fix from@remimarenco).069e7baAdd IUC standards to Planemo docs.2ae2b49Improve collection-related contents in documentation
(thanks in part to@martenson).fea51fc,13a5ae7Add documentation onGALAXY_SLOTSand running planemo
on a cluster.45135ff,e0acf91Revise command-line handling framework for consistency and
extension - allow extra options to be configured as
defaults~/.planemo.ymlincluding--job_config_fileandCondaconfiguration options.e769118,26e378eFixtool_initcommans options typos (thanks to
Nitesh Turaga).826d371Refactor galaxy-related modules into submodules of a newplanemo.galaxypackage.8e96864Fix error message typo (thanks to@blankenberg).b1c8f1dUpdate documentation for recent command additions.3f4ab44Rename option--galaxy_sqlite_databaseoption to--galaxy_database_seedand fix it so it actually works.f7554d1Add--extra_toolsoption toservecommand.02a08a0Update project testing to include linting documentation
(docs/), Python import order, and docstrings.a13a120,6e1e726,95d5cba0.24.2 (2016-04-25)Revert “check.shed.ymlowner against credentials during shed
creation”, test was incorrect and preventing uploads.Pull Request 425,Issue 2460.24.1 (2016-04-08)Fix test summary report.Pull Request 429Improve error reporting when runningshed_test.ce8e1beImproved code comments and tests for shed related functionality.89674cbRevgalaxy-libdependency to 16.4.1 to fix wget usage in
newer versions of wget.d76b4890.24.0 (2016-03-29)Drop support for Python 2.6.93b7bdaA variety of fixes forshed_update.Pull Request 428,Issue 416Fix reporting of metadata updates for invalid shed updates.Pull Request 426,Issue 420Check.shed.ymlowner against credentials during shed creation.Pull Request 425,Issue 246Fix logic error if there is a problem withshed_create.358a42cTool documentation improvements.0298510,a58a3b80.23.0 (2016-02-15)Fix duplicated attributes withCondaresolver (thanks
to Björn Grüning).Pull Request 403Upgrade to latest version ofgalaxy-libfor more linting.Attempt to better handle conditional dependency on cwltool.0.22.2 (2016-01-14)Fixed bug targetting forthcoming release of Galaxy 16.01.0.22.1 (2016-01-14)Fixed problem withPyPIbuild artifacts due to submodule’s not
being initialized during previous release.0.22.0 (2016-01-13)Add--skip_venvto support running Galaxy 16.01 inside of
conda environments.9f3957dImplement conda support.f99f6c1,ad3b2f0,5e0b6d1Update LICENSE for Planemo to match Galaxy.15d33c7Depend on newgalaxy-libonPyPIinstead of previous hacks….Pull Request 394Fix egg caching against master/15.10.6d0f502Fix bug causing shed publishing of.svndirectories.Issue 391Bug fixes forCondasupport thanks to@bgruening.63e456cFix document issues thanks to@einon.Pull Request 390Improve client for shed publishing to support newer shed backend
being developed by@hexylena.Pull Request 394Tool Shedrepo_idchange,@hexylena.Pull Request 398Various other small changes to testing, project structure, and
Python 3 support.0.21.1 (2015-11-29)Fix serious regression totestcommand.94097c7Small fixes to release process.4e1377c,94645ed0.21.0 (2015-11-29)Ifvirtualenvnot onPATH, have Planemo create one for Galaxy.5b97f2eAdd documentation section on testing tools installed in an existing
Galaxy instance.1927168When creating a virtualenv for Galaxy, prefer Python 2.7.e0577e7Documentation fixes and improvements thanks to@martenson.0f8cb10,01584c5,b757791Specify a minimumsixversion requirement.1c7ee5bAdd script to test a planemo as a wheel.6514ff5,Issue 184Fix empty macro loading.Issue 362Fix an issue when you runshed_diff--shed_targetlocalthanks
to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff.Pull Request 375Fixshed_diffprinting to stdout if-oisn’t specified.f3394e7Smallshed_diffimprovements to XML diffing and XUnit reporting.af7448c,83e227aMore logging ofshed_diffresults if--verboseflagged.9427b47Addtest_reportcommand for rebuilding reports from structured JSON.99ee51aFix option bug with Click 6.0 thanks to@bgruening.2a7c792Improved error messages for test commands.fdce74cVarious fixes for Python 3.2f66fc3,7572e99,8eda729,764ce01Use newer travis container infrastructure for testing.6d81a94Test case fixes.98fdc8c,0e4f70a0.20.0 (2015-11-11)More complete I/O capturing for XUnit.6409449Check for select parameter without options when linting tools.Issue 373Add--cwl_engineargument tocwl_runcommand.dd94ddcFixes for select parameter linting.8b31850Fix to demultiplexing repositories after tool uploads.Issue 361Fix to update planemo for Galaxy wheels.25ef0d5Various fixes for Python 2.6 and Python 3.c1713d2,916f610,c4448550.19.0 (2015-11-03)Initial implementation ofcwl_runcommand that runs a
