📦 Make graphviz optional

FCP-INDI · May 16, 2024 · 2e42754 · 2e42754
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commit 2e42754
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Showing 11 changed files with 13 additions and 9 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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 && \