2026-08-31T16:37:15,710 Created temporary directory: /tmp/pip-ephem-wheel-cache-0jlmm4qu 2026-08-31T16:37:15,712 Created temporary directory: /tmp/pip-build-tracker-pcqq_27j 2026-08-31T16:37:15,712 Initialized build tracking at /tmp/pip-build-tracker-pcqq_27j 2026-08-31T16:37:15,713 Created build tracker: /tmp/pip-build-tracker-pcqq_27j 2026-08-31T16:37:15,713 Entered build tracker: /tmp/pip-build-tracker-pcqq_27j 2026-08-31T16:37:15,714 Created temporary directory: /tmp/pip-wheel-625lkb7b 2026-08-31T16:37:15,717 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 2026-08-31T16:37:15,719 Created temporary directory: /tmp/pip-ephem-wheel-cache-59p9inp8 2026-08-31T16:37:15,741 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-31T16:37:15,745 2 location(s) to search for versions of topiary: 2026-08-31T16:37:15,745 * https://pypi.org/simple/topiary/ 2026-08-31T16:37:15,745 * https://www.piwheels.org/simple/topiary/ 2026-08-31T16:37:15,746 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-08-31T16:37:15,747 Getting page https://pypi.org/simple/topiary/ 2026-08-31T16:37:15,748 Found index url https://pypi.org/simple 2026-08-31T16:37:15,977 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-08-31T16:37:16,004 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,393 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.14-py3-none-any.whl#sha256=48e8744f89c7f03717c8e36a17ede28b495b845c7106cb5638c216db27054fad (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,393 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.13-py3-none-any.whl#sha256=588396661f87bea8be890d90c6800ac4825d06ae7db1c50c98a1978fe9c45bd3 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,394 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.10-py3-none-any.whl#sha256=56bea0cecf1273a44cd2e51ad294714c41e0fb7d9cc0b16382709573c4ec9443 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,395 Skipping link: No binaries permitted for topiary: 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https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,397 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.5-py3-none-any.whl#sha256=52f489eb5876b619e9988ee4c2fabec4df1a087c2f67f96cbb99ece92eb57576 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,398 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.4-py3-none-any.whl#sha256=5c94fb56e54399233efc5f88a6f6cfe2914773c5b2aa67a24f6ddf6089561b3b (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,398 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.3-py3-none-any.whl#sha256=197f9da38cd367d77acaec6282f0d22aefaf1e1ab6754379f671902958348f15 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,399 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.2-py3-none-any.whl#sha256=accaff90bafe6c929aece0f65b8ccedd45839064bf361d8f69bfefd543127ec2 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,400 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.1-py3-none-any.whl#sha256=6743a02aee34bc7567913bbe5c15a321924d9e1cb2c15f956e4ebb9b321707f4 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,400 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.0-py3-none-any.whl#sha256=a4de4e13dc8561c43fd350094d3cbc3267e0faacf5e65b94501ef15affdf51e6 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:37:16,401 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-08-31T16:37:16,402 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-08-31T16:37:16,432 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-08-31T16:37:16,450 Collecting topiary==5.29.0 2026-08-31T16:37:16,453 Created temporary directory: /tmp/pip-unpack-5euuorjp 2026-08-31T16:37:16,602 Downloading topiary-5.29.0.tar.gz (325 kB) 2026-08-31T16:37:16,984 Added topiary==5.29.0 from https://files.pythonhosted.org/packages/c8/ed/e425bba6fef623f969ed53ec35c546ebf3f11a6b8024b338ba04e35fabd5/topiary-5.29.0.tar.gz to build tracker '/tmp/pip-build-tracker-pcqq_27j' 2026-08-31T16:37:16,989 Created temporary directory: /tmp/pip-build-env-zg77jmu2 2026-08-31T16:37:16,994 Installing build dependencies: started 2026-08-31T16:37:16,995 Running command pip subprocess to install build dependencies 2026-08-31T16:37:18,370 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-08-31T16:37:18,858 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 2026-08-31T16:37:18,882 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-31T16:37:20,685 Collecting setuptools>=64 2026-08-31T16:37:20,686 Obtaining dependency information for setuptools>=64 from https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata 