diff --git a/.all-contributorsrc b/.all-contributorsrc index 27f1209d73..7d85506d8a 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -192,6 +192,13 @@ "login": "ali_khan", "name": "Ali Khan" }, + { + "contributions": [ + "tool" + ], + "login": "alizee_wickenheiser", + "name": "Alizee Wickenheiser" + }, { "contributions": [ "userTesting" @@ -443,6 +450,14 @@ "login": "carlo_miniussi", "name": "Carlo Miniussi" }, + { + "contributions": [ + "data", + "tool" + ], + "login": "cecile_madjar", + "name": "Cecile Madjar" + }, { "contributions": [ "doc" @@ -1002,7 +1017,8 @@ "tool", "eventOrganizing", "fundingFinding", - "infra" + "infra", + "talk" ], "login": "francopestilli", "name": "Franco Pestilli", @@ -1461,6 +1477,13 @@ "name": "Jeanette Mumford", "profile": "https://jeanettemumford.org/" }, + { + "contributions": [ + "tool" + ], + "login": "jefferson_casimir", + "name": "Jefferson Casimir" + }, { "contributions": [ "doc" @@ -1799,6 +1822,13 @@ "name": "Kurt Schilling", "profile": "https://github.com/schillkg" }, + { + "contributions": [ + "tool" + ], + "login": "laetitia_fesselier", + "name": "Laetitia Fesselier" + }, { "contributions": [ "financial" @@ -2728,6 +2758,17 @@ "login": "stephan_bickel", "name": "Stephan Bickel" }, + { + "contributions": [ + "bug", + "code", + "question", + "tool", + "userTesting" + ], + "login": "smeisler", + "name": "Steven Meisler" + }, { "avatar_url": "https://avatars.githubusercontent.com/u/11152799?v=4", "contributions": [ @@ -2987,6 +3028,14 @@ "name": "Tristan Glatard", "profile": "https://github.com/glatard" }, + { + "contributions": [ + "data", + "tool" + ], + "login": "tyler_collins", + "name": "Tyler Collins" + }, { "contributions": [ "doc" @@ -3091,7 +3140,14 @@ "tool", "question", "bug", - "code" + "code", + "data", + "fundingFinding", + "ideas", + "plugin", + "review", + "userTesting", + "infra" ], "login": "yarikoptic", "name": "Yaroslav O. Halchenko", diff --git a/.circleci/config.yml b/.circleci/config.yml index 9e6b41fa62..ee82d5b003 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,7 +2,7 @@ version: 2.1 jobs: build_docs: docker: - - image: cimg/python:3.8 + - image: cimg/python:3.12-node steps: # checkout code to default ~/project - checkout @@ -21,14 +21,15 @@ jobs: - persist_to_workspace: # the mkdocs build outputs are in ~/project/site root: ~/project - paths: site + paths: + - site - store_artifacts: path: ~/project/site/ destination: dev_docs check_links: docker: - - image: cimg/python:3.8 + - image: cimg/python:3.12 steps: # checkout code to default ~/project - checkout @@ -131,7 +132,8 @@ jobs: - persist_to_workspace: # raw generated changelog in ~/changelog_build/CHANGES.md root: ~/. - paths: changelog_build + paths: + - changelog_build # Lint and fix the auto generated changes.md file lint_generated_changelog: @@ -164,7 +166,8 @@ jobs: - persist_to_workspace: # linted and fixed changelog in ~/changelog_build/CHANGES.md root: ~/. - paths: changelog_build + paths: + - changelog_build # Push built changelog to repo commit_generated_changelog: @@ -178,7 +181,7 @@ jobs: - attach_workspace: # fixed+linted changelog in ~/changelog_build/CHANGES.md at: ~/. - - deploy: + - run: name: Changelog deployment # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI command: | @@ -197,7 +200,6 @@ jobs: fi workflows: - version: 2 search_build: jobs: - build_docs diff --git a/.codespellrc b/.codespellrc index 4092a9a7bf..22cd48ca96 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,6 +1,6 @@ [codespell] skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build -ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn +ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel builtin = clear,rare,en-GB_to_en-US # this overloads default dictionaries and I have not yet figured out # how to have multiple https://github.com/codespell-project/codespell/issues/2727 diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml index 8188370cdd..6cf4dbcd4c 100644 --- a/.github/workflows/schemacode_ci.yml +++ b/.github/workflows/schemacode_ci.yml @@ -26,8 +26,8 @@ jobs: os: ["ubuntu-latest"] python-version: ["3.11"] steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: "Install build dependencies" @@ -44,7 +44,7 @@ jobs: run: python -m build tools/schemacode - name: "Check distribution metadata" run: twine check tools/schemacode/dist/* - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: dist path: tools/schemacode/dist/ @@ -56,7 +56,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] include: - os: macos-latest python-version: 3 @@ -64,18 +64,19 @@ jobs: python-version: 3 name: ${{ matrix.os }} with Python ${{ matrix.python-version }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: "Set up Python" - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + allow-prereleases: true - name: "Display Python version" run: python -c "import sys; print(sys.version)" - name: "Fetch packages" - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: dist path: dist/ @@ -90,7 +91,7 @@ jobs: --cov-append --cov-report=xml --cov=bidsschematools --doctest-modules - name: Upload artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: unit_${{ matrix.os }}_${{ matrix.python-version }} path: coverage.xml @@ -107,7 +108,7 @@ jobs: python-version: ["3.11"] steps: - name: "Fetch packages" - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: dist path: dist/ @@ -129,12 +130,12 @@ jobs: runs-on: ubuntu-latest name: Validate schema steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set Up Python environment - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: "3.9" + python-version: "3.11" - name: Install the schemacode package run: | @@ -145,7 +146,7 @@ jobs: run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools - name: Upload artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: schema_validation path: coverage.xml @@ -157,13 +158,13 @@ jobs: needs: [test, validate_schema] steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Download artifacts - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 - name: Upload to CodeCov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} # not required but might help API rate limits fail_ci_if_error: true diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml index 8e48d85bb6..5be42a5b18 100644 --- a/.github/workflows/validation.yml +++ b/.github/workflows/validation.yml @@ -16,15 +16,15 @@ jobs: codespell: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: codespell-project/actions-codespell@master # Markdown formatting remark: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-node@v3 + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 with: node-version: 14 - name: Install dependencies @@ -36,8 +36,8 @@ jobs: yamllint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: 3 - name: Install dependencies @@ -49,8 +49,8 @@ jobs: python-style: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: 3 - run: python -m pip install --upgrade flake8 black isort[colors] @@ -63,8 +63,8 @@ jobs: latin-phrases: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: 3 - name: Install dependencies @@ -86,8 +86,8 @@ jobs: validate_cff: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: 3 - name: Install dependencies diff --git a/.gitignore b/.gitignore index 59fa1a1de3..9e8cf66a91 100644 --- a/.gitignore +++ b/.gitignore @@ -7,6 +7,7 @@ venvs pdf_build_src/bids-spec.pdf pdf_build_src/bids-spec_pandoc_log.json pdf_build_src/src_copy +pdf_build_src/tests/data/output # JS/NPM package-lock.json diff --git a/.lgtm.yml b/.lgtm.yml deleted file mode 100644 index 0734210407..0000000000 --- a/.lgtm.yml +++ /dev/null @@ -1,8 +0,0 @@ ---- -# This file contains configuration for the LGTM tool: https://lgtm.com/ -# The bids-specification repository is continuously scanned by the LGTM tool -# for any security and/or code vulnerabilities. You can find the alert here: -# https://lgtm.com/projects/g/bids-standard/bids-specification/ -queries: - # https://lgtm.com/rules/6770079/ - - exclude: py/unused-import diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a825e940d9..fcf475045e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,7 +3,7 @@ exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json' repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v4.6.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer @@ -13,7 +13,7 @@ repos: - id: check-added-large-files - id: check-case-conflict - repo: https://github.com/psf/black - rev: 23.7.0 + rev: 24.3.0 hooks: - id: black files: ^tools/(?!schemacode) @@ -23,7 +23,7 @@ repos: files: tools/schemacode args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"] - repo: https://github.com/pyCQA/isort - rev: 5.12.0 + rev: 5.13.2 hooks: - id: isort files: ^tools/(?!schemacode) @@ -33,22 +33,23 @@ repos: files: tools/schemacode args: ["--settings-file", "tools/schemacode/pyproject.toml"] - repo: https://github.com/pyCQA/flake8 - rev: 6.1.0 + rev: 7.0.0 hooks: - id: flake8 args: [--config=tools/schemacode/setup.cfg] - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.2 + rev: v4.0.0-alpha.8 hooks: - id: prettier + entry: env PRETTIER_LEGACY_CLI=1 prettier # temporary fix for https://github.com/prettier/prettier/issues/15742 files: src/schema/.*/.*\.yaml - repo: https://github.com/codespell-project/codespell - rev: v2.2.5 + rev: v2.2.6 hooks: - id: codespell args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"] - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.5.1 + rev: v1.9.0 hooks: - id: mypy # Sync with project.optional-dependencies.typing diff --git a/.remarkrc b/.remarkrc index fc065759c2..8d6c26487a 100644 --- a/.remarkrc +++ b/.remarkrc @@ -10,6 +10,7 @@ ["lint-maximum-heading-length", false], ["lint-no-shortcut-reference-link", false], ["lint-no-trailing-spaces"], + ["remark-lint-code-block-style", false], ["lint-no-undefined-references", false] ] } diff --git a/.tributors b/.tributors index b325271c22..fa5b1a18f2 100644 --- a/.tributors +++ b/.tributors @@ -174,6 +174,14 @@ ], "name": "Ali Khan" }, + "alizee_wickenheiser": { + "affiliation": "LORIS, MCIN, Montreal Neurological Institute, McGill University", + "contributions": [ + "tool" + ], + "email": "alizee.wickenheiser@mcin.ca", + "name": "Alizee Wickenheiser" + }, "ana_fouto": { "contributions": [ "userTesting" @@ -407,6 +415,15 @@ "name": "Carlo Miniussi", "orcid": "0000-0002-5436-4745" }, + "cecile_madjar": { + "affiliation": "LORIS, MCIN, Montreal Neurological Institute, McGill University", + "contributions": [ + "data", + "tool" + ], + "email": "cecile.madjar@mcin.ca", + "name": "Cecile Madjar" + }, "chloé_pasturel": { "contributions": [ "doc" @@ -953,7 +970,8 @@ "tool", "eventOrganizing", "fundingFinding", - "infra" + "infra", + "talk" ], "name": "Franco Pestilli" }, @@ -1401,6 +1419,14 @@ "name": "Jeanette Mumford", "publish_email": false }, + "jefferson_casimir": { + "affiliation": "LORIS, MCIN, Montreal Neurological Institute, McGill University", + "contributions": [ + "tool" + ], + "email": "jefferson.casimir@mcin.ca", + "name": "Jefferson Casimir" + }, "jeffrey_g_ojemann": { "contributions": [ "doc" @@ -1737,6 +1763,14 @@ ], "name": "Kurt Schilling" }, + "laetitia_fesselier": { + "affiliation": "LORIS, MCIN, Montreal Neurological Institute, McGill University", + "contributions": [ + "tool" + ], + "email": "laetitia.fesselier@mcin.ca", + "name": "Laetitia Fesselier" + }, "laura_and_john_arnold_foundation": { "contributions": [ "financial" @@ -2649,6 +2683,20 @@ ], "name": "Stephan Bickel" }, + "smeisler": { + "affiliation": "Program in Speech and Hearing Bioscience and Technology, Harvard University", + "contributions": [ + "bug", + "code", + "question", + "tool", + "userTesting" + ], + "email": "smeisler@g.harvard.edu", + "github": "smeisler", + "name": "Steven Meisler", + "orcid": "0000-0002-8888-1572" + }, "suyashdb": { "blog": "https://www.linkedin.com/in/suyashb/", "contributions": [ @@ -2907,6 +2955,15 @@ "name": "Tristan Glatard", "orcid": "0000-0003-2620-5883" }, + "tyler_collins": { + "affiliation": "BrockU, LORIS, MCIN, Montreal Neurological Institute, McGill University", + "contributions": [ + "data", + "tool" + ], + "email": "tyler.collins@mcin.ca", + "name": "Tyler Collins" + }, "ulrike_bingel": { "contributions": [ "doc" @@ -3006,7 +3063,14 @@ "tool", "question", "bug", - "code" + "code", + "data", + "fundingFinding", + "ideas", + "plugin", + "review", + "userTesting", + "infra" ], "email": "debian@onerussian.com", "name": "Yaroslav O. Halchenko", diff --git a/CITATION.cff b/CITATION.cff index ef9976621b..23f53ad4bd 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,22 +2,30 @@ cff-version: 1.2.0 -title: bids-specification +title: The Brain Imaging Data Structure (BIDS) Specification -abstract: - The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to - organize and describe data. +abstract: >- + The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to organize and describe data. -version: v1.8.1-dev +version: 1.10.0-dev license: CC-BY-4.0 repository-code: https://github.com/bids-standard/bids-specification -message: Please cite it as below. +message: >- + To cite the BIDS specification, please follow the instructions here: + https://bids-specification.rtfd.io/en/latest/introduction.html#citing-bids + HTML versions of the BIDS specification can be browsed following this link: + https://bids-specification.rtfd.io + PDF versions of the BIDS specification can be found in the Zenodo archives + listed under "identifiers" below in the present `CITATION.cff` file. identifiers: - - description: bids-specification + - description: PDFs of the BIDS specification for versions 1.9.0 and above + type: doi + value: 10.5281/zenodo.10175845 + - description: PDFs of the BIDS specification for versions 1.0.0 to 1.8.0 type: