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4b2be15a79fcbee8d4c987f449cd6bdbdd00f752
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343 Commits
Author SHA1 Message Date
Nicola Soranzo c329529e51 Packages: finish migration from `setup.cfg to pyproject.toml` 
Also:
- Drop now unnecessary ``packages/sync_pyprojects.py`` script.
 2026-06-08 08:58:40 +01:00
Nicola Soranzo 015ab515a2 Merge branch 'release_26.0' into release_26.1 2026-06-07 23:40:06 +01:00
Nicola Soranzo eec86f0b99 Merge branch 'release_26.0' into release_26.1 2026-06-05 15:08:38 +01:00
John Davis b884af499b Move classifiers and keywords from setup.cfg to pyproject.toml 
When a [project] table is present in pyproject.toml, setuptools
ignores fields in setup.cfg unless they are listed in the dynamic
array.  This applies to classifiers and keywords: the build was
silently dropping them from the wheel metadata.

Fix: define classifiers and keywords as static values directly in the
[project] section of each package's pyproject.toml, and remove them from
setup.cfg.

Alternate fix: add both to the dynamic list, keeping the definitions in
setup.cfg. However, I think the first is better since that keeps
pyproject.toml as the single source of truth.
 2026-06-05 09:32:41 -04:00
Nicola Soranzo 6b0d47911b Drop console scripts from packages' `setup.cfg` files 
Follow-up on https://github.com/galaxyproject/galaxy/pull/22825#issuecomment-4625193313
 2026-06-05 12:15:43 +01:00
John Davis 3e9e1ab6f9 Merge branch 'release_26.0' into release_26.1 
# Conflicts:
#	client/package.json
#	lib/galaxy/version/__init__.py
#	package.json
#	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/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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/test_selenium/HISTORY.rst
#	packages/test_selenium/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/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_client/HISTORY.rst
#	packages/web_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2026-06-04 23:25:03 -04:00
John Davis 09b9b3da46 Start work on 26.0.2.dev0 2026-06-04 23:24:59 -04:00
John Davis 57b0c3040d Create version 26.0.1 2026-06-04 23:24:54 -04:00
John Davis be90bf05cb Fix missing console scripts in built wheels 
When [project] is defined in pyproject.toml, setuptools does not include
[options.entry_points] from setup.cfg in the built wheel.

Solution: move console script definitions to [project.scripts] in
pyproject.toml for all affected packages.
 2026-06-04 13:49:08 -04:00
Nicola Soranzo e0681411fa Pin rocrate<0.15.0 until roc-validator supports RO-Crate Metadata Specification 1.2 
rocrate 0.15.0 produces crates conforming to 1.2 spec by default, which
causes roc-validator validation errors like:

```
The RO-Crate metadata file descriptor MUST have a `conformsTo` property with the RO-Crate specification version
```

xref https://github.com/crs4/rocrate-validator/issues/107

Also:
- Remove unused `BaseWorkflowPopulator.validate_invocation_crate_directory()` method.
 2026-04-21 16:45:52 +01:00
mvdbeek 8e5801c95f Add hvac to galaxy-data test extras 
The packaged galaxy-data test suite imports `hvac` (via the vault
tests), so installing the `test` extra needs to pull it in for the
package tests to pass in CI.
 2026-04-21 11:24:21 +02:00
Michael R. Crusoe b7f83c8469 python packages: convert to "src" layout 
As suggested at https://packaging.python.org/en/latest/guides/packaging-namespace-packages/#native-namespace-packages

Use setuptools-scm to automatically adds all the SCM-managed files to the sdist
instead of manually listing them in packages/*/MANIFEST.in
 2026-04-15 15:16:36 +02:00
Michael R. Crusoe dbfcdb8bc9 python packages: convert to pure namespace packages 
only directories in `lib/galaxy` & `packages/*/galaxy`
All other files removed or moved to their own module
All references to those files updated, especially galaxy/version.py
 2026-04-15 15:16:34 +02:00
Nicola Soranzo 35dcde758c Pin rocrate<0.15.0 until roc-validator supports RO-Crate Metadata Specification 1.2 
rocrate 0.15.0 produces crates conforming to 1.2 spec by default, which
causes roc-validator validation errors like:

```
The RO-Crate metadata file descriptor MUST have a `conformsTo` property with the RO-Crate specification version
```

