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‎.codespellrc

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[codespell]
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skip = .git,*.pdf,*.svg,*.html,dataset_description.json,*.bib
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# te - TE
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# Weill - name
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# reson - Reson. abbreviation in citation
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ignore-words-list = te,weill,reson

‎.dockerignore

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# python cache
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__pycache__/**/*
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__pycache__
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*.pyc
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# python distribution
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build/**/*
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build
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dist/**/*
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dist
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fmripost_template.egg-info/**/*
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fmripost_template.egg-info
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.eggs/**/*
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.eggs

‎.git-blame-ignore-revs

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# Tue Apr 1 10:16:12 2025 -0400 - markiewicz@stanford.edu - sty: ruff format [ignore-rev]
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3577bfbbac45ca1e2f9d8b6dd3c036eba5dcd7d2

‎.git_archival.txt

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node: $Format:%H$
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node-date: $Format:%cI$
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describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
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ref-names: $Format:%D$

‎.gitattributes

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.git_archival.txt export-subst

‎.github/ISSUE_TEMPLATE/bug_report.yml

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name: Bug Report
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description: File a report of a problem you encountered.
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labels: ["bug"]
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body:
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- type: markdown
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attributes:
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value: |
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# Thanks for taking the time to fill out this bug report!
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### The following information will help us in getting your issue resolved.
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- type: textarea
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id: what-happened
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attributes:
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label: What happened?
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description: A short description of what went wrong.
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validations:
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required: true
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- type: textarea
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id: command
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attributes:
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label: What command did you use?
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description: |
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If you're using `fmriprep-docker`, please include the `RUNNING: ...` line that is printed first.
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This helps us replicate the problem. This will be automatically formatted into code, so no need for backticks.
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render: shell
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validations:
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required: true
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- type: input
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id: version
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attributes:
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label: What version of fMRIPost-template are you running?
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validations:
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required: true
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- type: dropdown
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id: environment
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attributes:
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label: How are you running fMRIPost-template?
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options:
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- Docker
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- Singularity
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- Local installation ("bare-metal")
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- Other
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validations:
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required: true
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- type: dropdown
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id: bids-valid
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attributes:
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label: Is your data BIDS valid?
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description: |
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The BIDS validator can be found at: https://bids-standard.github.io/bids-validator/
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Errors should not be present, but warnings are acceptable.
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options:
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- "Yes"
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- "No"
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validations:
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required: true
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- type: dropdown
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id: reuse
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attributes:
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label: Are you reusing any previously computed results?
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description: |
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You can select multiple options.
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We recommend using a fresh working directory when upgrading to a new fMRIPost-template minor series.
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multiple: true
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options:
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- FreeSurfer
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- Anatomical derivatives
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- Work directory
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- "No"
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validations:
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required: true
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- type: textarea
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id: logs
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attributes:
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label: Please copy and paste any relevant log output.
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description: |
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Can you find some traces of the error reported in the visual report (at the bottom) or in *crashfiles*?
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This will be automatically formatted into code, so no need for backticks.
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render: shell
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- type: textarea
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id: addinfo
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attributes:
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label: Additional information / screenshots
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description: |
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If you would like to include any further information, such as any visual reports, please include them below.
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Alternatively, you can privately share with us at <nipreps@gmail.com>.
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Reports do not contain data usable with personal identification or other research purposes.

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: true
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contact_links:
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- name: Questions
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url: https://neurostars.org/tag/fmripost-template
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about: For general questions, please search Neurostars for existing posts before starting a new one.

‎.github/ISSUE_TEMPLATE/documentation.md

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---
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name: Documentation improvement
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about: Is the documentation of something missing, unclear, or lacking? This is the place.
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title: ''
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labels: 'documentation'
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assignees: ''
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---
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<!--
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For the Documentation request, please include the following:
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------------------------
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What would you like changed/added and why?
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Do you have any suggestions for the new documents?
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-->

