Add GH actions (#2)

.github/ISSUE_TEMPLATE/bug_report.yml

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

.github/ISSUE_TEMPLATE/documentation.md

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

.github/ISSUE_TEMPLATE/feature_request.yml

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

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      interval: 'monthly'
+    groups:
+      actions-infrastructure:
+        patterns:
+          - 'actions/*'
+  - package-ecosystem: 'pip'
+    directory: '/services/datalad'
+    schedule:
+      interval: 'monthly'
+    groups:
+      pipenv:
+        patterns:
+          - '*'

.github/pull_request_template.md

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+<!--
+Text in these brackets are comments, and won't be visible when you submit your pull request.
+If this is your first contribution, please take the time to read these, in particular the comment
+beginning "Welcome, new contributors!".
+-->
+
+## Changes proposed in this pull request
+
+<!--
+Please describe here the main features / changes proposed for review and integration in fMRIPost-template
+If this PR addresses some existing problem, please use GitHub's citing tools
+(eg. ref #, closes # or fixes #).
+If there is not an existing issue open describing the problem, please consider opening a new
+issue first and then link it from here (so the *fMRIPost-template* community has a better understanding
+of ongoing development efforts and possible overlaps between contributions).
+-->
+
+
+## Documentation that should be reviewed
+<!--
+Please summarize here the main changes to the documentation that the reviewers should be aware of.
+-->
+
+
+
+<!--
+Welcome, new contributors!
+
+We ask you to read through the Contributing Guide:
+https://github.com/nipreps/fmripost-template/blob/main/CONTRIBUTING.md
+
+These are guidelines intended to make communication easier by describing a consistent process, but
+don't worry if you don't get it everything exactly "right" on the first try.
+
+To boil it down, here are some highlights:
+
+1) Consider starting a conversation in the issues list before submitting a pull request. The discussion might save you a
+   lot of time coding.
+2) Please use descriptive prefixes in your pull request title, such as "ENH:" for an enhancement or "FIX:" for a bug fix.
+   (See the Contributing guide for the full set.) And consider adding a "WIP" tag for works-in-progress.
+3) Any code you submit will be licensed under the same terms (Apache License 2.0) as the rest of fMRIPost-template.
+4) We invite every contributor to add themselves to the `.zenodo.json` file
+   (https://github.com/nipreps/fmripost-template/blob/main/.zenodo.json), which will result in your being listed as an author
+   at the next release. Please add yourself as the next-to-last entry, just above Russ.
+
+A pull request is a conversation. We may ask you to make some changes before accepting your PR,
+and likewise, you should feel free to ask us any questions you have.
+
+-->

.github/release.yml

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

.github/workflows/contrib.yml

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

.github/workflows/docker.yml

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

.github/workflows/test.yml

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+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+      - maint/*
+  pull_request:
+    branches:
+      - main
+      - maint/*
+  # Allow job to be triggered manually from GitHub interface
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+# Force tox and pytest to use color
+env:
+  FORCE_COLOR: true
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  stable:
+    # Check each OS, all supported Python, minimum versions and latest releases
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.10', '3.11', '3.12']
+        dependencies: ['full', 'pre']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.10'
+            dependencies: 'min'
+
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install tox
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox tox-gh-actions
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v --exit-and-dump-after 1200
+      - uses: codecov/codecov-action@v4
+        if: ${{ always() }}
+        with:
+          files: cov.xml
+          token: ${{ secrets.CODECOV_TOKEN }}