2025-12-11T07:29:07,927 Created temporary directory: /tmp/pip-ephem-wheel-cache-kywbfcig
2025-12-11T07:29:07,929 Created temporary directory: /tmp/pip-build-tracker-8s7eioai
2025-12-11T07:29:07,929 Initialized build tracking at /tmp/pip-build-tracker-8s7eioai
2025-12-11T07:29:07,930 Created build tracker: /tmp/pip-build-tracker-8s7eioai
2025-12-11T07:29:07,930 Entered build tracker: /tmp/pip-build-tracker-8s7eioai
2025-12-11T07:29:07,931 Created temporary directory: /tmp/pip-wheel-_1ido393
2025-12-11T07:29:07,934 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
2025-12-11T07:29:07,936 Created temporary directory: /tmp/pip-ephem-wheel-cache-iq1befe8
2025-12-11T07:29:07,958 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-12-11T07:29:07,962 2 location(s) to search for versions of ragbio:
2025-12-11T07:29:07,962 * https://pypi.org/simple/ragbio/
2025-12-11T07:29:07,962 * https://www.piwheels.org/simple/ragbio/
2025-12-11T07:29:07,962 Fetching project page and analyzing links: https://pypi.org/simple/ragbio/
2025-12-11T07:29:07,963 Getting page https://pypi.org/simple/ragbio/
2025-12-11T07:29:07,965 Found index url https://pypi.org/simple
2025-12-11T07:29:08,178 Fetched page https://pypi.org/simple/ragbio/ as application/vnd.pypi.simple.v1+json
2025-12-11T07:29:08,179   Skipping link: No binaries permitted for ragbio: https://files.pythonhosted.org/packages/49/ef/b76938c77f3c7b1ea66f2f25e49ae4b169e1f8050de61183a14e6ac4d4fe/ragbio-0.1.12-py3-none-any.whl (from https://pypi.org/simple/ragbio/) (requires-python:>=3.9)
2025-12-11T07:29:08,180   Found link https://files.pythonhosted.org/packages/34/53/62f7f4e6ea6e004f8ef0bcfe3006736331f55847fa6dea5ab395b84f1663/ragbio-0.1.12.tar.gz (from https://pypi.org/simple/ragbio/) (requires-python:>=3.9), version: 0.1.12
2025-12-11T07:29:08,181   Skipping link: No binaries permitted for ragbio: https://files.pythonhosted.org/packages/dc/24/2258809d9b74a8ca4f242fff2e0710b7bf4931298e52997448b7aa979848/ragbio-0.1.13-py3-none-any.whl (from https://pypi.org/simple/ragbio/) (requires-python:>=3.9)
2025-12-11T07:29:08,182   Found link https://files.pythonhosted.org/packages/88/6a/2ec5f1bd89c003be226c58beb02fac2d381fbf82e0431448569082feccf9/ragbio-0.1.13.tar.gz (from https://pypi.org/simple/ragbio/) (requires-python:>=3.9), version: 0.1.13
2025-12-11T07:29:08,183 Fetching project page and analyzing links: https://www.piwheels.org/simple/ragbio/
2025-12-11T07:29:08,184 Getting page https://www.piwheels.org/simple/ragbio/
2025-12-11T07:29:08,185 Found index url https://www.piwheels.org/simple
2025-12-11T07:29:08,338 Fetched page https://www.piwheels.org/simple/ragbio/ as text/html
2025-12-11T07:29:08,340   Skipping link: No binaries permitted for ragbio: https://www.piwheels.org/simple/ragbio/ragbio-0.1.12-py3-none-any.whl#sha256=1342160fe2f337fa22045a27acec4b081fa922939b65d47324ece873fd3618be (from https://www.piwheels.org/simple/ragbio/) (requires-python:>=3.9)
2025-12-11T07:29:08,341 Skipping link: not a file: https://www.piwheels.org/simple/ragbio/
2025-12-11T07:29:08,341 Skipping link: not a file: https://pypi.org/simple/ragbio/
2025-12-11T07:29:08,360 Given no hashes to check 1 links for project 'ragbio': discarding no candidates
2025-12-11T07:29:08,378 Collecting ragbio==0.1.13
2025-12-11T07:29:08,381   Created temporary directory: /tmp/pip-unpack-7qlj0fg0
2025-12-11T07:29:08,594   Downloading ragbio-0.1.13.tar.gz (314 kB)
2025-12-11T07:29:08,753   Added ragbio==0.1.13 from https://files.pythonhosted.org/packages/88/6a/2ec5f1bd89c003be226c58beb02fac2d381fbf82e0431448569082feccf9/ragbio-0.1.13.tar.gz to build tracker '/tmp/pip-build-tracker-8s7eioai'
2025-12-11T07:29:08,758   Created temporary directory: /tmp/pip-build-env-vk8fjmj2
2025-12-11T07:29:08,762   Installing build dependencies: started
2025-12-11T07:29:08,764   Running command pip subprocess to install build dependencies
2025-12-11T07:29:09,937   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2025-12-11T07:29:10,570   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
2025-12-11T07:29:10,594   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-12-11T07:29:12,323   Collecting setuptools>=61.0
2025-12-11T07:29:12,420     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2025-12-11T07:29:12,696   Collecting wheel
2025-12-11T07:29:12,713     Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB)
2025-12-11T07:29:15,588   Installing collected packages: wheel, setuptools
2025-12-11T07:29:15,837     Creating /tmp/pip-build-env-vk8fjmj2/overlay/local/bin
2025-12-11T07:29:15,839     changing mode of /tmp/pip-build-env-vk8fjmj2/overlay/local/bin/wheel to 755
2025-12-11T07:29:19,549   Successfully installed setuptools-80.9.0 wheel-0.45.1
2025-12-11T07:29:19,825   Installing build dependencies: finished with status 'done'
2025-12-11T07:29:19,831   Getting requirements to build wheel: started
2025-12-11T07:29:19,832   Running command Getting requirements to build wheel
2025-12-11T07:29:20,441   /tmp/pip-build-env-vk8fjmj2/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-12-11T07:29:20,442   !!

