2026-02-08T21:10:09,928 Created temporary directory: /tmp/pip-ephem-wheel-cache-x7nqcrt_ 2026-02-08T21:10:09,930 Created temporary directory: /tmp/pip-build-tracker-ddx89aq8 2026-02-08T21:10:09,930 Initialized build tracking at /tmp/pip-build-tracker-ddx89aq8 2026-02-08T21:10:09,931 Created build tracker: /tmp/pip-build-tracker-ddx89aq8 2026-02-08T21:10:09,931 Entered build tracker: /tmp/pip-build-tracker-ddx89aq8 2026-02-08T21:10:09,932 Created temporary directory: /tmp/pip-wheel-faxk2ppq 2026-02-08T21:10:09,935 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 2026-02-08T21:10:09,937 Created temporary directory: /tmp/pip-ephem-wheel-cache-db3tck14 2026-02-08T21:10:09,961 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-08T21:10:09,965 2 location(s) to search for versions of aoptk: 2026-02-08T21:10:09,965 * https://pypi.org/simple/aoptk/ 2026-02-08T21:10:09,965 * https://www.piwheels.org/simple/aoptk/ 2026-02-08T21:10:09,966 Fetching project page and analyzing links: https://pypi.org/simple/aoptk/ 2026-02-08T21:10:09,967 Getting page https://pypi.org/simple/aoptk/ 2026-02-08T21:10:09,968 Found index url https://pypi.org/simple 2026-02-08T21:10:10,182 Fetched page https://pypi.org/simple/aoptk/ as application/vnd.pypi.simple.v1+json 2026-02-08T21:10:10,186 Skipping link: No binaries permitted for aoptk: https://files.pythonhosted.org/packages/4b/d6/384d5602117668d9368aaf2151a9b9eef9040cad1af0597c4a61a431dc32/aoptk-0.1.0-py3-none-any.whl (from https://pypi.org/simple/aoptk/) (requires-python:>=3.8) 2026-02-08T21:10:10,187 Found link https://files.pythonhosted.org/packages/3c/0b/6ee2e5619ce9230307113c992ace76e126a0afe211e6cff0114e5e21c555/aoptk-0.1.0.tar.gz (from https://pypi.org/simple/aoptk/) (requires-python:>=3.8), version: 0.1.0 2026-02-08T21:10:10,188 Skipping link: No binaries permitted for aoptk: https://files.pythonhosted.org/packages/39/08/e2621f4b2faf8e16aab6437af0245042fa1f56eb9e6d5b8a3497b0e4a42f/aoptk-0.1.1-py3-none-any.whl (from https://pypi.org/simple/aoptk/) (requires-python:>=3.8) 2026-02-08T21:10:10,189 Found link https://files.pythonhosted.org/packages/21/59/05f875bd1dd4c4edac306e1e85fc6c589b2fa00f94693287fd2249007416/aoptk-0.1.1.tar.gz (from https://pypi.org/simple/aoptk/) (requires-python:>=3.8), version: 0.1.1 2026-02-08T21:10:10,190 Skipping link: No binaries permitted for aoptk: https://files.pythonhosted.org/packages/25/8a/cc74e1935468567e709e4d0b0775fae7c7999f4d550d202554f26fc8807c/aoptk-0.1.3-py3-none-any.whl (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-08T21:10:10,191 Found link https://files.pythonhosted.org/packages/ab/ba/59d070d1e9e68886157fe9815f4808d34629cf444027b99cc6e37ff50fed/aoptk-0.1.3.tar.gz (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10), version: 0.1.3 2026-02-08T21:10:10,192 Skipping link: No binaries permitted for aoptk: https://files.pythonhosted.org/packages/09/18/831de8fac3196d62e7bcc5f701d724a681903a24f8f2f69ad527ac00b7e3/aoptk-0.1.4-py3-none-any.whl (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-08T21:10:10,193 Found link https://files.pythonhosted.org/packages/97/5c/d4ee4004b70af67a4020e8960783876dac154a7440079530302dd88e93b8/aoptk-0.1.4.tar.gz (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10), version: 0.1.4 2026-02-08T21:10:10,193 Skipping link: No binaries permitted for aoptk: https://files.pythonhosted.org/packages/08/a1/30a6bec86f370bdfa443cac60c93c5d03014808c364a2854ed0c2a5b91a9/aoptk-0.1.5-py3-none-any.whl (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-08T21:10:10,194 Found link https://files.pythonhosted.org/packages/a3/75/34369baf9135531f36e392c6ad20f1f9954e0b1fb7988f513bb84704507d/aoptk-0.1.5.tar.gz (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10), version: 0.1.5 2026-02-08T21:10:10,195 Skipping link: No binaries permitted for aoptk: https://files.pythonhosted.org/packages/66/ed/b715ba2c6486fcbb10cbceaca45f2230b1330c5be19054afb704e8ccfadf/aoptk-0.1.6-py3-none-any.whl (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-08T21:10:10,196 