From d639215fad0993fca4b6aea857483811edf65879 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Fri, 6 Sep 2024 15:07:15 -0400 Subject: [PATCH] :arrow_down: Keep `nitransforms` <24.0.0 Ref https://github.com/nipy/nitransforms/pull/203#discussion_r1747586808 --- .github/Dockerfiles/c-pac_api.latest.Dockerfile | 12 ++++++------ .github/Dockerfiles/c-pac_api.nightly.Dockerfile | 8 ++++---- README.rst | 4 ++-- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/Dockerfiles/c-pac_api.latest.Dockerfile b/.github/Dockerfiles/c-pac_api.latest.Dockerfile index 789c1e87..b78143e4 100644 --- a/.github/Dockerfiles/c-pac_api.latest.Dockerfile +++ b/.github/Dockerfiles/c-pac_api.latest.Dockerfile @@ -14,10 +14,10 @@ # 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/ubuntu:jammy-non-free as src -LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A DRY-RUN TESTING IMAGE \ +FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free AS src +LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A DRY-RUN TESTING IMAGE \ Dry-run C-PAC latest API." -LABEL org.opencontainers.image.source https://github.com/FCP-INDI/cpac +LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/cpac USER root COPY --from=fcpindi/c-pac:latest /code /code RUN mkdir -p /home/user/c-pac_user \ @@ -29,10 +29,10 @@ RUN mkdir -p /home/user/c-pac_user \ python3.10 \ python-is-python3 \ && rm -rf /var/lib/apt/lists/* -ENV PYTHONUSERBASE=/home/c-pac_user/.local -ENV PATH=$PATH:/home/c-pac_user/.local/bin \ +ENV PYTHONUSERBASE=/home/user/c-pac_user/.local +ENV PATH=$PATH:/home/user/c-pac_user/.local/bin \ PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages USER c-pac_user -RUN pip install -r /code/requirements.txt && pip install --user /code +RUN pip install "nitransforms>=21.0.0,<24.0.0" && pip install -r /code/requirements.txt && pip install --user /code ENV FSLDIR="/FSLDIR" ENTRYPOINT [ "/code/run.py" ] diff --git a/.github/Dockerfiles/c-pac_api.nightly.Dockerfile b/.github/Dockerfiles/c-pac_api.nightly.Dockerfile index b26865f1..3ca25e80 100644 --- a/.github/Dockerfiles/c-pac_api.nightly.Dockerfile +++ b/.github/Dockerfiles/c-pac_api.nightly.Dockerfile @@ -14,10 +14,10 @@ # 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/ubuntu:jammy-non-free as src -LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A DRY-RUN TESTING IMAGE \ +FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free AS src +LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A DRY-RUN TESTING IMAGE \ Dry-run C-PAC nightly API." -LABEL org.opencontainers.image.source https://github.com/FCP-INDI/cpac +LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/cpac USER root COPY --from=fcpindi/c-pac:nightly /code /code RUN mkdir -p /home/user/c-pac_user \ @@ -33,6 +33,6 @@ ENV PYTHONUSERBASE=/home/c-pac_user/.local ENV PATH=$PATH:/home/c-pac_user/.local/bin \ PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages USER c-pac_user -RUN pip install -r /code/requirements.txt && pip install --user /code +RUN pip install "nitransforms>=21.0.0,<24.0.0" && pip install -r /code/requirements.txt && pip install --user /code ENV FSLDIR="/FSLDIR" ENTRYPOINT [ "/code/CPAC/_entrypoints/run.py" ] diff --git a/README.rst b/README.rst index 6b6758da..72bd5dba 100644 --- a/README.rst +++ b/README.rst @@ -58,7 +58,7 @@ Usage cpac -B /path/to/data/configs:/configs \ --image fcpindi/c-pac --tag latest \ run /path/to/data /path/for/outputs \ - --data_config_file /configs/data_config.yml \ + --data_config_file /configs/data_config.yaml \ --save_working_dir Each command can take "--help" to provide additonal usage information, e.g., @@ -88,7 +88,7 @@ Usage gradients Run ba_timeseries_gradients. See "cpac [--platform "{docker,singularity}] gradients --help" for more information. - tsconcat Run ba-tsconcat (*) + tsconcat Run ba-tsconcat (<0.2.0,>=0.1.2) pull (upgrade) Upgrade your local C-PAC version to the latest version by pulling from Docker Hub or other repository. Use with "--image" and/or "--tag" to specify an image