2026-02-10T01:30:18,926 Created temporary directory: /tmp/pip-ephem-wheel-cache-1lyd04x2 2026-02-10T01:30:18,928 Created temporary directory: /tmp/pip-build-tracker-asp54b92 2026-02-10T01:30:18,929 Initialized build tracking at /tmp/pip-build-tracker-asp54b92 2026-02-10T01:30:18,930 Created build tracker: /tmp/pip-build-tracker-asp54b92 2026-02-10T01:30:18,930 Entered build tracker: /tmp/pip-build-tracker-asp54b92 2026-02-10T01:30:18,931 Created temporary directory: /tmp/pip-wheel-k7q59ahg 2026-02-10T01:30:18,934 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-10T01:30:18,938 Created temporary directory: /tmp/pip-ephem-wheel-cache-cq85lqwk 2026-02-10T01:30:18,960 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-10T01:30:18,964 2 location(s) to search for versions of aoptk: 2026-02-10T01:30:18,964 * https://pypi.org/simple/aoptk/ 2026-02-10T01:30:18,964 * https://www.piwheels.org/simple/aoptk/ 2026-02-10T01:30:18,965 Fetching project page and analyzing links: https://pypi.org/simple/aoptk/ 2026-02-10T01:30:18,965 Getting page https://pypi.org/simple/aoptk/ 2026-02-10T01:30:18,967 Found index url https://pypi.org/simple 2026-02-10T01:30:19,103 Fetched page https://pypi.org/simple/aoptk/ as application/vnd.pypi.simple.v1+json 2026-02-10T01:30:19,106 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) 2026-02-10T01:30:19,107 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 2026-02-10T01:30:19,108 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) 2026-02-10T01:30:19,109 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 2026-02-10T01:30:19,110 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) 2026-02-10T01:30:19,110 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 2026-02-10T01:30:19,111 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) 2026-02-10T01:30:19,112 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 2026-02-10T01:30:19,113 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) 2026-02-10T01:30:19,114 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 2026-02-10T01:30:19,115 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) 2026-02-10T01:30:19,116 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 2026-02-10T01:30:19,117 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) 2026-02-10T01:30:19,118 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 2026-02-10T01:30:19,118 Fetching project page and analyzing links: https://www.piwheels.org/simple/aoptk/ 2026-02-10T01:30:19,119 Getting page https://www.piwheels.org/simple/aoptk/ 2026-02-10T01:30:19,120 Found index url https://www.piwheels.org/simple 2026-02-10T01:30:19,272 Fetched page https://www.piwheels.org/simple/aoptk/ as text/html 2026-02-10T01:30:19,275 Skipping link: No binaries permitted for aoptk: https://www.piwheels.org/simple/aoptk/aoptk-0.1.5-py3-none-any.whl#sha256=7a17e4ff667b20151c38637fa7ba34a064bc1ab7faa6a6b8bd9ed90977af6091 (from https://www.piwheels.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-10T01:30:19,275 Skipping link: No binaries permitted for aoptk: https://www.piwheels.org/simple/aoptk/aoptk-0.1.4-py3-none-any.whl#sha256=017a7a258e33079170ed7b9a9cc2c447641f47b264928589234455dba69c24c3 (from https://www.piwheels.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-10T01:30:19,276 Skipping link: No binaries permitted for aoptk: https://www.piwheels.org/simple/aoptk/aoptk-0.1.3-py3-none-any.whl#sha256=c4498769b4890de65cc3350de686e24482781d49ec980ff56c661abd6dceda37 (from https://www.piwheels.org/simple/aoptk/) (requires-python:>=3.10) 2026-02-10T01:30:19,277 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) 2026-02-10T01:30:19,277 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) 2026-02-10T01:30:19,278 Skipping link: not a file: https://www.piwheels.org/simple/aoptk/ 