- 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
- Init & update submodules when installing and creating packages. Stop distributing eggs (thanks to @nsoranzo). 1ab8530
- 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
- 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
- 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
- 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 deprecatedload()
(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
- 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
- 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
- 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
- Fix username validation for shed linting (thanks to @martenson). Pull Request 899, Issue 898
- 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 forplanemo 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__
forTestCase
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
- 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
- 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
- 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
- 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
- Allow optional disabling of Galaxy single user mode. Pull Request 835
- Fix for path pasting options during workflow testing. Pull Request 834
- 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
, andmull
. Pull Request 828 - Add two new tutorials for Conda and Container 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 withSoftwareRequirement
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 withpip install toil
in Planemo's environment). Pull Request 831 - Add documentation 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
- Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container
--engine
.
- Fixes and small CLI tweaks to get the Docker Galaxy container working as an
--engine
for the run, serve, and test commands.
- Various small fixes for new external Galaxy engine type.
- Fix PyPI README rendering for 0.49.0 release changes.
- 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 withconda-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
- 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
andrun
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
- 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
- Rev to latest versions of bioblend and galaxy-lib for various fixes related to CWL.
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
- 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 justo
) 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
- Fix bug with
shed_lint --urls
introduced in 0.38.0. 84ebc1f
- 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
- 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
- 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
- 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
- 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).
- 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
- Implement
mull
command to build containers for tools based on Conda recipes matching requirement definitions. 08cef54 - Implement
--mulled_containers
flag ontest
,serve
, andrun
commands to run tools in "mulled" containers. Galaxy will first search locally cache containers (such as ones built withmull
), 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 onlint
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
- Fix HISTORY.rst link problem that prevented correct display of content on PyPI.
- 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
- 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
andpull_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. 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
- 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
- Implement new commands to
ci_find_repos
andci_find_tools
to ease CI scripting. Pull Request 555
- 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
- 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 forconda_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 thedependency_script
command (thanks to @peterjc). c2204b3 - Fixes for the Homebrew recipe updater. c262b6d
- Improved handling of Python 2.7 specific dependencies.
- 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
- 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 bytravis_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
- 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
- Implement
Engine
andRunnable
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 bygalaxy_root
having existing and incompatiblejob_conf.xml
files and makes it possible to specify defaults with fixed server name. c4dfd55 - Introduce profile commands (
profile_create
,profile_delete
, andprofile_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
- Implement Galaxy "profiles" - the ability to configure
perisistent, named environments for
serve
andtest
. 5d08b67 - Greatly improved
serve
command - maketest-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 toserve
command. 02a08a0 - Update project testing to include linting documentation
(
docs/
), Python import order, and docstrings. a13a120, 6e1e726, 95d5cba
- Revert "check
.shed.yml
owner against credentials during shed creation", test was incorrect and preventing uploads. Pull Request 425, Issue 246
- 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
- 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
- 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.
- Fixed bug targetting forthcoming release of Galaxy 16.01.
- Fixed problem with PyPI build artifacts due to submodule's not being initialized during previous release.
- 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.
- If
virtualenv
not onPATH
, 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
- More complete I/O capturing for XUnit. 6409449
- Check for select parameter without options when linting tools. Issue 373
- Add
--cwl_engine
argument tocwl_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
- Initial implementation of
cwl_run
command that runs a CWL tool and job file through Galaxy. 49c5c1e - Add
--cwl
flag toserve
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
andshed_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
totool_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
- Fix issue with test reporting not being populated. 19900a6
- 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
- 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
- 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
- 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
- Allow
-t
as shorthand for--shed_target
(thanks to Peter Cock). Pull Request 278 - Fix
tool_init
command to usefrom_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
- Fix project_init for missing files. cb5b906
- Various documentation improvements.
- Fix for
shed_init
producing non-standard type hints. Issue 243, f0610d7 - Fix tool linting for parameters that define an
argument
but not aname
. 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).
- 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 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
- Fix
shed_test
andshed_serve
for test and local tool sheds. f3cafaa
- Fix to ensure the tab completion script is in the Python source tarball (required for setting up tab-completion for Homebrew). 6b4e7a6
- Implement a
--failed
flag for thetest
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
andshed_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 toshed_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
- Fix default behavior for
planemo lint
to use current directory if explicit paths are not supplied. 1e3668a
- 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
- 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 verifydata
inputs specify aformat
attribute. 8117e03 - Docstring fix thanks to @peterjc. fe7ad46
- Add new logo to the README thanks to @petrkadlec from puradesign.cz 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 forshed_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 toshed_download
andshed_diff
commands and allow these commands to work with.shed.yml
files defining multipe repositories. 40a1f57 - Add
--port
option to theserve
andtool_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
- 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
- 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
- Fix bug with
config_init
command thanks to @bgruening. Pull Request 151 - Fix unnessecary
lint
warning aboutparallelism
tag reported by @peterjc. 9bf1eab
- Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
- Implement the new
shed_lint
command that verifies various aspects of tool shed repositories - including XSD validation ofrepository_dependencies.xml
andtool_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 itsPATH
. 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 maintained by @JeanFred. This requires the lxml library to be available to Planemo or the application xmllint to be on itsPATH
. 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 suchshed_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 arepository_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 toshed_create
andlint
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 whenconfigfiles
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 butinterpreter
). 4f61025 - Various design, documentation (including new documentation on Tool Shed publishing), and testing related improvements (test coverage has risen from 65% to over 80% during this release cycle).
- 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 forshed_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. Pull Request 113
- Omit
tool_test_output.json
from Tool Shed tar file created withshed_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
- 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 totool_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
- Implement
--version
option. Issue 78 - Implement
--no_cleanup
option fortest
andserve
commands to persist temp files. 2e41e0a - Fix bug that left temp files undeleted. Issue 80
- More improvements to release process. fba3874
- 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
- Fix README.rst so it renders properly on PyPI.
- Implement
tool_init
command for bootstrapping creation of new tools (with tutorial.) 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.
- Fixes to get PyPI workflow working properly.
- Add option (
-r
) to theshed_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 istest_data
). 834bfb2 - Use
tool_data_table_conf.xml.sample
file iftool_data_table_conf.xml.test
is unavailable. Should allow some new tools to be tested without modifying Galaxy's globaltool_data_table_conf.xml
file. ac4f828
- 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
- 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.
- Initial work on the project - commands for testing, linting, serving Galaxy tools - and more experimental features involving Docker and Homebrew. 7d07782