From 817c438558caa70ff1c970764873d22a452cb09c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 15:14:28 -0400
Subject: [PATCH 01/18] CI: Disable CircleCI

---
 .circleci/config.yml | 520 +------------------------------------------
 1 file changed, 5 insertions(+), 515 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 6d842d2389..302a7d3112 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,524 +1,14 @@
-# reusable anchors
-_machine_defaults: &machine_defaults
-  environment:
-    TZ: "/usr/share/zoneinfo/America/Los_Angeles"
-    SCRATCH: "/scratch"
-  machine:
-    image: ubuntu-2204:current
-    docker_layer_caching: true
-  working_directory: /tmp/src/sdcflows
-  resource_class: large
-
-_python_defaults: &python_defaults
-  docker:
-    - image: cimg/python:3.10.9
-  working_directory: /tmp/src/sdcflows
-
-_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/sdcflows
-    docker tag localhost:5000/sdcflows nipreps/sdcflows:latest
-
 version: 2.1
-orbs:
-  docker: circleci/docker@2.2.0
-  codecov: codecov/codecov@3.2.4
 
 jobs:
-  cache_test_data:
-    docker: # executor type
-      - image: nipreps/miniconda:py39_2209.01
-        auth:
-          username: $DOCKER_USER
-          password: $DOCKER_PAT
-
-    working_directory: /tmp/data
-    environment:
-      - TEMPLATEFLOW_HOME: /tmp/templateflow
-    steps:
-      - checkout:
-          path: /tmp/src/sdcflows
-
-      - run:
-          name: Configure git (pacify datalad)
-          command: |
-            git config --global user.name "First Last"
-            git config --global user.email "email@domain.com"
-
-      - restore_cache:
-          keys:
-            - data-v6-{{ .Branch }}-{{ .Revision }}
-            - data-v6--{{ .Revision }}
-            - data-v6-{{ .Branch }}-
-            - data-v6-main-
-            - data-v6-
-
-      - run:
-          name: Ensure some templates are cached
-          command: |
-            python -c "from templateflow import api as tfapi; \
-                       tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='brain', suffix='mask'); \
-                       tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='fMRIPrep', suffix='boldref');"
-
-      - run:
-          name: Install ds001600
-          command: |
-            datalad install -r https://github.com/nipreps-data/ds001600.git
-            datalad update -r --merge -d ds001600/
-            datalad get -r -d ds001600/ ds001600/sub-1/
-
-      - run:
-          name: Install HCP/sub-101006
-          command: |
-            datalad install -r https://github.com/nipreps-data/HCP101006.git
-            datalad update -r --merge -d HCP101006/
-            datalad get -r -d HCP101006
-
-      - run:
-          name: Install ds001771
-          command: |
-            datalad install -r https://github.com/nipreps-data/ds001771.git
-            datalad update -r --merge -d ds001771/
-            datalad get -r -d ds001771/ ds001771/sub-36/*
-            datalad get -r -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/*
-
-      - run:
-          name: Install ds000206
-          command: |
-            datalad install -r https://github.com/nipreps-data/ds000206.git
-            datalad update -r --merge -d ds000206/
-            datalad get -r -d ds000206/ ds000206/sub-05/*
-
-      - run:
-          name: Install ds000054
-          command: |
-            datalad install -r https://github.com/nipreps-data/ds000054.git
-            datalad update -r --merge -d ds000054/
-            datalad get -r -J 2 -d ds000054/ ds000054/* ds000054/derivatives/*
-
-      - run:
-          name: Install Brain extraction tests
-          command: |
-            datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests
-            datalad update --merge -d brain-extraction-tests/
-            datalad get -r -J 2 -d brain-extraction-tests
-
-      - run:
-          name: Install HCPh fieldmaps
-          command: |
-            datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
-            datalad update -r --merge -d hcph-pilot_fieldmaps/
-            datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*
-
-      - save_cache:
-          key: data-v6-{{ .Branch }}-{{ .Revision }}
-          paths:
-            - /tmp/data
-            - /tmp/templateflow
-
-      - restore_cache:
-          keys:
-            - freesurfer-v0-{{ .BuildNum }}
-            - freesurfer-v0-
-      - run:
-          name: Pull FreeSurfer down
-          command: |
-            if [[ ! -d /tmp/freesurfer ]]; then
-              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 /tmp \
-                   --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'
-              echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > /tmp/freesurfer/license.txt
-            else
-              echo "FreeSurfer was cached."
-              circleci step halt
-            fi
-      - save_cache:
-          key: freesurfer-v0-{{ .BuildNum }}
-          paths:
-            - /tmp/freesurfer
-
-  build_n_pytest:
-    <<: *machine_defaults
-    working_directory: /tmp/tests
+  empty:
+    machine:
+      image: ubuntu-2204:current
     steps:
-      - restore_cache:
-          keys:
-            - build-v2-{{ .Branch }}-{{ epoch }}
-            - build-v2-{{ .Branch }}-
-            - build-v2-master-
-            - build-v2-
-          paths:
-            - /tmp/docker
-      - docker/install-docker-credential-helper
-      - run: *docker_auth
-      - run: *setup_docker_registry
-      - run:
-          name: Pull Ubuntu/jammy image
-          command: |
-            set +e
-            docker pull localhost:5000/ubuntu
-            success=$?
-            set -e
-            if [[ "$success" = "0" ]]; then
-                echo "Pulling from local registry"
-                docker tag localhost:5000/ubuntu ubuntu:jammy
-            else
-                echo "Pulling from Docker Hub"
-                docker pull ubuntu:jammy
-                docker tag ubuntu:jammy localhost:5000/ubuntu
-                docker push localhost:5000/ubuntu
-            fi
-      - run:
-          name: Pull SDCFlows Docker image
-          command: |
-            set +e
-            docker pull localhost:5000/sdcflows
-            success=$?
-            set -e
-            if [[ "$success" = "0" ]]; then
-                echo "Pulling from local registry"
-                docker tag localhost:5000/sdcflows nipreps/sdcflows:latest
-                docker tag localhost:5000/sdcflows nipreps/sdcflows
-            else
-                echo "Pulling from Docker Hub"
-                docker pull nipreps/sdcflows:latest
-            fi
-      - checkout:
-          path: /tmp/src/sdcflows
-      - run:
-          name: Build Docker image
-          working_directory: /tmp/src/sdcflows
-          no_output_timeout: 60m
-          command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
-            python3 -m pip install -U build hatch hatchling pip twine docutils
-
-            # Get version, update files.
-            THISVERSION=$( python3 -m hatch version | tail -n1 | xargs )
-            if [[ ${THISVERSION:0:1} == "0" ]] ; then
-              echo "WARNING: latest git tag could not be found"
-              echo "Please, make sure you fetch all tags from upstream with"
-              echo "the command ``git fetch --tags --verbose`` and push"
-              echo "them to your fork with ``git push origin --tags``"
-            fi
-            # Build docker image
-            docker build --rm \
-                --cache-from=nipreps/sdcflows \
-                -t nipreps/sdcflows:latest \
-                --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
