History¶
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 1408Fix 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
andMaterials 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 1370fix 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 1329Add 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 1312Fix 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 1283Planemo 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
andplanemo.virtualenv
(thanks to @nsoranzo). Pull Request 1287Drop
conda_lint
command (thanks to @nsoranzo). Pull Request 1288Type 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
andplanemo.workflow_lint
(thanks to @nsoranzo). Pull Request 1291Make –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 1184Select 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 therun
command (thanks to @simonbray). Pull Request 1157Make 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 1154Revise 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
andci_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 thelist_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 1102Add
workflow_upload
command for publishing each workflow of a repository with many workflows to their own standalone repository. Pull Request 1091Update github commands to authenticate with a token rather than username/password (thanks to @simonbray). Pull Request 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
, andworkflow_test_init
(thanks to @simonbray). Pull Request 1101, Pull Request 1118, Pull Request 1121, Pull Request 1116, Pull Request 1064Allow outputting test results as Allure framework results. Pull Request 1115
Fix
run_tests.sh
invocation Pull Request 1099Tiny 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 1072Updating 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 1086Explicit tests for Galaxy 20.09. Pull Request 1093
Minor fix for
ci_find_repos
command. Pull Request 1094Fix 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 1114Fix
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 1052Workflow 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
andtest
. Pull Request 900, Pull Request 1029Remove 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 1001Change 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 toci_find_tools
(thanks to @bernt-matthias). Pull Request 1008Add shared data library path to the data upload box for training material (thanks to @shiltemann). Pull Request 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 989Drop planemo database seed option Pull Request 985
Don’t execute
untar_to()
subprocesses through the shell Pull Request 984Allow 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)¶
0.62.0 (2019-10-11)¶
Use
unicodify()
on exceptions and subprocess outputs (thanks to @nsoranzo) Pull Request 944Do not override
None
with empty string (thanks to @ic4f). Pull Request 950Update 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 deprecatedload()
(thanks to @nsoranzo). Pull Request 921Allow converting
tool_test_report.json
to xunit (thanks to @mvdbeek). Pull Request 918Fix 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
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 902Do 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 896New command (
workflow_edit
) to open workflow in a synchronized graphical editor. Pull Request 894Conda tutorial fixes (thanks to @nsoranzo). Pull Request 876
Enable
--conda_use_local
option forplanemo test
(thanks to @nsoranzo). Pull Request 876When 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 892Increase 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 888Add 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 877Improved XSD lint reporting. Pull Request 871
Fix Planemo writing a file called
gx_venv_None
. Pull Request 870Update 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. 72d2ca7Add 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 841Small 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
, andmull
. Pull Request 828Add 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, a5c72e3Add new engine type (
--engine toil
) for testing and running CWL tools (requires manually installing Toil withpip install toil
in Planemo’s environment). Pull Request 831Add 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 826Fix 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 801Log tool config in verbose logging mode. Pull Request 802
Replace
r
channel withconda-forge
(thanks to @bgruening). Pull Request 805Sync
galaxy.xsd
with latest Galaxy updates (thanks to @nsoranzo). Pull Request 806Use
requests.get()
when validating http URLs (thanks to @nsoranzo). Pull Request 809Do 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
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 764Record 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 776Implement 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 733Add ‘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 709Bugfix handle
None
requirement versions when registering containers (thanks to @bgruening). Pull Request 704Bugfix 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 680Conda documentation and option naming improvements. Pull Request 683
Implement
container_register
for tool repositories. Pull Request 675Fix
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 662Fix
filter_paths()
to not partial match paths when filtering shed repositories (thanks to @nsoranzo). Pull Request 665Fix 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. b4ae44dRun 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 642Allow Planemo to work with locally built Conda packages using the
