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Commit Graph
157 Commits
Author SHA1 Message Date
Nicola Soranzo 4ca163b9ca Add support for Python 3.11 
- Update Python dependencies that didn't have a cp311 wheel: h5py and
  psycopg2-binary.
- For packages for which there is no recent version that works on all
  Python versions supported by Galaxy (numpy and scipy), replace old
  requirement with multiple Python-version-specific requirements.
 2023-02-02 01:18:25 +00:00
Nicola Soranzo ee7d51f2f5 Merge branch 'release_22.05' into dev 2022-12-09 11:36:00 +00:00
Nicola Soranzo 1eceea2a45 Add/remove/pin/unpin Python requirements 2022-12-09 02:01:26 +00:00
mvdbeek 9c92c55a31 Reset all package HISTORY.rst file to 22.5.0.dev0 2022-12-08 13:24:06 +01:00
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
Nicola Soranzo 1048abe3cf Update cwltool pin 2022-11-10 01:13:41 +00:00
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 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
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
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
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
Michael R. Crusoe e955f87c19 pin schema-salad version 2022-07-23 13:59:20 -05:00
Michael R. Crusoe 62168de95d pin schema-salad version 2022-07-22 15:39:20 -05:00
Nicola Soranzo 933f9d4e88 Modernise build of galaxy-tool-util package 
Also:
- Add missing file to `MANIFEST.in`
 2022-06-09 23:48:22 +01:00
Nicola Soranzo 73bf57e9a0 Remove unused and unnecessary code 
- `PROJECT_OWNER`, `PROJECT_USERAME`, `RAW_CONTENT_URL` and `_version_re` are unused.
- `:changelog:` hyperlink target is unnecessary.
- `test_suite` and `tests_require` are deprecated since setuptools v41.5.0
 2022-06-09 22:55:07 +01:00
Nicola Soranzo e9b2262dd3 Move mypy configuration to `mypy.ini` 
So packages can use `setup.cfg` to replace `setup.py` .
 2022-06-08 10:35:18 +01:00
Nicola Soranzo aeef3318a2 Use setuptools custom package discovery instead of explicit listing 2022-06-06 23:48:37 +01:00
Nicola Soranzo 27b2ee0e9e Merge branch 'release_22.01' into dev 2022-06-06 19:18:55 +01:00
Nicola Soranzo 6a00e75410 Merge branch 'release_21.09' into release_22.01 2022-06-06 11:25:14 +01:00
Nuwan Goonasekera 16d9981c45 Fix missing biotools package 2022-06-06 11:45:55 +05:30
Nicola Soranzo 97e7dceb73 Fix packages' requirements 2022-05-30 22:40:28 +01:00
Nicola Soranzo f2a42ba67e Run mypy on all packages' files 
Also:
- mypy fixes.
- Use `with` statement to open/close files.
 2022-05-30 22:38:55 +01:00
Michael R. Crusoe dd77026527 galaxy-tool-util: better link in the README 2022-05-04 15:25:42 +02:00
Nicola Soranzo 6da2f0e98c Merge branch 'release_22.01' into dev 2022-04-22 18:23:33 +01:00
mvdbeek da61e77068 Fix persistent mulled cache unused for repo_has_name 2022-04-14 12:10:42 +02:00
mvdbeek 443119ccc9 Drop containers package, move to tool_util 2022-03-24 19:51:59 +01:00
mvdbeek 9690680ec7 Update version to 22.01. 2022-03-15 20:46:24 +01:00
Nicola Soranzo 0c80836c34 Upgrade syntax to Python 3.7 
using `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus`

Also more refactoring of Python files in `packages/` .
 2022-03-14 14:57:43 +00:00
John Chilton 213f3a17fc Allow legacy EDAM mappings. 2022-03-07 16:54:54 -05:00