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23441de
Initial notes taken and extended from https://github.com/bids-standar…
yarikoptic Mar 16, 2026
e6a414c
Clarifications and "deduplicate" as the mode
yarikoptic Mar 16, 2026
924dbbe
note that we need to adjust participants.tsv
yarikoptic Mar 17, 2026
8ce518b
add "audit" idea
yarikoptic Mar 18, 2026
edfbef9
clarification on potential trickiness in 'aggregate'
yarikoptic Mar 18, 2026
a40008a
Initialize spec-kit workflow with project constitution
yarikoptic Mar 21, 2026
f83736c
Clarify ecosystem relationships: PyBIDS adoption bar, bids2table, val…
yarikoptic Mar 21, 2026
ee60e74
mention rename-tool
yarikoptic Apr 2, 2026
efacca6
Add SemVer, DRY with duplication tooling, and automated releases to c…
yarikoptic Apr 2, 2026
3df1a53
[DATALAD RUNCMD] /speckit.constitution - clarify a little
yarikoptic Apr 2, 2026
888a641
Apply suggestions from code review
yarikoptic Apr 2, 2026
57d11df
[DATALAD RUNCMD] /speckit.specify ...
yarikoptic Apr 3, 2026
526163c
Reviewed/adjusted a few aspects of user stories
yarikoptic Apr 3, 2026
216e9b1
[DATALAD RUNCMD] yolo '/speckit.clarify - in prior commit...
yarikoptic Apr 3, 2026
4963045
some notes on the user stories
yarikoptic Apr 3, 2026
065efa2
[DATALAD RUNCMD] yolo '/speckit.clarify - in prior commit...
yarikoptic Apr 3, 2026
a9333c9
pointer to file-mapper @Lestropie mentioned
yarikoptic Apr 3, 2026
73fad0d
[DATALAD RUNCMD] /speckit.plan ...
yarikoptic Apr 4, 2026
95288bd
[DATALAD RUNCMD] yolo /speckit.tasks
yarikoptic Apr 4, 2026
a4cd9ab
Implement bids-utils: library + CLI for BIDS dataset manipulation
yarikoptic Apr 4, 2026
ba393a4
Fix lint/type/duplication failures; add pre-commit tox gate
yarikoptic Apr 4, 2026
0070482
fix: register CLI subcommands so they appear in --help
yarikoptic Apr 4, 2026
f8cb41a
gitignore uv.lock and .duct for now
yarikoptic Apr 4, 2026
4d8a240
Address speckit-analyze findings: tests, prompts, honest task marks
yarikoptic Apr 5, 2026
7fa7213
Broaden integration tests to cover non-MRI datasets; add skip reasons
yarikoptic Apr 7, 2026
65b19f8
Include exception message in integration test skip reasons
yarikoptic Apr 7, 2026
25fb67e
[DATALAD RUNCMD] yolo '/speckit.clarify there should be e...
yarikoptic Apr 7, 2026
0daa94c
[DATALAD RUNCMD] yolo /speckit.tasks
yarikoptic Apr 7, 2026
29bbfd5
[DATALAD RUNCMD] yolo -p '/speckit.implement T034 T035 —...
yarikoptic Apr 7, 2026
4b18c77
[DATALAD RUNCMD] yolo -p '/speckit.implement T054 T061 T0...
yarikoptic Apr 7, 2026
12e1ab3
[DATALAD RUNCMD] yolo -p /speckit.implement
yarikoptic Apr 7, 2026
d9a88f8
speckit.analyze: remediate spec gaps and inconsistencies
yarikoptic Apr 7, 2026
e657885
Implement shell completion (Phase 11: T083-T085)
yarikoptic Apr 10, 2026
b713dae
spec: add FR-022 — annexed content handling with --annexed option
yarikoptic Apr 10, 2026
e90e7ad
Implement annexed content handling (Phase 1b: T086-T091, FR-022)
yarikoptic Apr 10, 2026
f3824b9
Fix symlink bug, add --dry-run=detailed, annex logging (Phase 1c: T09…
yarikoptic Apr 10, 2026
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6 changes: 6 additions & 0 deletions .autorc
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"plugins": ["git-tag", "conventional-commits"],
"owner": "bids-standard",
"repo": "bids-utils",
"name": "bids-utils"
}
34 changes: 34 additions & 0 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
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name: CI

on:
push:
branches: [main]
pull_request:
branches: [main]

jobs:
test:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.10", "3.11", "3.12", "3.13"]

steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0

- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install uv
uses: astral-sh/setup-uv@v4

- name: Install CI dependencies
run: uv pip install --system -e ".[ci]"

- name: Run tox
run: tox
39 changes: 39 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
# Python
__pycache__/
*.pyc
*.pyo
*.egg-info/
dist/
build/
*.egg

# Virtual environments
.venv/
venv/
venvs/

# Testing
.tox/
.pytest_cache/
.coverage
htmlcov/
coverage.xml

# IDE
.vscode/
.idea/
*.swp
*.swo

# OS
.DS_Store
Thumbs.db

# npm (never commit)
.npm/

# Environment
.env
.env.*
uv.lock
.duct
3 changes: 3 additions & 0 deletions .gitmodules
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
[submodule "bids-examples"]
path = bids-examples
url = https://github.com/bids-standard/bids-examples.git
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