2025-12-03T02:25:26,901 Created temporary directory: /tmp/pip-ephem-wheel-cache-3gjpsy4v 2025-12-03T02:25:26,903 Created temporary directory: /tmp/pip-build-tracker-hyq1tw09 2025-12-03T02:25:26,903 Initialized build tracking at /tmp/pip-build-tracker-hyq1tw09 2025-12-03T02:25:26,904 Created build tracker: /tmp/pip-build-tracker-hyq1tw09 2025-12-03T02:25:26,904 Entered build tracker: /tmp/pip-build-tracker-hyq1tw09 2025-12-03T02:25:26,905 Created temporary directory: /tmp/pip-wheel-0zd5r70b 2025-12-03T02:25:26,908 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 2025-12-03T02:25:26,910 Created temporary directory: /tmp/pip-ephem-wheel-cache-sssvg4sj 2025-12-03T02:25:26,931 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-12-03T02:25:26,934 2 location(s) to search for versions of cassia: 2025-12-03T02:25:26,934 * https://pypi.org/simple/cassia/ 2025-12-03T02:25:26,934 * https://www.piwheels.org/simple/cassia/ 2025-12-03T02:25:26,935 Fetching project page and analyzing links: https://pypi.org/simple/cassia/ 2025-12-03T02:25:26,936 Getting page https://pypi.org/simple/cassia/ 2025-12-03T02:25:26,937 Found index url https://pypi.org/simple 2025-12-03T02:25:27,155 Fetched page https://pypi.org/simple/cassia/ as application/vnd.pypi.simple.v1+json 2025-12-03T02:25:27,162 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/fd/14/94da6522b1364498cddd2c537019fc450393500cdc692b689297115da8ec/CASSIA-0.1-py3-none-any.whl (from https://pypi.org/simple/cassia/) 2025-12-03T02:25:27,163 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/f7/1b/6997afb5835697ec0ef343b4ad8c02d0a29f3b86e89705d36ce76f95e311/CASSIA-0.1.0-py3-none-any.whl (from https://pypi.org/simple/cassia/) 2025-12-03T02:25:27,163 Found link https://files.pythonhosted.org/packages/26/97/db8e55429eee275f757c4447b74a395a0e5c21922c4f502d93f0977ae9b2/cassia-0.1.tar.gz (from https://pypi.org/simple/cassia/), version: 0.1 2025-12-03T02:25:27,164 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/bd/f9/d0cd59dd7ce3d19c2ffb54d448002a2396640796d331474044d229129192/CASSIA-0.1.1-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,165 Found link https://files.pythonhosted.org/packages/80/fa/494a5d4035fd6e11e7d80197728297196f244c54a072cf72d65ab0345b98/cassia-0.1.1.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.1 2025-12-03T02:25:27,166 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/6f/d8/4900dc3805e66254667d349f4d51c8ac8a5342ca145785e5b9d0f80e3aa1/CASSIA-0.1.2-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,167 Found link https://files.pythonhosted.org/packages/36/6b/b9f052c0de80cfab4026b64a8c0a2042c46275aba336623484a3013233f8/cassia-0.1.2.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.2 2025-12-03T02:25:27,168 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/dd/a7/23e6df5395de019994180ba12dfda49d85702fe01d3635ccf230133a76d5/CASSIA-0.1.3-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,169 Found link https://files.pythonhosted.org/packages/30/6c/a3d59df5aba1a664d3ec3494dfabc008a35f2391b095545c6de517345699/cassia-0.1.3.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.3 2025-12-03T02:25:27,169 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/73/95/c7a43ea77725d76db542aa209815aade50c2a857c320aa49a30d9b30311b/CASSIA-0.1.4-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,170 Found link https://files.pythonhosted.org/packages/b8/ac/bfc205400bd5a1856ef48e20a56f78971cdb98f6b7681936d0a8d36c5ad9/cassia-0.1.4.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.4 2025-12-03T02:25:27,171 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/58/a5/4c80ef7639de67ddcd728825d7c0054cb0f11ae6494e3c53b83ea0dd4a8c/CASSIA-0.1.5-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,172 Found link https://files.pythonhosted.org/packages/35/92/abce78e33564190569868bfa24fa1bb57197c46a56e245c04b674849c4ad/cassia-0.1.5.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.5 2025-12-03T02:25:27,172 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/b7/da/dff3b6ffc6a6958de824b5ca680bc8d0543799343ccc4a45f2aae940941a/CASSIA-0.1.6-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,173 Found link https://files.pythonhosted.org/packages/e8/b6/f39d8bf9410a597b9ff10da7a4a8a67939aa2d33214d20db4d645a1cec44/cassia-0.1.6.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.6 2025-12-03T02:25:27,174 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/96/1f/bb55e307a91d58477954d8786da585b9b4c4952bb3024a04cfe9461b9be9/CASSIA-0.1.7-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,175 Found link https://files.pythonhosted.org/packages/33/42/7ee57e8e2f32734268e4b486e0ea072869996ea2f0736fcc8502fbe28ccf/cassia-0.1.7.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.7 2025-12-03T02:25:27,175 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/70/04/7c91cc5853ad95a37f922e401379f6b618ade43b11445eef018cfb436d56/CASSIA-0.1.8-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,176 Found link https://files.pythonhosted.org/packages/5d/16/7c43c97b5902f6fd7c1be4d726071a66cc65a2ba85880aba619f486d12a0/cassia-0.1.8.