diff --git a/.circleci/config.yml b/.circleci/config.yml
index b8a719419..15ee642b8 100755
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,3 +1,4 @@
+# reusable anchors
 docs_deploy: &docs
   docker:
     - image: node:8.10.0
@@ -21,118 +22,235 @@ docs_deploy: &docs
         name: Deploy docs to gh-pages branch
         command: gh-pages --dotfiles --message "doc(update) [skip ci]" --dist docs/_build/html
 
+_machine_defaults: &machine_defaults
+  environment:
+    TZ: "/usr/share/zoneinfo/America/Los_Angeles"
+    SCRATCH: "/scratch"
+  machine:
+    image: default
+    docker_layer_caching: true
+  working_directory: /tmp/src/dmriprep
+  resource_class: large
+
+_python_defaults: &python_defaults
+  docker:
+    - image: cimg/python:3.12
+  working_directory: /tmp/src/dmriprep
+
+_docker_auth: &docker_auth
+  name: Docker authentication
+  command: |
+    if [[ -n $DOCKER_PAT ]]; then
+      echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
+    fi
+
+_setup_docker_registry: &setup_docker_registry
+  name: Set up Docker registry
+  command: |
+    if [[ -f /tmp/images/registry.tar.gz ]]; then
+      echo "Loading saved registry image"
+      docker load < /tmp/images/registry.tar.gz
+    else
+      echo "Pulling registry image from DockerHub"
+      docker pull registry:2
+    fi
+    docker run -d -p 5000:5000 --restart=always --name=registry \
+        -v /tmp/docker:/var/lib/registry registry:2
+
+_pull_from_registry: &pull_from_registry
+  name: Pull and tag image from local registry
+  command: |
+    docker pull localhost:5000/dmriprep
+    docker tag localhost:5000/dmriprep nipreps/dmriprep:latest
+
+_pull_test_image_from_registry: &pull_test_image_from_registry
+  name: Pull and tag image from local registry
+  command: |
+    docker pull localhost:5000/dmriprep-test
+    docker tag localhost:5000/dmriprep-test nipreps/dmriprep:test
+
+_check_skip_job: &check_skip_job
+  name: Check commit message and determine if job should be skipped
+  command: |
+    set +e
+    cd /tmp/src/dmriprep
+    COMMIT_MSG="$(git show -s --format=%s)"
+    DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
+    SKIP_ALL="$(echo ${COMMIT_MSG} | grep -i -E '\[skipcircle\]')"
+    SKIP_PYTEST="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?tests\]')"
+    SKIP_DS005="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds005\]' )"
+    SKIP_DS054="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )"
+    SKIP_DS210="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds210\]' )"
+    NO_FASTTRACK="$(echo ${COMMIT_MSG} | grep -i -E '\[no[ _-]?fasttrack\]' )"
+
+    # no skipping if tagged build
+    if [[ -n "$NO_FASTTRACK" ]]; then
+      touch /tmp/.nofasttrack
+      echo "Anatomical fasttrack reusing sMRIPrep's derivatives will not be used."
+    elif [[ -n "$CIRCLETAG" ]]; then
+      exit 0
+    elif [[ -n "$DOCSBUILD" ]]; then  # always try to skip docs builds
+      echo "Only docs build"
+      circleci step halt
+    elif [ -n "$SKIP_ALL" ]; then
+      echo "Skipping all!"
+      circleci step halt
+    elif [ -n "$CHECK_PYTEST" -a -n "$SKIP_PYTEST" ]; then
+      echo "Skipping pytest"
+      circleci step halt
+    elif [ -n "$CHECK_DS005" -a -n "$SKIP_DS005" ]; then
+      echo "Skipping DS005"
+      circleci step halt
+    elif [ -n "$CHECK_DS054" -a -n "$SKIP_DS054" ]; then
+      echo "Skipping DS054"
+      circleci step halt
+    elif [ -n "$CHECK_DS210" -a -n "$SKIP_DS210" ]; then
+      echo "Skipping DS210"
+      circleci step halt
+    fi
+    echo "No skip"
+
+_setup_dmriprep_docker: &setup_dmriprep_docker
+  name: Install dMRIPrep's docker wrapper
+  command: |
+    pyenv local 3
+    pip install --upgrade pip
+    pip install --upgrade /tmp/src/dmriprep/wrapper/
+
+_check_outputs: &check_outputs
+  name: Check outputs of dMRIPrep run
+  command: |
+    set +e -x
+    mkdir -p /tmp/${DATASET}/test
+    find /tmp/${DATASET}/${SUBDIR:-dmriprep} \
+      \( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) \
+      -prune -o -name "*" -print | cut -d/ -f 5- | sort > /tmp/${DATASET}/test/outputs.out
+
+    FASTTRACK_OUTPUTS="${DATASET}${VARIANT}_fasttrack_outputs.txt"
+    FULL_OUTPUTS="${DATASET}${VARIANT}_outputs.txt"
+    RET=1
+    if [ ! -f /tmp/.nofasttrack ]; then
+        echo "Checking fasttrack..."
+        sort /tmp/src/dmriprep/.circleci/${FASTTRACK_OUTPUTS} > /tmp/${DATASET}/test/fasttrack.out
+        diff /tmp/${DATASET}/test/{fasttrack,outputs}.out
+        RET=$?
+    fi
+    if [ $RET -ne 0 ]; then
+        echo "Checking full..."
+        sort /tmp/src/dmriprep/.circleci/${FULL_OUTPUTS} > /tmp/${DATASET}/test/full.out
+        diff /tmp/${DATASET}/test/{full,outputs}.out
+        RET=$?
+    fi
+    exit $RET
+
 version: 2.1
+aliases:
+  - &src "/tmp/src/dmriprep"
 orbs:
-  docker: circleci/docker@1.6.0
+  docker: circleci/docker@2.1.4
 
 jobs:
   build:
-    machine:
-      # https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
-      # upgrade Docker version
-      image: ubuntu-2004:202104-01
-    working_directory: /tmp/src/dmriprep
+    <<: *machine_defaults
     environment:
-      TZ: "/usr/share/zoneinfo/America/Los_Angeles"
-      SCRATCH: "/scratch"
+      DOCKER_BUILDKIT: 1
     steps:
-      - checkout
-      - run:
-          name: Check whether build should be skipped
-          command: |
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
-              echo "Only docs build"
-              circleci step halt
-            fi
+      - checkout:
+          path: *src
+      - run: *check_skip_job
       - restore_cache:
           keys:
-            - build-v1-{{ .Branch }}-{{ .Revision }}
-            - build-v1--{{ .Revision }}
-            - build-v1-{{ .Branch }}-
-            - build-v1-master-
-            - build-v1-
+            - build-v2-{{ .Branch }}-{{ .Revision }}
+            - build-v2--{{ .Revision }}
+            - build-v2-{{ .Branch }}-
+            - build-v2-master-
+            - build-v2-
           paths:
             - /tmp/docker
+            - /tmp/images
       - docker/install-docker-credential-helper
+      - run: *docker_auth
+      - run: *setup_docker_registry
       - run:
-          name: Login into Docker Hub
-          command: |
-            if [[ -n "$DOCKER_PAT" ]]; then
-              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
-            fi
-      - run:
-          name: Set-up a Docker registry
-          command: |
-            docker run -d -p 5000:5000 --restart=always --name=registry \
-                -v /tmp/docker:/var/lib/registry registry:2
-      - run:
-          name: Pull images
-          command: |
-            set +e
-            docker pull localhost:5000/ubuntu
-            success=$?
-            set -e
-            if [[ "$success" = "0" ]]; then
-                echo "Pulling from local registry"
-                docker tag localhost:5000/ubuntu ubuntu:xenial-20201030
-                docker pull localhost:5000/dmriprep
-                docker tag localhost:5000/dmriprep nipreps/dmriprep:latest
-                docker tag localhost:5000/dmriprep nipreps/dmriprep
-            else
-                echo "Pulling from Docker Hub"
-                docker pull ubuntu:xenial-20201030
-                docker tag ubuntu:xenial-20201030 localhost:5000/ubuntu
-                docker push localhost:5000/ubuntu
-                docker pull nipreps/dmriprep:latest
-            fi
-      - run:
-          name: Build Docker image
+          name: Build Docker image (production environment)
           no_output_timeout: 60m
           command: |
-            export PY3=$(pyenv versions | grep '3\.' |
-                         sed -e 's/.* 3\./3./' -e 's/ .*//')
-            pyenv local $PY3
+            pyenv local 3
+            pip install hatch
             # Get version, update files.
-            THISVERSION=$( python3 get_version.py )
-            if [[ ${THISVERSION:0:2} == "0+" ]] ; then
+            THISVERSION=$( hatch version )
+            if [[ ${THISVERSION:0:1} == "0" ]] ; then
               echo "WARNING: latest git tag could not be found"
               echo "Please, make sure you fetch all tags from upstream with"
               echo "the command ``git fetch --tags --verbose`` and push"
               echo "them to your fork with ``git push origin --tags``"
             fi
             # Build docker image
-            e=1 && for i in {1..5}; do
-              docker build --rm \
-                --cache-from=nipreps/dmriprep \
+            docker buildx build --load \
+                --cache-from localhost:5000/dmriprep \
+                --cache-from nipreps/dmriprep:latest \
                 -t nipreps/dmriprep:latest \
+                --platform linux/amd64 \
                 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                 --build-arg VCS_REF=`git rev-parse --short HEAD` \
-                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
-              && e=0 && break || sleep 15
-            done && [ "$e" -eq "0" ]
+                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" .
+      - run:
+          name: Build Docker image (test environment)
+          no_output_timeout: 60m
+          command: |
+            docker buildx build --load \
+                --cache-from localhost:5000/dmriprep \
+                --cache-from nipreps/dmriprep:latest \
+                -t nipreps/dmriprep:test \
+                --platform linux/amd64 \
+                --target test .
+      - run:
+          command: docker images
+      - run:
+          name: Check Docker image (production)
+          command: |
+            # Get version, update files.
+            THISVERSION=$( hatch version )
+            BUILT_VERSION=$( docker run --rm nipreps/dmriprep:latest --version )
+            BUILT_VERSION=${BUILT_VERSION%$'\r'}
+            BUILT_VERSION=${BUILT_VERSION#*"dMRIPrep v"}
+            BUILT_VERSION=${BUILT_VERSION%.d*}
+            echo "VERSION: \"$THISVERSION\""
+            echo "BUILT: \"$BUILT_VERSION\""
+            set -e
+            test "$BUILT_VERSION" = "$THISVERSION"
+      - run:
+          name: Check Docker image (test)
+          command: |
+            docker run --rm nipreps/dmriprep:test dmriprep --version
+            docker run --rm nipreps/dmriprep:test pytest --version
       - run:
           name: Docker push to local registry
           no_output_timeout: 40m
           command: |
             docker tag nipreps/dmriprep:latest localhost:5000/dmriprep
+            docker tag nipreps/dmriprep:test localhost:5000/dmriprep-test
             docker push localhost:5000/dmriprep
+            docker push localhost:5000/dmriprep-test
       - run:
           name: Docker registry garbage collection
           command: |
             docker exec -it registry /bin/registry garbage-collect --delete-untagged \
-                /etc/docker/registry/config.yml
-      - save_cache:
-         key: build-v1-{{ .Branch }}-{{ .Revision }}
-         paths:
-            - /tmp/docker
+              /etc/docker/registry/config.yml
+
       - persist_to_workspace:
           root: /tmp
           paths:
             - src/dmriprep
+      - save_cache:
+         key: build-v2-{{ .Branch }}-{{ .Revision }}
+         paths:
+            - /tmp/docker
+            - /tmp/images
 
   get_data:
     docker:
-      - image: continuumio/miniconda3:4.9.2-alpine
+      - image: continuumio/miniconda3:master-alpine
     working_directory: /tmp/data
     environment:
       - TEMPLATEFLOW_HOME: /tmp/templateflow
@@ -145,7 +263,7 @@ jobs:
       - run:
           name: Setup git-annex & DataLad
           command: |
-            conda install -y -c anaconda -c conda-forge git-annex datalad
+            conda install -y -c anaconda -c conda-forge git git-annex datalad
             python -m pip install --no-cache-dir -U datalad-osf
             git config --global user.name 'NiPreps Bot'
             git config --global user.email 'nipreps@gmail.com'
@@ -166,49 +284,36 @@ jobs:
 
       - restore_cache:
           keys:
-            - data-ds001771-v3-{{ .Branch }}-{{ .Revision }}
-            - data-ds001771-v3--{{ .Revision }}
-            - data-ds001771-v3-{{ .Branch }}-
-            - data-ds001771-v3-master-
-            - data-ds001771-v3-
+            - data-v0-{{ .Branch }}-{{ .Revision }}
+            - data-v0--{{ .Revision }}
+            - data-v0-{{ .Branch }}-
+            - data-v0-master-
+            - data-v0-
       - run:
           name: Install ds001771
           command: |
-            datalad install -r https://github.com/nipreps-data/ds001771.git
-            datalad update -r --merge -d ds001771/
-            datalad get -J 2 -r -d ds001771/ ds001771/sub-36/anat/*
-            datalad get -J 2 -r -d ds001771/ ds001771/sub-36/dwi/*
-            datalad get -J 2 -r -d ds001771/ ds001771/sub-36/fmap/*
-            datalad get -J 2 -r -d ds001771/derivatives/ ds001771/derivatives/smriprep-0.6.0/*
-            datalad get -J 2 -r -d ds001771/derivatives/ ds001771/derivatives/freesurfer-6.0.1/sub-36/mri/*
-            datalad get -J 2 -r -d ds001771/derivatives/ ds001771/derivatives/freesurfer-6.0.1/sub-36/surf/lh.white \
+            datalad install -r /tmp/data/ds001771 -s https://github.com/nipreps-data/ds001771.git
+            datalad update -r --merge -d /tmp/data/ds001771
+            datalad get -J 2 -r -d /tmp/data/ds001771 ds001771/sub-36/anat/*
+            datalad get -J 2 -r -d /tmp/data/ds001771 ds001771/sub-36/dwi/*
+            datalad get -J 2 -r -d /tmp/data/ds001771 ds001771/sub-36/fmap/*
+            datalad get -J 2 -r -d /tmp/data/ds001771/derivatives/ ds001771/derivatives/smriprep-0.6.0/*
+            datalad get -J 2 -r -d /tmp/data/ds001771/derivatives/ ds001771/derivatives/freesurfer-6.0.1/sub-36/mri/*
+            datalad get -J 2 -r -d /tmp/data/ds001771/derivatives/ ds001771/derivatives/freesurfer-6.0.1/sub-36/surf/lh.white \
                                                          ds001771/derivatives/freesurfer-6.0.1/sub-36/surf/rh.white \
                                                          ds001771/derivatives/freesurfer-6.0.1/sub-36/surf/lh.thickness \
                                                          ds001771/derivatives/freesurfer-6.0.1/sub-36/surf/rh.thickness
-
-      - save_cache:
-          key: data-ds001771-v3-{{ .Branch }}-{{ .Revision }}
-          paths:
-            - /tmp/data/ds001771
-
-      - restore_cache:
-          keys:
-            - data-ds000206-v2-{{ .Branch }}-{{ .Revision }}
-            - data-ds000206-v2--{{ .Revision }}-
-            - data-ds000206-v2-{{ .Branch }}-
-            - data-ds000206-v2-master-
-            - data-ds000206-v2-
       - run:
           name: Install ds000206
           command: |
-            datalad install -r https://github.com/nipreps-data/ds000206.git
-            datalad update -r --merge -d ds000206/
-            datalad get -J 2 -r -d ds000206/ ds000206/sub-05/*
-            datalad get -J 2 -r -d ds000206/derivatives/ ds000206/derivatives/freesurfer-6.0.1/sub-05/*
-
+            datalad install -r /tmp/data/ds000206 -s https://github.com/nipreps-data/ds000206.git
+            datalad update -r --merge -d /tmp/data/ds000206
+            datalad get -J 2 -r -d /tmp/data/ds000206/ ds000206/sub-05/*
+            datalad get -J 2 -r -d /tmp/data/ds000206/derivatives/ ds000206/derivatives/freesurfer-6.0.1/sub-05/*
       - save_cache:
-          key: data-ds000206-v2-{{ .Branch }}-{{ .Revision }}
+          key: data-v0-{{ .Branch }}-{{ .Revision }}
           paths:
+            - /tmp/data/ds001771
             - /tmp/data/ds000206
 