-                --build-arg VCS_REF=`git rev-parse --short HEAD` \
-                --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
-                | tee build-output.log
-            echo "${CIRCLE_TAG:-$THISVERSION}" >> /tmp/.local-version.txt
-      - run:
-          name: Check Docker image
-          working_directory: /tmp/src/sdcflows
-          command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
-            # Get version, update files.
-            THISVERSION=$( python3 -m hatch version | tail -n1 | xargs )
-            BUILT_VERSION=$( docker run --rm --entrypoint=python nipreps/sdcflows:latest -c "import sdcflows; print(sdcflows.__version__)" )
-            BUILT_VERSION=${BUILT_VERSION%$'\r'}
-            echo "VERSION: \"$THISVERSION\""
-            echo "BUILT: \"$BUILT_VERSION\""
-            set -e
-            test "$BUILT_VERSION" = "$THISVERSION"
-      - run:
-          name: Docker push to local registry
-          no_output_timeout: 40m
-          command: |
-            docker tag nipreps/sdcflows:latest localhost:5000/sdcflows
-            docker push localhost:5000/sdcflows
-      - run:
-          name: Docker registry garbage collection
-          command: |
-            docker exec -it registry /bin/registry garbage-collect --delete-untagged \
-                /etc/docker/registry/config.yml
-      - save_cache:
-          key: build-v2-{{ .Branch }}-{{ epoch }}
-          paths:
-            - /tmp/docker
-
-      - restore_cache:
-          keys:
-            - freesurfer-v0-{{ .BuildNum }}
-            - freesurfer-v0-
-      - restore_cache:
-          keys:
-            - data-v6-{{ .Branch }}-{{ .Revision }}
-            - data-v6--{{ .Revision }}
-            - data-v6-{{ .Branch }}-
-            - data-v6-main-
-            - data-v6-
-
-      - restore_cache:
-          keys:
-            - workdir-v3-{{ .Branch }}-
-            - workdir-v3-master-
-            - workdir-v3-
-      - run:
-          name: Refreshing cached intermediate results
-          working_directory: /tmp/src/sdcflows
-          command: |
-            COMMIT_MSG=$( git log --format=oneline -n 1 $CIRCLE_SHA1 )
-            set +e
-            do_refresh="$( echo "${COMMIT_MSG}" | grep -i -E '\[refresh[ _]?cache\]' )"
-            set -e
-            if [[ "x${do_refresh}" = "x" ]]; then
-              echo "Did not refresh the workdir."
-            else
-              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-                  -O /tmp/data/workdir.tar.gz "https://files.osf.io/v1/resources/9sy2a/providers/osfstorage/5dcabd60a1cd9e000c751b3c"
-              rm -rf /tmp/work
-              mkdir -p /tmp/work
-              pushd /tmp/work
-              tar xzfv /tmp/data/workdir.tar.gz --strip 1
-              popd
-            fi
-
-            wipe_dir=$( echo "${COMMIT_MSG}" | sed -n 's/.*\[wipe \([a-zA-Z0-9_\*]*\)\].*/\1/p' )
-            if [[ "x${wipe_dir}" != "x" ]]; then
-              path=/tmp/work/${wipe_dir}
-              echo "Found tag [wipe ${wipe_dir}] - clearing up $path ..."
-              rm -rf ${path}
-            fi
-      - run:
-          name: Run tests
-          no_output_timeout: 2h
-          command: |
-            mkdir -p /tmp/work
-            docker run -it --rm -w /src/sdcflows \
-                -e TEST_WORK_DIR=/work \
-                -e TEST_DATA_HOME=/data \
-                -e TEST_OUTPUT_DIR=/out \
-                -e COVERAGE_FILE=/out/.coverage \
-                -e FS_LICENSE=/opt/freesurfer/license.txt \
-                -v /tmp/data:/data:ro \
-                -v /tmp/src:/src \
-                -v /tmp/tests:/out \
-                -v /tmp/work:/work \
-                -v /tmp/freesurfer:/opt/freesurfer:ro  \
-                -v /tmp/templateflow:/home/sdcflows/.cache/templateflow \
-                nipreps/sdcflows:latest \
-                pytest -v --junit-xml=/out/pytest.xml \
-                       --cov sdcflows --cov-report xml:/out/unittests.xml \
-                       -n auto sdcflows/
-      - save_cache:
-          key: workdir-v3-{{ .Branch }}-{{ .BuildNum }}
-          paths:
-            - /tmp/work
-      - store_artifacts:
-          path: /tmp/tests
-      - store_test_results:
-          path: /tmp/tests
-
-      - codecov/upload:
-          file: /tmp/tests/unittests.xml
-          flags: unittests
-
-  build_docs:
-    <<: *python_defaults
-    working_directory: /tmp/gh-pages
-    environment:
-      - FSLOUTPUTTYPE: NIFTI
-      - SUBJECTS_DIR: /tmp/subjects
-    steps:
-      - checkout
-      - run:
-          name: Create subjects folder
-          command: mkdir -p $SUBJECTS_DIR
-      - run:
-          name: Install Graphviz & pandoc
-          command: |
-            sudo apt-get update -y
-            sudo apt-get install -y --no-install-recommends graphviz pandoc texlive
-      - run:
-          name: Install deps
-          command: |
-            python -m venv /tmp/venv
-            source /tmp/venv/bin/activate
-            python -m pip install -U build hatch hatchling pip twine docutils
-            python -m pip install .[docs]
-      - run:
-          name: Build only this commit
-          command: |
-            source /tmp/venv/bin/activate
-            python -m hatch version | tail -n1 | xargs
-            BRANCH=$( echo $CIRCLE_BRANCH | sed 's+/+_+g' )
-            python -c "from templateflow.api import get; get('MNI152NLin2009cAsym', desc='brain', resolution=1, suffix='T1w')"
-            make -C docs SPHINXOPTS="-W -v" BUILDDIR="$HOME/docs" OUTDIR=${CIRCLE_TAG:-$BRANCH} html
-      - store_artifacts:
-          path: ~/docs/
-
-  deploy_docker:
-    <<: *machine_defaults
-    steps:
-      - restore_cache:
-          keys:
-            - build-v2-{{ .Branch }}-{{ epoch }}
-            - build-v2-{{ .Branch }}-
-            - build-v2-master-
-            - build-v2-
-          paths:
-            - /tmp/docker
-      - docker/install-docker-credential-helper
-      - run: *docker_auth
-      - run: *setup_docker_registry
-      - run: *pull_from_registry
-      - run:
-          name: Deploy to Docker Hub
-          no_output_timeout: 40m
-          command: |
-            if [[ -n "$DOCKER_PAT" ]]; then
-              docker push nipreps/sdcflows:latest
-              docker tag nipreps/sdcflows nipreps/sdcflows:$CIRCLE_TAG
-              docker push nipreps/sdcflows:$CIRCLE_TAG
-            fi
-
-  test_package:
-    <<: *python_defaults
-    steps:
-      - checkout
-      - run:
-          name: Prepare environment & build
-          command: |
-            python -m venv /tmp/buildenv
-            source /tmp/buildenv/bin/activate
-            python3 -m pip install -U build hatch hatchling pip twine docutils
-            python3 -m build
-            twine check dist/sdcflows*
-      - store_artifacts:
-          path: /tmp/src/sdcflows/dist
-      - persist_to_workspace:
-          root: /tmp/src/sdcflows
-          paths: dist
-
-      - run:
-          name: Validate version
-          command: |
-            source /tmp/buildenv/bin/activate
-            THISVERSION=$( python -m hatch version | tail -n1 | xargs )
-            python -m pip install dist/*.whl
-            mkdir empty
-            cd empty
-            INSTALLED=$( python -c 'import sdcflows; print(sdcflows.__version__)' )
-            test "${CIRCLE_TAG:-$THISVERSION}" == "$INSTALLED"
-
-  deploy_pypi:
-    <<: *python_defaults
-    steps:
-      - attach_workspace:
-          at: /tmp/src/sdcflows
-      - run:
-          name: Upload to Pypi
-          command: |
-            python -m pip install twine
-            python -m twine check dist/*
-            python -m twine upload dist/* --non-interactive
+      - run: echo Not doing nothing.
 
