2025-12-02T01:40:13,820 Created temporary directory: /tmp/pip-ephem-wheel-cache-6uqogd8z 2025-12-02T01:40:13,822 Created temporary directory: /tmp/pip-build-tracker-8pzn80_w 2025-12-02T01:40:13,823 Initialized build tracking at /tmp/pip-build-tracker-8pzn80_w 2025-12-02T01:40:13,823 Created build tracker: /tmp/pip-build-tracker-8pzn80_w 2025-12-02T01:40:13,823 Entered build tracker: /tmp/pip-build-tracker-8pzn80_w 2025-12-02T01:40:13,824 Created temporary directory: /tmp/pip-wheel-0r6zdb_m 2025-12-02T01:40:13,827 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 2025-12-02T01:40:13,830 Created temporary directory: /tmp/pip-ephem-wheel-cache-b794w3xg 2025-12-02T01:40:13,851 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-12-02T01:40:13,855 2 location(s) to search for versions of cassia: 2025-12-02T01:40:13,855 * https://pypi.org/simple/cassia/ 2025-12-02T01:40:13,855 * https://www.piwheels.org/simple/cassia/ 2025-12-02T01:40:13,855 Fetching project page and analyzing links: https://pypi.org/simple/cassia/ 2025-12-02T01:40:13,856 Getting page https://pypi.org/simple/cassia/ 2025-12-02T01:40:13,857 Found index url https://pypi.org/simple 2025-12-02T01:40:14,075 Fetched page https://pypi.org/simple/cassia/ as application/vnd.pypi.simple.v1+json 2025-12-02T01:40:14,081 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/) 2025-12-02T01:40:14,082 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/) 2025-12-02T01:40:14,082 Found link https://files.pythonhosted.org/packages/26/97/db8e55429eee275f757c4447b74a395a0e5c21922c4f502d93f0977ae9b2/cassia-0.1.tar.gz (from https://pypi.org/simple/cassia/), version: 0.1 2025-12-02T01:40:14,083 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) 2025-12-02T01:40:14,084 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 2025-12-02T01:40:14,085 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) 2025-12-02T01:40:14,086 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 2025-12-02T01:40:14,086 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) 2025-12-02T01:40:14,087 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 2025-12-02T01:40:14,088 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) 2025-12-02T01:40:14,089 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 2025-12-02T01:40:14,090 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) 2025-12-02T01:40:14,091 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 2025-12-02T01:40:14,091 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) 2025-12-02T01:40:14,092 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 2025-12-02T01:40:14,093 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) 2025-12-02T01:40:14,093 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 2025-12-02T01:40:14,094 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) 2025-12-02T01:40:14,095 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 2025-12-02T01:40:14,095 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) 2025-12-02T01:40:14,096 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) 2025-12-02T01:40:14,097 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 2025-12-02T01:40:14,098 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) 2025-12-02T01:40:14,098 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) 2025-12-02T01:40:14,099 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 2025-12-02T01:40:14,100 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) 2025-12-02T01:40:14,101 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 2025-12-02T01:40:14,101 Fetching project page and analyzing links: https://www.piwheels.org/simple/cassia/ 2025-12-02T01:40:14,102 Getting page https://www.piwheels.org/simple/cassia/ 2025-12-02T01:40:14,103 Found index url https://www.piwheels.org/simple 2025-12-02T01:40:14,259 Fetched page https://www.piwheels.org/simple/cassia/ as text/html 2025-12-02T01:40:14,263 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) 2025-12-02T01:40:14,263 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) 2025-12-02T01:40:14,264 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) 