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Changelog

The format is based on Keep a Changelog.

Versioning currently follows X.Y.Z where

  • X is used for major changes, that contain breaking changes
  • Y should be the current bfabric release
  • Z is increased for feature releases, that should not break the API

[Unreleased]

[1.13.33] - 2025-08-26

Added

  • Add new field WorkunitDefinition.registration.user_id.
  • Add created/modified fields to Workunit entity.

Fixed

  • Legacy wrapper creator also writes the inputdataset name.

[1.13.32] - 2025-08-26

Added

  • New entities: Workflow, WorkflowStep, WorkflowTemplate, WorkflowTemplateStep
  • New relationship: HasUser to resolve user references (since these are modeled differently from other relationships).

Fixed

  • There was an issue in import_entity.py which made loading entities with additional uppercase characters in the type fail.
  • Fix compatibility in legacy wrapper creator for dataset-flow workunits.

[1.13.31] - 2025-09-20

Changed

  • The Bfabric.connect_webapp will use the caller field from the token data to set the base_url of the client.
    • Existing code should not break, but will emit a deprecation warning as we plan to remove the old parameters.
    • Theoretically, it changes the semantics, but in practice it should yield the same result for all known use cases.

Added

  • TokenData will include the caller url now.
  • Entity User has been added.

Fixed

  • Legacy wrapper creator creates "" rather than None for empty parameter values.

[1.13.30] - 2025-08-19

Fixed

  • Fix legacy wrapper creator for orders without projects.

[1.13.29] - 2025-07-04

Changed

  • bfabric.rest.token_data.get_token_data now only requires the base_url instead of the whole config.

[1.13.28] - 2025-06-27

Breaking

  • base_url is now a mandatory parameter in the configuration.

Added

  • It is now possible to configure ~/.bfabricpy.yml without a default environment. In that case it will always be necessary to specify the requested config environment to be used.
  • bfabric.entities.Executable has parameters relationship now

Removed

  • Some old submitter related functionality is deleted.

Changed

  • Columns of tables named after B-Fabric entities, containing only integers, will be set as the specified type when saving to B-Fabric (in experimental.upload_dataset).

[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.

[1.13.26] - 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

[1.13.24] - 2025-04-08

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.

[1.13.23] - 2025-03-25

Fixed

  • Unsuccessful deletions are detected by checking the B-Fabric response.
  • Handle problematic characters in Workunit.store_output_folder.
  • BfabricRequestError did not properly subclass RuntimeError.

Changed

  • WorkunitDefinition uses PathSafeStr to normalize app and workunit names.
  • Internal: ResultContainer has no optional constructor arguments anymore to avoid confusion.

Added

  • Generic functionality in bfabric.utils.path_safe_name to validate names for use in paths.
  • bfabric.entities.Dataset.{write_parquet, get_parquet} methods for writing parquet

[1.13.22] - 2025-02-19

Fixed

  • Correctly read datasets, if columns were swapped in B-Fabric.

Changed

  • Dataset.types was renamed to Dataset.column_types, since there is only 1 usage and it is recent, this is not considered breaking.

[1.13.21] - 2025-02-19

Added

  • Entity.load_yaml and Entity.dump_yaml
  • Bfabric.from_token to create a Bfabric instance from a token
  • bfabric.rest.token_data to get token data from the REST API, low-level functionality

Changed

  • Internally, the user password is now in a pydantic.SecretStr until we construct the API call. This should prevent some logging related accidents.

[1.13.20] - 2025-02-10

Breaking

  • the old bfabric.cli_formatting and bfabric.bfabric2 modules have been deleted

Changed

  • move use_client to bfabric.utils.cli_integration: this will allow reuse between bfabric-scripts and bfabric-app-runner
  • move functionality from bfabric.cli_formatting to bfabric.utils.cli_integration

[1.13.19] - 2025-02-06

Fixed

  • Config: Log messages of app runner are shown by default again.

[1.13.18] - 2025-01-28

Changed

  • bfabric_upload_resource.py does not print a list anymore, but rather only the dict of the uploaded resource.

Fixed

  • Some scripts were not Python 3.9 compatible, which is restored now. However, we can consider increasing the Python requirement soon.