       - run:
@@ -224,228 +329,110 @@ jobs:
             printf "[execution]\nstop_on_first_crash = true\n" > /tmp/config/nipype.cfg
             echo "poll_sleep_duration = 0.01" >> /tmp/config/nipype.cfg
             echo "hash_method = content" >> /tmp/config/nipype.cfg
+
       - persist_to_workspace:
           root: /tmp
           paths:
-            - templateflow
             - fslicense
             - config/nipype.cfg
-
-  ds000206:
-    machine:
-      # https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
-      # upgrade Docker version
-      image: ubuntu-2004:202104-01
-    working_directory: /tmp/ds000206
+  test_pytest:
+    <<: *machine_defaults
     environment:
-      - FS_LICENSE: /tmp/fslicense/license.txt
+      CHECK_PYTEST: true
     steps:
       - checkout:
-          path: /home/circleci/src/dmriprep
-      - run:
-          name: Check whether build should be skipped
-          command: |
-            cd /home/circleci/src/dmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
-              echo "Only docs build"
-              circleci step halt
-            fi
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds000206\]' )" != "" ]]; then
-              echo "Skipping ds000206 build"
-              circleci step halt
-            fi
+          path: *src
+      - run: *check_skip_job
       - attach_workspace:
           at: /tmp
       - restore_cache:
           keys:
-            - data-ds000206-v2-{{ .Branch }}-{{ .Revision }}
-            - data-ds000206-v2-{{ .Branch }}-{{ .Revision }}-
-            - data-ds000206-v2--{{ .Revision }}-
-            - data-ds000206-v2-{{ .Branch }}-
-            - data-ds000206-v2-master-
-            - data-ds000206-v2-
-      - restore_cache:
-          keys:
-            - build-v1-{{ .Branch }}-{{ .Revision }}
+            - build-v2-{{ .Branch }}-{{ .Revision }}
           paths:
             - /tmp/docker
-      - run:
-          name: Set-up a Docker registry
-          command: |
-            docker run -d -p 5000:5000 --restart=always --name=registry \
-                -v /tmp/docker:/var/lib/registry registry:2
-      - run:
-          name: Pull images from local registry
-          command: |
-            docker pull localhost:5000/dmriprep
-            docker tag localhost:5000/dmriprep nipreps/dmriprep:latest
+            - /tmp/images
       - restore_cache:
           keys:
-            - ds000206-anat-v01-{{ .Branch }}-{{ .Revision }}
-            - ds000206-anat-v01-{{ .Branch }}
-            - ds000206-anat-v01-master
-            - ds000206-anat-v01-
+            - data-v0-{{ .Branch }}-{{ .Revision }}
+      - docker/install-docker-credential-helper
+      - run: *docker_auth
+      - run: *setup_docker_registry
+      - run: *pull_from_registry
+      - run: *pull_test_image_from_registry
       - run:
-          name: Run anatomical workflow on ds000206
+          name: Run dMRIPrep tests
           no_output_timeout: 2h
           command: |
-            mkdir -p /tmp/ds000206/work /tmp/ds000206/derivatives
-            docker run -e FS_LICENSE=$FS_LICENSE --rm \
-                -v /tmp/data/ds000206:/data \
-                -v /tmp/ds000206/derivatives:/out \
-                -v /tmp/fslicense/license.txt:/tmp/fslicense/license.txt:ro \
-                -v /tmp/config/nipype.cfg:/home/dmriprep/.nipype/nipype.cfg \
-                -v /tmp/templateflow:/home/dmriprep/.cache/templateflow \
-                -v /tmp/ds000206/work:/work \
-                --user $(id -u):$(id -g) \
-                nipreps/dmriprep:latest /data /out participant -vv \
-                --fs-subjects-dir /data/derivatives/freesurfer-6.0.1 --sloppy --anat-only \
-                --notrack --skip-bids-validation -w /work --omp-nthreads 2 --nprocs 2
-      - run:
-          name: Clean-up after anatomical run
-          command: |
-            rm -rf /tmp/ds000206/work/dmriprep_wf/fsdir*
-            rm -rf /tmp/ds000206/work/reportlets
-          when: on_success
-      - save_cache:
-         key: ds000206-anat-v01-{{ .Branch }}-{{ .Revision }}
-         paths:
-            - /tmp/ds000206/work
-      - run:
-          name: Run full diffusion workflow on ds000206
-          no_output_timeout: 4h
-          command: |
-            eddy="--ignore eddy"
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[run[ _]?eddy\]' )" != "" ]]; then
-              eddy=""
-            fi
-            mkdir -p /tmp/ds000206/work /tmp/ds000206/derivatives
-            docker run -e FS_LICENSE=$FS_LICENSE --rm \
-                -v /tmp/data/ds000206:/data \
-                -v /tmp/ds000206/derivatives:/out \
-                -v /tmp/fslicense/license.txt:/tmp/fslicense/license.txt:ro \
-                -v /tmp/config/nipype.cfg:/home/dmriprep/.nipype/nipype.cfg \
-                -v /tmp/templateflow:/home/dmriprep/.cache/templateflow \
-                -v /tmp/ds000206/work:/work \
-                --user $(id -u):$(id -g) \
-                nipreps/dmriprep:latest /data /out participant -vv $eddy \
-                --fs-subjects-dir /data/derivatives/freesurfer-6.0.1 --sloppy \
-                --output-spaces MNI152NLin2009cAsym --use-syn-sdc \
-                --notrack --skip-bids-validation -w /work --omp-nthreads 2 --nprocs 2
-      - store_artifacts:
-          path: /tmp/ds000206/derivatives/dmriprep
-      - run:
-          name: Clean working directory
-          when: on_success
-          command: |
-            sudo rm -rf /tmp/ds000206/work
-      - run:
-          name: Clean working directory
-          when: on_fail
-          command: |
-            find /tmp/ds000206/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-                -exec sh -c 'rm -f {}; touch {}' \;
-            find /tmp/ds000206/work_partial \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-                -exec sh -c 'rm -f {}; touch {}' \;
+            docker run -ti --rm=false \
+              -e TEST_READONLY_FILESYSTEM=1 -v $HOME:/home/readonly:ro \
+              --entrypoint="pytest" nipreps/dmriprep:test \
+              --pyargs dmriprep -svx --doctest-modules
+
       - store_artifacts:
-          path: /tmp/ds000206/work
-
-  ds001771:
-    machine:
-      # https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
-      # upgrade Docker version
-      image: ubuntu-2004:202104-01
-    working_directory: /tmp/ds001771
+          path: /tmp/data/reports
+
+  build_docs:
+    docker:
+      - image: python:3.12
     environment:
-      - FS_LICENSE: /tmp/fslicense/license.txt
+      - FSLOUTPUTTYPE: NIFTI
+      - SUBJECTS_DIR: /tmp/subjects
     steps:
-      - checkout:
-          path: /home/circleci/src/dmriprep
-      - run:
-          name: Check whether build should be skipped
-          command: |
-            cd /home/circleci/src/dmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
-              echo "Only docs build"
-              circleci step halt
-            fi
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds001771\]' )" != "" ]]; then
-              echo "Skipping ds001771 build"
-              circleci step halt
-            fi
-      - attach_workspace:
-          at: /tmp
       - restore_cache:
           keys:
-            - data-ds001771-v3-{{ .Branch }}-{{ .Revision }}-
-            - data-ds001771-v3--{{ .Revision }}-
-            - data-ds001771-v3-{{ .Branch }}-
-            - data-ds001771-v3-master-
-            - data-ds001771-v3-
-      - restore_cache:
-          keys:
-            - build-v1-{{ .Branch }}-{{ .Revision }}
-            - build-v1--{{ .Revision }}
-            - build-v1-
+            - docs-v1-{{ .Branch }}-{{ .Revision }}
+            - docs-v1--{{ .Revision }}
+            - docs-v1-{{ .Branch }}-
+            - docs-v1-master
+            - docs-v1-
           paths:
-            - /tmp/docker
+            - ./docs/_build/_html
+      - checkout
       - run:
-          name: Set-up a Docker registry
-          command: |
-            docker run -d -p 5000:5000 --restart=always --name=registry \
-                -v /tmp/docker:/var/lib/registry registry:2
+          name: Create subjects folder
+          command: mkdir -p $SUBJECTS_DIR
       - run:
-          name: Pull images from local registry
-          command: |
-            docker pull localhost:5000/dmriprep
-            docker tag localhost:5000/dmriprep nipreps/dmriprep:latest
+          name: Install Graphviz
+          command: apt update && apt -y install graphviz
       - run:
-          name: Run full diffusion workflow on ds001771
-          no_output_timeout: 4h
-          command: |
-            eddy="--ignore eddy"
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[run[ _]?eddy\]' )" != "" ]]; then
-              eddy=""
-            fi
-            mkdir -p /tmp/ds001771/work /tmp/ds001771/derivatives
-            docker run -e FS_LICENSE=$FS_LICENSE --rm \
-                -v /tmp/data/ds001771:/data \
-                -v /tmp/ds001771/derivatives:/out \
-                -v /tmp/fslicense/license.txt:/tmp/fslicense/license.txt:ro \
-                -v /tmp/templateflow:/home/dmriprep/.cache/templateflow \
-                -v /tmp/config/nipype.cfg:/home/dmriprep/.nipype/nipype.cfg \
-                -v /tmp/ds001771/work:/work \
-                --user $(id -u):$(id -g) \
-                nipreps/dmriprep:latest /data /out participant -vv $eddy \
-                -w /work --omp-nthreads 2 --nprocs 2 \
-                --notrack --skip-bids-validation --sloppy \
-                --fs-subjects-dir /data/derivatives/freesurfer-6.0.1 \
-                --anat-derivatives /data/derivatives/smriprep-0.6.0
-      - store_artifacts:
-          path: /tmp/ds001771/derivatives/dmriprep
+          name: Install deps
+          command: pip install --no-cache-dir -r docs/requirements.txt
       - run:
-          name: Clean working directory
-          when: on_success
-          command: |
-            sudo rm -rf /tmp/ds001771/work
+          name: Build only this commit
+          command: make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html
+      - store_artifacts:
+          path: ./docs/_build/no_version_html
       - run:
-          name: Clean working directory
-          when: on_fail
+          name: Generate Versioned Docs
           command: |
-            sudo chown $(id -un):$(id -gn) -R /tmp/ds001771
-            find /tmp/ds001771/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-                -exec sh -c 'rm -f {}; touch {}' \;
-            find /tmp/ds001771/work_partial \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-                -exec sh -c 'rm -f {}; touch {}' \;
+            set +e
+            force_versioned="$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[docs?[ _]?versions?\]' )"
+            set -e
+            if [[ "x${CIRCLE_TAG}" = "x" && "${CIRCLE_BRANCH}" != "master" && "x${force_versioned}" = "x" ]]; then
+              echo "Not a tag or master branch - skipping versioned docs."
+              circleci step halt
+            else
+              make -f ./docs/Makefile versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH}
+            fi
+      - save_cache:
+          key: docs-v1-{{ .Branch }}-{{ .Revision }}
+          paths:
+            - ./docs/_build/_html
+      - persist_to_workspace:
+          root: docs/_build
+          paths: html
       - store_artifacts:
-          path: /tmp/ds001771/work
+          path: ./docs/_build/html
+
+  deploy_docs_tag:
+    <<: *docs
+
+  deploy_docs_master:
+    <<: *docs
 
   deploy_docker_patches:
-    machine:
-      # https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
-      # upgrade Docker version
-      image: ubuntu-2004:202104-01
-    working_directory: /tmp/src/dmriprep
+    <<: *machine_defaults
+    working_directory: *src
     steps:
       - run:
           name: Check whether image should be deployed to Docker Hub
@@ -454,141 +441,83 @@ jobs:
               echo "Nothing to deploy for $CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME."
               circleci step halt
             fi
-      - checkout:
-          path: /home/circleci/src/dmriprep
-      - run:
-          name: Check whether build should be skipped
-          command: |
-            cd /home/circleci/src/dmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
-              echo "Only docs build"
-              circleci step halt
-            fi
       - restore_cache:
           keys:
-            - build-v1-{{ .Branch }}-{{ .Revision }}
+            - build-v2-{{ .Branch }}-{{ .Revision }}
           paths:
             - /tmp/docker
+            - /tmp/images
       - docker/install-docker-credential-helper
-      - run:
-          name: Login into Docker Hub
-          command: |
-            if [[ -n "$DOCKER_PAT" ]]; then
-              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
-            fi
-      - run:
-          name: Set-up a Docker registry
-          command: |
-            docker run -d -p 5000:5000 --restart=always --name=registry \
-                -v /tmp/docker:/var/lib/registry registry:2
-      - run:
-          name: Pull images from local registry
-          command: |
-            docker pull localhost:5000/dmriprep
-            docker tag localhost:5000/dmriprep nipreps/dmriprep:latest
+      - run: *docker_auth
+      - run: *setup_docker_registry
+      - run: *pull_from_registry
       - run:
           name: Deploy to Docker Hub
           no_output_timeout: 40m
           command: |
-            docker tag nipreps/dmriprep nipreps/dmriprep:${CIRCLE_BRANCH#docker/}
-            docker push nipreps/dmriprep:${CIRCLE_BRANCH#docker/}
+            # Format: docker/[<version-like>+]<tag> -> nipreps/dmriprep:<tag>
+            # <version-like>+<tag> guides setuptools_scm to get the right major/minor
+            docker tag nipreps/dmriprep nipreps/dmriprep:${CIRCLE_BRANCH##*[/+]}
+            docker push nipreps/dmriprep:${CIRCLE_BRANCH##*[/+]}
 
   deploy_docker:
-    machine:
-      # https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
-      # upgrade Docker version
-      image: ubuntu-2004:202104-01
-    working_directory: /tmp/src/dmriprep
+    <<: *machine_defaults
     steps:
-      - run:
-          name: Check whether image should be deployed to Docker Hub
-          command: |
-            if [[ "$CIRCLE_PROJECT_USERNAME" != "nipreps" ]]; then
-              echo "Nothing to deploy for $CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME."
-              circleci step halt
-            fi
       - checkout:
-          path: /home/circleci/src/dmriprep
-      - run:
-          name: Check whether build should be skipped
-          command: |
-            cd /home/circleci/src/dmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
-              echo "Only docs build"
-              circleci step halt
-            fi
+          path: *src
+      - run: *check_skip_job
       - restore_cache:
           keys:
-            - build-v1-{{ .Branch }}-{{ .Revision }}
+            - build-v2-{{ .Branch }}-{{ .Revision }}
           paths:
             - /tmp/docker
+            - /tmp/images
       - docker/install-docker-credential-helper
-      - run:
-          name: Login into Docker Hub
-          command: |
-            if [[ -n "$DOCKER_PAT" ]]; then
-              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
-            fi
-      - run:
-          name: Set-up a Docker registry
-          command: |
-            docker run -d -p 5000:5000 --restart=always --name=registry \
-                -v /tmp/docker:/var/lib/registry registry:2
-      - run:
-          name: Pull images from local registry
-          command: |
-            docker pull localhost:5000/dmriprep
-            docker tag localhost:5000/dmriprep nipreps/dmriprep:latest
+      - run: *docker_auth
+      - run: *setup_docker_registry
+      - run: *pull_from_registry
       - run:
           name: Deploy to Docker Hub
           no_output_timeout: 40m
           command: |
-            docker tag nipreps/dmriprep nipreps/dmriprep:unstable
-            docker push nipreps/dmriprep:unstable
-            if [[ -n "$CIRCLE_TAG" ]]; then
-              docker push nipreps/dmriprep:latest
-              docker tag nipreps/dmriprep nipreps/dmriprep:$CIRCLE_TAG
-              docker push nipreps/dmriprep:$CIRCLE_TAG
+            if [[ -n "$DOCKER_PAT" ]]; then
+              echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
+              docker tag nipreps/dmriprep nipreps/dmriprep:unstable
+              docker push nipreps/dmriprep:unstable
+              if [[ -n "$CIRCLE_TAG" ]]; then
+                docker push nipreps/dmriprep:latest
+                docker tag nipreps/dmriprep nipreps/dmriprep:$CIRCLE_TAG
+                docker push nipreps/dmriprep:$CIRCLE_TAG
+              fi
             fi
 
   test_deploy_pypi:
-    docker:
-      - image: circleci/python:3.7.4
-    working_directory: /tmp/src/dmriprep
+    <<: *python_defaults
     steps:
       - checkout
       - run:
-          name: Install libhdf5
-          command: |
-            sudo apt-get install pkg-config libhdf5-103 libhdf5-dev
-      - run:
-          name: Start virtual environment
-          command: |
-            python -m venv /tmp/sdist
-            source /tmp/sdist/bin/activate
-            python -m pip install -U pip
-            python -m pip install "setuptools>=40.8.0" twine
+          name: Update build tools
+          command: pip install --upgrade build twine hatch
       - run:
           name: Build dMRIPrep
-          command: |
-            source /tmp/sdist/bin/activate
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
-            THISVERSION=${CIRCLE_TAG:-$THISVERSION}
-            echo "${CIRCLE_TAG:-$THISVERSION}" > dmriprep/VERSION
-            python setup.py sdist
-            pip wheel --no-deps -w dist/ .
+          command: python -m build
+      - run:
+          name: Twine check dmriprep
+          command: twine check dist/*
+      - run:
+          name: Pre-run hatch version
+          command: hatch version
       - store_artifacts:
           path: /tmp/src/dmriprep/dist
       - run:
           name: Check sdist distribution
           command: |
-            source /tmp/sdist/bin/activate
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
+            THISVERSION=$( hatch version )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
-            twine check dist/dmriprep*.tar.gz
-            pip install dist/dmriprep*.tar.gz
+            virtualenv --python=python sdist
+            source sdist/bin/activate
+            python -m pip install --upgrade pip
+            python -m pip install dist/dmriprep*.tar.gz
             which dmriprep | grep sdist\\/bin
             INSTALLED_VERSION=$(dmriprep --version)
             INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
@@ -599,15 +528,11 @@ jobs:
       - run:
           name: Check wheel distribution
           command: |
-            python -m venv /tmp/wheel
-            source /tmp/wheel/bin/activate
-            python -m pip install -U pip
-            python -m pip install "setuptools>=40.8.0" twine
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
+            THISVERSION=$( hatch version )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
-            twine check dist/dmriprep*.whl
-            pip install dist/dmriprep*.whl
+            virtualenv --python=python wheel
+            source wheel/bin/activate
+            python -m pip install dist/dmriprep*.whl
             which dmriprep | grep wheel\\/bin
             INSTALLED_VERSION=$(dmriprep --version)
             INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
@@ -615,37 +540,31 @@ jobs:
             echo "VERSION: \"$THISVERSION\""
             echo "INSTALLED: \"$INSTALLED_VERSION\""
             test "$INSTALLED_VERSION" = "$THISVERSION"
+      - run:
+          name: Build dmriprep-docker
+          command: python -m build wrapper
+      - run:
+          name: Twine check wrapper
+          command: twine check wrapper/dist/*
       - store_artifacts:
-          path: /tmp/src/dmriprep/dist
+          path: /tmp/src/dmriprep/wrapper/dist
 
   deploy_pypi:
-    docker:
-      - image: circleci/python:3.7.4
-    working_directory: /tmp/src/dmriprep
+    <<: *python_defaults
     steps:
       - checkout
       - run:
-          name: Start virtual environment
-          command: |
-            python -m venv /tmp/sdist
-            source /tmp/sdist/bin/activate
-            python -m pip install -U pip
-            python -m pip install "setuptools>=40.8.0" wheel twine
+          name: Update build tools
+          command: pip install --upgrade build twine
       - run:
           name: Build dMRIPrep
-          command: |
-            source /tmp/sdist/bin/activate
-            THISVERSION=$( python get_version.py )
-            THISVERSION=${THISVERSION%.dirty*}
-            THISVERSION=${CIRCLE_TAG:-$THISVERSION}
-            echo "${CIRCLE_TAG:-$THISVERSION}" > dmriprep/VERSION
-            python setup.py sdist
-            pip wheel --no-deps -w dist/ .
+          command: python -m build
+      - run:
+          name: Build dmriprep-docker
+          command: python -m build wrapper/
       - run:
           name: Upload packages to PyPI
-          command: |
-            source /tmp/sdist/bin/activate
-            twine upload dist/dmriprep*
+          command: python -m twine upload dist/dmriprep* wrapper/dist/dmriprep*
 
   deployable:
     docker:
@@ -653,70 +572,13 @@ jobs:
     steps:
       - run: echo Deploying!
 