CWL tool and job file through Galaxy.49c5c1eAdd--cwlflag toserveto experimentally serve CWL tools
in Galaxy.Pull Request 339Implement highly experimentalcwl_scriptcommand to convert
a CWL job to a bash script.508dce7Add name to all XUnit reports (thanks to@hexylena).Pull Request 343Capture stdout and stderr forshed_diffandshed_updateXUnit reports.Pull Request 344More tool linting (conditionals) thanks to@hexylena.Pull Request 350UTF-8 fixes when handling XUnit reports.Pull Request 345AddEpigeneticsas Tool Shed category.Pull Request 351Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to@natefoo).Pull Request 356Add--cite_urltotool_init.fdb1b51tool_initbug fix.f854138Fixsetup.pyfor cwltool andbioblendchanges.1a157d4Add option to specify template sqlite database locally.c23569fAdd example IPython notebooks to docs.c8640b60.18.1 (2015-10-22)Fix issue with test reporting not being populated.19900a60.18.0 (2015-10-20)Improvements todocker_shellusability (thanks to@kellrott).Pull Request 334Add docker pull attempt when missing Dockerfile (thanks to@kellrott).Pull Request 333Fix bug inferring which files are tool files (thanks to@hexylena).Pull Request 335,Issue 313Initial work toward automating brew recipe update.4d6f7d9,Issue 3290.17.0 (2015-10-19)Implement basic XUnit report option forshed_update(thanks to@martenson).Pull Request 322Fix issues with producing test outputs.572e754Xunit reporting improvements - refactoring, times, diff output (thanks to@hexylena).Pull Request 330Implement project governance policy and update developer code of conduct to
match that of the Galaxy project.Pull Request 316Update filters for account for new.txtand.mdtest outputs
(thanks to@hexylena).Pull Request 327Add verbose logging to galaxy test output handling problems.5d7db92Flake8 fixes (thanks to@martenson).949a36dRemove uses of deprecatedmktempPython standard library function
(thanks to@hexylena).Pull Request 3300.16.0 (2015-10-07)Adding new commanddependency_scriptto convert Tool Shed dependencies
into shell scripts - thanks to@peterjc.Pull Request 310,f798c7e,Issue 303Implement profiles in sheds section of the~/.planemo.yml.Pull Request 3140.15.0 (2015-10-01)Template framework for reporting including new markdown and plain
text reporting options for testing - thanks to@hexylena.Pull Request 304XUnit style reporting forshed_diffcommand - thanks to@hexylena.Pull Request 305Add newshed_buildcommand for building repository tarballs -
thanks to@kellrott.Pull Request 297Fix exit code handling forlintcommands - thanks to@mvdbeek.Pull Request 292Improved documentation forservecommand - thanks to@lparsons.Pull Request 312Tiny backward compatible Python 3 tweaks forTool Factory- thanks
to@peterjc.dad2d9dFixed detection of virtual environment inMakefile- thanks to@lparsons.Pull Request 311Updates to Galaxy XSD - thanks to@mr-c.Pull Request 309Allow reading shed key option from an environment variable.Pull Request 307Allow specifying host to serve Galaxy using-host- thanks in
part to@chambm.Pull Request 301Allow specifying defaults for-hostand--portin~/.planemo.yml.Pull Request 301Improve~/.planemo.ymlsample comments - thanks to@martenson.Pull Request 287Update tool shed categories - thanks to@bgruening.Pull Request 285Improved output readibility fordiffcommand - thanks to@martenson.Pull Request 2840.14.0 (2015-08-06)Allow-tas shorthand for--shed_target(thanks to Peter Cock).Pull Request 278Fixtool_initcommand to usefrom_work_dironly if file in command
(thanks to bug report and initial fix outline by Gildas Le Corguillé).Pull Request 277Various documentation fixes (thanks in part to Peter Cock and Daniel
Blankenberg).Pull Request 256,Pull Request 253,Pull Request 254,Pull Request 255,Pull Request 251,Issue 2720.13.2 (2015-07-06)Fix project_init for missing files.cb5b906Various documentation improvements.0.13.1 (2015-07-01)Fix forshed_initproducing non-standard type hints.Issue 243,f0610d7Fix tool linting for parameters that define anargumentbut not aname.Issue 245,aad1eedMany doc updates including a tutorial for developing tools in a test-driven
fashion and instructions for using the planemo appliance through Kitematic
(with Kitematic screenshots from E. Rasche).0.13.0 (2015-06-28)If planemo cannot find a Galaxy root, it will now automatically fetch