2026-02-10T01:30:19,278 Skipping link: not a file: https://pypi.org/simple/aoptk/ 2026-02-10T01:30:19,298 Given no hashes to check 1 links for project 'aoptk': discarding no candidates 2026-02-10T01:30:19,316 Collecting aoptk==0.1.6 2026-02-10T01:30:19,319 Created temporary directory: /tmp/pip-unpack-nqfkvxjr 2026-02-10T01:30:19,529 Downloading aoptk-0.1.6.tar.gz (167 kB) 2026-02-10T01:30:19,834 Added aoptk==0.1.6 from https://files.pythonhosted.org/packages/af/6a/a9593e3f2c2eeaaded381d65b77318caffde8f5a48d71a89bad93264fa60/aoptk-0.1.6.tar.gz to build tracker '/tmp/pip-build-tracker-asp54b92' 2026-02-10T01:30:19,842 Created temporary directory: /tmp/pip-build-env-e59o48ts 2026-02-10T01:30:19,847 Installing build dependencies: started 2026-02-10T01:30:19,848 Running command pip subprocess to install build dependencies 2026-02-10T01:30:21,030 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-10T01:30:21,570 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-10T01:30:21,593 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-10T01:30:23,324 Collecting setuptools>=64.0.0 2026-02-10T01:30:23,344 Using cached setuptools-82.0.0-py3-none-any.whl (1.0 MB) 2026-02-10T01:30:23,713 Collecting setuptools-scm 2026-02-10T01:30:23,729 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-9.2.2-py3-none-any.whl (62 kB) 2026-02-10T01:30:23,958 Collecting wheel 2026-02-10T01:30:23,976 Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB) 2026-02-10T01:30:24,168 Collecting packaging>=20 2026-02-10T01:30:24,183 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-02-10T01:30:27,259 Installing collected packages: setuptools, packaging, wheel, setuptools-scm 2026-02-10T01:30:30,635 Creating /tmp/pip-build-env-e59o48ts/overlay/local/bin 2026-02-10T01:30:30,637 changing mode of /tmp/pip-build-env-e59o48ts/overlay/local/bin/wheel to 755 2026-02-10T01:30:30,883 changing mode of /tmp/pip-build-env-e59o48ts/overlay/local/bin/setuptools-scm to 755 2026-02-10T01:30:30,913 Successfully installed packaging-26.0 setuptools-82.0.0 setuptools-scm-9.2.2 wheel-0.46.3 2026-02-10T01:30:31,199 Installing build dependencies: finished with status 'done' 2026-02-10T01:30:31,205 Getting requirements to build wheel: started 2026-02-10T01:30:31,206 Running command Getting requirements to build wheel 2026-02-10T01:30:31,818 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2026-02-10T01:30:31,858 /tmp/pip-build-env-e59o48ts/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-10T01:30:31,859 !! 2026-02-10T01:30:31,860 ******************************************************************************** 2026-02-10T01:30:31,861 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). 2026-02-10T01:30:31,862 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-10T01:30:31,863 or your builds will no longer be supported. 2026-02-10T01:30:31,864 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T01:30:31,864 ******************************************************************************** 2026-02-10T01:30:31,866 !! 2026-02-10T01:30:31,866 corresp(dist, value, root_dir) 2026-02-10T01:30:31,955 running egg_info 2026-02-10T01:30:31,962 writing src/aoptk.egg-info/PKG-INFO 2026-02-10T01:30:31,969 writing dependency_links to src/aoptk.egg-info/dependency_links.txt 2026-02-10T01:30:31,971 writing entry points to src/aoptk.egg-info/entry_points.txt 2026-02-10T01:30:31,974 writing requirements to src/aoptk.egg-info/requires.txt 2026-02-10T01:30:31,976 writing top-level names to src/aoptk.egg-info/top_level.txt 2026-02-10T01:30:32,030 listing git files failed - pretending there aren't any 2026-02-10T01:30:32,038 reading manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-10T01:30:32,047 reading manifest template 'MANIFEST.in' 2026-02-10T01:30:32,048 warning: no files found matching 'NOTICE' 2026-02-10T01:30:32,049 adding license file 'LICENSE' 2026-02-10T01:30:32,055 writing manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-10T01:30:32,156 Getting requirements to build wheel: finished with status 'done' 2026-02-10T01:30:32,160 Created temporary directory: /tmp/pip-modern-metadata-fz2qid_c 2026-02-10T01:30:32,162 Preparing metadata (pyproject.toml): started 2026-02-10T01:30:32,163 Running command Preparing metadata (pyproject.toml) 2026-02-10T01:30:32,751 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2026-02-10T01:30:32,791 /tmp/pip-build-env-e59o48ts/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-10T01:30:32,792 !! 2026-02-10T01:30:32,793 ******************************************************************************** 2026-02-10T01:30:32,793 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). 2026-02-10T01:30:32,794 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-10T01:30:32,795 or your builds will no longer be supported. 2026-02-10T01:30:32,797 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T01:30:32,797 ******************************************************************************** 2026-02-10T01:30:32,798 !! 2026-02-10T01:30:32,799 corresp(dist, value, root_dir) 2026-02-10T01:30:32,887 running dist_info 2026-02-10T01:30:32,900 creating /tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info 2026-02-10T01:30:32,901 writing /tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/PKG-INFO 2026-02-10T01:30:32,909 writing dependency_links to /tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/dependency_links.txt 2026-02-10T01:30:32,910 writing entry points to /tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/entry_points.txt 2026-02-10T01:30:32,914 writing requirements to /tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/requires.txt 2026-02-10T01:30:32,915 writing top-level names to /tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/top_level.txt 2026-02-10T01:30:32,916 writing manifest file '/tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/SOURCES.txt' 2026-02-10T01:30:32,966 listing git files failed - pretending there aren't any 2026-02-10T01:30:32,972 reading manifest file '/tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/SOURCES.txt' 2026-02-10T01:30:32,974 reading manifest template 'MANIFEST.in' 2026-02-10T01:30:32,975 warning: no files found matching 'NOTICE' 2026-02-10T01:30:32,976 adding license file 'LICENSE' 2026-02-10T01:30:32,980 writing manifest file '/tmp/pip-modern-metadata-fz2qid_c/aoptk.egg-info/SOURCES.txt' 2026-02-10T01:30:32,981 creating '/tmp/pip-modern-metadata-fz2qid_c/aoptk-0.1.6.dist-info' 2026-02-10T01:30:33,111 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-10T01:30:33,117 Source in /tmp/pip-wheel-k7q59ahg/aoptk_c3fb4011a4ec42c5a7c9fdea3bb8731a has version 0.1.6, which satisfies requirement aoptk==0.1.6 from https://files.pythonhosted.org/packages/af/6a/a9593e3f2c2eeaaded381d65b77318caffde8f5a48d71a89bad93264fa60/aoptk-0.1.6.tar.gz 2026-02-10T01:30:33,118 Removed aoptk==0.1.6 from https://files.pythonhosted.org/packages/af/6a/a9593e3f2c2eeaaded381d65b77318caffde8f5a48d71a89bad93264fa60/aoptk-0.1.6.tar.gz from build tracker '/tmp/pip-build-tracker-asp54b92' 2026-02-10T01:30:33,124 Created temporary directory: /tmp/pip-unpack-soitv89_ 2026-02-10T01:30:33,125 Building wheels for collected packages: aoptk 2026-02-10T01:30:33,129 Created temporary directory: /tmp/pip-wheel-2sb7nqnf 2026-02-10T01:30:33,130 Destination directory: /tmp/pip-wheel-2sb7nqnf 2026-02-10T01:30:33,132 Building wheel for aoptk (pyproject.toml): started 2026-02-10T01:30:33,133 Running command Building wheel for aoptk (pyproject.toml) 2026-02-10T01:30:33,695 toml section missing PosixPath('pyproject.toml') does not contain a tool.setuptools_scm section 2026-02-10T01:30:33,733 /tmp/pip-build-env-e59o48ts/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-10T01:30:33,733 !! 