From 739f48c7236075fe4b219cd7acdc471bae329d4d Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Wed, 5 Jun 2024 11:29:38 -0400 Subject: [PATCH 1/6] :package: Restore `bids-validator` installation --- .../Dockerfiles/Ubuntu.jammy-non-free.Dockerfile | 9 +++++++-- CHANGELOG.md | 13 ++++++++++--- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile b/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile index 4498fa0b92..366cdb76a9 100644 --- a/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile +++ b/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile @@ -29,7 +29,8 @@ FROM neurodebian:jammy-non-free LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \ Ubuntu Jammy base image" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC -ARG DEBIAN_FRONTEND=noninteractive +ARG BIDS_VALIDATOR_VERSION=1.14.6 \ + DEBIAN_FRONTEND=noninteractive ENV TZ=America/New_York \ PATH=$PATH:/.local/bin \ PYTHONPATH=$PYTHONPATH:/.local/lib/python3.10/site-packages @@ -61,7 +62,11 @@ RUN groupadd -r c-pac \ && echo $TZ > /etc/timezone \ && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \ && dpkg-reconfigure --frontend=noninteractive locales \ - && update-locale LANG="en_US.UTF-8" + && update-locale LANG="en_US.UTF-8" \ + # # install bids-validator + && curl -fsSL https://raw.githubusercontent.com/tj/n/master/bin/n | bash -s lts \ + && curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.7/install.sh | bash && \ + npm install -g "bids-validator@${BIDS_VALIDATOR_VERSION}" COPY --from=c-pac_templates /cpac_templates /cpac_templates COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global diff --git a/CHANGELOG.md b/CHANGELOG.md index 8b0c525e72..54417dcbd1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,13 +22,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed -- Supplied missing `subject_id` for longitudinal workflow logger and make that field optional for the logger. +- Restored `bids-validator` functionality. + +### Removed + +- Variant image recipes. + - `ABCD-HCP` + - `fMRIPrep-LTS` +- Typehinting support for Python < 3.10. ## [1.8.7] - 2024-05-03 ### Added -- `Robustfov` feature in `FSL-BET` to crop images ensuring removal of neck regions that may appear in the skull-stripped images. +- `Robustfov` feature in `FSL-BET` to crop images ensuring removal of neck regions that may appear in the skull-stripped images. - Ability to throttle nodes, estimating all available memory when threading. - Ability to configure FreeSurfer ingress from the command line. @@ -255,7 +262,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - In a given pipeline configuration, segmentation probability maps and binary tissue masks are warped to template space, and those warped masks are included in the output directory - if `registration_workflows['functional_registration']['EPI_registration']['run segmentation']` is `On` and `segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation']` includes `EPI_Template` - + and/or - if `registration_workflows['anatomical_registration']['run']` is `On` and `segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation']` includes `T1_Template` - Renamed connectivity matrices from `*_connectome.tsv` to `*_correlations.tsv` From 9ca6831571d32f260d66dae27bf640d11043d850 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Thu, 6 Jun 2024 11:34:19 -0400 Subject: [PATCH 2/6] :white_check_mark: Test subprocess call to `bids-validator` --- CPAC/utils/tests/test_bids_utils.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/CPAC/utils/tests/test_bids_utils.py b/CPAC/utils/tests/test_bids_utils.py index 0c6cabebbd..e701568815 100644 --- a/CPAC/utils/tests/test_bids_utils.py +++ b/CPAC/utils/tests/test_bids_utils.py @@ -1,5 +1,7 @@ """Tests for bids_utils""" import os +from subprocess import run + import pytest import yaml from CPAC.utils.bids_utils import bids_gen_cpac_sublist, \ @@ -45,7 +47,12 @@ def _prefix_entities(paths, path): ])), 'w') -@pytest.mark.parametrize('only_one_anat', [True, False]) +def test_bids_validator() -> None: + """Test subprocess call to `bids-validator`.""" + run(["bids-validator", "--version"], check=True) + + +@pytest.mark.parametrize("only_one_anat", [True, False]) def test_create_cpac_data_config_only_one_anat(tmp_path, only_one_anat): """Function to test 'only_one_anat' parameter of 'create_cpac_data_config' function""" From 5e54ecde790726c5cacad9db35c2c217d0dd86f3 