2026-08-31T16:37:20,701 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-08-31T16:37:20,942 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-31T16:37:21,030 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-31T16:37:23,765 Installing collected packages: setuptools 2026-08-31T16:37:26,010 Successfully installed setuptools-84.0.0 2026-08-31T16:37:26,282 Installing build dependencies: finished with status 'done' 2026-08-31T16:37:26,289 Getting requirements to build wheel: started 2026-08-31T16:37:26,290 Running command Getting requirements to build wheel 2026-08-31T16:37:26,999 /tmp/pip-build-env-zg77jmu2/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:37:26,999 !! 2026-08-31T16:37:27,000 ******************************************************************************** 2026-08-31T16:37:27,001 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:37:27,002 License :: OSI Approved :: Apache Software License 2026-08-31T16:37:27,003 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:37:27,003 ******************************************************************************** 2026-08-31T16:37:27,004 !! 2026-08-31T16:37:27,005 dist._finalize_license_expression() 2026-08-31T16:37:27,006 /tmp/pip-build-env-zg77jmu2/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:37:27,006 !! 2026-08-31T16:37:27,007 ******************************************************************************** 2026-08-31T16:37:27,008 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:37:27,009 License :: OSI Approved :: Apache Software License 2026-08-31T16:37:27,011 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:37:27,011 ******************************************************************************** 2026-08-31T16:37:27,013 !! 2026-08-31T16:37:27,013 self._finalize_license_expression() 2026-08-31T16:37:27,014 running egg_info 2026-08-31T16:37:27,019 writing topiary.egg-info/PKG-INFO 2026-08-31T16:37:27,023 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-08-31T16:37:27,025 writing entry points to topiary.egg-info/entry_points.txt 2026-08-31T16:37:27,027 writing requirements to topiary.egg-info/requires.txt 2026-08-31T16:37:27,028 writing top-level names to topiary.egg-info/top_level.txt 2026-08-31T16:37:27,058 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:37:27,066 adding license file 'LICENSE' 2026-08-31T16:37:27,073 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:37:27,177 Getting requirements to build wheel: finished with status 'done' 2026-08-31T16:37:27,181 Created temporary directory: /tmp/pip-modern-metadata-e9rko6iv 2026-08-31T16:37:27,183 Preparing metadata (pyproject.toml): started 2026-08-31T16:37:27,184 Running command Preparing metadata (pyproject.toml) 2026-08-31T16:37:27,876 /tmp/pip-build-env-zg77jmu2/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:37:27,876 !! 2026-08-31T16:37:27,878 ******************************************************************************** 2026-08-31T16:37:27,878 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:37:27,879 License :: OSI Approved :: Apache Software License 2026-08-31T16:37:27,880 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:37:27,880 ******************************************************************************** 2026-08-31T16:37:27,881 !! 2026-08-31T16:37:27,882 dist._finalize_license_expression() 2026-08-31T16:37:27,882 /tmp/pip-build-env-zg77jmu2/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:37:27,883 !! 2026-08-31T16:37:27,884 ******************************************************************************** 2026-08-31T16:37:27,884 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:37:27,885 License :: OSI Approved :: Apache Software License 2026-08-31T16:37:27,886 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:37:27,887 ******************************************************************************** 2026-08-31T16:37:27,888 !! 