📦️ PEP 518: Set [build-system] in pyproject.toml (#2111)

.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 && \

.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 && \

.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 && \

.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 && \

CHANGELOG.md

@@ -16,9 +16,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
+### Added
+
+- `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)
+- A bug in which AWS S3 encryption was looked for in Nipype config instead of pipeline config (only affected uploading logs).
 
 ## [1.8.7] - 2024-05-03
 

CPAC/info.py

@@ -197,8 +197,7 @@ def get_cpac_gitversion():
     "psutil",
     "PyBASC",
     "pybids",
-    "pygraphviz",
-    "PyPEER @ git+https://[email protected]/ChildMindInstitute/PyPEER.git@6965d2b2bea0fef824e885fec33a8e0e6bd50a97#egg=PyPEER",
+    "PyPEER @ https://github.com/shnizzedy/PyPEER/archive/6965d2b2bea0fef824e885fec33a8e0e6bd50a97.zip",
     "python-dateutil",
     "pyyaml",
     "scikit-learn",

CPAC/utils/versioning/dependencies.py

@@ -56,7 +56,7 @@ def cli_version(
     with Popen(command, stdout=PIPE, stderr=STDOUT, shell=True) as _command:
         _version = _command.stdout.read().decode("utf-8")
         _command_poll = _command.poll()
-        if _command_poll is None or int(_command_poll) == 127:
+        if _command_poll is None or int(_command_poll) == 127:  # noqa: PLR2004
             # handle missing command
             return {}
     if formatting is not None:
@@ -80,19 +80,23 @@ def last_line(stdout: str) -> str:
     return stdout
 
 
-def _version_sort(_version_item):
+def _version_sort(_version_item) -> str:
     """Key to report by case-insensitive dependecy name."""
     return _version_item[0].lower()
 
 
-PYTHON_PACKAGES = dict(
-    sorted(
-        {
-            getattr(d, "name", d.metadata["Name"]): d.version
-            for d in list(distributions())
-        }.items(),
-        key=_version_sort,
+def sorted_versions(versions: dict) -> dict:
+    """Sort versions by case-insensitive names."""
+    return dict(
+        sorted(
+            ((name, version) for name, version in versions.items() if name),
+            key=_version_sort,
+        )
     )
+
+
+PYTHON_PACKAGES = sorted_versions(
+    {getattr(d, "name", d.metadata["Name"]): d.version for d in list(distributions())}
 )
 
 
@@ -130,18 +134,16 @@ def requirements() -> dict:
     return reqs
 
 
-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("}"),
-            ),
-        }.items(),
-        key=_version_sort,
-    )
+REPORTED = sorted_versions(
+    {
+        **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("}"),
+        ),
+    }
 )
+
 REQUIREMENTS = requirements()

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 && \

dev/docker_data/unpinned_requirements.txt

@@ -20,7 +20,7 @@ prov
 psutil
 PyBASC
 pybids
-PyPEER @ git+https://git@github.com/ChildMindInstitute/PyPEER.git@6965d2b2bea0fef824e885fec33a8e0e6bd50a97
+PyPEER @ https://github.com/shnizzedy/PyPEER/archive/6965d2b2bea0fef824e885fec33a8e0e6bd50a97.zip
 python-dateutil
 PyYAML
 requests

pyproject.toml

@@ -0,0 +1,19 @@
+# Copyright (C) 2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+[build-system]
+requires = ["nipype", "numpy", "pyyaml", "setuptools", "voluptuous"]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -27,7 +27,7 @@ prov==2.0.0
 psutil==5.9.5
 PyBASC==0.6.1
 pybids==0.15.6
-PyPEER @ git+https://git@github.com/ChildMindInstitute/PyPEER.git@6965d2b2bea0fef824e885fec33a8e0e6bd50a97
+PyPEER @ https://github.com/shnizzedy/PyPEER/archive/6965d2b2bea0fef824e885fec33a8e0e6bd50a97.zip
 python-dateutil==2.8.2
 PyYAML==6.0
 requests==2.31.0

setup.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2022  C-PAC Developers
+# Copyright (C) 2022-2024  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -43,9 +43,12 @@ def configuration(parent_package="", top_path=None):
 
 def main(**extra_args):
     from glob import glob
+    import sys
 
     from numpy.distutils.core import setup
 
+    # prepend this file's parent directory to sys.path to find CPAC when building
+    sys.path.insert(0, os.path.abspath(os.path.dirname(__file__)))
     from CPAC.info import (
         AUTHOR,
         AUTHOR_EMAIL,
@@ -78,6 +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"]},

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 && \

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 && \

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 && \