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planemo

Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).

0.75.26
PyPI

Maintainers: 5

.. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png :alt: Planemo Logo :align: center :figwidth: 100% :target: https://github.com/galaxyproject/planemo

Command-line utilities to assist in developing Galaxy_ and Common Workflow Language_ artifacts - including tools, workflows, and training materials.

.. image:: https://readthedocs.org/projects/planemo/badge/?version=latest :target: http://planemo.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status

.. image:: https://badge.fury.io/py/planemo.svg :target: https://pypi.python.org/pypi/planemo/ :alt: Planemo on the Python Package Index (PyPI)

.. image:: https://github.com/galaxyproject/planemo/workflows/Python%20CI/badge.svg :target: https://github.com/galaxyproject/planemo/actions?query=workflow%3A%22Python+CI%22

Free software: MIT License
Documentation: https://planemo.readthedocs.io.
Code: https://github.com/galaxyproject/planemo

Quick Start

Obtaining

For a traditional Python installation of Planemo, first set up a virtualenv for planemo (this example creates a new one in .venv) containing Python 3.7 or newer and then install with pip. 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 planemo

For information on updating Planemo, installing the latest development release, or installing Planemo via Bioconda <https://github.com/bioconda/bioconda-recipes>__

checkout the installation <http://planemo.readthedocs.io/en/latest/installation.html>__ documentation.

Planemo is also available as a virtual appliance <https://planemo.readthedocs.io/en/latest/appliance.html>_ bundled with a preconfigured Galaxy server and set up for Galaxy_ and Common Workflow Language_ tool development. You can choose from open virtualization format (OVA_, .ova) or Docker_ appliances.

Basics - Galaxy

This 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 demonstrating planemo as follows project_init --template=demo mytools; cd mytools.

Planemo can check tool XML files for common problems and best practices using the lint command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>_ (also aliased as l).

$ planemo lint

Like many planemo commands - 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.xml

The lint command takes in additional options related to reporting levels, exit code, etc. These options are described in the docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>_ or (like with all commands) can be accessed by passing --help to it.

$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATH

Once tools are syntactically correct - it is time to test. The test command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>__ can be used to test a tool or a directory of tools.

$ planemo test --galaxy_root=../galaxy randomlines.xml

If no --galaxy_root is defined, Planemo will download and configure a disposable Galaxy instance for testing.

Planemo will create a HTML output report in the current directory named tool_test_output.html (override with --test_output). See an example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>_ of such a report for Tophat.

Once tools have been linted and tested - the tools can be viewed in a Galaxy interface using the serve (s) command <http://planemo.readthedocs.org/en/latest/commands.html#serve-command>__.

$ planemo serve

Like test, serve requires a Galaxy root and one can be explicitly specified with --galaxy_root or installed dynamically with --install_galaxy.

For more information on building Galaxy tools in general please check out Building Galaxy Tools Using Planemo_.

For more information on developing Galaxy workflows with Planemo checkout best practices for Galaxy Workflows_ and the description of Planemo's test format_. For information on developing Galaxy training materials checkout the contributing documentation <https://training.galaxyproject.org/training-material/topics/contributing/>__ on training.galaxyproject.org.

Basics - Common Workflow Language

This quick start will assume you have a directory with one or more Common Workflow Language_ YAML files. If no such directory is available, one can be quickly created for demonstrating planemo as follows planemo project_init --template=seqtk_complete_cwl mytools; cd mytools.

Planemo can check tools YAML files for common problems and best practices using the lint command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>_ (also aliased as l).

$ planemo lint

Like many planemo commands - 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.cwl

$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATH

$ planemo test --engine cwltool seqtk_seq.cwl

Planemo will create a HTML output report in the current directory named tool_test_output.html. Check out the file seqtk_seq_tests.yml for 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 the Commmon Workflow User Guide_ for more information on developing CWL tools in general and Building Common Workflow Language Tools_ for more information on using Planemo to develop CWL tools.

Tool Shed

Planemo can help you publish tools to the Galaxy Tool Shed. Check out Publishing to the Tool Shed_ for more information.

Conda

Planemo can help develop tools and Conda packages in unison. Check out the Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>__ or CWL <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>__ version of the "Dependencies and Conda" tutorial for more information.

Docker and Containers

Planemo can help develop tools that run in "Best Practice" containers for scientific workflows. Check out the Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>__ or CWL <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>__ version of the "Dependencies and Containers" tutorial for more information.

.. _Galaxy: http://galaxyproject.org/ .. _GitHub: https://github.com/ .. _Conda: http://conda.pydata.org/ .. _Docker: https://www.docker.com/ .. _Vagrant: https://www.vagrantup.com/ .. _Travis CI: http://travis-ci.org/ .. _tools-devteam: https://github.com/galaxyproject/tools-devteam .. _tools-iuc: https://github.com/galaxyproject/tools-iuc .. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html .. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html .. _Common Workflow Language: https://www.commonwl.org/ .. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/ .. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html .. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format .. _test format: https://planemo.readthedocs.io/en/latest/test_format.html .. _best practices for Galaxy Workflows: https://planemo.readthedocs.io/en/latest/best_practices_workflows.html

History

.. to_doc

0.75.26 (2024-09-24)

Fix up autopygen type annotation (thanks to @mvdbeek). Pull Request 1474
Fix autoupdate for workflows with overlapping tool updates (thanks to @bernt-matthias). Pull Request 1452
Display last lines of logs (thanks to @mvdbeek). Pull Request 1473

0.75.25 (2024-08-11)

Add a new single cell category (thanks to @pavanvidem). Pull Request 1457
Add extended-assertions requirements (thanks to @bernt-matthias). Pull Request 1471

0.75.24 (2024-07-04)

Workflow best practices: check that creator identifiers are URIs (thanks to @elichad). Pull Request 1458
Update pinning for Galaxy 24.1 (thanks to @bernt-matthias). Pull Request 1460
Add option to create a minimal markdown test report (thanks to @bernt-matthias). Pull Request 1462
Increase worflow linting (thanks to @lldelisle). Pull Request 1463
Run CI tests against newer Galaxy versions (thanks to @bernt-matthias). Pull Request 1466
Add the option to provide a history id to run the workflow in (thanks to @Delphine-L). Pull Request 1461
Make sure that skip list does not get [''] (if no skip is given) (thanks to @bernt-matthias). Pull Request 1453
Tool linting add --skip_file and remove lxml schema validation (thanks to @bernt-matthias). Pull Request 1420

0.75.23 (2024-05-08)

Implement run/test/workflow_edit/autoupdate from non default tool sheds (thanks to @mvdbeek). Pull Request 1445
Install prebuilt client by default (thanks to @mvdbeek). Pull Request 1450
Bump galaxy packages to allow for 24.0 (thanks to @bernt-matthias). Pull Request 1441
replace dead link in conclusions (thanks to @martenson). Pull Request 1447
Add text to autopygen exceptions (thanks to @bernt-matthias). Pull Request 1444
Drop circleci config (thanks to @mvdbeek). Pull Request 1443
Fix linting of asserts with children (thanks to @bernt-matthias). Pull Request 1442

0.75.22 (2024-04-04)

Fix parsing of training metadata.yaml files (thanks to @nsoranzo). Pull Request 1439
Fix markdown template: add missing closing details tag (thanks to @bernt-matthias). Pull Request 1440
Misc workflow linting improvements (thanks to @bernt-matthias). Pull Request 1437
Don't skip requirements with an environment marker (thanks to @nsoranzo). Pull Request 1433
Add --host parameter to allow listening on non-default hosts (thanks to @selten). Pull Request 1430

0.75.21 (2024-02-01)

Add option to pass extra arguments to docker run (thanks to @bernt-matthias). Pull Request 1428
Fix workflow_edit (thanks to @mvdbeek). Pull Request 1427
Update to black 2024 stable style (thanks to @nsoranzo). Pull Request 1425

0.75.20 (2024-01-30)

Fix use of package_name attribute on CondaTarget objects (thanks to @nsoranzo). Pull Request 1424
Don't crash autoupdate on non-PEP440-compliant tool versions (thanks to @nsoranzo). Pull Request 1422
Add now mandatory readthedocs config files (thanks to @nsoranzo). Pull Request 1419
Update action versions (thanks to @nsoranzo). Pull Request 1416

0.75.19 (2023-12-06)

Update upper bound for galaxy packages to < 23.2 (thanks to @bernt-matthias). Pull Request 1388
Fix workflow download when using instance id (thanks to @mvdbeek). Pull Request 1412
Remove introduction header from training init (thanks to @hexylena). Pull Request 1410

0.75.18 (2023-11-16)

Pretty-print workflow and use correct version of linked workflow in workflow_test_init (thanks to @mvdbeek). Pull Request 1408
Fix running workflow tests when there are multiple tests (thanks to @mvdbeek). Pull Request 1407
Fix matching of tool ids to autoupdate (thanks to @nsoranzo). Pull Request 1406

0.75.17 (2023-11-01)

Implement running tests against existing invocation (thanks to @mvdbeek). Pull Request 1401
Fix test result download (thanks to @mvdbeek). Pull Request 1402

0.75.16 (2023-11-01)

No changes

0.75.15 (2023-10-29)

Change info message for markdown readme in repo (thanks to @bernt-matthias). Pull Request 1398
Make test reports more resilient to failing invocations (thanks to @mvdbeek). Pull Request 1400
Fix zenodo test, drop explicit datatype mapping (thanks to @mvdbeek). Pull Request 1399
Fix linting rule selection (thanks to @bernt-matthias). Pull Request 1396
Add missing Astronomy, CLIP-seq and Materials science TS categories (thanks to @bernt-matthias). Pull Request 1397

