Merge branch 'master' into mnt/mark-tests-slow

Author: effigies

.circleci/config.yml

@@ -10,33 +10,19 @@ jobs:
 
     steps:
       - checkout
-      - restore_cache:
-          keys:
-            - env-v6-{{ .Branch }}-
-            - env-v6-master-
-            - env-v6-
+      - run:
+          name: Ensure uv is present
+          command: uv -V || curl -LsSf https://astral.sh/uv/install.sh | sh
       - run:
           name: Setup git-annex
           command: |
-              sudo apt update && sudo apt-get install apt-transport-https ca-certificates -y && sudo update-ca-certificates
-              if [[ ! -d /opt/circleci/git-annex.linux ]]; then
-                cd /tmp
-                wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
-                tar xzf git-annex-standalone-amd64.tar.gz -C /opt/circleci/
-              fi
+              uv tool install git-annex
               git config --global user.name 'NiPy'
               git config --global user.email '[email protected]'
       - run:
           name: Setup DataLad
           command: |
-              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-v6-{{ .Branch }}-{{ .BuildNum }}
-          paths:
-            - /opt/circleci/git-annex.linux
-            - /opt/circleci/.pyenv/versions
+              uv tool install --with-executables-from=datalad-osf,datalad-next datalad
 
       - restore_cache:
           keys:
@@ -46,9 +32,6 @@ jobs:
       - run:
           name: Install test data from GIN
           command: |
-              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
@@ -61,10 +44,10 @@ jobs:
 
       - restore_cache:
           keys:
-            - build-v1-{{ .Branch }}-{{ epoch }}
-            - build-v1-{{ .Branch }}-
-            - build-v1-master-
-            - build-v1-
+            - build-v2-{{ .Branch }}-{{ epoch }}
+            - build-v2-{{ .Branch }}-
+            - build-v2-master-
+            - build-v2-
           paths:
             - /tmp/docker
       - run:
@@ -81,13 +64,13 @@ jobs:
               set -e
               if [[ "$success" = "0" ]]; then
                   echo "Pulling from local registry"
-                  docker tag localhost:5000/ubuntu ubuntu:xenial-20200114
+                  docker tag localhost:5000/ubuntu ubuntu:jammy-20250730
                   docker pull localhost:5000/nitransforms
                   docker tag localhost:5000/nitransforms nitransforms:latest
               else
                   echo "Pulling from Docker Hub"
-                  docker pull ubuntu:xenial-20200114
-                  docker tag ubuntu:xenial-20200114 localhost:5000/ubuntu
+                  docker pull ubuntu:jammy-20250730
+                  docker tag ubuntu:jammy-20250730 localhost:5000/ubuntu
                   docker push localhost:5000/ubuntu
               fi
       - run:
@@ -99,7 +82,7 @@ jobs:
                   -t nitransforms:latest \
                   --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                   --build-arg VCS_REF=`git rev-parse --short HEAD` \
-                  --build-arg VERSION=$( python3 -m setuptools_scm ) . \
+                  --build-arg VERSION=$( uv run --no-project -w setuptools_scm -m setuptools_scm ) . \
                   && e=0 && break || sleep 15
               done && [ "$e" -eq "0" ]
               docker tag nitransforms:latest localhost:5000/nitransforms
@@ -110,13 +93,13 @@ jobs:
               docker exec -it registry /bin/registry garbage-collect --delete-untagged \
                   /etc/docker/registry/config.yml
       - save_cache:
-          key: build-v1-{{ .Branch }}-{{ epoch }}
+          key: build-v2-{{ .Branch }}-{{ epoch }}
           paths:
             - /tmp/docker
       - run:
           name: Check version packaged in Docker image
           command: |
-              THISVERSION=${CIRCLE_TAG:-$(python3 -m setuptools_scm)}
+              THISVERSION=${CIRCLE_TAG:-$( uv run --no-project -w setuptools_scm -m setuptools_scm )}
               INSTALLED_VERSION=$(\
                 docker run -it --rm --entrypoint=python nitransforms \
                     -c 'import nitransforms as nit; print(nit.__version__, end="")' )
@@ -136,21 +119,22 @@ jobs:
           name: Run unit tests
           no_output_timeout: 2h
           command: |
-            mkdir -p /tmp/tests/{artifacts,summaries}
+            mkdir -p /tmp/tests/{artifacts,summaries,coverage}
             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 \
+              -e COVERAGE_FILE=/tmp/coverage/.pytest.coverage \
+              -v /tmp/fslicense/license.txt:/usr/local/freesurfer/license.txt:ro \
               -v /tmp/tests:/tmp nitransforms:latest \
               pytest --junit-xml=/tmp/summaries/pytest.xml \
-                     --cov nitransforms --cov-report xml:/tmp/summaries/unittests.xml \
+                     --cov nitransforms --cov-report xml:/tmp/coverage/unittests.xml \
+                     -n auto \
                      nitransforms/
       - run:
           name: Submit unit test coverage
           command: |
             cd /tmp/src/nitransforms
-            python3 -m codecov --file /tmp/tests/summaries/unittests.xml \
+            python3 -m codecov --file /tmp/tests/coverage/unittests.xml \
                 --flags unittests -e CIRCLE_JOB
       - run:
           name: Clean up tests directory