‎.github/ISSUE_TEMPLATE/feature_request.yml

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name: Feature Request
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description: Suggest an idea for a new feature or a change to an existing one.
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labels: ["enhancement"]
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body:
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- type: markdown
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attributes:
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value: |
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## Thank you for your suggestion!
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We welcome any ideas about how to make *fMRIPost-template* better for the community.
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Please keep in mind that features may not get implemented immediately.
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- type: textarea
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id: summary
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attributes:
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label: What would you like to see added in fMRIPost-template?
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description: |
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What are you trying to achieve with fMRIPost-template?
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Is this a more convenient way to do something that is already possible, or is a workaround currently unfeasible?
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Does this feature adhere to the [NiPreps driving principles](https://www.nipreps.org/community/CONTRIBUTING/#driving-principles)?
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validations:
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required: true
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- type: dropdown
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id: interest
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attributes:
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label: Do you have any interest in helping implement the feature?
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description: |
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We appreciate any help you can offer!
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For information on how to contribute, please refer to our [contributing guidelines](https://www.nipreps.org/community/CONTRIBUTING/).
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options:
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- "Yes"
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- "Yes, but I would need guidance"
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- "No"
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validations:
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required: true
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- type: textarea
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id: addinfo
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attributes:
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label: Additional information / screenshots
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description: Add any additional information or context about the feature request here.

‎.github/config.yml

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# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
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# Comment to be posted to on PRs from first time contributors in your repository
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newPRWelcomeComment: >
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:wave: Welcome, and thank you for your first contribution!
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We ask you to take a moment to read through our Contributing Guide:
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:point_right: https://github.com/nipreps/fmripost-template/blob/main/CONTRIBUTING.md
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These guidelines help us maintain a consistent and collaborative workflow.
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But don't worry — you don't have to get everything perfect on the first try!
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:mag: Here are a few quick tips:
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1. **Start a conversation**: Consider opening an issue to discuss your idea
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before submitting a pull request. It might save you time.
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1. **Descriptive titles**: Please use a clear, descriptive title for your
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pull request. If it is still a work in progress, mark it as a "Draft".
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1. **Licensing**: All contributions will be licensed under the Apache 2.0
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license — the same as the rest of the project.
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1. **Authorship**: You're invited to add yourself to the `.zenodo.json` file.
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file. This will credit you as a co-author in the next release. Please add
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your name as the second-to-last entry, just above the last author.
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A pull request is a conversation. We may suggest changes before merging,
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and likewise, you should feel free to ask us any questions you have.
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:rocket: We're happy to have you here!

‎.github/dependabot.yml

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version: 2
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updates:
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- package-ecosystem: 'github-actions'
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directory: '/'
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schedule:
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interval: 'monthly'
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groups:
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actions-infrastructure:
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patterns:
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- 'actions/*'
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docker:
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patterns:
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- 'docker/*'

‎.github/pull_request_template.md

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Closes .
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## Changes proposed in this pull request
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<!--
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Please describe here the main features / changes proposed for review and integration in fMRIPost-template
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If this PR addresses some existing problem, please use GitHub's citing tools
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(e.g., ref #, closes # or fixes #).
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If there is not an existing issue open describing the problem, please consider opening a new
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issue first and then link it from here (so the *fMRIPost-template* community has a better understanding
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of ongoing development efforts and possible overlaps between contributions).
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-->
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## Documentation that should be reviewed
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<!--
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Please summarize here the main changes to the documentation that the reviewers should be aware of.
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-->

‎.github/release.yml

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changelog:
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exclude:
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labels:
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- ignore-for-release
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categories:
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- title: 🛠 Breaking Changes
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labels:
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- breaking-change
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- title: 🎉 Exciting New Features
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labels:
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- enhancement
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- title: 👎 Deprecations
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labels:
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- deprecation
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- title: 🐛 Bug Fixes
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labels:
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- bug
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- title: Other Changes
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labels:
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- "*"

‎.github/workflows/contrib.yml

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name: Contribution checks
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on:
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push:
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branches:
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- main
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- maint/*
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pull_request:
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branches:
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- main
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- maint/*
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defaults:
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run:
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shell: bash
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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contents: read
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jobs:
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style:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- run: pipx run ruff check .
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- run: pipx run ruff format --diff .
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codespell:
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name: Check for spelling errors
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Codespell
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uses: codespell-project/actions-codespell@v2

‎.github/workflows/docker.yml

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name: Publish Docker image
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on:
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push:
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branches: [ignore]
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# release:
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# types: [published]
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jobs:
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push_to_registry:
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name: Push Docker image to Docker Hub
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runs-on: ubuntu-latest
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permissions:
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packages: write
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contents: read
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attestations: write
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id-token: write
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3.10.0
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- name: Log in to Docker Hub
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uses: docker/login-action@v3.4.0
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with:
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username: niprepsbot
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password: ${{ secrets.DOCKER_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5.7.0
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with:
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images: nipreps/fmripost-template
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# generate Docker tags based on the following events/attributes
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tags: |
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type=ref,event=branch
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type=semver,pattern={{version}}
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- name: Build and push Docker image
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uses: docker/build-push-action@v6.15.0
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with:
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context: .
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}

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