 workflows:
   version: 2
   build_deploy:
     jobs:
-      - cache_test_data:
-          context:
-            - nipreps-common
-            - fs-license
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-            tags:
-              only: /.*/
-
-      - build_n_pytest:
-          requires:
-            - cache_test_data
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-            tags:
-              only: /.*/
-
-      - test_package:
-          context:
-            - nipreps-common
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-                - /tests?\/.*/
-            tags:
-              only: /.*/
-
-      - deploy_pypi:
-          context:
-            - nipreps-common
-          requires:
-            - build_docs
-            - test_package
-            - build_n_pytest
-          filters:
-            branches:
-              ignore: /.*/
-            tags:
-              only: /.*/
-
-      - deploy_docker:
-          context:
-            - nipreps-common
-          requires:
-            - deploy_pypi
-          filters:
-            branches:
-              ignore: /.*/
-            tags:
-              only: /.*/
-
-      - build_docs:
-          filters:
-            branches:
-              ignore:
-                - /tests?\/.*/
-            tags:
-              only: /.*/
+      - empty

From 8d8b1042add1a1bd03106620432a88c0108cef4d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 15:16:14 -0400
Subject: [PATCH 02/18] CI: Remove some GITHUB_ACTIONS skips

---
 sdcflows/interfaces/tests/test_bspline.py | 1 -
 sdcflows/tests/test_transform.py          | 1 -
 2 files changed, 2 deletions(-)

diff --git a/sdcflows/interfaces/tests/test_bspline.py b/sdcflows/interfaces/tests/test_bspline.py
index 67813a4c29..d10b49684b 100644
--- a/sdcflows/interfaces/tests/test_bspline.py
+++ b/sdcflows/interfaces/tests/test_bspline.py
@@ -138,7 +138,6 @@ def test_topup_coeffs(tmpdir, testdata_dir):
         _fix_topup_fieldcoeff("failing.nii.gz", str(testdata_dir / "epi.nii.gz"), "i")
 
 
-@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
 def test_topup_coeffs_interpolation(tmpdir, testdata_dir):
     """Check that our interpolation is not far away from TOPUP's."""
     tmpdir.chdir()
diff --git a/sdcflows/tests/test_transform.py b/sdcflows/tests/test_transform.py
index 72e44e0759..3169f8b42c 100644
--- a/sdcflows/tests/test_transform.py
+++ b/sdcflows/tests/test_transform.py
@@ -139,7 +139,6 @@ def test_displacements_field(tmpdir, testdata_dir, outdir, pe_dir, rotation, fli
         ).run()
 
 
-@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
 @pytest.mark.parametrize(
     "pe0",
     [

From 5407ec2b20e59ca7a102789036143362c8769026 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 15:18:06 -0400
Subject: [PATCH 03/18] CI: Report test durations