2026-08-31T16:37:27,888 self._finalize_license_expression() 2026-08-31T16:37:27,889 running dist_info 2026-08-31T16:37:27,899 creating /tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info 2026-08-31T16:37:27,900 writing /tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/PKG-INFO 2026-08-31T16:37:27,904 writing dependency_links to /tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/dependency_links.txt 2026-08-31T16:37:27,905 writing entry points to /tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/entry_points.txt 2026-08-31T16:37:27,907 writing requirements to /tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/requires.txt 2026-08-31T16:37:27,908 writing top-level names to /tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/top_level.txt 2026-08-31T16:37:27,909 writing manifest file '/tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/SOURCES.txt' 2026-08-31T16:37:27,935 reading manifest file '/tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/SOURCES.txt' 2026-08-31T16:37:27,937 adding license file 'LICENSE' 2026-08-31T16:37:27,944 writing manifest file '/tmp/pip-modern-metadata-e9rko6iv/topiary.egg-info/SOURCES.txt' 2026-08-31T16:37:27,945 creating '/tmp/pip-modern-metadata-e9rko6iv/topiary-5.29.0.dist-info' 2026-08-31T16:37:28,071 Preparing metadata (pyproject.toml): finished with status 'done' 2026-08-31T16:37:28,077 Source in /tmp/pip-wheel-625lkb7b/topiary_f2687b62f8004fa4a4babb93c4d57ccb has version 5.29.0, which satisfies requirement topiary==5.29.0 from https://files.pythonhosted.org/packages/c8/ed/e425bba6fef623f969ed53ec35c546ebf3f11a6b8024b338ba04e35fabd5/topiary-5.29.0.tar.gz 2026-08-31T16:37:28,078 Removed topiary==5.29.0 from https://files.pythonhosted.org/packages/c8/ed/e425bba6fef623f969ed53ec35c546ebf3f11a6b8024b338ba04e35fabd5/topiary-5.29.0.tar.gz from build tracker '/tmp/pip-build-tracker-pcqq_27j' 2026-08-31T16:37:28,086 Created temporary directory: /tmp/pip-unpack-8oeen20j 2026-08-31T16:37:28,087 Building wheels for collected packages: topiary 2026-08-31T16:37:28,092 Created temporary directory: /tmp/pip-wheel-ag4gi29w 2026-08-31T16:37:28,092 Destination directory: /tmp/pip-wheel-ag4gi29w 2026-08-31T16:37:28,095 Building wheel for topiary (pyproject.toml): started 2026-08-31T16:37:28,096 Running command Building wheel for topiary (pyproject.toml) 2026-08-31T16:37:28,735 /tmp/pip-build-env-zg77jmu2/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:37:28,735 !! 2026-08-31T16:37:28,736 ******************************************************************************** 2026-08-31T16:37:28,737 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:37:28,738 License :: OSI Approved :: Apache Software License 2026-08-31T16:37:28,739 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:37:28,739 ******************************************************************************** 2026-08-31T16:37:28,740 !! 2026-08-31T16:37:28,741 dist._finalize_license_expression() 2026-08-31T16:37:28,741 /tmp/pip-build-env-zg77jmu2/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:37:28,742 !! 2026-08-31T16:37:28,743 ******************************************************************************** 2026-08-31T16:37:28,743 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:37:28,744 License :: OSI Approved :: Apache Software License 2026-08-31T16:37:28,745 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:37:28,746 ******************************************************************************** 2026-08-31T16:37:28,746 !! 2026-08-31T16:37:28,747 self._finalize_license_expression() 2026-08-31T16:37:28,747 running bdist_wheel 2026-08-31T16:37:28,761 running build 2026-08-31T16:37:28,762 running build_py 2026-08-31T16:37:28,768 creating build/lib/topiary 2026-08-31T16:37:28,770 copying topiary/wide.py -> build/lib/topiary 2026-08-31T16:37:28,773 copying topiary/io.py -> build/lib/topiary 2026-08-31T16:37:28,775 copying topiary/self_proteome.py -> build/lib/topiary 2026-08-31T16:37:28,778 copying topiary/io_lens.py -> build/lib/topiary 2026-08-31T16:37:28,781 copying topiary/cached.py -> build/lib/topiary 2026-08-31T16:37:28,784 copying topiary/properties.py -> build/lib/topiary 2026-08-31T16:37:28,786 copying topiary/protein_fragment.py -> build/lib/topiary 2026-08-31T16:37:28,789 copying topiary/io_pvacseq.py -> build/lib/topiary 2026-08-31T16:37:28,792 copying topiary/filters.py -> build/lib/topiary 2026-08-31T16:37:28,794 copying topiary/__init__.py -> build/lib/topiary 2026-08-31T16:37:28,796 copying topiary/predictor.py -> build/lib/topiary 2026-08-31T16:37:28,800 copying topiary/sources.py -> build/lib/topiary 2026-08-31T16:37:28,802 copying topiary/result.py -> build/lib/topiary 2026-08-31T16:37:28,805 copying topiary/inputs.py -> build/lib/topiary 2026-08-31T16:37:28,808 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-08-31T16:37:28,810 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-08-31T16:37:28,814 creating build/lib/tests 2026-08-31T16:37:28,815 copying tests/test_kind_mhc_dependence.py -> build/lib/tests 2026-08-31T16:37:28,818 copying tests/test_wide.py -> build/lib/tests 2026-08-31T16:37:28,821 copying tests/test_cli_coverage.py -> build/lib/tests 2026-08-31T16:37:28,823 copying tests/test_lens_versions.py -> build/lib/tests 2026-08-31T16:37:28,825 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-08-31T16:37:28,827 copying tests/test_io.py -> build/lib/tests 2026-08-31T16:37:28,830 copying tests/test_lens_multi_version.py -> build/lib/tests 2026-08-31T16:37:28,832 copying tests/test_protein_fragment.py -> build/lib/tests 2026-08-31T16:37:28,835 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-08-31T16:37:28,837 copying tests/test_self_proteome.py -> build/lib/tests 2026-08-31T16:37:28,839 copying tests/test_group_keys.py -> build/lib/tests 2026-08-31T16:37:28,842 copying tests/common.py -> build/lib/tests 2026-08-31T16:37:28,844 copying tests/test_result.py -> build/lib/tests 2026-08-31T16:37:28,847 copying tests/test_ranking.py -> build/lib/tests 2026-08-31T16:37:28,852 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-08-31T16:37:28,854 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-08-31T16:37:28,856 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-08-31T16:37:28,858 copying tests/test_integration.py -> build/lib/tests 2026-08-31T16:37:28,860 copying tests/test_peptide_property_node.py -> build/lib/tests 2026-08-31T16:37:28,862 copying tests/test_self_nearest_population.py -> build/lib/tests 2026-08-31T16:37:28,864 copying tests/test_dataframe.py -> build/lib/tests 2026-08-31T16:37:28,866 copying tests/test_io_lens.py -> build/lib/tests 2026-08-31T16:37:28,868 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-08-31T16:37:28,871 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-08-31T16:37:28,872 copying tests/test_cli_script.py -> build/lib/tests 2026-08-31T16:37:28,874 copying tests/test_lazy_imports.py -> build/lib/tests 2026-08-31T16:37:28,876 copying tests/test_context_forwarding.py -> build/lib/tests 2026-08-31T16:37:28,878 copying tests/test_cli_ranking.py -> build/lib/tests 2026-08-31T16:37:28,881 copying tests/test_allele_class.py -> build/lib/tests 2026-08-31T16:37:28,883 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-08-31T16:37:28,885 copying tests/test_predictor_internals.py -> build/lib/tests 2026-08-31T16:37:28,887 copying tests/test_allele_free_kinds.py -> build/lib/tests 2026-08-31T16:37:28,890 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-08-31T16:37:28,892 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-08-31T16:37:28,894 copying tests/test_from_predictions.py -> build/lib/tests 2026-08-31T16:37:28,896 copying tests/test_padding.py -> build/lib/tests 2026-08-31T16:37:28,898 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-08-31T16:37:28,900 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-08-31T16:37:28,903 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-08-31T16:37:28,906 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-08-31T16:37:28,909 copying tests/test_dsl_polish.py -> build/lib/tests 2026-08-31T16:37:28,911 copying tests/test_args_outputs.py -> build/lib/tests 2026-08-31T16:37:28,913 copying tests/test_sources_optional.py -> build/lib/tests 2026-08-31T16:37:28,915 copying tests/test_allele_set.py -> build/lib/tests 2026-08-31T16:37:28,917 copying tests/data.py -> build/lib/tests 2026-08-31T16:37:28,919 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-08-31T16:37:28,921 copying tests/test_expression_integration.py -> build/lib/tests 2026-08-31T16:37:28,923 copying tests/test_sources.py -> build/lib/tests 2026-08-31T16:37:28,925 copying tests/test_deploy_script.py -> build/lib/tests 2026-08-31T16:37:28,927 copying tests/test_best_allele.py -> build/lib/tests 2026-08-31T16:37:28,930 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-08-31T16:37:28,932 copying tests/test_cached_predictor.py -> build/lib/tests 2026-08-31T16:37:28,936 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-08-31T16:37:28,938 copying tests/test_shared_context.py -> build/lib/tests 2026-08-31T16:37:28,940 copying tests/test_end_to_end.py -> build/lib/tests 2026-08-31T16:37:28,942 copying tests/__init__.py -> build/lib/tests 2026-08-31T16:37:28,944 copying tests/test_io_pvacseq.py -> build/lib/tests 2026-08-31T16:37:28,947 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-08-31T16:37:28,950 copying tests/test_scoped_filters.py -> build/lib/tests 2026-08-31T16:37:28,952 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-08-31T16:37:28,954 copying tests/test_peptide_view.py -> build/lib/tests 2026-08-31T16:37:28,957 copying tests/test_sort_ordering.py -> build/lib/tests 2026-08-31T16:37:28,959 copying