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.8 2025-12-03T02:25:27,177 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/70/da/c5c1418310e8615c77ad99119af127f3ac2bdb21d5c69725df82583ca76e/CASSIA-0.1.9-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,178 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/5a/81/dd2738b5a33767ed19eee3c6add0bc13397e7bc1144e82f045762875feee/cassia-0.1.9-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,179 Found link https://files.pythonhosted.org/packages/fa/c4/1d279642d823e5fb7816e5dc0c9cf96b7256f3cabc3422762a1c64f9d5b4/cassia-0.1.9.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.8), version: 0.1.9 2025-12-03T02:25:27,179 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/4d/89/acd0978a3887e8b2fbf2d13dbf2cae3c19e3a08d0ddb2556775382b3be6b/cassia-0.2.0-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,180 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/8c/7d/3a7f158a1eaacbc08841d040134a21f9f1fbdfe6626957b1859bd2f9ab33/cassia-0.3.1.dev5-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.9) 2025-12-03T02:25:27,181 Found link https://files.pythonhosted.org/packages/cf/72/ca0b05784b7d668e4a4db6f638a3d7755898428d4db3e16b6cb050f6b6e2/cassia-0.3.1.dev5.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.9), version: 0.3.1.dev5 2025-12-03T02:25:27,181 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/d5/49/cf25a7220924c494be409d4fedc2a0033036e2ab5969c426fb23a5d68e71/cassia-0.3.1-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.9) 2025-12-03T02:25:27,182 Found link https://files.pythonhosted.org/packages/c0/87/f4a8fc33d6d1d21317d07ca08e896e88a14f444c822bbac3156303bcc324/cassia-0.3.1.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.9), version: 0.3.1 2025-12-03T02:25:27,183 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/09/cb/15b1522b479d1d3c9b9b0974cbcda929d1b461846216e19dcb3e21bb8992/cassia-0.3.2-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.9) 2025-12-03T02:25:27,184 Found link https://files.pythonhosted.org/packages/97/a3/cf67e557f6834ff73840c487e10a9f3da2984c5547c4fe78f533a8a4d81f/cassia-0.3.2.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.9), version: 0.3.2 2025-12-03T02:25:27,185 Skipping link: No binaries permitted for cassia: https://files.pythonhosted.org/packages/20/35/030a33b1893a65a3b683a1a0392b81759aeb812d1c056135e874b3861e21/cassia-0.3.3-py3-none-any.whl (from https://pypi.org/simple/cassia/) (requires-python:>=3.9) 2025-12-03T02:25:27,185 Found link https://files.pythonhosted.org/packages/69/74/6cdb354fa394126745f6e9dbc376fc6155f7ee833c0f7a946158d9517509/cassia-0.3.3.tar.gz (from https://pypi.org/simple/cassia/) (requires-python:>=3.9), version: 0.3.3 2025-12-03T02:25:27,186 Fetching project page and analyzing links: https://www.piwheels.org/simple/cassia/ 2025-12-03T02:25:27,187 Getting page https://www.piwheels.org/simple/cassia/ 2025-12-03T02:25:27,188 Found index url https://www.piwheels.org/simple 2025-12-03T02:25:27,347 Fetched page https://www.piwheels.org/simple/cassia/ as text/html 2025-12-03T02:25:27,352 Skipping link: No binaries permitted for cassia: https://www.piwheels.org/simple/cassia/cassia-0.3.2-py3-none-any.whl#sha256=cfc4a3f0168f9bf5ff3b3e0599b3f6115003e76644a7d33ec72fb2a18418234e (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.9) 2025-12-03T02:25:27,352 Skipping link: No binaries permitted for cassia: https://www.piwheels.org/simple/cassia/cassia-0.3.1-py3-none-any.whl#sha256=23c05779907a878e9671bb268e9c289efeef9aae12d9fed32f154bab4801e7dc (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.9) 2025-12-03T02:25:27,353 Skipping link: No binaries permitted for cassia: https://www.piwheels.org/simple/cassia/cassia-0.3.1.dev5-py3-none-any.whl#sha256=a05494df3be28005ecfe1dbbf97be4915253c487124e6a21d8da527bfd0fae87 (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.9) 2025-12-03T02:25:27,354 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.9-py3-none-any.whl#sha256=4c587602b1448b8326ae2da0164231e380dafd18476e24c360e0d5feab208609 (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,354 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.8-py3-none-any.whl#sha256=cef2f4adcf97a44f0f82dd394894647453f715df43e0f5856d81585be13c751b (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,355 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.7-py3-none-any.whl#sha256=46ffccf6ecab46768cce8957600e3f5bb1acb23dbcca70881c3ab046159e76a6 (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,356 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.6-py3-none-any.whl#sha256=e677bff5ce5ec53e01b7f460be6137747a33b853bdacbb1fa3d11f02762ae789 (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,356 