Pybids

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Bug fix release in the 0.10.x series.

* FIX: Add Replace as exception to recursive JSON conversion (589)

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Bug fix release in the 0.10.x series.

This release just makes available some of the latest minor fixes and improvements.

* FIX: Replace ``os.path.sep`` with ``fwdslash`` because bids validator hardcodes fwd (582)
* FIX: Refactor of ``build_path`` and inner machinery (574)
* FIX: Domain entity, and slow ``__repr__`` (569)
* FIX: "strict" helptext in ``BIDSLayout.write_contents_to_file`` (566)
* FIX: typos in helpstrings and comments (564)
* FIX: Correct term "caret" to "angle bracket" in helpstrings (565)
* ENH: Extend ``build_path`` to generate lists of files (576)
* ENH: Add one parametric test of ``BIDSLayout.build_path`` (577)
* ENH: Enable partial metadata indexing (560)
* ENH: Upscale to collection sampling rate prior to resampling (568)
* ENH: Calculate default sampling rate for ``SparseRunVariable.to_dense`` (571)
* MNT: Add ``.vscode`` (for Visual Studio Code) to ``.gitignore`` (562)
* MNT: Ignore pip-wheel-metadata (581)
* DOC: Remove Python 2 support statement, now that v0.10.0 has dropped it (561)

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New feature release in the 0.10.x series.

This release removes Python 2 support.

* ENH: Helpful error for db argument mismatch, and add classmethod load_from_db (547)
* ENH: Add Resample transformation (373)
* ENH: Save BIDSLayout + Derivatives to folder (with init arguments) (540)
* ENH: Adds support for NONE and ANY query Enums (542)
* ENH: Transformation-related improvements (541)
* ENH: FEMA contrasts (520)
* STY: Minor PEP8 Fixes (545)
* MNT: Various (543)
* MNT: Remove Python 2.7 support (524)
* CI: Configure Circle Artifact Redirector (544)

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Bug fix release in the 0.9.x series.

Final planned release with Python 2 support.

* FIX: Filter before downsampling (529)
* FIX: Copy input dict in ``replace_entities``\ ; Typos in ``default_path_patterns`` (517)
* FIX: Use string dtype for all entities when using regex search (511)
* FIX: Update Sphinx docs for 2.2 (507)
* ENH: Enable automatic derivative database caching (523)
* ENH: Raise ValueError if BIDSLayout.build_path fails to match any pattern (508)
* RF: Subclass analysis Node from object (528)
* DOC: Unify docstring format (499)
* DOC: Auto-generate stubs (513)
* STY: .sql is a misleading extension to sqlite files (531)
* STY: General cleanups (526, 527)

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Bug fix release in the 0.9.x series.

* FIX: Ignore ``default_ignore`` paths by default (495)
* FIX: Filter and sort on scalar metadata in ``get_nodes()`` (488)
* FIX: Automatically sanitize dtype of ``get()`` arguments (492)
* FIX: Check that ``default_path_patterns`` is not ``None`` before using in ``build_path`` (485)
* FIX: Add CBV and phase modalities to func datatype path pattern (479)
* FIX: Drop bold suffix constraint from echo entity (477)
* ENH: Enforce dtypes on spec-defined columns when reading in DFs (494)
* ENH: Validate built paths (496)
* ENH: Update contrast enhancing agent query name (ceagent) (497)
* DOC: Add citation information to README (493)
* DOC: Improve wording in Python notebook example comment (484)
* DOC: Finish sentence in Python Notebook example documentation (483)
* DOC: Add JOSS Badge (472)
* STY: Apply syntax highlight to Python notebook example doc (482)
* MAINT: Move setup configuration to setup.cfg (448)
* MAINT: Additional Zenodo metadata (470)
* MAINT/CI: Use ``extras_require`` to declare dependencies for tests (471)

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This version includes a number of minor fixes and improvements, one of which
breaks the existing API (by renaming two entities; see 464). Changes
include:

* FIX: Avoid DB collisions for redundant entities (468)
* FIX: Minor changes to entity names in core spec (464)
* FIX: Make bids.reports work properly with .nii images (463)
* CI: Execute notebook in Travis (461)
* ENH: More sensible **repr** for Tag model (467)