Found link https://files.pythonhosted.org/packages/af/6a/a9593e3f2c2eeaaded381d65b77318caffde8f5a48d71a89bad93264fa60/aoptk-0.1.6.tar.gz (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10), version: 0.1.6 2026-02-08T21:10:10,197 Skipping link: No binaries permitted for aoptk: https://files.pythonhosted.org/packages/db/eb/cb6f29cfaa33e3b014a5a30fa04bb03949c0d67cf7a93ecdcfc1b6fed0c6/aoptk-0.2.0-py3-none-any.whl (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-08T21:10:10,198 Found link https://files.pythonhosted.org/packages/ae/42/125a9d1b24aa3905e135286d1d915015175a4813e16f7319679083a7fe42/aoptk-0.2.0.tar.gz (from https://pypi.org/simple/aoptk/) (requires-python:>=3.10), version: 0.2.0 2026-02-08T21:10:10,198 Fetching project page and analyzing links: https://www.piwheels.org/simple/aoptk/ 2026-02-08T21:10:10,199 Getting page https://www.piwheels.org/simple/aoptk/ 2026-02-08T21:10:10,200 Found index url https://www.piwheels.org/simple 2026-02-08T21:10:10,353 Fetched page https://www.piwheels.org/simple/aoptk/ as text/html 2026-02-08T21:10:10,355 Skipping link: No binaries permitted for aoptk: https://www.piwheels.org/simple/aoptk/aoptk-0.1.1-py3-none-any.whl#sha256=7985d9a26e118e074b99d4d1e744a5096f4fb94be10bf74b56cf5b6aa116705a (from https://www.piwheels.org/simple/aoptk/) (requires-python:>=3.8) 2026-02-08T21:10:10,356 Skipping link: No binaries permitted for aoptk: https://www.piwheels.org/simple/aoptk/aoptk-0.1.0-py3-none-any.whl#sha256=198d0fc25eadbf1d18fa9ad643921c7ef552f7e75b1184be0690a45dfbf94086 (from https://www.piwheels.org/simple/aoptk/) (requires-python:>=3.8) 2026-02-08T21:10:10,356 Skipping link: not a file: https://www.piwheels.org/simple/aoptk/ 2026-02-08T21:10:10,357 Skipping link: not a file: https://pypi.org/simple/aoptk/ 2026-02-08T21:10:10,377 Given no hashes to check 1 links for project 'aoptk': discarding no candidates 2026-02-08T21:10:10,395 Collecting aoptk==0.1.3 2026-02-08T21:10:10,397 Created temporary directory: /tmp/pip-unpack-jo8shjbj 2026-02-08T21:10:10,531 Downloading aoptk-0.1.3.tar.gz (167 kB) 2026-02-08T21:10:10,801 Added aoptk==0.1.3 from https://files.pythonhosted.org/packages/ab/ba/59d070d1e9e68886157fe9815f4808d34629cf444027b99cc6e37ff50fed/aoptk-0.1.3.tar.gz to build tracker '/tmp/pip-build-tracker-ddx89aq8' 2026-02-08T21:10:10,810 Created temporary directory: /tmp/pip-build-env-9c0kot1e 2026-02-08T21:10:10,814 Installing build dependencies: started 2026-02-08T21:10:10,816 Running command pip subprocess to install build dependencies 2026-02-08T21:10:12,165 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-08T21:10:12,734 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 2026-02-08T21:10:12,757 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-08T21:10:14,484 Collecting setuptools>=64.0.0 2026-02-08T21:10:14,504 Using cached setuptools-82.0.0-py3-none-any.whl (1.0 MB) 2026-02-08T21:10:14,883 Collecting setuptools-scm 2026-02-08T21:10:14,900 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-9.2.2-py3-none-any.whl (62 kB) 2026-02-08T21:10:15,156 Collecting wheel 2026-02-08T21:10:15,161 Using cached wheel-0.46.3-py3-none-any.whl (30 kB) 2026-02-08T21:10:15,353 Collecting packaging>=20 2026-02-08T21:10:15,359 Using cached packaging-26.0-py3-none-any.whl (74 kB) 2026-02-08T21:10:18,399 Installing collected packages: setuptools, packaging, wheel, setuptools-scm 2026-02-08T21:10:21,716 Creating /tmp/pip-build-env-9c0kot1e/overlay/local/bin 2026-02-08T21:10:21,718 changing mode of /tmp/pip-build-env-9c0kot1e/overlay/local/bin/wheel to 755 2026-02-08T21:10:21,969 changing mode of /tmp/pip-build-env-9c0kot1e/overlay/local/bin/setuptools-scm to 755 2026-02-08T21:10:21,998 Successfully installed packaging-26.0 setuptools-82.0.0 setuptools-scm-9.2.2 wheel-0.46.3 2026-02-08T21:10:22,299 Installing build dependencies: finished with status 'done' 2026-02-08T21:10:22,305 Getting requirements to build wheel: started 2026-02-08T21:10:22,306 Running command Getting requirements to build wheel 2026-02-08T21:10:22,931 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2026-02-08T21:10:22,967 /tmp/pip-build-env-9c0kot1e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-08T21:10:22,967 !! 