2025-08-31T02:16:47,514 Created temporary directory: /tmp/pip-build-tracker-mau2s3xf 2025-08-31T02:16:47,515 Initialized build tracking at /tmp/pip-build-tracker-mau2s3xf 2025-08-31T02:16:47,516 Created build tracker: /tmp/pip-build-tracker-mau2s3xf 2025-08-31T02:16:47,516 Entered build tracker: /tmp/pip-build-tracker-mau2s3xf 2025-08-31T02:16:47,517 Created temporary directory: /tmp/pip-wheel-r0d706jz 2025-08-31T02:16:47,521 Created temporary directory: /tmp/pip-ephem-wheel-cache-mjd6wm9q 2025-08-31T02:16:47,568 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-08-31T02:16:47,570 2 location(s) to search for versions of biodisco: 2025-08-31T02:16:47,570 * https://pypi.org/simple/biodisco/ 2025-08-31T02:16:47,570 * https://www.piwheels.org/simple/biodisco/ 2025-08-31T02:16:47,571 Fetching project page and analyzing links: https://pypi.org/simple/biodisco/ 2025-08-31T02:16:47,572 Getting page https://pypi.org/simple/biodisco/ 2025-08-31T02:16:47,573 Found index url https://pypi.org/simple/ 2025-08-31T02:16:47,853 Fetched page https://pypi.org/simple/biodisco/ as application/vnd.pypi.simple.v1+json 2025-08-31T02:16:47,854 Skipping link: No binaries permitted for biodisco: https://files.pythonhosted.org/packages/cb/60/fbe131f40c6d65d83eda4451d1720cd9ebadb7ee02cf3720ce6a3702f153/biodisco-0.1.0-py3-none-any.whl (from https://pypi.org/simple/biodisco/) (requires-python:>=3.11) 2025-08-31T02:16:47,855 Found link https://files.pythonhosted.org/packages/0e/26/64cb58d6af1dbe3d70d2aebf14986d792e7a5ab113e9e8e8c59b19f7534f/biodisco-0.1.0.tar.gz (from https://pypi.org/simple/biodisco/) (requires-python:>=3.11), version: 0.1.0 2025-08-31T02:16:47,856 Fetching project page and analyzing links: https://www.piwheels.org/simple/biodisco/ 2025-08-31T02:16:47,857 Getting page https://www.piwheels.org/simple/biodisco/ 2025-08-31T02:16:47,858 Found index url https://www.piwheels.org/simple/ 2025-08-31T02:16:48,022 Fetched page https://www.piwheels.org/simple/biodisco/ as text/html 2025-08-31T02:16:48,023 Skipping link: not a file: https://www.piwheels.org/simple/biodisco/ 2025-08-31T02:16:48,024 Skipping link: not a file: https://pypi.org/simple/biodisco/ 2025-08-31T02:16:48,041 Given no hashes to check 1 links for project 'biodisco': discarding no candidates 2025-08-31T02:16:48,043 Collecting biodisco==0.1.0 2025-08-31T02:16:48,045 Created temporary directory: /tmp/pip-unpack-cv0wxkfu 2025-08-31T02:16:48,269 Downloading biodisco-0.1.0.tar.gz (32 kB) 2025-08-31T02:16:48,479 Added biodisco==0.1.0 from https://files.pythonhosted.org/packages/0e/26/64cb58d6af1dbe3d70d2aebf14986d792e7a5ab113e9e8e8c59b19f7534f/biodisco-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-mau2s3xf' 2025-08-31T02:16:48,481 Running setup.py (path:/tmp/pip-wheel-r0d706jz/biodisco_7ad4bc65420342ce836020cead877853/setup.py) egg_info for package biodisco 2025-08-31T02:16:48,482 Created temporary directory: /tmp/pip-pip-egg-info-xm54u_o_ 2025-08-31T02:16:48,483 Preparing metadata (setup.py): started 2025-08-31T02:16:48,485 Running command python setup.py egg_info 2025-08-31T02:16:49,338 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T02:16:49,338 !! 2025-08-31T02:16:49,340 ******************************************************************************** 2025-08-31T02:16:49,340 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T02:16:49,341 License :: OSI Approved :: MIT License 2025-08-31T02:16:49,342 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T02:16:49,343 ******************************************************************************** 2025-08-31T02:16:49,344 !! 2025-08-31T02:16:49,345 self._finalize_license_expression() 2025-08-31T02:16:49,367 running egg_info 2025-08-31T02:16:49,393 creating /tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info 2025-08-31T02:16:49,394 writing /tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info/PKG-INFO 2025-08-31T02:16:49,398 writing dependency_links to /tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info/dependency_links.txt 2025-08-31T02:16:49,400 writing requirements to /tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info/requires.txt 2025-08-31T02:16:49,401 writing top-level names to /tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info/top_level.txt 2025-08-31T02:16:49,402 writing manifest file '/tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info/SOURCES.txt' 