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.5-py3-none-any.whl#sha256=c1fa353a8507b7eca9619d54936424e38712e556ac918e547bb5404d1ad82fa3 (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,357 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.4-py3-none-any.whl#sha256=123d4ecb5c6db6bf550344141a0cdc4fc41e704b0a40f39833d42d413e0e023d (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,358 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.3-py3-none-any.whl#sha256=8199c427ae36776b6c0278e67653729e138fb30e0a7769a9d13a85457163cc56 (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,358 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.2-py3-none-any.whl#sha256=6d708d28ac90607cc607a0eef783d50c308e58d3b6033e859b1dd9b9e43e13a6 (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,358 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1.1-py3-none-any.whl#sha256=dec9df705c4c727b15a27e8e00e5e5a596dfec5a1606399d07c55f3014e3966a (from https://www.piwheels.org/simple/cassia/) (requires-python:>=3.8) 2025-12-03T02:25:27,359 Skipping link: No binaries permitted for cassia: https://archive1.piwheels.org/simple/cassia/CASSIA-0.1-py3-none-any.whl#sha256=56cd7ee82de55f6979e4830559b1b507ee28ff730829f8effcbad8a045873a5a (from https://www.piwheels.org/simple/cassia/) 2025-12-03T02:25:27,359 Skipping link: not a file: https://www.piwheels.org/simple/cassia/ 2025-12-03T02:25:27,360 Skipping link: not a file: https://pypi.org/simple/cassia/ 2025-12-03T02:25:27,382 Given no hashes to check 1 links for project 'cassia': discarding no candidates 2025-12-03T02:25:27,401 Collecting cassia==0.3.3 2025-12-03T02:25:27,403 Created temporary directory: /tmp/pip-unpack-545ptnmu 2025-12-03T02:25:27,542 Downloading cassia-0.3.3.tar.gz (1.5 MB) 2025-12-03T02:25:28,014 Added cassia==0.3.3 from https://files.pythonhosted.org/packages/69/74/6cdb354fa394126745f6e9dbc376fc6155f7ee833c0f7a946158d9517509/cassia-0.3.3.tar.gz to build tracker '/tmp/pip-build-tracker-hyq1tw09' 2025-12-03T02:25:28,016 Running setup.py (path:/tmp/pip-wheel-0zd5r70b/cassia_f77205e8cb744e178db80eb586aceeed/setup.py) egg_info for package cassia 2025-12-03T02:25:28,016 Created temporary directory: /tmp/pip-pip-egg-info-31peq3kx 2025-12-03T02:25:28,017 Preparing metadata (setup.py): started 2025-12-03T02:25:28,018 Running command python setup.py egg_info 2025-12-03T02:25:28,928 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-03T02:25:28,928 !! 2025-12-03T02:25:28,929 ******************************************************************************** 2025-12-03T02:25:28,930 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-03T02:25:28,931 License :: OSI Approved :: MIT License 2025-12-03T02:25:28,933 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-03T02:25:28,933 ******************************************************************************** 2025-12-03T02:25:28,935 !! 2025-12-03T02:25:28,935 self._finalize_license_expression() 2025-12-03T02:25:28,959 running egg_info 2025-12-03T02:25:28,986 creating /tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info 2025-12-03T02:25:28,987 writing /tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info/PKG-INFO 2025-12-03T02:25:28,991 writing dependency_links to /tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info/dependency_links.txt 2025-12-03T02:25:28,993 writing requirements to /tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info/requires.txt 2025-12-03T02:25:28,994 writing top-level names to /tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info/top_level.txt 2025-12-03T02:25:28,996 writing manifest file '/tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info/SOURCES.txt' 2025-12-03T02:25:29,103 reading manifest file '/tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info/SOURCES.txt' 2025-12-03T02:25:29,109 writing manifest file '/tmp/pip-pip-egg-info-31peq3kx/CASSIA.egg-info/SOURCES.txt' 2025-12-03T02:25:29,218 Preparing metadata (setup.py): finished with status 'done' 2025-12-03T02:25:29,222 Source in /tmp/pip-wheel-0zd5r70b/cassia_f77205e8cb744e178db80eb586aceeed has version 0.3.3, which satisfies requirement cassia==0.3.3 from https://files.pythonhosted.org/packages/69/74/6cdb354fa394126745f6e9dbc376fc6155f7ee833c0f7a946158d9517509/cassia-0.3.3.tar.gz 2025-12-03T02:25:29,223 Removed cassia==0.3.3 from https://files.pythonhosted.org/packages/69/74/6cdb354fa394126745f6e9dbc376fc6155f7ee833c0f7a946158d9517509/cassia-0.3.3.tar.gz from build tracker '/tmp/pip-build-tracker-hyq1tw09' 2025-12-03T02:25:29,228 Created temporary directory: /tmp/pip-unpack-id4cqjh5 2025-12-03T02:25:29,229 Building wheels for collected packages: cassia 2025-12-03T02:25:29,233 Created temporary directory: /tmp/pip-wheel-qo8hxenp 2025-12-03T02:25:29,234 Building wheel for cassia (setup.py): started 2025-12-03T02:25:29,235 Destination directory: /tmp/pip-wheel-qo8hxenp 2025-12-03T02:25:29,235 Running command python setup.py bdist_wheel 2025-12-03T02:25:30,060 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-03T02:25:30,061 !! 