2025-12-02T01:40:14,264 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) 2025-12-02T01:40:14,265 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) 2025-12-02T01:40:14,266 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) 2025-12-02T01:40:14,266 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) 2025-12-02T01:40:14,267 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) 2025-12-02T01:40:14,268 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) 2025-12-02T01:40:14,268 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) 2025-12-02T01:40:14,269 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/) 2025-12-02T01:40:14,269 Skipping link: not a file: https://www.piwheels.org/simple/cassia/ 2025-12-02T01:40:14,270 Skipping link: not a file: https://pypi.org/simple/cassia/ 2025-12-02T01:40:14,291 Given no hashes to check 1 links for project 'cassia': discarding no candidates 2025-12-02T01:40:14,311 Collecting cassia==0.3.1 2025-12-02T01:40:14,314 Created temporary directory: /tmp/pip-unpack-7pqosj5q 2025-12-02T01:40:14,534 Downloading cassia-0.3.1.tar.gz (1.5 MB) 2025-12-02T01:40:15,093 Added cassia==0.3.1 from https://files.pythonhosted.org/packages/c0/87/f4a8fc33d6d1d21317d07ca08e896e88a14f444c822bbac3156303bcc324/cassia-0.3.1.tar.gz to build tracker '/tmp/pip-build-tracker-8pzn80_w' 2025-12-02T01:40:15,095 Running setup.py (path:/tmp/pip-wheel-0r6zdb_m/cassia_999333c66f9943f283e83a0db98933fd/setup.py) egg_info for package cassia 2025-12-02T01:40:15,096 Created temporary directory: /tmp/pip-pip-egg-info-67avign7 2025-12-02T01:40:15,097 Preparing metadata (setup.py): started 2025-12-02T01:40:15,098 Running command python setup.py egg_info 2025-12-02T01:40:15,975 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-02T01:40:15,975 !! 2025-12-02T01:40:15,976 ******************************************************************************** 2025-12-02T01:40:15,977 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-02T01:40:15,978 License :: OSI Approved :: MIT License 2025-12-02T01:40:15,979 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-02T01:40:15,979 ******************************************************************************** 2025-12-02T01:40:15,980 !! 2025-12-02T01:40:15,981 self._finalize_license_expression() 2025-12-02T01:40:16,005 running egg_info 2025-12-02T01:40:16,032 creating /tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info 2025-12-02T01:40:16,033 writing /tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info/PKG-INFO 2025-12-02T01:40:16,037 writing dependency_links to /tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info/dependency_links.txt 2025-12-02T01:40:16,039 writing requirements to /tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info/requires.txt 2025-12-02T01:40:16,040 writing top-level names to /tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info/top_level.txt 2025-12-02T01:40:16,041 writing manifest file '/tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info/SOURCES.txt' 2025-12-02T01:40:16,146 reading manifest file '/tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info/SOURCES.txt' 2025-12-02T01:40:16,151 writing manifest file '/tmp/pip-pip-egg-info-67avign7/CASSIA.egg-info/SOURCES.txt' 2025-12-02T01:40:16,259 Preparing metadata (setup.py): finished with status 'done' 2025-12-02T01:40:16,263 Source in /tmp/pip-wheel-0r6zdb_m/cassia_999333c66f9943f283e83a0db98933fd has version 0.3.1, which satisfies requirement cassia==0.3.1 from https://files.pythonhosted.org/packages/c0/87/f4a8fc33d6d1d21317d07ca08e896e88a14f444c822bbac3156303bcc324/cassia-0.3.1.tar.gz 2025-12-02T01:40:16,264 Removed cassia==0.3.1 from https://files.pythonhosted.org/packages/c0/87/f4a8fc33d6d1d21317d07ca08e896e88a14f444c822bbac3156303bcc324/cassia-0.3.1.tar.gz from build tracker '/tmp/pip-build-tracker-8pzn80_w' 2025-12-02T01:40:16,271 Created temporary directory: /tmp/pip-unpack-61f7qw41 2025-12-02T01:40:16,271 Building wheels for collected packages: cassia 2025-12-02T01:40:16,276 Created temporary directory: /tmp/pip-wheel-7mvu_sd1 2025-12-02T01:40:16,276 Building wheel for cassia (setup.py): started 2025-12-02T01:40:16,278 Destination directory: /tmp/pip-wheel-7mvu_sd1 2025-12-02T01:40:16,278 Running command python setup.py bdist_wheel 2025-12-02T01:40:17,116 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-02T01:40:17,116 !! 