Pybids

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Bug-fix release in 0.15.x series.

* FIX: Test and update sync_kwargs class variable on transformations (891)
* FIX: Filtering of DM columns (892)
* ENH: Enable using participants.tsv, scans.tsv & session.tsv values as grouping variables (894)
* REF: Rename incoming single contrast column to intercept (886)
* DOC: Update references to nistats with references to nilearn in docs (882)
* TST: some sort of QA for derivatives' default_path_patterns (879)
* MNT: Update git submodules (887)
* MNT: Codespell errors (885)
* MNT: Update git submodules (884)
* MNT: Update git submodules (883)
* CI: Update actions versions (897)

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Bug-fix release in 0.15.x series.

* FIX: Synchronize kwargs in transformations, e.g., in Assign (836)
* FIX: Add HRF derivatives to variable collection when created (838)
* FIX: Interpolate derivative pipeline name in error message (847)
* FIX: Match only within relative path when indexer is validating (859)
* FIX: Rename intercept in DummyContrast (866)
* FIX: Add variables to correct Node in load_tsv_variables (872)
* FIX: Repair variable IO so scans.tsv is found (869)
* FIX: Restore automodel functionality (853)
* FIX: Allow ``pybids layout --derivatives`` to be a boolean flag or accept a path (848)
* ENH: Add default path patterns to derivatives.json (605)
* ENH: Rename statsmodels contrasts if they cannot be uniquely identified downstream (861)
* ENH: Make intercept-only first level models throw a NotImplementedError (854)
* ENH: Update config to support microscopy, qMRI, PET, ASL (840)
* TEST: Add bids-examples submodule and bids_examples pytest fixture (842)
* TEST: Add tests for default path patterns (846)
* TEST: Update bids-examples and remove expected failing tests (845)
* MNT: Update git submodules (874)
* MNT: Add workflow top automatically update submodule (870)
* MNT: Remove deprecated no dot config (841)
* CI: Upgrade several GitHub actions to v3 (867)
* CI: Add cron jobs to avoid sneaky failures during low activity periods (860)

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Bug-fix release in the 0.15.x series.

* RF/FIX: Decompose filter construction for special queries and lists (826)
* ENH: Relax group_by rules, allowing any entity to be used (829)
* MNT: Replace deprecated DataFrame.append call (833)
* DOC: Fresh rerun of entire pybids_tutorial.ipynb (832)

* FIX: Clarify exception message (806)
* FIX: Catch UnicodeDecodeErrors along with JSONDecodeErrors for better reporting (796)
* FIX: Accept paths/strings for layout configuration files (799)
* ENH: Add __main__ to allow ``python -m bids`` to run CLI (794)

-------------------------------
Bug-fix release in the 0.14.x series.

* RF/FIX: Decompose filter construction for special queries and lists (826)

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New feature release in the 0.14.x series.

This release includes a significant refactor of BIDS Statistical Models,
replacing the ``bids.analysis`` module with ``bids.modeling``.

Changes to ``bids.layout`` are minimal, and we do not anticipate API breakage.

* FIX: LGTM.com warning: Implicit string concatenation in a list (785)
* FIX: Take the intersection of variables and Model.X,
ignoring missing variables (usually contrasts) (764)
* FIX: Associate "is_metadata" with Tag, not Entity; and only return
non-metadata entries for core Entities in ``get(return_type='id')`` (749)
* FIX: Only include regressors if they are TSV (752)
* FIX: ensure force_dense=True runs to_dense only on sparse variables (745)
* FIX: get unique, with conflicting meta-data (748)
* FIX: Clean up some deprecation and syntax warnings (738)
* ENH: Add ``pybids upgrade`` command (654)
* ENH: Add Lag transformation (759)
* ENH: Use indirect transformations structure (737)
* ENH: Add visualization for statsmodel graph (742)
* ENH: Permit explicit intercept (1) in Contrasts and DummyContrasts (743)
* ENH: Add meta-analysis model type (731)
* ENH: Contrast type is now test (733)
* REF: Use pathlib.Path internally when possible (746)
* REF: Remove group_by from edges and add filter (734)
* REF: Improved/refactored StatsModels module (722)
* MNT: Make sure codespell skips .git when run locally (787)
* MNT: LGTM.com recommendations (786)
* MNT: Better codespell configuration (782)
* MNT: Constrain formulaic version to 0.2.x . (784)
* MNT: Update versioneer: 0.18 → 0.20 (778)
* MNT: Add "codespell" tool to CI checks to catch typos sooner (776)
* MNT: Disable bids-nodot mode (769)
* MNT: Send codecov reports again (766)
* MNT: Set minimum version to Python 3.6 (739)