Select {{ labelTitle }} Label:
diff --git a/client/src/components/Tool/utilities.js b/client/src/components/Tool/utilities.js
index 1b0a6d5a0ad2..84f9d2bd3fd2 100644
--- a/client/src/components/Tool/utilities.js
+++ b/client/src/components/Tool/utilities.js
@@ -2,7 +2,9 @@ import { getAppRoot } from "onload/loadConfig";
import { copy } from "utils/clipboard";
export function copyLink(toolId, message) {
- copy(`${window.location.origin + getAppRoot()}root?tool_id=${toolId}`, message);
+ const link = `${window.location.origin + getAppRoot()}root?tool_id=${toolId}`;
+ // Encode the link to handle special characters in tool id
+ copy(encodeURI(link), message);
}
export function copyId(toolId, message) {
diff --git a/client/src/components/Tool/utilities.test.ts b/client/src/components/Tool/utilities.test.ts
new file mode 100644
index 000000000000..8295d1e2bfe6
--- /dev/null
+++ b/client/src/components/Tool/utilities.test.ts
@@ -0,0 +1,36 @@
+import { copyLink } from "./utilities";
+
+const writeText = jest.fn();
+
+Object.assign(navigator, {
+ clipboard: {
+ writeText,
+ },
+});
+
+describe("copyLink", () => {
+ beforeEach(() => {
+ (navigator.clipboard.writeText as jest.Mock).mockResolvedValue(undefined);
+ });
+
+ it("should copy the link to the clipboard", () => {
+ const toolId = "MyToolId";
+ copyLink(toolId);
+ expect(writeText).toHaveBeenCalledTimes(1);
+ expect(writeText).toHaveBeenCalledWith(expect.stringContaining(toolId));
+ });
+
+ it("should encode the tool id with spaces", () => {
+ const toolId = "My Tool Id";
+ copyLink(toolId);
+ expect(writeText).toHaveBeenCalledTimes(1);
+ expect(writeText).toHaveBeenCalledWith(expect.stringContaining("My%20Tool%20Id"));
+ });
+
+ it("should not encode the character '+' in the tool id", () => {
+ const toolId = "My Tool Id+1";
+ copyLink(toolId);
+ expect(writeText).toHaveBeenCalledTimes(1);
+ expect(writeText).toHaveBeenCalledWith(expect.stringContaining("My%20Tool%20Id+1"));
+ });
+});
diff --git a/client/src/components/Upload/DefaultBox.vue b/client/src/components/Upload/DefaultBox.vue
index cba474744251..5182b087a306 100644
--- a/client/src/components/Upload/DefaultBox.vue
+++ b/client/src/components/Upload/DefaultBox.vue
@@ -99,18 +99,22 @@ const listExtensions = computed(() => props.effectiveExtensions.filter((ext) =>
const showHelper = computed(() => Object.keys(uploadItems.value).length === 0);
const uploadValues = computed(() => Object.values(uploadItems.value));
-const queue = new UploadQueue({
- announce: eventAnnounce,
- chunkSize: props.chunkUploadSize,
- complete: eventComplete,
- error: eventError,
- get: (index) => uploadItems.value[index],
- historyId: historyId.value,
- multiple: props.multiple,
- progress: eventProgress,
- success: eventSuccess,
- warning: eventWarning,
-});
+const queue = computed(() => createUploadQueue());
+
+function createUploadQueue() {
+ return new UploadQueue({
+ announce: eventAnnounce,
+ chunkSize: props.chunkUploadSize,
+ complete: eventComplete,
+ error: eventError,
+ get: (index) => uploadItems.value[index],
+ historyId: historyId.value,
+ multiple: props.multiple,
+ progress: eventProgress,
+ success: eventSuccess,
+ warning: eventWarning,
+ });
+}
/** Add files to queue */
function addFiles(files, immediate = false) {