---
 .github/workflows/unittests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 716c30d92c..757ff642e9 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -175,7 +175,8 @@ jobs:
       run: |
         export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
         export PATH=$ANTSPATH:${AFNI_HOME}:/usr/lib/fsl/5.0:$PATH
-        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows
+        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
+          --durations=20 --durations-min=10
 
     - uses: codecov/codecov-action@v4
       with:

From 1c19ef0d573a4f9122b6af45d96c6c3bfe3cc325 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 19:18:13 -0400
Subject: [PATCH 04/18] ci: Add HCPH pilot and brain extraction tests

---
 .github/workflows/unittests.yml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 757ff642e9..6a3ecf8fc7 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -128,7 +128,7 @@ jobs:
     - uses: actions/cache@v4
       with:
         path: ${{ env.TEST_DATA_HOME }}
-        key: data-cache-v1
+        key: data-cache-v2
         restore-keys: |
           data-cache-
     - name: Install test data
@@ -162,6 +162,17 @@ jobs:
         datalad update -r --merge -d ds000206/
         datalad get -r -d ds000206/ ds000206/sub-05/
 
+        # Brain extraction tests
+        datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests
+        datalad update --merge -d brain-extraction-tests/
+        datalad get -r -J 2 -d brain-extraction-tests
+
+        # HCPH pilot
+        datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
+        datalad update -r --merge -d hcph-pilot_fieldmaps/
+        datalad get -r -d hcph-pilot_fieldmaps/
+
+
     - name: Install FreeSurfer's mri_robust_template
       env:
         MRI_ROBUST_TEMPLATE: sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2

From a99ebfd298ee7dccf8b68eebddd7cbcc248f1245 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 19:44:01 -0400
Subject: [PATCH 05/18] ci: Try un-disabling all tests on GHA

---
 sdcflows/tests/test_transform.py             | 1 -
 sdcflows/workflows/fit/tests/test_pepolar.py | 3 ---
 sdcflows/workflows/fit/tests/test_phdiff.py  | 3 ---
 sdcflows/workflows/fit/tests/test_syn.py     | 3 ---
 sdcflows/workflows/tests/test_ancillary.py   | 2 --
 sdcflows/workflows/tests/test_base.py        | 4 ----
 sdcflows/workflows/tests/test_integration.py | 2 --
 7 files changed, 18 deletions(-)

diff --git a/sdcflows/tests/test_transform.py b/sdcflows/tests/test_transform.py
index 3169f8b42c..18e1b71174 100644
--- a/sdcflows/tests/test_transform.py
+++ b/sdcflows/tests/test_transform.py
@@ -21,7 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Unit tests of the transform object."""
-import os
 from subprocess import check_call
 from itertools import product
 import pytest
diff --git a/sdcflows/workflows/fit/tests/test_pepolar.py b/sdcflows/workflows/fit/tests/test_pepolar.py
index 995c867f96..f7dc970d5b 100644
--- a/sdcflows/workflows/fit/tests/test_pepolar.py
+++ b/sdcflows/workflows/fit/tests/test_pepolar.py
@@ -21,15 +21,12 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test pepolar type of fieldmaps."""
-import os
 import pytest
 from nipype.pipeline import engine as pe
 
 from ..pepolar import init_topup_wf
 
 
-@pytest.mark.skipif(os.getenv("TRAVIS") == "true", reason="this is TravisCI")
-@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
 @pytest.mark.parametrize("ds", ("ds001771", "HCP101006"))
 def test_topup_wf(tmpdir, bids_layouts, workdir, outdir, ds):
     """Test preparation workflow."""
diff --git a/sdcflows/workflows/fit/tests/test_phdiff.py b/sdcflows/workflows/fit/tests/test_phdiff.py
index 94af79f2fd..ef278fbe8b 100644
--- a/sdcflows/workflows/fit/tests/test_phdiff.py
+++ b/sdcflows/workflows/fit/tests/test_phdiff.py
@@ -21,7 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test phase-difference type of fieldmaps."""
-import os
 from pathlib import Path
 from json import loads
 
@@ -30,8 +29,6 @@
 from ..fieldmap import init_fmap_wf, Workflow
 
 
-@pytest.mark.skipif(os.getenv("TRAVIS") == "true", reason="this is TravisCI")
-@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
 @pytest.mark.parametrize(
     "fmap_file",
     [
diff --git a/sdcflows/workflows/fit/tests/test_syn.py b/sdcflows/workflows/fit/tests/test_syn.py
index d1535983b2..065a594265 100644
--- a/sdcflows/workflows/fit/tests/test_syn.py
+++ b/sdcflows/workflows/fit/tests/test_syn.py
@@ -21,7 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test fieldmap-less SDC-SyN."""
-import os
 import json
 import pytest
 from nipype.pipeline import engine as pe
@@ -29,8 +28,6 @@
 from ..syn import init_syn_sdc_wf, init_syn_preprocessing_wf, _adjust_zooms, _set_dtype
 
 
-@pytest.mark.skipif(os.getenv("TRAVIS") == "true", reason="this is TravisCI")
-@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
 def test_syn_wf(tmpdir, datadir, workdir, outdir, sloppy_mode):
     """Build and run an SDC-SyN workflow."""
     derivs_path = datadir / "ds000054" / "derivatives"
diff --git a/sdcflows/workflows/tests/test_ancillary.py b/sdcflows/workflows/tests/test_ancillary.py
index f73d062989..50f01c87bc 100644
--- a/sdcflows/workflows/tests/test_ancillary.py
+++ b/sdcflows/workflows/tests/test_ancillary.py
@@ -21,7 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Check the tools submodule."""
-import os
 import pytest
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
@@ -29,7 +28,6 @@
 from ..ancillary import init_brainextraction_wf
 