tests/test_canonical_methods.py -> build/lib/tests 2026-08-31T16:37:28,961 copying tests/test_kind_support.py -> build/lib/tests 2026-08-31T16:37:28,964 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-08-31T16:37:28,966 copying tests/test_rna_helpers.py -> build/lib/tests 2026-08-31T16:37:28,968 copying tests/test_inputs.py -> build/lib/tests 2026-08-31T16:37:28,970 copying tests/test_expression_loader.py -> build/lib/tests 2026-08-31T16:37:28,972 copying tests/test_combine_predictor_results.py -> build/lib/tests 2026-08-31T16:37:28,975 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-08-31T16:37:28,978 creating build/lib/topiary/rna 2026-08-31T16:37:28,979 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-08-31T16:37:28,982 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-08-31T16:37:28,984 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-08-31T16:37:28,985 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-08-31T16:37:28,987 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-08-31T16:37:28,990 creating build/lib/topiary/cli 2026-08-31T16:37:28,991 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-08-31T16:37:28,993 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-08-31T16:37:28,995 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-08-31T16:37:28,998 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-08-31T16:37:29,000 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-08-31T16:37:29,002 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-08-31T16:37:29,004 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-08-31T16:37:29,006 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-08-31T16:37:29,008 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-08-31T16:37:29,010 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-08-31T16:37:29,012 creating build/lib/topiary/ranking 2026-08-31T16:37:29,013 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-08-31T16:37:29,017 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-08-31T16:37:29,020 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-08-31T16:37:29,022 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-08-31T16:37:29,024 running egg_info 2026-08-31T16:37:29,034 writing topiary.egg-info/PKG-INFO 2026-08-31T16:37:29,038 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-08-31T16:37:29,039 writing entry points to topiary.egg-info/entry_points.txt 2026-08-31T16:37:29,040 writing requirements to topiary.egg-info/requires.txt 2026-08-31T16:37:29,041 writing top-level names to topiary.egg-info/top_level.txt 2026-08-31T16:37:29,059 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:37:29,066 adding license file 'LICENSE' 2026-08-31T16:37:29,073 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:37:29,091 installing to build/bdist.linux-armv7l/wheel 2026-08-31T16:37:29,092 running install 2026-08-31T16:37:29,114 running install_lib 2026-08-31T16:37:29,119 creating build/bdist.linux-armv7l/wheel 2026-08-31T16:37:29,121 creating build/bdist.linux-armv7l/wheel/topiary 2026-08-31T16:37:29,123 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,125 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,128 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,130 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,133 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,136 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,138 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,141 copying build/lib/topiary/io_pvacseq.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,144 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-08-31T16:37:29,145 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:37:29,147 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:37:29,149 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:37:29,151 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:37:29,152 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:37:29,155 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,157 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,159 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-08-31T16:37:29,160 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,162 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,164 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,167 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,169 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,171 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,173 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,174 