2025-12-03T02:25:30,062 ******************************************************************************** 2025-12-03T02:25:30,062 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-03T02:25:30,063 License :: OSI Approved :: MIT License 2025-12-03T02:25:30,064 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-03T02:25:30,065 ******************************************************************************** 2025-12-03T02:25:30,066 !! 2025-12-03T02:25:30,066 self._finalize_license_expression() 2025-12-03T02:25:30,067 running bdist_wheel 2025-12-03T02:25:30,196 running build 2025-12-03T02:25:30,197 running build_py 2025-12-03T02:25:30,228 creating build/lib/CASSIA 2025-12-03T02:25:30,230 copying CASSIA/LLM_evaluation_test.py -> build/lib/CASSIA 2025-12-03T02:25:30,234 copying CASSIA/LLM_evaluation_getscore.py -> build/lib/CASSIA 2025-12-03T02:25:30,236 copying CASSIA/__init__.py -> build/lib/CASSIA 2025-12-03T02:25:30,238 copying CASSIA/generate_comparison.py -> build/lib/CASSIA 2025-12-03T02:25:30,241 copying CASSIA/run_full_test.py -> build/lib/CASSIA 2025-12-03T02:25:30,242 copying CASSIA/CASSIA_python_tutorial.py -> build/lib/CASSIA 2025-12-03T02:25:30,248 creating build/lib/CASSIA/data 2025-12-03T02:25:30,249 copying CASSIA/data/__init__.py -> build/lib/CASSIA/data 2025-12-03T02:25:30,251 creating build/lib/CASSIA/reference_agent 2025-12-03T02:25:30,252 copying CASSIA/reference_agent/reference_selector.py -> build/lib/CASSIA/reference_agent 2025-12-03T02:25:30,255 copying CASSIA/reference_agent/complexity_scorer.py -> build/lib/CASSIA/reference_agent 2025-12-03T02:25:30,258 copying CASSIA/reference_agent/utils.py -> build/lib/CASSIA/reference_agent 2025-12-03T02:25:30,260 copying CASSIA/reference_agent/section_extractor.py -> build/lib/CASSIA/reference_agent 2025-12-03T02:25:30,263 copying CASSIA/reference_agent/reference_agent.py -> build/lib/CASSIA/reference_agent 2025-12-03T02:25:30,265 copying CASSIA/reference_agent/__init__.py -> build/lib/CASSIA/reference_agent 2025-12-03T02:25:30,267 creating build/lib/CASSIA/evaluation 2025-12-03T02:25:30,268 copying CASSIA/evaluation/cell_type_comparison.py -> build/lib/CASSIA/evaluation 2025-12-03T02:25:30,271 copying CASSIA/evaluation/scoring.py -> build/lib/CASSIA/evaluation 2025-12-03T02:25:30,274 copying CASSIA/evaluation/__init__.py -> build/lib/CASSIA/evaluation 2025-12-03T02:25:30,276 copying CASSIA/evaluation/LLM_evaluation.py -> build/lib/CASSIA/evaluation 2025-12-03T02:25:30,280 creating build/lib/CASSIA/engine 2025-12-03T02:25:30,281 copying CASSIA/engine/main_function_code.py -> build/lib/CASSIA/engine 2025-12-03T02:25:30,284 copying CASSIA/engine/tools_function.py -> build/lib/CASSIA/engine 2025-12-03T02:25:30,286 copying CASSIA/engine/__init__.py -> build/lib/CASSIA/engine 2025-12-03T02:25:30,288 creating build/lib/CASSIA/config 2025-12-03T02:25:30,289 copying CASSIA/config/set_api_keys.py -> build/lib/CASSIA/config 2025-12-03T02:25:30,291 copying CASSIA/config/__init__.py -> build/lib/CASSIA/config 2025-12-03T02:25:30,293 creating build/lib/CASSIA/pipeline 2025-12-03T02:25:30,294 copying CASSIA/pipeline/pipeline.py -> build/lib/CASSIA/pipeline 2025-12-03T02:25:30,296 copying CASSIA/pipeline/__init__.py -> build/lib/CASSIA/pipeline 2025-12-03T02:25:30,299 creating build/lib/CASSIA/imaging 2025-12-03T02:25:30,299 copying CASSIA/imaging/llm_image.py -> build/lib/CASSIA/imaging 2025-12-03T02:25:30,302 copying CASSIA/imaging/__init__.py -> build/lib/CASSIA/imaging 2025-12-03T02:25:30,304 creating build/lib/CASSIA/hypothesis 2025-12-03T02:25:30,305 copying CASSIA/hypothesis/hypothesis_generation.py -> build/lib/CASSIA/hypothesis 2025-12-03T02:25:30,307 copying CASSIA/hypothesis/__init__.py -> build/lib/CASSIA/hypothesis 2025-12-03T02:25:30,309 copying CASSIA/hypothesis/summarize_hypothesis_runs.py -> build/lib/CASSIA/hypothesis 2025-12-03T02:25:30,312 creating build/lib/CASSIA/core 2025-12-03T02:25:30,313 copying CASSIA/core/model_settings.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,316 copying CASSIA/core/progress_tracker.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,318 copying CASSIA/core/logging_config.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,320 copying CASSIA/core/marker_utils.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,322 copying CASSIA/core/exceptions.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,324 copying CASSIA/core/utils.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,326 copying CASSIA/core/llm_utils.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,329 copying CASSIA/core/__init__.