one (specifing--galaxy_installwill still force a fetch).Pull Request 235Docuementationhas been updated to reflect new and vastly improved Docker and Vagrant
virtual appliances are now available, as well as a new VirtualBox OVA
variant.Update linting for new tool XML features (includingdetect_errorsand output collections).Issue 233,334f2d4Fixshed_testhelp text.Issue 223Fix code typo (thanks to Nicola Soranzo).Pull Request 230Improvements to algorithm used to guess if an XML file is a tool XML file.Issue 231Fix configuration file handling bug.Issue 2400.12.2 (2015-05-23)Fixshed_testandshed_servefor test and local tool sheds.f3cafaa0.12.1 (2015-05-21)Fix to ensure the tab completion script is in the Python source tarball
(required for setting up tab-completion for Homebrew).6b4e7a60.12.0 (2015-05-21)Implement a--failedflag for thetestcommand to rerun
previously faied tests.Pull Request 210Implementshed_updateto upload contents and update repository
metadata.Pull Request 216Implementshed_testandshed_servecommands to test and view
published artifacts in the Tool Shed.Pull Request 213,Issue 176Add shell tab-completion script.37dcc07Many more commands allow specifing multiple tool and/or repository targets.Issue 150Add -m as alias for –message in planemo shed_upload (thanks to
Peter Cock).Pull Request 200Add--ensure_metadataoption toshed_lintto ensure.shed.ymlfiles contain many repository.Pull Request 215More developer documentation, additionalmaketargets including ones
for setting up git pre-commit hooks.cc8abb6,Issue 209Small README improvement (thanks to Martin Čech)b53006dFixes for shed operation error handling (thanks to Martin Čech).Pull Request 203,Pull Request 206Fix for “smart”shed_diffnot in the repository root directory
(thanks to Peter Cock).Pull Request 207,Issue 205Recursiveshed_diffwith directories not yet in Tool Shed.Pull Request 208Improve error handling and reporting for problematic--shed_targetvalues.Issue 217Fix typos in lint messages.Issue 2110.11.1 (2015-05-12)Fix default behavior forplanemo lintto use current directory if
explicit paths are not supplied.1e3668a0.11.0 (2015-05-12)More compact syntax for defining multiple custom inclusions in.shed.ymlfiles - thanks to Peter Cock.Issue 180,Pull Request 185,Pull Request 196Prevent ambigous destinations when defining custom inclusions in.shed.yml- thanks to Peter Cock.Pull Request 186lintnow warns if tool ids contain whitespace.Pull Request 190Handle empty tar-balls gracefully on older Python versions - thanks
to Peter Cock.Pull Request 187Tweak quoting incpcommand - thanks to Peter Cock.6bcf699Fix regression causing testing to no longer produce “pretty” test
results under certain circumstances.Issue 188Fix for recursiveshed_difffolder naming.Issue 192Fix output definitions totool_initcommand.Issue 1890.10.0 (2015-05-06)Extendshed_lintto check for valid actions in tool_dependencies.xml
files.8117e03Extendshed_lintto check for required files based on repository type.Issue 156Ignore common editor backup files duringshed_upload.Issue 179Fix missing file when installing from source viaPyPI.Issue 181Fixlintto verifydatainputs specify aformatattribute.8117e03Docstring fix thanks to@peterjc.fe7ad460.9.0 (2015-05-03)Add new logo to the README thanks to@petrkadlecfrompuradesign.czand@carlfeberhardfrom the Galaxy Project.Issue 108Implement smartershed_diffcommand - it now produces a meaningful
exit codes and doesn’t report differences if these correspond to attributes
that will be automatically populated by the Tool Shed.Issue 167Use new smartershed_diffcode to implement a new--check_diffoption forshed_upload- to check for meaningful differences before
updating repositories.Issue 168Record git commit hash duringshed_uploadif the.shed.ymlis
located in a git repository.Issue 170Allowshed_operations to operate on git URLs directly.Issue 169Fail if missing file inclusion statements encountered during.shed.ymlrepository resolution - bug reported by@peterjc.Issue 158Improved exception handling for tool shed operations including new--fail_fastcommand-line option. *Issue 114,Pull Request 173Implement more validation when using theshed_initcommand.1cd0e2dAdd-r/--recursiveoption toshed_downloadandshed_diffcommands and allow these commands to work with.shed.ymlfiles defining
multipe repositories.40a1f57Add--portoption to theserveandtool_factorycommands.15804beFix problem introduced withsetup.pyduring the 0.9.0 development cycle