2026-02-08T21:10:22,968 ******************************************************************************** 2026-02-08T21:10:22,969 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-08T21:10:22,970 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-08T21:10:22,970 or your builds will no longer be supported. 2026-02-08T21:10:22,971 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T21:10:22,972 ******************************************************************************** 2026-02-08T21:10:22,973 !! 2026-02-08T21:10:22,974 corresp(dist, value, root_dir) 2026-02-08T21:10:23,069 running egg_info 2026-02-08T21:10:23,077 writing src/aoptk.egg-info/PKG-INFO 2026-02-08T21:10:23,084 writing dependency_links to src/aoptk.egg-info/dependency_links.txt 2026-02-08T21:10:23,086 writing entry points to src/aoptk.egg-info/entry_points.txt 2026-02-08T21:10:23,089 writing requirements to src/aoptk.egg-info/requires.txt 2026-02-08T21:10:23,091 writing top-level names to src/aoptk.egg-info/top_level.txt 2026-02-08T21:10:23,145 listing git files failed - pretending there aren't any 2026-02-08T21:10:23,152 reading manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-08T21:10:23,161 reading manifest template 'MANIFEST.in' 2026-02-08T21:10:23,163 warning: no files found matching 'NOTICE' 2026-02-08T21:10:23,164 adding license file 'LICENSE' 2026-02-08T21:10:23,170 writing manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-08T21:10:23,274 Getting requirements to build wheel: finished with status 'done' 2026-02-08T21:10:23,278 Created temporary directory: /tmp/pip-modern-metadata-v5v510sc 2026-02-08T21:10:23,280 Preparing metadata (pyproject.toml): started 2026-02-08T21:10:23,281 Running command Preparing metadata (pyproject.toml) 2026-02-08T21:10:23,870 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2026-02-08T21:10:23,903 /tmp/pip-build-env-9c0kot1e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-08T21:10:23,904 !! 2026-02-08T21:10:23,905 ******************************************************************************** 2026-02-08T21:10:23,906 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-08T21:10:23,907 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-08T21:10:23,908 or your builds will no longer be supported. 2026-02-08T21:10:23,909 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T21:10:23,909 ******************************************************************************** 2026-02-08T21:10:23,910 !! 2026-02-08T21:10:23,911 corresp(dist, value, root_dir) 2026-02-08T21:10:23,997 running dist_info 2026-02-08T21:10:24,010 creating /tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info 2026-02-08T21:10:24,010 writing /tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/PKG-INFO 2026-02-08T21:10:24,018 writing dependency_links to /tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/dependency_links.txt 2026-02-08T21:10:24,020 writing entry points to /tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/entry_points.txt 2026-02-08T21:10:24,023 writing requirements to /tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/requires.txt 2026-02-08T21:10:24,024 writing top-level names to /tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/top_level.txt 2026-02-08T21:10:24,025 writing manifest file '/tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/SOURCES.txt' 2026-02-08T21:10:24,075 listing git files failed - pretending there aren't any 2026-02-08T21:10:24,082 reading manifest file '/tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/SOURCES.txt' 2026-02-08T21:10:24,084 reading manifest template 'MANIFEST.in' 2026-02-08T21:10:24,084 warning: no files found matching 'NOTICE' 2026-02-08T21:10:24,085 adding license file 'LICENSE' 2026-02-08T21:10:24,090 writing manifest file '/tmp/pip-modern-metadata-v5v510sc/aoptk.egg-info/SOURCES.txt' 2026-02-08T21:10:24,091 creating '/tmp/pip-modern-metadata-v5v510sc/aoptk-0.1.3.dist-info' 2026-02-08T21:10:24,226 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-08T21:10:24,231 Source in /tmp/pip-wheel-faxk2ppq/aoptk_2f7c5370e05449ca9eaa61255db7a030 has version 0.1.3, which satisfies requirement aoptk==0.1.3 from https://files.pythonhosted.org/packages/ab/ba/59d070d1e9e68886157fe9815f4808d34629cf444027b99cc6e37ff50fed/aoptk-0.1.3.tar.gz 2026-02-08T21:10:24,232 Removed aoptk==0.1.3 from https://files.pythonhosted.org/packages/ab/ba/59d070d1e9e68886157fe9815f4808d34629cf444027b99cc6e37ff50fed/aoptk-0.1.3.tar.gz from build tracker '/tmp/pip-build-tracker-ddx89aq8' 2026-02-08T21:10:24,238 Created temporary directory: /tmp/pip-unpack-hvhsp2ix 2026-02-08T21:10:24,239 Building wheels for collected packages: aoptk 2026-02-08T21:10:24,244 Created temporary directory: /tmp/pip-wheel-ws8gb351 2026-02-08T21:10:24,245 Destination directory: /tmp/pip-wheel-ws8gb351 2026-02-08T21:10:24,247 Building wheel for aoptk (pyproject.toml): started 2026-02-08T21:10:24,249 Running command Building wheel for aoptk (pyproject.toml) 2026-02-08T21:10:24,818 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2026-02-08T21:10:24,851 /tmp/pip-build-env-9c0kot1e/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-08T21:10:24,851 !! 2026-02-08T21:10:24,853 ******************************************************************************** 2026-02-08T21:10:24,853 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-08T21:10:24,854 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-08T21:10:24,855 or your builds will no longer be supported. 2026-02-08T21:10:24,856 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T21:10:24,857 ******************************************************************************** 2026-02-08T21:10:24,858 !! 2026-02-08T21:10:24,859 corresp(dist, value, root_dir) 2026-02-08T21:10:24,932 running bdist_wheel 2026-02-08T21:10:24,955 running build 2026-02-08T21:10:24,955 running build_py 2026-02-08T21:10:24,962 creating build/lib/aoptk 2026-02-08T21:10:24,964 copying src/aoptk/sentence_generator.py -> build/lib/aoptk 2026-02-08T21:10:24,966 copying src/aoptk/sentence.py -> build/lib/aoptk 2026-02-08T21:10:24,968 copying src/aoptk/__init__.py -> build/lib/aoptk 2026-02-08T21:10:24,970 copying src/aoptk/spacy_processor.py -> build/lib/aoptk 2026-02-08T21:10:24,972 copying src/aoptk/effect.py -> build/lib/aoptk 2026-02-08T21:10:24,974 copying src/aoptk/chemical.py -> build/lib/aoptk 2026-02-08T21:10:24,976 copying src/aoptk/regex_sentence_generator.py -> build/lib/aoptk 2026-02-08T21:10:24,978 copying src/aoptk/find_chemical.py -> build/lib/aoptk 2026-02-08T21:10:24,980 creating build/lib/aoptk/normalization 2026-02-08T21:10:24,981 copying src/aoptk/normalization/mesh_terms.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,983 copying src/aoptk/normalization/provide_normalization_dataframe.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,985 copying src/aoptk/normalization/pubchem_abbreviation_short.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,987 copying src/aoptk/normalization/__init__.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,988 copying src/aoptk/normalization/provide_mesh_term_dataframe_from_xml.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,990 copying src/aoptk/normalization/pubchem_api.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,992 copying src/aoptk/normalization/normalize_chemical.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,994 copying src/aoptk/normalization/pubchem_abbreviation_uppercase.