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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 91ba4d49..5be42a5b 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 @@ -81,3 +81,18 @@ jobs: run: | python no-bad-latin.py working-directory: tools + + # Validate CITATION.cff + validate_cff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: 3 + - name: Install dependencies + run: | + python -m pip install --upgrade pip setuptools + pip3 install cffconvert + - name: Validate CITATION.cff + run: make validate_citation_cff diff --git a/.gitignore b/.gitignore index 59fa1a1d..9e8cf66a 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 07342104..00000000 --- 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 7252578b..baab7834 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: v4.5.0 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: 23.3.0 + 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: 6.0.0 + rev: 7.0.0 hooks: - id: flake8 args: [--config=tools/schemacode/setup.cfg] - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.0-alpha.9-for-vscode + 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: v1.4.1 + rev: v1.9.0 hooks: - id: mypy # Sync with project.optional-dependencies.typing diff --git a/.remarkrc b/.remarkrc index fc065759..8d6c2648 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 new file mode 100644 index 00000000..fa5b1a18 --- /dev/null +++ b/.tributors @@ -0,0 +1,3128 @@ +{ + "aaron_oliver-taylor": { + "contributions": [ + "doc" + ], + "name": "Aaron Oliver-Taylor" + }, + "adam2392": { + "bio": "I am a Postdoctoral Research Fellow at Columbia University in the Causal AI Lab. 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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 + +keywords: + - brain imaging data structure + - bids + - standards + - data-standards + +authors: + - given-names: Aaron + family-names: Oliver-Taylor + - given-names: Adam + family-names: Li + website: https://adam2392.github.io/ + - given-names: Adam + 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, 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, 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, + Juelich, 52428, Germany + email: adina.wagner@t-online.de + - given-names: Agah + family-names: Karakuzu + website: https://agahkarakuzu.github.io + orcid: https://orcid.org/0000-0001-7283-271X + email: agahkarakuzu@gmail.com + - given-names: Aki + family-names: Nikolaidis + website: https://github.com/AkiNikolaidis + orcid: https://orcid.org/0000-0001-8960-1934 + - given-names: Alberto + family-names: Lazari + - given-names: Alejandro + family-names: de la Vega + website: https://github.com/adelavega + - given-names: Alessio + family-names: Giacomel + website: https://github.com/alegiac95 + orcid: https://orcid.org/0000-0002-7784-2041 + affiliation: GlaxoSmithKline Research and Development + - given-names: Alex + family-names: Rockhill + website: https://github.com/alexrockhill + orcid: https://orcid.org/0000-0003-3868-7453 + email: aprockhill@mailbox.org + - given-names: Alexander + family-names: Jones + - given-names: Alexander L. + family-names: Cohen + website: https://bchcohenlab.com + orcid: https://orcid.org/0000-0001-6557-5866 + 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 + - given-names: Alexandre + family-names: Gramfort + website: http://alexandre.gramfort.net + orcid: https://orcid.org/0000-0001-9791-4404 + affiliation: Inria, Université Paris-Saclay + email: alexandre.gramfort@inria.fr + - given-names: Alexandre + family-names: Hutton + - given-names: Alexandre + family-names: Routier + website: https://github.com/alexandreroutier + orcid: https://orcid.org/0000-0003-1603-8049 + - given-names: Alexandru + family-names: Foias + website: https://github.com/alexfoias + 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 + family-names: Eklund + website: https://github.com/wanderine + - given-names: Andrea + family-names: Pigorini + - given-names: Andrew + family-names: Hoopes + - given-names: Andrew + family-names: Jahn + - given-names: Andrew + family-names: Janke + website: http://apjanke.net + email: andrew@apjanke.net + - given-names: Anibal + family-names: Sólon + website: https://anibalsolon.com/ + orcid: https://orcid.org/0000-0002-2050-0614 + email: anibalsolon@gmail.com + - given-names: Anthony + family-names: Galassi + website: https://github.com/bendhouseart + orcid: https://orcid.org/0000-0001-6550-4574 + - given-names: Ariel + 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 + email: arokem@uw.edu + - given-names: Arjen + family-names: Stolk + - given-names: Arnaud + family-names: Delorme + website: https://www.arnauddelorme.com + orcid: https://orcid.org/0000-0002-0799-3557 + affiliation: Swartz Center for Computational Neuroscience + email: adelorme@ucsd.edu + - given-names: Arnaud + family-names: Marcoux + website: https://github.com/arnaudmarcoux + - given-names: Arshitha + 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, USA + email: arsh2794@gmail.com + - given-names: Ashley G. + family-names: Gillman + website: https://github.com/ashgillman + - given-names: Athanasia + family-names: Monika Mowinckel + website: https://github.com/drmowinckels + orcid: https://orcid.org/0000-0002-5756-0223 + affiliation: University of Oslo + - given-names: Aysegul + family-names: Gunduz + - given-names: Azeez + family-names: Adebimpe + orcid: https://orcid.org/0000-0001-9049-0135 + affiliation: University of Pennsylvania + - given-names: B. + family-names: Nolan Nichols + - given-names: Balint + family-names: Kincses + - given-names: Benjamin + family-names: Beasley + website: https://github.com/musicinmybrain + - given-names: Benjamin + family-names: Dichter + - given-names: Benjamin + family-names: Gagl + orcid: https://orcid.org/0000-0002-2339-6293 + affiliation: University of Vienna + - given-names: Bertrand + family-names: Thirion + website: https://github.com/bthirion + orcid: https://orcid.org/0000-0001-5018-7895 + - given-names: Bradley + 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, + USA + - given-names: Brett L. + family-names: Foster + - given-names: Brian A. + family-names: Wandell + - given-names: Brian N. + family-names: Lundstrom + - given-names: Camille + family-names: Maumet + website: https://camillemaumet.com/ + orcid: https://orcid.org/0000-0002-6290-553X + affiliation: Inria, Univ Rennes, CNRS, Inserm, Rennes, 35042, France + - given-names: Carlo + 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 + family-names: Benjamin + - given-names: Chris + family-names: Gahnström + - given-names: Chris + family-names: Holdgraf + website: http://chrisholdgraf.com + orcid: https://orcid.org/0000-0002-9420-9301 + - given-names: Chris J. + family-names: Gorgolewski + website: http://chrisgorgolewski.org + orcid: https://orcid.org/0000-0003-3321-7583 + affiliation: Google LLC + email: krzysztof.gorgolewski@gmail.com + - given-names: Chris + 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, USA + email: crorden6@gmail.com + - given-names: Christian + family-names: Büchel + - given-names: Christian + family-names: Horea + website: http://www.chymera.eu + orcid: https://orcid.org/0000-0001-7037-2449 + 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 + 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 + 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 + - given-names: Christopher J. + family-names: Markiewicz + website: https://github.com/effigies + email: effigies@gmail.com + - given-names: Christopher + family-names: Lee-Messer + - given-names: Clara + family-names: Moreau + - given-names: Clint + family-names: Hansen + affiliation: Kiel University + email: c.hansen@neurologie.uni-kiel.de + - given-names: Cyril + 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 + email: wamcyril@gmail.com + - given-names: Cyrus + family-names: Eierud + website: https://trendscenter.org/cyrus-eierud/ + orcid: https://orcid.org/0000-0002-9942-676X + affiliation: Georgia State University + email: ceierud@gsu.edu + - given-names: D. + family-names: Sturgeon + website: https://dasturge.github.io + - given-names: Dan + 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, USA + email: dlevitas@iu.edu + - given-names: Dan + family-names: Lurie + website: https://github.com/danlurie + - given-names: Daniel A. + family-names: Handwerker + - given-names: David + family-names: Alsop + - given-names: David + family-names: Boas + website: http://bu.edu/neurophotonics + orcid: https://orcid.org/0000-0002-6709-7711 + 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 + email: david.m.groppe@gmail.com + - given-names: David + family-names: Keator + website: https://github.com/dbkeator + orcid: https://orcid.org/0000-0001-5281-5576 + affiliation: Change Your Brain, Change Your Life Foundation + - given-names: David + family-names: McAlpine + - given-names: David + family-names: Thomas + - given-names: Dejan + family-names: Draschkow + orcid: https://orcid.org/0000-0003-1354-4835 + affiliation: University of Oxford + - given-names: Dianne + 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 USA + email: dkp@arizona.edu + - given-names: Dimitri + family-names: Papadopoulos Orfanos + website: https://github.com/DimitriPapadopoulos + - given-names: Dmitry + family-names: Petrov + - given-names: Dora + family-names: Hermes + website: https://github.com/dorahermes + - given-names: Dorien + family-names: Huijser + website: https://github.com/DorienHuijser + orcid: https://orcid.org/0000-0003-3282-8083 + affiliation: Utrecht University + - given-names: Douglas N. + family-names: Greve + website: https://github.com/dngreve + - given-names: Duncan + family-names: Macleod + - given-names: Dung + family-names: Truong + website: https://github.com/dungscout96 + affiliation: Swartz Center for Computational Neuroscience + email: dutruong@ucsd.edu + - given-names: Dylan + family-names: Nielson + website: https://github.com/Shotgunosine + orcid: https://orcid.org/0000-0003-4613-6643 + - given-names: Eduard + family-names: Ort + website: https://github.com/eort + orcid: https://orcid.org/0000-0001-5546-3561 + 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 + - 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, + USA + - given-names: Elke + family-names: Warmerdam + affiliation: Saarland University + email: elke.warmerdam@uni-saarland.de + - given-names: Erdal + family-names: Karaca + website: https://github.com/erdalkaraca + - given-names: Eric A. + 