2026-02-10T01:30:33,735 ******************************************************************************** 2026-02-10T01:30:33,735 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). 2026-02-10T01:30:33,736 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-10T01:30:33,736 or your builds will no longer be supported. 2026-02-10T01:30:33,737 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T01:30:33,738 ******************************************************************************** 2026-02-10T01:30:33,739 !! 2026-02-10T01:30:33,739 corresp(dist, value, root_dir) 2026-02-10T01:30:33,812 running bdist_wheel 2026-02-10T01:30:33,835 running build 2026-02-10T01:30:33,835 running build_py 2026-02-10T01:30:33,842 creating build/lib/aoptk 2026-02-10T01:30:33,844 copying src/aoptk/__init__.py -> build/lib/aoptk 2026-02-10T01:30:33,846 copying src/aoptk/spacy_processor.py -> build/lib/aoptk 2026-02-10T01:30:33,848 copying src/aoptk/sentence_generator.py -> build/lib/aoptk 2026-02-10T01:30:33,850 copying src/aoptk/chemical.py -> build/lib/aoptk 2026-02-10T01:30:33,852 copying src/aoptk/find_chemical.py -> build/lib/aoptk 2026-02-10T01:30:33,853 copying src/aoptk/regex_sentence_generator.py -> build/lib/aoptk 2026-02-10T01:30:33,855 copying src/aoptk/effect.py -> build/lib/aoptk 2026-02-10T01:30:33,857 copying src/aoptk/sentence.py -> build/lib/aoptk 2026-02-10T01:30:33,859 creating build/lib/aoptk/application 2026-02-10T01:30:33,860 copying src/aoptk/application/__init__.py -> build/lib/aoptk/application 2026-02-10T01:30:33,862 copying src/aoptk/application/publication_tracker.py -> build/lib/aoptk/application 2026-02-10T01:30:33,864 copying src/aoptk/application/chemical_identifier.py -> build/lib/aoptk/application 2026-02-10T01:30:33,867 creating build/lib/aoptk/normalization 2026-02-10T01:30:33,868 copying src/aoptk/normalization/__init__.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,870 copying src/aoptk/normalization/pubchem_abbreviation_uppercase.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,872 copying src/aoptk/normalization/normalize_chemical.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,873 copying src/aoptk/normalization/pubchem_api.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,875 copying src/aoptk/normalization/provide_normalization_dataframe.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,877 copying src/aoptk/normalization/pubchem_abbreviation_short.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,879 copying src/aoptk/normalization/mesh_terms.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,880 copying src/aoptk/normalization/provide_mesh_term_dataframe_from_xml.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,882 copying src/aoptk/normalization/pubchem_local.py -> build/lib/aoptk/normalization 2026-02-10T01:30:33,884 creating build/lib/aoptk/literature 2026-02-10T01:30:33,885 copying src/aoptk/literature/publication.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,887 copying src/aoptk/literature/__init__.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,889 copying src/aoptk/literature/abbreviations.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,890 copying src/aoptk/literature/pdf.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,892 copying src/aoptk/literature/pdf_parser.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,894 copying src/aoptk/literature/get_id.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,895 copying src/aoptk/literature/pymupdf_parser.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,898 copying src/aoptk/literature/get_abstract.