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74,595 Commits 62 Branches 243 Tags
74766a3fb591839dfd5b15d8476a8d0eaf04423a
Commit Graph
819 Commits
Author SHA1 Message Date
Nicola Soranzo 3f0f789b82 Merge pull request #17556 from kostrykin/files_diff_images 
Add `image_diff` comparison method for test output verification using images
 2024-03-04 17:04:44 +00:00
Nicola Soranzo b02101ba69 Unpin Cheetah as the poetry bug was fixed 2024-03-04 13:14:48 +00:00
Nicola Soranzo 62c610c250 Move numpy and pillow requirements to new extended-assertions extra 
together pysam, which is also conditionally imported in
``lib/galaxy/tool_util/verify/__init__.py`` .
 2024-03-02 01:59:10 +00:00
Nicola Soranzo 1a3edae577 Add missing package requirements 2024-02-29 18:22:42 +00:00
Nicola Soranzo d37c2844b5 Install future from PyPI again 
now that 1.0.0 has been released with Python 3.12 support from my
fork.
 2024-02-22 14:04:01 +00:00
John Davis 49e0d4348a Merge branch 'release_23.2' into dev 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/auth/HISTORY.rst
#	packages/config/HISTORY.rst
#	packages/data/HISTORY.rst
#	packages/files/HISTORY.rst
#	packages/job_execution/HISTORY.rst
#	packages/job_metrics/HISTORY.rst
#	packages/navigation/HISTORY.rst
#	packages/objectstore/HISTORY.rst
#	packages/selenium/HISTORY.rst
#	packages/test_api/HISTORY.rst
#	packages/test_base/HISTORY.rst
#	packages/test_driver/HISTORY.rst
#	packages/tool_util/HISTORY.rst
#	packages/tours/HISTORY.rst
#	packages/util/HISTORY.rst
#	packages/web_apps/HISTORY.rst
#	packages/web_framework/HISTORY.rst
#	packages/web_stack/HISTORY.rst
 2024-02-21 19:30:17 -05:00
John Davis f0fbe773b6 Start work on 23.2.2.dev0 2024-02-21 19:30:14 -05:00
John Davis cb06b048b9 Create version 23.2.1 2024-02-21 19:30:11 -05:00
Nicola Soranzo f9384bb0df Disallow pydantic 2.6.0 and 2.6.1 
xref: https://github.com/pydantic/pydantic/issues/8760

Fix the following error when testing with mypy:

```
$ tox -e mypy
Deferral trace:
    cwltool.utils:62
    cwltool.utils:-1
    ...
    galaxy.model:666
    galaxy.model:666
    galaxy.model:666
    galaxy.model:666
lib/galaxy/model/__init__.py: error: INTERNAL ERROR: maximum semantic analysis
iteration count reached
Found 1 error in 1 file (errors prevented further checking)
```
 2024-02-14 00:57:47 +00:00
mvdbeek b278d8a2aa Merge branch 'release_23.2' into dev 2024-02-08 11:35:49 +01:00
Nicola Soranzo 5e14d03779 Merge branch 'release_23.1' into release_23.2 2024-02-07 22:50:08 +00:00
Nicola Soranzo 52933ed5fd Merge branch 'release_23.0' into release_23.1 2024-02-07 22:48:53 +00:00
Nicola Soranzo de8d4562b6 Add missing Werkzeug test requirement 
Used in `test/unit/util/test_get_url.py` since commit
69ebbb761a .

Pin Werkzeug in `lib/galaxy/dependencies/dev-requirements.txt`
to latest version compatible with pytest-httpserver 1.0.6 .

