diff --git a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile b/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile index 0c9eaff2ad..e1ec4a5d8c 100644 --- a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile @@ -16,7 +16,7 @@ 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 +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \ diff --git a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile b/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile index 6cd146cd19..21575938e4 100644 --- a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile @@ -16,7 +16,7 @@ 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 +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \ diff --git a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile index e8f4654778..838d8dcc4b 100644 --- a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile @@ -22,7 +22,7 @@ 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 +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \ diff --git a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile index 56dcebfbca..b58801b519 100644 --- a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile +++ b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile @@ -23,7 +23,7 @@ USER root COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml COPY . /code COPY --from=ghcr.io/fcp-indi/c-pac_templates:latest /cpac_templates /cpac_templates -RUN pip cache purge && pip install -e /code +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \ diff --git a/CHANGELOG.md b/CHANGELOG.md index fd5cf6a1fe..fa71fae192 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `pyproject.toml` file with `[build-system]` defined. +### Changed + +- Moved `pygraphviz` from requirements to `graphviz` optional dependencies group. + ### Fixed - A bug in which AWS S3 encryption was looked for in Nipype config instead of pipeline config (only affected uploading logs). diff --git a/CPAC/info.py b/CPAC/info.py index c9c6959996..d776ad9971 100644 --- a/CPAC/info.py +++ b/CPAC/info.py @@ -197,7 +197,6 @@ def get_cpac_gitversion(): "psutil", "PyBASC", "pybids", - "pygraphviz", "PyPEER @ https://github.com/shnizzedy/PyPEER/archive/6965d2b2bea0fef824e885fec33a8e0e6bd50a97.zip", "python-dateutil", "pyyaml", diff --git a/Dockerfile b/Dockerfile index e8f4654778..838d8dcc4b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,7 +22,7 @@ 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 +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \ diff --git a/setup.py b/setup.py index 2e37ac0ef8..17919395d2 100755 --- a/setup.py +++ b/setup.py @@ -81,6 +81,7 @@ def main(**extra_args): platforms=PLATFORMS, version=VERSION, install_requires=REQUIREMENTS, + extras_require={"graphviz": ["pygraphviz"]}, configuration=configuration, scripts=glob("scripts/*"), entry_points={"console_scripts": ["cpac = CPAC.__main__:main"]}, diff --git a/variant-ABCD-HCP.Dockerfile b/variant-ABCD-HCP.Dockerfile index 0c9eaff2ad..e1ec4a5d8c 100644 --- a/variant-ABCD-HCP.Dockerfile +++ b/variant-ABCD-HCP.Dockerfile @@ -16,7 +16,7 @@ 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 +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \ diff --git a/variant-fMRIPrep-LTS.Dockerfile b/variant-fMRIPrep-LTS.Dockerfile index 6cd146cd19..21575938e4 100644 --- a/variant-fMRIPrep-LTS.Dockerfile +++ b/variant-fMRIPrep-LTS.Dockerfile @@ -16,7 +16,7 @@ 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 +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \ diff --git a/variant-lite.Dockerfile b/variant-lite.Dockerfile index 56dcebfbca..b58801b519 100644 --- a/variant-lite.Dockerfile +++ b/variant-lite.Dockerfile @@ -23,7 +23,7 @@ USER root COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml COPY . /code COPY --from=ghcr.io/fcp-indi/c-pac_templates:latest /cpac_templates /cpac_templates -RUN pip cache purge && pip install -e /code +RUN pip cache purge && pip install -e "/code[graphviz]" # set up runscript COPY dev/docker_data /code/docker_data RUN rm -Rf /code/docker_data/checksum && \