 
-@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
 @pytest.mark.parametrize("folder", ["magnitude/ds000054", "magnitude/ds000217"])
 def test_brainmasker(tmpdir, datadir, workdir, outdir, folder):
     """Exercise the brain masking tool."""
diff --git a/sdcflows/workflows/tests/test_base.py b/sdcflows/workflows/tests/test_base.py
index b31222fecc..39f37348f2 100644
--- a/sdcflows/workflows/tests/test_base.py
+++ b/sdcflows/workflows/tests/test_base.py
@@ -22,7 +22,6 @@
 #
 """Test the base workflow."""
 from pathlib import Path
-import os
 import pytest
 from sdcflows import fieldmaps as fm
 from sdcflows.utils.wrangler import find_estimators
@@ -62,9 +61,6 @@ def test_fmap_wf(tmpdir, workdir, outdir, bids_layouts, dataset, subject):
     if workdir:
         wf.base_dir = str(workdir)
 
-    if os.getenv("GITHUB_ACTIONS") == "true":
-        return
-
     res = wf.run(plugin="Linear")
 
     # Regression test for when out_merge_fmap_coeff was flattened and would
diff --git a/sdcflows/workflows/tests/test_integration.py b/sdcflows/workflows/tests/test_integration.py
index 6263f7a5f9..86b21646f1 100644
--- a/sdcflows/workflows/tests/test_integration.py
+++ b/sdcflows/workflows/tests/test_integration.py
@@ -21,7 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test the base workflow."""
-import os
 from pathlib import Path
 import json
 import pytest
@@ -37,7 +36,6 @@
 )
 
 
-@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
 @pytest.mark.parametrize("pe0", ["LR", "PA"])
 @pytest.mark.parametrize("mode", ["pepolar", "phasediff"])
 def test_integration_wf(tmpdir, workdir, outdir, datadir, pe0, mode):

From b6140aa07b683b9ddd53cfc8a20c97d25bd31eed Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 20:04:35 -0400
Subject: [PATCH 06/18] CI: Update datalad get calls

---
 .github/workflows/unittests.yml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 6a3ecf8fc7..47589d774b 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -139,38 +139,39 @@ jobs:
         # ds001600
         datalad install -r https://github.com/nipreps-data/ds001600.git
         datalad update -r --merge -d ds001600/
-        datalad get -r -d ds001600/ ds001600/sub-1/
+        datalad get -r -J 2 -d ds001600/ ds001600/sub-1/
 
         # HCP/sub-101006
         datalad install -r https://github.com/nipreps-data/HCP101006.git
         datalad update -r --merge -d HCP101006/
-        datalad get -r -d HCP101006
+        datalad get -r -J 2 -d HCP101006 HCP101006/*
 
         # ds001771
         datalad install -r https://github.com/nipreps-data/ds001771.git
         datalad update -r --merge -d ds001771/
-        datalad get -r -d ds001771/ ds001771/sub-36/*
-        datalad get -r -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/*
+        datalad get -r -J 2 -d ds001771/ ds001771/sub-36/*
+        datalad get -r -J 2 -d ds001771/derivatives ds001771/derivatives/openneuro/sub-36/*
 
         # ds000054
         datalad install -r https://github.com/nipreps-data/ds000054.git
         datalad update --merge -d ds000054/
         datalad get -r -d ds000054/ ds000054/sub-100185/*
+        datalad get -r -J 2 -d ds000054/ ds000054/derivatives/smriprep-0.6/sub-100185/anat/
 
         # ds000206
         datalad install -r https://github.com/nipreps-data/ds000206.git
         datalad update -r --merge -d ds000206/
-        datalad get -r -d ds000206/ ds000206/sub-05/
+        datalad get -r -J 2 -d ds000206/ ds000206/sub-05/
 
         # Brain extraction tests
         datalad install -r https://gin.g-node.org/nipreps-data/brain-extraction-tests
         datalad update --merge -d brain-extraction-tests/
-        datalad get -r -J 2 -d brain-extraction-tests
+        datalad get -r -J 2 -d brain-extraction-tests brain-extraction-tests/*
 
         # HCPH pilot
         datalad install -r https://github.com/nipreps-data/hcph-pilot_fieldmaps.git
         datalad update -r --merge -d hcph-pilot_fieldmaps/
-        datalad get -r -d hcph-pilot_fieldmaps/
+        datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*
 
 
     - name: Install FreeSurfer's mri_robust_template

From 49b5390360feba1d1f3fb37e7acbe7db1dd6156d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 21:10:03 -0400
Subject: [PATCH 07/18] fix: Ensure FS_LICENSE is accessible

---
 .github/workflows/unittests.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 47589d774b..952c7b28c4 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -173,6 +173,8 @@ jobs:
         datalad update -r --merge -d hcph-pilot_fieldmaps/
         datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*
 
+    - name: Set FS_LICENSE variable
+      run: echo "FS_LICENSE=$HOME/.cache/freesurfer/license.txt" >> $GITHUB_ENV
 
     - name: Install FreeSurfer's mri_robust_template
       env:
@@ -180,8 +182,8 @@ jobs:
       run: |
         curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template
         sudo install mri_robust_template /usr/local/bin
-        mkdir -p $HOME/.cache/freesurfer/
-        echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $HOME/.cache/freesurfer/license.txt
+        mkdir -p $( dirname $FS_LICENSE )
+        echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $FS_LICENSE
 
     - name: Run pytest with coverage
       run: |

From e232f6e02665166b7767e929743d30c51322f592 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 21:10:23 -0400
Subject: [PATCH 08/18] CI: Install ANTs with conda

---
 .github/workflows/unittests.yml | 26 ++++++--------------------
 1 file changed, 6 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 952c7b28c4..89ce32bde5 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -30,7 +30,6 @@ jobs:
       AFNI_IMSAVE_WARNINGS: NO
       AFNI_TTATLAS_DATASET: /opt/afni/atlases
       AFNI_PLUGINPATH: /opt/afni/plugins
-      ANTSPATH: /opt/ants
     strategy:
       max-parallel: 5
       matrix:
@@ -66,19 +65,6 @@ jobs:
           tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME}
         fi
 
