Pybids

-----------------------------
This version includes a number of minor fixes and improvements.
EEG files are better handled, and ``BIDSLayout`` and ``BIDSFile`` play more
nicely with ``Path``\ -like objects.

With thanks to new contributor Cecile Madjar.

* FIX: Instantiate ``ignore``\ /\ ``force_index`` after root validation (457)
* FIX: Restore ``<entity>=None`` query returning files lacking the entity (458)
* ENH: Add ``BIDSJSONFile`` (444)
* ENH: Add ``BIDSFile.__fspath__`` to work with pathlib (449)
* ENH: Add ``eeg`` datatype to layout config (455)
* RF: Remove unused kwargs to BIDSFile (443)
* DOC: Improve docstring consistency, style (443)
* DOC: Address final JOSS review (453)
* STY: PEP8 Fixes (456)
* MAINT: Set name explicitly in setup.py (450)

----------------------------
Hotfix release:

* Fixed package deployment issues (446)
* Updated author list (447)

Thanks to new contributors Erin Dickie, Chadwick Boulay and Johannes Wennberg.

----------------------------
Version 0.9 replaces the native Python backend with a SQLite database managed
via SQLAlchemy. The layout module has been refactored (again), but API changes
are minimal. This release also adds many new features and closes a number of
open issues.

API CHANGES/DEPRECATIONS:

* The ``extensions`` argument has now been banished forever; instead, use
``extension``\ , which is now defined as a first-class entity. The former will
continue to work until at least the 0.11 release (closes 404).
* Relatedly, values for ``extension`` should no longer include a leading ``.``\ ,
though this should also continue to work for the time being.
* The ``BIDSLayout`` init argument ``index_associated`` has been removed as the
various other filtering/indexing options mean there is longer a good reason for
users to manipulate this.
* ``bids.layout.MetadataIndex`` no longer exists. It's unlikely that anyone will
notice this.
* ``BIDSLayout.get_metadata()`` no longer takes additional entities as optional
keyword arguments (they weren't necessary for anything).
* Direct access to most ``BIDSFile`` properties is discouraged, and in one case
is broken in 0.9 (for ``.metadata``\ , which was unavoidable, because it's reserved
by SQLAlchemy). Instead, users should use getters (\ ``get_metadata``\ , ``get_image``\ ,
``get_df``\ , etc.) whenever possible.

NEW FUNCTIONALITY:

* All file and metadata indexing and querying is now supported by a
relational (SQLite) database (see 422). While this has few API implications,
the efficiency of many operations is improved, and complex user-generated
queries can now be performed via the SQLAlchemy ``.session`` stored in each
``BIDSLayout``.
* Adds ``.save()`` method to the ``BIDSLayout`` that saves the current SQLite DB
to the specified location. Conversely, passing a filename as ``database_file`` at
init will use the specified store instead of re-indexing all files. This
eliminates the need for a pickling strategy (435).
* Related to the above, the ``BIDSLayout`` init adds a ``reset_database`` argument
that forces reindexing even if a ``database_file`` is specified.
* The ``BIDSLayout`` has a new ``index_metadata`` flag that controls whether or
not the contents of JSON metadata files are indexed.
* Added ``metadata`` flag to ``BIDSLayout.to_df()`` that controls whether or not
metadata columns are included in the returned pandas ``DataFrame`` (232).
* Added ``get_entities()`` method to ``BIDSLayout`` that allows retrieval of all
``Entity`` instances available within a specified scope (346).
* Adds ``drop_invalid_filters`` argument to ``BIDSLayout.get()``\ , enabling users to
(optionally) ensure that invalid filters don't clobber all search results
(402).
* ``BIDSFile`` instances now have a ``get_associations()`` method that returns
associated files (see 431).
* The ``BIDSFile`` class has been split into a hierarchy, with ``BIDSImageFile``
and ``BIDSDataFile`` subclasses. The former adds a ``get_image()`` method (returns
a NiBabel image); the latter adds a ``get_df()`` method (returns a pandas DF).
All ``BIDSFile`` instances now also have a ``get_entities()`` method.

BUG FIXES AND OTHER MINOR CHANGES:

* Metadata key/value pairs and file entities are now treated identically,
eliminating a source of ambiguity in search (see 398).
* Metadata no longer bleeds between raw and derivatives directories unless
explicitly specified (see 383).
* ``BIDSLayout.get_collections()`` no longer drops user-added columns (273).
* Various minor fixes/improvements/changes to tests.
* The tutorial Jupyter notebook has been fixed and updated to reflect the
latest changes.

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``.

---------------------------------

---------------------------------
This is a bug fix release in the 0.7 series. The primary API change is improved
handling of ``Path`` objects.

* FIX: Path validation (342)
* FIX: Ensure consistent entities at all levels (326)
* FIX: Edge case where a resampled column was too-long-by-one (365)
* FIX: Use BIDS metadata for TR over nii header (357)
* FIX: Add check for ``run_info`` to be a list, pass ``run_info`` in correct position. (353)
* FIX: If ``sampling_rate`` is ``'auto'``\ , set to first rate of ``DenseRunVariables`` (351)
* FIX: Get the absolute path of the test data directory (347)
* FIX: Update reports to be 0.7-compatible (341)
* ENH: Rename ``sr`` variable to more intuitive ``interval`` (366)
* ENH: Support ``pathlib.Path`` and other ``str``\ -castable types (307)
* MNT: Updates link to derivative config file in notebook (344)
* MNT: Add bids-validator dependency (363)
* MNT: Require pandas >= 0.23.0 (348)
* MNT: Bump grabbit version (338)
* CI: Ignore OSX Python 3.5 failures (372)
* CI: Build with Python 3.7 on Travis, deploy on 3.6 (337)