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, USA + email: eric.earl@nih.gov + - given-names: Eric + family-names: Achten + website: https://github.com/rikAchten + - given-names: Eric + family-names: Bridgeford + - given-names: Erin W. + family-names: Dickie + website: http://imaging-genetics.camh.ca/ + - given-names: Ethan + family-names: Blackwood + orcid: https://orcid.org/0000-0002-3049-0640 + affiliation: University of Pennsylvania + - given-names: Eugene P. + family-names: Duff + website: http://eduff.github.io + orcid: https://orcid.org/0000-0001-8795-5472 + affiliation: UK Dementia Research Institute, Imperial College London, UK + email: eduff@imperial.ac.uk + - given-names: Ezequiel + family-names: Mikulan + orcid: https://orcid.org/0000-0001-7259-6120 + affiliation: University of Milan + - given-names: Felipe + family-names: Orihuela-Espina + - given-names: Fidel + family-names: Alfaro Almagro + - given-names: Filip + family-names: Szczepankiewicz + orcid: https://orcid.org/0000-0002-5251-587X + affiliation: Lund University + - given-names: Filippo + 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, + Sesto Fiorentino, (FI), 50019, Italy + email: castelli@lens.unifi.it + - given-names: Franco + family-names: Pestilli + website: https://liberalarts.utexas.edu/psychology/faculty/fp4834 + - given-names: Franklin W. + family-names: Feingold + website: https://github.com/franklin-feingold + orcid: https://orcid.org/0000-0002-6533-2909 + affiliation: Stanford University + - given-names: François + family-names: Tadel + - given-names: Gaia + 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 + 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, USA + email: gangchen@mail.nih.gov + - given-names: Gaël + family-names: Varoquaux + website: https://github.com/GaelVaroquaux + - given-names: Ghislain + family-names: Vaillant + website: https://github.com/ghisvail + orcid: https://orcid.org/0000-0003-0267-3033 + - given-names: Giacomo + family-names: Bertazzoli + orcid: https://orcid.org/0000-0003-1624-2576 + affiliation: Centro San Giovanni di Dio Fatebenefratelli + - given-names: Giacomo + family-names: Guidali + orcid: https://orcid.org/0000-0002-3741-0404 + affiliation: IRCCS Centro San Giovanni di Dio Fatebenefratelli + - given-names: Giacomo + family-names: Mazzamuto + website: https://github.com/gmazzamuto + orcid: https://orcid.org/0000-0003-3077-3904 + affiliation: National Institute of Optics, National Research Council + email: mazzamuto@lens.unifi.it + - given-names: Gilles + family-names: de Hollander + website: https://github.com/Gilles86 + - given-names: Gio + family-names: Piantoni + - given-names: Gitte M. + family-names: Knudsen + - given-names: Giulio + family-names: Castegnaro + - given-names: Giuseppe + family-names: Gallitto + orcid: https://orcid.org/0000-0001-5185-0206 + affiliation: Essen University Hospital + - given-names: Graham + family-names: Searle + - given-names: Granville J. + family-names: Matheson + website: http://www.granvillematheson.com + - given-names: Gregory + family-names: Kiar + website: https://github.com/gkiar + orcid: https://orcid.org/0000-0001-8915-496X + affiliation: Child Mind Institute + - given-names: Gregory + family-names: Noack + website: https://github.com/thinknoack + - given-names: Greydon + family-names: Gilmore + website: http://greydongilmore.com + orcid: https://orcid.org/0000-0001-7523-5734 + email: ggilmore@uwo.ca + - given-names: Guillaume + family-names: Flandin + website: https://www.fil.ion.ucl.ac.uk/team/spm-team/ + orcid: https://orcid.org/0000-0003-0077-7859 + affiliation: University College London + - given-names: Gunnar + family-names: Schaefer + orcid: https://orcid.org/0000-0001-9661-2121 + - given-names: Gustav + family-names: Nilsonne + website: https://nilsonne.net/about/ + orcid: https://orcid.org/0000-0001-5273-0150 + affiliation: Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, + 17177, Sweden + email: gustav.nilsonne@ki.se + - given-names: Hamish + family-names: Innes-Brown + orcid: https://orcid.org/0000-0002-1512-2823 + affiliation: Oticon A/S, Eriksholm Research Centre, Snekkersten, Denmark + email: hain@eriksholm.com + - 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 + email: hanne.d.hansen@nru.dk + - given-names: Hanzhang + family-names: Lu + orcid: https://orcid.org/0000-0003-3871-1564 + affiliation: Johns Hopkins Medicine + - given-names: Hao-Ting + family-names: Wang + website: https://github.com/htwangtw + orcid: https://orcid.org/0000-0003-4078-2038 + affiliation: CRIUGM, Montreal, Quebec, H3W 1W5, Canada + email: htwangtw@gmail.com + - given-names: Helena + family-names: Cockx + website: https://github.com/helenacockx + orcid: https://orcid.org/0000-0001-7782-7178 + affiliation: Radboud University + email: helena.cockx@donders.ru.nl + - given-names: Henk + 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, + Amsterdam, 1013 EG, The Netherlands + email: h.j.mutsaerts@amsterdamumc.nl + - given-names: Hernando + family-names: Ombao + - given-names: Hugo + family-names: Boniface + website: https://github.com/Hboni + - given-names: Ilkay + family-names: Isik + website: https://github.com/ilkayisik + orcid: https://orcid.org/0000-0002-1652-9297 + affiliation: Max Planck Institute for Empirical Aesthetics + - given-names: Ilona + family-names: Lipp + website: https://github.com/IlonaLipp + - given-names: International + family-names: Neuroinformatics Coordinating Facility + website: https://github.com/INCF + - given-names: Iris + family-names: Groen + website: https://github.com/irisgroen + - given-names: Isla + family-names: Staden + orcid: https://orcid.org/0000-0002-0795-1154 + - given-names: Jaap + family-names: von der Aar + - given-names: Jakub + family-names: Kaczmarzyk + website: https://github.com/kaczmarj + orcid: https://orcid.org/0000-0002-5544-7577 + - given-names: James + family-names: Gholam + orcid: https://orcid.org/0000-0003-4513-2341 + - given-names: James + family-names: Kent + website: https://github.com/jdkent + - given-names: Jan + 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 + email: jm.schoffelen@gmail.com + - given-names: Jan + family-names: Petr + website: https://www.exploreasl.org + orcid: https://orcid.org/0000-0002-3201-6002 + affiliation: Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany + email: j.petr@hzdr.de + - given-names: Jan-Mathijs + family-names: Schoffelen + - given-names: Jean-Baptiste + family-names: Poline + website: https://github.com/jbpoline + orcid: https://orcid.org/0000-0002-9794-749X + - given-names: Jean-Christophe + family-names: Houde + website: http://scil.dinf.usherbrooke.ca/jchoude + orcid: https://orcid.org/0000-0003-3026-021X + affiliation: Université de Sherbrooke + email: jean.christophe.houde@gmail.com + - 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, USA + email: jean-dominique.gallezot@yale.edu + - given-names: Jean-Philippe + family-names: Lachaux + orcid: https://orcid.org/0000-0002-9459-0667 + affiliation: INSERM + - given-names: Jeanette + 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. + family-names: Grethe + website: http://profiles.ucsd.edu/jeffrey.grethe + - given-names: JegouA + website: https://github.com/JegouA + - given-names: Jelle + 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 + email: j.r.dalenberg@umcg.nl + - given-names: Jeremy + family-names: Moreau + - given-names: Jessica A. + family-names: Turner + - given-names: Jochem + family-names: Rieger + website: https://uol.de/en/applied-neurocognitive-psychology + orcid: https://orcid.org/0000-0003-0955-2306 + affiliation: Oldenburg University, Dept. of Psychology, 26129, Germany + email: jochem.rieger@uni-oldenburg.de + - given-names: John + family-names: Detre + orcid: https://orcid.org/0000-0002-8115-6343 + affiliation: University of Pennsylvania + - given-names: John + family-names: Pellman + orcid: https://orcid.org/0000-0001-6810-4461 + - given-names: John T. + family-names: Wodder + website: https://github.com/jwodder + - given-names: Joke + family-names: Durnez + website: https://github.com/jokedurnez + orcid: https://orcid.org/0000-0001-9030-2202 + affiliation: Stanford University + - given-names: Jon + 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, + (Québec), J1K 2R1, Canada + email: jon.haitz.legarreta@gmail.com + - given-names: Jonathan C. + family-names: Lau + - given-names: Jonathan + family-names: Winawer + website: https://github.com/JWinawer + - given-names: Joost + 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, + Amsterdam, 1081 HV, The Netherlands + email: jpa.kuijer@amsterdamumc.nl + - given-names: Jose + family-names: Manuel Saborit + - given-names: Joseph + family-names: Wexler + orcid: https://orcid.org/0000-0001-9086-8484 + affiliation: Loyola University Chicago + - given-names: Joseph + 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, + Oxford, UK + email: joseph.woods@ndcn.ox.ac.uk + - given-names: Julia + family-names: Guiomar Niso Galán + website: http://guiomarniso.com + orcid: https://orcid.org/0000-0001-5872-8924 + affiliation: Indiana University + - given-names: Julia + 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 + 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, + QC, Canada + - given-names: Julius + family-names: Welzel + website: https://github.com/JuliusWelzel + orcid: https://orcid.org/0000-0001-8958-0934 + affiliation: Kiel University + email: julius.welzel@gmail.com + - given-names: Kai J. + family-names: Miller + - given-names: Kangjoo + family-names: Lee + website: https://github.com/Kangjoo + orcid: https://orcid.org/0000-0002-7760-8079 + affiliation: Yale School of Medicine + - given-names: Katja + family-names: Heuer + website: https://github.com/katjaq + orcid: https://orcid.org/0000-0002-7237-0196 + affiliation: Institut Pasteur + - given-names: Kay + 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 USA + email: kay.robbins@utsa.edu + - given-names: Kevin + family-names: Larcher + - given-names: Kimberly + family-names: Ray + orcid: https://orcid.org/0000-0003-1302-2834 + affiliation: UT Austin + email: kimberlylray@gmail.com + - given-names: Kirstie + family-names: Whitaker + website: https://whitakerlab.github.io + orcid: https://orcid.org/0000-0001-8498-4059 + affiliation: University of Cambridge + email: kwhitaker@turing.ac.uk + - given-names: Klara + family-names: Gregorova + website: https://github.com/greckla + orcid: https://orcid.org/0000-0002-3828-9386 + - given-names: Klaus + family-names: Gramann + affiliation: Technical University Berlin + email: klaus.gramann@tu-berlin.de + - given-names: Kris + family-names: Thielemans + website: https://iris.ucl.ac.uk/iris/browse/profile?upi=KTHIE60 + - given-names: Kristofer + family-names: Bouchard + website: https://bouchardlab.lbl.gov + orcid: https://orcid.org/0000-0002-1974-4603 + affiliation: LBNL, Scientific Data Division + email: kristofer.bouchard@gmail.com + - 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 + (CUBRIC), UK + email: BeltrachiniL@cardiff.ac.uk + - given-names: Lee + family-names: Kamentsky + website: https://github.com/LeeKamentsky + orcid: https://orcid.org/0000-0002-8161-3604 + affiliation: MIT + - given-names: Lennart + family-names: Walger + orcid: https://orcid.org/0000-0002-3300-6877 + - given-names: Lennart + family-names: Wittkuhn + website: https://github.com/lnnrtwttkhn + orcid: https://orcid.org/0000-0003-2966-6888 + affiliation: Max Planck Institute for Human Development + - given-names: Liberty + family-names: Hamilton + website: https://github.com/libertyh + - given-names: Luca + 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, USA + email: lpollonini@uh.edu + - given-names: Luis + family-names: Hernandez-Garcia + - given-names: Luke J. + family-names: Edwards + orcid: https://orcid.org/0000-0002-8320-7298 + affiliation: Max Planck Institute for Human Cognitive and Brain Sciences + - given-names: Lyuba + family-names: Zehl + website: https://github.com/lzehl + orcid: https://orcid.org/0000-0002-5947-9939 + affiliation: Forschungszentrum Jülich + - given-names: Mainak + family-names: Jas + website: http://jasmainak.github.io/ + orcid: https://orcid.org/0000-0002-3199-9027 + - given-names: Manjari + family-names: Narayan + - given-names: Manuel + family-names: Mercier + orcid: https://orcid.org/0000-0001-6358-4734 + 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 + orcid: https://orcid.org/0000-0003-2122-740X + affiliation: Amsterdam UMC, locatie VUmc + - given-names: Marc + 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 + - 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 + 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 + email: delaiglesia_mar@gva.es + - given-names: Marie-Hélène + family-names: Bourget + website: https://github.com/mariehbourget + - given-names: Mark + 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, + USA + email: mam4041@med.cornell.edu + - given-names: Markus + family-names: Morawski + orcid: https://orcid.org/0000-0002-3817-5186 + affiliation: Universität Leipzig + - given-names: Marta + family-names: Bortoletto + orcid: https://orcid.org/0000-0002-8489-8043 + affiliation: IRCCS Centro S Giovanni di Dio Fatebenefratelli + - given-names: Martin + family-names: Craig + - given-names: Martin + 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, 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 + email: mail@martinszinte.net + - given-names: Martin + family-names: Wilson + - given-names: Martina + family-names: Bulgari + orcid: https://orcid.org/0000-0003-1594-9617 + affiliation: IRCCS Centro San Giovanni di Dio Fatebenefratelli + - given-names: Mateusz + family-names: Pawlik + website: https://github.com/mateuszpawlik + email: mateusz.pawlik@plus.ac.at + - given-names: Mathias + 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, + USA + email: mathiasg@stanford.edu + - given-names: Mathieu + family-names: Boudreau + website: https://github.com/mathieuboudreau + orcid: https://orcid.org/0000-0002-7726-4456 + affiliation: Polytechnique Montréal + - given-names: Matt + family-names: Sanderson + - given-names: Matteo + 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, + Switzerland + - given-names: Matthias + family-names: Günther + - given-names: Matthias + family-names: Van Osch + - given-names: Maureen + family-names: J Shader + - given-names: Maurice + family-names: Pasternak + - given-names: Max A. + 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, 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, + 2100, Denmark + - given-names: Michael + family-names: Chappell + - given-names: Michael + family-names: Hanke + website: https://github.com/mih + - given-names: Michael P. + family-names: Harms + - given-names: Michael P. + family-names: Milham + - given-names: Michael P. + family-names: Notter + - given-names: Michael + family-names: Schirner + website: https://www.brainsimulation.org + orcid: https://orcid.org/0000-0001-8227-8476 + affiliation: Charité—Universitätsmedizin Berlin, Department of Neurology, Berlin, + 10115, Germany + email: michael.schirner@charite.de + - given-names: Mikaël + family-names: Naveau + website: https://www.cyceron.fr + orcid: https://orcid.org/0000-0002-4685-0057 + affiliation: UAR3408-US50 CYCERON, Caen, 14000, France + - given-names: Nader + family-names: Pouratian + orcid: https://orcid.org/0000-0002-0426-3241 + - 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 + Utrecht, 3584 CX Utrecht, NL + - given-names: National + family-names: Institute of Mental Health + - given-names: Nell + family-names: Hardcastle + website: https://github.com/nellh + orcid: https://orcid.org/0000-0002-3837-0707 + - given-names: Nicholas + family-names: Traut + - given-names: Nick F. + family-names: Ramsey + - given-names: Nicole C. + family-names: Swann + - given-names: Nima + family-names: Bigdely Shamlo + orcid: https://orcid.org/0000-0001-6403-892X + - given-names: Olivier + family-names: David + - given-names: Orrin + family-names: Devinsky + orcid: https://orcid.org/0000-0003-0044-4632 + affiliation: NYU School of Medicine + - given-names: Oscar + 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 + email: phd@oscaresteban.es + - given-names: Pamela + family-names: LaMontagne + orcid: https://orcid.org/0000-0002-6752-8518 + - given-names: Parul + family-names: Sethi + website: https://github.com/parulsethi + - given-names: Patricia + 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 + University Hospital / Ghent University, Ghent, Belgium + email: patricia.clement@ugent.be + - given-names: Patrick + family-names: Park + website: https://github.com/Park-Patrick + - given-names: Paule-Joanne + family-names: Toussaint + orcid: https://orcid.org/0000-0002-7446-150X + 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 + 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 + email: petra.ritter@charite.de + - given-names: Pierre + family-names: Rioux + website: https://github.com/prioux + - given-names: Pieter + family-names: Vandemaele + website: https://github.com/pvdemael + orcid: https://orcid.org/0000-0002-4523-2476 + affiliation: Ghent University Hospital + - given-names: Pradeep + family-names: Reddy Raamana + website: https://github.com/raamana + - given-names: R. + family-names: Cameron Craddock + website: https://github.com/ccraddock + - given-names: Remi + family-names: Gau + website: https://remi-gau.github.io/ + orcid: https://orcid.org/0000-0002-1535-9767 + affiliation: Université catholique de Louvain + email: remi.gau@tuebingen.mpg.de + - given-names: Richard + family-names: Höchenberger + website: https://hoechenberger.net/ + orcid: https://orcid.org/0000-0002-0380-4798 + affiliation: Inria Saclay - Île-de-France Research Centre + email: richard.hoechenberger@gmail.com + - given-names: Richard N. + family-names: Henson + website: http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal + orcid: https://orcid.org/0000-0002-0712-2639 + affiliation: MRC CBU, University of Cambridge, UK + email: Rik.Henson@mrc-cbu.cam.ac.uk + - given-names: Robert B. + 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 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 + Neuroinformatics Laboratory, Heidelberg, Victoria, 3084, Australia + email: robert.smith@florey.edu.au + - given-names: Robert + family-names: Knight + - given-names: Robert + family-names: Luke + website: https://github.com/rob-luke + - given-names: Robert + 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 + email: r.oostenveld@donders.ru.nl + - given-names: Roberto + family-names: Toro + website: https://github.com/r03ert0 + - given-names: Rohan + family-names: Goyal + - given-names: Ross W. + family-names: Blair + website: https://github.com/rwblair + - given-names: Russell A. + family-names: Poldrack + website: http://www.poldracklab.org + orcid: https://orcid.org/0000-0001-6755-0259 + affiliation: Stanford University, Stanford, CA 94305 USA + email: russpold@stanford.edu + - given-names: Rémi + family-names: Adon + website: https://github.com/remiadon + - given-names: Samir + family-names: Das + website: https://github.com/samirdas + - given-names: Samuel + family-names: Garcia + - given-names: Samuel + family-names: Nastase + website: https://snastase.github.io/ + orcid: https://orcid.org/0000-0001-7013-5275 + affiliation: Princeton University + email: sam.nastase@gmail.com + - given-names: Sara + family-names: Elgayar + - 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, + 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, 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, USA + email: smakeig@gmail.com + - given-names: Sein + family-names: Jeung + website: https://github.com/sjeung + orcid: https://orcid.org/0000-0002-0247-087X + affiliation: Technical University Berlin + email: seinjeung@gmail.com + - given-names: Shashank + family-names: Bansal + - given-names: Sjoerd B. + 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, + and Analysis;Perth;WA;6009;Australia + - given-names: Soichi + family-names: Hayashi + website: https://github.com/soichih + orcid: https://orcid.org/0000-0003-3641-3491 + affiliation: Indiana University + - given-names: Stefan + family-names: Appelhoff + website: https://www.stefanappelhoff.com + orcid: https://orcid.org/0000-0001-8002-0877 + affiliation: Max Planck Institute for Human Development + 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/ + - given-names: Sylvain + family-names: Baillet + website: https://github.com/sbaillet + - given-names: Sylvain + family-names: Takerkart + website: https://github.com/SylvainTakerkart + orcid: https://orcid.org/0000-0001-8410-0962 + 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 + (DNC), Lausanne, 1007, Switzerland + email: sebastien.tourbier1@gmail.com + - given-names: Sören + family-names: Grothkopp + affiliation: Technical University Berlin + email: s.grothkopp@secure.mailbox.org + - given-names: Tal + family-names: Pal Attia + website: https://github.com/tpatpa + - given-names: Tal + family-names: Yarkoni + website: https://github.com/tyarkoni + orcid: https://orcid.org/0000-0002-6558-5113 + - given-names: Tamas + 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 + email: tamas.spisak@uk-essen.de + - given-names: Tamás + family-names: Józsa + - given-names: Taylor + 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 + email: tsalo006@fiu.edu + - given-names: Teon L. + family-names: Brooks + website: https://teonbrooks.com + orcid: https://orcid.org/0000-0001-7344-3230 + email: teon.brooks@gmail.com + - given-names: Thomas E. + family-names: Nichols + website: http://nisox.org + orcid: https://orcid.org/0000-0002-4516-5103 + affiliation: University of Oxford, Big Data Institute, Oxford, OX3 7LF, UK + email: thomas.nichols@BDI.OX.AC.UK + - given-names: Thomas + family-names: Funck + website: https://github.com/tfunck + - given-names: Thomas + family-names: Kirk + - given-names: Thomas + family-names: Okell + orcid: https://orcid.org/0000-0001-8258-0659 + affiliation: University of Oxford + - given-names: Tibor + 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, 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 + (INM-1), Jülich, 52428, Germany + email: t.dickscheid@fz-juelich.de + - given-names: Timotheus + family-names: Berg + website: https://github.com/timo-berg + orcid: https://orcid.org/0000-0002-0746-3679 + affiliation: Technical University Berlin + email: timo.berg@campus.tu-berlin.de + - given-names: Tobey + family-names: Betthauser + orcid: https://orcid.org/0000-0001-8856-1352 + affiliation: University of Wisconsin-Madison + - given-names: Tobias + family-names: Bengfort + website: http://tobib.spline.de + email: tobias.bengfort@posteo.de + - given-names: Tom + family-names: Hampshire + - given-names: Tor + family-names: Wager + website: https://github.com/torwager + - given-names: Travis + family-names: Riddle + orcid: https://orcid.org/0000-0001-8160-3986 + affiliation: National Police Foundation + - given-names: Tristan + 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 + - given-names: Vanessa + family-names: Sochat + website: https://github.com/vsoch + orcid: https://orcid.org/0000-0002-4387-3819 + - given-names: Vasudev + family-names: Raguram + - 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 + email: vcalhoun@gsu.edu + - given-names: Vittorio + family-names: Iacovella + orcid: https://orcid.org/0000-0002-0853-1573 + - given-names: Vladimir + family-names: Litvak + orcid: https://orcid.org/0000-0001-8535-7452 + affiliation: UCL Queen Square Institute of Neurology + - given-names: Wietske + family-names: van der Zwaag + - given-names: William + family-names: Clarke + - given-names: William + family-names: Triplett + - given-names: Wouter V. + family-names: Potters + website: https://www.wouterpotters.nl + orcid: https://orcid.org/0000-0003-1249-1196 + - given-names: Xiangrui + family-names: Li + website: https://github.com/xiangruili + 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 + email: debian@onerussian.com + - given-names: Yoni + family-names: Ashar + orcid: https://orcid.org/0000-0001-5602-5619 + - given-names: Yuan + family-names: Wang + - given-names: Zachary + family-names: Michael + - given-names: ezemikulan + website: https://github.com/ezemikulan + - given-names: josator2 + website: https://github.com/josator2 + - given-names: monkeyman192 + website: https://github.com/monkeyman192 + - given-names: Étienne + family-names: Bergeron + orcid: https://orcid.org/0000-0002-8329-7852 + affiliation: Collège Sainte-Anne de Lachine diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 89154c90..c34f9cb5 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 evert 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 d27da727..a29b4b86 100644 --- a/DECISION-MAKING.md +++ b/DECISION-MAKING.md @@ -29,6 +29,8 @@ Current and past members of the steering group can be found | Anthony Galassi ([@bendhouseart](https://github.com/bendhouseart)) | 3h/week | PET, Community development | Sep 2021 | | Eric Earl ([@ericearl](https://github.com/ericearl)) | 2h/week | | Dec 2021 | | Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/mo | Interoperability, EEG and multi-modal | Apr 2023 | +| Nell Hardcastle ([@nellh](https://github.com/nellh)) | 2h/week | | Jul 2023 | +| Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay)) | 1h/week | | Nov 2022 | In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group) classification of a maintainer, maintainers may declare a limited scope of responsibility. @@ -51,11 +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 d5919783..22091e01 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/Makefile b/Makefile index 2662661f..a56b672d 100644 --- a/Makefile +++ b/Makefile @@ -1,3 +1,12 @@ +.PHONY: tools/contributors.tsv + +validate_citation_cff: CITATION.cff + cffconvert --validate + +update_contributors: + python tools/add_contributors.py + python tools/print_contributors.py + yarn all-contributors generate runprettier: prettier --write "src/schema/**/*.yaml" diff --git a/README.md b/README.md index 4deedd70..6474f470 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 @@ -42,10 +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 @@ -56,7 +54,466 @@ 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. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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