doi value: 10.5281/zenodo.3686061 @@ -37,24 +45,20 @@ authors: family-names: Thomas website: https://cmn.nimh.nih.gov/dsst orcid: https://orcid.org/0000-0002-2850-1419 - affiliation: - NIMH, Intramural Research Program, Bethesda, MD, 20891, United States of - America + affiliation: NIMH, Intramural Research Program, Bethesda, MD, 20891, USA email: adamt@nih.gov - given-names: Adeen family-names: Flinker website: http://flinkerlab.org orcid: https://orcid.org/0000-0003-1247-1283 - affiliation: - New York University, Department of Neurology, New York City, New York, - 10016, United States of America + affiliation: New York University, Department of Neurology, New York City, New + York, 10016, USA email: adeen@nyu.edu - given-names: Adina S. family-names: Wagner website: https://www.adina-wagner.com orcid: https://orcid.org/0000-0003-2917-3450 - affiliation: - Institute of Neuroscience and Medicine (INM-7), Research Center Juelich, + affiliation: Institute of Neuroscience and Medicine (INM-7), Research Center Juelich, Juelich, 52428, Germany email: adina.wagner@t-online.de - given-names: Agah @@ -87,9 +91,8 @@ authors: family-names: Cohen website: https://bchcohenlab.com orcid: https://orcid.org/0000-0001-6557-5866 - affiliation: - Boston Children's Hospital, Department of Neurology, Boston, 02115, United - States of America + affiliation: Boston Children's Hospital, Department of Neurology, Boston, MA, + 02115, USA email: alexander.cohen2@childrens.harvard.edu - given-names: Alexander family-names: von Lautz @@ -111,6 +114,10 @@ authors: orcid: https://orcid.org/0000-0001-5160-1402 - given-names: Ali family-names: Khan + - given-names: Alizee + family-names: Wickenheiser + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: alizee.wickenheiser@mcin.ca - given-names: Ana family-names: Fouto - given-names: Anders @@ -139,9 +146,8 @@ authors: family-names: Rokem website: https://arokem.org/ orcid: https://orcid.org/0000-0003-0679-1985 - affiliation: - University of Washington, Psychology, Seattle, WA, 98107, United States of - America + affiliation: University of Washington, Psychology, Seattle, WA, 98107, United + States of America email: arokem@uw.edu - given-names: Arjen family-names: Stolk @@ -158,9 +164,7 @@ authors: family-names: Basavaraj website: https://github.com/Arshitha orcid: https://orcid.org/0000-0002-6984-7969 - affiliation: - NIMH, Data Science and Sharing Team, Bethesda, MD, 20892, United States of - America + affiliation: NIMH, Data Science and Sharing Team, Bethesda, MD, 20892, USA email: arsh2794@gmail.com - given-names: Ashley G. family-names: Gillman @@ -197,9 +201,8 @@ authors: family-names: Voytek website: https://www.voyteklab.com/ orcid: https://orcid.org/0000-0003-1640-2525 - affiliation: - UC San Diego, Cognitive Science and Data Science, La Jolla, CA, 92093, - United States of America + affiliation: UC San Diego, Cognitive Science and Data Science, La Jolla, CA, 92093, + USA - given-names: Brett L. family-names: Foster - given-names: Brian A. @@ -215,6 +218,10 @@ authors: family-names: Miniussi orcid: https://orcid.org/0000-0002-5436-4745 affiliation: University of Trento + - given-names: Cecile + family-names: Madjar + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: cecile.madjar@mcin.ca - given-names: Chloé family-names: Pasturel - given-names: Chris @@ -235,9 +242,8 @@ authors: family-names: Rorden website: https://www.mricro.com orcid: https://orcid.org/0000-0002-7554-6142 - affiliation: - University of South Carolina, Department of Psychology, Columbia, SC, - 29016, United States of America + affiliation: University of South Carolina, Department of Psychology, Columbia, + SC, 29016, USA email: crorden6@gmail.com - given-names: Christian family-names: Büchel @@ -245,29 +251,26 @@ authors: family-names: Horea website: http://www.chymera.eu orcid: https://orcid.org/0000-0001-7037-2449 - affiliation: Dartmouth College, PBS, Hanover, NH, United States of America + affiliation: Dartmouth College, PBS, Hanover NH/USA email: chr@chymera.eu - given-names: Christine family-names: Rogers orcid: https://orcid.org/0000-0002-9893-8448 - affiliation: - McGill Centre for Integrative Neuroscience, Montreal Neurological - Institute, Montréal, Québec, Canada + affiliation: McGill Centre for Integrative Neuroscience, Montreal Neurological + Institute email: christine.rogers@mcgill.ca - given-names: Christophe family-names: Phillips website: https://www.uliege.be/cms/c_9054334/en/directory/?uid=U016440 orcid: https://orcid.org/0000-0002-4990-425X - affiliation: - University of Liège, GIGA CRC in vivo imaging, Liège, 4000, Belgium + affiliation: University of Liège, GIGA CRC in vivo imaging, Liège, 4000, Belgium email: c.phillips@uliege.be - given-names: Christopher J. family-names: Honey website: https://www.honeylab.org orcid: https://orcid.org/0000-0002-0745-5089 - affiliation: - Johns Hopkins University, Psychological and Brain Sciences, Baltimore, MD, - 21218, United States of America + affiliation: Johns Hopkins University, Psychological and Brain Sciences, Baltimore, + MD, 21218, United States - given-names: Christopher J. family-names: Markiewicz website: https://github.com/effigies @@ -284,9 +287,8 @@ authors: family-names: Pernet website: https://cpernet.github.io/ orcid: https://orcid.org/0000-0003-4010-4632 - affiliation: - Neurobiology Research Unit, Copenhagen University Hospital - Rigshospitalet, DK-2100 Copenhagen, Denmark + affiliation: Neurobiology Research Unit, Copenhagen University Hospital Rigshospitalet, + DK-2100 Copenhagen, Denmark email: wamcyril@gmail.com - given-names: Cyrus family-names: Eierud @@ -301,9 +303,8 @@ authors: family-names: Levitas website: https://github.com/dlevitas orcid: https://orcid.org/0000-0003-2279-7447 - affiliation: - Indiana University, Psychological & Brain Sciences, Bloomington, IN, - 47405, United States of America + affiliation: Indiana University, Psychological & Brain Sciences, Bloomington, + IN, 47405, USA email: dlevitas@iu.edu - given-names: Dan family-names: Lurie @@ -316,16 +317,13 @@ authors: family-names: Boas website: http://bu.edu/neurophotonics orcid: https://orcid.org/0000-0002-6709-7711 - affiliation: - Boston University, Biomedical Engineering, Boston, 02215, United States of - America + affiliation: Boston University, Biomedical Engineering, Boston, MA 02215 USA email: dboas@bu.edu - given-names: David family-names: Groppe website: https://github.com/dmgroppe orcid: https://orcid.org/0000-0002-3282-2514 - affiliation: - Persyst Development Corporation, R&D, Toronto, ON M4K 1W8 Canada + affiliation: Persyst Development Corporation, R&D, Toronto, ON M4K 1W8 Canada email: david.m.groppe@gmail.com - given-names: David family-names: Keator @@ -344,8 +342,7 @@ authors: family-names: Patterson website: https://profiles.arizona.edu/person/dkp orcid: https://orcid.org/0000-0001-7518-3110 - affiliation: - University of Arizona, RII, Tucson Arizona 85721 United States of America + affiliation: University of Arizona, RII, Tucson Arizona 85721 USA email: dkp@arizona.edu - given-names: Dimitri family-names: Papadopoulos Orfanos @@ -378,23 +375,20 @@ authors: family-names: Ort website: https://github.com/eort orcid: https://orcid.org/0000-0001-5546-3561 - affiliation: - Heinrich-Heine-University, Department of Experimental Psychology, + affiliation: Heinrich-Heine-University, Department of Experimental Psychology, Dusseldorf, 40224, Germany - given-names: Eleonora family-names: Marcantoni orcid: https://orcid.org/0000-0003-1137-4983 - affiliation: - IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli di Brescia + affiliation: IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli di Brescia - given-names: Elizabeth family-names: Bock - given-names: Elizabeth family-names: DuPre website: https://elizabeth-dupre.com orcid: https://orcid.org/0000-0003-1358-196X - affiliation: - Stanford University, Department of Psychology, Stanford, CA, 94063, United - States of America + affiliation: Stanford University, Department of Psychology, Stanford, CA, 94063, + USA - given-names: Elke family-names: Warmerdam affiliation: Saarland University @@ -406,9 +400,7 @@ authors: family-names: Earl website: https://ericearl.github.io/ orcid: https://orcid.org/0000-0001-5512-0083 - affiliation: - NIMH Data Science & Sharing Team, Bethesda, MD, 20892, United States of - America + affiliation: NIMH Data Science & Sharing Team, Bethesda, MD, 20892, USA email: eric.earl@nih.gov - given-names: Eric family-names: Achten @@ -444,8 +436,7 @@ authors: family-names: Maria Castelli website: https://github.com/filippocastelli orcid: https://orcid.org/0000-0001-8170-8905 - affiliation: - University of Florence, European Laboratory for NonLinear Spectroscopy, + affiliation: University of Florence, European Laboratory for NonLinear Spectroscopy, Sesto Fiorentino, (FI), 50019, Italy email: castelli@lens.unifi.it - given-names: Franco @@ -462,16 +453,14 @@ authors: family-names: Rizzo website: http://fair.dei.unipd.it/gaia-rizzo/ orcid: https://orcid.org/0000-0001-7272-8576 - affiliation: - Invicro, Burlington Danes Building, Imperial College London, Hammersmith + affiliation: Invicro, Burlington Danes Building, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK - given-names: Gang family-names: Chen website: https://github.com/afni-gangc orcid: https://orcid.org/0000-0002-2960-089X - affiliation: - National Institutes of Health, Scientific and Statistical Computing Core, - NIMH, Bethesda, MD 20892, United States of America + affiliation: National Institutes of Health, Scientific and Statistical Computing + Core, NIMH, Bethesda, MD 20892, USA email: gangchen@mail.nih.gov - given-names: Gaël family-names: Varoquaux @@ -537,8 +526,7 @@ authors: family-names: Nilsonne website: https://nilsonne.net/about/ orcid: https://orcid.org/0000-0001-5273-0150 - affiliation: - Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, + affiliation: Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, 17177, Sweden email: gustav.nilsonne@ki.se - given-names: Hamish @@ -549,9 +537,8 @@ authors: - given-names: Hanne D. family-names: Hansen orcid: https://orcid.org/0000-0001-5564-7627 - affiliation: - Copenhagen University Hospital, Neurobiology Research Unit, Section 8057, - Blegdamsvej 9, 2100 Copenhagen, Denmark + affiliation: Copenhagen University Hospital, Neurobiology Research Unit, Section + 8057, Blegdamsvej 9, 2100 Copenhagen, Denmark email: hanne.d.hansen@nru.dk - given-names: Hanzhang family-names: Lu @@ -573,8 +560,7 @@ authors: family-names: Mutsaerts website: http://www.ExploreASL.org orcid: https://orcid.org/0000-0003-0894-0307 - affiliation: - Amsterdam University Medical Centers, Radiology and Nuclear Department, + affiliation: Amsterdam University Medical Centers, Radiology and Nuclear Department, Amsterdam, 1013 EG, The Netherlands email: h.j.mutsaerts@amsterdamumc.nl - given-names: Hernando @@ -615,9 +601,8 @@ authors: family-names: Mathijs Schoffelen website: https://github.com/schoffelen orcid: https://orcid.org/0000-0003-0923-6610 - affiliation: - Radboud University Nijmegen, Donders Institute, Nijmegen, 6500 HB, The - Netherlands + affiliation: Radboud University Nijmegen, Donders Institute, Nijmegen, 6500 HB, + The Netherlands email: jm.schoffelen@gmail.com - given-names: Jan family-names: Petr @@ -640,9 +625,8 @@ authors: - given-names: Jean-Dominique family-names: Gallezot orcid: https://orcid.org/0000-0003-0399-8374 - affiliation: - Yale School of Medicine, Department of Radiology and Biomedical Imaging, - New Haven, CT, 06511, United States of America + affiliation: Yale School of Medicine, Department of Radiology and Biomedical Imaging, + New Haven, CT, 06511, USA email: jean-dominique.gallezot@yale.edu - given-names: Jean-Philippe family-names: Lachaux @@ -652,6 +636,10 @@ authors: family-names: Mumford website: https://jeanettemumford.org/ affiliation: Stanford, Department of Psychology, Stanford, CA + - given-names: Jefferson + family-names: Casimir + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: jefferson.casimir@mcin.ca - given-names: Jeffrey G. family-names: Ojemann - given-names: Jeffrey S. @@ -663,10 +651,8 @@ authors: family-names: Dalenberg website: https://github.com/jrdalenberg orcid: https://orcid.org/0000-0001-8580-5358 - affiliation: - University of Groningen, University Medical Center Groningen, Department - of Neurology, Movement Disorders Groningen, Hanzeplein 1, 9713 GZ, - Groningen + affiliation: University of Groningen, University Medical Center Groningen, Department + of Neurology, Movement Disorders Groningen, Hanzeplein 1, 9713 GZ, Groningen email: j.r.dalenberg@umcg.nl - given-names: Jeremy family-names: Moreau @@ -697,8 +683,7 @@ authors: family-names: Haitz Legarreta Gorroño website: https://github.com/jhlegarreta orcid: https://orcid.org/0000-0002-9661-1396 - affiliation: - Université de Sherbrooke, Department of Computer Science, Sherbrooke, + affiliation: Université de Sherbrooke, Department of Computer Science, Sherbrooke, (Québec), J1K 2R1, Canada email: jon.haitz.legarreta@gmail.com - given-names: Jonathan C. @@ -710,8 +695,7 @@ authors: family-names: Kuijer website: https://github.com/wadqc orcid: https://orcid.org/0000-0002-4181-0427 - affiliation: - Amsterdam University Medical Centers, Radiology and Nuclear Medicine, + affiliation: Amsterdam University Medical Centers, Radiology and Nuclear Medicine, Amsterdam, 1081 HV, The Netherlands email: jpa.kuijer@amsterdamumc.nl - given-names: Jose @@ -724,8 +708,7 @@ authors: family-names: Woods website: https://www.ndcn.ox.ac.uk/team/joseph-woods orcid: https://orcid.org/0000-0002-0329-824X - affiliation: - University of Oxford, Nuffield Department of Clinical Neuroscience, + affiliation: University