- thanks to@peterjc.Pull Request 171Fix clone bug introduced during 0.9.0 development cycle - thanks to@bgruening.Pull Request 1750.8.4 (2015-04-30)Fix for Travis CI testing picking up invalid tests (reported by@takadonet).Issue 161Fix tar ordering for consistency (always sort by name) - thanks to@peterjc.Pull Request 164,Issue 159Fix exception handling related to tool shed operations - thanks to@peterjc.Pull Request 155,b86fe1f0.8.3 (2015-04-29)Fix bug whereshed_lintwas not respecting the-r/--recursiveflag.9ff0d2dFix bug where planemo was producing tar files incompatible with the Tool
Shed for package and suite repositories.a2ee1350.8.2 (2015-04-29)Fix bug withconfig_initcommand thanks to@bgruening.Pull Request 151Fix unnessecarylintwarning aboutparallelismtag reported by@peterjc.9bf1eab0.8.1 (2015-04-28)Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.0.8.0 (2015-04-27)Implement the newshed_lintcommand that verifies various aspects of tool
shed repositories - includingXSDvalidation ofrepository_dependencies.xmlandtool_dependencies.xmlfiles, best practices for README files, and the
contents of.shed.ymlfiles. This requires thelxmllibrary to be available
to Planemo or the applicationxmllintto be on itsPATH.Pull Request 130Issue 89Issue 91912df02d26929e36ac6d8Option to enable experimentalXSDbased validation of tools whenlintis executed with the new--xsdflag. This validation occurs against the
unofficialGalaxy Tool XSD projectmaintained by@JeanFred. This requires thelxmllibrary to be
available to Planemo or the applicationxmllintto be on itsPATH.Pull Request 130912df02Allow skipping specific linters when using thelintcommand using the new--skipoption.26e3cdbImplement sophisticated options in.shed.ymlto map a directory to many,
custom Tool Shed repositories during shed operaitons suchshed_uploadincluding automatically mapping tools to their own directories and automatically
building suites repositories.Pull Request 143Makeshed_uploadmore intelligent when building tar files so that package
and suite repositories may have README files in source control and they will
just be filtered out during upload.53edd99Implement a newshed_initcommand that will help bootstrap.shed.ymlfiles in the specified directory.cc1a447Extendshed_initto automatically build arepository_rependencies.xmlfile corresponding to a Galaxy workflow (.gafile).Issue 118988de1dIn addition to a single file or directory, allowlintto be passed multiple
files.343902dIssue 139Add-r/--recursiveoption toshed_createandlintcommands.63cd43101f2af9Improved output formatting and option to write diffs to a file for theshed_diffcommand.965511dFix lint problem when using new Galaxy testing features such as expecting
job failures and verifing job output.Issue 138Fix typo intesthelp thanks to first time contributor@pvanheus.Pull Request 1291982076Fix NPE on emptyhelpelement when linting tools.Issue 124Fixlintwarnings whenconfigfilesare defined in a tool.1a85493Fix for empty.shed.ymlfiles.b7d9e96Fix thetestcommand for newer versions ofnose.33294d2Update help content and documentation to be clearnormalizeshould not
be used to update the contents of tool files at this time.08de8deWarn on unknowncommandattributes when linting tools (anything butinterpreter).4f61025Various design, documentation (including new documentation on Tool Shedpublishing),
and testing related improvements (test coverage has risen from 65% to over
80% during this release cycle).0.7.0 (2015-04-13)Implementshed_createcommand to create Tool Shed repositories from.shed.ymlfiles (thanks to E. Rasche).Pull Request 101Allow automatic creation of missing repositories  duringshed_uploadwith the new--force_repository_creationflag (thanks to E. Rasche).Pull Request 102Allow specifying files to exclude in.shed.ymlwhen creating tar files