2025-12-02T01:40:17,117 ******************************************************************************** 2025-12-02T01:40:17,118 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-02T01:40:17,119 License :: OSI Approved :: MIT License 2025-12-02T01:40:17,120 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-02T01:40:17,121 ******************************************************************************** 2025-12-02T01:40:17,122 !! 2025-12-02T01:40:17,122 self._finalize_license_expression() 2025-12-02T01:40:17,123 running bdist_wheel 2025-12-02T01:40:17,250 running build 2025-12-02T01:40:17,251 running build_py 2025-12-02T01:40:17,282 creating build/lib/CASSIA 2025-12-02T01:40:17,284 copying CASSIA/LLM_evaluation_test.py -> build/lib/CASSIA 2025-12-02T01:40:17,287 copying CASSIA/LLM_evaluation_getscore.py -> build/lib/CASSIA 2025-12-02T01:40:17,289 copying CASSIA/__init__.py -> build/lib/CASSIA 2025-12-02T01:40:17,291 copying CASSIA/generate_comparison.py -> build/lib/CASSIA 2025-12-02T01:40:17,294 copying CASSIA/run_full_test.py -> build/lib/CASSIA 2025-12-02T01:40:17,296 copying CASSIA/CASSIA_python_tutorial.py -> build/lib/CASSIA 2025-12-02T01:40:17,300 creating build/lib/CASSIA/data 2025-12-02T01:40:17,301 copying CASSIA/data/__init__.py -> build/lib/CASSIA/data 2025-12-02T01:40:17,304 creating build/lib/CASSIA/reference_agent 2025-12-02T01:40:17,305 copying CASSIA/reference_agent/reference_selector.py -> build/lib/CASSIA/reference_agent 2025-12-02T01:40:17,308 copying CASSIA/reference_agent/complexity_scorer.py -> build/lib/CASSIA/reference_agent 2025-12-02T01:40:17,310 copying CASSIA/reference_agent/utils.py -> build/lib/CASSIA/reference_agent 2025-12-02T01:40:17,313 copying CASSIA/reference_agent/section_extractor.py -> build/lib/CASSIA/reference_agent 2025-12-02T01:40:17,315 copying CASSIA/reference_agent/reference_agent.py -> build/lib/CASSIA/reference_agent 2025-12-02T01:40:17,318 copying CASSIA/reference_agent/__init__.py -> build/lib/CASSIA/reference_agent 2025-12-02T01:40:17,320 creating build/lib/CASSIA/evaluation 2025-12-02T01:40:17,321 copying CASSIA/evaluation/cell_type_comparison.py -> build/lib/CASSIA/evaluation 2025-12-02T01:40:17,325 copying CASSIA/evaluation/scoring.py -> build/lib/CASSIA/evaluation 2025-12-02T01:40:17,327 copying CASSIA/evaluation/__init__.py -> build/lib/CASSIA/evaluation 2025-12-02T01:40:17,329 copying CASSIA/evaluation/LLM_evaluation.py -> build/lib/CASSIA/evaluation 2025-12-02T01:40:17,333 creating build/lib/CASSIA/engine 2025-12-02T01:40:17,335 copying CASSIA/engine/main_function_code.py -> build/lib/CASSIA/engine 2025-12-02T01:40:17,338 copying CASSIA/engine/tools_function.py -> build/lib/CASSIA/engine 2025-12-02T01:40:17,341 copying CASSIA/engine/__init__.py -> build/lib/CASSIA/engine 2025-12-02T01:40:17,343 creating build/lib/CASSIA/config 2025-12-02T01:40:17,344 copying CASSIA/config/set_api_keys.py -> build/lib/CASSIA/config 2025-12-02T01:40:17,346 copying CASSIA/config/__init__.py -> build/lib/CASSIA/config 2025-12-02T01:40:17,349 creating build/lib/CASSIA/pipeline 2025-12-02T01:40:17,350 copying CASSIA/pipeline/pipeline.py -> build/lib/CASSIA/pipeline 2025-12-02T01:40:17,353 copying CASSIA/pipeline/__init__.py -> build/lib/CASSIA/pipeline 2025-12-02T01:40:17,355 creating build/lib/CASSIA/imaging 2025-12-02T01:40:17,356 copying CASSIA/imaging/llm_image.py -> build/lib/CASSIA/imaging 2025-12-02T01:40:17,359 copying CASSIA/imaging/__init__.py -> build/lib/CASSIA/imaging 2025-12-02T01:40:17,361 creating build/lib/CASSIA/hypothesis 2025-12-02T01:40:17,362 copying CASSIA/hypothesis/hypothesis_generation.py -> build/lib/CASSIA/hypothesis 2025-12-02T01:40:17,365 copying CASSIA/hypothesis/__init__.py -> build/lib/CASSIA/hypothesis 2025-12-02T01:40:17,367 copying CASSIA/hypothesis/summarize_hypothesis_runs.py -> build/lib/CASSIA/hypothesis 2025-12-02T01:40:17,370 creating build/lib/CASSIA/core 2025-12-02T01:40:17,371 copying CASSIA/core/model_settings.