2025-12-11T07:29:20,443           ********************************************************************************
2025-12-11T07:29:20,444           Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

2025-12-11T07:29:20,445           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-12-11T07:29:20,445           or your builds will no longer be supported.

2025-12-11T07:29:20,447           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-12-11T07:29:20,448           ********************************************************************************

2025-12-11T07:29:20,449   !!
2025-12-11T07:29:20,450     corresp(dist, value, root_dir)
2025-12-11T07:29:20,538   running egg_info
2025-12-11T07:29:20,545   writing ragbio.egg-info/PKG-INFO
2025-12-11T07:29:20,549   writing dependency_links to ragbio.egg-info/dependency_links.txt
2025-12-11T07:29:20,551   writing requirements to ragbio.egg-info/requires.txt
2025-12-11T07:29:20,552   writing top-level names to ragbio.egg-info/top_level.txt
2025-12-11T07:29:20,580   reading manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T07:29:20,583   reading manifest template 'MANIFEST.in'
2025-12-11T07:29:20,585   adding license file 'LICENSE'
2025-12-11T07:29:20,588   writing manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T07:29:20,685   Getting requirements to build wheel: finished with status 'done'
2025-12-11T07:29:20,689   Created temporary directory: /tmp/pip-modern-metadata-cva2izu2
2025-12-11T07:29:20,692   Preparing metadata (pyproject.toml): started
2025-12-11T07:29:20,693   Running command Preparing metadata (pyproject.toml)
2025-12-11T07:29:21,260   /tmp/pip-build-env-vk8fjmj2/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-12-11T07:29:21,260   !!

2025-12-11T07:29:21,261           ********************************************************************************
2025-12-11T07:29:21,262           Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

2025-12-11T07:29:21,263           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-12-11T07:29:21,263           or your builds will no longer be supported.

