Merge branch 'master' into enh/89-collapse-nonlinear

Author: oesteban

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2
 jobs:
   build_pytest:
     machine:
-      image: ubuntu-2004:202107-02
+      image: default
     working_directory: /tmp/src/nitransforms
     environment:
       TZ: "/usr/share/zoneinfo/America/Los_Angeles"
@@ -12,9 +12,9 @@ jobs:
       - checkout
       - restore_cache:
           keys:
-            - env-v3-{{ .Branch }}-
-            - env-v3-master-
-            - env-v3-
+            - env-v6-{{ .Branch }}-
+            - env-v6-master-
+            - env-v6-
       - run:
           name: Setup git-annex
           command: |
@@ -29,17 +29,14 @@ jobs:
       - run:
           name: Setup DataLad
           command: |
-              export PY3=$(pyenv versions | grep '3\.' |
-                           sed -e 's/.* 3\./3./' -e 's/ .*//')
-              pyenv local $PY3
-              python -m pip install --no-cache-dir -U pip "setuptools >= 45.0" "setuptools_scm[toml] >= 3.4"
-              python -m pip install --no-cache-dir -U datalad datalad-osf
+              python3 -m pip install --no-cache-dir -U pip "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
+              python3 -m pip install --no-cache-dir -U datalad datalad-osf
 
       - save_cache:
-          key: env-v3-{{ .Branch }}-{{ .BuildNum }}
+          key: env-v6-{{ .Branch }}-{{ .BuildNum }}
           paths:
             - /opt/circleci/git-annex.linux
-            - /opt/circleci/.pyenv/versions/3.9.4
+            - /opt/circleci/.pyenv/versions
 
       - restore_cache:
           keys:
@@ -49,10 +46,9 @@ jobs:
       - run:
           name: Install test data from GIN
           command: |
-              export PY3=$(pyenv versions | grep '3\.' |
-                           sed -e 's/.* 3\./3./' -e 's/ .*//')
-              pyenv local $PY3
               export PATH=/opt/circleci/git-annex.linux:$PATH
+              pyenv local 3
+              eval "$(pyenv init --path)"
               mkdir -p /tmp/data
               cd /tmp/data
               datalad install -r https://gin.g-node.org/oesteban/nitransforms-tests
@@ -98,15 +94,12 @@ jobs:
           name: Build Docker image & push to registry
           no_output_timeout: 60m
           command: |
-              export PY3=$(pyenv versions | grep '3\.' |
-                           sed -e 's/.* 3\./3./' -e 's/ .*//')
-              pyenv local $PY3
               e=1 && for i in {1..5}; do
                   docker build --rm --cache-from=nitransforms:latest \
                   -t nitransforms:latest \
                   --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                   --build-arg VCS_REF=`git rev-parse --short HEAD` \
-                  --build-arg VERSION=$( python3 setup.py --version ) . \
+                  --build-arg VERSION=$( python3 -m setuptools_scm ) . \
                   && e=0 && break || sleep 15
               done && [ "$e" -eq "0" ]
               docker tag nitransforms:latest localhost:5000/nitransforms
@@ -123,10 +116,7 @@ jobs:
       - run:
           name: Check version packaged in Docker image
           command: |
-              export PY3=$(pyenv versions | grep '3\.' |
-                           sed -e 's/.* 3\./3./' -e 's/ .*//')
-              pyenv local $PY3
-              THISVERSION=${CIRCLE_TAG:-$(python3 setup.py --version)}
+              THISVERSION=${CIRCLE_TAG:-$(python3 -m setuptools_scm)}
               INSTALLED_VERSION=$(\
                 docker run -it --rm --entrypoint=python nitransforms \
                     -c 'import nitransforms as nit; print(nit.__version__, end="")' )
@@ -141,13 +131,14 @@ jobs:
               echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
       - run:
           name: Get codecov
-          command: python -m pip install codecov
+          command: python3 -m pip install codecov
       - run:
           name: Run unit tests
           no_output_timeout: 2h
           command: |
             mkdir -p /tmp/tests/{artifacts,summaries}
-            docker run -u $( id -u ) -it --rm -w /src/nitransforms \
+            docker run -u $( id -u ) -it --rm \
+              -w /src/nitransforms -v $PWD:/src/nitransforms \
               -v /tmp/data/nitransforms-tests:/data -e TEST_DATA_HOME=/data \
               -e COVERAGE_FILE=/tmp/summaries/.pytest.coverage \
               -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
@@ -159,7 +150,7 @@ jobs:
           name: Submit unit test coverage
           command: |
             cd /tmp/src/nitransforms
-            python -m codecov --file /tmp/tests/summaries/unittests.xml \
+            python3 -m codecov --file /tmp/tests/summaries/unittests.xml \
                 --flags unittests -e CIRCLE_JOB
       - run:
           name: Clean up tests directory
@@ -186,9 +177,9 @@ jobs:
           command: |
             python3 -m venv /tmp/buildenv
             source /tmp/buildenv/bin/activate
-            python3 -m pip install "setuptools >= 45.0" wheel "setuptools_scm[toml] >= 3.4" \
+            python3 -m pip install "setuptools >= 45.0" build wheel "setuptools_scm[toml] >= 6.2" \
                 "pip>=10.0.1" twine docutils
-            python setup.py sdist bdist_wheel
+            python3 -m build
             twine check dist/nitransforms*
       - store_artifacts:
           path: /tmp/src/nitransforms/dist
@@ -200,9 +191,9 @@ jobs:
           command: |
             python3 -m venv /tmp/install_sdist
             source /tmp/install_sdist/bin/activate
-            python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1"
+            python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1" "setuptools_scm[toml] >= 6.2"
 
