From 3cab41291c7cfeeac6c1e2ce1010fadc7052ee6c Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 4 Mar 2024 13:31:02 -0500
Subject: [PATCH] Add fMRIPrep workflows.

---
 .github/workflows/contrib.yml     | 40 +++++++++++++++++
 .github/workflows/pre-release.yml | 69 +++++++++++++++++++++++++++++
 .github/workflows/stable.yml      | 72 +++++++++++++++++++++++++++++++
 3 files changed, 181 insertions(+)
 create mode 100644 .github/workflows/contrib.yml
 create mode 100644 .github/workflows/pre-release.yml
 create mode 100644 .github/workflows/stable.yml

diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
new file mode 100644
index 0000000..ae7833e
--- /dev/null
+++ b/.github/workflows/contrib.yml
@@ -0,0 +1,40 @@
+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
diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
new file mode 100644
index 0000000..21842e1
--- /dev/null
+++ b/.github/workflows/pre-release.yml
@@ -0,0 +1,69 @@
+name: Pre-release checks
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+defaults:
+  run:
+    shell: bash
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  pre-release:
+    # Check pre-releases of dependencies on stable Python
+    runs-on: ${{ matrix.os }}
+    continue-on-error: true
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.10', '3.11', '3.12']
+        install: ['pip']
+        check: ['tests']
+        pip-flags: ['PRE_PIP_FLAGS']
+    env:
+      INSTALL_TYPE: ${{ matrix.install }}
+      CHECK_TYPE: ${{ matrix.check }}
+      EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
+      OS_TYPE: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Install dependencies
+        run: .maint/ci/install_dependencies.sh
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Create virtual environment
+        run: .maint/ci/create_venv.sh
+      - name: Build archive
+        run: |
+          source .maint/ci/build_archive.sh
+          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
+      - name: Install fMRIPrep
+        run: .maint/ci/install.sh
+      - name: Install extras
+        run: .maint/ci/install_extras.sh
+      - name: Run tests
+        run: .maint/ci/check.sh
+      - uses: codecov/codecov-action@v4
+        with:
+          file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ always() }}
diff --git a/.github/workflows/stable.yml b/.github/workflows/stable.yml
new file mode 100644
index 0000000..b09cad1
--- /dev/null
+++ b/.github/workflows/stable.yml
@@ -0,0 +1,72 @@
+name: Stable tests
+
+on:
+  push:
+    branches:
+      - main
+      - maint/*
+      - next
+  pull_request:
+    branches:
+      - main
+      - maint/*
+      - next
+
+defaults:
+  run:
+    shell: bash
+
+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']
+        install: ['pip']
+        check: ['tests']
+        pip-flags: ['']
+    env:
+      INSTALL_TYPE: ${{ matrix.install }}
+      CHECK_TYPE: ${{ matrix.check }}
+      EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
+      OS_TYPE: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Install dependencies
+        run: .maint/ci/install_dependencies.sh
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Create virtual environment
+        run: .maint/ci/create_venv.sh
+      - name: Build archive
+        run: |
+          source .maint/ci/build_archive.sh
+          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
+      - name: Install fMRIPrep
+        run: .maint/ci/install.sh
+      - name: Install extras
+        run: .maint/ci/install_extras.sh
+      - name: Run tests
+        run: .maint/ci/check.sh
+      - uses: codecov/codecov-action@v4
+        with:
+          file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ always() }}