0.75.14 (2023-10-19)

Fix workflow_lint for json output values (thanks to @mvdbeek). Pull Request 1395

0.75.13 (2023-10-18)

Add --skip to shed_lint (thanks to @bernt-matthias). Pull Request 1394
Remove API key requirement from training_init (thanks to @hexylena). Pull Request 1393
Try to fix planemo test workflow when output is collection with identical name (thanks to @lldelisle). Pull Request 1391

0.75.12 (2023-09-18)

Track subworkflow invocations after main invocation is scheduled (thanks to @mvdbeek). Pull Request 1389

0.75.11 (2023-09-14)

Implement automatic tool generation based on the source code of the tool (thanks to @Kulivox). Pull Request 1263
Support for testing workflows with conditional steps (thanks to @mvdbeek). Pull Request 1387

0.75.10 (2023-09-01)

Add pick_value to distro_tools (thanks to @mvdbeek). Pull Request 1385
Allow missing conda_exec (thanks to @mstabrin). Pull Request 1384
Fix profile version test (thanks to @bernt-matthias). Pull Request 1383
Fix type comparisons (thanks to @bernt-matthias). Pull Request 1382
Added a note that docker is required for docker and biocontainers option (thanks to @paulzierep). Pull Request 1355
Optimize disk space usage for planemo test (thanks to @bernt-matthias). Pull Request 1378
Fix for change of base_url in BioBlend 1.2.0 (thanks to @nsoranzo). Pull Request 1379

0.75.9 (2023-06-29)

Update collection operation tool list (thanks to @mvdbeek). Pull Request 1377
Officially support Python 3.10 and 3.11 (thanks to @nsoranzo). Pull Request 1375
Fix links (thanks to @nsoranzo). Pull Request 1374
Fix test_run_gxtool_randomlines test on Galaxy dev branch (thanks to @nsoranzo). Pull Request 1373

0.75.8 (2023-06-09)

Bump galaxy package requirements to allow for 23.0 (thanks to @bernt-matthias). Pull Request 1372
Sanitize and make output names unique (thanks to @mvdbeek). Pull Request 1371
Increase bioblend retries for bad networks (thanks to @hexylena). Pull Request 1369
Add --biocontainers option to shed_lint (thanks to @mvdbeek). Pull Request 1370
fix regex of orcid + add test (thanks to @lldelisle). Pull Request 1364
Drop allow_none for finding repository (thanks to @mvdbeek). Pull Request 1358

0.75.7 (2023-03-01)

Drop call to escape_non_unicode_symbols (thanks to @nsoranzo). Pull Request 1357

0.75.6 (2023-02-22)

Allow running autoupdate against external server (thanks to @mvdbeek). Pull Request 1265
Fix extraction of orcid identifiers for .dockstore.yml (thanks to @lldelisle). Pull Request 1350

0.75.5 (2023-02-10)

Bump galaxy packages to 22.05 (thanks to @bernt-matthias). Pull Request 1275

0.75.4 (2023-02-09)

Store datasets by UUID (thanks to @bernt-matthias). Pull Request 1347
Fix orcid regex for dockstore_init (thanks to @lldelisle). Pull Request 1348
Fix virtualenv dir bookkeeping (thanks to @wm75). Pull Request 1346
Deprecate introduction slides folder (thanks to @hexylena). Pull Request 1344
Remove note recommending installing dev versions from planemo run tutorial (thanks to @simonbray). Pull Request 1338
Rename configuration option removed in tox 4.0 (thanks to @nsoranzo). Pull Request 1337
Remove travis-ci.org badge from README.rst (thanks to @SimonWaldherr). Pull Request 1334

0.75.3 (2022-11-30)

Mount test data dir read-only in docker (thanks to @mvdbeek). Pull Request 1327
Add traceback to report template (thanks to @bernt-matthias). Pull Request 1332
Add indent and sort_keys to tool_test_json (thanks to @simonbray). Pull Request 1330
Fix planemo shed_test (thanks to @mvdbeek). Pull Request 1329
Add h5py dependency, required for comparing h5 files (thanks to @mvdbeek). Pull Request 1326
Update GitHub action versions (thanks to @nsoranzo). Pull Request 1322
Fix "glone" typo in error message (thanks to @bernt-matthias). Pull Request 1325
Type annotation for input staging-related code (thanks to @nsoranzo). Pull Request 1320
Add creator dockstore (thanks to @lldelisle). Pull Request 1314

0.75.2 (2022-11-02)

Compare versions, not tool ids to find latest tool ids (thanks to @mvdbeek). Pull Request 1313
Fix for_paths when path is directory of tools (thanks to @mvdbeek). Pull Request 1312
Fix workflow_lint with list + check elements in collection (thanks to @lldelisle). Pull Request 1310
Drop copy_tree workaround for tool sources (thanks to @mvdbeek). Pull Request 1308

0.75.1 (2022-10-31)

Use pytest.raises() instead of ad-hoc assert_raises_regexp() context manager (thanks to @nsoranzo). Pull Request 1302
Add planemo_ci_setup command (thanks to @mvdbeek). Pull Request 1304
Don't fail planemo autoupdate if tool version not found in tool shed (thanks to @lldelisle). Pull Request 1305
workflow_lint: ensure that tool shed tool ids are valid (thanks to @lldelisle). Pull Request 1306
Fix recording of virtual_env_dir (thanks to @mvdbeek). Pull Request 1307

0.75.0 (2022-10-28)

Restore running tool tests against directory (thanks to @mvdbeek). Pull Request 1303
Update outdated cuffmerge url (thanks to @martenson). Pull Request 1247
Set upstream branch when pushing workflows to GitHub (thanks to @simonbray). Pull Request 1249
restore --no_cleanup to set cleanup_job to never (thanks to @bernt-matthias). Pull Request 1255
Drop support for Python 3.6 (thanks to @simonbray). Pull Request 1257
Replace CoC with link to GalaxyProject's one (thanks to @nsoranzo). Pull Request 1259
Mains resource selector must be skipped (thanks to @hexylena). Pull Request 1260
Ignore cloudflare 503 status when checking links (thanks to @bernt-matthias). Pull Request 1262
Document the use of mandatory macro parameters and add named macro tokens (thanks to @bernt-matthias). Pull Request 1212
Bump galaxy package requirements to 22.01 (thanks to @bernt-matthias). Pull Request 1264
Run local galaxy via gravity (thanks to @mvdbeek). Pull Request 1232
Lint randomlines.xml file (thanks to @simonbray). Pull Request 1270
Check if main requirement is None (thanks to @bernt-matthias). Pull Request 1274
Planemo type annotation: module planemo.commands.cmd_autoupdate (thanks to @gallardoalba). Pull Request 1278
Planemo type annotation: module planemo.cli (thanks to @gallardoalba). Pull Request 1277
Planemo type annotation: module cmd_clone (thanks to @gallardoalba). Pull Request 1279
Planemo type annotation: module cmd_tool_init (thanks to @gallardoalba). Pull Request 1281
Add type annotations to planemo.autoupdate module (thanks to @nsoranzo). Pull Request 1283
Planemo type annotation: module cmd_normalize (thanks to @gallardoalba). Pull Request 1280
Planemo type annotation: module planemo.conda (thanks to @gallardoalba). Pull Request 1284
Add type annotations to planemo.glob and planemo.virtualenv (thanks to @nsoranzo). Pull Request 1287
Drop conda_lint command (thanks to @nsoranzo). Pull Request 1288
Type annotations for planemo.bioblend, planemo.git, and planemo.cwl.run (thanks to @adRn-s). Pull Request 1285
Add FAQ page to docs (thanks to @simonbray). Pull Request 1271
Add type annotations to planemo.runnable and planemo.workflow_lint (thanks to @nsoranzo). Pull Request 1291
Make --channels also affect mulled channels and update/extend howto use bioconda artifacts (thanks to @bernt-matthias). Pull Request 1227
Planemo 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 1293
Pre-create expected output file on disk (thanks to @mvdbeek). Pull Request 1276
Control publish setting in .dockstore.yml, fix first release not appearing on dockstore (thanks to @mvdbeek). Pull Request 1295
Fix disclosure css for summary elements (thanks to @mvdbeek). Pull Request 1294
Enable providing multiple --tool_data_table options (thanks to @mvdbeek). Pull Request 1296
Make startup timeout configurable (thanks to @mvdbeek). Pull Request 1298
Fix printing planemo test logs (thanks to @mvdbeek). Pull Request 1299
Fix workflow test when input is optional but also workflow output (thanks to @mvdbeek). Pull Request 1297

0.74.11 (2022-06-08)

Removing broken link, update it to current doc (thanks to @profgiuseppe). Pull Request 1244
Implement nested collection inputs and outputs in workflow_test_init Pull Request 1242_
More fixes for auto-generating workflow tests Pull Request 1241_
Fix workflow_test_init for collection outputs Pull Request 1239_

0.74.10 (2022-05-31)

