Pybids

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Bug-fix release in the 0.16.x series.

This release resolves a bug likely introduced in 0.9.0
(when PyBIDS started using SQL),
in which boolean metadata fields with values of ``False`` were read in as
``True``.

* FIX: Ensure values of boolean metadata fields are preserved (1034)
* FIX: update config for PET tracer entity (1018)
* ENH: Clearer BIDSValidation error message (1023)
* STY: pacify codespell (1029)
* CI: Build(deps): Bump bids-examples from `064db11` to `b6e5234` (1031)
* CI: Build(deps): Bump bids-examples from `d039879` to `064db11` (1028)
* CI: Build(deps): Bump bids-examples from `bfcc5c6` to `d039879` (1027)
* CI: Bump bids-examples from `502c917` to `bfcc5c6` (1026)
* CI: Bump bids-examples from `1c30c6e` to `502c917` (1025)
* CI: Bump bids-examples from `e857597` to `1c30c6e` (1021)
* CI: Bump bids-examples from `c557d1f` to `e857597` (1019)
* CI: Bump bids-examples from `75968b9` to `c557d1f` (1011)
* CI: Bump actions/checkout from 3 to 4 (1024)

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Bug-fix release in the 0.16.x series.

This release resolves a regression introduced in 0.16.2 when JSON sidecar files
contain ``null`` values.

* FIX: Drop JSON sidecar fields with null values during metadata indexing (1016)

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Bug-fix and performance release in the 0.16.x series.
Notably, indexing is now significantly faster (2-2.5x).

* ENH: Speed up indexing by bulk committing to database (1013)
* Include indexer in add_derivatives call (1009)
* Bump bids-examples from `8550641` to `75968b9` (1008)
* Bump bids-examples from `e96b702` to `8550641` (1007)
* Bump bids-examples from `d8455af` to `e96b702` (1005)
* Bump bids-examples from `bc36231` to `d8455af` (1003)
* CI: Use OIDC publishing instead of tokens (1001)

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Bug-fix release in the 0.16.x series.

* FIX: Improve parsing of suffix/extension in non-BIDS files (997)
* FIX: Support use of Query enums in filter lists (994)
* MNT: Clean up imports in documentation scripts (980)
* MNT: update zenodo (995)
* CI: Update Python version for doc/sdist/wheel tests (996)

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New feature release in the 0.16.x series.

* FIX: Adapt to SQLAlchemy 1.4+ (985)
* FIX: Fill na with zero for VIF (976)
* ENH: Only warn if missing values not explicitly set (977)
* ENH: Create run reports of whole graph / create HTML reports (918)
* ENH: Speed up Sparse to Dense BIDSVariable conversion (969)
* ENH: Update config to support motion and nirs modalities (965)
* REF: Add derivative subdatasets in a less ad hoc fashion (954)
* MNT: Update minimum dependencies, add CI job to test them (987)
* MNT: Drop jinja2/markupsafe constraints (986)
* MNT: Fix ruff issue E712 (981)
* MNT: A few Python3 updates (971)
* MNT: Drop Python 3.7 EOL (974)
* MNT: Fix repeat-word typo (968)
* MNT: Update vendored inflect to 5.6.2 (961)
* MNT: Fix flake8 issues found by ruff (955)
* MNT: Remove (large) unused PNG from doc directory (962)
* MNT: http:// → https:// (#960)
* MNT: Update git submodules (964)
* CI: Drop codecov PyPI package and appveyor config (979)
* CI: Add Python 3.11 (975)
* CI: Replace custom update_submodules action with dependabot action (967)
* CI: fix errors caused by changes in examples (963)
* CI: Update parameters to gh-action-pypi-publish (957)

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Bug-fix release in 0.15.x series.

* FIX: Exclude non-Hashables from set in .get(return_type='id') (948)
* FIX: Broken pattern matching (936)
* FIX: Coerce oversampling parameter in convolution to int (929)
* FIX: Allowing custom BIDS configuration files for derivative datasets (922)
* FIX: Address change in default pandas grouping behavior (917)
* ENH: Speed up BIDSLayout.get(return_type='id', ...) (942)
* ENH: Update default anat filename patterns in config (933)
* DOC: Make clear how to ignore folders (945)
* DOC: Fix tutorial link in README (944)
* DOC: Mention conda installation in README (928)
* MNT: Update git submodules (946 + 943 + 932)
* MNT: Move package metadata to pyproject.toml, unvendor versioneer (907)
* MNT: Bump formulaic max version constraint to include 0.5.x (916)