of Oxford, Nuffield Department of Clinical Neuroscience, Oxford, UK email: joseph.woods@ndcn.ox.ac.uk - given-names: Julia @@ -737,15 +720,13 @@ authors: family-names: Sprenger website: https://github.com/juliasprenger orcid: https://orcid.org/0000-0002-9986-7477 - affiliation: - Institute de Neuroscience de la Timone, CNRS, Marseille, 13005, France + affiliation: Institute de Neuroscience de la Timone, CNRS, Marseille, 13005, France email: julia.sprenger@univ-amu.fr - given-names: Julien family-names: Cohen-Adad website: https://www.neuro.polymtl.ca orcid: https://orcid.org/0000-0003-3662-9532 - affiliation: - Polytechnique Montreal, Department of Electrical Engineering, Montreal, + affiliation: Polytechnique Montreal, Department of Electrical Engineering, Montreal, QC, Canada - given-names: Julius family-names: Welzel @@ -769,9 +750,8 @@ authors: family-names: Robbins website: http://www.cs.utsa.edu/~krobbins orcid: https://orcid.org/0000-0002-7147-5797 - affiliation: - University of Texas at San Antonio Department of Computer Science San - Antonio, TX 78249 United States of America + affiliation: University of Texas at San Antonio Department of Computer Science + San Antonio, TX 78249 USA email: kay.robbins@utsa.edu - given-names: Kevin family-names: Larcher @@ -806,13 +786,16 @@ authors: - given-names: Kurt family-names: Schilling website: https://github.com/schillkg + - given-names: Laetitia + family-names: Fesselier + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: laetitia.fesselier@mcin.ca - given-names: Laura family-names: and John Arnold Foundation - given-names: Leandro family-names: Beltrachini orcid: https://orcid.org/0000-0003-4602-1416 - affiliation: - Cardiff University, Cardiff University Brain Research Imaging Centre + affiliation: Cardiff University, Cardiff University Brain Research Imaging Centre (CUBRIC), UK email: BeltrachiniL@cardiff.ac.uk - given-names: Lee @@ -835,9 +818,8 @@ authors: family-names: Pollonini website: https://polloninilab.com orcid: https://orcid.org/0000-0003-2955-6355 - affiliation: - University of Houston, Dept. of Engineering Technology, Houston TX 77204, - United States of America + affiliation: University of Houston, Dept. of Engineering Technology, Houston TX + 77204, USA email: lpollonini@uh.edu - given-names: Luis family-names: Hernandez-Garcia @@ -849,7 +831,7 @@ authors: family-names: Zehl website: https://github.com/lzehl orcid: https://orcid.org/0000-0002-5947-9939 - affiliation: Forschungszentrum Jülich, Jülich, 52428, Germany + affiliation: Forschungszentrum Jülich - given-names: Mainak family-names: Jas website: http://jasmainak.github.io/ @@ -859,8 +841,7 @@ authors: - given-names: Manuel family-names: Mercier orcid: https://orcid.org/0000-0001-6358-4734 - affiliation: - Dynamics of Cognitive Processes Group Institut de Neurosciences des + affiliation: Dynamics of Cognitive Processes Group Institut de Neurosciences des Systèmes, INS - UMR 1106 Inserm Aix-Marseille Université, France - given-names: Maqsood family-names: Yaqub @@ -870,22 +851,21 @@ authors: family-names: Lalancette website: https://github.com/Moo-Marc orcid: https://orcid.org/0000-0003-1161-3972 - affiliation: - Montreal Neurological Institute-Hospital, McConnell Brain Imaging Center, - Montreal, Quebec, H2A + affiliation: Montreal Neurological Institute-Hospital, McConnell Brain Imaging + Center, Montreal, Quebec, H2A - given-names: Marco family-names: Castellaro website: https://github.com/marcocastellaro orcid: https://orcid.org/0000-0002-1203-2670 - affiliation: - University of Padova, Department of Information Engineering, Padova, Italy + affiliation: University of Padova, Department of Information Engineering, Padova, + Italy email: marco.castellaro@gmail.com - given-names: Maria family-names: de la Iglesia website: https://bimcv.cipf.es orcid: https://orcid.org/0000-0003-4505-8399 - affiliation: - FISABIO, Join Unit Biomedical Imagin, Valencia, Valencia, 46006, Spain + affiliation: FISABIO, Join Unit Biomedical Imagin, Valencia, Valencia, 46006, + Spain email: delaiglesia_mar@gva.es - given-names: Marie-Hélène family-names: Bourget @@ -894,9 +874,8 @@ authors: family-names: Mikkelsen website: https://vivo.weill.cornell.edu/display/cwid-mam4041 orcid: https://orcid.org/0000-0002-0349-3782 - affiliation: - Weill Cornell Medicine, Department of Radiology, New York, NY, 10021, - United States of America + affiliation: Weill Cornell Medicine, Department of Radiology, New York, NY, 10021, + USA email: mam4041@med.cornell.edu - given-names: Markus family-names: Morawski @@ -912,16 +891,14 @@ authors: family-names: Noergaard website: https://profiles.stanford.edu/martin-noergaard orcid: https://orcid.org/0000-0003-2131-5688 - affiliation: - Stanford University, Department of Psychology, CA, 94304, United States of - America + affiliation: Stanford University, Department of Psychology, CA, 94304, USA email: noergard@stanford.edu - given-names: Martin family-names: Szinte website: http://www.martinszinte.net orcid: https://orcid.org/0000-0003-2040-4005 - affiliation: - CNRS, Institut des Neurosciences de la Timone, Marseille, 13008, France + affiliation: CNRS, Institut des Neurosciences de la Timone, Marseille, 13008, + France email: mail@martinszinte.net - given-names: Martin family-names: Wilson @@ -937,9 +914,8 @@ authors: family-names: Goncalves website: https://github.com/mgxd orcid: https://orcid.org/0000-0002-7252-7771 - affiliation: - Psychology Department, Stanford University, Palo Alto, CA, 94305, United - States of America + affiliation: Psychology Department, Stanford University, Palo Alto, CA, 94305, + USA email: mathiasg@stanford.edu - given-names: Mathieu family-names: Boudreau @@ -952,8 +928,7 @@ authors: family-names: Tonietto website: https://github.com/matteotonietto orcid: https://orcid.org/0000-0001-9591-5710 - affiliation: - Hoffmann-La Roche Ltd, Research and Early Development, Basel, 4070, + affiliation: Hoffmann-La Roche Ltd, Research and Early Development, Basel, 4070, Switzerland - given-names: Matthias family-names: Günther @@ -967,16 +942,13 @@ authors: family-names: van den Boom website: https://github.com/MaxvandenBoom orcid: https://orcid.org/0000-0001-5481-1659 - affiliation: - Mayo Clinic, Department of neurosurgery, Rochester, MN, United States of - America + affiliation: Mayo Clinic, Department of neurosurgery, Rochester, MN, USA email: m.a.vandenboom84@gmail.com - given-names: Melanie family-names: Ganz-Benjaminsen website: https://sites.google.com/view/melanieganz/home orcid: https://orcid.org/0000-0002-9120-8098 - affiliation: - University of Copenhagen, Department of Computer Science, Copenhagen, + affiliation: University of Copenhagen, Department of Computer Science, Copenhagen, 2100, Denmark - given-names: Michael family-names: Chappell @@ -993,8 +965,7 @@ authors: family-names: Schirner website: https://www.brainsimulation.org orcid: https://orcid.org/0000-0001-8227-8476 - affiliation: - Charité—Universitätsmedizin Berlin, Department of Neurology, Berlin, + affiliation: Charité—Universitätsmedizin Berlin, Department of Neurology, Berlin, 10115, Germany email: michael.schirner@charite.de - given-names: Mikaël @@ -1008,8 +979,7 @@ authors: - given-names: Natalia family-names: Petridou orcid: https://orcid.org/0000-0002-0783-0387 - affiliation: - High Field Dpt, Center for Image Sciences, University Medical Center + affiliation: High Field Dpt, Center for Image Sciences, University Medical Center Utrecht, 3584 CX Utrecht, NL - given-names: National family-names: Institute of Mental Health @@ -1036,9 +1006,8 @@ authors: family-names: Esteban website: http://www.axonlab.org orcid: https://orcid.org/0000-0001-8435-6191 - affiliation: - Department of Radiology, Lausanne University Hospital, Lausanne, CH-1011, - Switzerland + affiliation: Department of Radiology, Lausanne University Hospital, Lausanne, + CH-1011, Switzerland email: phd@oscaresteban.es - given-names: Pamela family-names: LaMontagne @@ -1050,8 +1019,7 @@ authors: family-names: Clement website: https://github.com/patsycle orcid: https://orcid.org/0000-0001-8546-0134 - affiliation: - Department of Medical Imaging / Department of Medical Sciences, Ghent + affiliation: Department of Medical Imaging / Department of Medical Sciences, Ghent University Hospital / Ghent University, Ghent, Belgium email: patricia.clement@ugent.be - given-names: Patrick @@ -1060,25 +1028,20 @@ authors: - given-names: Paule-Joanne family-names: Toussaint orcid: https://orcid.org/0000-0002-7446-150X - affiliation: - McGill University Faculty of Medicine and Health Sciences, Montréal, - Québec, Canada + affiliation: McGill University Faculty of Medicine and Health Sciences - given-names: Peer family-names: Herholz website: https://peerherholz.github.io/ orcid: https://orcid.org/0000-0002-9840-6257 - affiliation: - NeuroDataScience - ORIGAMI lab, McConnell Brain Imaging Centre, Montreal - Neurological Institute and Hospital, McGill University, Montreal, Québec, - Canada + affiliation: NeuroDataScience - ORIGAMI lab, McConnell Brain Imaging Centre, Montreal + Neurological Institute and Hospital, McGill University, Montreal, Québec, Canada email: herholz.peer@gmail.com - given-names: Petra family-names: Ritter website: https://www.brainsimulation.org orcid: https://orcid.org/0000-0002-4643-4782 - affiliation: - Charité University Medicine Berlin, Berlin Institute of Health, Berlin, - 10115, Germany + affiliation: Charité University Medicine Berlin, Berlin Institute of Health, + Berlin, 10115, Germany email: petra.ritter@charite.de - given-names: Pierre family-names: Rioux @@ -1116,16 +1079,13 @@ authors: family-names: Innis website: https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/mib/molecular-imaging-branch-mib orcid: https://orcid.org/0000-0003-1238-7209 - affiliation: - NIMH Intramural Research Program, Bethesda, MD 20850 United States of - America, MD 20892 United States of America + affiliation: NIMH Intramural Research Program, Bethesda, MD 20850 USA, MD 20892 USA email: robert.innis@nih.gov - given-names: Robert E. family-names: Smith website: http://www.mrtrix.org orcid: https://orcid.org/0000-0003-3636-4642 - affiliation: - The Florey Institute of Neuroscience and Mental Health, Epilepsy + affiliation: The Florey Institute of Neuroscience and Mental Health, Epilepsy Neuroinformatics Laboratory, Heidelberg, Victoria, 3084, Australia email: robert.smith@florey.edu.au - given-names: Robert @@ -1137,8 +1097,7 @@ authors: family-names: Oostenveld website: https://robertoostenveld.nl orcid: https://orcid.org/0000-0002-1974-1293 - affiliation: - Radboud University, Donders Institute, Nijmegen, 6525 EN, The Netherlands + affiliation: Radboud University, Donders Institute, Nijmegen, 6525 EN, The Netherlands email: r.oostenveld@donders.ru.nl - given-names: Roberto family-names: Toro @@ -1152,8 +1111,7 @@ authors: family-names: Poldrack website: http://www.poldracklab.org orcid: https://orcid.org/0000-0001-6755-0259 - affiliation: - Stanford University, Stanford, CA 94305 United States of America + affiliation: Stanford University, Stanford, CA 94305 USA email: russpold@stanford.edu - given-names: Rémi family-names: Adon @@ -1174,25 +1132,22 @@ authors: - given-names: Sasha family-names: D'Ambrosio orcid: https://orcid.org/0000-0002-6600-6419 - affiliation: - University of Milan, Department of Biomedical and Clinical Sciences, + affiliation: University of Milan, Department of Biomedical and Clinical Sciences, Milan, 20137, Italy email: sasha.dambrosio@unimi.it - given-names: Satrajit S. family-names: Ghosh website: https://satra.cogitatum.org orcid: https://orcid.org/0000-0002-5312-6729 - affiliation: - MIT, McGovern Institute for Brain Research, Cambridge, 02139, United - States of America + affiliation: MIT, McGovern Institute for Brain Research, Cambridge, MA 02139, + USA email: satra@mit.edu - given-names: Scott family-names: Makeig website: https://sccn.ucsd.edu/~scott orcid: https://orcid.org/0000-0002-9048-8438 - affiliation: - Institute for Neural Computation, University of California San Diego, La - Jolla, CA 92-93-0955, United States of America + affiliation: Institute for Neural Computation, University of California San Diego, + La Jolla, CA 92-93-0955, USA email: smakeig@gmail.com - given-names: Sein family-names: Jeung @@ -1206,8 +1161,7 @@ authors: family-names: Vos website: https://research-repository.uwa.edu.au/en/persons/sjoerd-vos orcid: https://orcid.org/0000-0002-8502-4487 - affiliation: - University of Western Australia;Centre for Microscopy, Characterisation, + affiliation: University of Western Australia;Centre for Microscopy, Characterisation, and Analysis;Perth;WA;6009;Australia - given-names: Soichi family-names: Hayashi @@ -1222,6 +1176,12 @@ authors: email: stefan.appelhoff@mailbox.org - given-names: Stephan family-names: Bickel + - given-names: Steven + family-names: Meisler + orcid: https://orcid.org/0000-0002-8888-1572 + affiliation: Program in Speech and Hearing Bioscience and Technology, Harvard + University + email: smeisler@g.harvard.edu - given-names: Suyash family-names: Bhogawar website: https://www.linkedin.com/in/suyashb/ @@ -1232,15 +1192,13 @@ authors: family-names: Takerkart website: https://github.com/SylvainTakerkart orcid: https://orcid.org/0000-0001-8410-0962 - affiliation: - CNRS, Institut des Neurosciences de la Timone, Marseille, France + affiliation: CNRS, Institut de Neurosciences de la Timone (INT), Marseille, France email: sylvain.takerkart@univ-amu.fr - given-names: Sébastien family-names: Tourbier website: https://github.com/sebastientourbier orcid: https://orcid.org/0000-0002-4441-899X - affiliation: - Lausanne University Hospital (CHUV), Department of Clinical Neurosciences + affiliation: Lausanne University Hospital (CHUV), Department of Clinical Neurosciences (DNC), Lausanne, 1007, Switzerland email: sebastien.tourbier1@gmail.com - given-names: Sören @@ -1258,10 +1216,8 @@ authors: family-names: Spisak website: https://pni-lab.github.io/ orcid: https://orcid.org/0000-0002-2942-0821 - affiliation: - University Hospital Essen, Center for Translational and Behavioral - Neuroscience, Department of Diagnostic and Interventional Radiology and - Neuroradiology + affiliation: University Hospital Essen, Center for Translational and Behavioral + Neuroscience, Department of Diagnostic and Interventional Radiology and Neuroradiology email: tamas.spisak@uk-essen.de - given-names: Tamás family-names: Józsa @@ -1269,9 +1225,8 @@ authors: family-names: Salo website: https://tsalo.github.io orcid: https://orcid.org/0000-0001-9813-3167 - affiliation: - University of Pennsylvania, Department of Psychiatry, Philadelphia, - Pennsylvania, 19104, United States of America + affiliation: University of Pennsylvania, Department of Psychiatry, Philadelphia, + Pennsylvania, 19104, United States email: tsalo006@fiu.edu - given-names: Teon L. family-names: Brooks @@ -1297,16 +1252,15 @@ authors: family-names: Auer website: https://tiborauer.github.io orcid: https://orcid.org/0000-0001-5153-1424 - affiliation: - University of Surrey, School of Psychology, Guildford, GU2 7XH, UK + affiliation: University of Surrey, School of Psychology, Guildford, GU2 7XH, United + Kingdom email: tibor.auer@gmail.com - given-names: Timo family-names: Dickscheid website: https://go.fzj.de/dickscheid orcid: https://orcid.org/0000-0002-9051-3701 - affiliation: - Forschungszentrum Jülich, Institute of Neuroscience and Medicine, Jülich, - 52428, Germany + affiliation: Forschungszentrum Jülich, Institute of Neuroscience and Medicine + (INM-1), Jülich, 52428, Germany email: t.dickscheid@fz-juelich.de - given-names: Timotheus family-names: Berg @@ -1335,6 +1289,10 @@ authors: family-names: Glatard website: https://github.com/glatard orcid: https://orcid.org/0000-0003-2620-5883 + - given-names: Tyler + family-names: Collins + affiliation: BrockU, LORIS, MCIN, Montreal Neurological Institute, McGill University + email: tyler.collins@mcin.ca - given-names: Ulrike family-names: Bingel orcid: https://orcid.org/0000-0002-9528-3204 @@ -1347,10 +1305,9 @@ authors: - given-names: Vince D. family-names: Calhoun website: http://trendscenter.org - affiliation: - Tri-institutional Center for Translational Research in Neuroimaging and - Data Science (TReNDS), Georgia State, Georgia Tech, and Emory, Atlanta, GA - 30030 + affiliation: Tri-institutional Center for Translational Research in Neuroimaging + and Data Science (TReNDS), Georgia State, Georgia Tech, and Emory, Atlanta, + GA 30030 email: vcalhoun@gsu.edu - given-names: Vittorio family-names: Iacovella @@ -1372,13 +1329,13 @@ authors: - given-names: Xiangrui family-names: Li website: https://github.com/xiangruili - affiliation: The Ohio State University, United States of America + affiliation: The Ohio State University email: xiangrui.li@gmail.com - given-names: Yaroslav O. family-names: Halchenko website: http://www.onerussian.com orcid: https://orcid.org/0000-0003-3456-2493 - affiliation: Dartmouth College, United States of America + affiliation: Dartmouth College email: debian@onerussian.com - given-names: Yoni family-names: Ashar diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 40fae2e3ea..c34f9cb514 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -163,7 +163,7 @@ The BIDS specification is written in American English. We follow certain "soft rules" in the way we format the specification in Markdown. -These rules are sometimes for internal consistency in terms of styling and aesthetics, +These rules are sometimes for internal consistency in terms of styling and esthetics, but several of them are also there because they help the workflow of tracking changes, reviewing them on GitHub, and making code suggestions. @@ -226,6 +226,37 @@ That would look like this: |--------------|----------------------------------------------------------| | Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) | + +#### MkDocs admonitions + +It is possible to use [Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end) +to highlight certain aspect of the specification. + +Admonitions are written like this: + +```` +!!! note "displayed heading is preceded by a keyword and 3 `!`" + + Body of the admonition + can be written on several lines, + but must be always preceded by 4 spaces. +```` + +The keyword for the heading must be one of the following: + +- note +- abstract +- info +- tip +- success +- question +- warning +- failure: octicons +- danger +- bug +- example +- quote + ## Using macros We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/) @@ -698,6 +729,8 @@ the `master` branch of the specification via a "Merge commit" see the [GitHub help page](https://help.github.com/en/articles/about-merge-methods-on-github) for more information on merge methods). +![merge-commit](release_images/merge_commit.png "merge-commit") + Note that for pull requests starting with `REL:`, no changelog is generated. To exclude pull requests from showing up in the changelog, they have to be labeled with @@ -709,16 +742,14 @@ BIDS follows the [all-contributors](https://github.com/kentcdodds/all-contributors) specification, so we welcome and recognize all contributions from documentation to testing to code development. -You can see a list of current contributors in the -[BIDS specification](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md). - -If you have made any type of contributions to the BIDS specifications, you can -either make a change to the -[contributors document](./src/appendices/contributors.md) and commit as -part of a pull request or you can edit this -[page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors) -of the specification WIKI. -The WIKI is then synced with the specification with every new release of the specifications. +You can see a list of contributors in the +[contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html) +of the BIDS specification. + +If you have made any type of contributions to BIDS, +we encourage you to enter or update your information in the +[Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors) +according to the instructions listed there. ## Thank you! diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md index 88474ac82f..a29b4b8632 100644 --- a/DECISION-MAKING.md +++ b/DECISION-MAKING.md @@ -53,11 +53,12 @@ Leaders of BIDS Extension Proposals are listed in the ### Contributors Group -Contributors are listed in the [Contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html) -of the BIDS specification. Contributors who have not yet entered their name -into this list are encouraged to edit the [Contributors WIKI page](https://github.com/bids-standard/bids-specification/wiki/Contributors) -with their name, using the emojis listed in the WIKI to indicate their -contributions. +Contributors are listed in the +[Contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html) +of the BIDS specification. +Contributors who have not yet entered their name into this list are encouraged to edit the +[Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors) +according to the instructions listed there. ### Other groups diff --git a/LICENSE b/LICENSE index d591978380..22091e01bb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ Attribution 4.0 International -Copyright (c) 2018-2022, BIDS Contributors. +Copyright (c) 2018, BIDS Contributors. ======================================================================= diff --git a/README.md b/README.md index 54b7bd11d7..6474f470a1 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ [![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml) [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification) -[![@BIDSstandard](http://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://twitter.com/BIDSstandard) +[![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard) +[![@BIDSstandard](https://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://x.com/BIDSstandard) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061) bids-logo @@ -12,7 +13,6 @@ organization of neuroimaging data. In this repository, we develop the [BIDS specification](https://bids-specification.readthedocs.io/en/latest/). - # When to use BIDS To organize your data in BIDS, all you need is neuro data, a computer, and the @@ -43,10 +43,7 @@ The specification is provided in the form of a webpage, built using 1. Read some introductory material, most likely the very basic problems have already been addressed! - [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit) for tutorials, wikis, templates, ... 2. Post your question in one of several channels where BIDS members are active - - the [NeuroStars](https://neurostars.org/tags/bids) discourse forum - - the [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html)) - - the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions surrounding BIDS - - the [specification repository issue page](https://github.com/bids-standard/bids-specification/issues), if you found inconsistencies, typos, or other issues with the BIDS specification itself + - see: [BIDS communication channels](#bids-communication-channels) # Contributing to BIDS @@ -57,11 +54,34 @@ For a current list of our contributors, please see our [Contributors appendix](h When you're ready to get started, check out [our contributing guidelines](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md). -We ask that all contributions to BIDS across all project-related spaces (including but not limited to: -[GitHub](https://github.com/bids-standard), -the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), and newsletter emails), +We ask that all contributions to BIDS across all project-related spaces +(including but not limited to: +[GitHub](https://github.com/bids-standard), and the +[Google group](https://groups.google.com/forum/#!forum/bids-discussion); see +[BIDS communication channels](#bids-communication-channels)) adhere to our [code of conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md). +# BIDS communication channels + +## Main communication channels + + - "Issue" pages on the different GitHub repositories of the [`bids-standard` GitHub organization](https://github.com/bids-standard), + such as the [BIDS specification repository](https://github.com/bids-standard/bids-specification/issues), + for reporting problems or making suggestions + - The [NeuroStars Discourse forum](https://neurostars.org/tags/bids), for asking usage questions + - The [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging + (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html)) + - The [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions and announcements surrounding BIDS + - The [BIDS website "news"](https://bids.neuroimaging.io/news.html), similar to the Google group, for broader discussions and announcements + +## Social media channels + +- [X](https://x.com/BIDSstandard) +- [Mastodon](https://fosstodon.org/@bidsstandard) +- [Bluesky](https://bsky.app/profile/bidsstandard.bsky.social) +- [Youtube](https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw) +- [Instagram](https://www.instagram.com/bidsstandard/) + ## Contributors Thanks goes to these wonderful people. @@ -72,415 +92,423 @@ Thanks goes to these wonderful people. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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Tal Yarkoni
💻 📖 🤔 🔍 🔌 👀 📢 🐛 🎨
Tamas Spisak
📖
Tamás Józsa
📓
Taylor Salo
💬 📖 🔌 💻
Teon L. Brooks
📖 💻 ⚠️ 💬 👀 🤔 🔧 🐛 📢

Thomas E. Nichols
📖 📢 🔧 👀 🚧 💻
Thomas Funck
📖
Thomas Kirk
📖
Thomas Okell
📖
Tibor Auer
💬 📖 💡 🔧 📢 🐛 🤔
Timo Dickscheid
📖
Timotheus Berg
📖 🤔 📓

Tobey Betthauser
📖
Tobias Bengfort
💻
Tom Hampshire
📖
Tor Wager
📖
Travis Riddle
📖 🔧 🐛
Tristan Glatard
📖 💻
Ulrike Bingel
📖

Vanessa Sochat
📖
Vasudev Raguram
💻 🎨 📖 🔧
Vince D. Calhoun
📖
Vittorio Iacovella
📖
Vladimir Litvak
📖
Wietske van der Zwaag
🔣 💬
William Clarke
📖

William Triplett
📖
Wouter V. Potters
💻 📖
Xiangrui Li
📖 💻
Yaroslav O. Halchenko
📖 📢 🔧 💬 🐛 💻
Yoni Ashar
📖
Yuan Wang
💻
Zachary Michael
📖

ezemikulan
💻
josator2
💻
monkeyman192
💻
Étienne Bergeron
🔣 💻		Aaron Oliver-Taylor
Aaron Oliver-Taylor
📖		Adam Li
Adam Li
📖 💻		Adam Thomas
Adam Thomas
📖		Adeen Flinker
Adeen Flinker
📖		Adina S. Wagner
Adina S. Wagner
🎨 💻		Agah Karakuzu
Agah Karakuzu
💬 📖 🔣 🤔 💻		Aki Nikolaidis
Aki Nikolaidis
📖
Alberto Lazari
Alberto Lazari
📖		Alejandro de la Vega
Alejandro de la Vega
🐛 💻 ⚠️		Alessio Giacomel
Alessio Giacomel
📖		Alex Rockhill
Alex Rockhill
📖 🔧 💻		Alexander Jones
Alexander Jones
💻 🐛		Alexander L. Cohen
Alexander L. Cohen
🐛 💻 📖 💬		Alexander von Lautz
Alexander von Lautz
📖
Alexandre Gramfort
Alexandre Gramfort
📖 💡		Alexandre Hutton
Alexandre Hutton
📖		Alexandre Routier
Alexandre Routier
📖		Alexandru Foias
Alexandru Foias
📖 🔣		Ali Khan
Ali Khan
📖		Alizee Wickenheiser
Alizee Wickenheiser
🔧		Ana Fouto
Ana Fouto
📓
Anders Eklund
Anders Eklund
📖 📢 💻		Andrea Pigorini
Andrea Pigorini
📖		Andrew Hoopes
Andrew Hoopes
📖		Andrew Jahn
Andrew Jahn
📓		Andrew Janke
Andrew Janke
📖 💻		Anibal Sólon
Anibal Sólon
💻 🐛		Anthony Galassi
Anthony Galassi
📖 💻
Ariel Rokem
Ariel Rokem
📖 💻		Arjen Stolk
Arjen Stolk
📖		Arnaud Delorme
Arnaud Delorme
📖 💡 🤔		Arnaud Marcoux
Arnaud Marcoux
📖		Arshitha Basavaraj
Arshitha Basavaraj
📖 🚇 💻		Ashley G. Gillman
Ashley G. Gillman
📖		Athanasia Monika Mowinckel
Athanasia Monika Mowinckel
📖
Aysegul Gunduz
Aysegul Gunduz
📖		Azeez Adebimpe
Azeez Adebimpe
📖		B. Nolan Nichols
B. Nolan Nichols
📖		Balint Kincses
Balint Kincses
📖		Benjamin Beasley
Benjamin Beasley
📖		Benjamin Dichter
Benjamin Dichter
