1.13.8

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

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

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• bfabric.endpoints list is deleted, since it was out of date and generally not so useful.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

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

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

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

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

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

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.

bfabricPy 0.13.8

Set version 0.13.8