forshed_upload(thanks to Björn Grüning).Pull Request 99Resolve symbolic links when building Tool Shed tar files withshed_upload(thanks to Dave Bouvier).Pull Request 104Add aContributor Code of Conduct.Pull Request 113Omittool_test_output.jsonfrom Tool Shed tar file created withshed_upload(thanks to Dave Bouvier).Pull Request 111Update required version ofbioblendto0.5.3. FixedIssue 88.Initial work on implementing tests cases for Tool Shed functionality.182fe57Fix incorrect link in HTML test report (thanks to Martin Čech).4c71299Download Galaxy from the new, official Github repository.7c69bf6Update travis_test to install stable planemo fromPyPI.39fedd2Enable caching on--install_galaxyby default (disable with--no_cache_galaxy).d755fe70.6.0 (2015-03-16)Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc…Fixtool_initto quote file names (thanks to Peter Cock).Pull Request 98.Allow ignoring file patterns in.shed.yml(thanks to Björn Grüning).Pull Request 99Add--macrosflag totool_initcommand to generate a macro file as part of tool generation.ec6e30fAdd linting of tag order for tool XML files.4823c5eAdd linting ofstdiotags in tool XML files.8207026More tests, much higher test coverage.0bd4ff00.5.0 (2015-02-22)Implement--versionoption.Issue 78Implement--no_cleanupoption fortestandservecommands to
persist temp files.2e41e0aFix bug that left temp files undeleted.Issue 80More improvements to release process.fba38740.4.2 (2015-02-21)Fixsetup.pyfor installing non-Python data fromPyPI(required newer
fortool_factorycommand and reStructuredText linting). Thanks to
Damion Dooley for the bug report.Issue 830.4.1 (2015-02-16)Fix README.rst so it renders properly onPyPI.0.4.0 (2015-02-16)Implementtool_initcommand for bootstrapping creation of new
tools (withtutorial.)78f8274Implementnormalizecommand for reorganizing tool XML and macro
debugging.e8c1d45Implementtool_factorycommand to spin up Galaxy pre-configured theTool Factory.9e746b4Added basic linting ofcommandblocks.b8d90abImproved linting ofhelpblocks, including verifying validreStructuredText.411a8daFix bug related toservecommand not killing Galaxy properly when complete.53a6766Haveservecommand display tools at the top level instead of in shallow sections.badc25fAdd additional dependencies tosetup.pymore functionality works out
of the box.85b9614Fix terrible error message related tobioblendbeing unavailable.Issue 70Various smaller documentation and project structure improvements.0.3.1 (2015-02-15)Fixes to getPyPIworkflow working properly.0.3.0 (2015-02-13)Add option (-r) to theshed_uploadcommand to recursively upload
subdirectories (thanks to E. Rasche).Pull Request 68Fix diff formatting in test reports (thanks to E. Rasche).Pull Request 63Grab updated test database to speed up testing (thanks to approach from
E. Rasche and Dannon Baker).Issue 61,dff4f33Fix test data command-line argument name (wastest-datanow it istest_data).834bfb2Usetool_data_table_conf.xml.samplefile iftool_data_table_conf.xml.testis unavailable. Should allow some
new tools to be tested without modifying Galaxy’s globaltool_data_table_conf.xmlfile.ac4f8280.2.0 (2015-01-13)Improvements to way Planemo loads its own copy of Galaxy modules to prevent
various conflicts when launching Galaxy from Planemo.Pull Request 56Allow setting various test output options in~/.planemo.ymland disabling
JSON output.21bb463More experimental Brew and Tool Shed options that should not be considered
part of Planemo’s stable API. See bit.ly/gxbrew1 for more details.Fixproject_initfor BSD tar (thanks to Nitesh Turaga for the bug
report.)a4110a8Documentation fixes for tool linting command (thanks to Nicola Soranzo).Pull Request 510.1.0 (2014-12-16)Moved repository URL tohttps://github.com/galaxyproject/planemo.Support for publishing to the Tool Shed.Pull Request 6Support for producing diffs (shed_diff) between local repositories and
the Tool Shed (based on scripts by Peter Cock).Pull Request 33Use tool’s local test data when available - add option for configuringtest-datatarget.Pull Request 1Support for testing tool features dependent on cached data.44de95cSupport for generating XUnit tool test reports.82e8b1fPrettier HTML reports for tool tests.05cc9f4Implementshare_testcommand for embedding test result links in pull
requests.Pull Request 40Fix for properly resolving links during Tool Shed publishing (thanks to Dave
Bouvier).Pull Request 29Fix for citation linter (thanks to Michael Crusoe for the bug report).af39061Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan
Blankenberg).a2c13e4Automate more of Travis CI testing so the scripts added to tool repository
can be smaller.20a8680Documentation fixes for Travis CI (thanks to Peter Cock).Pull Request 22,Pull Request 23Various documentation fixes (thanks to Martin Čech).36f7cb1,b9232e5Various smaller fixes for Docker support, tool linting, and documentation.0.0.1 (2014-10-04)Initial work on the project - commands for testing, linting, serving Galaxy
tools - and more experimental features involving Docker and Homebrew.7d07782