Harden datatype/derivatives extraction in filename parser

[gdevenyi]

Stacked on #27 (base align-bids-nomenclature). Fixes latent/fragile parsing in _libBIDSsh_parse_filename surfaced during the #21 review.

Bugs

_libBIDSsh_parse_filename derived the datatype and the derivatives pipeline with substring greps piped through head/awk:

1. Substring false-match (correctness). grep -oE "(anat|…|func|…)" matched the datatype anywhere in the path. A dataset path like study_func_proj/sub-01/anat/sub-01_T1w.nii.gz was reported as datatype=func instead of anat. The same flaw let myderivatives/… be read as a derivatives dataset.
2. SIGPIPE fragility. grep … | head -1 || echo "NA" can have grep killed by SIGPIPE when head closes the pipe; under set -o pipefail the pipeline reports failure and silently falls back to NA.

Fix

Anchored bash regex on the path — no subshells, no pipes, deterministic:

• datatype = file's immediate parent directory, matched as a whole component (^|/)<datatype>$;
• derivatives pipeline = component right after (^|/)derivatives/.

generate_entity_patterns.sh now emits the anchored datatype regex so the generated block stays in sync.

Tests

New test_parse_filename_datatype_derivatives covers: the func-substring false-match, emg detection, missing-datatype → NA, derivatives extraction, and the myderivatives non-match.

Verification

• bash -n + shellcheck clean on all three files.
• ./test_libBIDS.sh → 9/9 pass.
• Repro now returns datatype=anat.
• Real dataset ds000117 still extracts meg_derivatives / meg; ds001 datatype distribution unchanged (32 anat / 96 func).

🤖 Generated with Claude Code

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[Copilot]

Pull request overview

This PR hardens _libBIDSsh_parse_filename so datatype and derivatives are extracted from whole path components (avoiding substring false-matches) and avoids grep|head SIGPIPE fragility under set -o pipefail.

Changes:

• Replace substring/pipe-based datatype + derivatives parsing with anchored bash-regex extraction.
• Update generate_entity_patterns.sh to emit the anchored datatype regex for keeping generated blocks in sync.
• Add a focused regression test covering substring false-matches, emg, missing datatype → NA, derivatives extraction, and non-match for myderivatives.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
libBIDS.sh	Switches datatype/derivatives extraction to anchored bash regex matching.
generate_entity_patterns.sh	Emits anchored datatype regex intended for _libBIDSsh_parse_filename.
test_libBIDS.sh	Adds regression tests for datatype/derivatives extraction edge cases.

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