2025-12-11T07:29:21,264           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-12-11T07:29:21,265           ********************************************************************************

2025-12-11T07:29:21,266   !!
2025-12-11T07:29:21,266     corresp(dist, value, root_dir)
2025-12-11T07:29:21,353   running dist_info
2025-12-11T07:29:21,365   creating /tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info
2025-12-11T07:29:21,366   writing /tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info/PKG-INFO
2025-12-11T07:29:21,370   writing dependency_links to /tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info/dependency_links.txt
2025-12-11T07:29:21,372   writing requirements to /tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info/requires.txt
2025-12-11T07:29:21,373   writing top-level names to /tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info/top_level.txt
2025-12-11T07:29:21,374   writing manifest file '/tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info/SOURCES.txt'
2025-12-11T07:29:21,399   reading manifest file '/tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info/SOURCES.txt'
2025-12-11T07:29:21,401   reading manifest template 'MANIFEST.in'
2025-12-11T07:29:21,403   adding license file 'LICENSE'
2025-12-11T07:29:21,406   writing manifest file '/tmp/pip-modern-metadata-cva2izu2/ragbio.egg-info/SOURCES.txt'
2025-12-11T07:29:21,407   creating '/tmp/pip-modern-metadata-cva2izu2/ragbio-0.1.13.dist-info'
2025-12-11T07:29:21,530   Preparing metadata (pyproject.toml): finished with status 'done'
2025-12-11T07:29:21,535   Source in /tmp/pip-wheel-_1ido393/ragbio_efb5f01cd3a54c238cc29ec484a728c8 has version 0.1.13, which satisfies requirement ragbio==0.1.13 from https://files.pythonhosted.org/packages/88/6a/2ec5f1bd89c003be226c58beb02fac2d381fbf82e0431448569082feccf9/ragbio-0.1.13.tar.gz
2025-12-11T07:29:21,536   Removed ragbio==0.1.13 from https://files.pythonhosted.org/packages/88/6a/2ec5f1bd89c003be226c58beb02fac2d381fbf82e0431448569082feccf9/ragbio-0.1.13.tar.gz from build tracker '/tmp/pip-build-tracker-8s7eioai'
2025-12-11T07:29:21,541 Created temporary directory: /tmp/pip-unpack-sywfs8vv
2025-12-11T07:29:21,542 Building wheels for collected packages: ragbio
2025-12-11T07:29:21,547   Created temporary directory: /tmp/pip-wheel-wiqknadi
2025-12-11T07:29:21,547   Destination directory: /tmp/pip-wheel-wiqknadi
2025-12-11T07:29:21,549   Building wheel for ragbio (pyproject.toml): started
2025-12-11T07:29:21,551   Running command Building wheel for ragbio (pyproject.toml)
2025-12-11T07:29:22,093   /tmp/pip-build-env-vk8fjmj2/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-12-11T07:29:22,093   !!

2025-12-11T07:29:22,094           ********************************************************************************
2025-12-11T07:29:22,095           Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

2025-12-11T07:29:22,096           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-12-11T07:29:22,096           or your builds will no longer be supported.

2025-12-11T07:29:22,098           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-12-11T07:29:22,098           ********************************************************************************

