From 1771f7be37619bee50d9ac548ccdacc5f5bfe04c Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Wed, 26 Feb 2025 14:26:18 -0500 Subject: [PATCH 1/4] :bug: Restore outputs removed from "freesurfer_abcd_preproc" to "freesurfer_reconall" --- CPAC/anat_preproc/anat_preproc.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/CPAC/anat_preproc/anat_preproc.py b/CPAC/anat_preproc/anat_preproc.py index eda6ecf62..215e49544 100644 --- a/CPAC/anat_preproc/anat_preproc.py +++ b/CPAC/anat_preproc/anat_preproc.py @@ -2904,6 +2904,18 @@ def freesurfer_abcd_preproc(wf, cfg, strat_pool, pipe_num, opt=None): "pipeline-fs_brainmask", "pipeline-fs_wmparc", "pipeline-fs_T1", + *[ + f"pipeline-fs_hemi-{hemi}_{entity}" + for hemi in ["L", "R"] + for entity in [ + "desc-surface_curv", + *[ + f"desc-surfaceMesh_{_}" + for _ in ["pial", "smoothwm", "sphere", "white"] + ], + *[f"desc-surfaceMap_{_}" for _ in ["sulc", "thickness", "volume"]], + ] + ], *freesurfer_abcd_preproc.outputs, # we're grabbing the postproc outputs and appending them to # the reconall outputs From 43ed9ffc622590cd297e0907f65db1b8e195fdc5 Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Wed, 26 Feb 2025 15:17:47 -0500 Subject: [PATCH 2/4] :alien: Replace broken setup-conda action --- .github/workflows/smoke_test_participant.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/smoke_test_participant.yml b/.github/workflows/smoke_test_participant.yml index 347a489d0..f773ff7e6 100644 --- a/.github/workflows/smoke_test_participant.yml +++ b/.github/workflows/smoke_test_participant.yml @@ -145,7 +145,7 @@ jobs: echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV cat $GITHUB_ENV - name: setup-conda - uses: s-weigand/setup-conda@v1.2.3 + uses: conda-incubator/setup-miniconda@v3.1.1 - name: Set up datalad-OSF run: | git config --global user.email "CMI_CPAC_Support@childmind.org" @@ -203,7 +203,12 @@ jobs: echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV cat $GITHUB_ENV - name: setup-conda - uses: s-weigand/setup-conda@v1.2.3 + uses: conda-incubator/setup-miniconda@v3.1.1 + with: + activate-environment: datalad-osf + channels: conda-forge + conda-remove-defaults: "true" + python-version: 3.12 - name: Set up datalad-OSF run: | git config --global user.email "CMI_CPAC_Support@childmind.org" From ea3a304146422cfa00781eaa32ae7ece31bc5845 Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Thu, 27 Feb 2025 15:03:30 -0500 Subject: [PATCH 3/4] :loud_sound: Increase logging for `datalad clone` --- .github/workflows/smoke_test_participant.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/smoke_test_participant.yml b/.github/workflows/smoke_test_participant.yml index f773ff7e6..73ea99a88 100644 --- a/.github/workflows/smoke_test_participant.yml +++ b/.github/workflows/smoke_test_participant.yml @@ -217,6 +217,8 @@ jobs: pip install datalad-osf - name: Get rodent test data run: | + export GIT_TRACE=1 + export DATALAD_LOG_LEVEL=DEBUG datalad clone osf://uya3r test-data - name: Run rodent smoke test run: | From de9f5303cdc0abd40eb9e85b99156531ed97f902 Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Thu, 27 Feb 2025 16:02:53 -0500 Subject: [PATCH 4/4] :construction_worker: Install `git-annex` before `datalad-osf` [skip ci] --- .github/workflows/smoke_test_participant.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/smoke_test_participant.yml b/.github/workflows/smoke_test_participant.yml index 73ea99a88..e41292535 100644 --- a/.github/workflows/smoke_test_participant.yml +++ b/.github/workflows/smoke_test_participant.yml @@ -148,6 +148,7 @@ jobs: uses: conda-incubator/setup-miniconda@v3.1.1 - name: Set up datalad-OSF run: | + sudo apt-get update && sudo apt-get install -y git-annex git config --global user.email "CMI_CPAC_Support@childmind.org" git config --global user.name "Theodore (Machine User)" yes | conda install -c conda-forge datalad @@ -211,6 +212,7 @@ jobs: python-version: 3.12 - name: Set up datalad-OSF run: | + sudo apt-get update && sudo apt-get install -y git-annex git config --global user.email "CMI_CPAC_Support@childmind.org" git config --global user.name "Theodore (Machine User)" yes | conda install -c conda-forge datalad