Merge pull request #14 from tsalo/infrastructure

Work on infrastructure

.github/dependabot.yml

@@ -0,0 +1,18 @@
+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

@@ -0,0 +1,49 @@
+<!--
+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-AROMA
+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-AROMA* 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-aroma/blob/master/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-AROMA.
+4) We invite every contributor to add themselves to the `.zenodo.json` file
+   (https://github.com/nipreps/fmripost-aroma/blob/master/.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/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

.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 fMRIPost-AROMA
+        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() }}

.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 fMRIPost-AROMA
+        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() }}

.gitignore

@@ -1,5 +1,90 @@
+.DS_Store
 .*.swp
 .mypy_cache
 .pytest_cache
 .ruff_cache
 .coverage
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache/
+
+# C extensions
+*.so
+*.c
+
+# Distribution / packaging
+.Python
+env/
+# build/ # commented due to some strangeness with Docker/circle setup
+develop-eggs/
+dist/
+build/lib*
+build/temp*
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+pip-wheel-metadata/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+build/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+# pycharm project settings
+.idea
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+auth/
+secrets.py
+local_settings.py
+
+*.swp
+
+_version.py

.pre-commit-config.yaml

@@ -11,9 +11,9 @@ repos:
     rev: 23.1.0
     hooks:
     -   id: black
-        files: ^fmriprep/|^wrapper/
+        files: ^src/fmripost_aroma/
 -   repo: https://github.com/pycqa/isort
     rev: 5.12.0
     hooks:
     -   id: isort
-        files: ^fmriprep/|^wrapper/
+        files: ^src/fmripost_aroma/

Dockerfile

@@ -103,28 +103,8 @@ RUN apt-get update -qq \
     --exclude "fsl/tcl" \
     --exclude "fsl/bin/FSLeyes" \
     && find /opt/fsl-6.0.5.1/bin -type f -not \( \
-        -name "applywarp" -or \
-        -name "bet" -or \
-        -name "bet2" -or \
-        -name "convert_xfm" -or \
-        -name "fast" -or \
-        -name "flirt" -or \
-        -name "fsl_regfilt" -or \
-        -name "fslhd" -or \
-        -name "fslinfo" -or \
-        -name "fslmaths" -or \
-        -name "fslmerge" -or \
-        -name "fslroi" -or \
-        -name "fslsplit" -or \
-        -name "fslstats" -or \
-        -name "imtest" -or \
-        -name "mcflirt" -or \
         -name "melodic" -or \
-        -name "prelude" -or \
-        -name "remove_ext" -or \
-        -name "susan" -or \
-        -name "topup" -or \
-        -name "zeropad" \) -delete \
+        -name "susan" -or \) -delete \
     && find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
 ENV FSLDIR="/opt/fsl-6.0.5.1" \
     PATH="/opt/fsl-6.0.5.1/bin:$PATH" \