[1.13.17] - 2025-01-23

Added

  • bfabric-cli workunit export-definition to export workunit_definition.yml files
  • Executable.storage relationship

Fixed

  • Workunit.parameters and Workunit.resources are optional
  • bfabric-cli had unmet dependencies, that were not caught by the tests either

[1.13.16] - 2025-01-22

Added

  • Add missing Entity.__contains__ implementation to check if a key is present in an entity.
  • polars_utils.py which contains functionality to normalize relational fields in tables
  • Add bfabric-cli executable inspect command to inspect executables registered in B-Fabric.
  • Add bfabric-cli executable upload command to upload executables to B-Fabric.

Fixed

  • Order.project is optional

[1.13.15] - 2025-01-15

Added

  • Entity Sample
  • Relationship Resource.sample.
  • Extract logic for container resolution into HasContainerMixin which is right now shared between Sample and Workunit.

Fixed

  • Fix bug in bfabric_save_fasta.py.

[1.13.14] - 2025-01-08

Changed

  • Slurm submitter prints more diagnostics about PATH variable etc.

Fixed

  • Some commands in bfabric-cli are broken because __future__.annotations is imported and this breaks cyclopts.

[1.13.13] - 2024-12-18

Changed

  • Move bfabric-cli read to bfabric-cli api read.
  • (internal) use_client decorator is introduced to simplify and standardize the client usage in the new CLI code.

Added

  • Functionality to log by specifying the workunit instead of external job, which is used in some legacy scripts.
  • Add logging commands to bfabric-cli api log.
  • Add bfabric-cli api save.
  • Submitter script prints the id and hostname of apps, which in practice can be very useful.

Fixed

  • A bug in bfabric_save_workflowstep.py that crashed the script.

[1.13.12] - 2024-12-17

Changed

  • The submitter ensures that workunits always get set to processing.

Fixed

  • The script bfabric_setResourceStatus_available.py and other uses of report_resource, correctly search files which have a relative path starting with / as in the case of the legacy wrapper creator.

[1.13.11] - 2024-12-13

Fixed

  • The script bfabric_setWorkunitStatus.py did always set the status to available, instead of the specified status.

Changed

  • bfabric_setResourceStatus_available.py calls the report_resource function, in general this functionality has been refactored.

[1.13.10] - 2024-12-13

Fixed

  • If bfabricpy.yml contains a root-level key which is not a dictionary, a correct error message is shown instead of raising an exception.
  • A bug introduced while refactoring in slurm.py which passed Path objects to subprocess instead of strings.
  • Submitter
    • does not use unset JOB_ID environment variable anymore.
    • does not set unused STAMP environment variable anymore.
  • Fix bfabric_save_workflowstep.py bugs from refactoring.

Added

  • Experimental bfabric-cli interface. Please do not use it in production yet as it will need a lot of refinement.

[1.13.9] - 2024-12-10

From this release onwards, the experimental app runner is not part of the main bfabric package and instead a separate Python package with its individual changelog.

Added

  • Relationship: ExternalJob.executable
  • (experimental) EntityLookupCache that allows to cache entity lookups in a script to avoid redundant requests.
  • Specific use case script: bfabric_save_resource_description.py (the functionality will be available in a future CLI).

Fixed

  • Entity.find_all returns no values when an empty list is passed as an argument.

Changed

  • Except for macOS x86_64 (which we assume is Rosetta emulation nowadays), we use the faster polars instead of polars-lts-cpu.
  • BfabricRequestError is now a RuntimeError subclass.
  • Add py.typed marker.

Removed

  • bfabric_legacy.py has been removed.
  • math_helper.py has been removed.

[1.13.8] - 2024-10-03

This release contains mainly internal changes and ongoing development on the experimental app interface functionality.

Added

  • Entities can be compared and sorted by ID now.
  • Show Python version in version info string.
  • Caching for bfabric_list_not_existing_storage_directories.py.
  • (experimental) add initial code for a resource based application dispatch
  • (experimental) new app_runner cli that integrates all commands into a single interface

Fixed

  • bfabric_read.py is a bit more robust if "name" misses and tabular output is requested.

Changed

  • bfabric.scripts has been moved into a namespace package bfabric_scripts so we can later split it off.
  • (internal) migrate to src layout
  • (experimental) the former process step of the app runner has been split into a process and collect step where, the collect step is responsible for generating the output.yml file that will then be used to register the results.
  • (experimental) app runner apps by default reuse the default resource

[1.13.7] - 2024-09-17

Fixed

  • bfabric_save_csv2dataset.py considers all rows for schema inference, only considering the first 100 rows did cause problems with some files previously.