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,330 copying CASSIA/core/validation.py -> build/lib/CASSIA/core 2025-12-03T02:25:30,334 creating build/lib/CASSIA/comparison 2025-12-03T02:25:30,335 copying CASSIA/comparison/symphony_compare.py -> build/lib/CASSIA/comparison 2025-12-03T02:25:30,338 copying CASSIA/comparison/__init__.py -> build/lib/CASSIA/comparison 2025-12-03T02:25:30,340 creating build/lib/CASSIA/reports 2025-12-03T02:25:30,341 copying CASSIA/reports/generate_reports.py -> build/lib/CASSIA/reports 2025-12-03T02:25:30,344 copying CASSIA/reports/generate_hypothesis_report.py -> build/lib/CASSIA/reports 2025-12-03T02:25:30,346 copying CASSIA/reports/__init__.py -> build/lib/CASSIA/reports 2025-12-03T02:25:30,348 copying CASSIA/reports/generate_report_uncertainty.py -> build/lib/CASSIA/reports 2025-12-03T02:25:30,351 copying CASSIA/reports/generate_batch_report.py -> build/lib/CASSIA/reports 2025-12-03T02:25:30,354 creating build/lib/CASSIA/agents 2025-12-03T02:25:30,355 copying CASSIA/agents/__init__.py -> build/lib/CASSIA/agents 2025-12-03T02:25:30,358 creating build/lib/CASSIA/agents/reference_agent 2025-12-03T02:25:30,359 copying CASSIA/agents/reference_agent/reference_selector.py -> build/lib/CASSIA/agents/reference_agent 2025-12-03T02:25:30,361 copying CASSIA/agents/reference_agent/complexity_scorer.py -> build/lib/CASSIA/agents/reference_agent 2025-12-03T02:25:30,364 copying CASSIA/agents/reference_agent/utils.py -> build/lib/CASSIA/agents/reference_agent 2025-12-03T02:25:30,366 copying CASSIA/agents/reference_agent/section_extractor.py -> build/lib/CASSIA/agents/reference_agent 2025-12-03T02:25:30,368 copying CASSIA/agents/reference_agent/reference_agent.py -> build/lib/CASSIA/agents/reference_agent 2025-12-03T02:25:30,371 copying CASSIA/agents/reference_agent/__init__.py -> build/lib/CASSIA/agents/reference_agent 2025-12-03T02:25:30,373 creating build/lib/CASSIA/agents/subclustering 2025-12-03T02:25:30,374 copying CASSIA/agents/subclustering/subclustering.py -> build/lib/CASSIA/agents/subclustering 2025-12-03T02:25:30,377 copying CASSIA/agents/subclustering/__init__.py -> build/lib/CASSIA/agents/subclustering 2025-12-03T02:25:30,379 creating build/lib/CASSIA/agents/annotation_boost 2025-12-03T02:25:30,380 copying CASSIA/agents/annotation_boost/super_annotation_boost.py -> build/lib/CASSIA/agents/annotation_boost 2025-12-03T02:25:30,385 copying CASSIA/agents/annotation_boost/annotation_boost.py -> build/lib/CASSIA/agents/annotation_boost 2025-12-03T02:25:30,390 copying CASSIA/agents/annotation_boost/__init__.py -> build/lib/CASSIA/agents/annotation_boost 2025-12-03T02:25:30,392 creating build/lib/CASSIA/agents/merging 2025-12-03T02:25:30,393 copying CASSIA/agents/merging/merging_annotation.py -> build/lib/CASSIA/agents/merging 2025-12-03T02:25:30,396 copying CASSIA/agents/merging/__init__.py -> build/lib/CASSIA/agents/merging 2025-12-03T02:25:30,398 creating build/lib/CASSIA/agents/uncertainty 2025-12-03T02:25:30,399 copying CASSIA/agents/uncertainty/Uncertainty_quantification.py -> build/lib/CASSIA/agents/uncertainty 2025-12-03T02:25:30,402 copying CASSIA/agents/uncertainty/__init__.py -> build/lib/CASSIA/agents/uncertainty 2025-12-03T02:25:30,403 running egg_info 2025-12-03T02:25:30,430 writing CASSIA.egg-info/PKG-INFO 2025-12-03T02:25:30,433 writing dependency_links to CASSIA.egg-info/dependency_links.txt 2025-12-03T02:25:30,435 writing requirements to CASSIA.egg-info/requires.txt 2025-12-03T02:25:30,436 writing top-level names to CASSIA.egg-info/top_level.txt 2025-12-03T02:25:30,480 reading manifest file 'CASSIA.egg-info/SOURCES.txt' 2025-12-03T02:25:30,493 writing manifest file 'CASSIA.egg-info/SOURCES.txt' 2025-12-03T02:25:30,503 copying CASSIA/data/subcluster_results.csv -> build/lib/CASSIA/data 2025-12-03T02:25:30,507 copying CASSIA/data/processed.csv -> build/lib/CASSIA/data 2025-12-03T02:25:30,509 copying CASSIA/data/unprocessed.csv -> build/lib/CASSIA/data 2025-12-03T02:25:30,632 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-12-03T02:25:30,633 !! 2025-12-03T02:25:30,634 ******************************************************************************** 2025-12-03T02:25:30,635 Please avoid running ``setup.py`` directly. 2025-12-03T02:25:30,636 Instead, use pypa/build, pypa/installer or other 2025-12-03T02:25:30,636 standards-based tools. 2025-12-03T02:25:30,638 This deprecation is overdue, please update your project and remove deprecated 2025-12-03T02:25:30,638 calls to avoid build errors in the future. 2025-12-03T02:25:30,639 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-12-03T02:25:30,640 ******************************************************************************** 2025-12-03T02:25:30,641 !! 