@@ -119,9 +123,9 @@ function addFiles(files, immediate = false) {
eventReset();
}
if (props.multiple) {
- queue.add(files);
+ queue.value.add(files);
} else if (files.length > 0) {
- queue.add([files[0]]);
+ queue.value.add([files[0]]);
}
}
}
@@ -165,7 +169,7 @@ function eventComplete() {
/** Create a new file */
function eventCreate() {
- queue.add([{ name: DEFAULT_FILE_NAME, size: 0, mode: "new" }]);
+ queue.value.add([{ name: DEFAULT_FILE_NAME, size: 0, mode: "new" }]);
}
/** Error */
@@ -207,14 +211,14 @@ function eventRemove(index) {
counterAnnounce.value--;
}
Vue.delete(uploadItems.value, index);
- queue.remove(index);
+ queue.value.remove(index);
}
/** Show remote files dialog or FTP files */
function eventRemoteFiles() {
filesDialog(
(items) => {
- queue.add(
+ queue.value.add(
items.map((item) => {
const rval = {
mode: "url",
@@ -236,7 +240,7 @@ function eventReset() {
counterAnnounce.value = 0;
counterSuccess.value = 0;
counterError.value = 0;
- queue.reset();
+ queue.value.reset();
uploadItems.value = {};
extension.value = props.defaultExtension;
dbKey.value = props.defaultDbKey;
@@ -269,7 +273,7 @@ function eventStart() {
});
emit("progress", 0, "success");
counterRunning.value = counterAnnounce.value;
- queue.start();
+ queue.value.start();
}
}
@@ -278,7 +282,7 @@ function eventStop() {
if (isRunning.value) {
emit("progress", null, "info");
queueStopping.value = true;
- queue.stop();
+ queue.value.stop();
}
}
diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index d9032e0bfe88..76b1a8616903 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -12,6 +12,12 @@
root: ${user.preferences['owncloud|root']}
login: ${user.preferences['owncloud|username']}
password: ${user.preferences['owncloud|password']}
+ # By default, the plugin will use temp files to avoid loading entire files into memory.
+ # You can change the directory here or omit to use the default temp directory.
+ temp_path: /your/temp/path
+ # Set writable to true if you have write access to this source
+ # and want to allow exporting files to it, by default is read only.
+ writable: false
- type: posix
root: '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/'
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index c8cc90525a98..6e91ef9b5338 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -152,7 +152,7 @@ pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
python-jose==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
-python-multipart==0.0.6 ; python_version >= "3.8" and python_version < "3.13"
+python-multipart==0.0.7 ; python_version >= "3.8" and python_version < "3.13"
python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.13"
pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/files/sources/webdav.py b/lib/galaxy/files/sources/webdav.py
index 86ed55483e70..2e11a51d98b2 100644
--- a/lib/galaxy/files/sources/webdav.py
+++ b/lib/galaxy/files/sources/webdav.py
@@ -3,6 +3,7 @@
except ImportError:
WebDAVFS = None
+import tempfile
from typing import (
Optional,
Union,
@@ -22,6 +23,11 @@ class WebDavFilesSource(PyFilesystem2FilesSource):
def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
props = self._serialization_props(user_context)
+ use_temp_files = props.pop("use_temp_files", None)
+ if use_temp_files is None:
+ # Default to True to avoid memory issues with large files.