--conda_use_local
command. Pull Request 643, Issue 620Implement an
open
(or justo
) command to quickly open the last test results (or any file if supplied). Pull Request 641Linting 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. 6638caaAllow
conda_install
to work with packages as well as just tools. 8faf661Add
--global
option to conda_install to install requirements into global Conda setup instead of using an environment. 8faf661Implement
planemo lint --biocontainer
that checks that a tool has an available BioContainer registered. 0a1abfeAdd more options and more documentation to the
planemo mull
command. 0a1abfeHack around a bug in Conda 4.2 that makes it so
planemo mull
doesn’t work out of the box on Mac OS X. 0a1abfeAllow 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
. 04238d3Fix
MANIFEST.in
entry that was migrated to galaxy-lib. ced5ce2Various fixes for the command
conda_env
. Pull Request 640Improved command help - both formatting and content. Pull Request 639
Implement a
--no_dependency_resolution
option disabling conda dependency resolver. Pull Request 635, Issue 633Tests 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
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. 4595953Use 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 610Improved integration testing for
test
command. Pull Request 609Update 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. 08cef54Implement
--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. 9da8387Allow
conda_install
command over multiple tool paths. 2e4e5fcUpdate pip as part of setting virtual environment in
Makefile
target. 19b2ee9Add 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
). 1ef05d2Implement a
conda_lint
command to lint Conda recipes based on anaconda-verify. 6a6f164Implement
clone
andpull_request
commands to ease PRs (with documentation fixes from @martenson). e925ba1, ea5324fUpdate 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. ccdd2d5Update to latest Tool Factory code from tools-iuc. ca88b0c
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 566Migrate and update documentation related to tool XML macros and handling multiple outputs from the Galaxy wiki (with help from @bgruening, @mvdbeek, and @nsoranzo). Pull Request 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
andci_find_tools
to ease CI scripting. Pull Request 555
0.30.2 (2016-09-01)¶
0.30.1 (2016-09-01)¶
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 forconda_install
. ca19910Allow the environment variable
PLANEMO_CONDA_PREFIX
to set a default for--conda_prefix
. 24008abFix 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). c2204b3Fixes 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 545Fix 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)¶
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 528Minor polish to the
travis_init
command (thanks to @peterjc). Pull Request 512Update 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 513Improve and fix docs ahead of GCC 2016 (thanks to @martenson). Pull Request 498, 725b232
Add description of
expect_num_outputs
to planemo FAQ. a066afbRevise planemo tools docs to be more explicit about collection identifiers. a811e65
Add more docs on existing dynamic tool output features. Pull Request 526
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
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
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, 7be1bf5Fix 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. c4dfd55Introduce profile commands (
profile_create
,profile_delete
, andprofile_list
) and profile improvements (automatic postgres database creation support). Pull Request 480, a87899bRework Galaxy test reporting to use structured data instead of XUnit data. 4d29bf1
Refactor Galaxy configuration toward support for running Galaxy in docker-galaxy-stable. Pull Request 479
0.25.1 (2016-05-11)¶
0.25.0 (2016-05-11)¶
Implement Galaxy “profiles” - the ability to configure perisistent, named environments for
serve
andtest
. 5d08b67Greatly 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, f3c6917Add code and documentation for linting (
lint
) and building (tool_init
) CWL tools. a4e6958, b0b867e, 4cd571cIf needed for Conda workaround, shorten
config_directory
path (thanks to @mvdbeek). efc5f30Fix
--no_cache_galaxy
option (thanks to Gildas Le Corguillé). d8f2038Fix
cwltool
dependency version - upstream changes broke compatibility. 65b999dAdd 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, e0acf91Revise 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, 26e378eFix
tool_init
commans options typos (thanks to Nitesh Turaga). 826d371Refactor galaxy-related modules into submodules of a new
planemo.galaxy
package. 8e96864Fix 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. f7554d1Add
--extra_tools
option toserve
command. 02a08a0Update 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
. ce8e1beImproved 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 416Fix 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 246Fix logic error if there is a problem with
shed_create
. 358a42c
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. 9f3957dUpdate 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 391Bug 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 398Various other small changes to testing, project structure, and Python 3 support.