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,995 copying src/aoptk/normalization/pubchem_local.py -> build/lib/aoptk/normalization 2026-02-08T21:10:24,998 creating build/lib/aoptk/relationships 2026-02-08T21:10:24,999 copying src/aoptk/relationships/relationship.py -> build/lib/aoptk/relationships 2026-02-08T21:10:25,001 copying src/aoptk/relationships/find_relationship.py -> build/lib/aoptk/relationships 2026-02-08T21:10:25,003 copying src/aoptk/relationships/__init__.py -> build/lib/aoptk/relationships 2026-02-08T21:10:25,004 copying src/aoptk/relationships/zero_shot_classification.py -> build/lib/aoptk/relationships 2026-02-08T21:10:25,006 copying src/aoptk/relationships/zero_shot_classification_multiple.py -> build/lib/aoptk/relationships 2026-02-08T21:10:25,008 copying src/aoptk/relationships/zero_shot_classification_single.py -> build/lib/aoptk/relationships 2026-02-08T21:10:25,011 creating build/lib/aoptk/cleaning 2026-02-08T21:10:25,012 copying src/aoptk/cleaning/__init__.py -> build/lib/aoptk/cleaning 2026-02-08T21:10:25,013 copying src/aoptk/cleaning/html_tag_remover.py -> build/lib/aoptk/cleaning 2026-02-08T21:10:25,015 copying src/aoptk/cleaning/text_cleaner.py -> build/lib/aoptk/cleaning 2026-02-08T21:10:25,017 creating build/lib/aoptk/application 2026-02-08T21:10:25,018 copying src/aoptk/application/chemical_identifier.py -> build/lib/aoptk/application 2026-02-08T21:10:25,020 copying src/aoptk/application/__init__.py -> build/lib/aoptk/application 2026-02-08T21:10:25,022 copying src/aoptk/application/publication_tracker.py -> build/lib/aoptk/application 2026-02-08T21:10:25,025 creating build/lib/aoptk/abbreviations 2026-02-08T21:10:25,026 copying src/aoptk/abbreviations/abbreviation_translator_dictionary_generator.py -> build/lib/aoptk/abbreviations 2026-02-08T21:10:25,028 copying src/aoptk/abbreviations/abbreviation_translator_dictionary.py -> build/lib/aoptk/abbreviations 2026-02-08T21:10:25,029 copying src/aoptk/abbreviations/__init__.py -> build/lib/aoptk/abbreviations 2026-02-08T21:10:25,031 copying src/aoptk/abbreviations/abbreviation_translator.py -> build/lib/aoptk/abbreviations 2026-02-08T21:10:25,033 creating build/lib/aoptk/literature 2026-02-08T21:10:25,034 copying src/aoptk/literature/publication_metadata.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,036 copying src/aoptk/literature/get_pdf.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,038 copying src/aoptk/literature/get_id.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,040 copying src/aoptk/literature/id.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,041 copying src/aoptk/literature/utils.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,043 copying src/aoptk/literature/__init__.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,045 copying src/aoptk/literature/pdf.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,046 copying src/aoptk/literature/pymupdf_parser.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,048 copying src/aoptk/literature/publication.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,050 copying src/aoptk/literature/get_publication.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,052 copying src/aoptk/literature/get_abstract.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,054 copying src/aoptk/literature/abstract.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,055 copying src/aoptk/literature/pdf_parser.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,057 copying src/aoptk/literature/abbreviations.py -> build/lib/aoptk/literature 2026-02-08T21:10:25,059 creating build/lib/aoptk/literature/databases 2026-02-08T21:10:25,060 copying src/aoptk/literature/databases/pubmed.py -> build/lib/aoptk/literature/databases 2026-02-08T21:10:25,062 copying src/aoptk/literature/databases/europepmc.py -> build/lib/aoptk/literature/databases 2026-02-08T21:10:25,065 copying src/aoptk/literature/databases/__init__.py -> build/lib/aoptk/literature/databases 2026-02-08T21:10:25,066 running egg_info 2026-02-08T21:10:25,078 writing src/aoptk.egg-info/PKG-INFO 2026-02-08T21:10:25,085 writing dependency_links to src/aoptk.egg-info/dependency_links.txt 2026-02-08T21:10:25,086 writing entry points to src/aoptk.egg-info/entry_points.txt 2026-02-08T21:10:25,089 writing requirements to src/aoptk.egg-info/requires.txt 2026-02-08T21:10:25,090 