Allow specifying URL and API key with workflow autoupdate and docs improvements (thanks to @simonbray). Pull Request 1237
Pin planemo to last known working major galaxy version Pull Request 1230_
Drop unused Python dependencies and upgrade syntax to Python 3.6 Pull Request 1228_
Update best_practice_search() for changes in galaxy-tool-util Pull Request 1224_
Make galaxy config cleanup_job depend on --no_cleanup (thanks to @bernt-matthias). Pull Request 1226
Tool builder: add profile and suffix version (thanks to @gallardoalba). Pull Request 1222
training-init: add the FAQ index page to tutorial folder (thanks to @shiltemann). Pull Request 1217
Adding best practices and assertion checks to workflow_lint (thanks to @simonbray). Pull Request 1213
Updates to workflow autoupdate required for IWC bot (thanks to @simonbray). Pull Request 1214
Add test and fix for failing docker_galaxy engine (thanks to @simonbray). Pull Request 1215
Generate workflow test from invocation id (thanks to @simonbray). Pull Request 1209
Fixed minor typo in documentation (thanks to @stain). Pull Request 1206
Add missing ToolShed categories Pull Request 1207_
Use WorkflowId rather than StoredWorkflowId when autoupdating subworkflows (thanks to @simonbray). Pull Request 1205
Always use random id_secret for testing (thanks to @bernt-matthias). Pull Request 1198
Add rerun subcommand for rerunning jobs (thanks to @simonbray). Pull Request 1140

0.74.9 (2021-11-03)

Fix rendering of subworkflow steps for workflow testing report (thanks to @simonbray). Pull Request 1200
Replace Galaxy interactor galaxy_requests_post with make_post_request from BioBlend (thanks to @simonbray). Pull Request 1201

0.74.8 (2021-10-10)

Exclude click 8.0.2. Pull Request 1196_
Add tool version numbers to autoupdate logging (thanks to @simonbray). Pull Request 1188
Allow tool autoupdate without conda installation (thanks to @simonbray). Pull Request 1193
use correct key execution_problem in template (thanks to @bernt-matthias). Pull Request 1195

0.74.7 (2021-09-21)

Fix documentation to include --download_outputs flag (thanks to @simonbray). Pull Request 1184
Select refgenie config based on Galaxy version Pull Request 1187_
Extend autoupdate subcommand to workflows (thanks to @simonbray). Pull Request 1151

0.74.6 (2021-07-23)

Add JSON report for planemo run invocations (thanks to @simonbray). Pull Request 1153
Ignore failure to download output datasets Pull Request 1179_
Allow location to point to url for outputs Pull Request 1180_
Fix --shed_install for gxformat2 workflows Pull Request 1182_

0.74.5 (2021-06-25)

Remove iuc from default channels Pull Request 1170_
Fix parsing of changelog for git release Pull Request 1171_
Remove legacy commands, egg handling Pull Request 1172_
Use bioblend's invoke_workflow Pull Request 1173_
Create more useful output for failed invocations Pull Request 1174_
Improve dockstore_init Pull Request 1177_

0.74.4 (2021-06-01)

Relicense under the MIT license Pull Request 1169_
Revise log levels (thanks to @bernt-matthias). Pull Request 1165
Create upload_data subcommand (thanks to @simonbray). Pull Request 1164
Create --download_outputs flag for the run command (thanks to @simonbray). Pull Request 1157
Make simultaneous file upload configurable for the run and test commands (thanks to @simonbray). Pull Request 1156
Add option to add tags to a history with the run command (thanks to @simonbray). Pull Request 1154
Revise Allure_ reporting experience for workflows. Pull Request 1152_

0.74.3 (2021-02-25)

Load both cat1 versions when testing workflows Pull Request 1146_
Fix isolated virtualenv not getting activated Pull Request 1145_
Use bioblend's make_get_request for authenticated request Pull Request 1144_
Display live logs when Galaxy is run in background Pull Request 1142_

0.74.2 (2021-02-21)

Allow testing dir of workflows Pull Request 1095_
Fix container register for gh workflow Pull Request 1135, Pull Request 1133
Don't fail URL linting if blocked by CloudFlare Pull Request 1134_ 1133`_
Allow planemo run to stage exisiting datasets and relative paths (thanks to @simonbray). Pull Request 1128

0.74.1 (2021-01-03)

Fix ci_find_tools and ci_find_repos commands. Pull Request 1127_

0.74.0 (2020-12-30)

Allow running Galaxy workflow tests against externally defined workflows. Pull Request 1126, Pull Request 1125, Pull Request 1123_
Require Python tabulate package for the list_invocations command. Pull Request 1124_

0.73.0 (2020-12-28)

Integrate important features from gxwf_ for running workflows - including building up profile commands for creating aliases, allowing referencing workflows by external IDs, and listing invocations (thanks to @simonbray). Pull Request 1076
Documentation for using planemo run to execute workflows (thanks to @simonbray). Pull Request 1102
Add workflow_upload command for publishing each workflow of a repository with many workflows to their own standalone repository. Pull Request 1091_
Update github commands to authenticate with a token rather than username/password (thanks to @simonbray). Pull Request 1083
Document "advanced" tool test debugging (thanks to @bernt-matthias). Pull Request 1108
Various fixes for workflow commands - including workflow_convert, workflow_lint, workflow_job_init, and workflow_test_init (thanks to @simonbray). Pull Request 1101, Pull Request 1118, Pull Request 1121, Pull Request 1116, Pull Request 1064
Allow outputting test results as Allure_ framework results. Pull Request 1115_
Fix run_tests.sh invocation Pull Request 1099_
Tiny typo in debugging output (thanks to @abretaud). Pull Request 1066
Fix typo in 'planemo test' help text for --skip_venv (thanks to @peterjc). Pull Request 1068
Fixes for CLI when external_galaxy is used as the engine (thanks to @simonbray). Pull Request 1072
Updating base image to 20.05 for training topics (thanks to @bedroesb). Pull Request 1074
Changes to update_test_data testing mode (thanks to @simonbray). Pull Request 1079
Fix docker options when filling job_conf.xml template. Pull Request 1086_
Explicit tests for Galaxy 20.09. Pull Request 1093_
Minor fix for ci_find_repos command. Pull Request 1094_
Fix a couple of Cheetah_ urls in Galaxy tool documentation (thanks to @martenson). Pull Request 1096
Fix doc link from a redirect loop to a section (thanks to @martenson). Pull Request 1110
Clarify tutorial.md usage of citations (thanks to @blankenberg). Pull Request 1114
Fix ZeroDivisionError when no tests are executed (thanks to @simonbray). Pull Request 1120

0.72.0 (2020-08-04)

More documentation/support around running workflows including new command to initialize workflow jobs workflow_init_job. Pull Request 1052_
Workflow tests and documentation for tagging inputs. Pull Request 1058_
Various documentation improvements. Pull Request 1061, Pull Request 1062
Add mypy type checking. Pull Request 1060_
Progress decoupling Planemo's core from click & CLI interactions. Pull Request 1059_
Tests for workflow testing script. Pull Request 821_

0.71.0 (2020-08-03)

Drop Python 2 support. Pull Request 1026_
Rev 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 1034_
Workflow linting, best practices, and tooling to assist in following them. Pull Request 1028, Pull Request 1049, Pull Request 1051_ Pull Request 1044_
Substantial rewrites to Galaxy workflow input staging - including allow nested collection and composite inputs to Galaxy for run and test. Pull Request 900, Pull Request 1029
Remove assorted older, likely unused commands. Pull Request 1043_
Update installation.rst (thanks to @mblue9). Pull Request 1032
Automatic PyPI upload on tag using GitHub Actions. Pull Request 994_
Fix quay repository presence check for single target builds. Pull Request 993_
More fine grained options for --shed_install (thanks to @AndreasSko). Pull Request 1001
Change default Python version for Galaxy (thanks to @bernt-matthias). Pull Request 1021
Sort tests by id when merging (thanks to @bernt-matthias). Pull Request 1022
Add --group_tools option to ci_find_tools (thanks to @bernt-matthias). Pull Request 1008
Add shared data library path to the data upload box for training material (thanks to @shiltemann). Pull Request 1013
Add support for tool versions to tutorial template generator (thanks to @shiltemann). Pull Request 1041
Only copy test files if they don't exist. Pull Request 1037_
Improvements to loading stock tools for workflow testing and serving ( add new stock tools to list and check subworkflows). Pull Request 1031_
Fix link for composite data type docs (thanks to @bernt-matthias). Pull Request 1020
Do not use gi._make_url() internal BioBlend method.
Switch CWL examples to use https://schema.org/version/latest/schema.rdf (thanks to @mr-c). Pull Request 1015
Fix docs not to claim Galaxy can't run on Python 3. Pull Request 1023_
Improved abstractions around target Galaxy instance. Pull Request 1046_
Add empty refgenie config for tests (thanks to @blankenberg). Pull Request 1025
Substantial reworking of testing infrastructure. Pull Request 1024, Pull Request 1003, Pull Request 1011, Pull Request 1006, Pull Request 1040, Pull Request 1036, Pull Request 1042_

0.70.0 (2020-01-29)

Temporarily add galaxy-util requirement Pull Request 991_
Make symlinks in tool tree work for planemo test Pull Request 988_
Reduce use of shell=True in subprocesses Pull Request 989_
Drop planemo database seed option Pull Request 985_
Don't execute untar_to() subprocesses through the shell Pull Request 984_
Allow setting database_connection for planemo test runs Pull Request 986_
Fix copy-paste mistakes Pull Request 983_
Add planemo list_repos command Pull Request 982_
Make container_register build files with headers and include base_image Pull Request 980_
Replace deprecated galaxy-lib requirement with galaxy-tool-util Pull Request 978_
Close all opened files (thanks to @bernt-matthias). Pull Request 979
Build single requirement container, log if requirement not in best-practice channels Pull Request 977_
Use tojson jinja2 filter instead of json.dumps Pull Request 975_
Add merge_test_reports command Pull Request 974_
Implement github workflow and fix profile commands if psql unavailable Pull Request 976_
Fix planemo lint --biocontainers if no build number in container Pull Request 972_
Update a training command (thanks to @hexylena). Pull Request 973
Allow passing through GALAXY_VIRTUAL_ENV variable to venv setup Pull Request 971_
Correct help text (thanks to @hexylena). Pull Request 970
Remove unneeded html5lib requirement Pull Request 968_