0.21.1 (2015-11-29)¶
0.21.0 (2015-11-29)¶
If
virtualenv
not onPATH
, have Planemo create one for Galaxy. 5b97f2eAdd 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. 1c7ee5bFix 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 375Fix
shed_diff
printing to stdout if-o
isn’t specified. f3394e7Small
shed_diff
improvements to XML diffing and XUnit reporting. af7448c, 83e227aMore logging of
shed_diff
results if--verbose
flagged. 9427b47Add
test_report
command for rebuilding reports from structured JSON. 99ee51aFix 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
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 tocwl_run
command. dd94ddcFixes 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. 49c5c1eAdd
--cwl
flag toserve
to experimentally serve CWL tools in Galaxy. Pull Request 339Implement highly experimental
cwl_script
command to convert a CWL job to a bash script. 508dce7Add name to all XUnit reports (thanks to @hexylena). Pull Request 343
Capture stdout and stderr for
shed_diff
andshed_update
XUnit reports. Pull Request 344More 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
. fdb1b51tool_init
bug fix. f854138Add 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 334Add 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 322Fix 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 327Add 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 303Implement 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 305Add new
shed_build
command for building repository tarballs - thanks to @kellrott. Pull Request 297Fix exit code handling for
lint
commands - thanks to @mvdbeek. Pull Request 292Improved documentation for
serve
command - thanks to @lparsons. Pull Request 312Tiny backward compatible Python 3 tweaks for Tool Factory - thanks to @peterjc. dad2d9d
Fixed detection of virtual environment in
Makefile
- thanks to @lparsons. Pull Request 311Updates 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 301Allow specifying defaults for
-host
and--port
in~/.planemo.yml
. Pull Request 301Improve
~/.planemo.yml
sample comments - thanks to @martenson. Pull Request 287Update 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 278Fix
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 277Various documentation fixes (thanks in part to Peter Cock and Daniel Blankenberg). Pull Request 256, Pull Request 253, Pull Request 254, Pull Request 255, Pull Request 251, Issue 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, f0610d7Fix tool linting for parameters that define an
argument
but not aname
. Issue 245, aad1eedMany doc updates including a tutorial for developing tools in a test-driven fashion and instructions for using the planemo appliance through Kitematic (with Kitematic screenshots from E. Rasche).
0.13.0 (2015-06-28)¶
If planemo cannot find a Galaxy root, it will now automatically fetch one (specifing
--galaxy_install
will still force a fetch). Pull Request 235Docuementation 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, 334f2d4Fix
shed_test
help text. Issue 223Fix 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
andshed_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 thetest
command to rerun previously faied tests. Pull Request 210Implement
shed_update
to upload contents and update repository metadata. Pull Request 216Implement
shed_test
andshed_serve
commands to test and view published artifacts in the Tool Shed. Pull Request 213, Issue 176Add 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 215More developer documentation, additional
make
targets including ones for setting up git pre-commit hooks. cc8abb6, Issue 209Small 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 205Recursive
shed_diff
with directories not yet in Tool Shed. Pull Request 208Improve error handling and reporting for problematic
--shed_target
values. Issue 217Fix 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 196Prevent ambigous destinations when defining custom inclusions in
.shed.yml
- thanks to Peter Cock. Pull Request 186lint
now warns if tool ids contain whitespace. Pull Request 190Handle empty tar-balls gracefully on older Python versions - thanks to Peter Cock. Pull Request 187
Tweak quoting in
cp
command - thanks to Peter Cock. 6bcf699Fix regression causing testing to no longer produce “pretty” test results under certain circumstances. Issue 188
Fix for recursive
shed_diff
folder naming. Issue 192Fix 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. 8117e03Extend
shed_lint
to check for required files based on repository type. Issue 156Ignore common editor backup files during
shed_upload
. Issue 179Fix missing file when installing from source via PyPI. Issue 181
Fix
lint
to verifydata
inputs specify aformat
attribute. 8117e03
0.9.0 (2015-05-03)¶
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 167Use new smarter
shed_diff