📖		Benjamin Gagl
Benjamin Gagl
📖
Bertrand Thirion
Bertrand Thirion
📖		Bradley Voytek
Bradley Voytek
📖		Brett L. Foster
Brett L. Foster
📖		Brian A. Wandell
Brian A. Wandell
📖		Brian N. Lundstrom
Brian N. Lundstrom
📖		Camille Maumet
Camille Maumet
📖		Carlo Miniussi
Carlo Miniussi
📖
Cecile Madjar
Cecile Madjar
🔣 🔧		Chloé Pasturel
Chloé Pasturel
📖		Chris Benjamin
Chris Benjamin
📖		Chris Gahnström
Chris Gahnström
📖		Chris Holdgraf
Chris Holdgraf
📖 🤔 💻		Chris J. Gorgolewski
Chris J. Gorgolewski
📖 💻 💬 🤔 🔍 📢 📝 💡 🔌		Chris Rorden
Chris Rorden
📖 💻
Christian Büchel
Christian Büchel
📖		Christian Horea
Christian Horea
💻 📖		Christine Rogers
Christine Rogers
🔣 📖 🤔 🚇 🔧		Christophe Phillips
Christophe Phillips
📖		Christopher J. Honey
Christopher J. Honey
📖		Christopher J. Markiewicz
Christopher J. Markiewicz
💬 🐛 💻 📖 🎨 💡 🤔 🔌 👀 🔧 📢 🔣 📋 🚧		Christopher Lee-Messer
Christopher Lee-Messer
📖
Clara Moreau
Clara Moreau
📖		Clint Hansen
Clint Hansen
📖 🤔		Cyril Pernet
Cyril Pernet
💬 📝 📖 🎨 💡 📋 🤔 📢		Cyrus Eierud
Cyrus Eierud
📖		D. Sturgeon
D. Sturgeon
💻		Dan Levitas
Dan Levitas
📖		Dan Lurie
Dan Lurie
🤔 📖 🔧 🔌 💻 💬
Daniel A. Handwerker
Daniel A. Handwerker
📖		David Alsop
David Alsop
📖		David Boas
David Boas
📖		David Groppe
David Groppe
📖		David Keator
David Keator
📖		David McAlpine
David McAlpine
📖		David Thomas
David Thomas
📖 🔣
Dejan Draschkow
Dejan Draschkow
📖		Dianne Patterson
Dianne Patterson
📖		Dimitri Papadopoulos Orfanos
Dimitri Papadopoulos Orfanos
📖 💡 🤔 💬 💻		Dmitry Petrov
Dmitry Petrov
📖 💻		Dora Hermes
Dora Hermes
📖 💻 ✅ 🔍 🤔		Dorien Huijser
Dorien Huijser
📖		Douglas N. Greve
Douglas N. Greve
📖
Duncan Macleod
Duncan Macleod
📖 🚇		Dung Truong
Dung Truong
📖 💻 🔧 🤔		Dylan Nielson
Dylan Nielson
📖 💻 🔧		Eduard Ort
Eduard Ort
📖 💻		Eleonora Marcantoni
Eleonora Marcantoni
📖		Elizabeth Bock
Elizabeth Bock
📖 💡		Elizabeth DuPre
Elizabeth DuPre
📖 💡 🔍 🤔 💬 💻
Elke Warmerdam
Elke Warmerdam
🔣 📖		Erdal Karaca
Erdal Karaca
💻		Eric A. Earl
Eric A. Earl
📖 💬 🐛 🚧 🔧 🤔 💻		Eric Achten
Eric Achten
📖 🔣 📓		Eric Bridgeford
Eric Bridgeford
📖 🔧		Erin W. Dickie
Erin W. Dickie
📖 🤔 👀 📢 💬 💻		Ethan Blackwood
Ethan Blackwood
👀 📖
Eugene P. Duff
Eugene P. Duff
📖		Ezequiel Mikulan
Ezequiel Mikulan
📖 💻		Felipe Orihuela-Espina
Felipe Orihuela-Espina
📖		Fidel Alfaro Almagro
Fidel Alfaro Almagro
💬 📖 💡 🔌		Filip Szczepankiewicz
Filip Szczepankiewicz
📖		Filippo Maria Castelli
Filippo Maria Castelli
📖 🔣		Franco Pestilli
Franco Pestilli
📖 💻 🎨 💡 🤔 👀 🔧 📋 🔍 🚇 📢
Franklin W. Feingold
Franklin W. Feingold
📋 📝 ✅ 💬 🤔 🎨 📢 👀 🚇 🖋 📆 💻		François Tadel
François Tadel
📖 🔌 💡		Gaia Rizzo
Gaia Rizzo
📖		Gang Chen
Gang Chen
📖		Gaël Varoquaux
Gaël Varoquaux
📖		Ghislain Vaillant
Ghislain Vaillant
💻		Giacomo Bertazzoli
Giacomo Bertazzoli
📖
Giacomo Guidali
Giacomo Guidali
📖		Giacomo Mazzamuto
Giacomo Mazzamuto
📖 🔣		Gilles de Hollander
Gilles de Hollander
📖		Gio Piantoni
Gio Piantoni
📖		Gitte M. Knudsen
Gitte M. Knudsen
📖		Giulio Castegnaro
Giulio Castegnaro
📖		Giuseppe Gallitto
Giuseppe Gallitto
📖
Graham Searle
Graham Searle
📖		Granville J. Matheson
Granville J. Matheson
📖		Gregory Kiar
Gregory Kiar
📖 💻 🎨 🔧		Gregory Noack
Gregory Noack
📖 💻 ⚠️		Greydon Gilmore
Greydon Gilmore
📖 💻		Guillaume Flandin
Guillaume Flandin
📖 💻		Gunnar Schaefer
Gunnar Schaefer
📖
Gustav Nilsonne
Gustav Nilsonne
📖		Hamish Innes-Brown
Hamish Innes-Brown
📖		Hanne D. Hansen
Hanne D. Hansen
📖		Hanzhang Lu
Hanzhang Lu
📖		Hao-Ting Wang
Hao-Ting Wang
📖 🐛		Helena Cockx
Helena Cockx
📖 🤔 💬		Henk Mutsaerts
Henk Mutsaerts
💬 🐛 💻 📖 💡 📋 🤔 📆 📢 📓
Hernando Ombao
Hernando Ombao
📖		Hugo Boniface
Hugo Boniface
📖 💻		Ilkay Isik
Ilkay Isik
📖		Ilona Lipp
Ilona Lipp
📖		International Neuroinformatics Coordinating Facility
International Neuroinformatics Coordinating Facility
💵 📋		Iris Groen
Iris Groen
📖		Isla Staden
Isla Staden
📖
Jaap von der Aar
Jaap von der Aar
📖		Jakub Kaczmarzyk
Jakub Kaczmarzyk
📖 🔧 🚇		James Gholam
James Gholam
📖		James Kent
James Kent
💬 💻		Jan Mathijs Schoffelen
Jan Mathijs Schoffelen
📖		Jan Petr
Jan Petr
💬 🐛 💻 📖 🔣 💡 📋 🤔 📆 ⚠️ 📢		Jan-Mathijs Schoffelen
Jan-Mathijs Schoffelen
📖
Jean-Baptiste Poline
Jean-Baptiste Poline
📖 📢 🤔 🎨 💻		Jean-Christophe Houde
Jean-Christophe Houde
📖 💻		Jean-Dominique Gallezot
Jean-Dominique Gallezot
📖		Jean-Philippe Lachaux
Jean-Philippe Lachaux
📖		Jeanette Mumford
Jeanette Mumford
📖		Jefferson Casimir
Jefferson Casimir
🔧		Jeffrey G. Ojemann
Jeffrey G. Ojemann
📖
Jeffrey S. Grethe
Jeffrey S. Grethe
💬 🐛 ✅ 📢 💻		JegouA
JegouA
💻		Jelle Dalenberg
Jelle Dalenberg
📖		Jeremy Moreau
Jeremy Moreau
📖 💡		Jessica A. Turner
Jessica A. Turner
📖		Jochem Rieger
Jochem Rieger
📖		John Detre
John Detre
📖
John Pellman
John Pellman
📖		John T. Wodder
John T. Wodder
💻		Joke Durnez
Joke Durnez
📖 🔧 💻		Jon Haitz Legarreta Gorroño
Jon Haitz Legarreta Gorroño
💻 📖		Jonathan C. Lau
Jonathan C. Lau
📖		Jonathan Winawer
Jonathan Winawer
📖		Joost Kuijer
Joost Kuijer
📖
Jose Manuel Saborit
Jose Manuel Saborit
📖		Joseph Wexler
Joseph Wexler
📖 💡		Joseph Woods
Joseph Woods
📖		Julia Guiomar Niso Galán
Julia Guiomar Niso Galán
🤔 🎨 🔍 👀 📋 📝 🔧 🐛 💻 🔣 ✅ 💬 📖 💡 📢		Julia Sprenger
Julia Sprenger
📖		Julien Cohen-Adad
Julien Cohen-Adad
📖 🔣 🤔		Julius Welzel
Julius Welzel
📖 💡 🐛 💻 🔣 🤔 💬 📓
Kai J. Miller
Kai J. Miller
📖		Kangjoo Lee
Kangjoo Lee
📖		Katja Heuer
Katja Heuer
🔧		Kay Robbins
Kay Robbins
💻 📖 🐛		Kevin Larcher
Kevin Larcher
💬		Kimberly Ray
Kimberly Ray
📖 📋 🤔 📆		Kirstie Whitaker
Kirstie Whitaker
📖 💡 🔍 🤔 📢 💬 💻
Klara Gregorova
Klara Gregorova
📖		Klaus Gramann
Klaus Gramann
📖 🤔		Kris Thielemans
Kris Thielemans
📖		Kristofer Bouchard
Kristofer Bouchard
📖		Kurt Schilling
Kurt Schilling
📖		Laetitia Fesselier
Laetitia Fesselier
🔧		Laura and John Arnold Foundation
Laura and John Arnold Foundation
💵
Leandro Beltrachini
Leandro Beltrachini
📖		Lee Kamentsky
Lee Kamentsky
📖		Lennart Walger
Lennart Walger
📖		Lennart Wittkuhn
Lennart Wittkuhn
📖		Liberty Hamilton
Liberty Hamilton
📖		Luca Pollonini
Luca Pollonini
📖		Luis Hernandez-Garcia
Luis Hernandez-Garcia
📖 📓
Luke J. Edwards
Luke J. Edwards
📖 💬		Lyuba Zehl
Lyuba Zehl
📖		Mainak Jas
Mainak Jas
📖 💻		Manjari Narayan
Manjari Narayan
📖		Manuel Mercier
Manuel Mercier
📖 🤔		Maqsood Yaqub
Maqsood Yaqub
📖		Marc Lalancette
Marc Lalancette
📖 💻
Marco Castellaro
Marco Castellaro
💬 🐛 💻 📖 💡 ⚠️ 📢 🚇		Maria de la Iglesia
Maria de la Iglesia
📖		Marie-Hélène Bourget
Marie-Hélène Bourget
📖 🔣 💻 🤔		Mark Mikkelsen
Mark Mikkelsen
📖		Markus Morawski
Markus Morawski
📖		Marta Bortoletto
Marta Bortoletto
📖		Martin Craig
Martin Craig
🔣
Martin Noergaard
Martin Noergaard
📖 🔣 💻 🤔 📢		Martin Szinte
Martin Szinte
📖		Martin Wilson
Martin Wilson
📖		Martina Bulgari
Martina Bulgari
📖		Mateusz Pawlik
Mateusz Pawlik
📖 🐛 🤔 🚧 👀		Mathias Goncalves
Mathias Goncalves
💻 🔧 📢		Mathieu Boudreau
Mathieu Boudreau
💬 🤔 📢
Matt Sanderson
Matt Sanderson
📖 💻		Matteo Tonietto
Matteo Tonietto
📖		Matthias Günther
Matthias Günther
📖		Matthias Van Osch
Matthias Van Osch
📖		Maureen J Shader
Maureen J Shader
📖		Maurice Pasternak
Maurice Pasternak
📓		Max A. van den Boom
Max A. van den Boom
💻 👀 📖 🐛
Melanie Ganz-Benjaminsen
Melanie Ganz-Benjaminsen
📖 🔣 💻 🤔 📆 🔍 📢		Michael Chappell
Michael Chappell
📖 🔣 📆		Michael Hanke
Michael Hanke
📖 🤔 🔧 🐛 📢		Michael P. Harms
Michael P. Harms
📖 ⚠️ 🔧		Michael P. Milham
Michael P. Milham
💡 🔍		Michael P. Notter
Michael P. Notter
💬 📝 ✅ 📢 📖		Michael Schirner
Michael Schirner
📖
Mikaël Naveau
Mikaël Naveau
🐛		Nader Pouratian
Nader Pouratian
📖		Natalia Petridou
Natalia Petridou
📖		National Institute of Mental Health
National Institute of Mental Health
💵		Nell Hardcastle
Nell Hardcastle
💻 📖 🤔 🚇 👀 💬		Nicholas Traut
Nicholas Traut
📖 🔧 💻		Nick F. Ramsey
Nick F. Ramsey
📖
Nicole C. Swann
Nicole C. Swann
📖		Nima Bigdely Shamlo
Nima Bigdely Shamlo
📖		Olivier David
Olivier David
📖		Orrin Devinsky
Orrin Devinsky
📖		Oscar Esteban
Oscar Esteban
📖 🔧 🤔 💬 💻		Pamela LaMontagne
Pamela LaMontagne
📖 💡		Parul Sethi
Parul Sethi
📖 🔧 ⚠️ 💻
Patricia Clement
Patricia Clement
💬 🐛 💻 📖 🔣 💡 📋 🤔 📆 ⚠️ 📢		Patrick Park
Patrick Park
📖 💡 💬 💻		Paule-Joanne Toussaint
Paule-Joanne Toussaint
📖		Peer Herholz
Peer Herholz
💬 📖 👀 🔧 ✅ 📢		Petra Ritter
Petra Ritter
📖		Pierre Rioux
Pierre Rioux
📖		Pieter Vandemaele
Pieter Vandemaele
📖 💻
Pradeep Reddy Raamana
Pradeep Reddy Raamana
💻 🔧		R. Cameron Craddock
R. Cameron Craddock
📖 📢		Remi Gau
Remi Gau
📖 💻 💬 📢 🐛 💻 🚇 👀 🔧 🤔		Richard Höchenberger
Richard Höchenberger
📖 💻		Richard N. Henson
Richard N. Henson
📖		Robert B. Innis
Robert B. Innis
📖		Robert E. Smith
Robert E. Smith
💻 📖
Robert Knight
Robert Knight
📖		Robert Luke
Robert Luke
💻		Robert Oostenveld
Robert Oostenveld
📖 🔧 📢 💡 ✅ ⚠️ 🤔 💬 🐛 📝 💻 🖋 🔣 🎨 📋 🚇 👀 📓 📹		Roberto Toro
Roberto Toro
🔧		Rohan Goyal
Rohan Goyal
📖		Ross W. Blair
Ross W. Blair
💻		Russell A. Poldrack
Russell A. Poldrack
📖 🔍 📢
Rémi Adon
Rémi Adon
📖		Samir Das
Samir Das
📖		Samuel Garcia
Samuel Garcia
🤔 👀 📖		Samuel Nastase
Samuel Nastase
💻		Sara Elgayar
Sara Elgayar
📖		Sasha D'Ambrosio
Sasha D'Ambrosio
📖		Satrajit S. Ghosh
Satrajit S. Ghosh
📖 💻
Scott Makeig
Scott Makeig
📖		Sein Jeung
Sein Jeung
📖 💡 🐛 💻 🔣 🤔 💬 🔧 📓		Shashank Bansal
Shashank Bansal
📖		Sjoerd B. Vos
Sjoerd B. Vos
📖		Soichi Hayashi
Soichi Hayashi
📖 🔧 🐛		Stefan Appelhoff
Stefan Appelhoff
📖 💬 🤔 🐛 💡 💻 👀 ⚠️ 📢 ✅ 🔧 🔌 📝 🚧 🔣		Stephan Bickel
Stephan Bickel
📖
Steven Meisler
Steven Meisler
🐛 💻 💬 🔧 📓		Suyash Bhogawar
Suyash Bhogawar
📖 💡 ⚠️ 🔧 💬		Sylvain Baillet
Sylvain Baillet
📖 🔍		Sylvain Takerkart
Sylvain Takerkart
📖		Sébastien Tourbier
Sébastien Tourbier
🤔 👀 📢 🐛 💻 📖		Sören Grothkopp
Sören Grothkopp
📖 🔣 📓		Tal Pal Attia
Tal Pal Attia
📖
Tal Yarkoni
Tal Yarkoni
💻 📖 🤔 🔍 🔌 👀 📢 🐛 🎨		Tamas Spisak
Tamas Spisak
📖		Tamás Józsa
Tamás Józsa
📓		Taylor Salo
Taylor Salo
💬 📖 🔌 💻		Teon L. Brooks
Teon L. Brooks
📖 💻 ⚠️ 💬 👀 🤔 🔧 🐛 📢		Thomas E. Nichols
Thomas E. Nichols
📖 📢 🔧 👀 🚧 💻		Thomas Funck
Thomas Funck
📖
Thomas Kirk
Thomas Kirk
📖		Thomas Okell
Thomas Okell
📖		Tibor Auer
Tibor Auer
💬 📖 💡 🔧 📢 🐛 🤔		Timo Dickscheid
Timo Dickscheid
📖		Timotheus Berg
Timotheus Berg
📖 🤔 📓		Tobey Betthauser
Tobey Betthauser
📖		Tobias Bengfort
Tobias Bengfort
💻
Tom Hampshire
Tom Hampshire
📖		Tor Wager
Tor Wager
📖		Travis Riddle
Travis Riddle
📖 🔧 🐛		Tristan Glatard
Tristan Glatard
📖 💻		Tyler Collins
Tyler Collins
🔣 🔧		Ulrike Bingel
Ulrike Bingel
📖		Vanessa Sochat
Vanessa Sochat
📖
Vasudev Raguram
Vasudev Raguram
💻 🎨 📖 🔧		Vince D. Calhoun
Vince D. Calhoun
📖		Vittorio Iacovella
Vittorio Iacovella
📖		Vladimir Litvak
Vladimir Litvak
📖		Wietske van der Zwaag
Wietske van der Zwaag
🔣 💬		William Clarke
William Clarke
📖		William Triplett
William Triplett
📖
Wouter V. Potters
Wouter V. Potters
💻 📖		Xiangrui Li
Xiangrui Li
📖 💻		Yaroslav O. Halchenko
Yaroslav O. Halchenko
📖 📢 🔧 💬 🐛 💻 🔣 🔍 🤔 🔌 👀 📓 🚇		Yoni Ashar
Yoni Ashar
📖		Yuan Wang
Yuan Wang
💻		Zachary Michael
Zachary Michael
📖		ezemikulan
ezemikulan
💻
josator2
josator2
💻		monkeyman192
monkeyman192
💻		Étienne Bergeron
Étienne Bergeron
🔣 💻
diff --git a/Release_Protocol.md b/Release_Protocol.md index 5773da78e3..c93c039a48 100644 --- a/Release_Protocol.md +++ b/Release_Protocol.md @@ -8,10 +8,14 @@ The protocol assumes that you have a [fork](https://help.github.com/en/articles/ of the bids-standard/bids-specification repository and have [cloned](https://help.github.com/en/articles/cloning-a-repository) your fork locally to a directory called `bids-specification`. -NOTE: Before you start a release, you have to ensure that the automatically generated changelog is -**up to date**. See the relevant [section in CONTRIBUTING.md](CONTRIBUTING.md#how-is-the-changelog-generated) -for further information. In practice this means ensuring that the most recently merged pull request was -merged into the `master` branch using the "Merge commit" option. +### 0. Cleaning up the changelog + +Before you start a release, you have to ensure that the automatically generated changelog is **up to date**. +See the relevant [section in CONTRIBUTING.md](CONTRIBUTING.md#how-is-the-changelog-generated) for further information. +In practice this means ensuring that the most recently merged pull request +was merged into the `master` branch using the "Merge commit" option. + +![merge-commit](release_images/merge_commit.png.png "merge-commit") ### 1. Fetch the latest version of the [master branch of the BIDS-specification](https://github.com/bids-standard/bids-specification/tree/master) @@ -48,13 +52,13 @@ Update the version in CITATION.cff. Change the "Unreleased" heading in [src/CHANGES.md](https://github.com/bids-standard/bids-specification/blob/master/src/CHANGES.md) -to `v`, and link to the target ReadTheDocs URL. +to ``, and link to the target ReadTheDocs URL. If the target release date is known, include the date in YYYY-MM-DD in parentheses after the link. ```Diff - ## Unreleased -+ ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04) ++ ## [1.2.0](https://bids-specification.readthedocs.io/en/1.2.0/) (2019-03-04) ``` The date can be changed or added later, so accurate prediction is not necessary. @@ -63,7 +67,7 @@ Remove the `-dev` from the version in [mkdocs.yml](https://github.com/bids-standard/bids-specification/blob/master/mkdocs.yml) configuration, so the title will be correct for the released specification. If the version preceding the `-dev` is not the target version, update the version as well. -In the figure below, we update `v1.2.0-dev` to `v1.2.0`. +In the figure below, we update `1.2.0-dev` to `1.2.0`. ![dev-to-stable](release_images/site_name_release_1.2dev-1.2.png "dev-to-stable") Additionally, implement the same change in the version name perform above in the `src/schema/BIDS_VERSION` file. @@ -75,27 +79,35 @@ It will be generated once the GitHub release has been completed. #### 2.2 Update the contributors list -Synchronize the [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md) -with the [Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Contributors) -to ensure all contributors are duly credited. -Be sure not to remove credits if both have been edited. +We want to ensure that all contributors are duly credited. +To synchronize the +[Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md) +with the +[Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors), +please follow these steps: + +- be sure not to remove credits if both the contributors appendix AND + the contributors wiki page have been edited (or the `.tributors` or `.all-contributorsrc` files) - add new contributors info to the `tools/new_contributors.tsv` file. - make sure that you have installed - all the python packages listed in `tools/requirements.txt` - the [allcontributors](https://allcontributors.org/docs/en/cli/installation) package - run: + ```bash make update_contributors ``` + - you may need to fix some errors in the contributions names in case of crash - make sure to review the changes and not commit them blindly - commit the changes #### 2.3 Update the previous version URLs -Please change the previous version links from GitHub to ReadTheDocs. -In the figure below, we update v1.2.2. +In `src/CHANGES.md`, +please change the previous version links from GitHub to ReadTheDocs. +In the figure below, we update 1.2.2. ![github-to-rtd](release_images/GitHub_to_RTD_spec_rendering.png "github-to-rtd") #### 2.4 Update the Changelog @@ -115,7 +127,7 @@ discrepancies is reduced. ```Shell git add src/CHANGES.md mkdocs.yml src/appendices/contributors.md src/schema/BIDS_VERSION -git commit -m 'REL: v1.2.0' +git commit -m 'REL: 1.2.0' git push -u upstream rel/1.2.0 ``` @@ -123,7 +135,7 @@ git push -u upstream rel/1.2.0 **Important notes:** -1. The pull request title **must** be named "REL: vX.Y.Z" (for example, "REL: v1.2.0") +1. The pull request title **must** be named "REL: X.Y.Z" (for example, "REL: 1.2.0") 1. The pull request **must** get a GitHub label called `exclude-from-changelog` **This will open a period of discussion for 5 business days regarding if we are ready to release.