0.62.1 (2019-10-14)

Init & update submodules when installing and creating packages. Stop distributing eggs (thanks to @nsoranzo). 1ab8530

0.62.0 (2019-10-11)

Use unicodify() on exceptions and subprocess outputs (thanks to @nsoranzo) Pull Request 944
Do not override None with empty string (thanks to @ic4f). Pull Request 950
Update Docker template for training material generation (thanks to @bedroesb). Pull Request 958
Add support for suite of repos with different owners (thanks to @nsoranzo). Pull Request 959
Link for collection details updated in the docs (thanks to @martin-raden). Pull Request 963
Move most tests to Python 3.7, drop Python 3.4 (thanks to @nsoranzo). Pull Request 964
Remove confusing warning Pull Request 966_

0.61.0 (2019-07-08)

Training - fix empty repeat + some formatting (thanks to @bebatut). Pull Request 926
Training - add bibliography to tutorial template (thanks to @shiltemann). Pull Request 938
Training - support new class definition for input in workflow step (thanks to @bebatut). Pull Request 943
Various tool tutorial fixes ahead of GCC 2019 (thanks to @nsoranzo). Pull Request 940
Return validation error if doi is empty (thanks to @nsoranzo). Pull Request 937

0.60.0 (2019-05-31)

Return validation error if doi is empty Pull Request 937_
Add junit as test reporter (thanks to @selten). Pull Request 935
Update galaxy.xsd for new python 3 compatibility attribute (thanks to @martenson). Pull Request 931
Documentation: add a little warning for <param ... multiple="true"> (thanks to @bernt-matthias). Pull Request 930

0.59.0 (2019-05-09)

Add ability to test data manager tools (thanks to @mvdbeek). Pull Request 912
Update Training for new requirement definition (thanks to @bebatut). Pull Request 913
Drop amqp workaround (thanks to @mvdbeek). Pull Request 917
Use yaml.safe_load() instead of deprecated load() (thanks to @nsoranzo). Pull Request 921
Allow converting tool_test_report.json to xunit (thanks to @mvdbeek). Pull Request 918
Fix error if testcase.data.job does not exist (thanks to @mvdbeek). Pull Request 924
Fix deprecated getchildren() (thanks to @nsoranzo). Pull Request 925

0.58.2 (2019-03-01)

Fix display of tool ids in planemo html report (thanks to @mvdbeek). Pull Request 908
Single quotes for file names (thanks to @bernt-matthias). Pull Request 909
Fix doc linting (thanks to @mvdbeek). Pull Request 910
Update TS categories (thanks to @nsoranzo). 07dc6e0
Close tag in doc help, to help with copy&paste (thanks to @blankenberg). Pull Request 914
Update the tool XSD file (thanks to @bgruening). Pull Request 915

0.58.1 (2019-01-03)

Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to @nsoranzo). Pull Request 906
Fix command run by planemo test --skip_venv (thanks to @nsoranzo). Pull Request 907

0.58.0 (2019-01-01)

Remove deprecated sudo: false from .travis.yml (thanks to @nsoranzo). Pull Request 902
Do not skip Galaxy client build for planemo serve. Install Galaxy when the directory specified with --galaxy_root does not exist or is empty. (thanks to @nsoranzo). Pull Request 895, Issue 845_

0.57.1 (2018-11-23)

Fix username validation for shed linting (thanks to @martenson). Pull Request 899, Issue 898_

0.57.0 (2018-11-19)

Allow workflow_convert to convert a native .ga workflows to format 2 (yaml). Pull Request 896_
New command (workflow_edit) to open workflow in a synchronized graphical editor. Pull Request 894_
Conda tutorial fixes (thanks to @nsoranzo). Pull Request 876
Enable --conda_use_local option for planemo test (thanks to @nsoranzo). Pull Request 876
When testing, skip workflow outputs that do not have a label set (thanks to @bgruening). Pull Request 893
Add __repr__ for TestCase to improve debugging Planemo (thanks to @bgruening). Pull Request 892
Increase IO polling interval over time (thanks to @martenson). Pull Request 891
Sync galaxy xsd and fix tests (thanks to @mvdbeek). Pull Request 889
Linting fix for W605 (thanks to @martenson). Pull Request 888
Add icon for repeat parameters in training (thanks to @bebatut). Pull Request 887

0.56.0 (2018-10-30)

Allow selection of Python version when starting managed Galaxy (thanks to @mvdbeek). Pull Request 874
Change the channel priority of conda (again). (thanks to @bgruening). Pull Request 867
Some small english corrections (thanks to @hexylena). Pull Request 868
Print the list of excluded paths when running ci_find_repos (thanks to @nsoranzo). Pull Request 877
Improved XSD lint reporting. Pull Request 871_
Fix Planemo writing a file called gx_venv_None. Pull Request 870_
Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to @nsoranzo). Pull Request 864
Fix to make workflow testing more robust. Pull Request 882_

0.55.0 (2018-09-12)

Add commands to create Galaxy training materials (thanks to @bebatut). Pull Request 861
Fix planemo test when TEMP env variable contain spaces (thanks to @nsoranzo). Pull Request 851
Support testing a completely remote galaxy instance (thanks to @hexylena). Pull Request 856
Allow naming history from command line (thanks to @hexylena). Pull Request 860
Sync galaxy.xsd from galaxy repo (thanks to @nsoranzo). Pull Request 866
Fix ServeTestCase.test_shed_serve test (thanks to @nsoranzo). bad810a_

0.54.0 (2018-06-06)

Better support for testings against different versions of Galaxy efficiently and robustly. Pull Request 849_
New database version (thanks to @bgruening). Pull Request 847
Hyperlink DOIs against preferred resolver (thanks to @katrinleinweber). Pull Request 850
Tests for collection inputs to workflows. Pull Request 843_
Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust. b12b117_
More tutorial testing, tutorial updates. 016b923_, 324c776_, 2002b49_
More isolated test_shed_upload.py tests. 72d2ca7_
Add filetype support for workflow test inputs (thanks to @bgruening). Pull Request 842
Add --no_shed_install option, to prevent shed installs as part of workflow testing. Pull Request 841_
Small docs fix (thanks to @hexylena). Pull Request 848

0.53.0 (2018-05-22)

Make Planemo testing easier for CWL tools and workflows in various ways and update tutorials to reflect these simplifications. Pull Request 837_
Test and fix running workflow tests against externally managed Galaxy servers. Pull Request 833, Pull Request 836
Allow using URIs for inputs of workflow test. Pull Request 840_
Slide Galaxy testing window to include 18.05 and drop 17.09. Pull Request 838_

0.52.0 (2018-05-20)

Allow optional disabling of Galaxy single user mode. Pull Request 835_
Fix for path pasting options during workflow testing. Pull Request 834_

0.51.0 (2018-05-19)

Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between CWL_ and existing Galaxy functionality - fixes and enhances many commands including lint, conda_install, conda_env, test, run, and mull. Pull Request 828_
Add two new tutorials for Conda <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>__ and Container <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>__ development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new CWL exercises, answers, and example project templates. 347c622_
Improve the CWL generated by the tool_init command to properly deal with SoftwareRequirement s and generate more idiomatic CWL. Pull Request 820, a5c72e3
Add new engine type (--engine toil) for testing and running CWL_ tools (requires manually installing Toil_ with pip install toil in Planemo's environment). Pull Request 831_
Add documentation <http://planemo.readthedocs.io/en/latest/test_format.html>__ for the Galaxy Workflow and CWL_ test format files (includes information on configuring various test engines). Pull Request 832_
Better default logging config for CWL development. Pull Request 830_
Various fixes for the conda_search command. Pull Request 826_
Fix test coverage configuration. Pull Request 822_
Reorganize .travis.yml for clarity. Pull Request 829_
More isolated, robust unit tests that use git_. Pull Request 827, Pull Request 818
Fix default list of best-practice Conda channels. Pull Request 825_
Refactor tests to speed up quick tests - fewer buggy URLs fetched in "quick" mode. Pull Request 823_
Fix upload configuration of workflow testing to default (overrideable) external Galaxies to not use path pasting. Pull Request 816_
Fix test number parsing for workflow tests. Pull Request 817_

0.50.1 (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 --engine for 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)

Fix PyPI_ README rendering for 0.49.0 release changes.