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,899 copying src/aoptk/literature/get_pdf.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,901 copying src/aoptk/literature/publication_metadata.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,903 copying src/aoptk/literature/get_publication.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,904 copying src/aoptk/literature/abstract.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,906 copying src/aoptk/literature/utils.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,908 copying src/aoptk/literature/id.py -> build/lib/aoptk/literature 2026-02-10T01:30:33,910 creating build/lib/aoptk/relationships 2026-02-10T01:30:33,910 copying src/aoptk/relationships/find_relationship.py -> build/lib/aoptk/relationships 2026-02-10T01:30:33,912 copying src/aoptk/relationships/zero_shot_classification.py -> build/lib/aoptk/relationships 2026-02-10T01:30:33,914 copying src/aoptk/relationships/__init__.py -> build/lib/aoptk/relationships 2026-02-10T01:30:33,916 copying src/aoptk/relationships/zero_shot_classification_multiple.py -> build/lib/aoptk/relationships 2026-02-10T01:30:33,917 copying src/aoptk/relationships/relationship.py -> build/lib/aoptk/relationships 2026-02-10T01:30:33,919 copying src/aoptk/relationships/zero_shot_classification_single.py -> build/lib/aoptk/relationships 2026-02-10T01:30:33,921 creating build/lib/aoptk/cleaning 2026-02-10T01:30:33,922 copying src/aoptk/cleaning/__init__.py -> build/lib/aoptk/cleaning 2026-02-10T01:30:33,923 copying src/aoptk/cleaning/html_tag_remover.py -> build/lib/aoptk/cleaning 2026-02-10T01:30:33,925 copying src/aoptk/cleaning/text_cleaner.py -> build/lib/aoptk/cleaning 2026-02-10T01:30:33,927 creating build/lib/aoptk/abbreviations 2026-02-10T01:30:33,928 copying src/aoptk/abbreviations/__init__.py -> build/lib/aoptk/abbreviations 2026-02-10T01:30:33,930 copying src/aoptk/abbreviations/abbreviation_translator.py -> build/lib/aoptk/abbreviations 2026-02-10T01:30:33,931 copying src/aoptk/abbreviations/abbreviation_translator_dictionary_generator.py -> build/lib/aoptk/abbreviations 2026-02-10T01:30:33,933 copying src/aoptk/abbreviations/abbreviation_translator_dictionary.py -> build/lib/aoptk/abbreviations 2026-02-10T01:30:33,935 creating build/lib/aoptk/literature/databases 2026-02-10T01:30:33,936 copying src/aoptk/literature/databases/__init__.py -> build/lib/aoptk/literature/databases 2026-02-10T01:30:33,938 copying src/aoptk/literature/databases/europepmc.py -> build/lib/aoptk/literature/databases 2026-02-10T01:30:33,940 copying src/aoptk/literature/databases/pubmed.py -> build/lib/aoptk/literature/databases 2026-02-10T01:30:33,942 running egg_info 2026-02-10T01:30:33,954 writing src/aoptk.egg-info/PKG-INFO 2026-02-10T01:30:33,960 writing dependency_links to src/aoptk.egg-info/dependency_links.txt 2026-02-10T01:30:33,962 writing entry points to src/aoptk.egg-info/entry_points.txt 2026-02-10T01:30:33,965 writing requirements to src/aoptk.egg-info/requires.txt 2026-02-10T01:30:33,966 writing top-level names to src/aoptk.egg-info/top_level.txt 2026-02-10T01:30:34,003 listing git files failed - pretending there aren't any 2026-02-10T01:30:34,009 reading manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-10T01:30:34,016 reading manifest template 'MANIFEST.in' 2026-02-10T01:30:34,017 warning: no files found matching 'NOTICE' 2026-02-10T01:30:34,018 adding license file 'LICENSE' 2026-02-10T01:30:34,024 writing manifest file 'src/aoptk.egg-info/SOURCES.txt' 2026-02-10T01:30:34,045 installing to build/bdist.linux-armv7l/wheel 2026-02-10T01:30:34,045 running install 2026-02-10T01:30:34,068 running install_lib 2026-02-10T01:30:34,074 creating build/bdist.linux-armv7l/wheel 2026-02-10T01:30:34,077 