Added

  • Script logging configuration
    • If BFABRICPY_DEBUG environment variable is set, log messages in scripts will be set to debug mode.
    • Log messages from __main__ will also be shown by default.
  • bfabric.entities.MultiplexKit to extract multiplex kit information.
  • bfabric.entities.Workunit.store_output_folder implements the old rule, but more deterministically and reusable.
  • (Experimental) bfabric.experimental.app_interface core functionality is implemented
    • This can be used as a building block to standardize the input preparation for applications.

Changed

  • Correctly support optional workunit parameters.

Removed

  • bfabric.entities.Resource association application has been removed as it does not exist

[1.13.6] - 2024-08-29

Added

  • Entity.find_by has new parameter max_results.

Changed

  • bfabric_read.py prints non-output information exclusively through logger and does not restrict entity types anymore.
  • bfabric_delete.py accepts multiple ids at once and does not restrict entity types anymore.
  • Both engines raise a BfabricRequestError if the endpoint was not found.

Removed

  • bfabric.endpoints list is deleted, since it was out of date and generally not so useful.

[1.13.5] - 2024-08-13

Added

  • The Bfabric instance is now pickleable.
  • Entities mapping:
    • Add Entity.id and Entity.web_url properties.
    • Add Entity.__getitem__ and Entity.get to access fields from the data dictionary directly.
    • Add Entity.find_by to find entities by a query.
    • More types and relationships
    • Relationships defer imports to descriptor call, i.e. circular relationships are possible now.
    • HasOne and HasMany allow defining optional=True to indicate fields which can be missing under some circumstances.
  • Add nodelist column and application name to bfabric_list_not_available_proteomics_workunits.py output.

Changed

  • Entity.find_all supports more than 100 IDs now by using the experimental MultiQuery API.

[1.13.4] - 2024-08-05

Added

  • Add Workunit, Parameter, and Resource entities.
  • Add concept of has_many and has_one relationships to entities.
  • bfabric_slurm_queue_status.py to quickly check slurm queue status.
  • Bfabric.save provides method which can be set to checkandinsert for specific use cases.

Changed

  • Most messages are now logged to debug level.
  • The old verbose version information is now always logged, to INFO level, since it could entail useful information for error reporting.

[1.13.3] - 2024-07-18

Added

  • Flask
    • New endpoint GET /config/remote_base_url for testing

Changed

  • Flask
    • Simplify logging by using loguru only.
    • Simplified setup logic since the production use case should use a WSGI server.

Fixed

  • bfabric_save_csv2dataset.py had an undeclared dependency on numpy and a few bugs which was improved.

[1.13.2] - 2024-07-11

Added

  • Add bfabric.entities.Dataset to easily read datasets.
  • Pydantic-based configuration parsing
    • The config format did not change.
    • The code is easier to maintain now.
    • Additionally, there is a lot more validation of the configuration file now, that should catch errors early.
  • Make host and port configurable in bfabric_flask.py (currently only dev mode).

[1.13.1] - 2024-07-02

Changed

  • bfabric_save_csv2dataset will raise an error if problematic characters are found in any of the cells
  • Correctly define bfabric_setWorkunitStatus_available.py, and processing and failed variants.

Added

  • Add loguru for future logging refactoring.
  • Easily runnable tests with nox and standardized formatting using pre-commit.

Removed

  • Pandas is no longer a dependency, and has been replaced by polars.

[1.13.0] - 2024-05-24

This is a major release refactoring bfabricPy's API.

Changed

  • The Bfabric class operations now return ResultContainer objects.
    • These provide a list-like interface to access individual items or iterate over them.
    • Individual items are a dictionary, potentially nested, and not specific to suds/zeep anymore.
    • Convenience conversions, e.g. to a polars DataFrame, can be provided there.
  • Configuration is now defined in ~/.bfabricpy.yml and supports multiple configurations, which can be selected by the BFABRICPY_CONFIG_ENV environment variable. Please consult the README for an example configuration.
  • Use pyproject.toml for package configuration.
  • Scripts have been refactored on a case-by-case basis.

Added

  • Zeep can be used instead of suds for SOAP communication.
  • Bfabric can be instantiated without authentication, that can be provided later. This is useful in a server setup.
  • Pagination support in Bfabric, specify the number of max_results and a potential offset. Pages handling is abstracted away.
  • Detect errors in responses, e.g. invalid login.

Removed

  • Several old scripts have been moved into a deprecated_scripts folder.
  • Wrapper creator related code is currently not updated but has been extracted into a dedicated folder wrapper_creator as well.