2025-12-03T02:25:30,642 self.initialize_options() 2025-12-03T02:25:30,666 installing to build/bdist.linux-armv7l/wheel 2025-12-03T02:25:30,666 running install 2025-12-03T02:25:30,690 running install_lib 2025-12-03T02:25:30,718 creating build/bdist.linux-armv7l/wheel 2025-12-03T02:25:30,720 creating build/bdist.linux-armv7l/wheel/CASSIA 2025-12-03T02:25:30,722 creating build/bdist.linux-armv7l/wheel/CASSIA/data 2025-12-03T02:25:30,724 copying build/lib/CASSIA/data/subcluster_results.csv -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-03T02:25:30,729 copying build/lib/CASSIA/data/processed.csv -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-03T02:25:30,731 copying build/lib/CASSIA/data/unprocessed.csv -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-03T02:25:30,827 copying build/lib/CASSIA/data/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-03T02:25:30,829 creating build/bdist.linux-armv7l/wheel/CASSIA/reference_agent 2025-12-03T02:25:30,830 copying build/lib/CASSIA/reference_agent/reference_selector.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-03T02:25:30,833 copying build/lib/CASSIA/reference_agent/complexity_scorer.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-03T02:25:30,835 copying build/lib/CASSIA/reference_agent/utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-03T02:25:30,837 copying build/lib/CASSIA/reference_agent/section_extractor.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-03T02:25:30,840 copying build/lib/CASSIA/reference_agent/reference_agent.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-03T02:25:30,842 copying build/lib/CASSIA/reference_agent/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-03T02:25:30,844 creating build/bdist.linux-armv7l/wheel/CASSIA/evaluation 2025-12-03T02:25:30,845 copying build/lib/CASSIA/evaluation/cell_type_comparison.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-03T02:25:30,848 copying build/lib/CASSIA/evaluation/scoring.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-03T02:25:30,851 copying build/lib/CASSIA/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-03T02:25:30,852 copying build/lib/CASSIA/evaluation/LLM_evaluation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-03T02:25:30,856 creating build/bdist.linux-armv7l/wheel/CASSIA/engine 2025-12-03T02:25:30,857 copying build/lib/CASSIA/engine/main_function_code.py -> build/bdist.linux-armv7l/wheel/./CASSIA/engine 2025-12-03T02:25:30,859 copying build/lib/CASSIA/engine/tools_function.py -> build/bdist.linux-armv7l/wheel/./CASSIA/engine 2025-12-03T02:25:30,862 copying build/lib/CASSIA/engine/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/engine 2025-12-03T02:25:30,864 creating build/bdist.linux-armv7l/wheel/CASSIA/config 2025-12-03T02:25:30,866 copying build/lib/CASSIA/config/set_api_keys.py -> build/bdist.linux-armv7l/wheel/./CASSIA/config 2025-12-03T02:25:30,868 copying build/lib/CASSIA/config/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/config 2025-12-03T02:25:30,870 copying build/lib/CASSIA/LLM_evaluation_test.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-03T02:25:30,873 creating build/bdist.linux-armv7l/wheel/CASSIA/pipeline 2025-12-03T02:25:30,874 copying build/lib/CASSIA/pipeline/pipeline.py -> build/bdist.linux-armv7l/wheel/./CASSIA/pipeline 2025-12-03T02:25:30,876 copying build/lib/CASSIA/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/pipeline 2025-12-03T02:25:30,878 creating build/bdist.linux-armv7l/wheel/CASSIA/imaging 2025-12-03T02:25:30,879 copying build/lib/CASSIA/imaging/llm_image.py -> build/bdist.linux-armv7l/wheel/./CASSIA/imaging 2025-12-03T02:25:30,882 copying build/lib/CASSIA/imaging/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/imaging 2025-12-03T02:25:30,884 creating build/bdist.linux-armv7l/wheel/CASSIA/hypothesis 2025-12-03T02:25:30,885 copying build/lib/CASSIA/hypothesis/hypothesis_generation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/hypothesis 2025-12-03T02:25:30,887 copying build/lib/CASSIA/hypothesis/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/hypothesis 2025-12-03T02:25:30,889 copying build/lib/CASSIA/hypothesis/summarize_hypothesis_runs.py -> build/bdist.linux-armv7l/wheel/./CASSIA/hypothesis 2025-12-03T02:25:30,891 copying build/lib/CASSIA/LLM_evaluation_getscore.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-03T02:25:30,893 creating build/bdist.linux-armv7l/wheel/CASSIA/core 2025-12-03T02:25:30,894 copying build/lib/CASSIA/core/model_settings.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,897 copying build/lib/CASSIA/core/progress_tracker.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,899 copying build/lib/CASSIA/core/logging_config.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,901 copying build/lib/CASSIA/core/marker_utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,903 copying build/lib/CASSIA/core/exceptions.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,905 copying build/lib/CASSIA/core/utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,907 copying build/lib/CASSIA/core/llm_utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,909 copying build/lib/CASSIA/core/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,911 copying build/lib/CASSIA/core/validation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-03T02:25:30,913 copying build/lib/CASSIA/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-03T02:25:30,916 copying build/lib/CASSIA/generate_comparison.