+ props["use_temp_files"] = True
+ props["temp_path"] = props.get("temp_path", tempfile.TemporaryDirectory(prefix="webdav_"))
extra_props: Union[FilesSourceProperties, dict] = opts.extra_props or {} if opts else {}
handle = WebDAVFS(**{**props, **extra_props})
return handle
diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
index 985dc06387b6..5610108ec482 100644
--- a/lib/galaxy/webapps/galaxy/services/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -1433,8 +1433,12 @@ def _unhide(self, item: HistoryItemModel):
def _delete(self, item: HistoryItemModel, trans: ProvidesHistoryContext):
if isinstance(item, HistoryDatasetCollectionAssociation):
- return self.dataset_collection_manager.delete(trans, "history", item.id, recursive=True, purge=False)
- return self.hda_manager.delete(item, flush=self.flush)
+ self.dataset_collection_manager.delete(trans, "history", item.id, recursive=True, purge=False)
+ else:
+ self.hda_manager.delete(item, flush=self.flush)
+ # In the edge case where all selected items are already deleted we need to force an update
+ # otherwise the history will wait indefinitely for the items to be deleted
+ item.update()
def _undelete(self, item: HistoryItemModel):
if getattr(item, "purged", False):
diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
index 36584e4ada74..8441a9d276ac 100644
--- a/packages/app/HISTORY.rst
+++ b/packages/app/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -60,8 +59,6 @@ Enhancements
Bug fixes
=========
-*
-*
* read job_conf directly from `config_dir` instead of computing it again from `config_file` by `@bernt-matthias `_ in `#15596 `_
* Fix some drs handling issues by `@nuwang `_ in `#15777 `_
* Fix filesource file url support by `@nuwang `_ in `#15794 `_
@@ -117,8 +114,6 @@ Bug fixes
Enhancements
============
-*
-*
* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_
* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan `_ in `#15019 `_
* Add slack error reporting plugin by `@hexylena `_ in `#15025 `_
@@ -204,9 +199,6 @@ Other changes
Bug fixes
=========
-*
-*
-*
* Fix upload paramfile handling (for real user setups) by `@bernt-matthias `_ in `#16504 `_
* Fix extra files path handling by `@mvdbeek `_ in `#16541 `_
* Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek `_ in `#16569 `_
@@ -220,9 +212,6 @@ Bug fixes
Enhancements
============
-*
-*
-*
* Update pulsar client library to 0.15.5 by `@mvdbeek `_ in `#16701 `_
-------------------
@@ -234,10 +223,6 @@ Enhancements
Bug fixes
=========
-*
-*
-*
-*
* Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by `@bernt-matthias `_ in `#16403 `_
* Fix test discovery in vscode by `@mvdbeek `_ in `#16413 `_
* Fixes for (gitlab) error reporting by `@bernt-matthias `_ in `#16424 `_
@@ -251,11 +236,6 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
-*
* Fix default when statement evaluation by `@mvdbeek `_ in `#16332 `_
* Redact private role name and description when purging user by `@mvdbeek `_ in `#16349 `_
@@ -268,31 +248,18 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
-*
-*
* Bump galaxy-release-util version to 0.1.2 by `@mvdbeek `_ in `#16241 `_
============
Enhancements
============
-*
-*
-*
-*
* When importing tool data bundles, use the first loc file for the matching table by `@natefoo `_ in `#16247 `_
=============
Other changes
=============
-*
-*
-*
* Forward port of slugify username received from oidc by `@nuwang `_ in `#16271 `_
-------------------
@@ -304,26 +271,12 @@ Other changes
Bug fixes
=========
-*
-*
-*
-*
-*
-*
-*
* Fix ``Text File Busy`` errors at the source by `@mvdbeek `_ in `#16212 `_
============
Enhancements
============
-*
-*
-*
-*
-*
-*
-*
* Point release deps fixes and docs by `@mvdbeek `_ in `#16214 `_
* Use galaxy-release-util to upload python packages by `@mvdbeek `_ in `#16240 `_
@@ -336,14 +289,6 @@ Enhancements
Bug fixes
=========
-*
-*
-*
-*
-*
-*
-*
-*
* Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_
* Fix mixed outputs_to_working_directory pulsar destinations by `@mvdbeek `_ in `#15927 `_
* Update Gravity to 1.0.3 by `@natefoo `_ in `#15939 `_
@@ -367,13 +312,6 @@ Bug fixes