.github/workflows/tox.yml

@@ -83,7 +83,7 @@ jobs:
       DEPENDS: ${{ matrix.dependencies }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: recursive
           fetch-depth: 0
@@ -166,7 +166,7 @@ jobs:
         check: ['style']
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Install the latest version of uv
         uses: astral-sh/setup-uv@v6
       - name: Show tox config

CHANGES.rst

@@ -1,20 +1,48 @@
-25.0.0 (TBD)
-============
-A new major release with critical updates.
-The new release includes a critical hotfix for 4D resamplings.
-The second major improvement is the inclusion of a first implementation of the X5 format (BIDS).
-The X5 implementation is currently restricted to reading/writing of linear transforms.
+25.0.1 (August 14, 2025)
+========================
+A patch release addressing a critical issue in the ``ImageGrid`` class relating coordinates,
+and bolstered the testing of ANTs' generated displacements fields by cross-comparing against
+``antsApplyTransformsToPoints`` in several new tests.
+
+CHANGES
+-------
+* FIX: ``ImageGrid._coords`` was somehow overwritten + re-enable tests by @oesteban in https://github.com/nipy/nitransforms/pull/276
+* FIX: Revision of index and RAS coordinate grids generation by @oesteban in https://github.com/nipy/nitransforms/pull/271
+* ENH: Implement ITK densefields checks vs ``antsApplyTransformsToPoints`` by @oesteban in https://github.com/nipy/nitransforms/pull/277
+* ENH: Add unit test on dense fields (extracted from #266) by @oesteban in https://github.com/nipy/nitransforms/pull/274
+* RF: Move tests to better locations by @oesteban in https://github.com/nipy/nitransforms/pull/272
+* MNT: Minimal housekeeping of tests by @oesteban in https://github.com/nipy/nitransforms/pull/275
+* MNT: Fix coverage XML path in CircleCI by @oesteban in https://github.com/nipy/nitransforms/pull/265
+* MNT: Add test cases demonstrating ordering bug reading composite ITK's HDF5 files by @oesteban in https://github.com/nipy/nitransforms/pull/263
+* STY: Run ruff at the source root by @oesteban in https://github.com/nipy/nitransforms/pull/273
+
+**Full Changelog**: https://github.com/nipy/nitransforms/compare/25.0.0...25.0.1
+
+25.0.0 (July 22, 2025)
+======================
+A new major release introducing critical fixes and important new functionality.
+Most notably, it includes a hotfix for 4D resampling (also backported to 24.1.4) and adds **experimental support for the X5 format** (*BIDS*).
+The X5 support enables I/O for linear and nonlinear transforms and includes partial support for transformation chains—marking a first step
+toward full *BIDS* interoperability.
+This release also drops support for *Python* 3.9 and earlier, aligning with modern *Python* standards and paving the way for future improvements.
 
 CHANGES
 -------
+* FIX: BSpline mapping of individual points by @oesteban in https://github.com/nipy/nitransforms/pull/256
+* FIX: Remove implementation of an abstract class by @oesteban in https://github.com/nipy/nitransforms/pull/255
+* FIX: Add test for ``DenseFieldTransform`` handling of OOB points by @oesteban in https://github.com/nipy/nitransforms/pull/254
+* ENH: X5 read/write support of ``TransformChain`` by @oesteban in https://github.com/nipy/nitransforms/pull/253
 * ENH: Loading of X5 (linear) transforms by @oesteban in https://github.com/nipy/nitransforms/pull/243
 * ENH: Implement X5 representation and output to filesystem by @oesteban in https://github.com/nipy/nitransforms/pull/241
 * DOC: Fix references to ``os.PathLike`` by @oesteban in https://github.com/nipy/nitransforms/pull/242
+* MNT: Drop Python 3.9 by @oesteban in https://github.com/nipy/nitransforms/pull/259
 * MNT: Increase coverage by testing edge cases and adding docstrings by @oesteban in https://github.com/nipy/nitransforms/pull/248
 * MNT: Refactor io/lta to reduce one partial line by @oesteban in https://github.com/nipy/nitransforms/pull/246
 * MNT: Move flake8 config into ``pyproject.toml`` by @oesteban in https://github.com/nipy/nitransforms/pull/245
 * MNT: Configure coverage to omit tests by @oesteban in https://github.com/nipy/nitransforms/pull/244
 
+**Full Changelog**: https://github.com/nipy/nitransforms/compare/24.1.4...25.0.0
+
 24.1.4 (July 20, 2025)
 ======================
 Hotfix release addressing an issue in dense displacements fields.