0.49.0 (2018-05-06)

Implement external Galaxy engine. Pull Request 781_
Restructure serve testing code for reuse. Pull Request 795_
Improve test report handling for JSON generated via galaxy-lib testing script. Pull Request 799_
Improve how various branches of Galaxy are tested. Pull Request 800_
Added documentation for GALAXY_MEMORY_MB (thanks to @bernt-matthias). Pull Request 801
Log tool config in verbose logging mode. Pull Request 802_
Replace r channel with conda-forge (thanks to @bgruening). Pull Request 805
Sync galaxy.xsd with latest Galaxy updates (thanks to @nsoranzo). Pull Request 806
Use requests.get() when validating http URLs (thanks to @nsoranzo). Pull Request 809
Do not consider tools with "deprecated" in the path (thanks to @bgruening). Pull Request 810
Automatically load tools shipped with Galaxy when testing, running, or serving workflows that reference these tools. Pull Request 790_
Revise README and touch up documentation in general. Pull Request 787_
Various small changes to testing and test framework. Pull Request 792_
Various Python 3 fixes. 8cfe9e9_, 41f7df1_
Fixes for Galaxy 18.0X releases. Pull Request 803, dc443d6

0.48.0 (2018-02-28)

Run all CI tests against Python 3 (thanks to @nsoranzo). Pull Request 768 and Pull Request 774_
Python 3 fix - subprocess with universal_newlines=True (thanks to @peterjc). Pull Request 764
Record CWL_ conformance test results using JUnit xml (thanks to @mr-c). Pull Request 756
Restore run test case for simple Galaxy tools. Pull Request 769_
Enhancements to Galaxy profiles and workflow testing. Pull Request 773_
Fix resolving & installing shed repositories from workflows for test and run commands. Pull Request 776_
Implement planemo command to convert format 2 workflows into .ga workflows. Pull Request 771_
Add a native Galaxy workflow (.ga) testing test. Pull Request 770_
Drop Brew support but add more detailed install instructions. Pull Request 761_
Clean up CWL_ conformance test execution. Pull Request 753_
Assorted small CWL_ and deamon serve fixes. Pull Request 759_

0.47.0 (2017-11-18)

Update to the latest Galaxy tool XSD (thanks to @nsoranzo). Pull Request 747
Re-fix problem when shed_update would fail if nothing to update (thanks to @nsoranzo). Pull Request 747
Update instructions for installation via conda (thanks to @nsoranzo) . Pull Request 743
Bug fix for MacOS chmod doesn't support --recursive flag. (thanks to @dfornika). Pull Request 739
Bug fix to also socket.error when linting URLs (thanks to @nsoranzo). Pull Request 738
Disable broken tests. Pull Request 745_

0.46.1 (2017-09-26)

Rev to latest versions of bioblend_ and galaxy-lib_ for various fixes related to CWL_.

0.46.0 (2017-09-15)

Change behavior of --docker flag, 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 733_
Add 'Accept' header when linting doc URLs (thanks to @nsoranzo). Pull Request 725
Fix --conda_auto_install help (thanks to @nsoranzo). Pull Request 727
Incremental progress toward CWL support via Galaxy. Pull Request 729, Pull Request 732
Update galaxy-lib to latest version to fix various issues. Pull Request 730_
Fix lint detected problems with documentation. Pull Request 731_

0.45.0 (2017-09-06)

Update to the latest galaxy-lib_ for Conda fixes. (thanks @nsoranzo) and updated CWL utilities. Pull Request 716, Pull Request 723
Update Conda_ channel order to sync with Bioconda_ (thanks to @nsoranzo). Pull Request 715
Experimental support running CWL_ workflows through the CWL_ fork of Galaxy.
Mention planemo command --help in main help (thanks to @peterjc). Pull Request 709
Bugfix handle None requirement versions when registering containers (thanks to @bgruening). Pull Request 704
Bugfix for dependencies by pinning ruamel.yaml version (thanks to @mvdbeek). Pull Request 720

0.44.0 (2017-06-22)

Fix and improve Galaxy root option specification options. Pull Request 701, 8a608e0
Update planemo mull to use a default action of build-and-test since build no longer cleans up itself. ecc1bc2_
Add a command to pre-install Involucro_. Pull Request 702_

0.43.0 (2017-06-22)

Remove stdio from generated tools - just use exit_code for everything. 91b6fa0_
Implement some ad-hoc documentation tests. Pull Request 699_
A 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) 904d77a
Fix container_register to create pull requests against the newly finalized home of the multi-package-containers registry repository. 9636682_
Fix use_global_config and use_env_var for options with unspecified defaults. 475104c_

0.42.0 (2017-06-15)

Conda/Container documentation and option naming improvements. Pull Request 684_
Sync galaxy.xsd with latest upstream Galaxy updates (thanks to @nsoranzo). Pull Request 687
Fix ci_find_repos command to not filter repos whose only modifications where in subdirs (thanks to @nsoranzo). Pull Request 688
Update container_register for mulled version 2 and repository name changes. Pull Request 689_
Better pull request messages for the container_register command. Pull Request 690_

0.41.0 (2017-06-05)

Fix shed_update not fail if there is nothing to update (thanks to @nsoranzo). Issue 494, Pull Request 680_
Conda documentation and option naming improvements. Pull Request 683_
Implement container_register for tool repositories. Pull Request 675_
Fix hub binary installation for Mac OS X. Pull Request 682_

0.40.1 (2017-05-03)

Fix data manager configuration to not conflict with original Galaxy at galaxy_root (thanks to @nsoranzo). Pull Request 662
Fix filter_paths() to not partial match paths when filtering shed repositories (thanks to @nsoranzo). Pull Request 665
Fix description when creating .shed.yml files (thanks to @RJMW). Pull Request 664

0.40.0 (2017-03-16)

Implement instructions and project template for GA4GH Tool Execution Challenge Phase 1. 84c4a73_
Eliminate Conda hack forcing /tmp as temp directory. b4ae44d_
Run dependency script tests in isolated directories. 32f41c9_
Fix OS X bug in planemo run by reworking it to wait using urllib instead of sockets. 3129216_

0.39.0 (2017-03-15)

Implement documentation and examples for Conda-based dependency development (under "Advanced" topics). Pull Request 642, Pull Request 643
Implement documentation and examples for container-based dependency development (under "Advanced" topics). 0a1abfe_
Implement a planemo conda_search command for searching best practice channels from the command line. Pull Request 642_
Allow Planemo to work with locally built Conda packages using the --conda_use_local command. Pull Request 643, Issue 620
Implement an open (or just o) command to quickly open the last test results (or any file if supplied). Pull Request 641_
Linting improvements and fixes due to galaxy-lib_ update.
- 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
- Fix assert_command not detected as a valid test (fixes Issue 260_).
Have lint --conda_requirements check that at least one actual requirement is found. 6638caa_
Allow conda_install to work with packages as well as just tools. 8faf661_
Add --global option to conda_install to install requirements into global Conda setup instead of using an environment. 8faf661_
Implement planemo lint --biocontainer that checks that a tool has an available BioContainer registered. 0a1abfe_
Add more options and more documentation to the planemo mull command. 0a1abfe_
Hack around a bug in Conda 4.2 that makes it so planemo mull doesn't work out of the box on Mac OS X. 0a1abfe_
Allow URIs to be used instead of paths for a couple operations. ce0dc4e_
Implement non-strict CWL parsing option. 4c0f100_
Fixes for changes to cwltool_ and general CWL-relate functionality. 3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_
Eliminate deprecated XML-based abstraction from planemo.tools. 04238d3_
Fix MANIFEST.in entry that was migrated to galaxy-lib. ced5ce2_
Various fixes for the command conda_env. Pull Request 640_
Improved command help - both formatting and content. Pull Request 639_
Implement a --no_dependency_resolution option disabling conda dependency resolver. Pull Request 635, Issue 633
Tests for new linting logic. Pull Request 638_
Fix bug where tool IDs needs to be lowercase for the shed (thanks to @bgruening). Pull Request 649
Update seqtk version targetted by intro docs. e343b67_
Various other Conda usability improvements. Pull Request 634_

0.38.1 (2017-02-06)

Fix bug with shed_lint --urls introduced in 0.38.0. 84ebc1f_

0.38.0 (2017-02-06)

Trim down the default amount of logging during testing. Pull Request 629, Issue 515
Improved log messages during shed operations. 08c067c_
Update tool XSD against latest Galaxy. fca4183_, 03c9658_
Fix bug where shed_lint --tools for a suite lints the same tools multiple times. Issue 564, Pull Request 628

0.37.0 (2017-01-25)

Update to the latest galaxy-lib_ release. This means new installs start with Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many Conda_ related 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_init are effectively enabled by default now. 4595953_
Use the Galaxy cached dependency manager by default (thanks to @abretaud). Pull Request 612
Test 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. 32acd68_
Fix pip ignores for bioconda_scripts (thanks to @nturaga) Pull Request 614

0.36.1 (2016-12-12)

Fix move error when using project_init. Issue 388, Pull Request 610
Improved integration testing for test command. Pull Request 609_
Update CWL links to v1.0 (thanks to @mr-c). Pull Request 608

0.36.0 (2016-12-11)

Bring in latest tool XSD file from Galaxy (thanks to @peterjc). Pull Request 605
PEP8 fixes for various linting problems (thanks to @peterjc). Pull Request 606
Update tool syntax URL to new URL (thanks to @mvdbeek). Pull Request 602

0.35.0 (2016-11-14)

Native support for building bioconductor tools and recipes (thanks to @nturaga). Pull Request 570
Fixes for running Galaxy via docker-galaxy-stable (thanks to @bgruening). 50d3c4a
Import order linting fixes (thanks to @bgruening_).

0.34.1 (2016-10-12)

Mimic web browser to validate user help URLs fixing Issue 578_ (thanks to @peterjc). Pull Request 591
Fix for Bioconda recipes depending on conda-forge (thanks to @nsoranzo). Pull Request 590

0.34.0 (2016-10-05)

Implement mull command to build containers for tools based on Conda_ recipes matching requirement definitions. 08cef54_
Implement --mulled_containers flag on test, serve, and run commands to run tools in "mulled" containers. Galaxy will first search locally cache containers (such as ones built with mull), then search the mulled namespace of quay.io, and finally build one on-demand if needed using galaxy-lib and Involucro_ developed by @thriqon_.
Implement --conda_requirements flag on lint command to ensure requirements can be resolved in best practice channels. 9da8387_
Allow conda_install command over multiple tool paths. 2e4e5fc_
Update pip_ as part of setting virtual environment in Makefile target. 19b2ee9_
Add script to auto-update Bioconda_ recipe for Planemo and open a pull request. f0da66f_

0.33.2 (2016-09-28)

Fix HISTORY.rst link problem that prevented correct display of content on PyPI_.