Other changes
=============
-*
-*
-*
-*
-*
-*
-*
* Startup fix when tool removed between reboot by `@mvdbeek `_ in `#16175 `_
-------------------
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index 3dd7e40ee12e..d5e9717649ef 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-app
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
index 7a9a856cf816..d34767538af7 100644
--- a/packages/auth/HISTORY.rst
+++ b/packages/auth/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg
index 076669b4c250..adad08ddb323 100644
--- a/packages/auth/setup.cfg
+++ b/packages/auth/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-auth
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst
index 36133dd346dc..7de666556510 100644
--- a/packages/config/HISTORY.rst
+++ b/packages/config/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -48,8 +47,6 @@ Enhancements
Bug fixes
=========
-*
-*
* Fix some drs handling issues by `@nuwang `_ in `#15777 `_
* Improve container resolver documentation by `@mvdbeek `_ in `#16280 `_
* Limit tool document cache to tool configs with explicit cache path by `@mvdbeek `_ in `#16537 `_
@@ -60,8 +57,6 @@ Bug fixes
Enhancements
============
-*
-*
* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan `_ in `#15019 `_
* Add slack error reporting plugin by `@hexylena `_ in `#15025 `_
* Documents use of k8s_extra_job_envs in job_conf sample advanced by `@pcm32 `_ in `#15110 `_
@@ -105,9 +100,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
* Minor bug fix for default mail templates by `@neoformit `_ in `#16362 `_
-------------------
@@ -137,20 +129,12 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
-*
-*
* Change default watchdog inotify_buffer log level to info by `@mvdbeek `_ in `#15967 `_
============
Enhancements
============
-*
-*
-*
* Add ``ca_certs`` option for sentry client by `@mvdbeek `_ in `#15943 `_
-------------------
diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg
index a377dacfdabb..b1691b58d9a5 100644
--- a/packages/config/setup.cfg
+++ b/packages/config/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-config
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
index 5d18fbecce98..fb62bc58b6c7 100644
--- a/packages/data/HISTORY.rst
+++ b/packages/data/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -46,7 +45,6 @@ Bug fixes
Bug fixes
=========
-*
* Skip change_datatype things if we're not actually changing the extension by `@mvdbeek `_ in `#16931 `_
* Fix copying metadata to copied job outputs by `@mvdbeek `_ in `#17007 `_
* Update tar_to_directory dependency by `@mvdbeek `_ in `#17009 `_
@@ -70,8 +68,6 @@ Enhancements
Bug fixes
=========
-*
-*
* Fix bad auto-merge of dev. by `@jmchilton `_ in `#15386 `_
* Merge conflicting db migration branches into one by `@jdavcs `_ in `#15771 `_
* Enable ``strict_equality`` mypy option by `@nsoranzo `_ in `#15808 `_
@@ -102,8 +98,6 @@ Bug fixes
Enhancements
============
-*
-*
* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_
* Add Storage Dashboard visualizations for histories by `@davelopez `_ in `#14820 `_
* Towards decoupling datatypes and model by `@jdavcs `_ in `#15186 `_
@@ -162,9 +156,6 @@ Other changes
Bug fixes
=========
-*
-*
-*
* Fix extra files path handling by `@mvdbeek `_ in `#16541 `_
* Don't fail invocation message without dependent_workflow_step_id by `@mvdbeek `_ in `#16628 `_
@@ -177,10 +168,6 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
* Copy when_expression when copying workflow step by `@mvdbeek `_ in `#16377 `_
-------------------
@@ -210,11 +197,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
-*
-*
* Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_
* Fix folder listing via file browser by `@mvdbeek `_ in `#15950 `_
* Fix RO-crate invocation export with complex collections by `@davelopez `_ in `#15971 `_
diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
index 40befc738b9b..b7f5afea24c9 100644
--- a/packages/data/setup.cfg
+++ b/packages/data/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-data
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst
index 308d254390e3..92cfb088f68e 100644