2025-12-11T07:29:22,099   !!
2025-12-11T07:29:22,100     corresp(dist, value, root_dir)
2025-12-11T07:29:22,173   running bdist_wheel
2025-12-11T07:29:22,195   running build
2025-12-11T07:29:22,196   running build_py
2025-12-11T07:29:22,203   creating build/lib/ragbio
2025-12-11T07:29:22,205   copying ragbio/config.py -> build/lib/ragbio
2025-12-11T07:29:22,207   copying ragbio/__init__.py -> build/lib/ragbio
2025-12-11T07:29:22,210   creating build/lib/ragbio/utils
2025-12-11T07:29:22,211   copying ragbio/utils/update_config.py -> build/lib/ragbio/utils
2025-12-11T07:29:22,213   copying ragbio/utils/delete_neo4j_graph.py -> build/lib/ragbio/utils
2025-12-11T07:29:22,215   copying ragbio/utils/__init__.py -> build/lib/ragbio/utils
2025-12-11T07:29:22,216   copying ragbio/utils/rag_data_loader.py -> build/lib/ragbio/utils
2025-12-11T07:29:22,219   creating build/lib/ragbio/knowledge_graph
2025-12-11T07:29:22,220   copying ragbio/knowledge_graph/structured_drug_kg.py -> build/lib/ragbio/knowledge_graph
2025-12-11T07:29:22,224   creating build/lib/ragbio/embeddings
2025-12-11T07:29:22,225   copying ragbio/embeddings/embedding_engine.py -> build/lib/ragbio/embeddings
2025-12-11T07:29:22,227   copying ragbio/embeddings/__init__.py -> build/lib/ragbio/embeddings
2025-12-11T07:29:22,229   creating build/lib/ragbio/pipeline
2025-12-11T07:29:22,231   copying ragbio/pipeline/rag_neo4j_visualization.py -> build/lib/ragbio/pipeline
2025-12-11T07:29:22,234   copying ragbio/pipeline/rag_cytoscape_streamlit.py -> build/lib/ragbio/pipeline
2025-12-11T07:29:22,236   copying ragbio/pipeline/rag_pipeline.py -> build/lib/ragbio/pipeline
2025-12-11T07:29:22,238   running egg_info
2025-12-11T07:29:22,249   writing ragbio.egg-info/PKG-INFO
2025-12-11T07:29:22,252   writing dependency_links to ragbio.egg-info/dependency_links.txt
2025-12-11T07:29:22,254   writing requirements to ragbio.egg-info/requires.txt
2025-12-11T07:29:22,255   writing top-level names to ragbio.egg-info/top_level.txt
2025-12-11T07:29:22,270   reading manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T07:29:22,273   reading manifest template 'MANIFEST.in'
2025-12-11T07:29:22,275   adding license file 'LICENSE'
2025-12-11T07:29:22,279   writing manifest file 'ragbio.egg-info/SOURCES.txt'
2025-12-11T07:29:22,284   creating build/lib/ragbio/images
2025-12-11T07:29:22,285   copying ragbio/images/network_graph.png -> build/lib/ragbio/images
2025-12-11T07:29:22,306   installing to build/bdist.linux-armv7l/wheel
2025-12-11T07:29:22,307   running install
2025-12-11T07:29:22,331   running install_lib
2025-12-11T07:29:22,338   creating build/bdist.linux-armv7l/wheel
2025-12-11T07:29:22,340   creating build/bdist.linux-armv7l/wheel/ragbio
2025-12-11T07:29:22,342   creating build/bdist.linux-armv7l/wheel/ragbio/utils
2025-12-11T07:29:22,344   copying build/lib/ragbio/utils/update_config.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T07:29:22,346   copying build/lib/ragbio/utils/delete_neo4j_graph.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T07:29:22,348   copying build/lib/ragbio/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T07:29:22,350   copying build/lib/ragbio/utils/rag_data_loader.py -> build/bdist.linux-armv7l/wheel/./ragbio/utils
2025-12-11T07:29:22,353   creating build/bdist.linux-armv7l/wheel/ragbio/knowledge_graph
2025-12-11T07:29:22,355   copying build/lib/ragbio/knowledge_graph/structured_drug_kg.py -> build/bdist.linux-armv7l/wheel/./ragbio/knowledge_graph