creating build/bdist.linux-armv7l/wheel/aoptk 2026-02-10T01:30:34,078 creating build/bdist.linux-armv7l/wheel/aoptk/application 2026-02-10T01:30:34,079 copying build/lib/aoptk/application/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/application 2026-02-10T01:30:34,081 copying build/lib/aoptk/application/publication_tracker.py -> build/bdist.linux-armv7l/wheel/./aoptk/application 2026-02-10T01:30:34,083 copying build/lib/aoptk/application/chemical_identifier.py -> build/bdist.linux-armv7l/wheel/./aoptk/application 2026-02-10T01:30:34,086 creating build/bdist.linux-armv7l/wheel/aoptk/normalization 2026-02-10T01:30:34,087 copying build/lib/aoptk/normalization/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,088 copying build/lib/aoptk/normalization/pubchem_abbreviation_uppercase.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,090 copying build/lib/aoptk/normalization/normalize_chemical.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,091 copying build/lib/aoptk/normalization/pubchem_api.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,093 copying build/lib/aoptk/normalization/provide_normalization_dataframe.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,095 copying build/lib/aoptk/normalization/pubchem_abbreviation_short.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,096 copying build/lib/aoptk/normalization/mesh_terms.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,098 copying build/lib/aoptk/normalization/provide_mesh_term_dataframe_from_xml.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,100 copying build/lib/aoptk/normalization/pubchem_local.py -> build/bdist.linux-armv7l/wheel/./aoptk/normalization 2026-02-10T01:30:34,101 copying build/lib/aoptk/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,103 copying build/lib/aoptk/spacy_processor.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,105 copying build/lib/aoptk/sentence_generator.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,107 copying build/lib/aoptk/chemical.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,109 copying build/lib/aoptk/find_chemical.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,111 creating build/bdist.linux-armv7l/wheel/aoptk/literature 2026-02-10T01:30:34,113 copying build/lib/aoptk/literature/publication.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,114 copying build/lib/aoptk/literature/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,116 copying build/lib/aoptk/literature/abbreviations.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,117 copying build/lib/aoptk/literature/pdf.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,119 copying build/lib/aoptk/literature/pdf_parser.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,121 copying build/lib/aoptk/literature/get_id.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,123 copying build/lib/aoptk/literature/pymupdf_parser.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,125 copying build/lib/aoptk/literature/get_abstract.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,126 copying build/lib/aoptk/literature/get_pdf.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,128 copying build/lib/aoptk/literature/publication_metadata.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,130 creating build/bdist.linux-armv7l/wheel/aoptk/literature/databases 2026-02-10T01:30:34,131 copying build/lib/aoptk/literature/databases/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature/databases 2026-02-10T01:30:34,133 copying build/lib/aoptk/literature/databases/europepmc.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature/databases 2026-02-10T01:30:34,135 copying build/lib/aoptk/literature/databases/pubmed.