-    - uses: actions/cache@v4
-      with:
-        path: /opt/ants
-        key: ants-v1
-        restore-keys: |
-          ants-v1
-    - name: Install ANTS
-      run: |
-        if [[ ! -d "${ANTSPATH}" ]]; then
-          sudo mkdir -p $ANTSPATH
-          curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" | sudo tar -xzC $ANTSPATH --strip-components 1
-        fi
-
     - name: Git settings (pacify DataLad)
       run: |
         git config --global user.name 'NiPreps Bot'
@@ -89,11 +75,11 @@ jobs:
         auto-update-conda: true
         auto-activate-base: true
         python-version: ${{ matrix.python-version }}
-        channels: anaconda,https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
+        channels: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
     - uses: actions/cache@v4
       id: conda
       env:
-        CACHE_NUM: v4
+        CACHE_NUM: v5
       with:
         path: |
           ~/conda_pkgs_dir
@@ -105,9 +91,9 @@ jobs:
       run: |
         conda install git-annex=*=alldep* pip
         pip install datalad datalad-osf
-    - name: Install fsl
+    - name: Install fsl and ANTs
       run: |
-        conda install fsl-fugue fsl-topup
+        conda install fsl-fugue fsl-topup ants
     - uses: actions/checkout@v4
     - name: Install dependencies
       timeout-minutes: 5
@@ -187,8 +173,8 @@ jobs:
 
     - name: Run pytest with coverage
       run: |
-        export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
-        export PATH=$ANTSPATH:${AFNI_HOME}:/usr/lib/fsl/5.0:$PATH
+        export PATH=${AFNI_HOME}:$PATH
+        export FSLDIR=${CONDA_PREFIX}
         pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
           --durations=20 --durations-min=10
 

From 4b79240780100ab9efafdad5090ea06133067cbd Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 21:10:32 -0400
Subject: [PATCH 09/18] TEST: Mark slow tests and run in their own jobs

---
 .github/workflows/unittests.yml              | 10 +++++++++-
 pyproject.toml                               |  3 +++
 sdcflows/workflows/fit/tests/test_pepolar.py |  1 +
 sdcflows/workflows/fit/tests/test_phdiff.py  |  1 +
 sdcflows/workflows/fit/tests/test_syn.py     |  1 +
 sdcflows/workflows/tests/test_ancillary.py   |  1 +
 sdcflows/workflows/tests/test_base.py        |  1 +
 7 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 89ce32bde5..be3f82f4e4 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -34,6 +34,12 @@ jobs:
       max-parallel: 5
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
+        marks: ["not slow"]
+        include:
+          - python-version: "3.9"
+            marks: "slow"
+          - python-version: "3.12"
+            marks: "slow"
 
     steps:
     - uses: actions/cache@v4
@@ -176,7 +182,9 @@ jobs:
         export PATH=${AFNI_HOME}:$PATH
         export FSLDIR=${CONDA_PREFIX}
         pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
-          --durations=20 --durations-min=10
+          --durations=20 --durations-min=10 -m "$MARKS"
+      env:
+        MARKS: ${{ matrix.marks }}
 
     - uses: codecov/codecov-action@v4
       with:
diff --git a/pyproject.toml b/pyproject.toml
index fbdaae9e94..3a3c0b6ff8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -165,6 +165,9 @@ doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
 junit_family = "xunit2"
+markers = [
+  "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+]
 
 
 [tool.coverage.run]
diff --git a/sdcflows/workflows/fit/tests/test_pepolar.py b/sdcflows/workflows/fit/tests/test_pepolar.py
index f7dc970d5b..e95128d153 100644
--- a/sdcflows/workflows/fit/tests/test_pepolar.py
+++ b/sdcflows/workflows/fit/tests/test_pepolar.py
@@ -27,6 +27,7 @@
 from ..pepolar import init_topup_wf
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize("ds", ("ds001771", "HCP101006"))
 def test_topup_wf(tmpdir, bids_layouts, workdir, outdir, ds):
     """Test preparation workflow."""
diff --git a/sdcflows/workflows/fit/tests/test_phdiff.py b/sdcflows/workflows/fit/tests/test_phdiff.py
index ef278fbe8b..94932f6243 100644
--- a/sdcflows/workflows/fit/tests/test_phdiff.py
+++ b/sdcflows/workflows/fit/tests/test_phdiff.py
@@ -29,6 +29,7 @@
 from ..fieldmap import init_fmap_wf, Workflow
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize(
     "fmap_file",
     [
diff --git a/sdcflows/workflows/fit/tests/test_syn.py b/sdcflows/workflows/fit/tests/test_syn.py
index 065a594265..905c1d808b 100644
--- a/sdcflows/workflows/fit/tests/test_syn.py
+++ b/sdcflows/workflows/fit/tests/test_syn.py
@@ -28,6 +28,7 @@
 from ..syn import init_syn_sdc_wf, init_syn_preprocessing_wf, _adjust_zooms, _set_dtype
 
 
+@pytest.mark.slow
 def test_syn_wf(tmpdir, datadir, workdir, outdir, sloppy_mode):
     """Build and run an SDC-SyN workflow."""
     derivs_path = datadir / "ds000054" / "derivatives"
diff --git a/sdcflows/workflows/tests/test_ancillary.py b/sdcflows/workflows/tests/test_ancillary.py
index 50f01c87bc..7e407d86e3 100644
--- a/sdcflows/workflows/tests/test_ancillary.py
+++ b/sdcflows/workflows/tests/test_ancillary.py
@@ -28,6 +28,7 @@
 from ..ancillary import init_brainextraction_wf
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize("folder", ["magnitude/ds000054", "magnitude/ds000217"])
 def test_brainmasker(tmpdir, datadir, workdir, outdir, folder):
     """Exercise the brain masking tool."""
diff --git a/sdcflows/workflows/tests/test_base.py b/sdcflows/workflows/tests/test_base.py
index 39f37348f2..8b74ac9ddf 100644
--- a/sdcflows/workflows/tests/test_base.py
+++ b/sdcflows/workflows/tests/test_base.py
@@ -28,6 +28,7 @@
 from sdcflows.workflows.base import init_fmap_preproc_wf
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize(
     "dataset,subject", [("ds000054", "100185"), ("HCP101006", "101006")]
 )

From 606e5d8896df3e05fbe6ee260b45b7a6aa06f8ae Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 24 Sep 2024 21:30:17 -0400
Subject: [PATCH 10/18] CI: Define freesurfer home