2025-08-31T02:16:49,486 reading manifest file '/tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info/SOURCES.txt' 2025-08-31T02:16:49,488 reading manifest template 'MANIFEST.in' 2025-08-31T02:16:49,496 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-08-31T02:16:49,497 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-08-31T02:16:49,498 warning: no previously-included files found matching '.gitignore' 2025-08-31T02:16:49,498 warning: no previously-included files found matching '.git*' 2025-08-31T02:16:49,499 adding license file 'LICENSE' 2025-08-31T02:16:49,501 writing manifest file '/tmp/pip-pip-egg-info-xm54u_o_/biodisco.egg-info/SOURCES.txt' 2025-08-31T02:16:49,605 Preparing metadata (setup.py): finished with status 'done' 2025-08-31T02:16:49,610 Source in /tmp/pip-wheel-r0d706jz/biodisco_7ad4bc65420342ce836020cead877853 has version 0.1.0, which satisfies requirement biodisco==0.1.0 from https://files.pythonhosted.org/packages/0e/26/64cb58d6af1dbe3d70d2aebf14986d792e7a5ab113e9e8e8c59b19f7534f/biodisco-0.1.0.tar.gz 2025-08-31T02:16:49,611 Removed biodisco==0.1.0 from https://files.pythonhosted.org/packages/0e/26/64cb58d6af1dbe3d70d2aebf14986d792e7a5ab113e9e8e8c59b19f7534f/biodisco-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-mau2s3xf' 2025-08-31T02:16:49,619 Created temporary directory: /tmp/pip-unpack-to_c7vss 2025-08-31T02:16:49,620 Created temporary directory: /tmp/pip-unpack-wxn2lf3d 2025-08-31T02:16:49,621 Building wheels for collected packages: biodisco 2025-08-31T02:16:49,625 Created temporary directory: /tmp/pip-wheel-0zatsqjk 2025-08-31T02:16:49,626 DEPRECATION: Building 'biodisco' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'biodisco'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-08-31T02:16:49,627 Building wheel for biodisco (setup.py): started 2025-08-31T02:16:49,628 Destination directory: /tmp/pip-wheel-0zatsqjk 2025-08-31T02:16:49,629 Running command python setup.py bdist_wheel 2025-08-31T02:16:50,443 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T02:16:50,444 !! 2025-08-31T02:16:50,445 ******************************************************************************** 2025-08-31T02:16:50,445 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T02:16:50,447 License :: OSI Approved :: MIT License 2025-08-31T02:16:50,448 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T02:16:50,448 ******************************************************************************** 2025-08-31T02:16:50,450 !! 2025-08-31T02:16:50,450 self._finalize_license_expression() 2025-08-31T02:16:50,451 running bdist_wheel 2025-08-31T02:16:50,576 running build 2025-08-31T02:16:50,577 running build_py 2025-08-31T02:16:50,606 creating build/lib/BioDisco 2025-08-31T02:16:50,608 copying BioDisco/agents_evidence.py -> build/lib/BioDisco 2025-08-31T02:16:50,611 copying BioDisco/agents_auto_background.py -> build/lib/BioDisco 2025-08-31T02:16:50,614 copying BioDisco/__init__.py -> build/lib/BioDisco 2025-08-31T02:16:50,616 creating build/lib/BioDisco/utils 2025-08-31T02:16:50,617 copying BioDisco/utils/log_utils.py -> build/lib/BioDisco/utils 2025-08-31T02:16:50,619 copying BioDisco/utils/llm_config.py -> build/lib/BioDisco/utils 2025-08-31T02:16:50,621 copying BioDisco/utils/pubmed_query.py -> build/lib/BioDisco/utils 2025-08-31T02:16:50,623 copying BioDisco/utils/libraries.py -> build/lib/BioDisco/utils 2025-08-31T02:16:50,626 copying BioDisco/utils/__init__.py -> build/lib/BioDisco/utils 2025-08-31T02:16:50,627 copying BioDisco/utils/neo4j_query.py -> build/lib/BioDisco/utils 2025-08-31T02:16:50,631 running egg_info 2025-08-31T02:16:50,658 writing biodisco.egg-info/PKG-INFO 2025-08-31T02:16:50,661 writing dependency_links to biodisco.egg-info/dependency_links.txt 2025-08-31T02:16:50,663 writing requirements to biodisco.egg-info/requires.txt 2025-08-31T02:16:50,664 writing top-level names to biodisco.egg-info/top_level.txt 2025-08-31T02:16:50,694 reading manifest file 'biodisco.egg-info/SOURCES.txt' 2025-08-31T02:16:50,696 reading manifest template 'MANIFEST.in' 2025-08-31T02:16:50,705 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-08-31T02:16:50,706 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-08-31T02:16:50,707 warning: no previously-included files found matching '.gitignore' 2025-08-31T02:16:50,707 warning: no previously-included files found matching '.git*' 2025-08-31T02:16:50,708 adding license file 'LICENSE' 2025-08-31T02:16:50,711 writing manifest file 'biodisco.egg-info/SOURCES.txt' 2025-08-31T02:16:50,740 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-08-31T02:16:50,741 !! 