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-03T02:25:30,918 copying build/lib/CASSIA/run_full_test.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-03T02:25:30,920 creating build/bdist.linux-armv7l/wheel/CASSIA/comparison 2025-12-03T02:25:30,921 copying build/lib/CASSIA/comparison/symphony_compare.py -> build/bdist.linux-armv7l/wheel/./CASSIA/comparison 2025-12-03T02:25:30,924 copying build/lib/CASSIA/comparison/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/comparison 2025-12-03T02:25:30,926 creating build/bdist.linux-armv7l/wheel/CASSIA/reports 2025-12-03T02:25:30,927 copying build/lib/CASSIA/reports/generate_reports.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-03T02:25:30,930 copying build/lib/CASSIA/reports/generate_hypothesis_report.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-03T02:25:30,933 copying build/lib/CASSIA/reports/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-03T02:25:30,934 copying build/lib/CASSIA/reports/generate_report_uncertainty.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-03T02:25:30,937 copying build/lib/CASSIA/reports/generate_batch_report.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-03T02:25:30,941 creating build/bdist.linux-armv7l/wheel/CASSIA/agents 2025-12-03T02:25:30,942 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/reference_agent 2025-12-03T02:25:30,943 copying build/lib/CASSIA/agents/reference_agent/reference_selector.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-03T02:25:30,946 copying build/lib/CASSIA/agents/reference_agent/complexity_scorer.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-03T02:25:30,948 copying build/lib/CASSIA/agents/reference_agent/utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-03T02:25:30,951 copying build/lib/CASSIA/agents/reference_agent/section_extractor.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-03T02:25:30,953 copying build/lib/CASSIA/agents/reference_agent/reference_agent.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-03T02:25:30,955 copying build/lib/CASSIA/agents/reference_agent/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-03T02:25:30,958 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/subclustering 2025-12-03T02:25:30,959 copying build/lib/CASSIA/agents/subclustering/subclustering.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/subclustering 2025-12-03T02:25:30,961 copying build/lib/CASSIA/agents/subclustering/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/subclustering 2025-12-03T02:25:30,964 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/annotation_boost 2025-12-03T02:25:30,965 copying build/lib/CASSIA/agents/annotation_boost/super_annotation_boost.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/annotation_boost 2025-12-03T02:25:30,970 copying build/lib/CASSIA/agents/annotation_boost/annotation_boost.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/annotation_boost 2025-12-03T02:25:30,974 copying build/lib/CASSIA/agents/annotation_boost/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/annotation_boost 2025-12-03T02:25:30,977 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/merging 2025-12-03T02:25:30,978 copying build/lib/CASSIA/agents/merging/merging_annotation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/merging 2025-12-03T02:25:30,980 copying build/lib/CASSIA/agents/merging/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/merging 2025-12-03T02:25:30,982 copying build/lib/CASSIA/agents/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents 2025-12-03T02:25:30,984 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/uncertainty 2025-12-03T02:25:30,985 copying build/lib/CASSIA/agents/uncertainty/Uncertainty_quantification.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/uncertainty 2025-12-03T02:25:30,989 copying build/lib/CASSIA/agents/uncertainty/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/uncertainty 2025-12-03T02:25:30,990 copying build/lib/CASSIA/CASSIA_python_tutorial.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-03T02:25:30,996 running install_egg_info 2025-12-03T02:25:31,030 Copying CASSIA.egg-info to build/bdist.linux-armv7l/wheel/./CASSIA-0.3.3-py3.11.egg-info 2025-12-03T02:25:31,040 running install_scripts 2025-12-03T02:25:31,050 creating build/bdist.linux-armv7l/wheel/cassia-0.3.3.dist-info/WHEEL 2025-12-03T02:25:31,052 creating '/tmp/pip-wheel-qo8hxenp/cassia-0.3.