** @@ -158,13 +170,13 @@ The date should be placed after the link to the versioned URL. For example: ```Diff -- ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) -+ ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04) +- ## [1.2.0](https://bids-specification.readthedocs.io/en/1.2.0/) ++ ## [1.2.0](https://bids-specification.readthedocs.io/en/1.2.0/) (2019-03-04) ``` -Verify that the pull request title matches "REL: vX.Y.Z" and merge the pull request. +Verify that the pull request title matches "REL: X.Y.Z" and merge the pull request. -### 6. Get the built PDF +### 6. Get the built PDF and `CITATION.cff` file Upon each commit to the `master` branch, CircleCI builds a PDF version of the specification (see `.circleci/config.yml` and the `pdf_build_src` directory). @@ -178,6 +190,9 @@ jobs to finish and then check the built PDF using the following steps: 1. Download the PDF and check that the date and version on the first page are as expected 1. Hold the PDF ready for upload to our Zenodo archive (see the *Uploading the stable PDF to Zenodo* step below) +Furthermore, **copy the `CITATION.cff`** file in its current state from the root of the repository +and hold it ready for facilitating the upload of the PDF to our Zenodo archive. + ### 7. Tag the release GitHub's release mechanism does not have all of the features we need, so manually tag the release @@ -187,8 +202,8 @@ To do this, `fetch` the current state of `upstream` (see step 1), tag `upstream/ ```Shell git fetch upstream -git tag -a -m "v1.2.0 (2019-03-04)" v1.2.0 upstream/master -git push upstream v1.2.0 +git tag -a -m "1.2.0 (2019-03-04)" 1.2.0 upstream/master +git push upstream 1.2.0 ``` There are four components to the tag command: @@ -213,7 +228,7 @@ Click [Draft a new release](https://github.com/bids-standard/bids-specification/ ![GH-release-2](release_images/GH-release_2.png "GH-release-2") -Set the tag version and release title to "vX.Y.Z", and paste the current changelog as the +Set the tag version and release title to "X.Y.Z", and paste the current changelog as the description: ![GH-release-3](release_images/GH-release_3.png "GH-release-3") @@ -226,8 +241,14 @@ for `stable` and the most recent tag. ### 9. Edit the mkdocs.yml file site_name to set a new development version -Please commit to `master` with the title `REL: -dev`. +Please open a pull request and create a merge commit to `master` with the title `REL: -dev`. + +![merge-commit](release_images/merge_commit.png.png "merge-commit") + This should be the first commit in the new version. + +This will reset the URLs that were [manually changed before in step 2.3](#2.3-update-the-previous-version-URLs). + This process is illustrated below. ![stable-to-dev](release_images/site_name_release_1.2-1.3dev.png "stable-to-dev") @@ -243,22 +264,19 @@ Similarly update the version in CITATION.cff with a `dev` suffix. ### 10. Uploading the stable PDF to Zenodo -1. Open a private browser window -1. Log into https://github.com with the `bids-maintenance` user (credentials - are available from the BIDS maintainer group) -1. Open a new tab at https://zenodo.org and "log in via GitHub", you'll then - be on the `bids-maintenance` Zenodo account -1. Navigate to the [archive of our BIDS specification PDFs](https://doi.org/10.5281/zenodo.3686061) -1. Click on "add new version" -1. For a new version, upload the new PDF, naming it consistently with the other - PDFs: `BIDS-Specification-vX.X.X.pdf` (replace `X.X.X` with the new version) -1. Remove all other files from the upload -1. Edit the following fields: - 1. publication date - 1. version -1. Double check that everything is in order, then save and publish - -### 11. Sharing news of the release - -Please share news of the release on the [identified platforms](https://docs.google.com/spreadsheets/d/16SAGK3zG93WM2EWuoZDcRIC7ygPc5b7PDNGpFyC3obA/edit#gid=0). +1. In a previous step you have secured a PDF version of the BIDS specification and the corresponding `CITATION.cff` file. +1. Follow the steps described here: https://github.com/bids-standard/bids-specification-pdf-releases#release-instructions + +### 11. Update the BIDS website data + +Update the following files in the BIDS website repository (https://github.com/bids-standard/bids-website) if applicable: + +- `tools/timeline.csv` +- `_data/beps.yml` +- `_data/beps_completed.yml` +- `_data/beps_other.yml` + +### 12. Sharing news of the release + +Please share news of the release on the [identified platforms](https://github.com/bids-standard/bids-specification?tab=readme-ov-file#BIDS-communication-channels). Please use our previous release posts as a guide. diff --git a/mkdocs.yml b/mkdocs.yml index 04c07297ac..051aa2aaa6 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,115 +1,151 @@ -site_name: Brain Imaging Data Structure v1.9.0-dev +site_name: Brain Imaging Data Structure 1.10.0-dev site_url: https://bids-specification.readthedocs.io/en/stable/ +repo_url: https://github.com/bids-standard/bids-specification nav: - - The BIDS Specification: + - The BIDS Specification: - Introduction: introduction.md - Common principles: common-principles.md - Modality agnostic files: modality-agnostic-files.md - Modality specific files: - - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md - - Magnetoencephalography: modality-specific-files/magnetoencephalography.md - - Electroencephalography: modality-specific-files/electroencephalography.md - - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md - - Task events: modality-specific-files/task-events.md - - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md - - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md - - Genetic Descriptor: modality-specific-files/genetic-descriptor.md - - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md - - Microscopy: modality-specific-files/microscopy.md - - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md - - Motion: modality-specific-files/motion.md + - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md + - Magnetoencephalography: modality-specific-files/magnetoencephalography.md + - Electroencephalography: modality-specific-files/electroencephalography.md + - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md + - Task events: modality-specific-files/task-events.md + - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md + - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md + - Genetic Descriptor: modality-specific-files/genetic-descriptor.md + - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md + - Microscopy: modality-specific-files/microscopy.md + - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md + - Motion: modality-specific-files/motion.md - Derivatives: - - BIDS Derivatives: derivatives/introduction.md - - Common data types and metadata: derivatives/common-data-types.md - - Imaging data types: derivatives/imaging.md + - BIDS Derivatives: derivatives/introduction.md + - Common data types and metadata: derivatives/common-data-types.md + - Imaging data types: derivatives/imaging.md - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md - Glossary: glossary.md - BIDS Extension Proposals: extensions.md - Appendix: - - Schema: appendices/schema.md - - Contributors: appendices/contributors.md - - Licenses: appendices/licenses.md - - Entity table: appendices/entity-table.md - - Entities: appendices/entities.md - - File collections: appendices/file-collections.md - - Units: appendices/units.md - - Hierarchical Event Descriptors: appendices/hed.md - - MEG file formats: appendices/meg-file-formats.md - - MEG systems: appendices/meg-systems.md - - Coordinate systems: appendices/coordinate-systems.md - - Quantitative MRI: appendices/qmri.md - - Arterial Spin Labeling: appendices/arterial-spin-labeling.md - - Cross modality correspondence: appendices/cross-modality-correspondence.md + - Schema: appendices/schema.md + - Contributors: appendices/contributors.md + - Licenses: appendices/licenses.md + - Entity table: appendices/entity-table.md + - Entities: appendices/entities.md + - File collections: appendices/file-collections.md + - Units: appendices/units.md + - Hierarchical Event Descriptors: appendices/hed.md + - MEG file formats: appendices/meg-file-formats.md + - MEG systems: appendices/meg-systems.md + - Coordinate systems: appendices/coordinate-systems.md + - Quantitative MRI: appendices/qmri.md + - Arterial Spin Labeling: appendices/arterial-spin-labeling.md + - Cross modality correspondence: appendices/cross-modality-correspondence.md - Changelog: CHANGES.md - - The BIDS Starter Kit: - - Website: https://bids-standard.github.io/bids-starter-kit + - The BIDS Starter Kit: + - Website: https://bids-standard.github.io/bids-starter-kit/ - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html - GitHub repository: https://github.com/bids-standard/bids-starter-kit theme: - name: material - favicon: images/favicon.png - logo: images/logo.png - features: - - navigation.sections -copyright: Copyright © 2018-2022, BIDS Contributors - CC BY 4.0 + name: material + favicon: images/favicon.png + logo: images/logo.png + features: + - navigation.sections + - content.action.edit + icon: + repo: fontawesome/brands/github + edit: material/pencil + palette: + # Palette toggle for automatic mode + - media: (prefers-color-scheme) + toggle: + icon: material/brightness-auto + name: Switch to light mode + # Palette toggle for light mode + - media: "(prefers-color-scheme: light)" + scheme: default + toggle: + icon: material/brightness-7 + name: Switch to dark mode + # Palette toggle for dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + toggle: + icon: material/brightness-4 + name: Switch to system preference + +edit_uri: https://github.com/bids-standard/bids-specification/edit/master/src/ + +copyright: Copyright © BIDS Contributors - CC BY 4.0 + extra: - generator: false - social: - - icon: fontawesome/brands/twitter - link: https://twitter.com/BIDSstandard/ - - icon: fontawesome/brands/github - link: https://github.com/bids-standard/bids-specification/ - - icon: fontawesome/brands/google - link: https://groups.google.com/g/bids-discussion + generator: false + social: + - icon: fontawesome/brands/github + link: https://github.com/bids-standard/bids-specification/ + - icon: fontawesome/brands/x-twitter + link: https://x.com/BIDSstandard/ + - icon: fontawesome/brands/mastodon + link: https://fosstodon.org/@bidsstandard + - icon: fontawesome/brands/google + link: https://groups.google.com/g/bids-discussion + - icon: fontawesome/brands/instagram + link: https://www.instagram.com/bidsstandard/ + - icon: fontawesome/brands/youtube + link: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw + extra_javascript: - - js/jquery-3.6.0.min.js + - js/jquery-3.6.0.min.js markdown_extensions: - - toc: - anchorlink: true - - pymdownx.superfences + - toc: + anchorlink: true + - pymdownx.superfences + - admonition + - pymdownx.details plugins: - - search - - branchcustomization: - update_config: - - branch: /(?!