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,374 copying CASSIA/core/progress_tracker.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,376 copying CASSIA/core/logging_config.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,379 copying CASSIA/core/marker_utils.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,381 copying CASSIA/core/exceptions.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,383 copying CASSIA/core/utils.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,385 copying CASSIA/core/llm_utils.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,388 copying CASSIA/core/__init__.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,389 copying CASSIA/core/validation.py -> build/lib/CASSIA/core 2025-12-02T01:40:17,393 creating build/lib/CASSIA/comparison 2025-12-02T01:40:17,394 copying CASSIA/comparison/symphony_compare.py -> build/lib/CASSIA/comparison 2025-12-02T01:40:17,397 copying CASSIA/comparison/__init__.py -> build/lib/CASSIA/comparison 2025-12-02T01:40:17,399 creating build/lib/CASSIA/reports 2025-12-02T01:40:17,400 copying CASSIA/reports/generate_reports.py -> build/lib/CASSIA/reports 2025-12-02T01:40:17,403 copying CASSIA/reports/generate_hypothesis_report.py -> build/lib/CASSIA/reports 2025-12-02T01:40:17,405 copying CASSIA/reports/__init__.py -> build/lib/CASSIA/reports 2025-12-02T01:40:17,407 copying CASSIA/reports/generate_batch_report.py -> build/lib/CASSIA/reports 2025-12-02T01:40:17,411 creating build/lib/CASSIA/agents 2025-12-02T01:40:17,412 copying CASSIA/agents/__init__.py -> build/lib/CASSIA/agents 2025-12-02T01:40:17,415 creating build/lib/CASSIA/agents/reference_agent 2025-12-02T01:40:17,416 copying CASSIA/agents/reference_agent/reference_selector.py -> build/lib/CASSIA/agents/reference_agent 2025-12-02T01:40:17,418 copying CASSIA/agents/reference_agent/complexity_scorer.py -> build/lib/CASSIA/agents/reference_agent 2025-12-02T01:40:17,421 copying CASSIA/agents/reference_agent/utils.py -> build/lib/CASSIA/agents/reference_agent 2025-12-02T01:40:17,423 copying CASSIA/agents/reference_agent/section_extractor.py -> build/lib/CASSIA/agents/reference_agent 2025-12-02T01:40:17,426 copying CASSIA/agents/reference_agent/reference_agent.py -> build/lib/CASSIA/agents/reference_agent 2025-12-02T01:40:17,429 copying CASSIA/agents/reference_agent/__init__.py -> build/lib/CASSIA/agents/reference_agent 2025-12-02T01:40:17,431 creating build/lib/CASSIA/agents/subclustering 2025-12-02T01:40:17,432 copying CASSIA/agents/subclustering/subclustering.py -> build/lib/CASSIA/agents/subclustering 2025-12-02T01:40:17,435 copying CASSIA/agents/subclustering/__init__.py -> build/lib/CASSIA/agents/subclustering 2025-12-02T01:40:17,438 creating build/lib/CASSIA/agents/annotation_boost 2025-12-02T01:40:17,439 copying CASSIA/agents/annotation_boost/super_annotation_boost.py -> build/lib/CASSIA/agents/annotation_boost 2025-12-02T01:40:17,443 copying CASSIA/agents/annotation_boost/annotation_boost.py -> build/lib/CASSIA/agents/annotation_boost 2025-12-02T01:40:17,447 copying CASSIA/agents/annotation_boost/__init__.py -> build/lib/CASSIA/agents/annotation_boost 2025-12-02T01:40:17,449 creating build/lib/CASSIA/agents/merging 2025-12-02T01:40:17,451 copying CASSIA/agents/merging/merging_annotation.py -> build/lib/CASSIA/agents/merging 2025-12-02T01:40:17,453 copying CASSIA/agents/merging/__init__.py -> build/lib/CASSIA/agents/merging 2025-12-02T01:40:17,456 creating build/lib/CASSIA/agents/uncertainty 2025-12-02T01:40:17,457 copying CASSIA/agents/uncertainty/Uncertainty_quantification.py -> build/lib/CASSIA/agents/uncertainty 2025-12-02T01:40:17,460 copying CASSIA/agents/uncertainty/__init__.py -> build/lib/CASSIA/agents/uncertainty 2025-12-02T01:40:17,462 running egg_info 2025-12-02T01:40:17,490 writing CASSIA.egg-info/PKG-INFO 2025-12-02T01:40:17,493 writing dependency_links to CASSIA.egg-info/dependency_links.txt 2025-12-02T01:40:17,496 writing requirements