Version 1.0.1

[v1.0.1] - 2024-07-18

API-breaking changes:

• The output data frames produced by the dgd_get_recount3_data executable now contain both gene expression data and metadata unless otherwise filtered (see below).

Other changes:

• Now the experiment_attributes column, if present in the metadata columns of an SRA study, will be split into its constituent components when writing the output data frames for the dgd_get_recount3_data executable (as it is already the case with the sample_attributes column).

• The user can now pass a YAML file to dgd_get_recount3_data to download data from the Recount3 platform in bulk and filter them.

• The user can now pass metadata_to_keep and metadata_to_drop lists of metadata columns in the input file to dgd_get_recount3_data to keep or drop specific metadata columns in the output data frames. These can be passed both as columns if the input file is a CSV file or as specific keywords if the input file is a YAML file.

• The recount3.util.get_metadata function now returns the metadata data frame with the recount3_project_name and recount3_samples_category columns added.

• The model_untrained.yaml configuration file was added to the examples of configuration files available within the package.

Internal changes (for contributors):

• Two new internal functions in the bulkDGD.recount3.util module (_load_samples_batches_csv'and load_samples_batches_yaml) were introduced to parse the input files to dgd_get_recount3_data. The public function load_samples_batches simply calls one of them depending on the file's extension.

• The bulkDGD.util.get_handlers function now accepts two new arguments, log_level_console and log_level_file instead of the old log_level to have more fine-grained control over the log level of the handlers.

• The log level of the console handler for the _dgd_get_recount3_data_single_batch executable was changed to ERROR so as not to clutter the console too much with all the INFO messages from the subprocesses (which get logged to their own log files anyway if the overall log level is INFO or below).

• The header of the bulkDGD/recount3/data/sra_metadata_fields.txt file was changed to better describe the metadata fields included in it.

Documentation:

• The documentation was updated to reflect the user-facing changes.

• The readme files for the configurations were removed because of the redundancy in the content of the documentation and the configuration files themselves.