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Changelog

Source: NEWS.md

bidser 0.5.0

  • Windows: normalize project and resolved paths with forward slashes (winslash = "/") so full paths returned by query_files(full_path = TRUE), func_scans(), n_volumes(), and resolve_bids_uri() use a consistent separator instead of mixing \ and /. Fixes several R CMD check test failures on Windows.

  • Make query_files() reuse the index built when the project was constructed instead of re-scanning the filesystem on every call. Repeated queries are now roughly two orders of magnitude faster (an indexed lookup rather than a full stat of the dataset on each query). The default query surface is a snapshot; use refresh = TRUE to re-scan the manifest and pick up additions, content changes, and removals without rebuilding the project object. query_files() also now honours index = "none" and prefers each project’s own construction-time snapshot, so two project objects sharing a path no longer perturb each other’s query results.

  • Build the query manifest from a direct filesystem path scan instead of only the parsed data tree. This keeps bidser’s tree-focused accessors intact while making query_files() and broad search_files() see pybids-visible layout files such as README, CHANGES, dataset_description.json, participants.tsv, *_scans.tsv, JSON sidecars, root .bval/.bvec files, and extensionless files under subject datatypes. On ds005, the raw file-count parity surface is now 142/142 against vendored pybids.

  • Make indexed query_files() honour strict = TRUE for missing entity filters, so broad subject/task queries do not accidentally include root layout files.

  • Fix wildcard entity filters such as task = ".*" in fallback/no-index query_files() calls so they match indexed query semantics, and remove the unused tree-derived manifest builder left behind by the filesystem-backed manifest path.

  • Fix require_entity = TRUE being silently ignored on the indexed query_files() path when an entity filter used the .* wildcard (e.g. task = ".*"). It now requires the entity to be present as documented, matching the non-indexed path, so entity-less files (such as anatomical scans, which lack task) are correctly excluded.

  • Add raw DWI files as a built-in datatype, so bids_project() and query_files() index dwi/ files (.nii.gz, .nii, .json, .bval, .bvec) without user-side register_datatype() setup.

  • Speed up index construction by deriving manifest/sidecar entities directly from paths and by lazily ingesting JSON sidecar contents only when metadata APIs need them. This keeps query-oriented project construction focused on the file manifest while preserving indexed metadata inheritance on demand.

  • Speed up bids_project() construction by replacing generic tree/table conversions and repeated tree searches with leaf-specific extractors, by using vectorized manifest row construction, and by trimming parser/directory-listing overhead in constructor hot paths.

  • Further speed up indexed query_files() by avoiding per-query manifest re-finalization and by applying indexed filters with a single logical mask.

  • Add tools/benchmark-pybids-parity.R, a repeatable local harness for comparing bidser construction/query timings and basic file-count parity against the vendored pybids checkout via uv.

bidser 0.4.0

  • Add bids_entities() for vectorized path-to-entity parsing, returning one typed tibble row per path.
  • Add n_volumes() for reading functional scan volume counts from NIfTI headers, with a bids_project method for raw or preprocessed scan discovery.
  • Make search_files() fall back to a filesystem regex scan when the parsed BIDS tree has no match, so ad hoc regex searches can find valid but currently unparsed files such as masks.
  • Expose common filtering arguments on the read_events() and read_confounds() generics, and have read_events() return bare metadata aliases alongside the legacy dotted columns.
  • Change confound_set("dvars") to select only std_dvars, with explicit std_dvars, raw_dvars, non_std_dvars, and vx_wisestd_dvars selectors for callers that want a specific variant.
  • Add confound_set("legacy_default"), a public, version-robust handle for the 26 canonical confound names historically exposed only as the unexported bidser:::DEFAULT_CVARS2. Code that depended on bidser:::DEFAULT_CVARS2 should switch to confound_set("legacy_default"), which returns the identical set. DEFAULT_CVARS2 is retained (unexported) for now but is superseded.
  • Express the read_confounds() cvars default via confound_set("legacy_default") and remove the internal DEFAULT_CVARS constant. The default now resolves through canonical confound names; the set of columns returned for a no-cvars call is unchanged in practice on fMRIPrep outputs. ?read_confounds now documents the recommended modern default confound_strategy("pcabasic80") (noting it is not equivalent to the legacy default) and cross-references the confound_set()/confound_strategy()/list_confound_sets()/ list_confound_strategies() helpers.
  • Change read_preproc_scans() to return a file-ordered list of NeuroVec objects, one per matched preprocessed scan, instead of collapsing multiple files into a single container.
  • Fix derivative discovery and legacy fMRIPrep helpers for datasets that place derivative subject folders directly under derivatives/ with prep_dir = "derivatives".
  • Make read_confounds() raise informative, selection-aware errors when no matching participants, confound files, or usable requested confounds are found.
  • Add run-level confound diagnostics and cleaning via check_confounds(), clean_confounds(), and read_confounds(..., clean = ), with zero-variance confounds dropped by default and recorded in a confound_diagnostics attribute.
  • Fix create_preproc_mask() to ignore matching JSON sidecars and only read actual NIfTI mask images.
  • Add query_files() as the recommended explicit query API for new workflows, with match_mode, require_entity, and raw/derivatives scope controls.
  • Add get_metadata() for inheritance-aware BIDS metadata resolution with deterministic nearest-sidecar precedence.
  • Extend read_sidecar() with inheritance-aware resolution via inherit and inherit_scope.
  • Add permissive bids_project(..., strict_participants = FALSE) loading for datasets that omit participants.tsv, while keeping compliance reporting explicit.
  • Add derivative discovery via bids_project(..., derivatives = "auto") and derivative_pipelines(), while preserving legacy fmriprep helpers when an fMRIPrep pipeline is present.
  • Add persistent file indexing with bids_index() and indexed query_files() lookups.
  • Add variables_table() and bids_report_data() / bids_report() for tidy run-level inventory and lightweight dataset reporting.
  • Expand acceptance coverage for metadata inheritance, missing-sidecar cases, conflict handling, and derivative-scope behavior.
  • Keep search_files() available for backward compatibility while steering new examples and docs toward query_files().

bidser 0.3.0

  • Fix load_all_events() and read_events() to use tab delimiter for BIDS TSV event files instead of space delimiter.
  • Fix read_sidecar() to handle JSON sidecars containing vector-valued fields (e.g. SliceTiming) by storing them as list-columns instead of failing with a “differing number of rows” error.

bidser 0.2.0

CRAN release: 2026-02-19

  • TBD.

bidser 0.1.0

  • Initial CRAN release.
  • Read, validate, and query BIDS-compliant neuroimaging projects.
  • Support for fMRIPrep derivatives including confound tables, preprocessed scans, and brain masks.
  • Mock BIDS project creation for testing (create_mock_bids()).
  • Confound processing with PCA reduction and canonical variable aliasing.
  • Visualization of PCA confound scores and loadings (plot.bids_confounds()).
  • Search and filter BIDS files by subject, session, task, run, space, and other entities.