to CASSIA.egg-info/requires.txt 2025-12-02T01:40:17,497 writing top-level names to CASSIA.egg-info/top_level.txt 2025-12-02T01:40:17,541 reading manifest file 'CASSIA.egg-info/SOURCES.txt' 2025-12-02T01:40:17,553 writing manifest file 'CASSIA.egg-info/SOURCES.txt' 2025-12-02T01:40:17,563 copying CASSIA/data/subcluster_results.csv -> build/lib/CASSIA/data 2025-12-02T01:40:17,567 copying CASSIA/data/processed.csv -> build/lib/CASSIA/data 2025-12-02T01:40:17,569 copying CASSIA/data/unprocessed.csv -> build/lib/CASSIA/data 2025-12-02T01:40:17,659 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-12-02T01:40:17,660 !! 2025-12-02T01:40:17,661 ******************************************************************************** 2025-12-02T01:40:17,661 Please avoid running ``setup.py`` directly. 2025-12-02T01:40:17,662 Instead, use pypa/build, pypa/installer or other 2025-12-02T01:40:17,662 standards-based tools. 2025-12-02T01:40:17,663 This deprecation is overdue, please update your project and remove deprecated 2025-12-02T01:40:17,664 calls to avoid build errors in the future. 2025-12-02T01:40:17,664 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-12-02T01:40:17,665 ******************************************************************************** 2025-12-02T01:40:17,666 !! 2025-12-02T01:40:17,667 self.initialize_options() 2025-12-02T01:40:17,689 installing to build/bdist.linux-armv7l/wheel 2025-12-02T01:40:17,689 running install 2025-12-02T01:40:17,713 running install_lib 2025-12-02T01:40:17,740 creating build/bdist.linux-armv7l/wheel 2025-12-02T01:40:17,743 creating build/bdist.linux-armv7l/wheel/CASSIA 2025-12-02T01:40:17,744 creating build/bdist.linux-armv7l/wheel/CASSIA/data 2025-12-02T01:40:17,745 copying build/lib/CASSIA/data/subcluster_results.csv -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-02T01:40:17,750 copying build/lib/CASSIA/data/processed.csv -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-02T01:40:17,752 copying build/lib/CASSIA/data/unprocessed.csv -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-02T01:40:17,809 copying build/lib/CASSIA/data/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/data 2025-12-02T01:40:17,812 creating build/bdist.linux-armv7l/wheel/CASSIA/reference_agent 2025-12-02T01:40:17,813 copying build/lib/CASSIA/reference_agent/reference_selector.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-02T01:40:17,815 copying build/lib/CASSIA/reference_agent/complexity_scorer.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-02T01:40:17,818 copying build/lib/CASSIA/reference_agent/utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-02T01:40:17,820 copying build/lib/CASSIA/reference_agent/section_extractor.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-02T01:40:17,823 copying build/lib/CASSIA/reference_agent/reference_agent.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-02T01:40:17,825 copying build/lib/CASSIA/reference_agent/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reference_agent 2025-12-02T01:40:17,828 creating build/bdist.linux-armv7l/wheel/CASSIA/evaluation 2025-12-02T01:40:17,829 copying build/lib/CASSIA/evaluation/cell_type_comparison.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-02T01:40:17,832 copying build/lib/CASSIA/evaluation/scoring.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-02T01:40:17,835 copying build/lib/CASSIA/evaluation/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-02T01:40:17,837 copying build/lib/CASSIA/evaluation/LLM_evaluation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/evaluation 2025-12-02T01:40:17,840 creating build/bdist.linux-armv7l/wheel/CASSIA/engine 2025-12-02T01:40:17,842 copying build/lib/CASSIA/engine/main_function_code.py -> build/bdist.linux-armv7l/wheel/./CASSIA/engine 2025-12-02T01:40:17,844 copying build/lib/CASSIA/engine/tools_function.py -> build/bdist.linux-armv7l/wheel/./CASSIA/engine 2025-12-02T01:40:17,847 copying build/lib/CASSIA/engine/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/engine 2025-12-02T01:40:17,850 creating build/bdist.linux-armv7l/wheel/CASSIA/config 2025-12-02T01:40:17,850 copying build/lib/CASSIA/config/set_api_keys.py -> build/bdist.linux-armv7l/wheel/./CASSIA/config 2025-12-02T01:40:17,852 copying build/lib/CASSIA/config/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/config 2025-12-02T01:40:17,854 copying build/lib/CASSIA/LLM_evaluation_test.