2025-09-16T23:25:30,069 Created temporary directory: /tmp/pip-ephem-wheel-cache-v79qjq8u 2025-09-16T23:25:30,071 Created temporary directory: /tmp/pip-build-tracker-fe5wcsq6 2025-09-16T23:25:30,072 Initialized build tracking at /tmp/pip-build-tracker-fe5wcsq6 2025-09-16T23:25:30,072 Created build tracker: /tmp/pip-build-tracker-fe5wcsq6 2025-09-16T23:25:30,073 Entered build tracker: /tmp/pip-build-tracker-fe5wcsq6 2025-09-16T23:25:30,073 Created temporary directory: /tmp/pip-wheel-bbx9feob 2025-09-16T23:25:30,076 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2025-09-16T23:25:30,079 Created temporary directory: /tmp/pip-ephem-wheel-cache-wlaa1z5r 2025-09-16T23:25:30,102 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-16T23:25:30,106 2 location(s) to search for versions of rcsb-workflow: 2025-09-16T23:25:30,106 * https://pypi.org/simple/rcsb-workflow/ 2025-09-16T23:25:30,106 * https://www.piwheels.org/simple/rcsb-workflow/ 2025-09-16T23:25:30,107 Fetching project page and analyzing links: https://pypi.org/simple/rcsb-workflow/ 2025-09-16T23:25:30,107 Getting page https://pypi.org/simple/rcsb-workflow/ 2025-09-16T23:25:30,109 Found index url https://pypi.org/simple 2025-09-16T23:25:30,324 Fetched page https://pypi.org/simple/rcsb-workflow/ as application/vnd.pypi.simple.v1+json 2025-09-16T23:25:30,335 Skipping link: No binaries permitted for rcsb-workflow: 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2025-09-16T23:25:30,605 Given no hashes to check 1 links for project 'rcsb-workflow': discarding no candidates 2025-09-16T23:25:30,623 Collecting rcsb-workflow==0.61 2025-09-16T23:25:30,627 Created temporary directory: /tmp/pip-unpack-2mvsy8q8 2025-09-16T23:25:30,834 Downloading rcsb_workflow-0.61.tar.gz (34 kB) 2025-09-16T23:25:30,916 Added rcsb-workflow==0.61 from https://files.pythonhosted.org/packages/d0/9d/16fc2923c1f241b92672286107977c190430ab6b5c9c383c5eb884c68875/rcsb_workflow-0.61.tar.gz to build tracker '/tmp/pip-build-tracker-fe5wcsq6' 2025-09-16T23:25:30,918 Running setup.py (path:/tmp/pip-wheel-bbx9feob/rcsb-workflow_490f4e7166e545fc9a76b89f198dc373/setup.py) egg_info for package rcsb-workflow 2025-09-16T23:25:30,919 Created temporary directory: /tmp/pip-pip-egg-info-nc858rnx 2025-09-16T23:25:30,919 Preparing metadata (setup.py): started 2025-09-16T23:25:30,921 Running command python setup.py egg_info 2025-09-16T23:25:31,478 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-16T23:25:31,478 warnings.warn(msg) 2025-09-16T23:25:31,479 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-16T23:25:31,479 warnings.warn(msg) 2025-09-16T23:25:31,787 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-16T23:25:31,788 !! 2025-09-16T23:25:31,789 ******************************************************************************** 2025-09-16T23:25:31,790 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-16T23:25:31,791 License :: OSI Approved :: Apache Software License 2025-09-16T23:25:31,792 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-16T23:25:31,793 ******************************************************************************** 2025-09-16T23:25:31,794 !! 