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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
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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
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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
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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
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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
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Vasudev Raguram
💻 🎨 📖 🔧		Vince D. Calhoun
Vince D. Calhoun
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Vittorio Iacovella
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Wietske van der Zwaag
🔣 💬		William Clarke
William Clarke
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William Triplett
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Wouter V. Potters
💻 📖		Xiangrui Li
Xiangrui Li
📖 💻		Yaroslav O. Halchenko
Yaroslav O. Halchenko
📖 📢 🔧 💬 🐛 💻 🔣 🔍 🤔 🔌 👀 📓 🚇		Yoni Ashar
Yoni Ashar
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josator2
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💻		monkeyman192
monkeyman192
💻		Étienne Bergeron
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+ + + + + diff --git a/Release_Protocol.md b/Release_Protocol.md index cb1363f7..c93c039a 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) @@ -42,15 +46,19 @@ git checkout -b rel/1.2.0 upstream/master ### 2. Update the version, contributors list, previous version URLs, and the Changelog +#### 2.1 Update the version + +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. @@ -59,22 +67,51 @@ 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. -Note: this will make our continuous integration ([CircleCI](https://circleci.com/)) fail. This fails because the URL of the new ReadTheDocs rendering has not been generated at this time. It will be generated once the GitHub release has been completed. +Note: +this will make our continuous integration ([CircleCI](https://circleci.com/)) fail. +This fails because the URL of the new ReadTheDocs rendering has not been generated at this time. +It will be generated once the GitHub release has been completed. + +#### 2.2 Update the contributors list + +We want to ensure that all contributors are duly credited. -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. +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: -Please change the previous version links from GitHub to ReadTheDocs. -In the figure below, we update v1.2.2. +- 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 + +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 + Review `src/CHANGES.md` to ensure that the document produces a changelog that is useful to a reader of the specification. For example, several small PRs fixing typos might be merged into a single line-item, or less @@ -90,7 +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 ``` @@ -98,7 +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.** @@ -133,13 +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). @@ -153,6 +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 @@ -162,8 +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: @@ -188,7 +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") @@ -201,8 +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") @@ -214,24 +260,23 @@ on the expected next version. Additionally, the same version name set above in `mkdocs.yaml` should be set in the `src/schema/BIDS_VERSION` schema version file. +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 1a246973..051aa2aa 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,114 +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: - - 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 b7b1842b..e9710482 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 5d30aabc..705daa8b 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 00000000..1942f8b5 --- /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 00000000..e995e422 --- /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 00000000..37fadc29 --- /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 00000000..d70af64a --- /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 00000000..cab48172 --- /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 00000000..bfc1b850 --- /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 cc3f461f..5611c595 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 00000000..3df09bab Binary files /dev/null and b/release_images/merge_commit.png differ diff --git a/src/CHANGES.md b/src/CHANGES.md index ea117357..087368ff 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -1,14 +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)) +- \[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)) +- \[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)) @@ -17,25 +47,25 @@ - \[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] 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-\