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-02T01:40:17,858 creating build/bdist.linux-armv7l/wheel/CASSIA/pipeline 2025-12-02T01:40:17,859 copying build/lib/CASSIA/pipeline/pipeline.py -> build/bdist.linux-armv7l/wheel/./CASSIA/pipeline 2025-12-02T01:40:17,862 copying build/lib/CASSIA/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/pipeline 2025-12-02T01:40:17,864 creating build/bdist.linux-armv7l/wheel/CASSIA/imaging 2025-12-02T01:40:17,865 copying build/lib/CASSIA/imaging/llm_image.py -> build/bdist.linux-armv7l/wheel/./CASSIA/imaging 2025-12-02T01:40:17,867 copying build/lib/CASSIA/imaging/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/imaging 2025-12-02T01:40:17,870 creating build/bdist.linux-armv7l/wheel/CASSIA/hypothesis 2025-12-02T01:40:17,871 copying build/lib/CASSIA/hypothesis/hypothesis_generation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/hypothesis 2025-12-02T01:40:17,873 copying build/lib/CASSIA/hypothesis/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/hypothesis 2025-12-02T01:40:17,875 copying build/lib/CASSIA/hypothesis/summarize_hypothesis_runs.py -> build/bdist.linux-armv7l/wheel/./CASSIA/hypothesis 2025-12-02T01:40:17,877 copying build/lib/CASSIA/LLM_evaluation_getscore.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-02T01:40:17,880 creating build/bdist.linux-armv7l/wheel/CASSIA/core 2025-12-02T01:40:17,881 copying build/lib/CASSIA/core/model_settings.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,883 copying build/lib/CASSIA/core/progress_tracker.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,886 copying build/lib/CASSIA/core/logging_config.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,888 copying build/lib/CASSIA/core/marker_utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,890 copying build/lib/CASSIA/core/exceptions.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,892 copying build/lib/CASSIA/core/utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,894 copying build/lib/CASSIA/core/llm_utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,896 copying build/lib/CASSIA/core/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,898 copying build/lib/CASSIA/core/validation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/core 2025-12-02T01:40:17,901 copying build/lib/CASSIA/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-02T01:40:17,903 copying build/lib/CASSIA/generate_comparison.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-02T01:40:17,906 copying build/lib/CASSIA/run_full_test.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-02T01:40:17,908 creating build/bdist.linux-armv7l/wheel/CASSIA/comparison 2025-12-02T01:40:17,909 copying build/lib/CASSIA/comparison/symphony_compare.py -> build/bdist.linux-armv7l/wheel/./CASSIA/comparison 2025-12-02T01:40:17,912 copying build/lib/CASSIA/comparison/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/comparison 2025-12-02T01:40:17,914 creating build/bdist.linux-armv7l/wheel/CASSIA/reports 2025-12-02T01:40:17,915 copying build/lib/CASSIA/reports/generate_reports.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-02T01:40:17,919 copying build/lib/CASSIA/reports/generate_hypothesis_report.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-02T01:40:17,921 copying build/lib/CASSIA/reports/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-02T01:40:17,923 copying build/lib/CASSIA/reports/generate_batch_report.py -> build/bdist.linux-armv7l/wheel/./CASSIA/reports 2025-12-02T01:40:17,927 creating build/bdist.linux-armv7l/wheel/CASSIA/agents 2025-12-02T01:40:17,929 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/reference_agent 2025-12-02T01:40:17,930 copying build/lib/CASSIA/agents/reference_agent/reference_selector.