-  build_docs:
-    docker:
-      - image: python:3.7.4
-    environment:
-      - FSLOUTPUTTYPE: NIFTI
-      - SUBJECTS_DIR: /tmp/subjects
-    steps:
-      - restore_cache:
-          keys:
-            - docs-v1-{{ .Branch }}-{{ .Revision }}
-            - docs-v1--{{ .Revision }}
-            - docs-v1-{{ .Branch }}-
-            - docs-v1-master
-            - docs-v1-
-          paths:
-            - ./docs/_build/_html
-      - checkout
-      - run:
-          name: Create subjects folder
-          command: mkdir -p $SUBJECTS_DIR
-      - run:
-          name: Install Graphviz
-          command: apt update && apt -y install graphviz
-      - run:
-          name: Install deps
-          command: pip install --no-cache-dir -r docs/requirements.txt
-      - run:
-          name: Build only this commit
-          command: make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html
-      - store_artifacts:
-          path: ./docs/_build/no_version_html
-      - run:
-          name: Generate Versioned Docs
-          command: |
-            set +e
-            force_versioned="$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[docs?[ _]?versions?\]' )"
-            set -e
-            if [[ "x${CIRCLE_TAG}" = "x" && "${CIRCLE_BRANCH}" != "master" && "x${force_versioned}" = "x" ]]; then
-              echo "Not a tag or master branch - skipping versioned docs."
-              circleci step halt
-            else
-              make -f ./docs/Makefile versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH}
-            fi
-      - save_cache:
-          key: docs-v1-{{ .Branch }}-{{ .Revision }}
-          paths:
-            - ./docs/_build/_html
-      - persist_to_workspace:
-          root: docs/_build
-          paths: html
-      - store_artifacts:
-          path: ./docs/_build/html
-
-  deploy_docs_tag:
-    <<: *docs
-
-  deploy_docs_master:
-    <<: *docs
-
 workflows:
   version: 2
   build_test_deploy:
     jobs:
       - build:
+          context:
+            - nipreps-common
           filters:
             branches:
               ignore:
@@ -734,96 +596,100 @@ workflows:
             tags:
               only: /.*/
 
-      - ds000206:
-          requires:
-            - build
-            - get_data
+
+      - test_deploy_pypi:
+          context:
+            - nipreps-common
           filters:
             branches:
-              ignore:
-                - /docs?\/.*/
-                - /tests?\/.*/
-                - /docker\/.*/
+              only:
+                - /rel\/.*/
+                - /maint\/.*/
             tags:
               only: /.*/
-      - ds001771:
+
+      - test_pytest:
+          context:
+            - nipreps-common
           requires:
             - build
-            - get_data
           filters:
             branches:
               ignore:
                 - /docs?\/.*/
-                - /tests?\/.*/
+                - /ds001771\/.*/
+                - /ds000206\/.*/
                 - /docker\/.*/
             tags:
               only: /.*/
-      - test_deploy_pypi:
+
+      - build_docs:
+          context:
+            - nipreps-common
           filters:
             branches:
-              only:
-                - /rel\/.*/
-                - /maint\/.*/
+              ignore:
+                - /tests?\/.*/
+                - /ds000206\/.*/
+                - /ds001771\/.*/
             tags:
               only: /.*/
 
-      - deploy_docker_patches:
-          requires:
-            - build
-          filters:
-            branches:
-              only: /docker\/.*/
-
-      - deployable:
+      - deploy_docs_master:
+          context:
+            - nipreps-common
           requires:
-            - build
             - build_docs
             - test_deploy_pypi
           filters:
             branches:
-              only: master
+              only: /master/
             tags:
-              only: /.*/
+              ignore: /.*/
 
-      - deploy_docker:
+      - deploy_docs_tag:
           requires:
             - deployable
           filters:
             branches:
-              only: master
+              ignore: /.*/
             tags:
               only: /.*/
 
-      - deploy_pypi:
+
+      - deploy_docker_patches:
+          context:
+            - nipreps-common
           requires:
-            - deployable
+            - build
           filters:
             branches:
-              ignore: /.*/
-            tags:
-              only: /.*/
+              only: /docker\/.*/
 
-      - build_docs:
+      - deployable:
+          requires:
+            - test_deploy_pypi
+            - test_pytest
           filters:
             branches:
-              ignore:
-                - /tests?\/.*/
-                - /ds000206\/.*/
-                - /ds001771\/.*/
+              only: master
             tags:
               only: /.*/
 
-      - deploy_docs_master:
+      - deploy_docker:
+          context:
+            - nipreps-common
           requires:
-            - build_docs
-            - test_deploy_pypi
+            - deployable
           filters:
             branches:
-              only: /master/
+              only: master
             tags:
-              ignore: /.*/
+              only: /.*/
 
-      - deploy_docs_tag:
+      - deploy_pypi:
+          context:
+            - nipreps-common
           requires:
             - deployable
           filters:
diff --git a/.docker/fsl-6.0/bin/eddy_openmp b/.docker/fsl-6.0/bin/eddy_openmp
deleted file mode 100755
index dbca89210..000000000
Binary files a/.docker/fsl-6.0/bin/eddy_openmp and /dev/null differ
diff --git a/.docker/fsl-6.0/bin/imglob b/.docker/fsl-6.0/bin/imglob
deleted file mode 100755
index 718c453b5..000000000
--- a/.docker/fsl-6.0/bin/imglob
+++ /dev/null
@@ -1,132 +0,0 @@
-#!/usr/bin/env python
-#   imglob - expand list of image filenames
-#   Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group
-#   Copyright (C) 2009 University of Oxford 
-#   Part of FSL - FMRIB's Software Library
-#   http://www.fmrib.ox.ac.uk/fsl
-#   fsl@fmrib.ox.ac.uk
-#   
-#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
-#   Imaging of the Brain), Department of Clinical Neurology, Oxford
-#   University, Oxford, UK
-#   
-#   
-#   LICENCE
-#   
-#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
-#   Oxford (the "Software")
-#   
-#   The Software remains the property of the University of Oxford ("the
-#   University").
-#   
-#   The Software is distributed "AS IS" under this Licence solely for
-#   non-commercial use in the hope that it will be useful, but in order
-#   that the University as a charitable foundation protects its assets for
-#   the benefit of its educational and research purposes, the University
-#   makes clear that no condition is made or to be implied, nor is any
-#   warranty given or to be implied, as to the accuracy of the Software,
-#   or that it will be suitable for any particular purpose or for use
-#   under any specific conditions. Furthermore, the University disclaims
-#   all responsibility for the use which is made of the Software. It
-#   further disclaims any liability for the outcomes arising from using
-#   the Software.
-#   
-#   The Licensee agrees to indemnify the University and hold the
-#   University harmless from and against any and all claims, damages and
-#   liabilities asserted by third parties (including claims for
-#   negligence) which arise directly or indirectly from the use of the
-#   Software or the sale of any products based on the Software.
-#   
-#   No part of the Software may be reproduced, modified, transmitted or
-#   transferred in any form or by any means, electronic or mechanical,
-#   without the express permission of the University. The permission of
-#   the University is not required if the said reproduction, modification,
-#   transmission or transference is done without financial return, the
-#   conditions of this Licence are imposed upon the receiver of the
-#   product, and all original and amended source code is included in any
-#   transmitted product. You may be held legally responsible for any
-#   copyright infringement that is caused or encouraged by your failure to
-#   abide by these terms and conditions.
-#   
-#   You are not permitted under this Licence to use this Software
-#   commercially. Use for which any financial return is received shall be
-#   defined as commercial use, and includes (1) integration of all or part
-#   of the source code or the Software into a product for sale or license
-#   by or on behalf of Licensee to third parties or (2) use of the
-#   Software or any derivative of it for research with the final aim of
-#   developing software products for sale or license to a third party or
-#   (3) use of the Software or any derivative of it for research with the
-#   final aim of developing non-software products for sale or license to a
-#   third party, or (4) use of the Software to provide any service to an
-#   external organisation for which payment is received. If you are
-#   interested in using the Software commercially, please contact Isis
-#   Innovation Limited ("Isis"), the technology transfer company of the
-#   University, to negotiate a licence. Contact details are:
-#   innovation@isis.ox.ac.uk quoting reference DE/9564.
-
-import sys
-import os
-import glob
-
-setAvailable=True
-if sys.version_info < (2, 4):
-   import sets
-   from sets import Set
-   setAvailable=False
-
-def usage():
-    print("Usage: $0 [-extension/extensions] <list of names>")
-    print("       -extension for one image with full extension")
-    print("       -extensions for image list with full extensions")
-    sys.exit(1)
-
-def isImage(input,allExtensions):       #Returns whether an input filename has an image extension ( and the basename and extension pair )
-    for extension in allExtensions:
-       if input[-len(extension):] == extension:
-          return True, input[:-len(extension)], extension
-    return False, input, ''
-
-def removeImageExtension(input,allExtensions):
-    return isImage(input,allExtensions)[1]
-
-if len(sys.argv) <= 1:
-    usage()
-
-deleteExtensions=True
-primaryExtensions=['.nii.gz', '.nii', '.hdr.gz', '.hdr']
-secondaryExtensions=['.img.gz', '.img']
-allExtensions=primaryExtensions+secondaryExtensions
-validExtensions=primaryExtensions
-startingArg=1
-
-if sys.argv[1] == "-extensions":
-   validExtensions=allExtensions
-   deleteExtensions=False
-   startingArg=2
-if sys.argv[1] == "-extension":
-   deleteExtensions=False
-   startingArg=2
-    
-filelist=[]
-for arg in range(startingArg, len(sys.argv)):
-#      if isImage(sys.argv[arg],allExtensions)[0]:          #These enable a "pedantic" style mode currently not used
-#         filelist.extend(glob.glob(sys.argv[arg]))
-#      else:
-#         for currentExtension in validExtensions:
-#            filelist.extend(glob.glob(sys.argv[arg]+currentExtension))
-    for currentExtension in validExtensions:
-       filelist.extend(glob.glob(removeImageExtension(sys.argv[arg],allExtensions)+currentExtension))
-
-if deleteExtensions:
-    for file in range(0, len(filelist)):
-        filelist[file]=removeImageExtension(filelist[file],allExtensions)
-if setAvailable:
-   filelist=list(set(filelist))
-else:
-   filelist=list(Set(filelist))
-filelist.sort()
-
-for file in range(0, len(filelist)):
-    print(filelist[file], end=' ')
-    if file < len(filelist)-1:
-       print(" ", end=' ')
diff --git a/.docker/fsl-6.0/bin/topup b/.docker/fsl-6.0/bin/topup
deleted file mode 100755
index fed01a44c..000000000
Binary files a/.docker/fsl-6.0/bin/topup and /dev/null differ
diff --git a/.docker/fsl-6.0/lib/libgfortran.so.3 b/.docker/fsl-6.0/lib/libgfortran.so.3
deleted file mode 100755
index ae186d1b7..000000000
Binary files a/.docker/fsl-6.0/lib/libgfortran.so.3 and /dev/null differ
diff --git a/.docker/fsl-6.0/lib/libopenblas.so.0 b/.docker/fsl-6.0/lib/libopenblas.so.0
deleted file mode 100755
index d898087b7..000000000
Binary files a/.docker/fsl-6.0/lib/libopenblas.so.0 and /dev/null differ
diff --git a/.docker/neurodebian.gpg b/.docker/neurodebian.gpg
deleted file mode 100644
index c546d45d2..000000000
--- a/.docker/neurodebian.gpg
+++ /dev/null
@@ -1,71 +0,0 @@
------BEGIN PGP PUBLIC KEY BLOCK-----
-Version: GnuPG v1
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diff --git a/.dockerignore b/.dockerignore
index 21177b527..08977af76 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -12,43 +12,16 @@ dmriprep.egg-info/**/*
 dmriprep.egg-info
 .eggs/**/*
 .eggs
+
+.pixi
+.tox
+
+# python distribution
 .pytest_cache/**/*
 .pytest_cache
 .ipynb_checkpoints/**/*
 .ipynb_checkpoints
 
-
-# housekeeping tools
-.maintenance/**/*
-.maintenance
-get_version.py
-tox.ini
-
-# pip installs
-src/**/*
-src/
-
 # git
 .gitignore
-.git/**/*
-.git
-.github/**/*
-.github
 .mailmap
-
-# other
-work/**/*
-work
-out/**/*
-out/
-
-# CI, etc.
-.circleci
-.circleci/**/*
-.codecov.yml
-.coveragerc
-.pep8speaks.yml
-.travis.yml
-.zenodo.json
-
-.afq
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 000000000..887a2c18f
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
deleted file mode 100644
index 61706914d..000000000
--- a/.github/workflows/pythonpackage.yml
+++ /dev/null
@@ -1,101 +0,0 @@
-name: Python package
-
-on:
-  push:
-    branches: [ '*' ]
-    tags: [ '*' ]
-  pull_request:
-    branches: [ master, 'maint/*' ]
-
-jobs:
-  build:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.7, 3.8]
-        pip: ["pip~=20.3", "pip~=21.0"]
-
-    steps:
-    - name: Install hdf5 libraries
-      run: |
-        sudo apt-get install pkg-config libhdf5-103 libhdf5-dev
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v2
-      with:
-        ssh-key: "${{ secrets.NIPREPS_DEPLOY }}"
-    - name: Fetch all tags (for versioneer to work)
-      if: "!startsWith(github.ref, 'refs/tags/')"
-      run: |
-        /usr/bin/git -c protocol.version=2 fetch --tags --prune --unshallow origin
-    - name: Build in confined, updated environment and interpolate version
-      run: |
-        python -m venv /tmp/buildenv
-        source /tmp/buildenv/bin/activate
-        python -m pip install -U setuptools pip wheel twine docutils
-        python setup.py sdist bdist_wheel
-        python -m twine check dist/dmriprep*
-        # Interpolate version
-        if [[ "$GITHUB_REF" == refs/tags/* ]]; then
-          TAG=${GITHUB_REF##*/}
-        fi
-        THISVERSION=$( python get_version.py )
-        THISVERSION=${TAG:-$THISVERSION}
-        echo "Expected VERSION: \"${THISVERSION}\""
-        echo "THISVERSION=${THISVERSION}" >> ${GITHUB_ENV}
-    - name: Install in confined environment [sdist]
-      run: |
-        python -m venv /tmp/install_sdist
-        source /tmp/install_sdist/bin/activate
-        python -m pip install "${{ matrix.pip }}" setuptools
-        python -m pip install dist/dmriprep*.tar.gz
-        INSTALLED_VERSION=$(python -c 'import dmriprep; print(dmriprep.__version__, end="")')
-        echo "VERSION: \"${THISVERSION}\""
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-    - name: Install in confined environment [wheel]
-      run: |
-        python -m venv /tmp/install_wheel
-        source /tmp/install_wheel/bin/activate
-        python -m pip install "${{ matrix.pip }}" setuptools
-        python -m pip install dist/dmriprep*.whl
-        INSTALLED_VERSION=$(python -c 'import dmriprep; print(dmriprep.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-    - name: Install in confined environment [setup.py - install]
-      run: |
-        python -m venv /tmp/setup_install
-        source /tmp/setup_install/bin/activate
-        python -m pip install "${{ matrix.pip }}" setuptools
-        python -m pip install numpy scipy "Cython >= 0.28.5" # sklearn needs this
-        python -m pip install scikit-learn  # otherwise it attempts to build it
-        python setup.py install
-        INSTALLED_VERSION=$(python -c 'import dmriprep; print(dmriprep.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-    - name: Install in confined environment [setup.py - develop]
-      run: |
-        python -m venv /tmp/setup_develop
-        source /tmp/setup_develop/bin/activate
-        python -m pip install "${{ matrix.pip }}" setuptools
-        # sklearn needs these dependencies
-        python -m pip install numpy scipy "Cython >= 0.28.5"
-        python -m pip install scikit-learn  # otherwise it attempts to build it
-        python setup.py develop
-        INSTALLED_VERSION=$(python -c 'import dmriprep; print(dmriprep.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${THISVERSION}"
-  flake8:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.7
-    - run: pip install flake8
-    - run: flake8 dmriprep
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 000000000..40474ca74
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,98 @@
+name: Stable tests
+
+on:
+  push:
+    branches:
+      - master
+      - maint/*
+      - next
+  pull_request:
+    branches:
+      - master
+      - maint/*
+      - next
+
+defaults:
+  run:
+    shell: bash
+
+# Force tox and pytest to use color
+env:
+  FORCE_COLOR: true
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    # 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', '3.13']
+        dependencies: ['latest', 'pre']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.10'
+            dependencies: 'min'
+
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/templateflow
+          key: templateflow-v1
+      - name: Install dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends graphviz
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        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 --with=tox-uv --with=tox-gh-actions tox
+      - 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", "spellcheck"]
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          persist-credentials: false
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install tox
+        run: uv tool install tox --with=tox-uv
+      - name: Show tox config
+        run: tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: tox -e ${{ matrix.check }}
diff --git a/.gitignore b/.gitignore
index 71450ef6d..d8240e12e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -107,3 +107,6 @@ ENV/
 
