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Merge remote-tracking branch 'upstream/main' into dev
2 parents 7cba507 + ed14a14 commit 9734fba

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‎.git-blame-ignore-revs‎

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# Tue Mar 25 15:43:26 2025 -0400 - [email protected] - chore(fmt): deno fmt [ignore-rev]
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51510f5ecd91027f6ab4bfd1d0d287aaf6300e8d
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# Wed Aug 28 11:37:33 2024 -0400 - [email protected] - chore(fmt): deno fmt [ignore-rev]
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ff6015b9b2d9b1f215905d71e7dc7a14b8f29f56
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# Fri Aug 16 17:23:33 2024 -0400 - [email protected] - chore(fmt): deno fmt [ignore-rev]

‎.github/scripts/scriv_check.sh‎

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#!/usr/bin/env bash
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# Modified from https://github.com/tarides/changelog-check-action/tree/main
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set -uo pipefail
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if [ "${NO_CHANGELOG_LABEL}" = "true" ]; then
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# 'no changelog' set, so finish successfully
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exit 0
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else
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# a changelog check is required
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# fail if the diff is empty
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if git diff --exit-code "origin/${BASE_REF}" -- "changelog.d/"; then
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cat <<END >&2
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User-visible changes should come with an entry in the changelog.
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Create a changelog blurb with "uvx scriv create --edit".
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If no changelog entry is needed, then set the "no changelog" label.
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END
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exit 1
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fi
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fi

‎.github/workflows/deno_tests.yml‎

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run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --deny-net' >> $GITHUB_ENV
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if: ${{ ! matrix.allow-net }}
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- name: Disable example that requires network access
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run: touch tests/data/bids-examples/xeeg_hed_score/.SKIP_VALIDATION
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run: |
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for DS in eeg_ds003645s_hed_library xeeg_hed_score; do
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touch tests/data/bids-examples/${DS}/.SKIP_VALIDATION
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done
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if: ${{ ! matrix.allow-net }}
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- name: Disable unreleased examples
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run: touch tests/data/bids-examples/dwi_deriv/.SKIP_VALIDATION
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run: |
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for DS in dwi_deriv pheno004; do
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touch tests/data/bids-examples/${DS}/.SKIP_VALIDATION
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done
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if: github.ref_name != 'dev' && github.base_ref != 'dev'
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- run: deno test --node-modules-dir=auto $PERMS --coverage=cov/ src/
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- name: Collect coverage

‎.github/workflows/validation.yml‎

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python-version: 3
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- name: Validate CITATION.cff
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run: pipx run cffconvert --validate
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check_change_log:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Check for changes in changelog
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env:
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BASE_REF: ${{ github.event.pull_request.base.ref }}
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NO_CHANGELOG_LABEL: ${{ contains(github.event.pull_request.labels.*.name, 'no changelog') }}
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run: .github/scripts/scriv_check.sh
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shell: bash

‎.github/workflows/wheels.yml‎

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name: Build wheels
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on:
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push:
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branches: [main, dev]
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tags: ['*']
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pull_request:
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branches: [main, dev]
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workflow_dispatch:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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MACOSX_DEPLOYMENT_TARGET: '10.12'
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defaults:
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run:
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shell: bash
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jobs:
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build_sdist:
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name: Build & verify package
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runs-on: ubuntu-latest
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permissions:
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attestations: write
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id-token: write
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: hynek/build-and-inspect-python-package@v2
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with:
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attest-build-provenance-github: ${{ github.event_name != 'pull_request' }}
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skip-wheel: true
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build_wheels:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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needs: [build_sdist]
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strategy:
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matrix:
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os:
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- ubuntu-latest
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- ubuntu-24.04-arm
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- windows-latest
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- macos-13
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- macos-latest
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fail-fast: false
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permissions:
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attestations: write
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id-token: write
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steps:
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- name: Download sdist
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uses: actions/download-artifact@v4
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with:
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name: Packages
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path: dist
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- name: Unpack sdist
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run: |
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tar --strip-components=1 -xzvf dist/*.tar.gz
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rm -r dist
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- name: Build wheels from sdist
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uses: pypa/[email protected]
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- name: Generate artifact attestation for wheels
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if: ${{ github.event_name != 'pull_request' }}
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uses: actions/attest-build-provenance@c074443f1aee8d4aeeae555aebba3282517141b2 # v2.2.3
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with:
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subject-path: "wheelhouse/bids_validator_deno-*.whl"
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- uses: actions/upload-artifact@v4
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with:
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name: wheel-${{ matrix.os }}
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path: ./wheelhouse
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test-publish:
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name: Push package to test.pypi.org
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if: github.event_name == 'push'
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runs-on: ubuntu-latest
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needs: [build_wheels]
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permissions:
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id-token: write
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steps:
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- name: Download sdist
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uses: actions/download-artifact@v4
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with:
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name: Packages
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path: dist
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- name: Download wheels
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uses: actions/download-artifact@v4
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with:
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pattern: wheel-*
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path: dist
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- run: |
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mv dist/*/* dist/
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rmdir dist/*/
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- name: Upload package to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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repository-url: https://test.pypi.org/legacy/
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skip-existing: true
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publish:
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name: Publish released package to pypi.org
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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runs-on: ubuntu-latest
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needs: [build_wheels]
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permissions:
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id-token: write
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steps:
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- name: Download sdist
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uses: actions/download-artifact@v4
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with:
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name: Packages
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path: dist
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- name: Download wheels
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uses: actions/download-artifact@v4
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with:
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pattern: wheel-*
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path: dist
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- run: |
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mv dist/*/* dist/
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rmdir dist/*/
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- name: Upload package to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎CHANGELOG.md‎

