Releases · fgcz/bfabricPy

[0.0.23] - 2025-06-02

Added

bfabric_app_runner.bfabric_integration.slurm and associated packages.
Command bfabric-app-runner run workunit to run the whole app end-to-end for a workunit.

Removed

AppVersion does not have a submitter field anymore.
Some old submitter related functionality is deleted.

[1.13.27] - 2025-05-21

Added

Attribute Bfabric.config_data to obtain a ConfigData object directly.
TokenData.load_entity convenience method to load an entity from the token data.
Entities Instrument, Plate, Run were added (but with no extra functionality).
Workunit.{application_parameters, submitter_parameters} to access parameter values.

Changed

Submitter parameters will not be written any longer to WorkunitExecution parameters.

Fixed

Compatibility with upcoming change that Application can have multiple technology values.

Deprecated

Workunit.parameter_values will be removed in favor of Workunit.application_parameters and Workunit.submitter_parameters in a future version.

[1.13.28] - 2025-05-21

Removed

Removed bfabric_delete.py. Use bfabric-cli api delete instead.
Removed bfabric_list_not_available_proteomics_workunits.py. Use bfabric-cli workunit not-available instead.

Changed

Update bfabric to 1.13.27.
bfabric-cli api delete will use the type of the entity in CLI messages.

[0.0.22] - 2025-05-21

Added

Apps can now be referred to by module path rather than just file paths. This is going to be a primary building block
to very simple package-based deployment of apps.
The static_file input spec type has been integrated properly.
Missing integration for file input spec type has been added.
The workunit makefile now directly shows how to use the GitHub app runner version instead, which is sometimes required
while debugging.
CommandExec allows prepending paths to PATH and setting environment variables and is less ambiguous than she 8000 ll.
bfabric-app-runner action interface which standardizes the various actions of running app steps.
bfabric-app-runner prepare workunit to prepare a workunit execution and sets up a app_env.yml and Makefile.
bfabric-app-runner deploy build-app-zip experimental command to build an app zip file which can be deployed, for a
particular Python application.

Changed

Silently interpolate_config_strings log messages.
Update bfabric dependency to 1.13.27.
App versions do not always require a version key as it will default to "latest", but only one version can have a
particular version key per app definition.

Fixed

Use most recent cyclopts version again, i.e. issue 168 is fixed.
Compatibility with pandera 0.24.0 was restored.

[1.13.26] - 2025-04-26

This release introduces an environment variable BFABRICPY_CONFIG_OVERRIDE to configure the Bfabric client completely,
along with a new method for creating an instance of the Bfabric client, Bfabric.connect().
This will allow us to propagate any configuration to subprocesses reliably. BFABRICPY_CONFIG_ENV remains available
with the same semantics, but lower priority than BFABRICPY_CONFIG_OVERRIDE.

This also simplifies the logic that was present in Bfabric.from_config which is why this introduced with a new API
to prevent configuration mix-ups.

Added

New environment variable BFABRICPY_CONFIG_OVERRIDE to configure the Bfabric client completely
New method Bfabric.connect() for creating an instance of the Bfabric client

Changed

Renamed Bfabric.from_token to Bfabric.connect_webapp() (along with some changes, no known users of this API yet)
Disallowed default as an environment config name
bfabric.cli_integration.utils.use_client uses Bfabric.connect() instead of Bfabric.from_config()

Deprecated

Bfabric.from_config is now deprecated in favor of Bfabric.connect()

[1.13.25] - 2025-04-22

Breaking

Bfabric.from_token returns the TokenData in addition to the client instance. While this is breaking, I'm not aware
of any existing users of this API and I noticed that this information is going to be needed in this context often.

Added

bfabric.experimental.upload_dataset.warn_on_trailing_spaces function used by bfabric-scripts to validate

[1.13.27] - 2025-04-22

Changed

bfabric-cli dataset upload will print warnings when trailing whitespace is detected and not print the whole
response anymore, but rather the important information only.

Added

Optional support for uploading xlsx (currently behind excel optional feature).

Removed

cyclopts is not a dependency of bfabric anymore, but rather of bfabric-scripts and bfabric-app-runner.

Changed

Bfabric client now does not take engine argument anymore, but rather this information comes from ClientConfig.
For compatibility reasons, the engine argument is still accepted in Bfabric.from_config and
Bfabric.from_token.

Changed

Update bfabric to 1.13.24.

Removed

Remove bfabric-cli api save -> use bfabric-cli api create and bfabric-cli api update instead.

Fixed

Temporary workaround for #168.

Releases: fgcz/bfabricPy

bfabric_app_runner/0.0.23

[0.0.23] - 2025-06-02

Added

Removed

Uh oh!

bfabric/1.13.27

[1.13.27] - 2025-05-21

Added

Changed

Fixed

Deprecated

Uh oh!

bfabric_scripts/1.13.28

[1.13.28] - 2025-05-21

Removed

Changed

Uh oh!

bfabric_app_runner/0.0.22

[0.0.22] - 2025-05-21

Added

Changed

Fixed

Uh oh!

bfabric/1.13.26

[1.13.26] - 2025-04-26

Added

Changed

Deprecated

Uh oh!

bfabric/1.13.25

[1.13.25] - 2025-04-22

Breaking

Added

Uh oh!

bfabric_scripts/1.13.27

[1.13.27] - 2025-04-22

Changed

Added

Uh oh!

bfabric/1.13.24

Removed

Changed

Uh oh!

bfabric_scripts/1.13.26

Changed

Removed

Uh oh!

bfabric_scripts/1.13.25

Fixed

Uh oh!