-            THISVERSION=$( python3 setup.py --version )
+            THISVERSION=$( python3 -m setuptools_scm )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
             python3 -m pip install dist/nitransforms*.tar.gz
             INSTALLED_VERSION=$(python3 -c 'import nitransforms as nit; print(nit.__version__, end="")')
@@ -214,9 +205,9 @@ jobs:
           command: |
             python3 -m venv /tmp/install_wheel
             source /tmp/install_wheel/bin/activate
-            python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1"
+            python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1" "setuptools_scm[toml] >= 6.2"
 
-            THISVERSION=$( python3 setup.py --version )
+            THISVERSION=$( python3 -m setuptools_scm )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
             python3 -m pip install dist/nitransforms*.whl
             INSTALLED_VERSION=$(python3 -c 'import nitransforms as nit; print(nit.__version__, end="")')

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      actions-infrastructure:
+        patterns:
+          - "actions/*"

.github/workflows/pythonpackage.yml

@@ -0,0 +1,129 @@
+name: Tox
+
+on:
+  push:
+    branches: [ master, main, 'maint/*' ]
+    tags: [ '*' ]
+  pull_request:
+    branches: [ master, main, 'maint/*' ]
+  schedule:
+    - cron: '0 0 * * *'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+env:
+  # Force tox and pytest to use color
+  FORCE_COLOR: true
+  TEST_DATA_HOME: /home/runner/testdata/nitransforms-tests
+
+jobs:
+  cache-test-data:
+    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+    runs-on: ubuntu-latest
+    outputs:
+      SHA: ${{ steps.test-head.outputs.SHA }}
+    steps:
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Git settings (pacify DataLad)
+        run: |
+          git config --global user.name 'NiPreps Bot'
+          git config --global user.email 'nipreps@gmail.com'
+      - name: Install DataLad
+        run: |
+          $CONDA/bin/conda install -c conda-forge git-annex
+          uv tool install --with=datalad-next --with=datalad-osf datalad
+      - name: Check remote HEAD
+        id: test-head
+        run: |
+          git ls-remote https://gin.g-node.org/oesteban/nitransforms-tests \
+            | awk '/HEAD/{ print "SHA=" $1 }' >> $GITHUB_OUTPUT
+
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.TEST_DATA_HOME }}
+          key: data-cache-v2-${{ steps.test-head.outputs.SHA }}
+          restore-keys: |
+            data-cache-v2-${{ steps.test-head.outputs.SHA }}
+            data-cache-v2
+
+      - name: Install test data
+        run: |
+          export PATH=$CONDA/bin:$PATH
+          mkdir -p /home/runner/testdata
+
+          datalad install -s https://gin.g-node.org/oesteban/nitransforms-tests $TEST_DATA_HOME
+          datalad update --merge -d $TEST_DATA_HOME
+          datalad get -J 2 -d $TEST_DATA_HOME
+
+  test:
+    runs-on: ubuntu-latest
+    needs: [cache-test-data]
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        dependencies: [latest, pre]
+        include:
+          - python-version: "3.9"
+            dependencies: min
+        exclude:
+          # Do not test pre-releases for versions out of SPEC0
+          - python-version: "3.9"
+            dependencies: pre
+          - python-version: "3.10"
+            dependencies: pre
+
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - uses: actions/cache/restore@v4
+        with:
+          path: ${{ env.TEST_DATA_HOME }}
+          key: data-cache-v2-${{ needs.cache-test-data.outputs.SHA }}
+      - 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: Install tox
+        run: |
+          uv tool install tox --with=tox-uv --with=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@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ always() }}
+
+  checks:
+    runs-on: 'ubuntu-latest'
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ['style']
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Show tox config
+        run: uvx tox c
+      - name: Show tox config (this call)
+        run: uvx tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: uvx tox -e ${{ matrix.check }}