^master$)/ - +extra_css: - - css/watermark.css - - macros: - module_name: tools/mkdocs_macros_bids/main - - redirects: - redirect_maps: - '01-introduction.md': 'introduction.md' - '02-common-principles.md': 'common-principles.md' - '03-modality-agnostic-files.md': 'modality-agnostic-files.md' - '04-modality-specific-files/01-magnetic-resonance-imaging-data.md': 'modality-specific-files/magnetic-resonance-imaging-data.md' - '04-modality-specific-files/02-magnetoencephalography.md': 'modality-specific-files/magnetoencephalography.md' - '04-modality-specific-files/03-electroencephalography.md': 'modality-specific-files/electroencephalography.md' - '04-modality-specific-files/04-intracranial-electroencephalography.md': 'modality-specific-files/intracranial-electroencephalography.md' - '04-modality-specific-files/05-task-events.md': 'modality-specific-files/task-events.md' - '04-modality-specific-files/06-physiological-and-other-continuous-recordings.md': 'modality-specific-files/physiological-and-other-continuous-recordings.md' - '04-modality-specific-files/07-behavioral-experiments.md': 'modality-specific-files/behavioral-experiments.md' - '04-modality-specific-files/08-genetic-descriptor.md': 'modality-specific-files/genetic-descriptor.md' - '04-modality-specific-files/09-positron-emission-tomography.md': 'modality-specific-files/positron-emission-tomography.md' - '04-modality-specific-files/10-microscopy.md': 'modality-specific-files/microscopy.md' - '04-modality-specific-files/11-near-infrared-spectroscopy.md': 'modality-specific-files/near-infrared-spectroscopy.md' - '05-derivatives/01-introduction.md': 'derivatives/introduction.md' - '05-derivatives/02-common-data-types.md': 'derivatives/common-data-types.md' - '05-derivatives/03-imaging.md': 'derivatives/imaging.md' - '06-longitudinal-and-multi-site-studies.md': 'longitudinal-and-multi-site-studies.md' - '07-extensions.md': 'extensions.md' - '99-appendices/14-glossary.md': 'glossary.md' - '99-appendices/01-contributors.md': 'appendices/contributors.md' - '99-appendices/02-licenses.md': 'appendices/licenses.md' - '99-appendices/03-hed.md': 'appendices/hed.md' - '99-appendices/04-entity-table.md': 'appendices/entity-table.md' - '99-appendices/05-units.md': 'appendices/units.md' - '99-appendices/06-meg-file-formats.md': 'appendices/meg-file-formats.md' - '99-appendices/07-meg-systems.md': 'appendices/meg-systems.md' - '99-appendices/08-coordinate-systems.md': 'appendices/coordinate-systems.md' - '99-appendices/09-entities.md': 'appendices/entities.md' - '99-appendices/10-file-collections.md': 'appendices/file-collections.md' - '99-appendices/11-qmri.md': 'appendices/qmri.md' - '99-appendices/12-arterial-spin-labeling.md': 'appendices/arterial-spin-labeling.md' - '99-appendices/13-cross-modality-correspondence.md': 'appendices/cross-modality-correspondence.md' -docs_dir: 'src' + - search + - branchcustomization: + update_config: + - branch: /(?!^master$)/ + +extra_css: + - css/watermark.css + - macros: + module_name: tools/mkdocs_macros_bids/main + - redirects: + redirect_maps: + "01-introduction.md": "introduction.md" + "02-common-principles.md": "common-principles.md" + "03-modality-agnostic-files.md": "modality-agnostic-files.md" + "04-modality-specific-files/01-magnetic-resonance-imaging-data.md": "modality-specific-files/magnetic-resonance-imaging-data.md" + "04-modality-specific-files/02-magnetoencephalography.md": "modality-specific-files/magnetoencephalography.md" + "04-modality-specific-files/03-electroencephalography.md": "modality-specific-files/electroencephalography.md" + "04-modality-specific-files/04-intracranial-electroencephalography.md": "modality-specific-files/intracranial-electroencephalography.md" + "04-modality-specific-files/05-task-events.md": "modality-specific-files/task-events.md" + "04-modality-specific-files/06-physiological-and-other-continuous-recordings.md": "modality-specific-files/physiological-and-other-continuous-recordings.md" + "04-modality-specific-files/07-behavioral-experiments.md": "modality-specific-files/behavioral-experiments.md" + "04-modality-specific-files/08-genetic-descriptor.md": "modality-specific-files/genetic-descriptor.md" + "04-modality-specific-files/09-positron-emission-tomography.md": "modality-specific-files/positron-emission-tomography.md" + "04-modality-specific-files/10-microscopy.md": "modality-specific-files/microscopy.md" + "04-modality-specific-files/11-near-infrared-spectroscopy.md": "modality-specific-files/near-infrared-spectroscopy.md" + "05-derivatives/01-introduction.md": "derivatives/introduction.md" + "05-derivatives/02-common-data-types.md": "derivatives/common-data-types.md" + "05-derivatives/03-imaging.md": "derivatives/imaging.md" + "06-longitudinal-and-multi-site-studies.md": "longitudinal-and-multi-site-studies.md" + "07-extensions.md": "extensions.md" + "99-appendices/14-glossary.md": "glossary.md" + "99-appendices/01-contributors.md": "appendices/contributors.md" + "99-appendices/02-licenses.md": "appendices/licenses.md" + "99-appendices/03-hed.md": "appendices/hed.md" + "99-appendices/04-entity-table.md": "appendices/entity-table.md" + "99-appendices/05-units.md": "appendices/units.md" + "99-appendices/06-meg-file-formats.md": "appendices/meg-file-formats.md" + "99-appendices/07-meg-systems.md": "appendices/meg-systems.md" + "99-appendices/08-coordinate-systems.md": "appendices/coordinate-systems.md" + "99-appendices/09-entities.md": "appendices/entities.md" + "99-appendices/10-file-collections.md": "appendices/file-collections.md" + "99-appendices/11-qmri.md": "appendices/qmri.md" + "99-appendices/12-arterial-spin-labeling.md": "appendices/arterial-spin-labeling.md" + "99-appendices/13-cross-modality-correspondence.md": "appendices/cross-modality-correspondence.md" +docs_dir: "src" use_directory_urls: false diff --git a/pdf_build_src/pandoc_script.py b/pdf_build_src/pandoc_script.py index b7b1842b96..e9710482ab 100644 --- a/pdf_build_src/pandoc_script.py +++ b/pdf_build_src/pandoc_script.py @@ -2,6 +2,7 @@ This is done once the duplicate src directory is processed. """ + import subprocess import yaml from pathlib import Path @@ -11,9 +12,7 @@ def _find(path, filename): return next( - parent / filename - for parent in path.parents - if Path.is_file(parent / filename) + parent / filename for parent in path.parents if Path.is_file(parent / filename) ) diff --git a/pdf_build_src/process_markdowns.py b/pdf_build_src/process_markdowns.py index 5d30aabc21..705daa8b22 100644 --- a/pdf_build_src/process_markdowns.py +++ b/pdf_build_src/process_markdowns.py @@ -17,6 +17,8 @@ import numpy as np +from remove_admonitions import remove_admonitions + sys.path.append("../tools/") # functions from module macros are called by eval() later on from mkdocs_macros_bids import macros # noqa: F401 @@ -585,9 +587,9 @@ def edit_titlepage(): data = file.readlines() data[-1] = ( - fr"\textsc{{\large {version_number}}}" + rf"\textsc{{\large {version_number}}}" r"\\[0.5cm]" - fr"{{\large {build_date}}}" + rf"{{\large {build_date}}}" r"\\[2cm]" r"\vfill" r"\end{titlepage}" @@ -679,33 +681,38 @@ def process_macros(duplicated_src_dir_path): duplicated_src_dir_path = "src_copy/src" - # Step 1: make a copy of the src directory in the current directory + # make a copy of the src directory in the current directory copy_src() - # Step 2: run mkdocs macros embedded in markdown files + # run mkdocs macros embedded in markdown files process_macros(duplicated_src_dir_path) - # Step 3: copy BIDS_logo to images directory of the src_copy directory + # remove mkdocs admonition + remove_admonitions( + input_folder=duplicated_src_dir_path, output_folder=duplicated_src_dir_path + ) + + # copy BIDS_logo to images directory of the src_copy directory copy_bids_logo() - # Step 4: copy images from subdirectories of src_copy directory + # copy images from subdirectories of src_copy directory copy_images(duplicated_src_dir_path) subprocess.call("mv src_copy/src/images/images/* src_copy/src/images/", shell=True) - # Step 5: extract the latest version number, date and title + # extract the latest version number, date and title extract_header_string() add_header() edit_titlepage() - # Step 6: modify changelog to be a level 1 heading to facilitate section + # modify changelog to be a level 1 heading to facilitate section # separation modify_changelog() - # Step 7: remove all internal links + # remove all internal links assert_no_multiline_links(duplicated_src_dir_path) remove_internal_links_inline(duplicated_src_dir_path) remove_internal_links_reference(duplicated_src_dir_path) - # Step 8: correct number of dashes and fences alignment for rendering tables in PDF + # correct number of dashes and fences alignment for rendering tables in PDF correct_tables(duplicated_src_dir_path) diff --git a/pdf_build_src/remove_admonitions.py b/pdf_build_src/remove_admonitions.py new file mode 100644 index 0000000000..1942f8b5b0 --- /dev/null +++ b/pdf_build_src/remove_admonitions.py @@ -0,0 +1,64 @@ +"""Script to remove all mkdocs admonition from the markdown files in a directory. + +See the pdf_build_src/tests/data/input directory to see what admonitions look like. +""" + +from __future__ import annotations + +import shutil +from pathlib import Path + +INDENT = " " + +ADMONITION_DELIMITERS = ["!!!", "???", "???+"] + + +def remove_admonitions( + input_folder: str | Path, output_folder: str | Path, indent: str = None +): + + if indent is None: + indent = INDENT + + md_files = Path(input_folder).glob("**/*.md") + + for file in md_files: + + with open(file, "r", encoding="utf8") as f: + content = f.readlines() + + output_file = Path(output_folder) / file.relative_to(input_folder) + output_file.parent.mkdir(parents=True, exist_ok=True) + print(f"processing: {file}\n to: {output_file}") + + with open(output_file, "w", encoding="utf8") as f: + + is_admonition = False + counter = 0 + for line in content: + + if any(line.startswith(x) for x in ADMONITION_DELIMITERS): + is_admonition = True + counter = 0 + continue + + # skip first line after admonition + if is_admonition and counter == 0: + counter += 1 + continue + + if line != "\n" and not line.startswith(indent): + is_admonition = False + + if is_admonition: + line = line.lstrip(indent) + + f.write(line) + + +if __name__ == "__main__": + """If run as a script this will just run the main function on test data.""" + input_folder = Path(__file__).parent / "tests" / "data" / "input" + output_folder = Path(__file__).parent / "tests" / "data" / "output" + shutil.rmtree(output_folder) + remove_admonitions(input_folder, output_folder) diff --git a/pdf_build_src/test_remove_admonitions.py b/pdf_build_src/test_remove_admonitions.py new file mode 100644 index 0000000000..e995e42246 --- /dev/null +++ b/pdf_build_src/test_remove_admonitions.py @@ -0,0 +1,25 @@ +from pathlib import Path + +from remove_admonitions import remove_admonitions + + +def test_remove_admonitions(tmp_path): + input_folder = Path(__file__).parent / "tests" / "data" / "input" + expected_folder = Path(__file__).parent / "tests" / "data" / "expected" + + remove_admonitions(input_folder, tmp_path) + + generated_files = list(tmp_path.glob("**/*.md")) + + for file in generated_files: + + expected = expected_folder / file.relative_to(tmp_path) + + with open(expected, "r", encoding="utf8") as f: + expected_content = f.readlines() + + with open(file, "r", encoding="utf8") as f: + generated_content = f.readlines() + + for expected_line, generated_line in zip(expected_content, generated_content): + assert generated_line == expected_line diff --git a/pdf_build_src/tests/data/expected/README.md b/pdf_build_src/tests/data/expected/README.md new file mode 100644 index 0000000000..37fadc295d --- /dev/null +++ b/pdf_build_src/tests/data/expected/README.md @@ -0,0 +1,32 @@ +# Test inputs + +This input directory contains data to use for testing the pdf build code of the BIDS specification. + +For example the following admonition should be removed by `pdf_build_src/remove_admonitions.py`. + +Lorem ipsum dolor sit amet, consectetur adipiscing elit. +Nulla et euismod nulla. +Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, +nec semper lorem quam in massa. + +The `expected` directory should contain the documents +as they should look like after processing. + +[Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end) +come in different type. In aaddtion of the classical admonitions show above you have also: + +Collapsible admonitions start with 3 questions marks (`???`). + +Collapsible admonitions that will be shown as expanded +start with 3 questions marks and a plus sign (`???+`). + + + +Let's see + +- [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) +- foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) + +More of the admonition + +And here we resume normal thing. diff --git a/pdf_build_src/tests/data/expected/modality-specific-files/magnetic-resonance-imaging-data.md b/pdf_build_src/tests/data/expected/modality-specific-files/magnetic-resonance-imaging-data.md new file mode 100644 index 0000000000..d70af64a49 --- /dev/null +++ b/pdf_build_src/tests/data/expected/modality-specific-files/magnetic-resonance-imaging-data.md @@ -0,0 +1,8 @@ +# Magnetic Resonance Imaging + +## Common metadata fields + +Lorem ipsum dolor sit amet, consectetur adipiscing elit. +Nulla et euismod nulla. +Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, +nec semper lorem quam in massa. diff --git a/pdf_build_src/tests/data/input/README.md b/pdf_build_src/tests/data/input/README.md new file mode 100644 index 0000000000..cab4817282 --- /dev/null +++ b/pdf_build_src/tests/data/input/README.md @@ -0,0 +1,40 @@ +# Test inputs + +This input directory contains data to use for testing the pdf build code of the BIDS specification. + +For example the following admonition should be removed by `pdf_build_src/remove_admonitions.py`. + +!!! note + + Lorem ipsum dolor sit amet, consectetur adipiscing elit. + Nulla et euismod nulla. + Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, + nec semper lorem quam in massa. + +The `expected` directory should contain the documents +as they should look like after processing. + +[Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end) +come in different type. In aaddtion of the classical admonitions show above you have also: + +??? note "Collapsible admonitions" + + Collapsible admonitions start with 3 questions marks (`???`). + +???+ note "Expanded collapsible admonitions" + + Collapsible admonitions that will be shown as expanded + start with 3 questions marks and a plus sign (`???