 #kubernetes stuff
 kubernetes/jobs/
+# pixi environments
+.pixi/*
+!.pixi/config.toml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 000000000..c501a7c41
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,19 @@
+exclude: ".*/data/.*|.maint/.*_author.*.py|.vscode/.*.json"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: '.*\.svg'
+      - id: end-of-file-fixer
+        exclude: '.*\.svg'
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.3
+    hooks:
+      - id: ruff-check
+        args: [ --fix ]
+      - id: ruff-format
diff --git a/Dockerfile b/Dockerfile
index 54fc7a75d..defc43f56 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,7 +2,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2021 The NiPreps Developers
+# Copyright (c) The NiPreps Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -22,187 +22,108 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-# Use Ubuntu 16.04 LTS
-FROM ubuntu:xenial-20201030
+ARG BASE_IMAGE=ghcr.io/nipreps/fmriprep-base:20251006
 
-# Prepare environment
+#
+# Build pixi environment
+# The Pixi environment includes:
+#   - Python
+#     - Scientific Python stack (via conda-forge)
+#     - General Python dependencies (via PyPI)
+#   - NodeJS
+#     - bids-validator
+#     - svgo
+#   - FSL (via fslconda)
+#   - ants (via conda-forge)
+#   - connectome-workbench (via conda-forge)
+#   - ...
+#
+FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    autoconf \
-                    build-essential \
-                    bzip2 \
                     ca-certificates \
-                    curl \
-                    cython3 \
-                    git \
-                    libtool \
-                    lsb-release \
-                    pkg-config \
-                    xvfb && \
+                    git && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+# Run post-link scripts during install, but use global to keep out of source tree
+RUN pixi config set --global run-post-link-scripts insecure
+
+# Install dependencies before the package itself to leverage caching
+RUN mkdir /app
+COPY pixi.lock pyproject.toml /app
+WORKDIR /app
+RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e dmriprep -e test --frozen --skip dmriprep
+RUN --mount=type=cache,target=/root/.npm pixi run --as-is -e dmriprep npm install -g svgo@^3.2.0 bids-validator@1.14.10
+# Note that PATH gets hard-coded. Remove it and re-apply in final image
+RUN pixi shell-hook -e dmriprep --as-is | grep -v PATH > /shell-hook.sh
+RUN pixi shell-hook -e test --as-is | grep -v PATH > /test-shell-hook.sh
+
+# Finally, install the package
+COPY . /app
+RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e dmriprep -e test --frozen
 
-# Installing freesurfer
-RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
-    --exclude='freesurfer/diffusion' \
-    --exclude='freesurfer/docs' \
-    --exclude='freesurfer/fsfast' \
-    --exclude='freesurfer/lib/cuda' \
-    --exclude='freesurfer/lib/qt' \
-    --exclude='freesurfer/matlab' \
-    --exclude='freesurfer/mni/share/man' \
-    --exclude='freesurfer/subjects/fsaverage_sym' \
-    --exclude='freesurfer/subjects/fsaverage3' \
-    --exclude='freesurfer/subjects/fsaverage4' \
-    --exclude='freesurfer/subjects/cvs_avg35' \
-    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
-    --exclude='freesurfer/subjects/bert' \
-    --exclude='freesurfer/subjects/lh.EC_average' \
-    --exclude='freesurfer/subjects/rh.EC_average' \
-    --exclude='freesurfer/subjects/sample-*.mgz' \
-    --exclude='freesurfer/subjects/V1_average' \
-    --exclude='freesurfer/trctrain'
-
-ENV FSL_DIR="/usr/share/fsl/5.0" \
-    OS="Linux" \
-    FS_OVERRIDE=0 \
-    FIX_VERTEX_AREA="" \
-    FSF_OUTPUT_FORMAT="nii.gz" \
-    FREESURFER_HOME="/opt/freesurfer"
-ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
-    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
-    MNI_DIR="$FREESURFER_HOME/mni" \
-    LOCAL_DIR="$FREESURFER_HOME/local" \
-    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
-    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
-    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
-ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
-
-# Pre-cache neurodebian key
-COPY .docker/neurodebian.gpg /usr/local/etc/neurodebian.gpg
-# Installing Neurodebian packages (FSL, AFNI, git)
-RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key add /usr/local/etc/neurodebian.gpg && \
-    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
+#
+# Pre-fetch templates
+#
+FROM ghcr.io/astral-sh/uv:python3.12-alpine AS templates
+ENV TEMPLATEFLOW_HOME="/templateflow"
+RUN uv pip install --system templateflow
+RUN templateflow ls MNI152Lin
+# COPY scripts/fetch_templates.py fetch_templates.py
+# RUN python fetch_templates.py
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-                    fsl-core=5.0.9-5~nd16.04+1 \
-                    fsl-mni152-templates=5.0.7-2 \
-                    afni=16.2.07~dfsg.1-5~nd16.04+1 \
-                    convert3d && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-ENV FSLDIR="/usr/share/fsl/5.0" \
-    FSLOUTPUTTYPE="NIFTI_GZ" \
-    FSLMULTIFILEQUIT="TRUE" \
-    POSSUMDIR="/usr/share/fsl/5.0" \
-    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
-    FSLTCLSH="/usr/bin/tclsh" \
-    FSLWISH="/usr/bin/wish" \
-    AFNI_MODELPATH="/usr/lib/afni/models" \
-    AFNI_IMSAVE_WARNINGS="NO" \
-    AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
-    AFNI_PLUGINPATH="/usr/lib/afni/plugins"
-ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
-
-COPY .docker/fsl-6.0/bin/topup /usr/share/fsl/5.0/bin/topup
-COPY .docker/fsl-6.0/bin/imglob /usr/share/fsl/5.0/bin/imglob
-COPY .docker/fsl-6.0/bin/eddy_openmp  /usr/lib/fsl/5.0/eddy_openmp
-COPY .docker/fsl-6.0/lib/* /usr/lib/fsl/5.0/
-
-# Installing ANTs 2.3.3 (NeuroDocker build)
-# Note: the URL says 2.3.4 but it is actually 2.3.3
-ENV ANTSPATH=/usr/lib/ants
-RUN mkdir -p $ANTSPATH && \
-    curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
-    | tar -xzC $ANTSPATH --strip-components 1
-ENV PATH=$ANTSPATH:$PATH
+#
+# Main stage
+#
+FROM ${BASE_IMAGE} AS base
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users dmriprep
 WORKDIR /home/dmriprep
 ENV HOME="/home/dmriprep"
 
-# Installing and setting up miniconda
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
-    bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda3-4.5.11-Linux-x86_64.sh
-
-# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
-ENV PATH="/usr/local/miniconda/bin:$PATH" \
-    CPATH="/usr/local/miniconda/include/:$CPATH" \
-    LANG="C.UTF-8" \
-    LC_ALL="C.UTF-8" \
-    PYTHONNOUSERSITE=1
-
-# Installing precomputed python packages
-RUN conda install -y -c anaconda -c conda-forge \
-                     python=3.7.1 \
-                     graphviz=2.40 \
-                     git-annex \
-                     libxml2=2.9.8 \
-                     libxslt=1.1.32 \
-                     matplotlib=2.2 \
-                     mkl \
-                     mkl-service \
-                     nodejs \
-                     numpy=1.20 \
-                     pandoc=2.11 \
-                     pip=20.3 \
-                     scikit-learn=0.19 \
-                     scipy=1.5 \
-                     setuptools=51.1 \
-                     traits=4.6.0 \
-                     zlib; sync && \
-    chmod -R a+rX /usr/local/miniconda; sync && \
-    chmod +x /usr/local/miniconda/bin/*; sync && \
-    conda build purge-all; sync && \
-    conda clean -tipsy && sync
+COPY --link --from=templates /templateflow /home/dmriprep/.cache/templateflow
+
+RUN chmod -R go=u $HOME
 
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
-# Precaching fonts, set 'Agg' as default backend for matplotlib
-RUN python -c "from matplotlib import font_manager" && \
-    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+WORKDIR /tmp
 
-# Installing SVGO
-RUN npm install -g svgo
+FROM base AS test
 
-# Installing bids-validator
-RUN npm install -g bids-validator@1.4.0
+COPY --link --from=build /app/.pixi/envs/test /app/.pixi/envs/test
+COPY --link --from=build /test-shell-hook.sh /shell-hook.sh
+RUN cat /shell-hook.sh >> $HOME/.bashrc
+ENV PATH="/app/.pixi/envs/test/bin:$PATH"
 
-# Refresh linked libraries
-RUN ldconfig
+ENV FSLDIR="/app/.pixi/envs/test"
 
-WORKDIR /src
+FROM base AS dmriprep
 
-# Installing dMRIPrep
-COPY . /src/dmriprep
-ARG VERSION
-# Force static versioning within container
-RUN echo "${VERSION}" > /src/dmriprep/dmriprep/VERSION && \
-    echo "include dmriprep/VERSION" >> /src/dmriprep/MANIFEST.in && \
-    cd /src/dmriprep && \
-    pip install --no-cache-dir .[all]
+# Keep synced with wrapper's PKG_PATH
+COPY --link --from=build /app/.pixi/envs/dmriprep /app/.pixi/envs/dmriprep
+COPY --link --from=build /shell-hook.sh /shell-hook.sh
+RUN cat /shell-hook.sh >> $HOME/.bashrc
+ENV PATH="/app/.pixi/envs/dmriprep/bin:$PATH"
+
+ENV FSLDIR="/app/.pixi/envs/dmriprep"
 
-RUN find $HOME -type d -exec chmod go=u {} + && \
-    find $HOME -type f -exec chmod go=u {} +
+# For detecting the container
+ENV IS_DOCKER_8395080871=1
 
-WORKDIR /tmp/
-ENTRYPOINT ["/usr/local/miniconda/bin/dmriprep"]
+ENTRYPOINT ["/app/.pixi/envs/dmriprep/bin/dmriprep"]
 
 ARG BUILD_DATE
 ARG VCS_REF
 ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.name="dMRIPrep" \
-      org.label-schema.description="dMRIPrep - robust dMRI preprocessing tool" \
-      org.label-schema.url="http://dmriprep.org" \
+      org.label-schema.description="dMRIPrep - robust fMRI preprocessing tool" \
+      org.label-schema.url="https://www.nipreps.org/dmriprep/" \
       org.label-schema.vcs-ref=$VCS_REF \
       org.label-schema.vcs-url="https://github.com/nipreps/dmriprep" \
       org.label-schema.version=$VERSION \
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index a24694ff4..000000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1 +0,0 @@
-include versioneer.py
diff --git a/NOTICE b/NOTICE
index 63430138c..ebe04b695 100644
--- a/NOTICE
+++ b/NOTICE
@@ -1,18 +1,9 @@
 dMRIPrep
-Copyright 2021 The NiPreps Developers.
+Copyright The NiPreps Developers.
 
 This product includes software developed by
 the NiPreps Community (https://nipreps.org/).
 
-Portions of this software were developed at the Department of
-Psychology at Stanford University, Stanford, CA, US.
-
-This software redistributes the versioneer Python package, which is
-Public domain source code.
-
 This software is also distributed as a Docker container image.
-The bootstraping file for the image ("Dockerfile") is licensed
+The bootstrapping file for the image ("Dockerfile") is licensed
 under the MIT License.
-
-This software may be distributed through an add-on package called
-"Docker Wrapper" that is under the BSD 3-clause License.
diff --git a/dmriprep/__about__.py b/dmriprep/__about__.py
deleted file mode 100644
index fbaf58f46..000000000
--- a/dmriprep/__about__.py
+++ /dev/null
@@ -1,39 +0,0 @@
-# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft=python sts=4 ts=4 sw=4 et:
-#
-# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-# We support and encourage derived works from this project, please read
-# about our expectations at
-#
-#     https://www.nipreps.org/community/licensing/
-#
-"""Base module variables."""
-from ._version import get_versions
-
-__version__ = get_versions()["version"]
-del get_versions
-
-__packagename__ = "dmriprep"
-__copyright__ = "Copyright 2019, The dMRIPrep developers"
-__credits__ = (
-    "Contributors: please check the ``.zenodo.json`` file at the top-level folder"
-    "of the repository"
-)
-__url__ = "https://github.com/nipreps/dmriprep"
-
-DOWNLOAD_URL = f"https://github.com/nipreps/{__packagename__}/archive/{__version__}.tar.gz"
-
-__ga_id__ = "UA-156165436-1"
diff --git a/dmriprep/__init__.py b/dmriprep/__init__.py
index d8a714e65..2afc7fea2 100644
--- a/dmriprep/__init__.py
+++ b/dmriprep/__init__.py
@@ -1,14 +1,28 @@
-"""Top-level package for dmriprep."""
-from .__about__ import (
-    __version__,
-    __copyright__,
-    __credits__,
-    __packagename__,
-)
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <nipreps@gmail.com>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Top-module metadata."""
 