xref https://github.com/crs4/rocrate-validator/issues/107

Also:
- Remove unused `BaseWorkflowPopulator.validate_invocation_crate_directory()` method.
 2026-04-13 17:21:08 +01:00
Nate Coraor 99af84d1bd Merge remote-tracking branch 'upstream/release_26.0' into dev 2026-04-13 11:34:46 -04:00
Nicola Soranzo 59b0074b16 Fix missing package dependencies 2026-04-12 22:44:45 +01:00
Nicola Soranzo 349a5daec1 Merge branch 'release_26.0' into dev 2026-04-10 18:08:40 +01:00
guerler 4211127ac2 Bump dev cycle from 26.0.1.dev0 to 26.0.1.dev1 
The 26.0.1.dev0 PyPI packages were already published during the
earlier broken release attempt, so the version string is permanently
burned: PyPI does not allow re-uploading the same version, even for
pre-releases.  Bump the dev counter to .dev1 so the release branch
ends at a version that has not been published yet and future dev
builds from this branch can be uploaded.

This commit only changes the four dev0 version strings introduced by
the previous commit:
  - lib/galaxy/version.py:        VERSION_MINOR = "1.dev0" -> "1.dev1"
  - client/package.json:          "26.0.1.dev0" -> "26.0.1.dev1"
  - packages/*/setup.cfg:         version = 26.0.1.dev0 -> 26.0.1.dev1
  - packages/*/HISTORY.rst:       26.0.1.dev0 header -> 26.0.1.dev1

The pulsar-galaxy-lib>=0.15.0.dev0 dependency pin in
packages/app/setup.cfg and the historical 22.9.0.dev0 changelog
entries in packages/navigation/HISTORY.rst and packages/tours/HISTORY.rst
are deliberately left untouched — they refer to unrelated versions.
 2026-04-09 23:59:50 +03:00
guerler 08f930027b Re-apply version bump to 26.0.1.dev0 after v26.0.0 retag 
Companion to the previous commit.  After v26.0.0 is retagged onto the
restoration commit and the PyPI publish workflow produces the correct
26.0.0 artifacts, this commit returns the release branch to
26.0.1.dev0 so future development on the 26.0 line continues from a
post-release dev version, matching the state established by
f4478f5d09 ("Start work on 26.0.1.dev0").

This is a fresh commit with the same content as f4478f5d09; it is not
a cherry-pick and does not reuse the original hash or author metadata.

After the v26.0.0 tag has been moved and a successful publish is
verified, the branch HEAD is once again at 26.0.1.dev0 just like
before this two-commit sequence — but now the v26.0.0 tag points at a
commit that actually contains version = 26.0.0.
 2026-04-09 23:41:25 +03:00
guerler 854899453b Restore version to 26.0.0 for v26.0.0 retag 
The original v26.0.0 tag was retagged from 52e970855b to HEAD because
of bugs in the GitHub Actions release workflow.  Unfortunately HEAD
already contained the post-release version bump from f4478f5d09
("Start work on 26.0.1.dev0"), so PyPI builds from the retagged HEAD
publish wheels labeled 26.0.1.dev0 instead of 26.0.0.

This commit restores the version files to their 26.0.0 state so the
v26.0.0 tag can be moved to point at this commit and the publish
workflow can produce correctly labeled artifacts.

The next commit re-applies the dev0 bump so the release branch ends
back at 26.0.1.dev0 and future development continues normally.