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Thu, 6 Jun 2024 11:39:25 -0400 Subject: [PATCH 3/6] :memo: Add `bids-validator` to dependencies with reported versions [rebuild Ubuntu.jammy-non-free] [rebuild base-lite] [rebuild base-standard] --- .github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile | 3 +-- CPAC/utils/versioning/dependencies.py | 11 +++++++---- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile b/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile index 366cdb76a9..cd9e1317ee 100644 --- a/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile +++ b/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile @@ -65,8 +65,7 @@ RUN groupadd -r c-pac \ && update-locale LANG="en_US.UTF-8" \ # # install bids-validator && curl -fsSL https://raw.githubusercontent.com/tj/n/master/bin/n | bash -s lts \ - && curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.7/install.sh | bash && \ - npm install -g "bids-validator@${BIDS_VALIDATOR_VERSION}" + && npm install -g "bids-validator@${BIDS_VALIDATOR_VERSION}" COPY --from=c-pac_templates /cpac_templates /cpac_templates COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global diff --git a/CPAC/utils/versioning/dependencies.py b/CPAC/utils/versioning/dependencies.py index 115160336a..d95add1961 100644 --- a/CPAC/utils/versioning/dependencies.py +++ b/CPAC/utils/versioning/dependencies.py @@ -119,9 +119,12 @@ def requirements() -> dict: REPORTED = dict(sorted({ - **cli_version('ldd --version', formatting=first_line), - 'Python': sys.version.replace('\n', ' ').replace(' ', ' '), - **cli_version('3dECM -help', delimiter='_', - formatting=lambda _: last_line(_).split('{')[-1].rstrip('}')) + **cli_version("bids-validator --version", dependency="bids-validator", + in_result=False, formatting=first_line), + **cli_version("ldd --version", formatting=first_line), + "Python": sys.version.replace("\n", " ").replace(" ", " "), + **cli_version("3dECM -help", delimiter="_", + formatting=lambda _: last_line(_).split("{")[-1].rstrip("}")) }.items(), key=_version_sort)) + REQUIREMENTS = requirements() From 4b0ba7b7a6f7906ae99cbbd0a66691c902681e44 Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Wed, 11 Dec 2024 16:12:40 -0500 Subject: [PATCH 4/6] :construction_worker: Skip pre-commit CI --- .github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile | 2 +- .../Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile | 2 +- .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile | 2 +- .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile | 2 +- .github/Dockerfiles/base-standard.Dockerfile | 2 +- .pre-commit-config.yaml | 5 ++++- Dockerfile | 2 +- variant-ABCD-HCP.Dockerfile | 2 +- variant-fMRIPrep-LTS.Dockerfile | 2 +- variant-lite.Dockerfile | 2 +- 10 files changed, 13 insertions(+), 10 deletions(-) diff --git a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile b/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile index 27631dacd5..1114ae5dac 100644 --- a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile b/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile index 3071f2de78..824bbf6721 100644 --- a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile index 6de7379c1d..3bcfdf79c9 100644 --- a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile index 98d4ed9f8f..a3b38ee247 100644 --- a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/.github/Dockerfiles/base-standard.Dockerfile b/.github/Dockerfiles/base-standard.Dockerfile index 2a448e1186..c01e250dc6 100644 --- a/.github/Dockerfiles/base-standard.Dockerfile +++ b/.github/Dockerfiles/base-standard.Dockerfile @@ -16,7 +16,7 @@ # License along with C-PAC. If not, see . FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy as FreeSurfer -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \ Standard software dependencies for C-PAC standard images" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7357d71417..0db56cf902 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,7 +14,10 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . - +ci: + skip: + - autoversioning + - update-yaml-comments repos: - repo: local hooks: diff --git a/Dockerfile b/Dockerfile index 6de7379c1d..3bcfdf79c9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/variant-ABCD-HCP.Dockerfile b/variant-ABCD-HCP.Dockerfile index 27631dacd5..1114ae5dac 100644 --- a/variant-ABCD-HCP.Dockerfile +++ b/variant-ABCD-HCP.