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,176 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,178 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:37:29,180 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,183 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,186 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,188 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,191 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,193 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:37:29,195 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-08-31T16:37:29,196 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:37:29,200 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:37:29,203 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:37:29,205 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:37:29,209 creating build/bdist.linux-armv7l/wheel/tests 2026-08-31T16:37:29,210 copying build/lib/tests/test_kind_mhc_dependence.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,212 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,215 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,217 copying build/lib/tests/test_lens_versions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,219 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,221 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,224 copying build/lib/tests/test_lens_multi_version.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,226 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,229 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,230 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,233 copying build/lib/tests/test_group_keys.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,235 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,237 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,239 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,243 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,245 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,247 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,249 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,251 copying build/lib/tests/test_peptide_property_node.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,253 copying build/lib/tests/test_self_nearest_population.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,255 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,257 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,259 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,261 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,263 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,265 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,266 copying build/lib/tests/test_context_forwarding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,269 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,271 copying build/lib/tests/test_allele_class.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,273 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,275 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,277 copying build/lib/tests/test_allele_free_kinds.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,279 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,282 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,283 copying build/lib/tests/test_from_predictions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,286 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,287 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,289 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,292 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,294 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,297 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,299 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,301 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,302 copying build/lib/tests/test_allele_set.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,305 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,306 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,308 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,310 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,312 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,314 copying build/lib/tests/test_best_allele.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,316 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,318 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,320 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,322 copying build/lib/tests/test_shared_context.