2025-08-31T02:16:50,742 ******************************************************************************** 2025-08-31T02:16:50,743 Please avoid running ``setup.py`` directly. 2025-08-31T02:16:50,744 Instead, use pypa/build, pypa/installer or other 2025-08-31T02:16:50,744 standards-based tools. 2025-08-31T02:16:50,745 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-08-31T02:16:50,746 or your builds will no longer be supported. 2025-08-31T02:16:50,747 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-08-31T02:16:50,748 ******************************************************************************** 2025-08-31T02:16:50,749 !! 2025-08-31T02:16:50,750 self.initialize_options() 2025-08-31T02:16:50,769 installing to build/bdist.linux-armv7l/wheel 2025-08-31T02:16:50,770 running install 2025-08-31T02:16:50,792 running install_lib 2025-08-31T02:16:50,819 creating build/bdist.linux-armv7l/wheel 2025-08-31T02:16:50,821 creating build/bdist.linux-armv7l/wheel/BioDisco 2025-08-31T02:16:50,823 creating build/bdist.linux-armv7l/wheel/BioDisco/utils 2025-08-31T02:16:50,824 copying build/lib/BioDisco/utils/log_utils.py -> build/bdist.linux-armv7l/wheel/./BioDisco/utils 2025-08-31T02:16:50,826 copying build/lib/BioDisco/utils/llm_config.py -> build/bdist.linux-armv7l/wheel/./BioDisco/utils 2025-08-31T02:16:50,828 copying build/lib/BioDisco/utils/pubmed_query.py -> build/bdist.linux-armv7l/wheel/./BioDisco/utils 2025-08-31T02:16:50,830 copying build/lib/BioDisco/utils/libraries.py -> build/bdist.linux-armv7l/wheel/./BioDisco/utils 2025-08-31T02:16:50,833 copying build/lib/BioDisco/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./BioDisco/utils 2025-08-31T02:16:50,835 copying build/lib/BioDisco/utils/neo4j_query.py -> build/bdist.linux-armv7l/wheel/./BioDisco/utils 2025-08-31T02:16:50,837 copying build/lib/BioDisco/agents_evidence.py -> build/bdist.linux-armv7l/wheel/./BioDisco 2025-08-31T02:16:50,840 copying build/lib/BioDisco/agents_auto_background.py -> build/bdist.linux-armv7l/wheel/./BioDisco 2025-08-31T02:16:50,843 copying build/lib/BioDisco/__init__.py -> build/bdist.linux-armv7l/wheel/./BioDisco 2025-08-31T02:16:50,844 running install_egg_info 2025-08-31T02:16:50,877 Copying biodisco.egg-info to build/bdist.linux-armv7l/wheel/./biodisco-0.1.0-py3.11.egg-info 2025-08-31T02:16:50,888 running install_scripts 2025-08-31T02:16:50,900 creating build/bdist.linux-armv7l/wheel/biodisco-0.1.0.dist-info/WHEEL 2025-08-31T02:16:50,903 creating '/tmp/pip-wheel-0zatsqjk/biodisco-0.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-08-31T02:16:50,905 adding 'BioDisco/__init__.py' 2025-08-31T02:16:50,907 adding 'BioDisco/agents_auto_background.py' 2025-08-31T02:16:50,912 adding 'BioDisco/agents_evidence.py' 2025-08-31T02:16:50,914 adding 'BioDisco/utils/__init__.py' 2025-08-31T02:16:50,916 adding 'BioDisco/utils/libraries.py' 2025-08-31T02:16:50,917 adding 'BioDisco/utils/llm_config.py' 2025-08-31T02:16:50,918 adding 'BioDisco/utils/log_utils.py' 2025-08-31T02:16:50,921 adding 'BioDisco/utils/neo4j_query.py' 2025-08-31T02:16:50,923 adding 'BioDisco/utils/pubmed_query.py' 2025-08-31T02:16:50,926 adding 'biodisco-0.1.0.dist-info/licenses/LICENSE' 2025-08-31T02:16:50,927 adding 'biodisco-0.1.0.dist-info/METADATA' 2025-08-31T02:16:50,928 adding 'biodisco-0.1.0.dist-info/WHEEL' 2025-08-31T02:16:50,929 adding 'biodisco-0.1.0.dist-info/top_level.txt' 2025-08-31T02:16:50,930 adding 'biodisco-0.1.0.dist-info/RECORD' 2025-08-31T02:16:50,932 removing build/bdist.linux-armv7l/wheel 2025-08-31T02:16:51,045 Building wheel for biodisco (setup.py): finished with status 'done' 2025-08-31T02:16:51,048 Created wheel for biodisco: filename=biodisco-0.1.0-py3-none-any.whl size=34214 sha256=b292747f00ac31e86e9ae4281cceff364a6d1ab17f79c66dad5a606c66d2d028 2025-08-31T02:16:51,049 Stored in directory: /tmp/pip-ephem-wheel-cache-mjd6wm9q/wheels/84/76/a4/4c029d9f7c4023119bc01b5dca8b487b24cb0cebe386fc7695 2025-08-31T02:16:51,062 Successfully built biodisco 2025-08-31T02:16:51,066 Removed build tracker: '/tmp/pip-build-tracker-mau2s3xf'