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature/databases 2026-02-10T01:30:34,137 copying build/lib/aoptk/literature/get_publication.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,139 copying build/lib/aoptk/literature/abstract.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,141 copying build/lib/aoptk/literature/utils.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,142 copying build/lib/aoptk/literature/id.py -> build/bdist.linux-armv7l/wheel/./aoptk/literature 2026-02-10T01:30:34,145 creating build/bdist.linux-armv7l/wheel/aoptk/relationships 2026-02-10T01:30:34,145 copying build/lib/aoptk/relationships/find_relationship.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-10T01:30:34,147 copying build/lib/aoptk/relationships/zero_shot_classification.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-10T01:30:34,149 copying build/lib/aoptk/relationships/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-10T01:30:34,150 copying build/lib/aoptk/relationships/zero_shot_classification_multiple.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-10T01:30:34,152 copying build/lib/aoptk/relationships/relationship.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-10T01:30:34,154 copying build/lib/aoptk/relationships/zero_shot_classification_single.py -> build/bdist.linux-armv7l/wheel/./aoptk/relationships 2026-02-10T01:30:34,155 copying build/lib/aoptk/regex_sentence_generator.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,157 creating build/bdist.linux-armv7l/wheel/aoptk/cleaning 2026-02-10T01:30:34,158 copying build/lib/aoptk/cleaning/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/cleaning 2026-02-10T01:30:34,160 copying build/lib/aoptk/cleaning/html_tag_remover.py -> build/bdist.linux-armv7l/wheel/./aoptk/cleaning 2026-02-10T01:30:34,162 copying build/lib/aoptk/cleaning/text_cleaner.py -> build/bdist.linux-armv7l/wheel/./aoptk/cleaning 2026-02-10T01:30:34,163 copying build/lib/aoptk/effect.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,165 copying build/lib/aoptk/sentence.py -> build/bdist.linux-armv7l/wheel/./aoptk 2026-02-10T01:30:34,167 creating build/bdist.linux-armv7l/wheel/aoptk/abbreviations 2026-02-10T01:30:34,168 copying build/lib/aoptk/abbreviations/__init__.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-10T01:30:34,170 copying build/lib/aoptk/abbreviations/abbreviation_translator.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-10T01:30:34,171 copying build/lib/aoptk/abbreviations/abbreviation_translator_dictionary_generator.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-10T01:30:34,173 copying build/lib/aoptk/abbreviations/abbreviation_translator_dictionary.py -> build/bdist.linux-armv7l/wheel/./aoptk/abbreviations 2026-02-10T01:30:34,175 running install_egg_info 2026-02-10T01:30:34,181 Copying src/aoptk.egg-info to build/bdist.linux-armv7l/wheel/./aoptk-0.1.6-py3.11.egg-info 2026-02-10T01:30:34,192 running install_scripts 2026-02-10T01:30:34,203 creating build/bdist.linux-armv7l/wheel/aoptk-0.1.6.dist-info/WHEEL 2026-02-10T01:30:34,206 creating '/tmp/pip-wheel-2sb7nqnf/.tmp-rmpkmfeu/aoptk-0.1.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-10T01:30:34,209 adding 'aoptk/__init__.py' 2026-02-10T01:30:34,210 adding 'aoptk/chemical.py' 2026-02-10T01:30:34,211 adding 'aoptk/effect.py' 2026-02-10T01:30:34,213 adding 'aoptk/find_chemical.py' 2026-02-10T01:30:34,214 adding 'aoptk/regex_sentence_generator.py' 2026-02-10T01:30:34,215 adding 'aoptk/sentence.py' 2026-02-10T01:30:34,217 adding 'aoptk/sentence_generator.py' 2026-02-10T01:30:34,218 adding 'aoptk/spacy_processor.py' 2026-02-10T01:30:34,220 adding 'aoptk/abbreviations/__init__.py' 2026-02-10T01:30:34,221 adding 'aoptk/abbreviations/abbreviation_translator.py' 2026-02-10T01:30:34,223 adding 'aoptk/abbreviations/abbreviation_translator_dictionary.py' 