CRAN Release 0.9.0

raveio 0.9.0

We are close to a major release.

Major changes:

• Pipeline supports Python now! (I think this deserves the first place)

• Referencing electrodes does not require users to run wavelet anymore (this one wins the second as it allows for more flexible data processing pipelines)

• Added PipelineCollections, allowing users to build and run multiple pipelines

• run_wavelet will trigger caching existing references

• The pipeline errors is properly handled

• Pipeline error messages also print out the expressions causing the issues

• Clears pipeline object directory when related errors are raised; in this case pipeline is rescheduled automatically

• Pipeline also reports warning messages

• Allow pipelines to fork

• Added external data path (extdata) to pipeline to store large temporary data

• Added prepare_subject_phase and prepare_subject_wavelet to support loading phase and time-frequency data (besides amplitude)

• Pipeline shared scripts uses script directory as working directory

• Added lapply_async that can run in parallel standalone while is compatible with with_future_parallel; this function replaces dipsaus::lapply_async2

• Added a new subject class RAVEMetaSubject for meta-analysis

• Added support for FreeSurfer recon-all-clinical.sh, allowing users to apply super-resolution to their clinical MRI before surface reconstruction

• Supports when one NSx block data contains multiple recordings (discontinued/paused recording in one block)

• rave_export exports summary in Matlab format as well (thanks @Kaitlyn)

• Added cmd_run_r to generate reproducible shell scripts that run code

• Added pipeline$visualize to view the target relationships and schedule graphs

• Added pipeline$shared_env to obtain shared environment

Minor changes:

• Default pipeline repository user name has been changed to rave-ieeg
• Updated Github action configurations
• Copy MRI to derivative folder when importing images from NIfTI format (before imaging segmentation and CT to MRI registration)
• Updated pipeline template to display the latest pipeline dependency
• Pipeline dependency are installed at the same directory as ravemanager
• Removed improper S3generics in validate_raw_file_lfp
• Pipeline root searching path can be set with temporary values
• Added is_on_cran, allowing certain examples and tests to be suppressed during CRAN check, while these code are enabled in the local tests - this helps me to keep examples up-to-date

Bug fixes:

• Fixed template module UI having extra padding on bottom
• Fixed Blackrock NEV-3.0 specification configurations
• Fixed errors when subject set_default and get_default raise errors when configuration files are corrupted
• Fixed a potential code injection issue
• Fixed parallel code not closing socket connections correctly

raveio 0.1.0

Major changes:

• Added pipeline target format interface; an example for rave-subject has been implemented
• rewrote as_rave_subject such that the subject information will be updated when called
• Revised error handlers in pipeline generating engine, so that when errors occur, the enclosing target expressions and back-trace will be printed
• Supported brain viewer to be loaded without electrodes via include_electrodes argument
• Added coregistration via ANTs
• Supports MRI registering to templates via non-linear transforms

Minor changes:

• When importing electrodes from other formats, the subject used to be required. However, this is totally unnecessary; removed such requirement
• Fixed a small typo that may cause inconsistent electrode labels (Nolabel to NoLabel)

Bug fixes:

• When executing pipeline shared script, it is possible to leak some variables to the global environment; fixed
• Fixing a bug where shared scripts might not be loaded properly in pipeline_run