--- a/packages/files/HISTORY.rst
+++ b/packages/files/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -46,8 +45,6 @@ Bug fixes
Bug fixes
=========
-*
-*
* Fix some drs handling issues by `@nuwang `_ in `#15777 `_
* Fix filesource file url support by `@nuwang `_ in `#15794 `_
* Fix unittest mocks to support us checking geturl() by `@dannon `_ in `#16726 `_
@@ -92,9 +89,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
* Fix dropbox import to support newer versions by `@nuwang `_ in `#16239 `_
-------------------
diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg
index 41dd76202a23..f294659aa77f 100644
--- a/packages/files/setup.cfg
+++ b/packages/files/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-files
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
index 7cfc0c2ce106..e153373a4889 100644
--- a/packages/job_execution/HISTORY.rst
+++ b/packages/job_execution/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -43,8 +42,6 @@ Bug fixes
Bug fixes
=========
-*
-*
* Fix tags ownership by `@davelopez `_ in `#16339 `_
* Push to object store even if ``set_meta`` fails by `@mvdbeek `_ in `#16667 `_
* Fix metadata setting in extended metadata + outputs_to_working_directory mode by `@mvdbeek `_ in `#16678 `_
@@ -73,9 +70,6 @@ Enhancements
Bug fixes
=========
-*
-*
-*
* Fix extra files path handling by `@mvdbeek `_ in `#16541 `_
* Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek `_ in `#16569 `_
* Fixes for extra files handling and cached object stores by `@mvdbeek `_ in `#16595 `_
diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg
index 4be22661024a..40c3be56f524 100644
--- a/packages/job_execution/setup.cfg
+++ b/packages/job_execution/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-job-execution
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
index d81bff83430b..e44fe3049ab9 100644
--- a/packages/job_metrics/HISTORY.rst
+++ b/packages/job_metrics/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg
index 4d16b381adcc..476eea3712ad 100644
--- a/packages/job_metrics/setup.cfg
+++ b/packages/job_metrics/setup.cfg
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-job-metrics
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/meta/HISTORY.rst b/packages/meta/HISTORY.rst
index 3fbd85e0bc3b..7297421a7487 100644
--- a/packages/meta/HISTORY.rst
+++ b/packages/meta/HISTORY.rst
@@ -3,9 +3,9 @@ History
.. to_doc
----------------------
-22.5.0.dev0
----------------------
+---------
+23.2.dev0
+---------
diff --git a/packages/meta/setup.cfg b/packages/meta/setup.cfg
index a5ac9edb2620..260765e0f7d2 100644
--- a/packages/meta/setup.cfg
+++ b/packages/meta/setup.cfg
@@ -29,7 +29,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy
url = https://github.com/galaxyproject/galaxy
-version = 22.5.0.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst
index 58bc52e4a963..6ce702dca0cf 100644
--- a/packages/navigation/HISTORY.rst
+++ b/packages/navigation/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg
index 2c8c32db2fab..a2635d9e49fe 100644
--- a/packages/navigation/setup.cfg
+++ b/packages/navigation/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-navigation
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
index 28f440463183..d036a4451c51 100644
--- a/packages/objectstore/HISTORY.rst
+++ b/packages/objectstore/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -67,9 +66,6 @@ Other changes
Bug fixes
=========
-*
-*
-*
* Fix extra files path handling by `@mvdbeek `_ in `#16541 `_
* Fixes for extra files handling and cached object stores by `@mvdbeek `_ in `#16595 `_
diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg
index 2122a4c390b4..2257e1f6efd5 100644
--- a/packages/objectstore/setup.cfg
+++ b/packages/objectstore/setup.cfg
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-objectstore
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst
index e947a90a461d..a23b80b80131 100644
--- a/packages/schema/HISTORY.rst
+++ b/packages/schema/HISTORY.rst
@@ -3,8 +3,8 @@ History
.. to_doc
----------------------
-21.1.0.dev0
----------------------
+---------
+23.2.dev0
+---------
* First release.
diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg
index d732f5a8cdc3..e374603fc2d0 100644
--- a/packages/schema/setup.cfg
+++ b/packages/schema/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-schema
url = https://github.com/galaxyproject/galaxy
-version = 23.1.0.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
index 3c43f57b307a..d8a77c091d9e 100644
--- a/packages/selenium/HISTORY.rst
+++ b/packages/selenium/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -92,9 +91,6 @@ No recorded changes since last release
Enhancements
============
-*
-*
-*
* Port selenium setup to non-deprecated selenium options by `@mvdbeek `_ in `#16215 `_
-------------------
@@ -106,14 +102,6 @@ Enhancements
Enhancements
============
-*
-*
-*
-*
-*
-*
-*
-*
* Add support for launching workflows via Tutorial Mode by `@hexylena `_ in `#15684 `_
-------------------
diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg
index 79cabcad10b7..07fab81680d9 100644
--- a/packages/selenium/setup.cfg
+++ b/packages/selenium/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-selenium
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst
index bbc4d919acbb..13160613feb4 100644
--- a/packages/test_api/HISTORY.rst
+++ b/packages/test_api/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -54,8 +53,6 @@ Enhancements
Bug fixes
=========
-*
-*
* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_
* allow anon access for api/datasets/get_content_as_text by `@martenson `_ in `#16226 `_
* qualify querying for an api-key by `@martenson `_ in `#16320 `_
@@ -77,8 +74,6 @@ Bug fixes
Enhancements
============
-*
-*
* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_
* Outline Deployment Tests by `@jmchilton `_ in `#15420 `_
* Unify url handling with filesources by `@nuwang `_ in `#15497 `_
@@ -131,9 +126,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
* Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_
* Fix folder listing via file browser by `@mvdbeek `_ in `#15950 `_
* Fix case sensitive filtering by name in histories by `@davelopez `_ in `#16036 `_
@@ -144,9 +136,6 @@ Bug fixes
Enhancements
============
-*
-*
-*
* Add support for launching workflows via Tutorial Mode by `@hexylena `_ in `#15684 `_
* Allow setting auto_decompress property in staging interface by `@mvdbeek `_ in `#16014 `_
diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg
index f429b01114ba..a6754d91250f 100644
--- a/packages/test_api/setup.cfg
+++ b/packages/test_api/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-api
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst
index 056191917442..beb7c49f68c6 100644
--- a/packages/test_base/HISTORY.rst
+++ b/packages/test_base/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -41,8 +40,6 @@ Bug fixes
Bug fixes
=========
-*
-*
* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_
============
@@ -103,9 +100,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
* Ensure history export contains all expected datasets by `@davelopez `_ in `#16013 `_
* Fix extended metadata file size handling by `@mvdbeek `_ in `#16109 `_
diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg
index d0e46454cb0a..f5e3b8b0c9da 100644
--- a/packages/test_base/setup.cfg
+++ b/packages/test_base/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-base
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst
index ed2c3738f32a..6af909c4c5fd 100644
--- a/packages/test_driver/HISTORY.rst
+++ b/packages/test_driver/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -41,8 +40,6 @@ Bug fixes
Bug fixes
=========
-*
-*
* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_
* Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_
diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg
index 9d79fb553c16..6f4efce2cfab 100644
--- a/packages/test_driver/setup.cfg
+++ b/packages/test_driver/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-driver
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/test_selenium/HISTORY.rst b/packages/test_selenium/HISTORY.rst
index 8672d24edec0..a47664bd7ead 100644
--- a/packages/test_selenium/HISTORY.rst
+++ b/packages/test_selenium/HISTORY.rst
@@ -3,9 +3,9 @@ History
.. to_doc
----------------------
-22.5.0.dev0
----------------------
+---------
+23.2.dev0
+---------
diff --git a/packages/test_selenium/setup.cfg b/packages/test_selenium/setup.cfg
index f8993d8da273..03134c45bb19 100644
--- a/packages/test_selenium/setup.cfg
+++ b/packages/test_selenium/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-selenium
url = https://github.com/galaxyproject/galaxy
-version = 22.5.0.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst
index 7fccc8db62eb..a23b80b80131 100644
--- a/packages/tool_shed/HISTORY.rst
+++ b/packages/tool_shed/HISTORY.rst
@@ -3,8 +3,8 @@ History
.. to_doc
----------------------
-23.1.0.dev0
----------------------
+---------
+23.2.dev0
+---------
* First release.
diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg
index 784c1d0edaec..4e78a7c84c29 100644
--- a/packages/tool_shed/setup.cfg
+++ b/packages/tool_shed/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-shed
url = https://github.com/galaxyproject/galaxy
-version = 23.1.0.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
index 845892ccb87f..a97ccaa5ba05 100644
--- a/packages/tool_util/HISTORY.rst
+++ b/packages/tool_util/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -54,8 +53,6 @@ Enhancements
Bug fixes
=========
-*
-*
* Fixes for two framework test tools by `@bernt-matthias `_ in `#15483 `_
* add missing f for f-string by `@bernt-matthias `_ in `#15584 `_
* Fix call to `docker_cached_container_description` by `@bernt-matthias `_ in `#15598 `_
@@ -77,8 +74,6 @@ Bug fixes
Enhancements
============
-*
-*
* Decompress history data for testing assertions by `@bernt-matthias `_ in `#15085 `_
* OIDC tokens by `@SergeyYakubov `_ in `#15300 `_
* Fix for new style conda packages by `@bernt-matthias `_ in `#15446 `_
@@ -115,9 +110,6 @@ Other changes
Bug fixes
=========
-*
-*
-*
* Fixes for extra files handling and cached object stores by `@mvdbeek `_ in `#16595 `_
* Fix create/install commands for conda 23.9.0 by `@nsoranzo `_ in `#16831 `_
@@ -130,10 +122,6 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
* Allow duplicate labels in linter if outputs contain filters by `@bernt-matthias `_ in `#15933 `_
* Fix parsing tool metadata from bio.tools by `@kysrpex `_ in `#16449 `_
* Linter: fix regex for profile version by `@bernt-matthias `_ in `#16480 `_
@@ -154,11 +142,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
-*
-*
* xsd: add missing `sep` attribute for `has_n_columns` by `@bernt-matthias `_ in `#16262 `_
* Missing init prevents models.py being bundled into tool_util by `@nuwang `_ in `#16308 `_
@@ -166,9 +149,6 @@ Bug fixes
Enhancements
============
-*
-*
-*
* When importing tool data bundles, use the first loc file for the matching table by `@natefoo `_ in `#16247 `_
-------------------
@@ -180,13 +160,6 @@ Enhancements
Bug fixes
=========
-*
-*
-*
-*
-*
-*
-*
* Don't fail CWL tool parsing when Cheetah not installed by `@mvdbeek `_ in `#16219 `_
* Allow skipping ``expect_num_outputs`` when ``expect_failure`` is set in tool test by `@bernt-matthias `_ in `#16237 `_
@@ -199,14 +172,6 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
-*
-*
-*
-*
* Fix assertion linting to not fail on byte suffixes by `@bernt-matthias `_ in `#15873 `_
* Fix ``get_test_from_anaconda()`` and ``base_image_for_targets()`` functions by `@nsoranzo `_ in `#16125 `_
* Fix test search for mulled container hashes by `@mvdbeek `_ in `#16170 `_
@@ -215,13 +180,6 @@ Bug fixes
Enhancements
============
-*
-*
-*
-*
-*
-*
-*
* Allow setting auto_decompress property in staging interface by `@mvdbeek `_ in `#16014 `_
-------------------
diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
index 442c1ef95a46..e338e4989d36 100644
--- a/packages/tool_util/setup.cfg
+++ b/packages/tool_util/setup.cfg
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-util
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst
index 99e6d8503d9b..3bc82b6c4f18 100644
--- a/packages/tours/HISTORY.rst
+++ b/packages/tours/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg
index af106a9a8aa8..8ec2300750ff 100644
--- a/packages/tours/setup.cfg
+++ b/packages/tours/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tours
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst
index 356538eaab5b..0be43a48e4ed 100644
--- a/packages/util/HISTORY.rst
+++ b/packages/util/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -55,8 +54,6 @@ Bug fixes
Enhancements
============
-*
-*
* Various Tool Shed Cleanup by `@jmchilton `_ in `#15247 `_
* Protection against problematic boolean parameters. by `@jmchilton `_ in `#15493 `_
* Unify url handling with filesources by `@nuwang `_ in `#15497 `_