2025-09-16T23:25:31,795 self._finalize_license_expression() 2025-09-16T23:25:31,817 running egg_info 2025-09-16T23:25:31,844 creating /tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info 2025-09-16T23:25:31,845 writing /tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/PKG-INFO 2025-09-16T23:25:31,849 writing dependency_links to /tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/dependency_links.txt 2025-09-16T23:25:31,851 writing entry points to /tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/entry_points.txt 2025-09-16T23:25:31,853 writing requirements to /tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/requires.txt 2025-09-16T23:25:31,854 writing top-level names to /tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/top_level.txt 2025-09-16T23:25:31,856 writing manifest file '/tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/SOURCES.txt' 2025-09-16T23:25:31,957 reading manifest file '/tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/SOURCES.txt' 2025-09-16T23:25:31,958 reading manifest template 'MANIFEST.in' 2025-09-16T23:25:31,959 adding license file 'LICENSE' 2025-09-16T23:25:31,962 writing manifest file '/tmp/pip-pip-egg-info-nc858rnx/rcsb.workflow.egg-info/SOURCES.txt' 2025-09-16T23:25:32,066 Preparing metadata (setup.py): finished with status 'done' 2025-09-16T23:25:32,070 Source in /tmp/pip-wheel-bbx9feob/rcsb-workflow_490f4e7166e545fc9a76b89f198dc373 has version 0.61, which satisfies requirement rcsb-workflow==0.61 from https://files.pythonhosted.org/packages/d0/9d/16fc2923c1f241b92672286107977c190430ab6b5c9c383c5eb884c68875/rcsb_workflow-0.61.tar.gz 2025-09-16T23:25:32,070 Removed rcsb-workflow==0.61 from https://files.pythonhosted.org/packages/d0/9d/16fc2923c1f241b92672286107977c190430ab6b5c9c383c5eb884c68875/rcsb_workflow-0.61.tar.gz from build tracker '/tmp/pip-build-tracker-fe5wcsq6' 2025-09-16T23:25:32,075 Created temporary directory: /tmp/pip-unpack-jomkaf0a 2025-09-16T23:25:32,076 Building wheels for collected packages: rcsb-workflow 2025-09-16T23:25:32,080 Created temporary directory: /tmp/pip-wheel-b_gli0di 2025-09-16T23:25:32,080 Building wheel for rcsb-workflow (setup.py): started 2025-09-16T23:25:32,082 Destination directory: /tmp/pip-wheel-b_gli0di 2025-09-16T23:25:32,082 Running command python setup.py bdist_wheel 2025-09-16T23:25:32,614 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-16T23:25:32,615 warnings.warn(msg) 2025-09-16T23:25:32,615 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-16T23:25:32,616 warnings.warn(msg) 2025-09-16T23:25:32,909 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-16T23:25:32,909 !! 2025-09-16T23:25:32,910 ******************************************************************************** 2025-09-16T23:25:32,911 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-16T23:25:32,912 License :: OSI Approved :: Apache Software License 2025-09-16T23:25:32,914 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-16T23:25:32,914 ******************************************************************************** 2025-09-16T23:25:32,915 !! 2025-09-16T23:25:32,916 self._finalize_license_expression() 2025-09-16T23:25:32,917 running bdist_wheel 2025-09-16T23:25:32,991 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:135: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated 2025-09-16T23:25:32,992 !! 2025-09-16T23:25:32,993 ******************************************************************************** 2025-09-16T23:25:32,994 With Python 2.7 end-of-life, support for building universal wheels 2025-09-16T23:25:32,994 (i.e., wheels that support both Python 2 and Python 3) 2025-09-16T23:25:32,995 is being obviated. 2025-09-16T23:25:32,995 Please discontinue using this option, or if you still need it, 2025-09-16T23:25:32,996 file an issue with pypa/setuptools describing your use case. 2025-09-16T23:25:32,997 This deprecation is overdue, please update your project and remove deprecated 2025-09-16T23:25:32,998 calls to avoid build errors in the future. 