code to implement a new--check_diff
option forshed_upload
- to check for meaningful differences before updating repositories. Issue 168Record git commit hash during
shed_upload
if the.shed.yml
is located in a git repository. Issue 170Allow
shed_
operations to operate on git URLs directly. Issue 169Fail if missing file inclusion statements encountered during
.shed.yml
repository resolution - bug reported by @peterjc. Issue 158Improved exception handling for tool shed operations including new
--fail_fast
command-line option. * Issue 114, Pull Request 173Implement more validation when using the
shed_init
command. 1cd0e2dAdd
-r/--recursive
option toshed_download
andshed_diff
commands and allow these commands to work with.shed.yml
files defining multipe repositories. 40a1f57Add
--port
option to theserve
andtool_factory
commands. 15804beFix 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)¶
0.8.2 (2015-04-29)¶
Fix bug with
config_init
command thanks to @bgruening. Pull Request 151Fix unnessecary
lint
warning aboutparallelism
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 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 36ac6d8Option 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 912df02Allow skipping specific linters when using the
lint
command using the new--skip
option. 26e3cdbImplement 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 143Make
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. 53edd99Implement a new
shed_init
command that will help bootstrap.shed.yml
files in the specified directory. cc1a447Extend
shed_init
to automatically build arepository_rependencies.xml
file corresponding to a Galaxy workflow (.ga
file). Issue 118 988de1dIn addition to a single file or directory, allow
lint
to be passed multiple files. 343902d Issue 139Add
-r/--recursive
option toshed_create
andlint
commands. 63cd431 01f2af9Improved output formatting and option to write diffs to a file for the
shed_diff
command. 965511dFix 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 1982076Fix NPE on empty
help
element when linting tools. Issue 124Fix
lint
warnings whenconfigfiles
are defined in a tool. 1a85493Fix for empty
.shed.yml
files. b7d9e96Update help content and documentation to be clear
normalize
should not be used to update the contents of tool files at this time. 08de8deWarn on unknown
command
attributes when linting tools (anything butinterpreter
). 4f61025Various 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).
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 101Allow automatic creation of missing repositories during
shed_upload
with the new--force_repository_creation
flag (thanks to E. Rasche). Pull Request 102Allow specifying files to exclude in
.shed.yml
when creating tar files forshed_upload
(thanks to Björn Grüning). Pull Request 99Resolve symbolic links when building Tool Shed tar files with
shed_upload
(thanks to Dave Bouvier). Pull Request 104Omit
tool_test_output.json
from Tool Shed tar file created withshed_upload
(thanks to Dave Bouvier). Pull Request 111Update 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 99Add
--macros
flag totool_init
command to generate a macro file as part of tool generation. ec6e30fAdd linting of tag order for tool XML files. 4823c5e
Add linting of
stdio
tags in tool XML files. 8207026More tests, much higher test coverage. 0bd4ff0
0.5.0 (2015-02-22)¶
0.4.2 (2015-02-21)¶
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.) 78f8274Implement
normalize
command for reorganizing tool XML and macro debugging. e8c1d45Implement
tool_factory
command to spin up Galaxy pre-configured the Tool Factory. 9e746b4Added basic linting of
command
blocks. b8d90abImproved linting of
help
blocks, including verifying valid reStructuredText. 411a8daFix bug related to
serve
command not killing Galaxy properly when complete. 53a6766Have
serve
command display tools at the top level instead of in shallow sections. badc25fAdd additional dependencies to
setup.py
more functionality works out of the box. 85b9614Fix 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 theshed_upload
command to recursively upload subdirectories (thanks to E. Rasche). Pull Request 68Fix 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
). 834bfb2Use
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
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. 21bb463More experimental Brew and Tool Shed options that should not be considered part of Planemo’s stable API. See bit.ly/gxbrew1 for more details.
Fix
project_init
for BSD tar (thanks to Nitesh Turaga for the bug report.) a4110a8Documentation 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 33Use tool’s local test data when available - add option for configuring
test-data
target. Pull Request 1Support 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 40Fix 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