-__all__ = [
-    "__version__",
-    "__copyright__",
-    "__credits__",
-    "__packagename__",
-]
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ = '0+unknown'
diff --git a/dmriprep/_version.py b/dmriprep/_version.py
deleted file mode 100644
index 34ee6ff95..000000000
--- a/dmriprep/_version.py
+++ /dev/null
@@ -1,530 +0,0 @@
-
-# This file helps to compute a version number in source trees obtained from
-# git-archive tarball (such as those provided by githubs download-from-tag
-# feature). Distribution tarballs (built by setup.py sdist) and build
-# directories (produced by setup.py build) will contain a much shorter file
-# that just contains the computed version number.
-
-# This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
-
-"""Git implementation of _version.py."""
-
-import errno
-import os
-import re
-import subprocess
-import sys
-
-
-def get_keywords():
-    """Get the keywords needed to look up the version information."""
-    # these strings will be replaced by git during git-archive.
-    # setup.py/versioneer.py will grep for the variable names, so they must
-    # each be defined on a line of their own. _version.py will just call
-    # get_keywords().
-    git_refnames = "$Format:%d$"
-    git_full = "$Format:%H$"
-    git_date = "$Format:%ci$"
-    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
-    return keywords
-
-
-class VersioneerConfig:
-    """Container for Versioneer configuration parameters."""
-
-
-def get_config():
-    """Create, populate and return the VersioneerConfig() object."""
-    # these strings are filled in when 'setup.py versioneer' creates
-    # _version.py
-    cfg = VersioneerConfig()
-    cfg.VCS = "git"
-    cfg.style = "pep440"
-    cfg.tag_prefix = ""
-    cfg.parentdir_prefix = ""
-    cfg.versionfile_source = "dmriprep/_version.py"
-    cfg.verbose = False
-    return cfg
-
-
-class NotThisMethod(Exception):
-    """Exception raised if a method is not valid for the current scenario."""
-
-
-LONG_VERSION_PY = {}
-HANDLERS = {}
-
-
-def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
-    def decorate(f):
-        """Store f in HANDLERS[vcs][method]."""
-        if vcs not in HANDLERS:
-            HANDLERS[vcs] = {}
-        HANDLERS[vcs][method] = f
-        return f
-    return decorate
-
-
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
-    """Call the given command(s)."""
-    assert isinstance(commands, list)
-    p = None
-    for c in commands:
-        try:
-            dispcmd = str([c] + args)
-            # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
-            break
-        except EnvironmentError:
-            e = sys.exc_info()[1]
-            if e.errno == errno.ENOENT:
-                continue
-            if verbose:
-                print(f"unable to run {dispcmd}")
-                print(e)
-            return None, None
-    else:
-        if verbose:
-            print(f"unable to find command, tried {commands}")
-        return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
-        if verbose:
-            print(f"unable to run {dispcmd} (error)")
-            print(f"stdout was {stdout}")
-        return None, p.returncode
-    return stdout, p.returncode
-
-
-def versions_from_parentdir(parentdir_prefix, root, verbose):
-    """Try to determine the version from the parent directory name.
-
-    Source tarballs conventionally unpack into a directory that includes both
-    the project name and a version string. We will also support searching up
-    two directory levels for an appropriately named parent directory
-    """
-    rootdirs = []
-
-    for i in range(3):
-        dirname = os.path.basename(root)
-        if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
-
-    if verbose:
-        print(f"Tried directories {rootdirs} but none started with prefix {parentdir_prefix}")
-    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-
-
-@register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
-    """Extract version information from the given file."""
-    # the code embedded in _version.py can just fetch the value of these
-    # keywords. When used from setup.py, we don't want to import _version.py,
-    # so we do it with a regexp instead. This function is not used from
-    # _version.py.
-    keywords = {}
-    try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
-        pass
-    return keywords
-
-
-@register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
-    """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
-    date = keywords.get("date")
-    if date is not None:
-        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
-        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
-        # -like" string, which we must then edit to make compliant), because
-        # it's been around since git-1.5.3, and it's too difficult to
-        # discover which version we're using, or to work around using an
-        # older one.
-        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-    refnames = keywords["refnames"].strip()
-    if refnames.startswith("$Format"):
-        if verbose:
-            print("keywords are unexpanded, not using")
-        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
-    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
-    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
-    TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
-    if not tags:
-        # Either we're using git < 1.8.3, or there really are no tags. We use
-        # a heuristic: assume all version tags have a digit. The old git %d
-        # expansion behaves like git log --decorate=short and strips out the
-        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
-        # between branches and tags. By ignoring refnames without digits, we
-        # filter out many common branch names like "release" and
-        # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
-        if verbose:
-            print(f"discarding '{','.join(refs - tags)}', no digits")
-    if verbose:
-        print(f"likely tags: {','.join(sorted(tags))}")
-    for ref in sorted(tags):
-        # sorting will prefer e.g., "2.0" over "2.0rc1"
-        if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
-            if verbose:
-                print(f"picking {r}")
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
-    # no suitable tags, so version is "0+unknown", but full hex is still there
-    if verbose:
-        print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
-
-
-@register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
-    """Get version from 'git describe' in the root of the source tree.
-
-    This only gets called if the git-archive 'subst' keywords were *not*
-    expanded, and _version.py hasn't already been rewritten with a short
-    version string, meaning we're inside a checked out source tree.
-    """
-    GITS = ["git"]
-    if sys.platform == "win32":
-        GITS = ["git.cmd", "git.exe"]
-
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
-    if rc != 0:
-        if verbose:
-            print(f"Directory {root} not under git control")
-        raise NotThisMethod("'git rev-parse --git-dir' returned error")
-
-    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
-    # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", f"{tag_prefix}*"],
-                                   cwd=root)
-    # --long was added in git-1.5.5
-    if describe_out is None:
-        raise NotThisMethod("'git describe' failed")
-    describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
-    if full_out is None:
-        raise NotThisMethod("'git rev-parse' failed")
-    full_out = full_out.strip()
-
-    pieces = {}
-    pieces["long"] = full_out
-    pieces["short"] = full_out[:7]  # maybe improved later
-    pieces["error"] = None
-
-    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
-    # TAG might have hyphens.
-    git_describe = describe_out
-
-    # look for -dirty suffix
-    dirty = git_describe.endswith("-dirty")
-    pieces["dirty"] = dirty
-    if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
-
-    # now we have TAG-NUM-gHEX or HEX
-
-    if "-" in git_describe:
-        # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
-        if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = f"unable to parse git-describe output: '{describe_out}'"
-            return pieces
-
-        # tag
-        full_tag = mo.group(1)
-        if not full_tag.startswith(tag_prefix):
-            if verbose:
-                print(
-                    f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'")
-            pieces["error"] = (f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'"
-            return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
-
-        # distance: number of commits since tag
-        pieces["distance"] = int(mo.group(2))
-
-        # commit: short hex revision ID
-        pieces["short"] = mo.group(3)
-
-    else:
-        # HEX: no tags
-        pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
-        pieces["distance"] = int(count_out)  # total number of commits
-
-    # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
-                       cwd=root)[0].strip()
-    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-
-    return pieces
-
-
-def plus_or_dot(pieces):
-    """Return a + if we don't already have one, else return a ."""
-    if "+" in pieces.get("closest-tag", ""):
-        return "."
-    return "+"
-
-
-def render_pep440(pieces):
-    """Build up version string, with post-release "local version identifier".
-
-    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
-    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
-
-    Exceptions:
-    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += plus_or_dot(pieces)
-            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
-            if pieces["dirty"]:
-                rendered += ".dirty"
-    else:
-        # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
-        if pieces["dirty"]:
-            rendered += ".dirty"
-    return rendered
-
-
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
-
-    Exceptions:
-    1: no tags. 0.post.devDISTANCE
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
-    else:
-        # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
-    return rendered
-
-
-def render_pep440_post(pieces):
-    """TAG[.postDISTANCE[.dev0]+gHEX] .
-
-    The ".dev0" means dirty. Note that .dev0 sorts backwards
-    (a dirty tree will appear "older" than the corresponding clean one),
-    but you shouldn't be releasing software with -dirty anyways.
-
-    Exceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%d" % pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-            rendered += plus_or_dot(pieces)
-            rendered += f"g{pieces['short']}"
-    else:
-        # exception #1
-        rendered = "0.post%d" % pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-        rendered += f"+g{pieces['short']}"
-    return rendered
-
-
-def render_pep440_old(pieces):
-    """TAG[.postDISTANCE[.dev0]] .
-
-    The ".dev0" means dirty.
-
-    Eexceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%d" % pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-    else:
-        # exception #1
-        rendered = "0.post%d" % pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-    return rendered
-
-
-def render_git_describe(pieces):
-    """TAG[-DISTANCE-gHEX][-dirty].
-
-    Like 'git describe --tags --dirty --always'.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-def render_git_describe_long(pieces):
-    """TAG-DISTANCE-gHEX[-dirty].
-
-    Like 'git describe --tags --dirty --always -long'.
-    The distance/hash is unconditional.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-def render(pieces, style):
-    """Render the given version pieces into the requested style."""
-    if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
-
-    if not style or style == "default":
-        style = "pep440"  # the default
-
-    if style == "pep440":
-        rendered = render_pep440(pieces)
-    elif style == "pep440-pre":
-        rendered = render_pep440_pre(pieces)
-    elif style == "pep440-post":
-        rendered = render_pep440_post(pieces)
-    elif style == "pep440-old":
-        rendered = render_pep440_old(pieces)
-    elif style == "git-describe":
-        rendered = render_git_describe(pieces)
-    elif style == "git-describe-long":
-        rendered = render_git_describe_long(pieces)
-    else:
-        raise ValueError(f"unknown style '{style}'")
-
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
-
-
-def get_versions():
-    """Get version information or return default if unable to do so."""
-    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
-    # __file__, we can work backwards from there to the root. Some
-    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
-    # case we can only use expanded keywords.
-
-    cfg = get_config()
-    verbose = cfg.verbose
-    root = os.path.realpath(__file__)
-
-    root_dir = os.path.dirname(root)
-    if os.path.isfile(os.path.join(root_dir, 'VERSION')):
-        with open(os.path.join(root_dir, 'VERSION')) as vfile:
-            version = vfile.readline().strip()
-
-        return {
-            "version": version,
-            "full-revisionid": None,
-            "dirty": None,
-            "error": None,
-            "date": None
-        }
-
-    try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
-                                          verbose)
-    except NotThisMethod:
-        pass
-
-    try:
-        # versionfile_source is the relative path from the top of the source
-        # tree (where the .git directory might live) to this file. Invert
-        # this to find the root from __file__.
-        for i in cfg.versionfile_source.split('/'):
-            root = os.path.dirname(root)
-    except NameError:
-        return {"version": "0+unknown", "full-revisionid": None,
-                "dirty": None,
-                "error": "unable to find root of source tree",
-                "date": None}
-
-    try:
-        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
-        return render(pieces, cfg.style)
-    except NotThisMethod:
-        pass
-
-    try:
-        if cfg.parentdir_prefix:
-            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
-    except NotThisMethod:
-        pass
-
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to compute version", "date": None}
diff --git a/get_version.py b/get_version.py
deleted file mode 100644
index 34c95fa25..000000000
--- a/get_version.py
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env python
-# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft=python sts=4 ts=4 sw=4 et:
-"""A convenience tool for querying dMRIPrep's version."""
-import sys
-import os.path as op
-
-
-def main():
-    """Print current dMRIPrep version."""
-    sys.path.insert(0, op.abspath("."))
-    from dmriprep.__about__ import __version__
-
-    print(__version__)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/long_description.rst b/long_description.rst
new file mode 100644
index 000000000..43d135e3d
--- /dev/null
+++ b/long_description.rst
@@ -0,0 +1,38 @@
+Preprocessing of diffusion MRI (dMRI) involves numerous steps to clean and standardize
+the data before voxel-wise diffusion modeling.
+Generally, researchers create ad hoc preprocessing workflows for each dataset,
+building upon a large inventory of available tools.
+The complexity of these workflows has snowballed with rapid advances in
+acquisition and processing.
+dMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and
+reproducible preprocessing for dMRI data.
+dMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of
+virtually any dataset, ensuring high-quality preprocessing without manual intervention.
+dMRIPrep robustly produces high-quality results on diverse dMRI data.
+Additionally, dMRIPrep introduces less uncontrolled spatial smoothness than observed
+with commonly used preprocessing tools.
+dMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing
+workflow, which can help ensure the validity of inference and the interpretability
+of results.
+
+License information
+-------------------
+*dMRIPrep* adheres to the
+`general licensing guidelines <https://www.nipreps.org/community/licensing/>`__
+of the *NiPreps framework*.
+
+License
+~~~~~~~
+Copyright (c) the *NiPreps* Developers.
+
+*dMRIPrep* is licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+`http://www.apache.org/licenses/LICENSE-2.0
+<http://www.apache.org/licenses/LICENSE-2.0>`__.
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 000000000..67ac4b857
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,7229 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+    - url: https://conda.anaconda.org/mrtrix3/
+    - url: https://conda.anaconda.org/conda-forge/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.11.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/backports.tarfile-1.2.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb03c661_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb03c661_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brunsli-0.1-he3183e4_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.21.3-h4cfbee9_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2025.10.5-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py313hf01b4d8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/charls-2.4.2-h59595ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.0-pyh707e725_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.3-py313h7037e92_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cryptography-46.0.2-py313hafb0bba_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/dbus-1.16.2-h3c4dab8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/deepdiff-8.6.1-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/dipy-1.11.0-np2py313h73dcb5b_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.19.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.60.1-py313h3dea7bd_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.16.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/h5py-3.14.0-nompi_py313h253c126_101.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/hatch-1.14.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/hatchling-1.27.0-pypyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.6-nompi_h6e4c0c1_103.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/httpcore-1.0.9-pyh29332c3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/httpx-0.28.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/hyperlink-21.0.0-pyh29332c3_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/imagecodecs-2025.8.2-py313h718aa22_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/imageio-2.37.0-pyhfb79c49_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.7.0-pyhe01879c_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.5.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.classes-3.4.0-pyhd8ed1ab_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.context-6.0.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.functools-4.3.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jeepney-0.9.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/joblib-1.5.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/jxrlib-1.1-hd590300_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/keyring-25.6.0-pyha804496_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.9-py313hc8edb43_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/lazy-loader-0.4-pyhd8ed1ab_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda
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+  sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
+  md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 567578
+  timestamp: 1742433379869
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-h6491c7d_2.conda
+  sha256: 0d02046f57f7a1a3feae3e9d1aa2113788311f3cf37a3244c71e61a93177ba67
+  md5: e6f69c7bcccdefa417f056fa593b40f0
+  depends:
+  - __osx >=11.0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 399979
+  timestamp: 1742433432699
diff --git a/pyproject.toml b/pyproject.toml
index 3a682f14f..8bd30e407 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,4 +1,247 @@
 [build-system]
-# setuptools can be configured with setup.cfg when >=30.3
-# Most bugfixes regarding setup.cfg are included before 38.3
-requires = ["setuptools >= 40.8.0", "wheel"]
+requires = ["hatchling>=1.27", "hatch-vcs", "nipreps-versions"]
+build-backend = "hatchling.build"
+
+[project]
+name = "dmriprep"
+description = "A robust and easy-to-use pipeline for preprocessing of diverse fMRI data"
+readme = "long_description.rst"
+authors = [{name = "The NiPreps Developers", email = "nipreps@gmail.com"}]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+dependencies = [
+    "dipy >=1.0.0",
+    "looseversion >= 1.3",
+    "h5py",
+    "nibabel >= 5.1.1",
+    "nipype >= 1.9.0",
+    "nireports >= 24.1.0",
+    "nitransforms >= 25.0.1",
+    "niworkflows >= 1.14.2",
+    "numpy >= 2.0",
+    "packaging >= 24",
+    "pandas >= 2.2",
+    "psutil >= 5.4",
+    "pyyaml",
+    "pybids >= 0.16",
+    "requests >= 2.27",
+    "sdcflows >= 2.15.0",
+    "smriprep >= 0.19.2",
+    "templateflow >= 24.2.2",
+    "transforms3d >= 0.4.2",
+    "toml >= 0.10",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/nipreps/dmriprep"
+Documentation = "https://www.nipreps.org/dmriprep"
+"Docker Images" = "https://hub.docker.com/r/nipreps/dmriprep/tags/"
+NiPreps = "https://www.nipreps.org/"
+
+[project.optional-dependencies]
+doc = [
+    "pydot >= 1.2.3",
+    "sphinx >= 5",
+    "sphinx-argparse !=0.5.0",
+    "sphinx_rtd_theme>=0.5.2",
+]
+dev = [
+    "ruff",
+    "pre-commit",
+]
+duecredit = ["duecredit"]
+resmon = []
+container = [
+    "dmriprep[telemetry]",
+    # templateflow extras
+    "datalad",
+    "datalad-osf",
+]
+telemetry = [
+    "migas >= 0.4.0",
+    "sentry-sdk >= 1.3",
+]
+test = [
+    "coverage[toml] >= 5.2.1",
+    "pytest >= 8.1",
+    "pytest-cov >= 2.11",
+    "pytest-env",
+    "pytest-xdist >= 2.5",
+]
+maint = [
+    "fuzzywuzzy",
+    "python-Levenshtein",
+]
+# Aliases
+docs = ["dmriprep[doc]"]
+tests = ["dmriprep[test]"]
+all = ["dmriprep[doc,maint,telemetry,test]"]
+
+[project.scripts]
+dmriprep = "dmriprep.cli.run:main"
+
+#
+# Hatch configurations
+#
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.sdist]