This is purely additive — no history is rewritten and the existing
26.0.1.dev0 commit (f4478f5d09) is left untouched.
 2026-04-09 23:40:45 +03:00
guerler 6a23ae0d6e Merge branch 'release_26.0' 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/meta/HISTORY.rst
#	packages/navigation/HISTORY.rst
#	packages/objectstore/HISTORY.rst
#	packages/schema/HISTORY.rst
#	packages/selenium/HISTORY.rst
#	packages/test_api/HISTORY.rst
#	packages/test_base/HISTORY.rst
#	packages/test_driver/HISTORY.rst
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_util/HISTORY.rst
#	packages/tool_util_models/HISTORY.rst
#	packages/tours/HISTORY.rst
#	packages/util/HISTORY.rst
#	packages/web_apps/HISTORY.rst
#	packages/web_client/HISTORY.rst
#	packages/web_framework/HISTORY.rst
#	packages/web_stack/HISTORY.rst
 2026-04-08 02:01:44 +03:00
guerler f4478f5d09 Start work on 26.0.1.dev0 2026-04-08 02:01:36 +03:00
guerler 52e970855b Create version 26.0.0 2026-04-08 02:01:25 +03:00
mvdbeek 8de15ef52c Merge branch 'release_26.0' into dev 2026-03-09 17:33:09 +01:00
mvdbeek 3124ebcec6 Merge branch 'release_25.1' into release_26.0 
# Conflicts:
#	client/package.json
#	lib/galaxy/version.py
#	package.json
#	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/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/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_client/HISTORY.rst
#	packages/web_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2026-03-09 17:33:06 +01:00
mvdbeek 1134ffb67c Start work on 25.1.3.dev0 2026-03-09 17:33:02 +01:00
mvdbeek 8d2170b52c Create version 25.1.2 2026-03-09 17:32:58 +01:00
mvdbeek 9b03fe65f0 Merge branch 'release_26.0' into dev 2026-03-09 17:27:59 +01:00
Michael R. Crusoe 7f40e45a7f Switch to only MIT license 2026-03-06 19:05:20 +01:00
Michael R. Crusoe 4d6519ae77 Switch to only MIT license 2026-02-23 14:35:30 +01:00
mvdbeek e162e02ce0 Merge branch 'release_26.0' into dev 2026-02-03 15:05:58 +01:00
mvdbeek 081ca1a041 Merge branch 'release_25.1' into release_26.0 
# Conflicts:
#	client/package.json
#	lib/galaxy/version.py
#	package.json
#	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/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/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_client/HISTORY.rst
#	packages/web_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2026-02-03 15:05:47 +01:00
mvdbeek ef9f099631 Start work on 25.1.2.dev0 2026-02-03 15:05:40 +01:00
mvdbeek 5f2adab86e Create version 25.1.1 2026-02-03 15:05:37 +01:00
Leonid Kostrykin 1d7a944b31 Merge branch 'dev' into feat/dicom 2026-01-20 11:30:52 +01:00
Nicola Soranzo eb9fde1dcd Drop support for Python 3.9 2026-01-19 18:39:16 +00:00
Leonid Kostrykin 09d6b2f76f Add pydicom as a package dependency 2026-01-19 17:56:27 +01:00
Leonid Kostrykin fadcf16070 Update deps with lib/galaxy/dependencies/update.sh -p pydicom 2026-01-19 17:49:27 +01:00
Leonid Kostrykin f08ae16a60 Add pydicom dependency 2026-01-19 17:40:51 +01:00
Nicola Soranzo 0de53df7b8 Add support for Python 3.14 2025-12-24 15:15:11 +00:00
Ahmed Awan 9e1089ad38 Merge branch 'release_25.1' 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/meta/HISTORY.rst
#	packages/navigation/HISTORY.rst
#	packages/objectstore/HISTORY.rst
#	packages/schema/HISTORY.rst
#	packages/selenium/HISTORY.rst
#	packages/test_api/HISTORY.rst
#	packages/test_base/HISTORY.rst
#	packages/test_driver/HISTORY.rst
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_util/HISTORY.rst
#	packages/tool_util_models/HISTORY.rst
#	packages/tours/HISTORY.rst
#	packages/util/HISTORY.rst
#	packages/web_apps/HISTORY.rst
#	packages/web_client/HISTORY.rst
#	packages/web_framework/HISTORY.rst
#	packages/web_stack/HISTORY.rst
 2025-12-12 23:29:08 +05:00
Ahmed Awan 9c07488a50 Start work on 25.1.1.dev0 2025-12-12 23:28:53 +05:00
Ahmed Awan 7d5ed76b41 Create version 25.1.0 2025-12-12 23:28:31 +05:00
mvdbeek bef42b43ca Merge branch 'release_25.1' into dev 2025-11-18 16:02:31 +01:00
mvdbeek 231ea7db6e Merge branch 'release_25.0' into release_25.1 
# Conflicts:
#	client/package.json
#	lib/galaxy/version.py
#	package.json
#	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/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/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_client/HISTORY.rst
#	packages/web_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2025-11-18 16:02:27 +01:00
mvdbeek f764acd337 Start work on 25.0.5.dev0 2025-11-18 16:02:22 +01:00
mvdbeek cca180264e Create version 25.0.4 2025-11-18 16:02:15 +01:00
Nicola Soranzo 560006530f Cleanup formatting of pyproject.toml files 2025-10-29 12:45:48 +00:00
John Chilton 760fff8b87 More documentation and QOL improvements for package-centric dev. 2025-10-23 21:18:01 -04:00
John Chilton e90db6180f Drop now redundant test-requirements.txt files. 2025-10-23 21:18:01 -04:00