2026-02-10T01:30:34,224 adding 'aoptk/abbreviations/abbreviation_translator_dictionary_generator.py' 2026-02-10T01:30:34,226 adding 'aoptk/application/__init__.py' 2026-02-10T01:30:34,227 adding 'aoptk/application/chemical_identifier.py' 2026-02-10T01:30:34,229 adding 'aoptk/application/publication_tracker.py' 2026-02-10T01:30:34,230 adding 'aoptk/cleaning/__init__.py' 2026-02-10T01:30:34,231 adding 'aoptk/cleaning/html_tag_remover.py' 2026-02-10T01:30:34,232 adding 'aoptk/cleaning/text_cleaner.py' 2026-02-10T01:30:34,234 adding 'aoptk/literature/__init__.py' 2026-02-10T01:30:34,235 adding 'aoptk/literature/abbreviations.py' 2026-02-10T01:30:34,236 adding 'aoptk/literature/abstract.py' 2026-02-10T01:30:34,237 adding 'aoptk/literature/get_abstract.py' 2026-02-10T01:30:34,238 adding 'aoptk/literature/get_id.py' 2026-02-10T01:30:34,239 adding 'aoptk/literature/get_pdf.py' 2026-02-10T01:30:34,240 adding 'aoptk/literature/get_publication.py' 2026-02-10T01:30:34,242 adding 'aoptk/literature/id.py' 2026-02-10T01:30:34,243 adding 'aoptk/literature/pdf.py' 2026-02-10T01:30:34,244 adding 'aoptk/literature/pdf_parser.py' 2026-02-10T01:30:34,245 adding 'aoptk/literature/publication.py' 2026-02-10T01:30:34,246 adding 'aoptk/literature/publication_metadata.py' 2026-02-10T01:30:34,248 adding 'aoptk/literature/pymupdf_parser.py' 2026-02-10T01:30:34,249 adding 'aoptk/literature/utils.py' 2026-02-10T01:30:34,250 adding 'aoptk/literature/databases/__init__.py' 2026-02-10T01:30:34,252 adding 'aoptk/literature/databases/europepmc.py' 2026-02-10T01:30:34,253 adding 'aoptk/literature/databases/pubmed.py' 2026-02-10T01:30:34,255 adding 'aoptk/normalization/__init__.py' 2026-02-10T01:30:34,256 adding 'aoptk/normalization/mesh_terms.py' 2026-02-10T01:30:34,257 adding 'aoptk/normalization/normalize_chemical.py' 2026-02-10T01:30:34,259 adding 'aoptk/normalization/provide_mesh_term_dataframe_from_xml.py' 2026-02-10T01:30:34,260 adding 'aoptk/normalization/provide_normalization_dataframe.py' 2026-02-10T01:30:34,261 adding 'aoptk/normalization/pubchem_abbreviation_short.py' 2026-02-10T01:30:34,262 adding 'aoptk/normalization/pubchem_abbreviation_uppercase.py' 2026-02-10T01:30:34,263 adding 'aoptk/normalization/pubchem_api.py' 2026-02-10T01:30:34,265 adding 'aoptk/normalization/pubchem_local.py' 2026-02-10T01:30:34,266 adding 'aoptk/relationships/__init__.py' 2026-02-10T01:30:34,267 adding 'aoptk/relationships/find_relationship.py' 2026-02-10T01:30:34,269 adding 'aoptk/relationships/relationship.py' 2026-02-10T01:30:34,270 adding 'aoptk/relationships/zero_shot_classification.py' 2026-02-10T01:30:34,271 adding 'aoptk/relationships/zero_shot_classification_multiple.py' 2026-02-10T01:30:34,272 adding 'aoptk/relationships/zero_shot_classification_single.py' 2026-02-10T01:30:34,275 adding 'aoptk-0.1.6.dist-info/licenses/LICENSE' 2026-02-10T01:30:34,276 adding 'aoptk-0.1.6.dist-info/METADATA' 2026-02-10T01:30:34,277 adding 'aoptk-0.1.6.dist-info/WHEEL' 2026-02-10T01:30:34,278 adding 'aoptk-0.1.6.dist-info/entry_points.txt' 2026-02-10T01:30:34,279 adding 'aoptk-0.1.6.dist-info/top_level.txt' 2026-02-10T01:30:34,281 adding 'aoptk-0.1.6.dist-info/RECORD' 2026-02-10T01:30:34,283 removing build/bdist.linux-armv7l/wheel 2026-02-10T01:30:34,397 Building wheel for aoptk (pyproject.toml): finished with status 'done' 2026-02-10T01:30:34,402 Created wheel for aoptk: filename=aoptk-0.1.6-py3-none-any.whl size=37709 sha256=61640d337a55be5eeb1d7b61b631712248a89395751a90c633216c8b43de50f6 2026-02-10T01:30:34,404 Stored in directory: /tmp/pip-ephem-wheel-cache-cq85lqwk/wheels/4c/d1/99/ebf6b0c6a3ff84f8637c31b0b3efb2a307beab800410f5f563 2026-02-10T01:30:34,417 Successfully built aoptk 2026-02-10T01:30:34,421 Removed build tracker: '/tmp/pip-build-tracker-asp54b92'