---
 .github/workflows/unittests.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index be3f82f4e4..620992c3d9 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -165,8 +165,10 @@ jobs:
         datalad update -r --merge -d hcph-pilot_fieldmaps/
         datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*
 
-    - name: Set FS_LICENSE variable
-      run: echo "FS_LICENSE=$HOME/.cache/freesurfer/license.txt" >> $GITHUB_ENV
+    - name: Set FreeSurfer variables
+      run: |
+        echo "FREESURFER_HOME=$HOME/.cache/freesurfer" >> $GITHUB_ENV
+        echo "FS_LICENSE=$HOME/.cache/freesurfer/license.txt" >> $GITHUB_ENV
 
     - name: Install FreeSurfer's mri_robust_template
       env:

From bc24ff61f36d029b19c0919b8b31b106072be385 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 07:53:37 -0400
Subject: [PATCH 11/18] TEST: More slow marks, add veryslow

---
 pyproject.toml                               | 3 ++-
 sdcflows/workflows/fit/tests/test_syn.py     | 1 +
 sdcflows/workflows/tests/test_base.py        | 1 +
 sdcflows/workflows/tests/test_integration.py | 1 +
 4 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3a3c0b6ff8..ef65fce49e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -160,13 +160,14 @@ per-file-ignores = [
 
 [tool.pytest.ini_options]
 norecursedirs = [".git"]
-addopts = "-svx --doctest-modules"
+addopts = "-svx --doctest-modules --strict-markers"
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
 junit_family = "xunit2"
 markers = [
   "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+  "veryslow: marks tests as very slow (>5min)",
 ]
 
 
diff --git a/sdcflows/workflows/fit/tests/test_syn.py b/sdcflows/workflows/fit/tests/test_syn.py
index 905c1d808b..262890d03a 100644
--- a/sdcflows/workflows/fit/tests/test_syn.py
+++ b/sdcflows/workflows/fit/tests/test_syn.py
@@ -28,6 +28,7 @@
 from ..syn import init_syn_sdc_wf, init_syn_preprocessing_wf, _adjust_zooms, _set_dtype
 
 
+@pytest.mark.veryslow
 @pytest.mark.slow
 def test_syn_wf(tmpdir, datadir, workdir, outdir, sloppy_mode):
     """Build and run an SDC-SyN workflow."""
diff --git a/sdcflows/workflows/tests/test_base.py b/sdcflows/workflows/tests/test_base.py
index 8b74ac9ddf..2cb77cf089 100644
--- a/sdcflows/workflows/tests/test_base.py
+++ b/sdcflows/workflows/tests/test_base.py
@@ -28,6 +28,7 @@
 from sdcflows.workflows.base import init_fmap_preproc_wf
 
 
+@pytest.mark.veryslow
 @pytest.mark.slow
 @pytest.mark.parametrize(
     "dataset,subject", [("ds000054", "100185"), ("HCP101006", "101006")]
diff --git a/sdcflows/workflows/tests/test_integration.py b/sdcflows/workflows/tests/test_integration.py
index 86b21646f1..ac61a48034 100644
--- a/sdcflows/workflows/tests/test_integration.py
+++ b/sdcflows/workflows/tests/test_integration.py
@@ -36,6 +36,7 @@
 )
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize("pe0", ["LR", "PA"])
 @pytest.mark.parametrize("mode", ["pepolar", "phasediff"])
 def test_integration_wf(tmpdir, workdir, outdir, datadir, pe0, mode):

From 3c9dfeda3c6768bdd7718fb0d4b34b96d89b6427 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 07:57:22 -0400
Subject: [PATCH 12/18] CI: Run slow and veryslow on two separate jobs

---
 .github/workflows/unittests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 620992c3d9..c037561af9 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -37,9 +37,9 @@ jobs:
         marks: ["not slow"]
         include:
           - python-version: "3.9"
-            marks: "slow"
+            marks: "slow and not veryslow"
           - python-version: "3.12"
-            marks: "slow"
+            marks: "veryslow"
 
     steps:
     - uses: actions/cache@v4

From 7742627cbab45d21efc4f2dc1e473a00957b8c9c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 07:57:45 -0400
Subject: [PATCH 13/18] CI: Allow all jobs to run simultaneously

---
 .github/workflows/unittests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index c037561af9..76c4755903 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -31,7 +31,7 @@ jobs:
       AFNI_TTATLAS_DATASET: /opt/afni/atlases
       AFNI_PLUGINPATH: /opt/afni/plugins
     strategy:
-      max-parallel: 5
+      max-parallel: 6
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         marks: ["not slow"]

From e11a7783519fb485dff657d91b3e236abb10a21a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 09:37:56 -0400
Subject: [PATCH 14/18] CI: Update config in prep for merge

---
 .github/workflows/unittests.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 76c4755903..12c8b84c01 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -5,6 +5,12 @@ on:
   pull_request:
   schedule:
     - cron: 0 0 * * 0
+  # Allow job to be triggered manually from GitHub interface
+  workflow_dispatch:
+
+# Force pytest to use color
+env:
+  FORCE_COLOR: true
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -18,7 +24,7 @@ defaults:
     shell: bash -el {0}
 
 jobs:
-  build-linux:
+  test:
     if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))"
     runs-on: ubuntu-latest
     env:

From 186c36d8db1b238838538702b5a5d5679d24418d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 09:58:11 -0400
Subject: [PATCH 15/18] CI: Add build/publish jobs

---
 .github/workflows/unittests.yml | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
index 12c8b84c01..d3d5a03551 100644
--- a/.github/workflows/unittests.yml
+++ b/.github/workflows/unittests.yml
@@ -24,6 +24,19 @@ defaults:
     shell: bash -el {0}
 
 jobs:
+  build-package:
+    name: Build & inspect package
+    runs-on: ubuntu-latest
+    permissions:
+      attestations: write
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: hynek/build-and-inspect-python-package@v2
+
   test:
     if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))"
     runs-on: ubuntu-latest
@@ -199,3 +212,23 @@ jobs:
         file: cov.xml
         token: ${{ secrets.CODECOV_TOKEN }}
       if: ${{ always() }}
+
+  publish:
+    name: Publish released package to pypi.org
+    environment: release-pypi
+    if: github.event.action == 'published'
+    runs-on: ubuntu-latest
+    needs: [build-package, test]
+    permissions:
+      attestations: write
+      id-token: write
+
+    steps:
+      - name: Download packages built by build-and-inspect-python-package
+        uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - name: Upload package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