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<a id='changelog-2.0.4'></a>
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# 2.0.5 — 2025-03-31
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A hot-fix release that adds missing entries to the 2.0.4 changelog and fixes publication to PyPI.
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<a id='changelog-2.0.4'></a>
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# 2.0.4 — 2025-03-31
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## Added
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- Validate directory names names according to `schema.rules.directories` entries.
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Use rules to identify "opaque" directories whose contents are unspecified by BIDS.
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([#180])
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[#180]: https://github.com/bids-standard/bids-validator/pull/180
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- Report field descriptions for missing or invalid metadata. ([#177])
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[#177]: https://github.com/bids-standard/bids-validator/pull/177
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- Publish validator to PyPI as `bids-validator-deno`. ([#186])
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[#186]: https://github.com/bids-standard/bids-validator/pull/186
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## Changed
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- Update to HED Validator 4.0.0. ([#173])
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[#173]: https://github.com/bids-standard/bids-validator/pull/173
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<a id='changelog-2.0.3'></a>
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# 2.0.3 — 2025-02-24

‎README.md‎

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```
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Deno by default sandboxes applications like a web browser.
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`-E`, `-R`, '-W', and `-N` allow the validator to read environment variables,
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`-E`, `-R`, `-W`, and `-N` allow the validator to read environment variables,
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read/write local files, and read network locations.
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A pre-compiled binary is published to [PyPI][] and may be installed with:
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```
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pip install bids-validator-deno
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bids-validator-deno --help
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```
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### Configuration file
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The schema validator accepts a JSON configuration file that reclassifies issues as
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[BIDS Validator]: https://bids-standard.github.io/bids-validator/
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[Deno]: https://deno.com/
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[Deno - Installation]: https://docs.deno.com/runtime/getting_started/installation/
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[PyPI]: https://pypi.org/project/bids-validator-deno/

‎changelog.d/scriv.ini‎

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[scriv]
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format = md
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main_branches = master, main, dev
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version = literal: deno.json: version
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version = command: jq .version deno.json
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categories = Added, Changed, Fixed, Deprecated, Removed, Security, Infrastructure

‎deno.json‎

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"@bids/schema": "jsr:@bids/[email protected]+1a202531",
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"@cliffy/command": "jsr:@effigies/[email protected]",
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"@cliffy/table": "jsr:@effigies/[email protected]",
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"@hed/validator": "npm:hed-validator@3.15.5",
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"@hed/validator": "npm:hed-validator@4.0.1",
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"@ignore": "npm:[email protected]",
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"@libs/xml": "jsr:@libs/[email protected]",
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"@mango/nifti": "npm:@bids/[email protected]",
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"@std/assert": "jsr:@std/[email protected].7",
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"@std/fmt": "jsr:@std/[email protected].5",
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"@std/fs": "jsr:@std/[email protected].13",
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"@std/assert": "jsr:@std/[email protected].12",
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"@std/fmt": "jsr:@std/[email protected].6",
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"@std/fs": "jsr:@std/[email protected].15",
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"@std/io": "jsr:@std/[email protected]",
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"@std/log": "jsr:@std/[email protected]",
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"@std/path": "jsr:@std/[email protected]",

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