0.8.0

Release notes

Version 0.8 refactors much of the layout module. It drops the grabbit
dependency, overhauls the file indexing process, and features a number of other
improvements. However, changes to the public API are very minimal, and in the
vast majority of cases, 0.8 should be a drop-in replacement for 0.7.*.

API-breaking changes

• Changes to (rarely-used) BIDSLayout initialization arguments:
  • include and exclude have been replaced with ignore and
    force_index. Paths passed to ignore will be ignored from indexing;
    paths passed to force_index will be forcibly indexed even if they are
    otherwise BIDS-non-compliant. force_index takes precedence over ignore.
• Most querying/selection methods add a new scope argument that controls
  scope of querying (e.g., 'raw', 'derivatives', 'all', etc.). In some
  cases this replaces the more limited derivatives argument.
• No more domains: with the grabbit removal (see below), the notion of a
  'domain' has been removed. This should impact few users, but those who need
  to restrict indexing or querying to specific parts of a BIDS project should be
  able to use the scope argument more effectively.

Other changes

• FIX: Path indexing issues in get_file() (#379)
• FIX: Duplicate file returns under certain conditions (#350)
• FIX: Pass new variable args as kwargs in split() (#386) @effigies
• TEST: Update naming conventions for synthetic dataset (#385) @effigies
• REF: The grabbit package is no longer a dependency; as a result, much of the
  functionality from grabbit has been ported over to pybids.
• REF: Required functionality from six and inflect is now bundled with pybids
  in bids.external, minimizing external dependencies.
• REF: Core modules have been reorganized. Key data structures and containers
  (e.g., BIDSFile, Entity, etc.) are now in a new bids.layout.core module.
• REF: A new Config class has been introduced to house the information
  found in bids.json and other layout configuration files.
• REF: The file-indexing process has been completely refactored. A new
  hierarchy of BIDSNode objects has been introduced. While this has no real
  impact on the public API, and isn't really intended for public consumption yet,
  it will in future make it easier for users to work with BIDS projects in a
  tree-like way, while also laying the basis for a more sensible approach to
  reading and accessing associated BIDS data (e.g., .tsv files).
• MNT: All invocations of pd.read_table have been replaced with read_csv.