From 5a65956fd884abdbc8d63a45b92bc69f3c350f3c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 09:58:57 -0400
Subject: [PATCH 16/18] CI: Rename workflows

---
 .github/workflows/{unittests.yml => build-test-publish.yml} | 0
 .github/workflows/{pythonpackage.yml => validate.yml}       | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{unittests.yml => build-test-publish.yml} (100%)
 rename .github/workflows/{pythonpackage.yml => validate.yml} (100%)

diff --git a/.github/workflows/unittests.yml b/.github/workflows/build-test-publish.yml
similarity index 100%
rename from .github/workflows/unittests.yml
rename to .github/workflows/build-test-publish.yml
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/validate.yml
similarity index 100%
rename from .github/workflows/pythonpackage.yml
rename to .github/workflows/validate.yml

From ee166de9d3ec3585dea5cf729fd11ed277024878 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 10:00:46 -0400
Subject: [PATCH 17/18] CI: Reduce validation workflow

---
 .github/workflows/validate.yml | 116 ++-------------------------------
 1 file changed, 5 insertions(+), 111 deletions(-)

diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml
index 26a7f11751..bd8b7c2b0c 100644
--- a/.github/workflows/validate.yml
+++ b/.github/workflows/validate.yml
@@ -1,14 +1,13 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python package
+name: Validations
 
 on:
   push:
     branches: [ '*' ]
-    tags: [ '*' ]
   pull_request:
-    branches: [ master, 'maint/*' ]
+    branches: [ master, main, 'maint/*' ]
+
+env:
+  FORCE_COLOR: true
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -18,115 +17,10 @@ permissions:
   contents: read
 
 jobs:
-  job_metadata:
-    if: github.repository == 'nipreps/sdcflows'
-    runs-on: ubuntu-latest
-    outputs:
-      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
-      version: ${{ steps.show_version.outputs.version }}
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - name: Print head git commit message
-        id: get_commit_message
-        run: |
-          if [[ -z "$COMMIT_MSG" ]]; then
-            COMMIT_MSG=$(git show -s --format=%s $REF)
-          fi
-          echo commit_message=$COMMIT_MSG | tee -a $GITHUB_OUTPUT
-        env:
-          COMMIT_MSG: ${{ github.event.head_commit.message }}
-          REF: ${{ github.event.pull_request.head.sha }}
-      - name: Detect version
-        id: show_version
-        run: |
-          if [[ "$GITHUB_REF" == refs/tags/* ]]; then
-            VERSION=${GITHUB_REF##*/}
-          else
-            pip install -U build hatch hatchling pip twine docutils
-            VERSION=$( python -m hatch version | tail -n1 | xargs )
-          fi
-          echo version=$VERSION | tee -a $GITHUB_OUTPUT
-
-  build:
-    if: github.repository == 'nipreps/sdcflows'
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-    - name: Set up Python 3
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3
-    - name: Display Python version
-      run: python -c "import sys; print(sys.version)"
-    - name: Build sdcflows
-      run: pipx run build
-    - name: Check distributions
-      run: pipx run twine check dist/*
-    - uses: actions/upload-artifact@v4
-      with:
-        name: dist
-        path: dist/
-
-  test:
-    if: "!startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]')"
-    needs: [build, job_metadata]
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9", "3.12"]
-        install: [repo, sdist, wheel, editable]
-
-    env:
-      INSTALL_TYPE: ${{ matrix.install }}
-
-    steps:
-    - uses: actions/checkout@v4
-      if: matrix.install == 'repo' || matrix.install == 'editable'
-      with:
-        fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Fetch packages
-      if: matrix.install == 'sdist' || matrix.install == 'wheel'
-      uses: actions/download-artifact@v4
-      with:
-        name: dist
-        path: dist/
-    - name: Select archive
-      run: |
-        if [ "$INSTALL_TYPE" = "sdist" ]; then
-          ARCHIVE=$( ls dist/*.tar.gz )
-        elif [ "$INSTALL_TYPE" = "wheel" ]; then
-          ARCHIVE=$( ls dist/*.whl )
-        elif [ "$INSTALL_TYPE" = "repo" ]; then
-          ARCHIVE="."
-        elif [ "$INSTALL_TYPE" = "editable" ]; then
-          ARCHIVE="-e ."
-        fi
-        echo "ARCHIVE=$ARCHIVE" | tee -a $GITHUB_ENV
-    - name: Install package
-      run: python -m pip install $ARCHIVE
-    - name: Check version
-      run: |
-        INSTALLED_VERSION=$(python -c 'import sdcflows; print(sdcflows.__version__, end="")')
-        echo "INSTALLED: \"${INSTALLED_VERSION}\""
-        test "${INSTALLED_VERSION}" = "${VERSION}"
-      env:
-        VERSION: ${{ needs.job_metadata.outputs.version }}
-
   flake8:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
     - run: pipx run flake8-pyproject sdcflows/
 
   # codespell:

From 2b7e23ed514e4c32b50ad7bc201553add714758b Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 25 Sep 2024 10:40:09 -0400
Subject: [PATCH 18/18] MNT: Configure check-wheel-contents not to complain
 about test data

---
 pyproject.toml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index ef65fce49e..fa54d89b70 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -195,3 +195,8 @@ ignore-words-list = 'nd,mapp,reson'
 skip = """
 ./.git,*.pdf,*.svg,*.min.js,*.ipynb,ORIGINAL_LICENSE,\
 ./docs/source/_static/example_anatreport.html"""
+
+[tool.check-wheel-contents]
+ignore = [
+  "W002",  # Test data contains duplicates
+]