0.33.1 (2016-09-28)

Fix lint --urls false positives by being more restrictive with what is considered a URL (fixed by @hexylena_ after detailed report from @peterjc). Issue 573, Pull Request 579_

0.33.0 (2016-09-23)

Enable XSD validation of tools by default (restore old behavior with planemo lint --no_xsd). 1ef05d2_
Implement a conda_lint command to lint Conda_ recipes based on anaconda-verify. 6a6f164
Implement clone and pull_request commands to ease PRs (with documentation fixes from @martenson). e925ba1, ea5324f_
Update galaxy.xsd_ to allow version_command's to have an interpreter attribute. 7cca2e4_
Apply improvement from @nsoranzo_ for Planemo's use of git diff <https://git-scm.com/docs/git-diff>__. 6f91719_
Pull in downstream refactoring of tool_init code from @nturaga's Bioconductor work. ccdd2d5_
Update to latest Tool Factory_ code from tools-iuc. ca88b0c
Small code cleanups. b6d8294_, d6da3a8_
Fixup docs in planemo.xml.validation.
Allow skipping newly required lxml_ dependency in setup.py. 34538de

0.32.0 (2016-09-16)

Enhance planemo lint --xsd to use a fairly complete and newly official XSD definition. Pull Request 566_
Migrate 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 559
Documentation fixes (thanks to @ramezrawas). Pull Request 561
Do not fail URL linting in case of too many requests (thanks to @nsoranzo). Pull Request 565

0.31.0 (2016-09-06)

Implement new commands to ci_find_repos and ci_find_tools to ease CI scripting. Pull Request 555_

0.30.2 (2016-09-01)

Fix another problem with Conda_ prefix handling when using --conda_dependency_resolution. f7b6c7e_

0.30.1 (2016-09-01)

Fix a problem with Conda_ prefix handling when using --conda_dependency_resolution. f7b6c7e_
Fix for quote problem in update_planemo_recipe.bash. 6c03de8_
Fix to restore linting of tests/ directory and fix import order throughout module. ef4b9f4_

0.30.0 (2016-09-01)

Update to the latest galaxy-lib_ release and change Conda_ semantics to match recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+ with Galaxy 16.07 or master. 07d94bd_
Implement the --conda_auto_init flag for conda_install. ca19910_
Allow the environment variable PLANEMO_CONDA_PREFIX to set a default for --conda_prefix. 24008ab_
Fixup documentation regarding installs and Conda_. ce44e87_
Fix and lint Python module import order throughout project. Pull Request 550_
Use cp rather than symlink to $DOWNLOAD_CACHE in the dependency_script command (thanks to @peterjc). c2204b3
Fixes for the Homebrew recipe updater. c262b6d_

0.29.1 (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 539
An assortment fixes and enhancements to the dependency_script command (thanks to @peterjc). Pull Request 541, Pull Request 545_
Fix shed_build to respect exclude: in .shed.yml (thanks to @nsoranzo). Pull Request 540
Fix linting of tool URLs (thanks to @nsoranzo). Pull Request 546

0.28.0 (2016-08-17)

Fixes for bioblend_ v0.8.0 (thanks to @nsoranzo). 9fdf490
Enable shed repo type update (thanks to @nsoranzo). 3ceaa40
Create suite repositories with repository_suite_definition type by default (thanks to @nsoranzo). 057f4f0
Include shed_lint in script run by travis_init (thanks to @peterjc). Pull Request 528
Minor polish to the travis_init command (thanks to @peterjc). Pull Request 512
Update pip_ and setuptools on TravisCI; fix travis_init (thanks to @peterjc). Pull Request 521
Shorten command one line descriptions for main help (thanks to @peterjc). Pull Request 510
Use planemo test --no_cache_galaxy under TravisCI (thanks to @peterjc). Pull Request 513
Improve and fix docs ahead of GCC 2016 (thanks to @martenson). Pull Request 498, 725b232_
Add description of expect_num_outputs to planemo FAQ. a066afb_
Revise planemo tools docs to be more explicit about collection identifiers. a811e65_
Add more docs on existing dynamic tool output features. Pull Request 526_
Fix serve command doc (thanks to @nsoranzo). 8c088c6
Fix make lint-readme (RST link errors) (thanks to @peterjc). Pull Request 525
Add union bedgraph example to project templates (for GCC demo example). d53bcd6_
Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as shed categories (thanks to @bgruening, @gregvonkuster, and @nsoranzo). e890ab5, 08bb354_, e2398fb_
Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to Paul Stewart @pstew). Pull Request 507

0.27.0 (2016-06-22)

Use ephemeris to handle syncing shed tools for workflow actions. 1c6cfbb_
More planemo testing enhancements for testing artifacts that aren't Galaxy tools. Pull Request 491_
Implement docker_galaxy engine type. eb039c0_, Issue 15_
Enhance profiles to be Dockerized Galaxy-aware. Pull Request 488_
Add linter for DOI type citation - thanks to @mvdbeek. Pull Request 484

0.26.0 (2016-05-20)

Implement Engine and Runnable abstractions - Planemo now has beta support for testing Galaxy workflows and CWL_ tools with Galaxy and any CWL_ artifact with cwltool_. Pull Request 454, 7be1bf5
Fix missing command_line in test output json. e38c436_
More explicit Galaxy job_conf.xml handling, fixes bugs caused by galaxy_root having existing and incompatible job_conf.xml files and makes it possible to specify defaults with fixed server name. c4dfd55_
Introduce profile commands (profile_create, profile_delete, and profile_list) and profile improvements (automatic postgres database creation support). Pull Request 480, a87899b
Rework Galaxy test reporting to use structured data instead of XUnit data. 4d29bf1_
Refactor Galaxy configuration toward support for running Galaxy in docker-galaxy-stable. Pull Request 479_

0.25.1 (2016-05-11)

Tweak dependencies to try to fix cwltool_ related issues - such as Issue 475_.

0.25.0 (2016-05-11)

Implement Galaxy "profiles" - the ability to configure perisistent, named environments for serve and test. 5d08b67_
Greatly improved serve command - make test-data available 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 --daemon mode).
Two fixes to ensure more consistent, dependable test output. Pull Request 472, f3c6917
Add code and documentation for linting (lint) and building (tool_init) CWL_ tools. a4e6958_, b0b867e_, 4cd571c_
If needed for Conda_ workaround, shorten config_directory path (thanks to @mvdbeek). efc5f30
Fix --no_cache_galaxy option (thanks to Gildas Le Corguillé). d8f2038_
Target draft 3 of CWL_ instead of draft 2. 775bf49_
Fix cwltool dependency version - upstream changes broke compatibility. 65b999d_
Add documentation section and slides about recent Galaxy tool framework changes (with fix from @remimarenco). 069e7ba
Add IUC standards to Planemo docs. 2ae2b49_
Improve collection-related contents in documentation (thanks in part to @martenson). fea51fc, 13a5ae7_
Add documentation on GALAXY_SLOTS and running planemo on a cluster. 45135ff_, e0acf91_
Revise command-line handling framework for consistency and extension - allow extra options to be configured as defaults ~/.planemo.yml including --job_config_file and Conda_ configuration options. e769118_, 26e378e_
Fix tool_init commans options typos (thanks to Nitesh Turaga). 826d371_
Refactor galaxy-related modules into submodules of a new planemo.galaxy package. 8e96864_
Fix error message typo (thanks to @blankenberg). b1c8f1d
Update documentation for recent command additions. 3f4ab44_
Rename option --galaxy_sqlite_database option to --galaxy_database_seed and fix it so it actually works. f7554d1_
Add --extra_tools option to serve command. 02a08a0_
Update project testing to include linting documentation (docs/), Python import order, and docstrings. a13a120_, 6e1e726_, 95d5cba_

0.24.2 (2016-04-25)

Revert "check .shed.yml owner against credentials during shed creation", test was incorrect and preventing uploads. Pull Request 425, Issue 246

0.24.1 (2016-04-08)

Fix test summary report. Pull Request 429_
Improve error reporting when running shed_test. ce8e1be_
Improved code comments and tests for shed related functionality. 89674cb_
Rev galaxy-lib_ dependency to 16.4.1 to fix wget usage in newer versions of wget. d76b489_

0.24.0 (2016-03-29)

Drop support for Python 2.6. 93b7bda_
A variety of fixes for shed_update. Pull Request 428, Issue 416
Fix reporting of metadata updates for invalid shed updates. Pull Request 426, Issue 420
Check .shed.yml owner against credentials during shed creation. Pull Request 425, Issue 246
Fix logic error if there is a problem with shed_create. 358a42c_
Tool documentation improvements. 0298510_, a58a3b8_

0.23.0 (2016-02-15)

Fix duplicated attributes with Conda_ resolver (thanks to Björn Grüning). Pull Request 403_
Upgrade to latest version of galaxy-lib_ for 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 with PyPI_ build artifacts due to submodule's not being initialized during previous release.