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-02T01:40:17,932 copying build/lib/CASSIA/agents/reference_agent/complexity_scorer.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-02T01:40:17,935 copying build/lib/CASSIA/agents/reference_agent/utils.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-02T01:40:17,937 copying build/lib/CASSIA/agents/reference_agent/section_extractor.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-02T01:40:17,940 copying build/lib/CASSIA/agents/reference_agent/reference_agent.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-02T01:40:17,942 copying build/lib/CASSIA/agents/reference_agent/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/reference_agent 2025-12-02T01:40:17,945 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/subclustering 2025-12-02T01:40:17,946 copying build/lib/CASSIA/agents/subclustering/subclustering.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/subclustering 2025-12-02T01:40:17,949 copying build/lib/CASSIA/agents/subclustering/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/subclustering 2025-12-02T01:40:17,951 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/annotation_boost 2025-12-02T01:40:17,952 copying build/lib/CASSIA/agents/annotation_boost/super_annotation_boost.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/annotation_boost 2025-12-02T01:40:17,957 copying build/lib/CASSIA/agents/annotation_boost/annotation_boost.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/annotation_boost 2025-12-02T01:40:17,961 copying build/lib/CASSIA/agents/annotation_boost/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/annotation_boost 2025-12-02T01:40:17,964 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/merging 2025-12-02T01:40:17,965 copying build/lib/CASSIA/agents/merging/merging_annotation.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/merging 2025-12-02T01:40:17,967 copying build/lib/CASSIA/agents/merging/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/merging 2025-12-02T01:40:17,969 copying build/lib/CASSIA/agents/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents 2025-12-02T01:40:17,972 creating build/bdist.linux-armv7l/wheel/CASSIA/agents/uncertainty 2025-12-02T01:40:17,973 copying build/lib/CASSIA/agents/uncertainty/Uncertainty_quantification.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/uncertainty 2025-12-02T01:40:17,976 copying build/lib/CASSIA/agents/uncertainty/__init__.py -> build/bdist.linux-armv7l/wheel/./CASSIA/agents/uncertainty 2025-12-02T01:40:17,978 copying build/lib/CASSIA/CASSIA_python_tutorial.py -> build/bdist.linux-armv7l/wheel/./CASSIA 2025-12-02T01:40:17,982 running install_egg_info 2025-12-02T01:40:18,016 Copying CASSIA.egg-info to build/bdist.linux-armv7l/wheel/./CASSIA-0.3.1-py3.11.egg-info 2025-12-02T01:40:18,027 running install_scripts 2025-12-02T01:40:18,037 creating build/bdist.linux-armv7l/wheel/cassia-0.3.1.dist-info/WHEEL 2025-12-02T01:40:18,040 creating '/tmp/pip-wheel-7mvu_sd1/cassia-0.3.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-12-02T01:40:18,052 adding 'CASSIA/CASSIA_python_tutorial.py' 2025-12-02T01:40:18,055 adding 'CASSIA/LLM_evaluation_getscore.py' 2025-12-02T01:40:18,058 adding 'CASSIA/LLM_evaluation_test.py' 2025-12-02T01:40:18,061 adding 'CASSIA/__init__.py' 2025-12-02T01:40:18,064 adding 'CASSIA/generate_comparison.py' 2025-12-02T01:40:18,066 adding 'CASSIA/run_full_test.py' 2025-12-02T01:40:18,068 adding 'CASSIA/agents/__init__.py' 2025-12-02T01:40:18,070 adding 'CASSIA/agents/annotation_boost/__init__.py' 2025-12-02T01:40:18,081 adding 'CASSIA/agents/annotation_boost/annotation_boost.py' 2025-12-02T01:40:18,094 adding 'CASSIA/agents/annotation_boost/super_annotation_boost.py' 2025-12-02T01:40:18,097 adding 'CASSIA/agents/merging/__init__.py' 2025-12-02T01:40:18,100 adding 'CASSIA/agents/merging/merging_annotation.py' 2025-12-02T01:40:18,102 adding 'CASSIA/agents/reference_agent/__init__.py' 2025-12-02T01:40:18,105 adding 'CASSIA/agents/reference_agent/complexity_scorer.py' 2025-12-02T01:40:18,108 adding 'CASSIA/agents/reference_agent/reference_agent.py' 