writing top-level names to src/aoptk.egg-info/top_level.txt 2026-02-08T21:10:25,127 listing git files failed - pretending there aren't any 2026-02-08T21:10:25,134 reading manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-08T21:10:25,141 reading manifest template 'MANIFEST.in' 2026-02-08T21:10:25,142 warning: no files found matching 'NOTICE' 2026-02-08T21:10:25,142 adding license file 'LICENSE' 2026-02-08T21:10:25,148 writing manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-08T21:10:25,169 installing to build/bdist.linux-armv7l/wheel 2026-02-08T21:10:25,170 running install 2026-02-08T21:10:25,193 running install_lib 2026-02-08T21:10:25,200 creating build/bdist.linux-armv7l/wheel 2026-02-08T21:10:25,202 creating build/bdist.linux-armv7l/wheel/aoptk 2026-02-08T21:10:25,204 creating build/bdist.linux-armv7l/wheel/aoptk/normalization 2026-02-08T21:10:25,205 copying build/lib/aoptk/normalization/mesh_terms.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,207 copying build/lib/aoptk/normalization/provide_normalization_dataframe.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,208 copying build/lib/aoptk/normalization/pubchem_abbreviation_short.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,210 copying build/lib/aoptk/normalization/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,212 copying build/lib/aoptk/normalization/provide_mesh_term_dataframe_from_xml.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,214 copying build/lib/aoptk/normalization/pubchem_api.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,215 copying build/lib/aoptk/normalization/normalize_chemical.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,217 copying build/lib/aoptk/normalization/pubchem_abbreviation_uppercase.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,219 copying build/lib/aoptk/normalization/pubchem_local.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-08T21:10:25,221 copying build/lib/aoptk/sentence_generator.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,222 copying build/lib/aoptk/sentence.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,225 creating build/bdist.linux-armv7l/wheel/aoptk/relationships 2026-02-08T21:10:25,226 copying build/lib/aoptk/relationships/relationship.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-08T21:10:25,227 copying build/lib/aoptk/relationships/find_relationship.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-08T21:10:25,229 copying build/lib/aoptk/relationships/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-08T21:10:25,231 copying build/lib/aoptk/relationships/zero_shot_classification.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-08T21:10:25,233 copying build/lib/aoptk/relationships/zero_shot_classification_multiple.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-08T21:10:25,234 copying build/lib/aoptk/relationships/zero_shot_classification_single.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-08T21:10:25,236 copying build/lib/aoptk/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,238 creating build/bdist.linux-armv7l/wheel/aoptk/cleaning 2026-02-08T21:10:25,239 copying build/lib/aoptk/cleaning/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/cleaning 2026-02-08T21:10:25,241 copying build/lib/aoptk/cleaning/html_tag_remover.py -> build/bdist.linux-armv7l/wheel/./aoptk/cleaning 2026-02-08T21:10:25,243 copying build/lib/aoptk/cleaning/text_cleaner.py -> build/bdist.linux-armv7l/wheel/./aoptk/cleaning 2026-02-08T21:10:25,245 copying build/lib/aoptk/spacy_processor.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,247 copying build/lib/aoptk/effect.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,248 copying build/lib/aoptk/chemical.