0.22.0 (2016-01-13)

Add --skip_venv to support running Galaxy 16.01 inside of conda environments. 9f3957d_
Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_
Update LICENSE for Planemo to match Galaxy. 15d33c7_
Depend on new galaxy-lib_ on PyPI_ instead of previous hacks.... Pull Request 394_
Fix egg caching against master/15.10. 6d0f502_
Fix bug causing shed publishing of .svn directories. Issue 391_
Bug fixes for Conda_ support thanks to @bgruening. 63e456c
Fix document issues thanks to @einon. Pull Request 390
Improve client for shed publishing to support newer shed backend being developed by @hexylena. Pull Request 394
Tool Shed repo_id change, @hexylena. Pull Request 398
Various other small changes to testing, project structure, and Python 3 support.

0.21.1 (2015-11-29)

Fix serious regression to test command. 94097c7_
Small fixes to release process. 4e1377c_, 94645ed_

0.21.0 (2015-11-29)

If virtualenv not on PATH, have Planemo create one for Galaxy. 5b97f2e_
Add documentation section on testing tools installed in an existing Galaxy instance. 1927168_
When creating a virtualenv for Galaxy, prefer Python 2.7. e0577e7_
Documentation fixes and improvements thanks to @martenson. 0f8cb10, 01584c5_, b757791_
Specify a minimum six version requirement. 1c7ee5b_
Add script to test a planemo as a wheel. 6514ff5_, Issue 184_
Fix empty macro loading. Issue 362_
Fix an issue when you run shed_diff --shed_target local thanks to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff. Pull Request 375_
Fix shed_diff printing to stdout if -o isn't specified. f3394e7_
Small shed_diff improvements to XML diffing and XUnit reporting. af7448c_, 83e227a_
More logging of shed_diff results if --verbose flagged. 9427b47_
Add test_report command for rebuilding reports from structured JSON. 99ee51a_
Fix option bug with Click 6.0 thanks to @bgruening. 2a7c792
Improved error messages for test commands. fdce74c_
Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_
Use newer travis container infrastructure for testing. 6d81a94_
Test case fixes. 98fdc8c_, 0e4f70a_

0.20.0 (2015-11-11)

More complete I/O capturing for XUnit. 6409449_
Check for select parameter without options when linting tools. Issue 373_
Add --cwl_engine argument to cwl_run command. dd94ddc_
Fixes for select parameter linting. 8b31850_
Fix to demultiplexing repositories after tool uploads. Issue 361_
Fix to update planemo for Galaxy wheels. 25ef0d5_
Various fixes for Python 2.6 and Python 3. c1713d2_, 916f610_, c444855_

0.19.0 (2015-11-03)

Initial implementation of cwl_run command that runs a CWL tool and job file through Galaxy. 49c5c1e_
Add --cwl flag to serve to experimentally serve CWL tools in Galaxy. Pull Request 339_
Implement highly experimental cwl_script command to convert a CWL job to a bash script. 508dce7_
Add name to all XUnit reports (thanks to @hexylena). Pull Request 343
Capture stdout and stderr for shed_diff and shed_update XUnit reports. Pull Request 344_
More tool linting (conditionals) thanks to @hexylena. Pull Request 350
UTF-8 fixes when handling XUnit reports. Pull Request 345_
Add Epigenetics as Tool Shed category. Pull Request 351_
Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to @natefoo). Pull Request 356
Add --cite_url to tool_init. fdb1b51_
tool_init bug fix. f854138_
Fix setup.py_ for cwltool and bioblend_ changes. 1a157d4_
Add option to specify template sqlite database locally. c23569f_
Add example IPython notebooks to docs. c8640b6_

0.18.1 (2015-10-22)

Fix issue with test reporting not being populated. 19900a6_

0.18.0 (2015-10-20)

Improvements to docker_shell usability (thanks to @kellrott). Pull Request 334
Add docker pull attempt when missing Dockerfile (thanks to @kellrott). Pull Request 333
Fix bug inferring which files are tool files (thanks to @hexylena). Pull Request 335, Issue 313_
Initial work toward automating brew recipe update. 4d6f7d9_, Issue 329_

0.17.0 (2015-10-19)

Implement basic XUnit report option for shed_update (thanks to @martenson). Pull Request 322
Fix issues with producing test outputs. 572e754_
Xunit reporting improvements - refactoring, times, diff output (thanks to @hexylena). Pull Request 330
Implement project governance policy and update developer code of conduct to match that of the Galaxy project. Pull Request 316_
Update filters for account for new .txt and .md test outputs (thanks to @hexylena). Pull Request 327
Add verbose logging to galaxy test output handling problems. 5d7db92_
Flake8 fixes (thanks to @martenson). 949a36d
Remove uses of deprecated mktemp Python standard library function (thanks to @hexylena). Pull Request 330

0.16.0 (2015-10-07)

Adding new command dependency_script to convert Tool Shed dependencies into shell scripts - thanks to @peterjc. Pull Request 310, f798c7e_, Issue 303_
Implement profiles in sheds section of the ~/.planemo.yml. Pull Request 314_

0.15.0 (2015-10-01)

Template framework for reporting including new markdown and plain text reporting options for testing - thanks to @hexylena. Pull Request 304
XUnit style reporting for shed_diff command - thanks to @hexylena. Pull Request 305
Add new shed_build command for building repository tarballs - thanks to @kellrott. Pull Request 297
Fix exit code handling for lint commands - thanks to @mvdbeek. Pull Request 292
Improved documentation for serve command - thanks to @lparsons. Pull Request 312
Tiny backward compatible Python 3 tweaks for Tool Factory_ - thanks to @peterjc. dad2d9d
Fixed detection of virtual environment in Makefile - thanks to @lparsons. Pull Request 311
Updates to Galaxy XSD - thanks to @mr-c. Pull Request 309
Allow reading shed key option from an environment variable. Pull Request 307_
Allow specifying host to serve Galaxy using -host - thanks in part to @chambm. Pull Request 301
Allow specifying defaults for -host and --port in ~/.planemo.yml. Pull Request 301_
Improve ~/.planemo.yml sample comments - thanks to @martenson. Pull Request 287
Update tool shed categories - thanks to @bgruening. Pull Request 285
Improved output readibility for diff command - thanks to @martenson. Pull Request 284

0.14.0 (2015-08-06)

Allow -t as shorthand for --shed_target (thanks to Peter Cock). Pull Request 278_
Fix tool_init command to use from_work_dir only if file in command (thanks to bug report and initial fix outline by Gildas Le Corguillé). Pull Request 277_
Various 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 272

0.13.2 (2015-07-06)

Fix project_init for missing files. cb5b906_
Various documentation improvements.

0.13.1 (2015-07-01)

Fix for shed_init producing non-standard type hints. Issue 243, f0610d7
Fix tool linting for parameters that define an argument but not a name. Issue 245, aad1eed
Many 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_install will still force a fetch). Pull Request 235_
Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>__ has 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 (including detect_errors and output collections). Issue 233, 334f2d4
Fix shed_test help text. Issue 223_
Fix code typo (thanks to Nicola Soranzo). Pull Request 230_
Improvements to algorithm used to guess if an XML file is a tool XML file. Issue 231_
Fix configuration file handling bug. Issue 240_

0.12.2 (2015-05-23)

Fix shed_test and shed_serve for test and local tool sheds. f3cafaa_

0.12.1 (2015-05-21)

Fix to ensure the tab completion script is in the Python source tarball (required for setting up tab-completion for Homebrew). 6b4e7a6_

0.12.0 (2015-05-21)

Implement a --failed flag for the test command to rerun previously faied tests. Pull Request 210_
Implement shed_update to upload contents and update repository metadata. Pull Request 216_
Implement shed_test and shed_serve commands to test and view published artifacts in the Tool Shed. Pull Request 213, Issue 176
Add shell tab-completion script. 37dcc07_
Many more commands allow specifing multiple tool and/or repository targets. Issue 150_
Add -m as alias for --message in planemo shed_upload (thanks to Peter Cock). Pull Request 200_
Add --ensure_metadata option to shed_lint to ensure .shed.yml files contain many repository. Pull Request 215_
More developer documentation, additional make targets including ones for setting up git pre-commit hooks. cc8abb6_, Issue 209_
Small README improvement (thanks to Martin Čech) b53006d_
Fixes for shed operation error handling (thanks to Martin Čech). Pull Request 203, Pull Request 206
Fix for "smart" shed_diff not in the repository root directory (thanks to Peter Cock). Pull Request 207, Issue 205
Recursive shed_diff with directories not yet in Tool Shed. Pull Request 208_
Improve error handling and reporting for problematic --shed_target values. Issue 217_
Fix typos in lint messages. Issue 211_

0.11.1 (2015-05-12)

Fix default behavior for planemo lint to use current directory if explicit paths are not supplied. 1e3668a_

0.11.0 (2015-05-12)

More compact syntax for defining multiple custom inclusions in .shed.yml files - thanks to Peter Cock. Issue 180, Pull Request 185, Pull Request 196_
Prevent ambigous destinations when defining custom inclusions in .shed.yml- thanks to Peter Cock. Pull Request 186_
lint now warns if tool ids contain whitespace. Pull Request 190_
Handle empty tar-balls gracefully on older Python versions - thanks to Peter Cock. Pull Request 187_
Tweak quoting in cp command - thanks to Peter Cock. 6bcf699_
Fix regression causing testing to no longer produce "pretty" test results under certain circumstances. Issue 188_
Fix for recursive shed_diff folder naming. Issue 192_
Fix output definitions to tool_init command. Issue 189_

0.10.0 (2015-05-06)

Extend shed_lint to check for valid actions in tool_dependencies.xml files. 8117e03_
Extend shed_lint to check for required files based on repository type. Issue 156_
Ignore common editor backup files during shed_upload. Issue 179_
Fix missing file when installing from source via PyPI_. Issue 181_
Fix lint to verify data inputs specify a format attribute. 8117e03_
Docstring fix thanks to @peterjc. fe7ad46