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/variant-fMRIPrep-LTS.Dockerfile b/variant-fMRIPrep-LTS.Dockerfile index 3071f2de78..824bbf6721 100644 --- a/variant-fMRIPrep-LTS.Dockerfile +++ b/variant-fMRIPrep-LTS.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/variant-lite.Dockerfile b/variant-lite.Dockerfile index 98d4ed9f8f..a3b38ee247 100644 --- a/variant-lite.Dockerfile +++ b/variant-lite.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root From acb6413f381bffe8923d1a4c831d1ac973a7784d Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Thu, 12 Dec 2024 10:45:45 -0500 Subject: [PATCH 5/6] :pencil2: Fix repeated `.dev3` --- .../C-PAC.develop-ABCD-HCP-bionic.Dockerfile | 33 ----------------- ...PAC.develop-fMRIPrep-LTS-xenial.Dockerfile | 35 ------------------- .../C-PAC.develop-jammy.Dockerfile | 2 +- .../C-PAC.develop-lite-jammy.Dockerfile | 2 +- .github/Dockerfiles/base-standard.Dockerfile | 2 +- Dockerfile | 2 +- variant-ABCD-HCP.Dockerfile | 33 ----------------- variant-fMRIPrep-LTS.Dockerfile | 35 ------------------- variant-lite.Dockerfile | 2 +- 9 files changed, 5 insertions(+), 141 deletions(-) delete mode 100644 .github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile delete mode 100644 .github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile delete mode 100644 variant-ABCD-HCP.Dockerfile delete mode 100644 variant-fMRIPrep-LTS.Dockerfile diff --git a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile b/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile deleted file mode 100644 index 1114ae5dac..0000000000 --- a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile +++ /dev/null @@ -1,33 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3.dev3.dev3 -LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)" -LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC -USER root - -# install C-PAC -COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml -COPY . /code -RUN pip cache purge && pip install -e /code -# set up runscript -COPY dev/docker_data /code/docker_data -RUN rm -Rf /code/docker_data/checksum && \ - mv /code/docker_data/* /code && \ - rm -Rf /code/docker_data && \ - chmod +x /code/run.py && \ - chmod +x /code/run-with-freesurfer.sh -ENTRYPOINT ["/code/run-with-freesurfer.sh"] - -# Link libraries for Singularity images -RUN ldconfig \ - && apt-get clean \ - && apt-get autoremove -y \ - && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/pip/* \ - && chmod 777 / \ - && chmod -R 777 /home/c-pac_user \ - && chmod 777 $(ls / | grep -v sys | grep -v proc) -ENV PYTHONUSERBASE=/home/c-pac_user/.local -ENV PATH=$PATH:/home/c-pac_user/.local/bin \ - PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages - -# set user -WORKDIR /home/c-pac_user -# USER c-pac_user diff --git a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile b/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile deleted file mode 100644 index 824bbf6721..0000000000 --- a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile +++ /dev/null @@ -1,35 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3.dev3.dev3 -LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)" -LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC -USER root - -# install C-PAC & set up runscript -COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml -COPY . /code -RUN pip cache purge && pip install -e /code -# set up runscript -COPY dev/docker_data /code/docker_data -RUN rm -Rf /code/docker_data/checksum && \ - mv /code/docker_data/* /code && \ - rm -Rf /code/docker_data && \ - chmod +x /code/run.py && \ - chmod +x /code/run-with-freesurfer.sh -ENTRYPOINT ["/code/run-with-freesurfer.sh"] - -# link libraries & clean up -RUN sed -i 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \ - && locale-gen \ - && apt-get clean \ - && apt-get autoremove -y \ - && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/pip/* \ - && ldconfig \ - && chmod 777 / \ - && chmod -R 777 /home/c-pac_user \ - && chmod 777 $(ls / | grep -v sys | grep -v proc) -ENV PYTHONUSERBASE=/home/c-pac_user/.local -ENV PATH=$PATH:/home/c-pac_user/.local/bin \ - PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages - -# set user -WORKDIR /home/c-pac_user -# USER c-pac_user diff --git a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile index 3bcfdf79c9..6de7379c1d 100644 --- a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "Full C-PAC image" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile index a3b38ee247..98d4ed9f8f 100644 --- a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/.github/Dockerfiles/base-standard.Dockerfile b/.github/Dockerfiles/base-standard.Dockerfile index c01e250dc6..2a448e1186 100644 --- a/.github/Dockerfiles/base-standard.Dockerfile +++ b/.github/Dockerfiles/base-standard.Dockerfile @@ -16,7 +16,7 @@ # License along with C-PAC. If not, see . FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy as FreeSurfer -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \ Standard software dependencies for C-PAC standard images" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC diff --git a/Dockerfile b/Dockerfile index 3bcfdf79c9..6de7379c1d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "Full C-PAC image" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root diff --git a/variant-ABCD-HCP.Dockerfile b/variant-ABCD-HCP.Dockerfile deleted file mode 100644 index 1114ae5dac..0000000000 --- a/variant-ABCD-HCP.Dockerfile +++ /dev/null @@ -1,33 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.7.post1.dev3.dev3.dev3 -LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)" -LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC -USER root - -# install C-PAC -COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml -COPY . /code -RUN pip cache purge && pip install -e /code -# set up runscript -COPY dev/docker_data /code/docker_data -RUN rm -Rf /code/docker_data/checksum && \ - mv /code/docker_data/* /code && \ - rm -Rf /code/docker_data && \ - chmod +x /code/run.py && \ - chmod +x /code/run-with-freesurfer.sh -ENTRYPOINT ["/code/run-with-freesurfer.sh"] - -# Link libraries for Singularity images -RUN ldconfig \ - && apt-get clean \ - && apt-get autoremove -y \ - && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/pip/* \ - && chmod 777 / \ - && chmod -R 777 /home/c-pac_user \ - && chmod 777 $(ls / | grep -v sys | grep -v proc) -ENV PYTHONUSERBASE=/home/c-pac_user/.local -ENV PATH=$PATH:/home/c-pac_user/.local/bin \ - PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages - -# set user -WORKDIR /home/c-pac_user -# USER c-pac_user diff --git a/variant-fMRIPrep-LTS.Dockerfile b/variant-fMRIPrep-LTS.Dockerfile deleted file mode 100644 index 824bbf6721..0000000000 --- a/variant-fMRIPrep-LTS.Dockerfile +++ /dev/null @@ -1,35 +0,0 @@ -FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.7.post1.dev3.dev3.dev3 -LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)" -LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC -USER root - -# install C-PAC & set up runscript -COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml -COPY . /code -RUN pip cache purge && pip install -e /code -# set up runscript -COPY dev/docker_data /code/docker_data -RUN rm -Rf /code/docker_data/checksum && \ - mv /code/docker_data/* /code && \ - rm -Rf /code/docker_data && \ - chmod +x /code/run.py && \ - chmod +x /code/run-with-freesurfer.sh -ENTRYPOINT ["/code/run-with-freesurfer.sh"] - -# link libraries & clean up -RUN sed -i 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \ - && locale-gen \ - && apt-get clean \ - && apt-get autoremove -y \ - && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/pip/* \ - && ldconfig \ - && chmod 777 / \ - && chmod -R 777 /home/c-pac_user \ - && chmod 777 $(ls / | grep -v sys | grep -v proc) -ENV PYTHONUSERBASE=/home/c-pac_user/.local -ENV PATH=$PATH:/home/c-pac_user/.local/bin \ - PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages - -# set user -WORKDIR /home/c-pac_user -# USER c-pac_user diff --git a/variant-lite.Dockerfile b/variant-lite.Dockerfile index a3b38ee247..98d4ed9f8f 100644 --- a/variant-lite.Dockerfile +++ b/variant-lite.Dockerfile @@ -14,7 +14,7 @@ # You should have received a copy of the GNU Lesser General Public # License along with C-PAC. If not, see . -FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3.dev3.dev3 +FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.7.post1.dev3 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer" LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC USER root From 8b84256fe7db012f188b93812bc76a0f7b4fae8e Mon Sep 17 00:00:00 2001 From: Jon Cluce Date: Thu, 12 Dec 2024 12:09:57 -0500 Subject: [PATCH 6/6] :construction_worker: :package: Rebuild stages [rebuild base-standard] [rebuild Ubuntu.jammy-non-free] [rebuild AFNI.23.3.09-jammy]