+`). + + + +!!! example "non ordered list should be handle propeler" + + Let's see + + - [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) + - foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) + + More of the admonition + +And here we resume normal thing. diff --git a/pdf_build_src/tests/data/input/modality-specific-files/magnetic-resonance-imaging-data.md b/pdf_build_src/tests/data/input/modality-specific-files/magnetic-resonance-imaging-data.md new file mode 100644 index 0000000000..bfc1b8509a --- /dev/null +++ b/pdf_build_src/tests/data/input/modality-specific-files/magnetic-resonance-imaging-data.md @@ -0,0 +1,10 @@ +# Magnetic Resonance Imaging + +## Common metadata fields + +!!! warning "foo bar" + + Lorem ipsum dolor sit amet, consectetur adipiscing elit. + Nulla et euismod nulla. + Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, + nec semper lorem quam in massa. diff --git a/readthedocs.yml b/readthedocs.yml index cc3f461fc7..5611c59505 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -2,11 +2,14 @@ version: 2 build: os: ubuntu-22.04 + apt_packages: + - jq tools: python: "3.11" jobs: pre_build: - bst -v export --output src/schema.json + - tools/no-bad-schema-paths.sh src/schema.json # README.md might need fixing mkdocs: configuration: mkdocs.yml diff --git a/release_images/merge_commit.png b/release_images/merge_commit.png new file mode 100644 index 0000000000..3df09babf9 Binary files /dev/null and b/release_images/merge_commit.png differ diff --git a/src/CHANGES.md b/src/CHANGES.md index f6b0a97cd4..087368ffea 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -1,24 +1,44 @@ # Changelog -## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) - +## [v1.9.0](https://github.com/bids-standard/bids-specification/tree/v1.9.0) (2023-11-20) + +- \[FIX] mention phenotype dir in folder structure [#1644](https://github.com/bids-standard/bids-specification/pull/1644) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] add `ElectricalStimulation` and `\*Parameters` metadata to MEEG jsons [#1638](https://github.com/bids-standard/bids-specification/pull/1638) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] years and degrees Units and unit to be singular to match the rest [#1631](https://github.com/bids-standard/bids-specification/pull/1631) ([yarikoptic](https://github.com/yarikoptic)) +- \[FIX] Hierarchical Event Descriptors (HED) page update [#1623](https://github.com/bids-standard/bids-specification/pull/1623) ([effigies](https://github.com/effigies)) +- \[ENH] Add `descriptions.tsv` file relating to the `desc-\` entity [#1613](https://github.com/bids-standard/bids-specification/pull/1613) ([CPernet](https://github.com/CPernet)) +- \[FIX] Do not require notch frequencies to be parsed as numbers, accommodating multiples [#1605](https://github.com/bids-standard/bids-specification/pull/1605) ([effigies](https://github.com/effigies)) +- \[ENH] Allow Levels field of column descriptions to be objects with TermURLs for each level [#1603](https://github.com/bids-standard/bids-specification/pull/1603) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Add optional low_cutoff and high_cutoff columns for fnirs channels.tsv [#1597](https://github.com/bids-standard/bids-specification/pull/1597) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Recommend SliceTiming if MRAcquisitionType is "2D" [#1594](https://github.com/bids-standard/bids-specification/pull/1594) ([tsalo](https://github.com/tsalo)) +- \[ENH] Add Level objects to channels.json for motion [#1591](https://github.com/bids-standard/bids-specification/pull/1591) ([effigies](https://github.com/effigies)) +- \[ENH] Add "chunk" entity to MRI datatype [#1586](https://github.com/bids-standard/bids-specification/pull/1586) ([valosekj](https://github.com/valosekj)) +- \[SCHEMA]\[ENH] Remove atlas entity and replace it with seg in prep of BEP038 [#1579](https://github.com/bids-standard/bids-specification/pull/1579) ([melanieganz](https://github.com/melanieganz)) +- \[FIX] Correct PDw suffix description [#1578](https://github.com/bids-standard/bids-specification/pull/1578) ([jeremie-fouquet](https://github.com/jeremie-fouquet)) +- \[FIX] improve longitudinal example [#1576](https://github.com/bids-standard/bids-specification/pull/1576) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[INFRA] Adds Kim Ray as maintainer. [#1571](https://github.com/bids-standard/bids-specification/pull/1571) ([arokem](https://github.com/arokem)) +- \[ENH] Allow for "echo" entity to be used with T1w and other nonparametric anatomical suffixes [#1570](https://github.com/bids-standard/bids-specification/pull/1570) ([yarikoptic](https://github.com/yarikoptic)) +- \[FIX] Update `templates` in modality-agnostic-files [#1564](https://github.com/bids-standard/bids-specification/pull/1564) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] Clarify that electrodes.tsv is optional for MEG, for use with simultaneous (i)EEG [#1555](https://github.com/bids-standard/bids-specification/pull/1555) ([effigies](https://github.com/effigies)) +- \[ENH] Allow UNKNOWN and NONE ContrastBolusIngredients [#1547](https://github.com/bids-standard/bids-specification/pull/1547) ([Remi-Gau](https://github.com/Remi-Gau)) - \[FIX] Update links to BIDS examples [#1545](https://github.com/bids-standard/bids-specification/pull/1545) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] add schema in appendix [#1543](https://github.com/bids-standard/bids-specification/pull/1543) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] add "visual correction" and "head stabilization" metadata [#1539](https://github.com/bids-standard/bids-specification/pull/1539) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] Clarify meaning of raw vs derivative datasets [#1537](https://github.com/bids-standard/bids-specification/pull/1537) ([CPernet](https://github.com/CPernet)) - \[FIX] match subject label in folder and filename in func example [#1536](https://github.com/bids-standard/bids-specification/pull/1536) ([Remi-Gau](https://github.com/Remi-Gau)) -- FIX: Trail MEG directory formats with `/` [#1534](https://github.com/bids-standard/bids-specification/pull/1534) ([effigies](https://github.com/effigies)) +- \[FIX] Trail MEG directory formats with `/` [#1534](https://github.com/bids-standard/bids-specification/pull/1534) ([effigies](https://github.com/effigies)) - \[ENH] Permit CITATION.cff as structured alternative to some dataset_description fields [#1525](https://github.com/bids-standard/bids-specification/pull/1525) ([effigies](https://github.com/effigies)) - \[FIX] Add missing column description in physio example [#1514](https://github.com/bids-standard/bids-specification/pull/1514) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] Clarify that data files must be uniquely identified by entities/suffix [#1508](https://github.com/bids-standard/bids-specification/pull/1508) ([sappelhoff](https://github.com/sappelhoff)) -- DOC: Auto-generate full API docs [#1505](https://github.com/bids-standard/bids-specification/pull/1505) ([effigies](https://github.com/effigies)) - \[INFRA] Publish schema tools API docs to additional ReadTheDocs site [#1491](https://github.com/bids-standard/bids-specification/pull/1491) ([bendhouseart](https://github.com/bendhouseart)) - \[FIX] Remove references to unspecified aslcontext.json [#1485](https://github.com/bids-standard/bids-specification/pull/1485) ([Remi-Gau](https://github.com/Remi-Gau)) +- ENH: Define channel column for events and Delimiter field for column descriptions [#1483](https://github.com/bids-standard/bids-specification/pull/1483) ([effigies](https://github.com/effigies)) - \[FIX] Revert index (entity format) definition to be a non-negative number, permitting zero [#1482](https://github.com/bids-standard/bids-specification/pull/1482) ([TheChymera](https://github.com/TheChymera)) -- ENH: Add version list to schema.meta and a warning on unknown BIDSVersion [#1472](https://github.com/bids-standard/bids-specification/pull/1472) ([effigies](https://github.com/effigies)) - \[FIX] Clean up qMRI RB1COR notes [#1465](https://github.com/bids-standard/bids-specification/pull/1465) ([lukeje](https://github.com/lukeje)) - \[ENH] Allow fractional seconds in StartTime [#1459](https://github.com/bids-standard/bids-specification/pull/1459) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] consistently list filename templates; `ext` --> `extension`; `\_photo.jpg` --> `\_photo.\` [#1458](https://github.com/bids-standard/bids-specification/pull/1458) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Demote `sample` and `value` columns in `events.tsv` from OPTIONAL to arbitrary [#1457](https://github.com/bids-standard/bids-specification/pull/1457) ([sappelhoff](https://github.com/sappelhoff)) -- ENH: Clarify shape of PDT2 images and recommend acq entity for split PDw/T2w images [#1448](https://github.com/bids-standard/bids-specification/pull/1448) ([effigies](https://github.com/effigies)) +- \[ENH] Clarify shape of PDT2 images and recommend acq entity for split PDw/T2w images [#1448](https://github.com/bids-standard/bids-specification/pull/1448) ([effigies](https://github.com/effigies)) - \[ENH] clarify guiding principles for requirement levels [#1444](https://github.com/bids-standard/bids-specification/pull/1444) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Clarify that dataset_description.Genetics object is required for genetics data [#1442](https://github.com/bids-standard/bids-specification/pull/1442) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] Clarify that BIDS specification is in American English [#1439](https://github.com/bids-standard/bids-specification/pull/1439) ([yarikoptic](https://github.com/yarikoptic)) @@ -27,25 +47,22 @@ - \[FIX] Rename `channels.tsv` column: `orientation\_component` to `component` [#1417](https://github.com/bids-standard/bids-specification/pull/1417) ([sjeung](https://github.com/sjeung)) - \[ENH] Some missing docstrings for bidsschematools [#1413](https://github.com/bids-standard/bids-specification/pull/1413) ([anibalsolon](https://github.com/anibalsolon)) - \[FIX] fixing some minor issues introduced recently [#1411](https://github.com/bids-standard/bids-specification/pull/1411) ([yarikoptic](https://github.com/yarikoptic)) -- SCHEMA: Implement some fairly easy rules [#1410](https://github.com/bids-standard/bids-specification/pull/1410) ([effigies](https://github.com/effigies)) -- \[REF] refactor institution and task tables [#1397](https://github.com/bids-standard/bids-specification/pull/1397) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] Add paragraph about richness versus distinctness in filenames [#1392](https://github.com/bids-standard/bids-specification/pull/1392) ([CPernet](https://github.com/CPernet)) - \[FIX] Updated HED score library version [#1390](https://github.com/bids-standard/bids-specification/pull/1390) ([VisLab](https://github.com/VisLab)) - \[FIX] Updated links and fixed typos in hed appendix [#1383](https://github.com/bids-standard/bids-specification/pull/1383) ([VisLab](https://github.com/VisLab)) - \[ENH] add screen parameters metadata [#1369](https://github.com/bids-standard/bids-specification/pull/1369) ([Remi-Gau](https://github.com/Remi-Gau)) -- RF: allow for any "recording" file to be listed in \_scans.tsv not just "neural recording" [#1368](https://github.com/bids-standard/bids-specification/pull/1368) ([yarikoptic](https://github.com/yarikoptic)) +- \[MISC] allow for any "recording" file to be listed in \_scans.tsv not just "neural recording" [#1368](https://github.com/bids-standard/bids-specification/pull/1368) ([yarikoptic](https://github.com/yarikoptic)) - \[FIX] wrong usage of DOI in SourceDatasets example [#1361](https://github.com/bids-standard/bids-specification/pull/1361) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] make references to Neuromag/Elekta/MEGIN consistent [#1359](https://github.com/bids-standard/bids-specification/pull/1359) ([sappelhoff](https://github.com/sappelhoff)) -- \[DOC] link to steering group section on bids website [#1358](https://github.com/bids-standard/bids-specification/pull/1358) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] Add reference for ASL BEP [#1357](https://github.com/bids-standard/bids-specification/pull/1357) ([Remi-Gau](https://github.com/Remi-Gau)) - \[FIX] remove redundant entity definitions in behavioral page [#1356](https://github.com/bids-standard/bids-specification/pull/1356) ([Remi-Gau](https://github.com/Remi-Gau)) - \[FIX] add missing processing entity for MEG physio files and render physio filename templates for fNIRS [#1355](https://github.com/bids-standard/bids-specification/pull/1355) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] Recommend gzip header fields be set to empty values [#1349](https://github.com/bids-standard/bids-specification/pull/1349) ([kousu](https://github.com/kousu)) - \[FIX] clarify TriggerChannelCount and TRIG type [#1342](https://github.com/bids-standard/bids-specification/pull/1342) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] Add qMRI fieldmap filename templates [#1336](https://github.com/bids-standard/bids-specification/pull/1336) ([Remi-Gau](https://github.com/Remi-Gau)) -- ENH: Introduce GIFTI formats in derivatives [#1333](https://github.com/bids-standard/bids-specification/pull/1333) ([effigies](https://github.com/effigies)) +- \[ENH] Introduce GIFTI formats in derivatives [#1333](https://github.com/bids-standard/bids-specification/pull/1333) ([effigies](https://github.com/effigies)) - \[ENH] Add ParallelReductionFactorOutOfPlane to MRI metadata [#1221](https://github.com/bids-standard/bids-specification/pull/1221) ([lukeje](https://github.com/lukeje)) -- \[ENH]\[SCHEMA] Adding an OPTIONAL \_task-\