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,324 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,327 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,328 copying build/lib/tests/test_io_pvacseq.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,331 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,333 copying build/lib/tests/test_scoped_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,335 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,337 copying build/lib/tests/test_peptide_view.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,339 copying build/lib/tests/test_sort_ordering.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,342 copying build/lib/tests/test_canonical_methods.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,344 copying build/lib/tests/test_kind_support.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,346 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,349 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,351 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,353 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,355 copying build/lib/tests/test_combine_predictor_results.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,357 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:37:29,360 running install_egg_info 2026-08-31T16:37:29,365 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.29.0-py3.11.egg-info 2026-08-31T16:37:29,377 running install_scripts 2026-08-31T16:37:29,389 creating build/bdist.linux-armv7l/wheel/topiary-5.29.0.dist-info/WHEEL 2026-08-31T16:37:29,392 creating '/tmp/pip-wheel-ag4gi29w/.tmp-rfnync8v/topiary-5.29.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-08-31T16:37:29,395 adding 'tests/__init__.py' 2026-08-31T16:37:29,396 adding 'tests/common.py' 2026-08-31T16:37:29,398 adding 'tests/data.py' 2026-08-31T16:37:29,399 adding 'tests/test_allele_class.py' 2026-08-31T16:37:29,401 adding 'tests/test_allele_free_kinds.py' 2026-08-31T16:37:29,403 adding 'tests/test_allele_set.py' 2026-08-31T16:37:29,405 adding 'tests/test_args_outputs.py' 2026-08-31T16:37:29,407 adding 'tests/test_best_allele.py' 2026-08-31T16:37:29,411 adding 'tests/test_cached_predictor.py' 2026-08-31T16:37:29,413 adding 'tests/test_canonical_methods.py' 2026-08-31T16:37:29,415 adding 'tests/test_cli_cached_predictor.py' 2026-08-31T16:37:29,417 adding 'tests/test_cli_coverage.py' 2026-08-31T16:37:29,418 adding 'tests/test_cli_protein_changes.py' 2026-08-31T16:37:29,419 adding 'tests/test_cli_ranking.py' 2026-08-31T16:37:29,421 adding 'tests/test_cli_script.py' 2026-08-31T16:37:29,423 adding 'tests/test_combine_predictor_results.py' 2026-08-31T16:37:29,425 adding 'tests/test_contains_mutant_residues.py' 2026-08-31T16:37:29,426 adding 'tests/test_context_forwarding.py' 2026-08-31T16:37:29,428 adding 'tests/test_coverage_gaps.py' 2026-08-31T16:37:29,430 adding 'tests/test_dataframe.py' 2026-08-31T16:37:29,431 adding 'tests/test_deploy_script.py' 2026-08-31T16:37:29,432 adding 'tests/test_direct_input_regressions.py' 2026-08-31T16:37:29,435 adding 'tests/test_dsl_extensions.py' 2026-08-31T16:37:29,437 adding 'tests/test_dsl_polish.py' 2026-08-31T16:37:29,439 adding 'tests/test_dsl_roundtrip.py' 2026-08-31T16:37:29,441 adding 'tests/test_edge_case_fixtures.py' 2026-08-31T16:37:29,442 adding 'tests/test_effect_expression_filters.py' 2026-08-31T16:37:29,444 adding 'tests/test_end_to_end.py' 2026-08-31T16:37:29,445 adding 'tests/test_epitopes_from_commandline_args.py' 2026-08-31T16:37:29,446 adding 'tests/test_expression_integration.py' 2026-08-31T16:37:29,448 adding 'tests/test_expression_loader.py' 2026-08-31T16:37:29,451 adding 'tests/test_frameshift_fragments.py' 2026-08-31T16:37:29,452 adding 'tests/test_from_predictions.py' 2026-08-31T16:37:29,455 adding 'tests/test_group_keys.py' 2026-08-31T16:37:29,456 adding 'tests/test_inputs.py' 2026-08-31T16:37:29,458 adding 'tests/test_integration.py' 2026-08-31T16:37:29,460 adding 'tests/test_io.py' 2026-08-31T16:37:29,462 adding 'tests/test_io_lens.py' 2026-08-31T16:37:29,465 adding 'tests/test_io_pvacseq.py' 2026-08-31T16:37:29,467 adding 'tests/test_kind_mhc_dependence.py' 2026-08-31T16:37:29,469 adding 'tests/test_kind_support.py' 2026-08-31T16:37:29,470 adding 'tests/test_lazy_imports.py' 2026-08-31T16:37:29,472 adding 'tests/test_lens_multi_version.py' 2026-08-31T16:37:29,474 adding 'tests/test_lens_versions.py' 2026-08-31T16:37:29,475 adding 'tests/test_load_cufflinks_fpkm.py' 2026-08-31T16:37:29,476 