+exclude = [".git_archival.txt"]  # No longer needed in sdist
+
+[tool.hatch.build.targets.wheel]
+packages = ["dmriprep"]
+exclude = [
+    "dmriprep/data/tests/work",  # Large test data directory
+]
+
+##  The following two sections configure setuptools_scm in the hatch way
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { version_scheme = "nipreps-calver" }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "dmriprep/_version.py"
+
+#
+# Developer tool configurations
+#
+
+# Disable black
+[tool.black]
+exclude = ".*"
+
+[tool.pytest.ini_options]
+minversion = "6"
+testpaths = ["dmriprep"]
+log_cli_level = "INFO"
+xfail_strict = true
+norecursedirs = [".git"]
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  # Config pytest-cov
+  "--cov=dmriprep",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+junit_family = "xunit2"
+
+[tool.ruff]
+line-length = 99
+
+[tool.ruff.lint]
+extend-select = [
+  "I",
+  "UP",
+  "YTT",
+  "S",
+  "BLE",
+  "B",
+  "A",
+  "C4",
+  # "CPY",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "FA",
+  "ISC",
+  "ICN",
+  "LOG",
+  "PIE",
+  "PYI",
+  "PT",
+  "Q",
+  # "SIM",
+  # "TID",
+  "FLY",
+  # "PD",
+  "PERF",
+  "W",
+  "PGH",
+  "PLC",
+  "PLE",
+  "PLW",
+  "FURB",
+  "RUF",
+]
+ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "S603",
+  "PIE790",
+  "PERF203",
+  "PLC0415",
+  "PLW2901",
+  "RUF005",
+  "RUF012",
+]
+
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+"dmriprep/utils/debug.py" = ["A002", "T100"]
+"docs/conf.py" = ["A001"]
+"docs/sphinxext/github_link.py" = ["BLE001"]
+
+[tool.ruff.format]
+quote-style = "single"
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/_version.py"
+]
+
+[tool.coverage.paths]
+source = [
+  "dmriprep",
+  "**/site-packages/dmriprep"
+]
+
+[tool.pixi.workspace]
+channels = ["https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public", "mrtrix3", "conda-forge"]
+platforms = ["linux-64", "osx-arm64"]
+
+[tool.pixi.activation.env]
+FSLDIR = "$CONDA_PREFIX"
+
+[tool.pixi.feature.editable.pypi-dependencies]
+dmriprep = { path = ".", editable = true }
+[tool.pixi.feature.production.pypi-dependencies]
+dmriprep = { path = ".", editable = false }
+
+[tool.pixi.environments]
+# Local installs will use editable
+default = { features = ["editable"], solve-group = "default" }
+test = { features = ["editable", "test"], solve-group = "default" }
+# Use "dmriprep" feature for production environment, so it is identifiable
+dmriprep = { features = ["production", "container", "telemetry"], solve-group = "production" }
+
+[tool.pixi.tasks]
+
+[tool.pixi.dependencies]
+dipy = ">=1.11.0,<2"
+nodejs = ">=24.4.1,<24.10"
+hatch = ">=1.14.1,<2"
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 0a2bbe260..000000000
--- a/setup.cfg
+++ /dev/null
@@ -1,140 +0,0 @@
-[metadata]
-author = The NiPreps developers
-author_email = nipreps@gmail.com
-classifiers =
-    Development Status :: 3 - Alpha
-    Intended Audience :: Science/Research
-    Topic :: Scientific/Engineering :: Image Recognition
-    License :: OSI Approved :: Apache Software License
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-description = dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data.
-license = Apache License, Version 2.0
-long_description = file:README.rst
-long_description_content_type = text/x-rst; charset=UTF-8
-name = dmriprep
-project_urls =
-    Home = https://github.com/nipreps/dmriprep
-    Documentation = https://www.nipreps.org/dmriprep
-
-[options]
-python_requires = >=3.7
-install_requires =
-    dipy >=1.0.0
-    h5py
-    indexed_gzip >=0.8.8
-    nibabel ~= 3.0
-    nipype >= 1.5.1, < 2.0
-    niworkflows >= 1.4.0rc6, <1.5
-    numpy
-    pybids >= 0.11.1
-    pyyaml
-    sdcflows ~= 2.0.4
-    smriprep >= 0.8.0rc2
-    svgutils != 0.3.2
-    templateflow ~= 0.6
-    toml
-setup_requires =
-    setuptools >= 40.8.0
-test_requires =
-    codecov
-    coverage
-    pytest
-packages = find:
-
-[options.packages.find]
-exclude =
-    *.tests
-
-[options.package_data]
-dmriprep =
-    VERSION
-    config/reports-spec.yml
-    data/boilerplate.bib
-    data/flirtsch/*.cnf
-    data/tests/config.toml
-    data/tests/THP/*
-    data/tests/THP/sub-THP0005/anat/*
-    data/tests/THP/sub-THP0005/dwi/*
-
-[options.exclude_package_data]
-* = tests
-
-[options.extras_require]
-datalad = datalad
-doc =
-    nbsphinx
-    packaging
-    pydot >= 1.2.3
-    pydotplus
-    sphinx >=2.1.2,<3.0
-    sphinx-argparse
-    sphinx_rtd_theme
-    sphinxcontrib-apidoc ~= 0.3.0
-    sphinxcontrib-napoleon
-    sphinxcontrib-versioning
-docs =
-    %(doc)s
-duecredit = duecredit
-resmon = psutil >=5.4
-popylar = popylar >= 0.2
-style =
-    flake8 >= 3.7.0
-test =
-    pytest >= 4.4
-    pytest-xdist >= 2.0
-    pytest-cov >= 2.10.1
-    pytest-env
-    coverage
-tests =
-    %(test)s
-all =
-    %(datalad)s
-    %(doc)s
-    %(duecredit)s
-    %(resmon)s
-    %(popylar)s
-    %(tests)s
-
-[options.entry_points]
-console_scripts =
-    dmriprep=dmriprep.cli.run:main
-
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = dmriprep/_version.py
-versionfile_build = dmriprep/_version.py
-tag_prefix =
-parentdir_prefix =
-
-[flake8]
-max-line-length = 99
-doctests = False
-ignore =
-    W503
-    E231
-    E203
-exclude =
-    *build/
-    docs/sphinxext/
-    docs/tools/
-per-file-ignores =
-    **/__init__.py : F401
-    docs/conf.py : E265
-
-[tool:pytest]
-norecursedirs = .git
-addopts = -vsx --doctest-modules
-doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE NUMBER
-env =
-    PYTHONHASHSEED=0
-filterwarnings =
-    ignore::DeprecationWarning
-    ignore::PendingDeprecationWarning
-    ignore:cmp not installed:UserWarning
-    ignore:This has not been fully tested:UserWarning
-
-[coverage:run]
-concurrency = multiprocessing
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 07c88269c..000000000
--- a/setup.py
+++ /dev/null
@@ -1,13 +0,0 @@
-"""dMRIPrep's setup script."""
-import sys
-from setuptools import setup
-import versioneer
-
-if __name__ == "__main__":
-    setupargs = {
-        "version": versioneer.get_version(),
-        "cmdclass": versioneer.get_cmdclass(),
-    }
-    if "bdist_wheel" in sys.argv:
-        setupargs["setup_requires"] = ["setuptools >= 40.8", "wheel"]
-    setup(**setupargs)
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 000000000..1e814e351
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,111 @@
+[tox]
+requires =
+  tox>=4
+envlist =
+  py3{10,11,12,13}-{latest,pre}
+  py310-min
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.10: py310
+  3.11: py311
+  3.12: py312
+  3.13: py313
+
+[gh-actions:env]
+DEPENDS =
+  min: min
+  latest: latest
+  pre: pre
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pip_pre =
+  pre: true
+pass_env =
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  PYTHON_GIL
+deps =
+  py313: traits @ git+https://github.com/enthought/traits.git@10954eb
+extras = test
+setenv =
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: UV_INDEX=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: UV_INDEX_STRATEGY=unsafe-best-match
+  NO_ET=1
+uv_resolution =
+  min: lowest-direct
+
+commands_pre =
+  # Use py* to disable for other environments
+  py3{10,11,12,13}: python scripts/fetch_templates.py
+commands =
+  pytest --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto}
+
+[testenv:style]
+description = Check our style guide
+labels = check
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --diff
+  ruff format --diff
+
+[testenv:style-fix]
+description = Auto-apply style guide to the extent possible
+labels = pre-release
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --fix
+  ruff format
+
+[testenv:spellcheck]
+description = Check spelling
+labels = check
+deps =
+  codespell[toml]
+skip_install = true
+commands =
+  codespell . {posargs}
+
+[testenv:build{,-strict}]
+labels =
+  check
+  pre-release
+deps =
+  build
+  twine
+skip_install = true
+set_env =
+  # Ignore specific known warnings:
+  # https://github.com/pypa/pip/issues/11684
+  # https://github.com/pypa/pip/issues/12243
+  strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
+commands =
+  python -m build
+  python -m twine check dist/*
+
+[testenv:publish]
+depends = build
+labels = release
+deps =
+  twine
+skip_install = true
+commands =
+  python -m twine upload dist/*
diff --git a/versioneer.py b/versioneer.py
deleted file mode 100644
index f654ff30b..000000000
--- a/versioneer.py
+++ /dev/null
@@ -1,1827 +0,0 @@
-
-# Version: 0.18
-
-"""The Versioneer - like a rocketeer, but for versions.
-
-The Versioneer
-==============
-
-* like a rocketeer, but for versions!
-* https://github.com/warner/python-versioneer
-* Brian Warner
-* License: Public Domain
-* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
-* [![Latest Version]
-(https://pypip.in/version/versioneer/badge.svg?style=flat)
-](https://pypi.python.org/pypi/versioneer/)
-* [![Build Status]
-(https://travis-ci.org/warner/python-versioneer.png?branch=master)
-](https://travis-ci.org/warner/python-versioneer)
-
-This is a tool for managing a recorded version number in distutils-based
-python projects. The goal is to remove the tedious and error-prone "update
-the embedded version string" step from your release process. Making a new
-release should be as easy as recording a new tag in your version-control
-system, and maybe making new tarballs.
-
-
-## Quick Install
-
-* `pip install versioneer` to somewhere to your $PATH
-* add a `[versioneer]` section to your setup.cfg (see below)
-* run `versioneer install` in your source tree, commit the results
-
-## Version Identifiers
-
-Source trees come from a variety of places:
-
-* a version-control system checkout (mostly used by developers)
-* a nightly tarball, produced by build automation
-* a snapshot tarball, produced by a web-based VCS browser, like github's
-  "tarball from tag" feature
-* a release tarball, produced by "setup.py sdist", distributed through PyPI
-
-Within each source tree, the version identifier (either a string or a number,
-this tool is format-agnostic) can come from a variety of places:
-
-* ask the VCS tool itself, e.g., "git describe" (for checkouts), which knows
-  about recent "tags" and an absolute revision-id
-* the name of the directory into which the tarball was unpacked
-* an expanded VCS keyword ($Id$, etc)
-* a `_version.py` created by some earlier build step
-
-For released software, the version identifier is closely related to a VCS
-tag. Some projects use tag names that include more than just the version
-string (e.g., "myproject-1.2" instead of just "1.2"), in which case the tool
-needs to strip the tag prefix to extract the version identifier. For
-unreleased software (between tags), the version identifier should provide
-enough information to help developers recreate the same tree, while also
-giving them an idea of roughly how old the tree is (after version 1.2, before
-version 1.3). Many VCS systems can report a description that captures this,
-for example `git describe --tags --dirty --always` reports things like
-"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the
-0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has
-uncommitted changes.
-
-The version identifier is used for multiple purposes:
-
-* to allow the module to self-identify its version: `myproject.__version__`
-* to choose a name and prefix for a 'setup.py sdist' tarball
-
-## Theory of Operation
-
-Versioneer works by adding a special `_version.py` file into your source
-tree, where your `__init__.py` can import it. This `_version.py` knows how to
-dynamically ask the VCS tool for version information at import time.
-
-`_version.py` also contains `$Revision$` markers, and the installation
-process marks `_version.py` to have this marker rewritten with a tag name
-during the `git archive` command. As a result, generated tarballs will
-contain enough information to get the proper version.
-
-To allow `setup.py` to compute a version too, a `versioneer.py` is added to
-the top level of your source tree, next to `setup.py` and the `setup.cfg`
-that configures it. This overrides several distutils/setuptools commands to
-compute the version when invoked, and changes `setup.py build` and `setup.py
-sdist` to replace `_version.py` with a small static file that contains just
-the generated version data.
-
-## Installation
-
-See [INSTALL.md](./INSTALL.md) for detailed installation instructions.
-
-## Version-String Flavors
-
-Code which uses Versioneer can learn about its version string at runtime by
-importing `_version` from your main `__init__.py` file and running the
-`get_versions()` function. From the "outside" (e.g., in `setup.py`), you can
-import the top-level `versioneer.py` and run `get_versions()`.
-
-Both functions return a dictionary with different flavors of version
-information:
-
-* `['version']`: A condensed version string, rendered using the selected
-  style. This is the most commonly used value for the project's version
-  string. The default "pep440" style yields strings like `0.11`,
-  `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section
-  below for alternative styles.
-
-* `['full-revisionid']`: detailed revision identifier. For Git, this is the
-  full SHA1 commit id, e.g., "1076c978a8d3cfc70f408fe5974aa6c092c949ac".
-
-* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the
-  commit date in ISO 8601 format. This will be None if the date is not
-  available.
-
-* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that
-  this is only accurate if run in a VCS checkout, otherwise it is likely to
-  be False or None
-
-* `['error']`: if the version string could not be computed, this will be set
-  to a string describing the problem, otherwise it will be None. It may be
-  useful to throw an exception in setup.py if this is set, to avoid e.g.
-  creating tarballs with a version string of "unknown".
-
-Some variants are more useful than others. Including `full-revisionid` in a
-bug report should allow developers to reconstruct the exact code being tested
-(or indicate the presence of local changes that should be shared with the
-developers). `version` is suitable for display in an "about" box or a CLI
-`--version` output: it can be easily compared against release notes and lists
-of bugs fixed in various releases.
-
-The installer adds the following text to your `__init__.py` to place a basic
-version in `YOURPROJECT.__version__`:
-
-    from ._version import get_versions
-    __version__ = get_versions()['version']
-    del get_versions
-
-## Styles
-
-The setup.cfg `style=` configuration controls how the VCS information is
-rendered into a version string.
-
-The default style, "pep440", produces a PEP440-compliant string, equal to the
-un-prefixed tag name for actual releases, and containing an additional "local
-version" section with more detail for in-between builds. For Git, this is
-TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags
---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the
-tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and
-that this commit is two revisions ("+2") beyond the "0.11" tag. For released
-software (exactly equal to a known tag), the identifier will only contain the
-stripped tag, e.g., "0.11".
-
-Other styles are available. See [details.md](details.md) in the Versioneer
-source tree for descriptions.
-
-## Debugging
-
-Versioneer tries to avoid fatal errors: if something goes wrong, it will tend
-to return a version of "0+unknown". To investigate the problem, run `setup.py
-version`, which will run the version-lookup code in a verbose mode, and will
-display the full contents of `get_versions()` (including the `error` string,
-which may help identify what went wrong).
-
-## Known Limitations
-
-Some situations are known to cause problems for Versioneer. This details the
-most significant ones. More can be found on Github
-[issues page](https://github.com/warner/python-versioneer/issues).
-
-### Subprojects
-
-Versioneer has limited support for source trees in which `setup.py` is not in
-the root directory (e.g., `setup.py` and `.git/` are *not* siblings). The are
-two common reasons why `setup.py` might not be in the root:
-
-* Source trees which contain multiple subprojects, such as
-  [Buildbot](https://github.com/buildbot/buildbot), which contains both
-  "master" and "slave" subprojects, each with their own `setup.py`,
-  `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI
-  distributions (and upload multiple independently-installable tarballs).
-* Source trees whose main purpose is to contain a C library, but which also
-  provide bindings to Python (and perhaps other langauges) in subdirectories.
-
-Versioneer will look for `.git` in parent directories, and most operations
-should get the right version string. However `pip` and `setuptools` have bugs
-and implementation details which frequently cause `pip install .` from a
-subproject directory to fail to find a correct version string (so it usually
-defaults to `0+unknown`).
-
-`pip install --editable .` should work correctly. `setup.py install` might
-work too.
-
-Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in
-some later version.
-
-[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking
-this issue. The discussion in
-[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the
-issue from the Versioneer side in more detail.
-[pip PR#3176](https://github.com/pypa/pip/pull/3176) and
-[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve
-pip to let Versioneer work correctly.
-
-Versioneer-0.16 and earlier only looked for a `.git` directory next to the
-`setup.cfg`, so subprojects were completely unsupported with those releases.
-
-### Editable installs with setuptools <= 18.5
-
-`setup.py develop` and `pip install --editable .` allow you to install a
-project into a virtualenv once, then continue editing the source code (and
-test) without re-installing after every change.
-
-"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a
-convenient way to specify executable scripts that should be installed along
-with the python package.
-
-These both work as expected when using modern setuptools. When using
-setuptools-18.5 or earlier, however, certain operations will cause
-`pkg_resources.DistributionNotFound` errors when running the entrypoint
-script, which must be resolved by re-installing the package. This happens
-when the install happens with one version, then the egg_info data is
-regenerated while a different version is checked out. Many setup.py commands
-cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into
-a different virtualenv), so this can be surprising.
-
-[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes
-this one, but upgrading to a newer version of setuptools should probably
-resolve it.
-
-### Unicode version strings
-
-While Versioneer works (and is continually tested) with both Python 2 and
-Python 3, it is not entirely consistent with bytes-vs-unicode distinctions.
-Newer releases probably generate unicode version strings on py2. It's not
-clear that this is wrong, but it may be surprising for applications when then
-write these strings to a network connection or include them in bytes-oriented
-APIs like cryptographic checksums.
-
-[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates
-this question.
-
-
-## Updating Versioneer
-
-To upgrade your project to a new release of Versioneer, do the following:
-
-* install the new Versioneer (`pip install -U versioneer` or equivalent)
-* edit `setup.cfg`, if necessary, to include any new configuration settings
-  indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details.
-* re-run `versioneer install` in your source tree, to replace
-  `SRC/_version.py`
-* commit any changed files
-
-## Future Directions
-
-This tool is designed to make it easily extended to other version-control
-systems: all VCS-specific components are in separate directories like
-src/git/ . The top-level `versioneer.py` script is assembled from these
-components by running make-versioneer.py . In the future, make-versioneer.py
-will take a VCS name as an argument, and will construct a version of
-`versioneer.py` that is specific to the given VCS. It might also take the
-configuration arguments that are currently provided manually during
-installation by editing setup.py . Alternatively, it might go the other
-direction and include code from all supported VCS systems, reducing the
-number of intermediate scripts.
-
-
-## License
-
-To make Versioneer easier to embed, all its code is dedicated to the public
-domain. The `_version.py` that it creates is also in the public domain.
-Specifically, both are released under the Creative Commons "Public Domain
-Dedication" license (CC0-1.0), as described in
-https://creativecommons.org/publicdomain/zero/1.0/ .
-
-"""
-try:
-    import configparser
-except ImportError:
-    import ConfigParser as configparser
-import errno
-import json
-import os
-import re
-import subprocess
-import sys
-from pathlib import Path
-
-
-class VersioneerConfig:
-    """Container for Versioneer configuration parameters."""
-
-
-def get_root():
-    """Get the project root directory.
-
-    We require that all commands are run from the project root, i.e., the
-    directory that contains setup.py, setup.cfg, and versioneer.py .
-    """
-    root = os.path.realpath(os.path.abspath(os.getcwd()))
-    setup_py = os.path.join(root, "setup.py")
-    versioneer_py = os.path.join(root, "versioneer.py")
-    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
-        # allow 'python path/to/setup.py COMMAND'
-        root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0])))
-        setup_py = os.path.join(root, "setup.py")
-        versioneer_py = os.path.join(root, "versioneer.py")
-    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
-        err = ("Versioneer was unable to run the project root directory. "
-               "Versioneer requires setup.py to be executed from "
-               "its immediate directory (like 'python setup.py COMMAND'), "
-               "or in a way that lets it use sys.argv[0] to find the root "
-               "(like 'python path/to/setup.py COMMAND').")
-        raise VersioneerBadRootError(err)
-    try:
-        # Certain runtime workflows (setup.py install/develop in a setuptools
-        # tree) execute all dependencies in a single python process, so
-        # "versioneer" may be imported multiple times, and python's shared
-        # module-import table will cache the first one. So we can't use
-        # os.path.dirname(__file__), as that will find whichever