2025-09-16T23:25:32,998 ******************************************************************************** 2025-09-16T23:25:33,000 !! 2025-09-16T23:25:33,000 self.finalize_options() 2025-09-16T23:25:33,052 running build 2025-09-16T23:25:33,053 running build_py 2025-09-16T23:25:33,082 creating build/lib/rcsb 2025-09-16T23:25:33,084 copying rcsb/__init__.py -> build/lib/rcsb 2025-09-16T23:25:33,086 creating build/lib/rcsb/workflow 2025-09-16T23:25:33,087 copying rcsb/workflow/__init__.py -> build/lib/rcsb/workflow 2025-09-16T23:25:33,090 creating build/lib/rcsb/workflow/chem 2025-09-16T23:25:33,091 copying rcsb/workflow/chem/ChemCompImageWorkflow.py -> build/lib/rcsb/workflow/chem 2025-09-16T23:25:33,094 copying rcsb/workflow/chem/ChemCompFileWorkflow.py -> build/lib/rcsb/workflow/chem 2025-09-16T23:25:33,096 copying rcsb/workflow/chem/ChemCompSearchIndexWorkflow.py -> build/lib/rcsb/workflow/chem 2025-09-16T23:25:33,098 copying rcsb/workflow/chem/__init__.py -> build/lib/rcsb/workflow/chem 2025-09-16T23:25:33,100 creating build/lib/rcsb/workflow/bcif 2025-09-16T23:25:33,101 copying rcsb/workflow/bcif/task_functions.py -> build/lib/rcsb/workflow/bcif 2025-09-16T23:25:33,103 copying rcsb/workflow/bcif/__init__.py -> build/lib/rcsb/workflow/bcif 2025-09-16T23:25:33,105 creating build/lib/rcsb/workflow/targets 2025-09-16T23:25:33,106 copying rcsb/workflow/targets/ProteinTargetSequenceWorkflow.py -> build/lib/rcsb/workflow/targets 2025-09-16T23:25:33,109 copying rcsb/workflow/targets/__init__.py -> build/lib/rcsb/workflow/targets 2025-09-16T23:25:33,111 copying rcsb/workflow/targets/ProteinTargetSequenceExecutionWorkflow.py -> build/lib/rcsb/workflow/targets 2025-09-16T23:25:33,114 creating build/lib/rcsb/workflow/wuw 2025-09-16T23:25:33,115 copying rcsb/workflow/wuw/PdbCsmImageWorkflow.py -> build/lib/rcsb/workflow/wuw 2025-09-16T23:25:33,117 copying rcsb/workflow/wuw/BcifWorkflow.py -> build/lib/rcsb/workflow/wuw 2025-09-16T23:25:33,119 copying rcsb/workflow/wuw/WuwUtils.py -> build/lib/rcsb/workflow/wuw 2025-09-16T23:25:33,121 copying rcsb/workflow/wuw/ExDbWorkflow.py -> build/lib/rcsb/workflow/wuw 2025-09-16T23:25:33,124 copying rcsb/workflow/wuw/__init__.py -> build/lib/rcsb/workflow/wuw 2025-09-16T23:25:33,126 creating build/lib/rcsb/workflow/cli 2025-09-16T23:25:33,127 copying rcsb/workflow/cli/ExDbExec.py -> build/lib/rcsb/workflow/cli 2025-09-16T23:25:33,130 copying rcsb/workflow/cli/ImgExec.py -> build/lib/rcsb/workflow/cli 2025-09-16T23:25:33,132 copying rcsb/workflow/cli/BcifExec.py -> build/lib/rcsb/workflow/cli 2025-09-16T23:25:33,134 copying rcsb/workflow/cli/__init__.py -> build/lib/rcsb/workflow/cli 2025-09-16T23:25:33,181 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-16T23:25:33,181 !! 2025-09-16T23:25:33,183 ******************************************************************************** 2025-09-16T23:25:33,183 Please avoid running ``setup.py`` directly. 2025-09-16T23:25:33,184 Instead, use pypa/build, pypa/installer or other 2025-09-16T23:25:33,184 standards-based tools. 2025-09-16T23:25:33,186 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-16T23:25:33,186 or your builds will no longer be supported. 2025-09-16T23:25:33,187 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-16T23:25:33,188 ******************************************************************************** 2025-09-16T23:25:33,189 !! 