Merge remote-tracking branch 'upstream/master' into enh/multi_sliceor…

…ientationpatient

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,.venv,venvs,*.svg,_build
+# te -- TE as codespell is case insensitive
+ignore-words-list = bu,nd,te

.github/ISSUE_TEMPLATE.md

@@ -1,4 +1,4 @@
-<!-- DO NOT DELETE THIS! 
+<!-- DO NOT DELETE THIS!
 This template is used to facilitate issue resolution.
 All text in <!-> tags will not be displayed.
 -->
@@ -20,5 +20,5 @@ Choose one:
 - [ ] Container
 <!-- If selected, please provide container name and tag"-->
 
-- Heudiconv version: 
+- Heudiconv version:
 <!-- To check: run heudiconv with just the --version flag -->

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    commit-message:
+      prefix: "[gh-actions]"
+      include: scope
+    labels:
+      - internal

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

.github/workflows/docker.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -20,12 +20,22 @@ jobs:
         working-directory: utils
 
       - name: Build Docker image
-        run: docker build -t nipy/heudiconv:master .
+        run: |
+          # build only if not release tag, i.e. has some "-" in describe
+          # so we do not duplicate work with release workflow.
+          git describe --match 'v[0-9]*' | grep -q -e - && \
+              docker build \
+                -t nipy/heudiconv:master \
+                -t nipy/heudiconv:unstable \
+                .
 
       - name: Push Docker image
         run: |
-          docker login -u "$DOCKER_LOGIN" --password-stdin <<<"$DOCKER_TOKEN"
-          docker push nipy/heudiconv:master
+          git describe --match 'v[0-9]*' | grep -q -e - && (
+              docker login -u "$DOCKER_LOGIN" --password-stdin <<<"$DOCKER_TOKEN"
+              docker push nipy/heudiconv:master
+              docker push nipy/heudiconv:unstable
+          )
         env:
           DOCKER_LOGIN: ${{ secrets.DOCKER_LOGIN }}
           DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Linters
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up environment
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.7'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade tox
+
+      - name: Run linters
+        run: tox -e lint

.github/workflows/release.yml

@@ -12,7 +12,7 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -28,13 +28,13 @@ jobs:
         id: auto-version
         run: |
           version="$(~/auto version)"
-          echo "::set-output name=version::$version"
+          echo "version=$version" >> "$GITHUB_OUTPUT"
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Set up Python
         if: steps.auto-version.outputs.version != ''
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: '^3.7'
 
@@ -67,8 +67,9 @@ jobs:
         run: |
           docker build \
             -t nipy/heudiconv:master \
+            -t nipy/heudiconv:unstable \
             -t nipy/heudiconv:latest \
-            -t nipy/heudiconv:"$(git describe)" \
+            -t nipy/heudiconv:"$(git describe | sed -e 's,^v,,g')" \
             .
 
       - name: Push Docker images

.github/workflows/test.yml

@@ -0,0 +1,61 @@
+name: Test
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    env:
+      BOTO_CONFIG: /tmp/nowhere
+      DATALAD_TESTS_SSH: '1'
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - '3.7'
+          - '3.8'
+          - '3.9'
+          - '3.10'
+          - '3.11'
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install git-annex
+        run: |
+          # The ultimate one-liner setup for NeuroDebian repository
+          bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+          sudo apt-get update -qq
+          sudo apt-get install git-annex-standalone dcm2niix
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          pip install -r dev-requirements.txt
+          pip install requests # below installs pyld but that assumes we have requests already
+          pip install datalad
+          pip install coverage pytest
+
+      - name: Configure Git identity
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub Almighty"
+
+      - name: Run tests with coverage
+        run: coverage run `which pytest` -s -v heudiconv
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: false
+
+# vim:set et sts=2:

.github/workflows/typing.yml

@@ -0,0 +1,27 @@
+name: Type-check
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  typing:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.7'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade tox
+
+      - name: Run type checker
+        run: tox -e typing

.gitignore

@@ -1,11 +1,13 @@
+*.egg-info/
 *.pyc
 .cache/
 .coverage
-*.egg-info/
 .idea/
-venvs/
+.tox/
+.vscode/
 _build/
+_version.py
 build/
 dist/
-.vscode/
-_version.py
+sample_nifti.json
+venvs/

.mailmap

@@ -3,3 +3,9 @@ Matteo Visconti di Oleggio Castello <[email protected]>
 Matteo Visconti di Oleggio Castello <[email protected]>
 Matteo Visconti di Oleggio Castello <[email protected]>
 Chris Filo Gorgolewski <[email protected]> Chris Gorgolewski <[email protected]>
+Pablo Velasco <[email protected]>
+Pablo Velasco <[email protected]>
+Dae Houlihan <[email protected]>
+Dae Houlihan <[email protected]>
+Mathias Goncalves <[email protected]>
+Mathias Goncalves <[email protected]>

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          - flake8-bugbear
+          - flake8-builtins
+          - flake8-unused-arguments

.readthedocs.yaml

@@ -8,7 +8,7 @@ python:
 build:
   os: ubuntu-20.04
   tools:
-    python: "3"
+    python: "3.9"
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: true