-        # versioneer.py was first imported, even in later projects.
-        me = os.path.realpath(os.path.abspath(__file__))
-        me_dir = os.path.normcase(os.path.splitext(me)[0])
-        vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
-        if me_dir != vsr_dir:
-            print("Warning: build in %s is using versioneer.py from %s"
-                  % (os.path.dirname(me), versioneer_py))
-    except NameError:
-        pass
-    return root
-
-
-def get_config_from_root(root):
-    """Read the project setup.cfg file to determine Versioneer config."""
-    # This might raise EnvironmentError (if setup.cfg is missing), or
-    # configparser.NoSectionError (if it lacks a [versioneer] section), or
-    # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
-    # the top of versioneer.py for instructions on writing your setup.cfg .
-    setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
-    with open(setup_cfg, "r") as f:
-        parser.readfp(f)
-    VCS = parser.get("versioneer", "VCS")  # mandatory
-
-    def get(parser, name):
-        if parser.has_option("versioneer", name):
-            return parser.get("versioneer", name)
-        return None
-    cfg = VersioneerConfig()
-    cfg.VCS = VCS
-    cfg.style = get(parser, "style") or ""
-    cfg.versionfile_source = get(parser, "versionfile_source")
-    cfg.versionfile_build = get(parser, "versionfile_build")
-    cfg.tag_prefix = get(parser, "tag_prefix")
-    if cfg.tag_prefix in ("''", '""'):
-        cfg.tag_prefix = ""
-    cfg.parentdir_prefix = get(parser, "parentdir_prefix")
-    cfg.verbose = get(parser, "verbose")
-    return cfg
-
-
-class NotThisMethod(Exception):
-    """Exception raised if a method is not valid for the current scenario."""
-
-
-# these dictionaries contain VCS-specific tools
-LONG_VERSION_PY = {}
-HANDLERS = {}
-
-
-def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
-    def decorate(f):
-        """Store f in HANDLERS[vcs][method]."""
-        if vcs not in HANDLERS:
-            HANDLERS[vcs] = {}
-        HANDLERS[vcs][method] = f
-        return f
-    return decorate
-
-
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
-    """Call the given command(s)."""
-    assert isinstance(commands, list)
-    p = None
-    for c in commands:
-        try:
-            dispcmd = str([c] + args)
-            # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
-            break
-        except EnvironmentError:
-            e = sys.exc_info()[1]
-            if e.errno == errno.ENOENT:
-                continue
-            if verbose:
-                print("unable to run %s" % dispcmd)
-                print(e)
-            return None, None
-    else:
-        if verbose:
-            print("unable to find command, tried %s" % (commands,))
-        return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
-        if verbose:
-            print("unable to run %s (error)" % dispcmd)
-            print("stdout was %s" % stdout)
-        return None, p.returncode
-    return stdout, p.returncode
-
-
-LONG_VERSION_PY['git'] = '''
-# This file helps to compute a version number in source trees obtained from
-# git-archive tarball (such as those provided by githubs download-from-tag
-# feature). Distribution tarballs (built by setup.py sdist) and build
-# directories (produced by setup.py build) will contain a much shorter file
-# that just contains the computed version number.
-
-# This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
-
-"""Git implementation of _version.py."""
-
-import errno
-import os
-import re
-import subprocess
-import sys
-
-
-def get_keywords():
-    """Get the keywords needed to look up the version information."""
-    # these strings will be replaced by git during git-archive.
-    # setup.py/versioneer.py will grep for the variable names, so they must
-    # each be defined on a line of their own. _version.py will just call
-    # get_keywords().
-    git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s"
-    git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s"
-    git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s"
-    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
-    return keywords
-
-
-class VersioneerConfig:
-    """Container for Versioneer configuration parameters."""
-
-
-def get_config():
-    """Create, populate and return the VersioneerConfig() object."""
-    # these strings are filled in when 'setup.py versioneer' creates
-    # _version.py
-    cfg = VersioneerConfig()
-    cfg.VCS = "git"
-    cfg.style = "%(STYLE)s"
-    cfg.tag_prefix = "%(TAG_PREFIX)s"
-    cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s"
-    cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s"
-    cfg.verbose = False
-    return cfg
-
-
-class NotThisMethod(Exception):
-    """Exception raised if a method is not valid for the current scenario."""
-
-
-LONG_VERSION_PY = {}
-HANDLERS = {}
-
-
-def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
-    def decorate(f):
-        """Store f in HANDLERS[vcs][method]."""
-        if vcs not in HANDLERS:
-            HANDLERS[vcs] = {}
-        HANDLERS[vcs][method] = f
-        return f
-    return decorate
-
-
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
-    """Call the given command(s)."""
-    assert isinstance(commands, list)
-    p = None
-    for c in commands:
-        try:
-            dispcmd = str([c] + args)
-            # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
-            break
-        except EnvironmentError:
-            e = sys.exc_info()[1]
-            if e.errno == errno.ENOENT:
-                continue
-            if verbose:
-                print("unable to run %%s" %% dispcmd)
-                print(e)
-            return None, None
-    else:
-        if verbose:
-            print("unable to find command, tried %%s" %% (commands,))
-        return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
-        if verbose:
-            print("unable to run %%s (error)" %% dispcmd)
-            print("stdout was %%s" %% stdout)
-        return None, p.returncode
-    return stdout, p.returncode
-
-
-def versions_from_parentdir(parentdir_prefix, root, verbose):
-    """Try to determine the version from the parent directory name.
-
-    Source tarballs conventionally unpack into a directory that includes both
-    the project name and a version string. We will also support searching up
-    two directory levels for an appropriately named parent directory
-    """
-    rootdirs = []
-
-    for i in range(3):
-        dirname = os.path.basename(root)
-        if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
-
-    if verbose:
-        print("Tried directories %%s but none started with prefix %%s" %%
-              (str(rootdirs), parentdir_prefix))
-    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-
-
-@register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
-    """Extract version information from the given file."""
-    # the code embedded in _version.py can just fetch the value of these
-    # keywords. When used from setup.py, we don't want to import _version.py,
-    # so we do it with a regexp instead. This function is not used from
-    # _version.py.
-    keywords = {}
-    try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
-        pass
-    return keywords
-
-
-@register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
-    """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
-    date = keywords.get("date")
-    if date is not None:
-        # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant
-        # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601
-        # -like" string, which we must then edit to make compliant), because
-        # it's been around since git-1.5.3, and it's too difficult to
-        # discover which version we're using, or to work around using an
-        # older one.
-        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-    refnames = keywords["refnames"].strip()
-    if refnames.startswith("$Format"):
-        if verbose:
-            print("keywords are unexpanded, not using")
-        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
-    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
-    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
-    TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
-    if not tags:
-        # Either we're using git < 1.8.3, or there really are no tags. We use
-        # a heuristic: assume all version tags have a digit. The old git %%d
-        # expansion behaves like git log --decorate=short and strips out the
-        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
-        # between branches and tags. By ignoring refnames without digits, we
-        # filter out many common branch names like "release" and
-        # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
-        if verbose:
-            print("discarding '%%s', no digits" %% ",".join(refs - tags))
-    if verbose:
-        print("likely tags: %%s" %% ",".join(sorted(tags)))
-    for ref in sorted(tags):
-        # sorting will prefer e.g., "2.0" over "2.0rc1"
-        if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
-            if verbose:
-                print("picking %%s" %% r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
-    # no suitable tags, so version is "0+unknown", but full hex is still there
-    if verbose:
-        print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
-
-
-@register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
-    """Get version from 'git describe' in the root of the source tree.
-
-    This only gets called if the git-archive 'subst' keywords were *not*
-    expanded, and _version.py hasn't already been rewritten with a short
-    version string, meaning we're inside a checked out source tree.
-    """
-    GITS = ["git"]
-    if sys.platform == "win32":
-        GITS = ["git.cmd", "git.exe"]
-
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
-    if rc != 0:
-        if verbose:
-            print("Directory %%s not under git control" %% root)
-        raise NotThisMethod("'git rev-parse --git-dir' returned error")
-
-    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
-    # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", "%%s*" %% tag_prefix],
-                                   cwd=root)
-    # --long was added in git-1.5.5
-    if describe_out is None:
-        raise NotThisMethod("'git describe' failed")
-    describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
-    if full_out is None:
-        raise NotThisMethod("'git rev-parse' failed")
-    full_out = full_out.strip()
-
-    pieces = {}
-    pieces["long"] = full_out
-    pieces["short"] = full_out[:7]  # maybe improved later
-    pieces["error"] = None
-
-    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
-    # TAG might have hyphens.
-    git_describe = describe_out
-
-    # look for -dirty suffix
-    dirty = git_describe.endswith("-dirty")
-    pieces["dirty"] = dirty
-    if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
-
-    # now we have TAG-NUM-gHEX or HEX
-
-    if "-" in git_describe:
-        # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
-        if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%%s'"
-                               %% describe_out)
-            return pieces
-
-        # tag
-        full_tag = mo.group(1)
-        if not full_tag.startswith(tag_prefix):
-            if verbose:
-                fmt = "tag '%%s' doesn't start with prefix '%%s'"
-                print(fmt %% (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'"
-                               %% (full_tag, tag_prefix))
-            return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
-
-        # distance: number of commits since tag
-        pieces["distance"] = int(mo.group(2))
-
-        # commit: short hex revision ID
-        pieces["short"] = mo.group(3)
-
-    else:
-        # HEX: no tags
-        pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
-        pieces["distance"] = int(count_out)  # total number of commits
-
-    # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"],
-                       cwd=root)[0].strip()
-    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-
-    return pieces
-
-
-def plus_or_dot(pieces):
-    """Return a + if we don't already have one, else return a ."""
-    if "+" in pieces.get("closest-tag", ""):
-        return "."
-    return "+"
-
-
-def render_pep440(pieces):
-    """Build up version string, with post-release "local version identifier".
-
-    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
-    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
-
-    Exceptions:
-    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += plus_or_dot(pieces)
-            rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"])
-            if pieces["dirty"]:
-                rendered += ".dirty"
-    else:
-        # exception #1
-        rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"],
-                                          pieces["short"])
-        if pieces["dirty"]:
-            rendered += ".dirty"
-    return rendered
-
-
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
-
-    Exceptions:
-    1: no tags. 0.post.devDISTANCE
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += ".post.dev%%d" %% pieces["distance"]
-    else:
-        # exception #1
-        rendered = "0.post.dev%%d" %% pieces["distance"]
-    return rendered
-
-
-def render_pep440_post(pieces):
-    """TAG[.postDISTANCE[.dev0]+gHEX] .
-
-    The ".dev0" means dirty. Note that .dev0 sorts backwards
-    (a dirty tree will appear "older" than the corresponding clean one),
-    but you shouldn't be releasing software with -dirty anyways.
-
-    Exceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%%d" %% pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-            rendered += plus_or_dot(pieces)
-            rendered += "g%%s" %% pieces["short"]
-    else:
-        # exception #1
-        rendered = "0.post%%d" %% pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-        rendered += "+g%%s" %% pieces["short"]
-    return rendered
-
-
-def render_pep440_old(pieces):
-    """TAG[.postDISTANCE[.dev0]] .
-
-    The ".dev0" means dirty.
-
-    Eexceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%%d" %% pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-    else:
-        # exception #1
-        rendered = "0.post%%d" %% pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-    return rendered
-
-
-def render_git_describe(pieces):
-    """TAG[-DISTANCE-gHEX][-dirty].
-
-    Like 'git describe --tags --dirty --always'.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-def render_git_describe_long(pieces):
-    """TAG-DISTANCE-gHEX[-dirty].
-
-    Like 'git describe --tags --dirty --always -long'.
-    The distance/hash is unconditional.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-def render(pieces, style):
-    """Render the given version pieces into the requested style."""
-    if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
-
-    if not style or style == "default":
-        style = "pep440"  # the default
-
-    if style == "pep440":
-        rendered = render_pep440(pieces)
-    elif style == "pep440-pre":
-        rendered = render_pep440_pre(pieces)
-    elif style == "pep440-post":
-        rendered = render_pep440_post(pieces)
-    elif style == "pep440-old":
-        rendered = render_pep440_old(pieces)
-    elif style == "git-describe":
-        rendered = render_git_describe(pieces)
-    elif style == "git-describe-long":
-        rendered = render_git_describe_long(pieces)
-    else:
-        raise ValueError("unknown style '%%s'" %% style)
-
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
-
-
-def get_versions():
-    """Get version information or return default if unable to do so."""
-    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
-    # __file__, we can work backwards from there to the root. Some
-    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
-    # case we can only use expanded keywords.
-
-    cfg = get_config()
-    verbose = cfg.verbose
-
-    try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
-                                          verbose)
-    except NotThisMethod:
-        pass
-
-    try:
-        root = os.path.realpath(__file__)
-        # versionfile_source is the relative path from the top of the source
-        # tree (where the .git directory might live) to this file. Invert
-        # this to find the root from __file__.
-        for i in cfg.versionfile_source.split('/'):
-            root = os.path.dirname(root)
-    except NameError:
-        return {"version": "0+unknown", "full-revisionid": None,
-                "dirty": None,
-                "error": "unable to find root of source tree",
-                "date": None}
-
-    try:
-        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
-        return render(pieces, cfg.style)
-    except NotThisMethod:
-        pass
-
-    try:
-        if cfg.parentdir_prefix:
-            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
-    except NotThisMethod:
-        pass
-
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to compute version", "date": None}
-'''
-
-
-@register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
-    """Extract version information from the given file."""
-    # the code embedded in _version.py can just fetch the value of these
-    # keywords. When used from setup.py, we don't want to import _version.py,
-    # so we do it with a regexp instead. This function is not used from
-    # _version.py.
-    keywords = {}
-    try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
-        pass
-    return keywords
-
-
-@register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
-    """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
-    date = keywords.get("date")
-    if date is not None:
-        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
-        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
-        # -like" string, which we must then edit to make compliant), because
-        # it's been around since git-1.5.3, and it's too difficult to
-        # discover which version we're using, or to work around using an
-        # older one.
-        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-    refnames = keywords["refnames"].strip()
-    if refnames.startswith("$Format"):
-        if verbose:
-            print("keywords are unexpanded, not using")
-        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
-    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
-    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
-    TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
-    if not tags:
-        # Either we're using git < 1.8.3, or there really are no tags. We use
-        # a heuristic: assume all version tags have a digit. The old git %d
-        # expansion behaves like git log --decorate=short and strips out the
-        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
-        # between branches and tags. By ignoring refnames without digits, we
-        # filter out many common branch names like "release" and
-        # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
-        if verbose:
-            print("discarding '%s', no digits" % ",".join(refs - tags))
-    if verbose:
-        print("likely tags: %s" % ",".join(sorted(tags)))
-    for ref in sorted(tags):
-        # sorting will prefer e.g., "2.0" over "2.0rc1"
-        if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
-            if verbose:
-                print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
-    # no suitable tags, so version is "0+unknown", but full hex is still there
-    if verbose:
-        print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
-
-
-@register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
-    """Get version from 'git describe' in the root of the source tree.
-
-    This only gets called if the git-archive 'subst' keywords were *not*
-    expanded, and _version.py hasn't already been rewritten with a short
-    version string, meaning we're inside a checked out source tree.
-    """
-    GITS = ["git"]
-    if sys.platform == "win32":
-        GITS = ["git.cmd", "git.exe"]
-
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
-    if rc != 0:
-        if verbose:
-            print("Directory %s not under git control" % root)
-        raise NotThisMethod("'git rev-parse --git-dir' returned error")
-
-    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
-    # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", "%s*" % tag_prefix],
-                                   cwd=root)
-    # --long was added in git-1.5.5
-    if describe_out is None:
-        raise NotThisMethod("'git describe' failed")
-    describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
-    if full_out is None:
-        raise NotThisMethod("'git rev-parse' failed")
-    full_out = full_out.strip()
-
-    pieces = {}
-    pieces["long"] = full_out
-    pieces["short"] = full_out[:7]  # maybe improved later
-    pieces["error"] = None
-
-    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
-    # TAG might have hyphens.
-    git_describe = describe_out
-
-    # look for -dirty suffix
-    dirty = git_describe.endswith("-dirty")
-    pieces["dirty"] = dirty
-    if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
-
-    # now we have TAG-NUM-gHEX or HEX
-
-    if "-" in git_describe:
-        # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
-        if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
-            return pieces
-
-        # tag
-        full_tag = mo.group(1)
-        if not full_tag.startswith(tag_prefix):
-            if verbose:
-                fmt = "tag '%s' doesn't start with prefix '%s'"
-                print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
-            return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
-
-        # distance: number of commits since tag
-        pieces["distance"] = int(mo.group(2))
-
-        # commit: short hex revision ID
-        pieces["short"] = mo.group(3)
-
-    else:
-        # HEX: no tags
-        pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
-        pieces["distance"] = int(count_out)  # total number of commits
-
-    # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