2025-09-16T23:25:33,190 self.initialize_options() 2025-09-16T23:25:33,211 installing to build/bdist.linux-armv7l/wheel 2025-09-16T23:25:33,212 running install 2025-09-16T23:25:33,235 running install_lib 2025-09-16T23:25:33,264 creating build/bdist.linux-armv7l/wheel 2025-09-16T23:25:33,266 creating build/bdist.linux-armv7l/wheel/rcsb 2025-09-16T23:25:33,267 creating build/bdist.linux-armv7l/wheel/rcsb/workflow 2025-09-16T23:25:33,269 creating build/bdist.linux-armv7l/wheel/rcsb/workflow/chem 2025-09-16T23:25:33,270 copying build/lib/rcsb/workflow/chem/ChemCompImageWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/chem 2025-09-16T23:25:33,273 copying build/lib/rcsb/workflow/chem/ChemCompFileWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/chem 2025-09-16T23:25:33,275 copying build/lib/rcsb/workflow/chem/ChemCompSearchIndexWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/chem 2025-09-16T23:25:33,277 copying build/lib/rcsb/workflow/chem/__init__.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/chem 2025-09-16T23:25:33,278 creating build/bdist.linux-armv7l/wheel/rcsb/workflow/bcif 2025-09-16T23:25:33,279 copying build/lib/rcsb/workflow/bcif/task_functions.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/bcif 2025-09-16T23:25:33,282 copying build/lib/rcsb/workflow/bcif/__init__.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/bcif 2025-09-16T23:25:33,284 creating build/bdist.linux-armv7l/wheel/rcsb/workflow/targets 2025-09-16T23:25:33,285 copying build/lib/rcsb/workflow/targets/ProteinTargetSequenceWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/targets 2025-09-16T23:25:33,288 copying build/lib/rcsb/workflow/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/targets 2025-09-16T23:25:33,289 copying build/lib/rcsb/workflow/targets/ProteinTargetSequenceExecutionWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/targets 2025-09-16T23:25:33,292 creating build/bdist.linux-armv7l/wheel/rcsb/workflow/wuw 2025-09-16T23:25:33,293 copying build/lib/rcsb/workflow/wuw/PdbCsmImageWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/wuw 2025-09-16T23:25:33,295 copying build/lib/rcsb/workflow/wuw/BcifWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/wuw 2025-09-16T23:25:33,297 copying build/lib/rcsb/workflow/wuw/WuwUtils.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/wuw 2025-09-16T23:25:33,298 copying build/lib/rcsb/workflow/wuw/ExDbWorkflow.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/wuw 2025-09-16T23:25:33,301 copying build/lib/rcsb/workflow/wuw/__init__.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/wuw 2025-09-16T23:25:33,303 creating build/bdist.linux-armv7l/wheel/rcsb/workflow/cli 2025-09-16T23:25:33,304 copying build/lib/rcsb/workflow/cli/ExDbExec.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/cli 2025-09-16T23:25:33,307 copying build/lib/rcsb/workflow/cli/ImgExec.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/cli 2025-09-16T23:25:33,308 copying build/lib/rcsb/workflow/cli/BcifExec.