2025-12-11T07:29:22,358   creating build/bdist.linux-armv7l/wheel/ragbio/images
2025-12-11T07:29:22,359   copying build/lib/ragbio/images/network_graph.png -> build/bdist.linux-armv7l/wheel/./ragbio/images
2025-12-11T07:29:22,366   copying build/lib/ragbio/config.py -> build/bdist.linux-armv7l/wheel/./ragbio
2025-12-11T07:29:22,368   copying build/lib/ragbio/__init__.py -> build/bdist.linux-armv7l/wheel/./ragbio
2025-12-11T07:29:22,370   creating build/bdist.linux-armv7l/wheel/ragbio/embeddings
2025-12-11T07:29:22,371   copying build/lib/ragbio/embeddings/embedding_engine.py -> build/bdist.linux-armv7l/wheel/./ragbio/embeddings
2025-12-11T07:29:22,374   copying build/lib/ragbio/embeddings/__init__.py -> build/bdist.linux-armv7l/wheel/./ragbio/embeddings
2025-12-11T07:29:22,376   creating build/bdist.linux-armv7l/wheel/ragbio/pipeline
2025-12-11T07:29:22,377   copying build/lib/ragbio/pipeline/rag_neo4j_visualization.py -> build/bdist.linux-armv7l/wheel/./ragbio/pipeline
2025-12-11T07:29:22,379   copying build/lib/ragbio/pipeline/rag_cytoscape_streamlit.py -> build/bdist.linux-armv7l/wheel/./ragbio/pipeline
2025-12-11T07:29:22,381   copying build/lib/ragbio/pipeline/rag_pipeline.py -> build/bdist.linux-armv7l/wheel/./ragbio/pipeline
2025-12-11T07:29:22,384   running install_egg_info
2025-12-11T07:29:22,389   Copying ragbio.egg-info to build/bdist.linux-armv7l/wheel/./ragbio-0.1.13-py3.11.egg-info
2025-12-11T07:29:22,400   running install_scripts
2025-12-11T07:29:22,410   creating build/bdist.linux-armv7l/wheel/ragbio-0.1.13.dist-info/WHEEL
2025-12-11T07:29:22,412   creating '/tmp/pip-wheel-wiqknadi/.tmp-5g8fx40z/ragbio-0.1.13-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-12-11T07:29:22,415   adding 'ragbio/__init__.py'
2025-12-11T07:29:22,416   adding 'ragbio/config.py'
2025-12-11T07:29:22,418   adding 'ragbio/embeddings/__init__.py'
2025-12-11T07:29:22,420   adding 'ragbio/embeddings/embedding_engine.py'
2025-12-11T07:29:22,453   adding 'ragbio/images/network_graph.png'
2025-12-11T07:29:22,457   adding 'ragbio/knowledge_graph/structured_drug_kg.py'
2025-12-11T07:29:22,459   adding 'ragbio/pipeline/rag_cytoscape_streamlit.py'
2025-12-11T07:29:22,461   adding 'ragbio/pipeline/rag_neo4j_visualization.py'
2025-12-11T07:29:22,463   adding 'ragbio/pipeline/rag_pipeline.py'
2025-12-11T07:29:22,465   adding 'ragbio/utils/__init__.py'
2025-12-11T07:29:22,466   adding 'ragbio/utils/delete_neo4j_graph.py'
2025-12-11T07:29:22,468   adding 'ragbio/utils/rag_data_loader.py'
2025-12-11T07:29:22,469   adding 'ragbio/utils/update_config.py'
2025-12-11T07:29:22,472   adding 'ragbio-0.1.13.dist-info/licenses/LICENSE'
2025-12-11T07:29:22,473   adding 'ragbio-0.1.13.dist-info/METADATA'
2025-12-11T07:29:22,474   adding 'ragbio-0.1.13.dist-info/WHEEL'
2025-12-11T07:29:22,474   adding 'ragbio-0.1.13.dist-info/top_level.txt'
2025-12-11T07:29:22,475   adding 'ragbio-0.1.13.dist-info/RECORD'
2025-12-11T07:29:22,480   removing build/bdist.linux-armv7l/wheel
2025-12-11T07:29:22,585   Building wheel for ragbio (pyproject.toml): finished with status 'done'
2025-12-11T07:29:22,598   Created wheel for ragbio: filename=ragbio-0.1.13-py3-none-any.whl size=312770 sha256=912866e12d366e61f3649d8b9072c4b60371a424bb5c6890f10ca07a27263b17
2025-12-11T07:29:22,599   Stored in directory: /tmp/pip-ephem-wheel-cache-iq1befe8/wheels/6c/c2/33/beb15ff7d88fe498c2e626ec10f7b71341c91791e9e7e1da52
2025-12-11T07:29:22,610 Successfully built ragbio
2025-12-11T07:29:22,625 Removed build tracker: '/tmp/pip-build-tracker-8s7eioai'