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-08-31T16:37:29,477 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-08-31T16:37:29,479 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-08-31T16:37:29,480 adding 'tests/test_padding.py' 2026-08-31T16:37:29,481 adding 'tests/test_peptide_mutation_interval.py' 2026-08-31T16:37:29,483 adding 'tests/test_peptide_property_node.py' 2026-08-31T16:37:29,486 adding 'tests/test_peptide_view.py' 2026-08-31T16:37:29,489 adding 'tests/test_predict_from_fragments.py' 2026-08-31T16:37:29,492 adding 'tests/test_predict_from_variants_refactor.py' 2026-08-31T16:37:29,494 adding 'tests/test_predictor_internals.py' 2026-08-31T16:37:29,496 adding 'tests/test_protein_fragment.py' 2026-08-31T16:37:29,505 adding 'tests/test_ranking.py' 2026-08-31T16:37:29,508 adding 'tests/test_result.py' 2026-08-31T16:37:29,510 adding 'tests/test_rna_helpers.py' 2026-08-31T16:37:29,511 adding 'tests/test_scoped_filters.py' 2026-08-31T16:37:29,513 adding 'tests/test_self_nearest_population.py' 2026-08-31T16:37:29,516 adding 'tests/test_self_proteome.py' 2026-08-31T16:37:29,517 adding 'tests/test_sequence_helpers.py' 2026-08-31T16:37:29,519 adding 'tests/test_shared_context.py' 2026-08-31T16:37:29,520 adding 'tests/test_sort_ordering.py' 2026-08-31T16:37:29,522 adding 'tests/test_sources.py' 2026-08-31T16:37:29,523 adding 'tests/test_sources_optional.py' 2026-08-31T16:37:29,525 adding 'tests/test_validation_and_edge_cases.py' 2026-08-31T16:37:29,526 adding 'tests/test_variant_expression_filters.py' 2026-08-31T16:37:29,528 adding 'tests/test_wide.py' 2026-08-31T16:37:29,530 adding 'topiary/__init__.py' 2026-08-31T16:37:29,536 adding 'topiary/cached.py' 2026-08-31T16:37:29,538 adding 'topiary/filters.py' 2026-08-31T16:37:29,540 adding 'topiary/inputs.py' 2026-08-31T16:37:29,542 adding 'topiary/io.py' 2026-08-31T16:37:29,544 adding 'topiary/io_lens.py' 2026-08-31T16:37:29,546 adding 'topiary/io_protein_fragment.py' 2026-08-31T16:37:29,549 adding 'topiary/io_pvacseq.py' 2026-08-31T16:37:29,557 adding 'topiary/predictor.py' 2026-08-31T16:37:29,559 adding 'topiary/properties.py' 2026-08-31T16:37:29,562 adding 'topiary/protein_fragment.py' 2026-08-31T16:37:29,565 adding 'topiary/result.py' 2026-08-31T16:37:29,569 adding 'topiary/self_proteome.py' 2026-08-31T16:37:29,571 adding 'topiary/sequence_helpers.py' 2026-08-31T16:37:29,573 adding 'topiary/sources.py' 2026-08-31T16:37:29,575 adding 'topiary/wide.py' 2026-08-31T16:37:29,577 adding 'topiary/cli/__init__.py' 2026-08-31T16:37:29,580 adding 'topiary/cli/args.py' 2026-08-31T16:37:29,582 adding 'topiary/cli/cached_predictor.py' 2026-08-31T16:37:29,584 adding 'topiary/cli/errors.py' 2026-08-31T16:37:29,585 adding 'topiary/cli/filtering.py' 2026-08-31T16:37:29,587 adding 'topiary/cli/outputs.py' 2026-08-31T16:37:29,588 adding 'topiary/cli/protein_changes.py' 2026-08-31T16:37:29,590 adding 'topiary/cli/rna.py' 2026-08-31T16:37:29,591 adding 'topiary/cli/script.py' 2026-08-31T16:37:29,592 adding 'topiary/cli/sequence.py' 2026-08-31T16:37:29,594 adding 'topiary/ranking/__init__.py' 2026-08-31T16:37:29,597 adding 'topiary/ranking/apply.py' 2026-08-31T16:37:29,612 adding 'topiary/ranking/nodes.py' 2026-08-31T16:37:29,616 adding 'topiary/ranking/parser.py' 2026-08-31T16:37:29,618 adding 'topiary/rna/__init__.py' 2026-08-31T16:37:29,619 adding 'topiary/rna/common.py' 2026-08-31T16:37:29,621 adding 'topiary/rna/cufflinks.py' 2026-08-31T16:37:29,623 adding 'topiary/rna/expression_loader.py' 2026-08-31T16:37:29,624 adding 'topiary/rna/gtf.py' 2026-08-31T16:37:29,628 adding 'topiary-5.29.0.dist-info/licenses/LICENSE' 2026-08-31T16:37:29,631 adding 'topiary-5.29.0.dist-info/METADATA' 2026-08-31T16:37:29,632 adding 'topiary-5.29.0.dist-info/WHEEL' 2026-08-31T16:37:29,633 adding 'topiary-5.29.0.dist-info/entry_points.txt' 2026-08-31T16:37:29,634 adding 'topiary-5.29.0.dist-info/top_level.txt' 2026-08-31T16:37:29,636 adding 'topiary-5.29.0.dist-info/RECORD' 2026-08-31T16:37:29,642 removing build/bdist.linux-armv7l/wheel 2026-08-31T16:37:29,765 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-08-31T16:37:29,777 Created wheel for topiary: filename=topiary-5.29.0-py3-none-any.whl size=363698 sha256=19a7f12827764e0f12920fe48404aa6607e31ffd04f04fed96d084327f8fc436 2026-08-31T16:37:29,778 Stored in directory: /tmp/pip-ephem-wheel-cache-59p9inp8/wheels/5f/92/ed/6929c4daae706829abe5a7fd3f3907bc04f346afe2c80a3749 2026-08-31T16:37:29,796 Successfully built topiary 2026-08-31T16:37:29,811 Removed build tracker: '/tmp/pip-build-tracker-pcqq_27j'