2025-12-02T01:40:18,110 adding 'CASSIA/agents/reference_agent/reference_selector.py' 2025-12-02T01:40:18,112 adding 'CASSIA/agents/reference_agent/section_extractor.py' 2025-12-02T01:40:18,114 adding 'CASSIA/agents/reference_agent/utils.py' 2025-12-02T01:40:18,117 adding 'CASSIA/agents/subclustering/__init__.py' 2025-12-02T01:40:18,121 adding 'CASSIA/agents/subclustering/subclustering.py' 2025-12-02T01:40:18,128 adding 'CASSIA/agents/uncertainty/Uncertainty_quantification.py' 2025-12-02T01:40:18,130 adding 'CASSIA/agents/uncertainty/__init__.py' 2025-12-02T01:40:18,133 adding 'CASSIA/comparison/__init__.py' 2025-12-02T01:40:18,136 adding 'CASSIA/comparison/symphony_compare.py' 2025-12-02T01:40:18,138 adding 'CASSIA/config/__init__.py' 2025-12-02T01:40:18,139 adding 'CASSIA/config/set_api_keys.py' 2025-12-02T01:40:18,142 adding 'CASSIA/core/__init__.py' 2025-12-02T01:40:18,143 adding 'CASSIA/core/exceptions.py' 2025-12-02T01:40:18,146 adding 'CASSIA/core/llm_utils.py' 2025-12-02T01:40:18,147 adding 'CASSIA/core/logging_config.py' 2025-12-02T01:40:18,150 adding 'CASSIA/core/marker_utils.py' 2025-12-02T01:40:18,152 adding 'CASSIA/core/model_settings.py' 2025-12-02T01:40:18,154 adding 'CASSIA/core/progress_tracker.py' 2025-12-02T01:40:18,156 adding 'CASSIA/core/utils.py' 2025-12-02T01:40:18,159 adding 'CASSIA/core/validation.py' 2025-12-02T01:40:18,161 adding 'CASSIA/data/__init__.py' 2025-12-02T01:40:18,163 adding 'CASSIA/data/processed.csv' 2025-12-02T01:40:18,193 adding 'CASSIA/data/subcluster_results.csv' 2025-12-02T01:40:18,849 adding 'CASSIA/data/unprocessed.csv' 2025-12-02T01:40:18,873 adding 'CASSIA/engine/__init__.py' 2025-12-02T01:40:18,876 adding 'CASSIA/engine/main_function_code.py' 2025-12-02T01:40:18,881 adding 'CASSIA/engine/tools_function.py' 2025-12-02T01:40:18,887 adding 'CASSIA/evaluation/LLM_evaluation.py' 2025-12-02T01:40:18,889 adding 'CASSIA/evaluation/__init__.py' 2025-12-02T01:40:18,893 adding 'CASSIA/evaluation/cell_type_comparison.py' 2025-12-02T01:40:18,896 adding 'CASSIA/evaluation/scoring.py' 2025-12-02T01:40:18,898 adding 'CASSIA/hypothesis/__init__.py' 2025-12-02T01:40:18,901 adding 'CASSIA/hypothesis/hypothesis_generation.py' 2025-12-02T01:40:18,903 adding 'CASSIA/hypothesis/summarize_hypothesis_runs.py' 2025-12-02T01:40:18,905 adding 'CASSIA/imaging/__init__.py' 2025-12-02T01:40:18,907 adding 'CASSIA/imaging/llm_image.py' 2025-12-02T01:40:18,909 adding 'CASSIA/pipeline/__init__.py' 2025-12-02T01:40:18,911 adding 'CASSIA/pipeline/pipeline.py' 2025-12-02T01:40:18,913 adding 'CASSIA/reference_agent/__init__.py' 2025-12-02T01:40:18,916 adding 'CASSIA/reference_agent/complexity_scorer.py' 2025-12-02T01:40:18,918 adding 'CASSIA/reference_agent/reference_agent.py' 2025-12-02T01:40:18,921 adding 'CASSIA/reference_agent/reference_selector.py' 2025-12-02T01:40:18,923 adding 'CASSIA/reference_agent/section_extractor.py' 2025-12-02T01:40:18,925 adding 'CASSIA/reference_agent/utils.py' 2025-12-02T01:40:18,927 adding 'CASSIA/reports/__init__.py' 2025-12-02T01:40:18,931 adding 'CASSIA/reports/generate_batch_report.py' 2025-12-02T01:40:18,933 adding 'CASSIA/reports/generate_hypothesis_report.py' 2025-12-02T01:40:18,938 adding 'CASSIA/reports/generate_reports.py' 2025-12-02T01:40:18,940 adding 'cassia-0.3.1.dist-info/METADATA' 2025-12-02T01:40:18,941 adding 'cassia-0.3.1.dist-info/WHEEL' 2025-12-02T01:40:18,942 adding 'cassia-0.3.1.dist-info/top_level.txt' 2025-12-02T01:40:18,943 adding 'cassia-0.3.1.dist-info/RECORD' 2025-12-02T01:40:19,008 removing build/bdist.linux-armv7l/wheel 2025-12-02T01:40:19,140 Building wheel for cassia (setup.py): finished with status 'done' 2025-12-02T01:40:19,183 Created wheel for cassia: filename=cassia-0.3.1-py3-none-any.whl size=1545217 sha256=23c05779907a878e9671bb268e9c289efeef9aae12d9fed32f154bab4801e7dc 2025-12-02T01:40:19,185 Stored in directory: /tmp/pip-ephem-wheel-cache-b794w3xg/wheels/3e/8b/74/415ac6243e62aba931fdb8b0b2882812714a6ceee7c084323b 2025-12-02T01:40:19,196 Successfully built cassia 2025-12-02T01:40:19,229 Removed build tracker: '/tmp/pip-build-tracker-8pzn80_w'