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-12-03T02:25:31,064 adding 'CASSIA/CASSIA_python_tutorial.py' 2025-12-03T02:25:31,067 adding 'CASSIA/LLM_evaluation_getscore.py' 2025-12-03T02:25:31,070 adding 'CASSIA/LLM_evaluation_test.py' 2025-12-03T02:25:31,072 adding 'CASSIA/__init__.py' 2025-12-03T02:25:31,074 adding 'CASSIA/generate_comparison.py' 2025-12-03T02:25:31,076 adding 'CASSIA/run_full_test.py' 2025-12-03T02:25:31,078 adding 'CASSIA/agents/__init__.py' 2025-12-03T02:25:31,079 adding 'CASSIA/agents/annotation_boost/__init__.py' 2025-12-03T02:25:31,090 adding 'CASSIA/agents/annotation_boost/annotation_boost.py' 2025-12-03T02:25:31,103 adding 'CASSIA/agents/annotation_boost/super_annotation_boost.py' 2025-12-03T02:25:31,106 adding 'CASSIA/agents/merging/__init__.py' 2025-12-03T02:25:31,108 adding 'CASSIA/agents/merging/merging_annotation.py' 2025-12-03T02:25:31,110 adding 'CASSIA/agents/reference_agent/__init__.py' 2025-12-03T02:25:31,112 adding 'CASSIA/agents/reference_agent/complexity_scorer.py' 2025-12-03T02:25:31,114 adding 'CASSIA/agents/reference_agent/reference_agent.py' 2025-12-03T02:25:31,117 adding 'CASSIA/agents/reference_agent/reference_selector.py' 2025-12-03T02:25:31,119 adding 'CASSIA/agents/reference_agent/section_extractor.py' 2025-12-03T02:25:31,120 adding 'CASSIA/agents/reference_agent/utils.py' 2025-12-03T02:25:31,122 adding 'CASSIA/agents/subclustering/__init__.py' 2025-12-03T02:25:31,126 adding 'CASSIA/agents/subclustering/subclustering.py' 2025-12-03T02:25:31,133 adding 'CASSIA/agents/uncertainty/Uncertainty_quantification.py' 2025-12-03T02:25:31,135 adding 'CASSIA/agents/uncertainty/__init__.py' 2025-12-03T02:25:31,137 adding 'CASSIA/comparison/__init__.py' 2025-12-03T02:25:31,139 adding 'CASSIA/comparison/symphony_compare.py' 2025-12-03T02:25:31,141 adding 'CASSIA/config/__init__.py' 2025-12-03T02:25:31,142 adding 'CASSIA/config/set_api_keys.py' 2025-12-03T02:25:31,144 adding 'CASSIA/core/__init__.py' 2025-12-03T02:25:31,146 adding 'CASSIA/core/exceptions.py' 2025-12-03T02:25:31,148 adding 'CASSIA/core/llm_utils.py' 2025-12-03T02:25:31,149 adding 'CASSIA/core/logging_config.py' 2025-12-03T02:25:31,151 adding 'CASSIA/core/marker_utils.py' 2025-12-03T02:25:31,154 adding 'CASSIA/core/model_settings.py' 2025-12-03T02:25:31,155 adding 'CASSIA/core/progress_tracker.py' 2025-12-03T02:25:31,157 adding 'CASSIA/core/utils.py' 2025-12-03T02:25:31,160 adding 'CASSIA/core/validation.py' 2025-12-03T02:25:31,163 adding 'CASSIA/data/__init__.py' 2025-12-03T02:25:31,164 adding 'CASSIA/data/processed.csv' 2025-12-03T02:25:31,209 adding 'CASSIA/data/subcluster_results.csv' 2025-12-03T02:25:31,875 adding 'CASSIA/data/unprocessed.csv' 2025-12-03T02:25:31,900 adding 'CASSIA/engine/__init__.py' 2025-12-03T02:25:31,903 adding 'CASSIA/engine/main_function_code.py' 2025-12-03T02:25:31,907 adding 'CASSIA/engine/tools_function.py' 2025-12-03T02:25:31,914 adding 'CASSIA/evaluation/LLM_evaluation.py' 2025-12-03T02:25:31,916 adding 'CASSIA/evaluation/__init__.py' 2025-12-03T02:25:31,920 adding 'CASSIA/evaluation/cell_type_comparison.py' 2025-12-03T02:25:31,922 adding 'CASSIA/evaluation/scoring.py' 2025-12-03T02:25:31,924 adding 'CASSIA/hypothesis/__init__.py' 2025-12-03T02:25:31,926 adding 'CASSIA/hypothesis/hypothesis_generation.py' 2025-12-03T02:25:31,928 adding 'CASSIA/hypothesis/summarize_hypothesis_runs.py' 2025-12-03T02:25:31,929 adding 'CASSIA/imaging/__init__.py' 2025-12-03T02:25:31,931 adding 'CASSIA/imaging/llm_image.py' 2025-12-03T02:25:31,933 adding 'CASSIA/pipeline/__init__.py' 2025-12-03T02:25:31,935 adding 'CASSIA/pipeline/pipeline.py' 2025-12-03T02:25:31,937 adding 'CASSIA/reference_agent/__init__.py' 2025-12-03T02:25:31,939 adding 'CASSIA/reference_agent/complexity_scorer.py' 2025-12-03T02:25:31,942 adding 'CASSIA/reference_agent/reference_agent.py' 2025-12-03T02:25:31,944 adding 'CASSIA/reference_agent/reference_selector.py' 2025-12-03T02:25:31,946 adding 'CASSIA/reference_agent/section_extractor.py' 2025-12-03T02:25:31,947 adding 'CASSIA/reference_agent/utils.py' 2025-12-03T02:25:31,949 adding 'CASSIA/reports/__init__.py' 2025-12-03T02:25:31,954 adding 'CASSIA/reports/generate_batch_report.py' 2025-12-03T02:25:31,955 adding 'CASSIA/reports/generate_hypothesis_report.py' 2025-12-03T02:25:31,959 adding 'CASSIA/reports/generate_report_uncertainty.py' 2025-12-03T02:25:31,963 adding 'CASSIA/reports/generate_reports.py' 2025-12-03T02:25:31,965 adding 'cassia-0.3.3.dist-info/METADATA' 2025-12-03T02:25:31,966 adding 'cassia-0.3.3.dist-info/WHEEL' 2025-12-03T02:25:31,967 adding 'cassia-0.3.3.dist-info/top_level.txt' 2025-12-03T02:25:31,969 adding 'cassia-0.3.3.dist-info/RECORD' 2025-12-03T02:25:31,989 removing build/bdist.linux-armv7l/wheel 2025-12-03T02:25:32,122 Building wheel for cassia (setup.py): finished with status 'done' 2025-12-03T02:25:32,140 Created wheel for cassia: filename=cassia-0.3.3-py3-none-any.whl size=1554531 sha256=8e7163a499a36ef67a2a8582dac289c8db2919b9547f50cb58a2ec9f8fbe95f7 2025-12-03T02:25:32,141 Stored in directory: /tmp/pip-ephem-wheel-cache-sssvg4sj/wheels/f6/84/91/2ea0bdbcadcfbabc6330c79a1e85f47118196b35dd25b67868 2025-12-03T02:25:32,155 Successfully built cassia 2025-12-03T02:25:32,207 Removed build tracker: '/tmp/pip-build-tracker-hyq1tw09'