-                       cwd=root)[0].strip()
-    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-
-    return pieces
-
-
-def do_vcs_install(manifest_in, versionfile_source, ipy):
-    """Git-specific installation logic for Versioneer.
-
-    For Git, this means creating/changing .gitattributes to mark _version.py
-    for export-subst keyword substitution.
-    """
-    GITS = ["git"]
-    if sys.platform == "win32":
-        GITS = ["git.cmd", "git.exe"]
-    files = [manifest_in, versionfile_source]
-    if ipy:
-        files.append(ipy)
-    try:
-        me = __file__
-        if me.endswith(".pyc") or me.endswith(".pyo"):
-            me = os.path.splitext(me)[0] + ".py"
-        versioneer_file = os.path.relpath(me)
-    except NameError:
-        versioneer_file = "versioneer.py"
-    files.append(versioneer_file)
-    present = False
-    try:
-        f = open(".gitattributes", "r")
-        for line in f.readlines():
-            if line.strip().startswith(versionfile_source):
-                if "export-subst" in line.strip().split()[1:]:
-                    present = True
-        f.close()
-    except EnvironmentError:
-        pass
-    if not present:
-        f = open(".gitattributes", "a+")
-        f.write("%s export-subst\n" % versionfile_source)
-        f.close()
-        files.append(".gitattributes")
-    run_command(GITS, ["add", "--"] + files)
-
-
-def versions_from_parentdir(parentdir_prefix, root, verbose):
-    """Try to determine the version from the parent directory name.
-
-    Source tarballs conventionally unpack into a directory that includes both
-    the project name and a version string. We will also support searching up
-    two directory levels for an appropriately named parent directory
-    """
-    rootdirs = []
-
-    for i in range(3):
-        dirname = os.path.basename(root)
-        if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
-
-    if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
-    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-
-
-SHORT_VERSION_PY = """
-# This file was generated by 'versioneer.py' (0.18) from
-# revision-control system data, or from the parent directory name of an
-# unpacked source archive. Distribution tarballs contain a pre-generated copy
-# of this file.
-
-import json
-
-version_json = '''
-%s
-'''  # END VERSION_JSON
-
-
-def get_versions():
-    return json.loads(version_json)
-"""
-
-
-def versions_from_file(filename):
-    """Try to determine the version from _version.py if present."""
-    try:
-        with open(filename) as f:
-            contents = f.read()
-    except EnvironmentError:
-        raise NotThisMethod("unable to read _version.py")
-    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON",
-                   contents, re.M | re.S)
-    if not mo:
-        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
-                       contents, re.M | re.S)
-    if not mo:
-        raise NotThisMethod("no version_json in _version.py")
-    return json.loads(mo.group(1))
-
-
-def write_to_version_file(filename, versions):
-    """Write the given version number to the given _version.py file."""
-    os.unlink(filename)
-    contents = json.dumps(versions, sort_keys=True,
-                          indent=1, separators=(",", ": "))
-    with open(filename, "w") as f:
-        f.write(SHORT_VERSION_PY % contents)
-
-    print("set %s to '%s'" % (filename, versions["version"]))
-
-
-def plus_or_dot(pieces):
-    """Return a + if we don't already have one, else return a ."""
-    if "+" in pieces.get("closest-tag", ""):
-        return "."
-    return "+"
-
-
-def render_pep440(pieces):
-    """Build up version string, with post-release "local version identifier".
-
-    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
-    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
-
-    Exceptions:
-    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += plus_or_dot(pieces)
-            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
-            if pieces["dirty"]:
-                rendered += ".dirty"
-    else:
-        # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
-        if pieces["dirty"]:
-            rendered += ".dirty"
-    return rendered
-
-
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
-
-    Exceptions:
-    1: no tags. 0.post.devDISTANCE
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
-    else:
-        # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
-    return rendered
-
-
-def render_pep440_post(pieces):
-    """TAG[.postDISTANCE[.dev0]+gHEX] .
-
-    The ".dev0" means dirty. Note that .dev0 sorts backwards
-    (a dirty tree will appear "older" than the corresponding clean one),
-    but you shouldn't be releasing software with -dirty anyways.
-
-    Exceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%d" % pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-            rendered += plus_or_dot(pieces)
-            rendered += "g%s" % pieces["short"]
-    else:
-        # exception #1
-        rendered = "0.post%d" % pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-        rendered += "+g%s" % pieces["short"]
-    return rendered
-
-
-def render_pep440_old(pieces):
-    """TAG[.postDISTANCE[.dev0]] .
-
-    The ".dev0" means dirty.
-
-    Eexceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%d" % pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-    else:
-        # exception #1
-        rendered = "0.post%d" % pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-    return rendered
-
-
-def render_git_describe(pieces):
-    """TAG[-DISTANCE-gHEX][-dirty].
-
-    Like 'git describe --tags --dirty --always'.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-def render_git_describe_long(pieces):
-    """TAG-DISTANCE-gHEX[-dirty].
-
-    Like 'git describe --tags --dirty --always -long'.
-    The distance/hash is unconditional.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-def render(pieces, style):
-    """Render the given version pieces into the requested style."""
-    if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
-
-    if not style or style == "default":
-        style = "pep440"  # the default
-
-    if style == "pep440":
-        rendered = render_pep440(pieces)
-    elif style == "pep440-pre":
-        rendered = render_pep440_pre(pieces)
-    elif style == "pep440-post":
-        rendered = render_pep440_post(pieces)
-    elif style == "pep440-old":
-        rendered = render_pep440_old(pieces)
-    elif style == "git-describe":
-        rendered = render_git_describe(pieces)
-    elif style == "git-describe-long":
-        rendered = render_git_describe_long(pieces)
-    else:
-        raise ValueError("unknown style '%s'" % style)
-
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
-
-
-class VersioneerBadRootError(Exception):
-    """The project root directory is unknown or missing key files."""
-
-
-def get_versions(verbose=False):
-    """Get the project version from whatever source is available.
-
-    Returns dict with two keys: 'version' and 'full'.
-    """
-    ver_file = Path(__file__).parent / 'dmriprep' / 'VERSION'
-
-    if ver_file.is_file():
-        ver = ver_file.read_text().splitlines()[0].strip()
-        return {"version": ver, 'full': ver}
-
-    if "versioneer" in sys.modules:
-        # see the discussion in cmdclass.py:get_cmdclass()
-        del sys.modules["versioneer"]
-
-    root = get_root()
-    cfg = get_config_from_root(root)
-
-    assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg"
-    handlers = HANDLERS.get(cfg.VCS)
-    assert handlers, "unrecognized VCS '%s'" % cfg.VCS
-    verbose = verbose or cfg.verbose
-    assert cfg.versionfile_source is not None, \
-        "please set versioneer.versionfile_source"
-    assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
-
-    versionfile_abs = os.path.join(root, cfg.versionfile_source)
-
-    # extract version from first of: _version.py, VCS command (e.g., 'git
-    # describe'), parentdir. This is meant to work for developers using a
-    # source checkout, for users of a tarball created by 'setup.py sdist',
-    # and for users of a tarball/zipball created by 'git archive' or github's
-    # download-from-tag feature or the equivalent in other VCSes.
-
-    get_keywords_f = handlers.get("get_keywords")
-    from_keywords_f = handlers.get("keywords")
-    if get_keywords_f and from_keywords_f:
-        try:
-            keywords = get_keywords_f(versionfile_abs)
-            ver = from_keywords_f(keywords, cfg.tag_prefix, verbose)
-            if verbose:
-                print("got version from expanded keyword %s" % ver)
-            return ver
-        except NotThisMethod:
-            pass
-
-    try:
-        ver = versions_from_file(versionfile_abs)
-        if verbose:
-            print("got version from file %s %s" % (versionfile_abs, ver))
-        return ver
-    except NotThisMethod:
-        pass
-
-    from_vcs_f = handlers.get("pieces_from_vcs")
-    if from_vcs_f:
-        try:
-            pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
-            ver = render(pieces, cfg.style)
-            if verbose:
-                print("got version from VCS %s" % ver)
-            return ver
-        except NotThisMethod:
-            pass
-
-    try:
-        if cfg.parentdir_prefix:
-            ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
-            if verbose:
-                print("got version from parentdir %s" % ver)
-            return ver
-    except NotThisMethod:
-        pass
-
-    if verbose:
-        print("unable to compute version")
-
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None, "error": "unable to compute version",
-            "date": None}
-
-
-def get_version():
-    """Get the short version string for this project."""
-    return get_versions()["version"]
-
-
-def get_cmdclass():
-    """Get the custom setuptools/distutils subclasses used by Versioneer."""
-    if "versioneer" in sys.modules:
-        del sys.modules["versioneer"]
-        # this fixes the "python setup.py develop" case (also 'install' and
-        # 'easy_install .'), in which subdependencies of the main project are
-        # built (using setup.py bdist_egg) in the same python process. Assume
-        # a main project A and a dependency B, which use different versions
-        # of Versioneer. A's setup.py imports A's Versioneer, leaving it in
-        # sys.modules by the time B's setup.py is executed, causing B to run
-        # with the wrong versioneer. Setuptools wraps the sub-dep builds in a
-        # sandbox that restores sys.modules to it's pre-build state, so the
-        # parent is protected against the child's "import versioneer". By
-        # removing ourselves from sys.modules here, before the child build
-        # happens, we protect the child from the parent's versioneer too.
-        # Also see https://github.com/warner/python-versioneer/issues/52
-
-    cmds = {}
-
-    # we add "version" to both distutils and setuptools
-    from distutils.core import Command
-
-    class cmd_version(Command):
-        description = "report generated version string"
-        user_options = []
-        boolean_options = []
-
-        def initialize_options(self):
-            pass
-
-        def finalize_options(self):
-            pass
-
-        def run(self):
-            vers = get_versions(verbose=True)
-            print("Version: %s" % vers["version"])
-            print(" full-revisionid: %s" % vers.get("full-revisionid"))
-            print(" dirty: %s" % vers.get("dirty"))
-            print(" date: %s" % vers.get("date"))
-            if vers["error"]:
-                print(" error: %s" % vers["error"])
-    cmds["version"] = cmd_version
-
-    # we override "build_py" in both distutils and setuptools
-    #
-    # most invocation pathways end up running build_py:
-    #  distutils/build -> build_py
-    #  distutils/install -> distutils/build ->..
-    #  setuptools/bdist_wheel -> distutils/install ->..
-    #  setuptools/bdist_egg -> distutils/install_lib -> build_py
-    #  setuptools/install -> bdist_egg ->..
-    #  setuptools/develop -> ?
-    #  pip install:
-    #   copies source tree to a tempdir before running egg_info/etc
-    #   if .git isn't copied too, 'git describe' will fail
-    #   then does setup.py bdist_wheel, or sometimes setup.py install
-    #  setup.py egg_info -> ?
-
-    # we override different "build_py" commands for both environments
-    if "setuptools" in sys.modules:
-        from setuptools.command.build_py import build_py as _build_py
-    else:
-        from distutils.command.build_py import build_py as _build_py
-
-    class cmd_build_py(_build_py):
-        def run(self):
-            root = get_root()
-            cfg = get_config_from_root(root)
-            versions = get_versions()
-            _build_py.run(self)
-            # now locate _version.py in the new build/ directory and replace
-            # it with an updated value
-            if cfg.versionfile_build:
-                target_versionfile = os.path.join(self.build_lib,
-                                                  cfg.versionfile_build)
-                print("UPDATING %s" % target_versionfile)
-                write_to_version_file(target_versionfile, versions)
-    cmds["build_py"] = cmd_build_py
-
-    if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
-        from cx_Freeze.dist import build_exe as _build_exe
-        # nczeczulin reports that py2exe won't like the pep440-style string
-        # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
-        # setup(console=[{
-        #   "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION
-        #   "product_version": versioneer.get_version(),
-        #   ...
-
-        class cmd_build_exe(_build_exe):
-            def run(self):
-                root = get_root()
-                cfg = get_config_from_root(root)
-                versions = get_versions()
-                target_versionfile = cfg.versionfile_source
-                print("UPDATING %s" % target_versionfile)
-                write_to_version_file(target_versionfile, versions)
-
-                _build_exe.run(self)
-                os.unlink(target_versionfile)
-                with open(cfg.versionfile_source, "w") as f:
-                    LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
-        cmds["build_exe"] = cmd_build_exe
-        del cmds["build_py"]
-
-    if 'py2exe' in sys.modules:  # py2exe enabled?
-        try:
-            from py2exe.distutils_buildexe import py2exe as _py2exe  # py3
-        except ImportError:
-            from py2exe.build_exe import py2exe as _py2exe  # py2
-
-        class cmd_py2exe(_py2exe):
-            def run(self):
-                root = get_root()
-                cfg = get_config_from_root(root)
-                versions = get_versions()
-                target_versionfile = cfg.versionfile_source
-                print("UPDATING %s" % target_versionfile)
-                write_to_version_file(target_versionfile, versions)
-
-                _py2exe.run(self)
-                os.unlink(target_versionfile)
-                with open(cfg.versionfile_source, "w") as f:
-                    LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
-        cmds["py2exe"] = cmd_py2exe
-
-    # we override different "sdist" commands for both environments
-    if "setuptools" in sys.modules:
-        from setuptools.command.sdist import sdist as _sdist
-    else:
-        from distutils.command.sdist import sdist as _sdist
-
-    class cmd_sdist(_sdist):
-        def run(self):
-            versions = get_versions()
-            self._versioneer_generated_versions = versions
-            # unless we update this, the command will keep using the old
-            # version
-            self.distribution.metadata.version = versions["version"]
-            return _sdist.run(self)
-
-        def make_release_tree(self, base_dir, files):
-            root = get_root()
-            cfg = get_config_from_root(root)
-            _sdist.make_release_tree(self, base_dir, files)
-            # now locate _version.py in the new base_dir directory
-            # (remembering that it may be a hardlink) and replace it with an
-            # updated value
-            target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
-            print("UPDATING %s" % target_versionfile)
-            write_to_version_file(target_versionfile,
-                                  self._versioneer_generated_versions)
-    cmds["sdist"] = cmd_sdist
-
-    return cmds
-
-
-CONFIG_ERROR = """
-setup.cfg is missing the necessary Versioneer configuration. You need
-a section like:
-
- [versioneer]
- VCS = git
- style = pep440
- versionfile_source = src/myproject/_version.py
- versionfile_build = myproject/_version.py
- tag_prefix =
- parentdir_prefix = myproject-
-
-You will also need to edit your setup.py to use the results:
-
- import versioneer
- setup(version=versioneer.get_version(),
-       cmdclass=versioneer.get_cmdclass(), ...)
-
-Please read the docstring in ./versioneer.py for configuration instructions,
-edit setup.cfg, and re-run the installer or 'python versioneer.py setup'.
-"""
-
-SAMPLE_CONFIG = """
-# See the docstring in versioneer.py for instructions. Note that you must
-# re-run 'versioneer.py setup' after changing this section, and commit the
-# resulting files.
-
-[versioneer]
-#VCS = git
-#style = pep440
-#versionfile_source =
-#versionfile_build =
-#tag_prefix =
-#parentdir_prefix =
-
-"""
-
-INIT_PY_SNIPPET = """
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
-"""
-
-
-def do_setup():
-    """Main VCS-independent setup function for installing Versioneer."""
-    root = get_root()
-    try:
-        cfg = get_config_from_root(root)
-    except (EnvironmentError, configparser.NoSectionError,
-            configparser.NoOptionError) as e:
-        if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
-            print("Adding sample versioneer config to setup.cfg",
-                  file=sys.stderr)
-            with open(os.path.join(root, "setup.cfg"), "a") as f:
-                f.write(SAMPLE_CONFIG)
-        print(CONFIG_ERROR, file=sys.stderr)
-        return 1
-
-    print(" creating %s" % cfg.versionfile_source)
-    with open(cfg.versionfile_source, "w") as f:
-        LONG = LONG_VERSION_PY[cfg.VCS]
-        f.write(LONG % {"DOLLAR": "$",
-                        "STYLE": cfg.style,
-                        "TAG_PREFIX": cfg.tag_prefix,
-                        "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                        "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        })
-
-    ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
-                       "__init__.py")
-    if os.path.exists(ipy):
-        try:
-            with open(ipy, "r") as f:
-                old = f.read()
-        except EnvironmentError:
-            old = ""
-        if INIT_PY_SNIPPET not in old:
-            print(" appending to %s" % ipy)
-            with open(ipy, "a") as f:
-                f.write(INIT_PY_SNIPPET)
-        else:
-            print(" %s unmodified" % ipy)
-    else:
-        print(" %s doesn't exist, ok" % ipy)
-        ipy = None
-
-    # Make sure both the top-level "versioneer.py" and versionfile_source
-    # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so
-    # they'll be copied into source distributions. Pip won't be able to
-    # install the package without this.
-    manifest_in = os.path.join(root, "MANIFEST.in")
-    simple_includes = set()
-    try:
-        with open(manifest_in, "r") as f:
-            for line in f:
-                if line.startswith("include "):
-                    for include in line.split()[1:]:
-                        simple_includes.add(include)
-    except EnvironmentError:
-        pass
-    # That doesn't cover everything MANIFEST.in can do
-    # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
-    # it might give some false negatives. Appending redundant 'include'
-    # lines is safe, though.
-    if "versioneer.py" not in simple_includes:
-        print(" appending 'versioneer.py' to MANIFEST.in")
-        with open(manifest_in, "a") as f:
-            f.write("include versioneer.py\n")
-    else:
-        print(" 'versioneer.py' already in MANIFEST.in")
-    if cfg.versionfile_source not in simple_includes:
-        print(" appending versionfile_source ('%s') to MANIFEST.in" %
-              cfg.versionfile_source)
-        with open(manifest_in, "a") as f:
-            f.write("include %s\n" % cfg.versionfile_source)
-    else:
-        print(" versionfile_source already in MANIFEST.in")
-
-    # Make VCS-specific changes. For git, this means creating/changing
-    # .gitattributes to mark _version.py for export-subst keyword
-    # substitution.
-    do_vcs_install(manifest_in, cfg.versionfile_source, ipy)
-    return 0
-
-
-def scan_setup_py():
-    """Validate the contents of setup.py against Versioneer's expectations."""
-    found = set()
-    setters = False
-    errors = 0
-    with open("setup.py", "r") as f:
-        for line in f.readlines():
-            if "import versioneer" in line:
-                found.add("import")
-            if "versioneer.get_cmdclass()" in line:
-                found.add("cmdclass")
-            if "versioneer.get_version()" in line:
-                found.add("get_version")
-            if "versioneer.VCS" in line:
-                setters = True
-            if "versioneer.versionfile_source" in line:
-                setters = True
-    if len(found) != 3:
-        print("")
-        print("Your setup.py appears to be missing some important items")
-        print("(but I might be wrong). Please make sure it has something")
-        print("roughly like the following:")
-        print("")
-        print(" import versioneer")
-        print(" setup( version=versioneer.get_version(),")
-        print("        cmdclass=versioneer.get_cmdclass(),  ...)")
-        print("")
-        errors += 1
-    if setters:
-        print("You should remove lines like 'versioneer.VCS = ' and")
-        print("'versioneer.versionfile_source = ' . This configuration")
-        print("now lives in setup.cfg, and should be removed from setup.py")
-        print("")
-        errors += 1
-    return errors
-
-
-if __name__ == "__main__":
-    cmd = sys.argv[1]
-    if cmd == "setup":
-        errors = do_setup()
-        errors += scan_setup_py()
-        if errors:
-            sys.exit(1)