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662 Commits
Author SHA1 Message Date
John Davis 0aa0feb610 Merge pull request #15004 from jdavcs/dev_mypy_workflow 
Run mypy on a fully loaded galaxy venv for stricter type checking
 2022-11-30 22:30:37 -05:00
Nicola Soranzo 3d5bcff5c1 Add pkce to dev/test requirements 
So `test_authenticate_set_pkce_verifier_cookie` unit test is not skipped.
 2022-11-30 16:34:32 +00:00
John DavisandNicola Soranzo 786a3e4375 Don't pip-install lint requirements for package tests 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 11:31:22 -05:00
John Davis 724ff9e17b Install mypy for package tests 2022-11-29 18:40:18 -05:00
John Davis 03732a7516 Re-add jinja2 to config package requirements 2022-11-21 18:12:04 -05:00
John Davis b934b27ea0 Move custom tempates unit test into app; rm jinja2 package dep from config 2022-11-21 18:12:04 -05:00
John Davis 86cc0f2b69 Move custom templates into the config package 2022-11-21 18:12:04 -05:00
Nicola Soranzo 2b362fbd1d Merge branch 'release_22.05' into dev 2022-11-17 22:50:45 +00:00
Nicola Soranzo 988f4e583c Merge branch 'release_22.01' into release_22.05 2022-11-17 22:48:35 +00:00
mvdbeek df7712927b Start work on galaxy-tool-util 22.1.6 2022-11-14 10:28:55 +01:00
mvdbeek 642c28a3e9 Release galaxy-tool-util-22.1.5 2022-11-14 10:22:28 +01:00
John Davis b11c18eb21 Merge pull request #14825 from neoformit/dev-html-email 
Looks great! Thanks, @neoformit 

For future ref/todo: we do need a more systematic/unified approach to handling path construction that handles tests that are arun both as standalone unit tests and as part of package tests (as per observation by @neoformit)
 2022-11-10 11:30:42 -05:00
Nicola Soranzo 1048abe3cf Update cwltool pin 2022-11-10 01:13:41 +00:00
Nicola Soranzo afa7b713bc Replace `GALAXY_TEST_INCLUDE_SLOW env variable with external_dependency_management` pytest marker 
Fix mulled tests missing tests in `test/unit/tool_util/test_conda_resolution.py` .

Also:
- Add `coverage` tox factor to generate coverage report.
 2022-11-03 21:43:37 +00:00
Nicola Soranzo f5deb24dbb Use dnspython to check specifically for an "MX" DNS record 
when validating the domain name of the email address for a new user.

Fix https://github.com/galaxyproject/galaxy/issues/14829 .
 2022-11-03 12:08:35 +01:00
Nicola Soranzo 5ca0aea54a Drop nose 
It's deprecated and unmaintained, and is broken under Python 3.10 .
 2022-11-01 18:45:07 +00:00
John Davis da83e159da Add jijna2 requirement to package install requirements 2022-11-01 10:31:28 -04:00
Cameron Hyde c03c94d0d9 Add jinja2 to test-requirements.txt 2022-11-01 13:58:31 +10:00
Nicola Soranzo 11597099a1 Merge branch 'release_22.05' into dev 2022-10-28 13:27:44 +01:00
Nicola Soranzo 06f518220f Merge branch 'release_22.01' into release_22.05 2022-10-28 13:25:16 +01:00
mvdbeek 238ab85379 Start work on galaxy-tool-util 22.1.5 2022-10-28 10:31:56 +02:00
mvdbeek 52f60b50a4 Release tool-util package 22.1.4 2022-10-28 10:30:23 +02:00
Nicola Soranzo 895a18c7e8 Add missing `unittest_utils` package to galaxy-tool-util 
Fix:

```
ModuleNotFoundError: No module named 'galaxy.tool_util.unittest_utils'
```

in https://github.com/conda-forge/galaxy-tool-util-feedstock/pull/4 .
 2022-10-28 00:23:21 +01:00
mvdbeek 7ff1026296 Start work on galaxy-tool-util 22.1.4 2022-10-27 18:30:21 +02:00
mvdbeek 9bf0b4ed1f Release tool-util package 22.1.3 2022-10-27 18:29:48 +02:00
Nicola Soranzo 5c43d2961f Use dnspython to check specifically for an "MX" DNS record 
when validating the domain name of the email address for a new user.

Fix https://github.com/galaxyproject/galaxy/issues/14829 .
 2022-10-27 11:17:14 +01:00
John Chilton 5a3069d283 Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes. 
Updating the Pulsar job runner/client for https://github.com/galaxyproject/pulsar/pull/302 and as described in the new docs at https://pulsar.readthedocs.io/en/latest/containers.html.
 2022-10-16 09:56:58 +02:00
davelopezandNicola Soranzo 5dc7dae7c1 Use pydantic[email] instead of email-validator 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2022-10-14 12:20:24 +02:00
John Chilton 61b9e57c7f Implement Workflow Invocation -> BCO export. 2022-10-14 12:20:24 +02:00
Nicola Soranzo d266eb7f80 Add missing package requirements 
Packages that are imported directly in galaxy-tool-util that were already
required through the galaxy-util dependency.
 2022-10-12 18:13:46 +01:00
Nate Coraor 61b1417d1f Relocate container_monitor from galaxy_ext, but keep it runnable from 
galaxy_ext. Add entrypoitn galaxy-container-monitor to job_execution
package.
 2022-09-21 17:32:21 -04:00
John Chilton 3dbe2891e7 Implement RO Crate export of Galaxy histories and invocations. 2022-09-13 19:20:48 -04:00
Nicola Soranzo fcfaede15b Merge branch 'release_22.05' into dev 2022-09-13 13:46:02 +01:00
Nicola Soranzo 463779b1b5 Merge branch 'release_22.01' into release_22.05 2022-09-13 12:28:05 +01:00
Nicola Soranzo 77553d1711 Pin CacheControl to prevent missing dependency 
schema-salad currently requires:
- "CacheControl >= 0.11.7, < 0.13"
- "lockfile >= 0.9", which is needed for CacheControl's FileCache until 0.12.11

but CacheControl 0.12.12 replaced lockfile with filelock.