@@ -108,9 +105,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
* Replace httpbin service with pytest-httpserver by `@mvdbeek `_ in `#16042 `_
-------------------
diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
index ffa6c59a3346..e7b174ffbfc5 100644
--- a/packages/util/setup.cfg
+++ b/packages/util/setup.cfg
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-util
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/util/test-requirements.txt b/packages/util/test-requirements.txt
index 779ccfa23c7e..2b7d321b4f1a 100644
--- a/packages/util/test-requirements.txt
+++ b/packages/util/test-requirements.txt
@@ -1,3 +1,4 @@
pytest
pytest-httpserver
responses
+Werkzeug
diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst
index 64f90b5badd8..a4302f2eae08 100644
--- a/packages/web_apps/HISTORY.rst
+++ b/packages/web_apps/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -40,7 +39,6 @@ Bug fixes
Bug fixes
=========
-*
* Provide error message instead of internal server error by `@mvdbeek `_ in `#16905 `_
* Fix input dates in notifications: consider timezone offset by `@davelopez `_ in `#17088 `_
@@ -59,8 +57,6 @@ Enhancements
Bug fixes
=========
-*
-*
* Create ToolSuccess route and refactor component by `@ahmedhamidawan `_ in `#15484 `_
* fix premature return in user API by `@martenson `_ in `#15781 `_
* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_
@@ -81,8 +77,6 @@ Bug fixes
Enhancements
============
-*
-*
* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_
* Add Storage Dashboard visualizations for histories by `@davelopez `_ in `#14820 `_
* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan `_ in `#15019 `_
@@ -140,9 +134,6 @@ Other changes
Bug fixes
=========
-*
-*
-*
* Fix incorrect ASGI request host by `@davelopez `_ in `#16574 `_
* Allow the legacy DELETE dataset endpoint to accept any string for the history_id by `@assuntad23 `_ in `#16593 `_
@@ -155,10 +146,6 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
* Fix active step display in workflow editor side panel by `@mvdbeek `_ in `#16364 `_
-------------------
@@ -170,11 +157,6 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
-*
* Fix folder access for anonymous user by `@mvdbeek `_ in `#16330 `_
-------------------
@@ -186,21 +168,12 @@ Bug fixes
Bug fixes
=========
-*
-*
-*
-*
-*
-*
* Fix converting Enum value to str for Python 3.11 by `@nsoranzo `_ in `#16284 `_
============
Enhancements
============
-*
-*
-*
* When importing tool data bundles, use the first loc file for the matching table by `@natefoo `_ in `#16247 `_
-------------------
@@ -218,13 +191,6 @@ No recorded changes since last release
Bug fixes
=========
-*
-*
-*
-*
-*
-*
-*
* Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_
* Various fixes to path prefix handling by `@mvdbeek `_ in `#16033 `_
* Fix dataype_change not updating HDCA update_time by `@mvdbeek `_ in `#16099 `_
diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
index 29caba4e5960..79a0bddbd172 100644
--- a/packages/web_apps/setup.cfg
+++ b/packages/web_apps/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-apps
url = https://github.com/galaxyproject/galaxy
-version = 23.1.dev0
+version = 23.2.dev0
[options]
include_package_data = True
diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst
index 454ed9753779..ef338c1005da 100644
--- a/packages/web_framework/HISTORY.rst
+++ b/packages/web_framework/HISTORY.rst
@@ -4,11 +4,10 @@ History
.. to_doc
---------
-23.3.dev0
+24.0.dev0
---------
-
-------------------
23.1.4 (2024-01-04)
-------------------
@@ -47,8 +46,6 @@ Enhancements
Bug fixes
=========
-*
-*
* Fix some drs handling issues by `@nuwang `_ in `#15777 `_
* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_
@@ -56,8 +53,6 @@ Bug fixes
Enhancements
============
-*
-*
* Update Python dependencies by `@galaxybot `_ in `#15435 `_
* Don't error on missing parameters or unused parameters in UI controllers by `@mvdbeek