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,251 creating build/bdist.linux-armv7l/wheel/aoptk/application 2026-02-08T21:10:25,252 copying build/lib/aoptk/application/chemical_identifier.py -> build/bdist.linux-armv7l/wheel/./aoptk/application 2026-02-08T21:10:25,255 copying build/lib/aoptk/application/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/application 2026-02-08T21:10:25,256 copying build/lib/aoptk/application/publication_tracker.py -> build/bdist.linux-armv7l/wheel/./aoptk/application 2026-02-08T21:10:25,259 creating build/bdist.linux-armv7l/wheel/aoptk/abbreviations 2026-02-08T21:10:25,260 copying build/lib/aoptk/abbreviations/abbreviation_translator_dictionary_generator.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-08T21:10:25,262 copying build/lib/aoptk/abbreviations/abbreviation_translator_dictionary.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-08T21:10:25,264 copying build/lib/aoptk/abbreviations/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-08T21:10:25,265 copying build/lib/aoptk/abbreviations/abbreviation_translator.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-08T21:10:25,267 copying build/lib/aoptk/regex_sentence_generator.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,270 creating build/bdist.linux-armv7l/wheel/aoptk/literature 2026-02-08T21:10:25,270 copying build/lib/aoptk/literature/publication_metadata.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,272 copying build/lib/aoptk/literature/get_pdf.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,274 copying build/lib/aoptk/literature/get_id.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,276 copying build/lib/aoptk/literature/id.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,278 copying build/lib/aoptk/literature/utils.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,280 copying build/lib/aoptk/literature/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,281 copying build/lib/aoptk/literature/pdf.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,283 copying build/lib/aoptk/literature/pymupdf_parser.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,285 copying build/lib/aoptk/literature/publication.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,286 copying build/lib/aoptk/literature/get_publication.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,288 copying build/lib/aoptk/literature/get_abstract.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,289 copying build/lib/aoptk/literature/abstract.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,291 copying build/lib/aoptk/literature/pdf_parser.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,293 copying build/lib/aoptk/literature/abbreviations.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-08T21:10:25,295 creating build/bdist.linux-armv7l/wheel/aoptk/literature/databases 2026-02-08T21:10:25,296 copying build/lib/aoptk/literature/databases/pubmed.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature/databases 2026-02-08T21:10:25,298 copying build/lib/aoptk/literature/databases/europepmc.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature/databases 2026-02-08T21:10:25,300 copying build/lib/aoptk/literature/databases/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature/databases 2026-02-08T21:10:25,302 copying build/lib/aoptk/find_chemical.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-08T21:10:25,304 running install_egg_info 2026-02-08T21:10:25,309 Copying src/aoptk.egg-info to build/bdist.linux-armv7l/wheel/./aoptk-0.1.3-py3.11.egg-info 2026-02-08T21:10:25,320 running install_scripts 2026-02-08T21:10:25,332 creating build/bdist.linux-armv7l/wheel/aoptk-0.1.3.dist-info/WHEEL 2026-02-08T21:10:25,335 creating '/tmp/pip-wheel-ws8gb351/.tmp-5iz079do/aoptk-0.1.