Fix unit test collection error on Python 3.11:
```
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/pytest_httpserver/httpserver.py", line 26, in <module>
    from werkzeug.http import parse_authorization_header
ImportError: cannot import name 'parse_authorization_header' from 'werkzeug.http' (/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/werkzeug/http.py)
```
 2024-02-07 05:44:42 +00:00
John Davis 019c49594f Fix formatting around new version in HISTORY.rst 2024-02-02 10:12:34 -05:00
John Davis ac15c87379 Update package versions to 23.2.dev0 
Update setup.cfg, HISTORY.rst.
Make all dev package versions consistent.
 2024-02-01 22:50:21 -05:00
John Davis b83073f4d2 Change version for schema and TS packages 
To make them consistent with other package versions:
23.1.0.dev0 >> 23.1.dev0.
The extra "0" was likely added automatically by running the
build_packages.sh script.
 2024-02-01 18:34:11 -05:00
John Davis 121e38d570 Drop empty bullet points from package HISTORY.rst files 2024-02-01 16:44:49 -05:00
John Davis 2337c9ca83 Partially remove bash-specific syntax 2024-02-01 12:22:21 -05:00
John Davis 01402e279c Use if/then/fi for readability; minor linting 2024-02-01 09:34:04 -05:00
John Davis 2783fb6018 Ignore lines starting with # in build packages script 2024-01-31 18:55:21 -05:00
John Davis a354d12a4e Merge branch 'release_23.2' into dev 2024-01-31 18:19:54 -05:00
John Davis c1081c3289 Reverse conditional to skip empty lines 2024-01-30 22:03:47 -05:00
John Davis adf175fdc2 Ignore empty lines in packages_by_dep_dag file 2024-01-30 18:44:24 -05:00
John Davis 568480f923 Merge branch 'release_23.2' into dev_merge_23.2 2024-01-24 16:28:01 +00:00
mvdbeek 7e9c02b75c Use python-isal for fast zip deflate compression in rocrate export 2024-01-23 11:16:26 +01:00
Ubuntu 6860c9a0fb Add support for Python 3.12 2024-01-21 11:57:59 +00:00
Nicola Soranzo 4eb94cde5f Install future from my fork with Python 3.12 patches 2024-01-21 11:57:58 +00:00
Nicola Soranzo bbf02a0fdb Use venv module instead of virtualenv 2024-01-15 17:31:57 +00:00
mvdbeek 5cd6254e69 Fix merge conflicts in packages/web_apps/setup.cfg 2024-01-10 17:30:02 +01:00
mvdbeek b70680c5f8 Import IdEncodingHelper for type-checking only 2024-01-10 17:27:58 +01:00
mvdbeek 6863ac4c5f Add pycryptodome dependency to galaxy-schema 2024-01-08 11:33:45 +01:00
mvdbeek 46dc767a4c Update pydantic package dependencies 2024-01-08 11:33:45 +01:00
mvdbeek 9dfdd7dcba Update dependencies 2024-01-08 11:33:41 +01:00
mvdbeek e63c3ba9d4 Update fastapi and pydantic dependencies 2024-01-08 11:33:34 +01:00
mvdbeek 5afce686b0 Merge branch 'release_23.2' into dev 2024-01-04 16:15:31 +01:00
mvdbeek 7fc0b15be7 Merge branch 'release_23.1' into release_23.2 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2024-01-04 16:15:26 +01:00
mvdbeek 20e560c2e2 Start work on 23.1.5.dev0 2024-01-04 16:15:18 +01:00
mvdbeek 5dccc48db7 Create version 23.1.4 2024-01-04 16:15:11 +01:00
John Chilton 4bb1c4b4ce Merge pull request #17205 from jdavcs/dev_cbv 
Vendorize fastapi-utls.cbv
 2023-12-22 10:28:32 -05:00
John Davis 52d7fa704f Bump graphene-sqlalchemy to 3.0.0rc1 2023-12-19 12:37:49 -05:00
John Davis 377d7d134f Remove fastapi-utils from pyproject.toml, packages 2023-12-18 14:52:01 -05:00
Nicola Soranzo ddbcb39fb3 Merge pull request #17058 from davelopez/remove_web_dependency_from_tools 
Remove web framework dependency from tools
 2023-12-01 12:29:26 +00:00
mvdbeek ca6f9b3586 Merge branch 'release_23.2' into dev 2023-12-01 11:54:53 +01:00
mvdbeek 87c98787a4 Merge branch 'release_23.1' into release_23.2 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-12-01 11:54:51 +01:00
mvdbeek 316f8c1a2c Start work on 23.1.4.dev0 2023-12-01 11:54:46 +01:00
mvdbeek d7cc988979 Create version 23.1.3 2023-12-01 11:54:43 +01:00
davelopez aedfa820f5 Add symlink to short_term_storage in app package 
Temporarily include it in app until the STS goes into its own package.
 2023-11-30 17:01:29 +01:00
mvdbeek dbe1e7464f Merge branch 'release_23.2' into dev 2023-11-29 19:20:17 +01:00
mvdbeek 64a813e763 Merge branch 'release_23.1' into release_23.2 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-11-29 19:20:15 +01:00
mvdbeek cb1bb4a6ab Start work on 23.1.3.dev0 2023-11-29 19:20:10 +01:00