0.9.0 (2015-05-03)

Add new logo to the README thanks to @petrkadlec_ from puradesign.cz <http://puradesign.cz/en>__ and @carlfeberhard_ from the Galaxy Project. Issue 108_
Implement smarter shed_diff command - 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 167_
Use new smarter shed_diff code to implement a new --check_diff option for shed_upload - to check for meaningful differences before updating repositories. Issue 168_
Record git commit hash during shed_upload if the .shed.yml is located in a git repository. Issue 170_
Allow shed_ operations to operate on git URLs directly. Issue 169_
Fail if missing file inclusion statements encountered during .shed.yml repository resolution - bug reported by @peterjc. Issue 158
Improved exception handling for tool shed operations including new --fail_fast command-line option. * Issue 114, Pull Request 173
Implement more validation when using the shed_init command. 1cd0e2d_
Add -r/--recursive option to shed_download and shed_diff commands and allow these commands to work with .shed.yml files defining multipe repositories. 40a1f57_
Add --port option to the serve and tool_factory commands. 15804be_
Fix problem introduced with setup.py_ during the 0.9.0 development cycle
- thanks to @peterjc. Pull Request 171
Fix clone bug introduced during 0.9.0 development cycle - thanks to @bgruening. Pull Request 175

0.8.4 (2015-04-30)

Fix for Travis CI testing picking up invalid tests (reported by @takadonet). Issue 161
Fix tar ordering for consistency (always sort by name) - thanks to @peterjc. Pull Request 164, Issue 159_
Fix exception handling related to tool shed operations - thanks to @peterjc. Pull Request 155, b86fe1f_

0.8.3 (2015-04-29)

Fix bug where shed_lint was not respecting the -r/--recursive flag. 9ff0d2d_
Fix bug where planemo was producing tar files incompatible with the Tool Shed for package and suite repositories. a2ee135_

0.8.2 (2015-04-29)

Fix bug with config_init command thanks to @bgruening. Pull Request 151
Fix unnessecary lint warning about parallelism tag reported by @peterjc. 9bf1eab

0.8.1 (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 new shed_lint command that verifies various aspects of tool shed repositories - including XSD_ validation of repository_dependencies.xml and tool_dependencies.xml files, best practices for README files, and the contents of .shed.yml files. This requires the lxml_ library to be available to Planemo or the application xmllint_ to be on its PATH. Pull Request 130_ Issue 89_ Issue 91_ 912df02_ d26929e_ 36ac6d8_
Option to enable experimental XSD_ based validation of tools when lint is executed with the new --xsd flag. This validation occurs against the unofficial Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>__ maintained by @JeanFred. This requires the lxml library to be available to Planemo or the application xmllint_ to be on its PATH. Pull Request 130_ 912df02_
Allow skipping specific linters when using the lint command using the new --skip option. 26e3cdb_
Implement sophisticated options in .shed.yml to map a directory to many, custom Tool Shed repositories during shed operaitons such shed_upload including automatically mapping tools to their own directories and automatically building suites repositories. Pull Request 143_
Make shed_upload more 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. 53edd99_
Implement a new shed_init command that will help bootstrap .shed.yml files in the specified directory. cc1a447_
Extend shed_init to automatically build a repository_rependencies.xml file corresponding to a Galaxy workflow (.ga file). Issue 118_ 988de1d_
In addition to a single file or directory, allow lint to be passed multiple files. 343902d_ Issue 139_
Add -r/--recursive option to shed_create and lint commands. 63cd431_ 01f2af9_
Improved output formatting and option to write diffs to a file for the shed_diff command. 965511d_
Fix lint problem when using new Galaxy testing features such as expecting job failures and verifing job output. Issue 138_
Fix typo in test help thanks to first time contributor @pvanheus. Pull Request 129 1982076_
Fix NPE on empty help element when linting tools. Issue 124_
Fix lint warnings when configfiles are defined in a tool. 1a85493_
Fix for empty .shed.yml files. b7d9e96_
Fix the test command for newer versions of nose_. 33294d2_
Update help content and documentation to be clear normalize should not be used to update the contents of tool files at this time. 08de8de_
Warn on unknown command attributes when linting tools (anything but interpreter). 4f61025_
Various design, documentation (including new documentation on Tool Shed publishing <http://planemo.readthedocs.org/en/latest/publishing.html>__), and testing related improvements (test coverage has risen from 65% to over 80% during this release cycle).

0.7.0 (2015-04-13)

Implement shed_create command to create Tool Shed repositories from .shed.yml files (thanks to E. Rasche). Pull Request 101_
Allow automatic creation of missing repositories during shed_upload with the new --force_repository_creation flag (thanks to E. Rasche). Pull Request 102_
Allow specifying files to exclude in .shed.yml when creating tar files for shed_upload (thanks to Björn Grüning). Pull Request 99_
Resolve symbolic links when building Tool Shed tar files with shed_upload (thanks to Dave Bouvier). Pull Request 104_
Add a Contributor Code of Conduct <https://planemo.readthedocs.org/en/latest/conduct.html>__. Pull Request 113_
Omit tool_test_output.json from Tool Shed tar file created with shed_upload (thanks to Dave Bouvier). Pull Request 111_
Update required version of bioblend_ to 0.5.3. Fixed Issue 88_.
Initial work on implementing tests cases for Tool Shed functionality. 182fe57_
Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_
Download Galaxy from the new, official Github repository. 7c69bf6_
Update travis_test to install stable planemo from PyPI_. 39fedd2_
Enable caching on --install_galaxy by default (disable with --no_cache_galaxy). d755fe7_

0.6.0 (2015-03-16)

Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...
Fix tool_init to quote file names (thanks to Peter Cock). Pull Request 98_.
Allow ignoring file patterns in .shed.yml (thanks to Björn Grüning). Pull Request 99_
Add --macros flag to tool_init command to generate a macro file as part of tool generation. ec6e30f_
Add linting of tag order for tool XML files. 4823c5e_
Add linting of stdio tags in tool XML files. 8207026_
More tests, much higher test coverage. 0bd4ff0_

0.5.0 (2015-02-22)

Implement --version option. Issue 78_
Implement --no_cleanup option for test and serve commands to persist temp files. 2e41e0a_
Fix bug that left temp files undeleted. Issue 80_
More improvements to release process. fba3874_

0.4.2 (2015-02-21)

Fix setup.py_ for installing non-Python data from PyPI_ (required newer for tool_factory command and reStructuredText linting). Thanks to Damion Dooley for the bug report. Issue 83_

0.4.1 (2015-02-16)

Fix README.rst so it renders properly on PyPI_.

0.4.0 (2015-02-16)

Implement tool_init command for bootstrapping creation of new tools (with tutorial <http://planemo.readthedocs.org/en/latest/writing.html>.) 78f8274
Implement normalize command for reorganizing tool XML and macro debugging. e8c1d45_
Implement tool_factory command to spin up Galaxy pre-configured the Tool Factory. 9e746b4
Added basic linting of command blocks. b8d90ab_
Improved linting of help blocks, including verifying valid reStructuredText. 411a8da_
Fix bug related to serve command not killing Galaxy properly when complete. 53a6766_
Have serve command display tools at the top level instead of in shallow sections. badc25f_
Add additional dependencies to setup.py more functionality works out of the box. 85b9614_
Fix terrible error message related to bioblend_ being unavailable. Issue 70_
Various smaller documentation and project structure improvements.

0.3.1 (2015-02-15)

Fixes to get PyPI_ workflow working properly.

0.3.0 (2015-02-13)

Add option (-r) to the shed_upload command to recursively upload subdirectories (thanks to E. Rasche). Pull Request 68_
Fix diff formatting in test reports (thanks to E. Rasche). Pull Request 63_
Grab updated test database to speed up testing (thanks to approach from E. Rasche and Dannon Baker). Issue 61, dff4f33
Fix test data command-line argument name (was test-data now it is test_data). 834bfb2_
Use tool_data_table_conf.xml.sample file if tool_data_table_conf.xml.test is unavailable. Should allow some new tools to be tested without modifying Galaxy's global tool_data_table_conf.xml file. ac4f828_

0.2.0 (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 56_
Allow setting various test output options in ~/.planemo.yml and disabling JSON output. 21bb463_
More experimental Brew and Tool Shed options that should not be considered part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
Fix project_init for BSD tar (thanks to Nitesh Turaga for the bug report.) a4110a8_
Documentation fixes for tool linting command (thanks to Nicola Soranzo). Pull Request 51_

0.1.0 (2014-12-16)

Moved repository URL to https://github.com/galaxyproject/planemo.
Support for publishing to the Tool Shed. Pull Request 6_
Support for producing diffs (shed_diff) between local repositories and the Tool Shed (based on scripts by Peter Cock). Pull Request 33_
Use tool's local test data when available - add option for configuring test-data target. Pull Request 1_
Support for testing tool features dependent on cached data. 44de95c_
Support for generating XUnit tool test reports. 82e8b1f_
Prettier HTML reports for tool tests. 05cc9f4_
Implement share_test command for embedding test result links in pull requests. Pull Request 40_
Fix for properly resolving links during Tool Shed publishing (thanks to Dave Bouvier). Pull Request 29_
Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_
Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan Blankenberg). a2c13e4_
Automate more of Travis CI testing so the scripts added to tool repository can be smaller. 20a8680_
Documentation fixes for Travis CI (thanks to Peter Cock). Pull Request 22, Pull Request 23
Various documentation fixes (thanks to Martin Čech). 36f7cb1_, b9232e5_
Various 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_

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