Prevent the following traceback:

```
self = <cachecontrol.caches.file_cache.FileCache object at 0x7fe36ac5d190>
directory = PosixPath('/tmp/.cache/salad'), forever = False, filemode = 384
dirmode = 448, lock_class = None

    def __init__(
        self,
        directory,
        forever=False,
        filemode=0o0600,
        dirmode=0o0700,
        lock_class=None,
    ):

        try:
            if lock_class is None:
>               from filelock import FileLock
E               ModuleNotFoundError: No module named 'filelock'

/tmp/gxpkgtestenvcy0lxY/lib/python3.7/site-packages/cachecontrol/caches/file_cache.py:74: ModuleNotFoundError
```
 2022-09-12 21:57:43 +01:00
Nicola Soranzo dda6feb391 Remove redundant license info from package READMEs 
The license is already specified in `setup.cfg` , which is the
canonical place.
This will simplify the transition to the MIT license.
 2022-09-09 17:20:24 +01:00
Nicola Soranzo 0df5c9a5fb Updates for Poetry 1.2.0 
Also:
- Export only dev requirements to `lib/galaxy/dependencies/dev-requirements.txt` .
- Packages don't have a `requirements.txt` file.
 2022-09-05 17:23:18 +01:00
Björn Grüning 7e76fdae82 Merge pull request #13977 from jmchilton/ts_api_tests 
Implement initial tool shed API tests.
 2022-08-30 21:51:33 +02:00
mvdbeek b43dfa2613 Merge branch 'release_22.05' into dev 2022-08-30 20:37:56 +02:00
mvdbeek d1b4f05345 Merge branch 'release_22.01' into release_22.05 2022-08-30 20:32:39 +02:00
Marius van den Beek 609c90fa25 Update packages/tool_util/HISTORY.rst 2022-08-30 17:25:10 +02:00
John Chilton 12b34ff47c API tests for the tool shed. 2022-08-29 09:51:20 -04:00
mvdbeek c07fd27806 Touch up tool util packaging fixes 2022-08-29 13:12:01 +02:00
mvdbeek 0a69d3d882 Update version to 22.1.2.dev0 2022-08-22 21:57:17 +02:00
mvdbeek dc56fc4e61 Update version to 22.01.1 2022-08-22 21:47:47 +02:00
mvdbeek a351bd1ce9 Merge branch 'release_22.05' into dev 2022-08-09 15:12:15 +02:00
Nicola Soranzo f68f573827 Merge pull request #14379 from mr-c/patch-1 2022-07-27 15:15:38 +01:00
Michael R. Crusoe 0c9b5c517e Remove schem-salad pin 
That release regressed for everyone, and it has been yanked from PyPI
 2022-07-27 10:46:52 +02:00
Michael R. Crusoe 59ac92c1c8 mark galaxy packages as containing typing information 2022-07-26 23:27:36 +01:00
Nicola Soranzo 09c0ed0b00 Temporarily pin schema-salad to 8.3.20220717184004 
Fix the following traceback when running
`pytest test/unit/tool_util/test_cwl.py`:

```
    def test_boolean_defaults():
>       proxy = workflow_proxy(_cwl_tool_path("v1.2/tests/conditionals/cond-wf-002_nojs.cwl"))

test/unit/tool_util/test_cwl.py:244:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/tool_util/cwl/parser.py:760: in workflow_proxy
    return _to_cwl_workflow_object(workflow_path, strict_cwl_validation=strict_cwl_validation)
lib/galaxy/tool_util/cwl/parser.py:851: in _to_cwl_workflow_object
    cwl_workflow = _schema_loader(strict_cwl_validation).tool(path=workflow_path)
lib/galaxy/tool_util/cwl/schema.py:86: in tool
    process_definition = self.process_definition(raw_process_reference)
lib/galaxy/tool_util/cwl/schema.py:68: in process_definition
    loading_context, uri = resolve_and_validate_document(
.venv/lib/python3.8/site-packages/cwltool/load_tool.py:384: in resolve_and_validate_document
    document_loader.resolve_all(workflowobj, fileuri)
schema_salad/ref_resolver.py:965: in resolve_all
    ???
schema_salad/ref_resolver.py:1197: in validate_links
    ???
schema_salad/ref_resolver.py:1124: in validate_links
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

>   ???
E   schema_salad.exceptions.ValidationException: test/functional/tools/cwl_tools/v1.2/tests/conditionals/cond-wf-002_nojs.cwl:2:1: Field `cwlVersion`
E                                                                                     contains undefined
E                                                                                     reference to
E                                                                                     `file:///usr/users/ga002/soranzon/software/nsoranzo_galaxy/test/functional/tools/cwl_tools/v1.2/tests/conditionals/v1.2`

schema_salad/ref_resolver.py:1062: ValidationException
```

Note that the unit test doesn't fail if run on its own with
`pytest test/unit/tool_util/test_cwl.py::test_boolean_defaults` .
 2022-07-25 13:13:48 +01:00