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/cli 2025-09-16T23:25:33,311 copying build/lib/rcsb/workflow/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow/cli 2025-09-16T23:25:33,312 copying build/lib/rcsb/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/./rcsb/workflow 2025-09-16T23:25:33,314 copying build/lib/rcsb/__init__.py -> build/bdist.linux-armv7l/wheel/./rcsb 2025-09-16T23:25:33,316 running install_egg_info 2025-09-16T23:25:33,349 running egg_info 2025-09-16T23:25:33,376 writing rcsb.workflow.egg-info/PKG-INFO 2025-09-16T23:25:33,379 writing dependency_links to rcsb.workflow.egg-info/dependency_links.txt 2025-09-16T23:25:33,381 writing entry points to rcsb.workflow.egg-info/entry_points.txt 2025-09-16T23:25:33,383 writing requirements to rcsb.workflow.egg-info/requires.txt 2025-09-16T23:25:33,385 writing top-level names to rcsb.workflow.egg-info/top_level.txt 2025-09-16T23:25:33,426 reading manifest file 'rcsb.workflow.egg-info/SOURCES.txt' 2025-09-16T23:25:33,429 reading manifest template 'MANIFEST.in' 2025-09-16T23:25:33,430 adding license file 'LICENSE' 2025-09-16T23:25:33,434 writing manifest file 'rcsb.workflow.egg-info/SOURCES.txt' 2025-09-16T23:25:33,435 Copying rcsb.workflow.egg-info to build/bdist.linux-armv7l/wheel/./rcsb.workflow-0.61-py3.11.egg-info 2025-09-16T23:25:33,447 running install_scripts 2025-09-16T23:25:33,460 creating build/bdist.linux-armv7l/wheel/rcsb_workflow-0.61.dist-info/WHEEL 2025-09-16T23:25:33,464 creating '/tmp/pip-wheel-b_gli0di/rcsb_workflow-0.61-py2.py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-16T23:25:33,466 adding 'rcsb/__init__.py' 2025-09-16T23:25:33,468 adding 'rcsb/workflow/__init__.py' 2025-09-16T23:25:33,470 adding 'rcsb/workflow/bcif/__init__.py' 2025-09-16T23:25:33,472 adding 'rcsb/workflow/bcif/task_functions.py' 2025-09-16T23:25:33,474 adding 'rcsb/workflow/chem/ChemCompFileWorkflow.py' 2025-09-16T23:25:33,476 adding 'rcsb/workflow/chem/ChemCompImageWorkflow.py' 2025-09-16T23:25:33,478 adding 'rcsb/workflow/chem/ChemCompSearchIndexWorkflow.py' 2025-09-16T23:25:33,479 adding 'rcsb/workflow/chem/__init__.py' 2025-09-16T23:25:33,481 adding 'rcsb/workflow/cli/BcifExec.py' 2025-09-16T23:25:33,483 adding 'rcsb/workflow/cli/ExDbExec.py' 2025-09-16T23:25:33,485 adding 'rcsb/workflow/cli/ImgExec.py' 2025-09-16T23:25:33,486 adding 'rcsb/workflow/cli/__init__.py' 2025-09-16T23:25:33,488 adding 'rcsb/workflow/targets/ProteinTargetSequenceExecutionWorkflow.py' 2025-09-16T23:25:33,491 adding 'rcsb/workflow/targets/ProteinTargetSequenceWorkflow.py' 2025-09-16T23:25:33,492 adding 'rcsb/workflow/targets/__init__.py' 2025-09-16T23:25:33,494 adding 'rcsb/workflow/wuw/BcifWorkflow.py' 2025-09-16T23:25:33,496 adding 'rcsb/workflow/wuw/ExDbWorkflow.py' 2025-09-16T23:25:33,498 adding 'rcsb/workflow/wuw/PdbCsmImageWorkflow.py' 2025-09-16T23:25:33,499 adding 'rcsb/workflow/wuw/WuwUtils.py' 2025-09-16T23:25:33,500 adding 'rcsb/workflow/wuw/__init__.py' 2025-09-16T23:25:33,503 adding 'rcsb_workflow-0.61.dist-info/licenses/LICENSE' 2025-09-16T23:25:33,505 adding 'rcsb_workflow-0.61.dist-info/METADATA' 2025-09-16T23:25:33,506 adding 'rcsb_workflow-0.61.dist-info/WHEEL' 2025-09-16T23:25:33,506 adding 'rcsb_workflow-0.61.dist-info/entry_points.txt' 2025-09-16T23:25:33,507 adding 'rcsb_workflow-0.61.dist-info/top_level.txt' 2025-09-16T23:25:33,508 adding 'rcsb_workflow-0.61.dist-info/RECORD' 2025-09-16T23:25:33,510 removing build/bdist.linux-armv7l/wheel 2025-09-16T23:25:33,624 Building wheel for rcsb-workflow (setup.py): finished with status 'done' 2025-09-16T23:25:33,627 Created wheel for rcsb-workflow: filename=rcsb_workflow-0.61-py2.py3-none-any.whl size=39873 sha256=29829c9ef6cee7f998a6317619a5d9de2e9487506b3dc872f7cf8bd6b758b445 2025-09-16T23:25:33,628 Stored in directory: /tmp/pip-ephem-wheel-cache-wlaa1z5r/wheels/ed/d0/c0/c3a10d52fc027ce80da5370ad9098085dd2e36d0722b43eeae 2025-09-16T23:25:33,640 Successfully built rcsb-workflow 2025-09-16T23:25:33,645 Removed build tracker: '/tmp/pip-build-tracker-fe5wcsq6'