chore: Transition to pyproject.toml and tox, support numpy 2, python 3.13

.github/workflows/tox.yml

@@ -0,0 +1,130 @@
+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@v3
+      - name: Git settings (pacify DataLad)
+        run: |
+          git config --global user.name 'NiPreps Bot'
+          git config --global user.email '[email protected]'
+      - 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@v3
+      - 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@v4
+        with:
+          file: coverage.xml
+          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@v3
+      - 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 }}

.readthedocs.yaml

@@ -1,19 +1,21 @@
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-lts-latest
   tools:
-    python: "3.8"
-
-sphinx:
-   configuration: docs/conf.py
+    python: latest
 
-python:
-   install:
-      - path: .
-        extra_requirements:
-          - all
-      - requirements: docs/requirements.txt
+  jobs:
+    pre_create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+      # Turn `python -m virtualenv` into `python -c pass`
+      - truncate --size 0 $( dirname $( uv python find ) )/../lib/python3*/site-packages/virtualenv/__main__.py
+    post_create_environment:
+      - uv venv $READTHEDOCS_VIRTUALENV_PATH
+      # Turn `python -m pip` into `python -c pass`
+      - truncate --size 0 $( ls -d $READTHEDOCS_VIRTUALENV_PATH/lib/python3* )/site-packages/pip.py
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache .[niftiext]
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache -r docs/requirements.txt

docs/conf.py

@@ -76,7 +76,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/requirements.txt

@@ -4,5 +4,5 @@ packaging
 pydot>=1.2.3
 pydotplus
 sphinx-argparse
-sphinx ~= 4.0
-sphinx_rtd_theme
+sphinx~=7.0
+sphinx_rtd_theme