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-08T21:10:25,337 adding 'aoptk/__init__.py' 2026-02-08T21:10:25,339 adding 'aoptk/chemical.py' 2026-02-08T21:10:25,340 adding 'aoptk/effect.py' 2026-02-08T21:10:25,341 adding 'aoptk/find_chemical.py' 2026-02-08T21:10:25,342 adding 'aoptk/regex_sentence_generator.py' 2026-02-08T21:10:25,344 adding 'aoptk/sentence.py' 2026-02-08T21:10:25,345 adding 'aoptk/sentence_generator.py' 2026-02-08T21:10:25,346 adding 'aoptk/spacy_processor.py' 2026-02-08T21:10:25,348 adding 'aoptk/abbreviations/__init__.py' 2026-02-08T21:10:25,349 adding 'aoptk/abbreviations/abbreviation_translator.py' 2026-02-08T21:10:25,350 adding 'aoptk/abbreviations/abbreviation_translator_dictionary.py' 2026-02-08T21:10:25,352 adding 'aoptk/abbreviations/abbreviation_translator_dictionary_generator.py' 2026-02-08T21:10:25,354 adding 'aoptk/application/__init__.py' 2026-02-08T21:10:25,355 adding 'aoptk/application/chemical_identifier.py' 2026-02-08T21:10:25,356 adding 'aoptk/application/publication_tracker.py' 2026-02-08T21:10:25,358 adding 'aoptk/cleaning/__init__.py' 2026-02-08T21:10:25,359 adding 'aoptk/cleaning/html_tag_remover.py' 2026-02-08T21:10:25,360 adding 'aoptk/cleaning/text_cleaner.py' 2026-02-08T21:10:25,362 adding 'aoptk/literature/__init__.py' 2026-02-08T21:10:25,363 adding 'aoptk/literature/abbreviations.py' 2026-02-08T21:10:25,364 adding 'aoptk/literature/abstract.py' 2026-02-08T21:10:25,366 adding 'aoptk/literature/get_abstract.py' 2026-02-08T21:10:25,367 adding 'aoptk/literature/get_id.py' 2026-02-08T21:10:25,368 adding 'aoptk/literature/get_pdf.py' 2026-02-08T21:10:25,369 adding 'aoptk/literature/get_publication.py' 2026-02-08T21:10:25,371 adding 'aoptk/literature/id.py' 2026-02-08T21:10:25,372 adding 'aoptk/literature/pdf.py' 2026-02-08T21:10:25,373 adding 'aoptk/literature/pdf_parser.py' 2026-02-08T21:10:25,374 adding 'aoptk/literature/publication.py' 2026-02-08T21:10:25,375 adding 'aoptk/literature/publication_metadata.py' 2026-02-08T21:10:25,377 adding 'aoptk/literature/pymupdf_parser.py' 2026-02-08T21:10:25,378 adding 'aoptk/literature/utils.py' 2026-02-08T21:10:25,380 adding 'aoptk/literature/databases/__init__.py' 2026-02-08T21:10:25,381 adding 'aoptk/literature/databases/europepmc.py' 2026-02-08T21:10:25,383 adding 'aoptk/literature/databases/pubmed.py' 2026-02-08T21:10:25,384 adding 'aoptk/normalization/__init__.py' 2026-02-08T21:10:25,385 adding 'aoptk/normalization/mesh_terms.py' 2026-02-08T21:10:25,386 adding 'aoptk/normalization/normalize_chemical.py' 2026-02-08T21:10:25,387 adding 'aoptk/normalization/provide_mesh_term_dataframe_from_xml.py' 2026-02-08T21:10:25,389 adding 'aoptk/normalization/provide_normalization_dataframe.py' 2026-02-08T21:10:25,390 adding 'aoptk/normalization/pubchem_abbreviation_short.py' 2026-02-08T21:10:25,391 adding 'aoptk/normalization/pubchem_abbreviation_uppercase.py' 2026-02-08T21:10:25,392 adding 'aoptk/normalization/pubchem_api.py' 2026-02-08T21:10:25,393 adding 'aoptk/normalization/pubchem_local.py' 2026-02-08T21:10:25,395 adding 'aoptk/relationships/__init__.py' 2026-02-08T21:10:25,396 adding 'aoptk/relationships/find_relationship.py' 2026-02-08T21:10:25,397 adding 'aoptk/relationships/relationship.py' 2026-02-08T21:10:25,398 adding 'aoptk/relationships/zero_shot_classification.py' 2026-02-08T21:10:25,400 adding 'aoptk/relationships/zero_shot_classification_multiple.py' 2026-02-08T21:10:25,401 adding 'aoptk/relationships/zero_shot_classification_single.py' 2026-02-08T21:10:25,403 adding 'aoptk-0.1.3.dist-info/licenses/LICENSE' 2026-02-08T21:10:25,405 adding 'aoptk-0.1.3.dist-info/METADATA' 2026-02-08T21:10:25,406 adding 'aoptk-0.1.3.dist-info/WHEEL' 2026-02-08T21:10:25,407 adding 'aoptk-0.1.3.dist-info/entry_points.txt' 2026-02-08T21:10:25,408 adding 'aoptk-0.1.3.dist-info/top_level.txt' 2026-02-08T21:10:25,409 adding 'aoptk-0.1.3.dist-info/RECORD' 2026-02-08T21:10:25,411 removing build/bdist.linux-armv7l/wheel 2026-02-08T21:10:25,531 Building wheel for aoptk (pyproject.toml): finished with status 'done' 2026-02-08T21:10:25,536 Created wheel for aoptk: filename=aoptk-0.1.3-py3-none-any.whl size=37702 sha256=c4498769b4890de65cc3350de686e24482781d49ec980ff56c661abd6dceda37 2026-02-08T21:10:25,537 Stored in directory: /tmp/pip-ephem-wheel-cache-db3tck14/wheels/6d/8e/33/b5df7c85420256da85e204766007d881bc12d40589df64ad3e 2026-02-08T21:10:25,551 Successfully built aoptk 2026-02-08T21:10:25,555 Removed build tracker: '/tmp/pip-build-tracker-ddx89aq8'