2026-05-09T03:47:24,261 Created temporary directory: /tmp/pip-ephem-wheel-cache-vguyuces 2026-05-09T03:47:24,263 Created temporary directory: /tmp/pip-build-tracker-ep7ygech 2026-05-09T03:47:24,263 Initialized build tracking at /tmp/pip-build-tracker-ep7ygech 2026-05-09T03:47:24,264 Created build tracker: /tmp/pip-build-tracker-ep7ygech 2026-05-09T03:47:24,264 Entered build tracker: /tmp/pip-build-tracker-ep7ygech 2026-05-09T03:47:24,265 Created temporary directory: /tmp/pip-wheel-dhi85yzf 2026-05-09T03:47:24,268 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. 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https://archive1.piwheels.org/simple/topiary/topiary-0.0.8-py3-none-any.whl#sha256=12b4f283d8fbedbd316649be8833a17fee852097f1e5cd8963264e6c4a2721e0 (from https://www.piwheels.org/simple/topiary/) 2026-05-09T03:47:24,886 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.7-py3-none-any.whl#sha256=6e23dbd38e19c12b658a8373b501f1e929c6fd3420749dee506a82b60b190d42 (from https://www.piwheels.org/simple/topiary/) 2026-05-09T03:47:24,887 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.6-py3-none-any.whl#sha256=f3b597a0744c3a7540c3ffe571b8f4fad3d2ad40ddc6198952e2aee7c96ff82c (from https://www.piwheels.org/simple/topiary/) 2026-05-09T03:47:24,887 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/) 2026-05-09T03:47:24,888 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/) 2026-05-09T03:47:24,888 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/) 2026-05-09T03:47:24,889 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/) 2026-05-09T03:47:24,889 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/) 2026-05-09T03:47:24,890 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/) 2026-05-09T03:47:24,890 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-05-09T03:47:24,891 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-05-09T03:47:24,918 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-05-09T03:47:24,936 Collecting topiary==5.12.0 2026-05-09T03:47:24,939 Created temporary directory: /tmp/pip-unpack-uj065qp2 2026-05-09T03:47:25,178 Downloading topiary-5.12.0.tar.gz (224 kB) 2026-05-09T03:47:25,488 Added topiary==5.12.0 from https://files.pythonhosted.org/packages/f8/b4/023a32e2dbe29176e05aac6b437d722f07ac5412efa25afe37df47012fdf/topiary-5.12.0.tar.gz to build tracker '/tmp/pip-build-tracker-ep7ygech' 2026-05-09T03:47:25,493 Created temporary directory: /tmp/pip-build-env-oso9y7lo 2026-05-09T03:47:25,497 Installing build dependencies: started 2026-05-09T03:47:25,499 Running command pip subprocess to install build dependencies 2026-05-09T03:47:26,653 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-09T03:47:27,093 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 2026-05-09T03:47:27,117 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-09T03:47:28,890 Collecting setuptools>=64 2026-05-09T03:47:28,966 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-09T03:47:31,878 Installing collected packages: setuptools 2026-05-09T03:47:34,981 Successfully installed setuptools-82.0.1 2026-05-09T03:47:35,246 Installing build dependencies: finished with status 'done' 2026-05-09T03:47:35,253 Getting requirements to build wheel: started 2026-05-09T03:47:35,254 Running command Getting requirements to build wheel 2026-05-09T03:47:35,975 /tmp/pip-build-env-oso9y7lo/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-09T03:47:35,975 !! 2026-05-09T03:47:35,977 ******************************************************************************** 2026-05-09T03:47:35,977 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-09T03:47:35,978 License :: OSI Approved :: Apache Software License 2026-05-09T03:47:35,979 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-09T03:47:35,980 ******************************************************************************** 2026-05-09T03:47:35,981 !! 2026-05-09T03:47:35,981 dist._finalize_license_expression() 2026-05-09T03:47:35,982 /tmp/pip-build-env-oso9y7lo/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-09T03:47:35,982 !! 2026-05-09T03:47:35,983 ******************************************************************************** 2026-05-09T03:47:35,984 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-09T03:47:35,985 License :: OSI Approved :: Apache Software License 2026-05-09T03:47:35,985 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-09T03:47:35,986 ******************************************************************************** 2026-05-09T03:47:35,987 !! 2026-05-09T03:47:35,987 self._finalize_license_expression() 2026-05-09T03:47:35,988 running egg_info 2026-05-09T03:47:35,994 writing topiary.egg-info/PKG-INFO 2026-05-09T03:47:35,998 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-09T03:47:36,000 writing entry points to topiary.egg-info/entry_points.txt 2026-05-09T03:47:36,002 writing requirements to topiary.egg-info/requires.txt 2026-05-09T03:47:36,003 writing top-level names to topiary.egg-info/top_level.txt 2026-05-09T03:47:36,032 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-09T03:47:36,038 adding license file 'LICENSE' 2026-05-09T03:47:36,045 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-09T03:47:36,141 Getting requirements to build wheel: finished with status 'done' 2026-05-09T03:47:36,145 Created temporary directory: /tmp/pip-modern-metadata-kvo_wyh5 2026-05-09T03:47:36,147 Preparing metadata (pyproject.toml): started 2026-05-09T03:47:36,149 Running command Preparing metadata (pyproject.toml) 2026-05-09T03:47:36,797 /tmp/pip-build-env-oso9y7lo/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-09T03:47:36,797 !! 2026-05-09T03:47:36,798 ******************************************************************************** 2026-05-09T03:47:36,799 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-09T03:47:36,800 License :: OSI Approved :: Apache Software License 2026-05-09T03:47:36,801 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-09T03:47:36,801 ******************************************************************************** 2026-05-09T03:47:36,803 !! 2026-05-09T03:47:36,803 dist._finalize_license_expression() 2026-05-09T03:47:36,804 /tmp/pip-build-env-oso9y7lo/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-09T03:47:36,805 !! 2026-05-09T03:47:36,806 ******************************************************************************** 2026-05-09T03:47:36,807 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-09T03:47:36,808 License :: OSI Approved :: Apache Software License 2026-05-09T03:47:36,809 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-09T03:47:36,810 ******************************************************************************** 2026-05-09T03:47:36,810 !! 2026-05-09T03:47:36,811 self._finalize_license_expression() 2026-05-09T03:47:36,813 running dist_info 2026-05-09T03:47:36,823 creating /tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info 2026-05-09T03:47:36,824 writing /tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/PKG-INFO 2026-05-09T03:47:36,829 writing dependency_links to /tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/dependency_links.txt 2026-05-09T03:47:36,830 writing entry points to /tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/entry_points.txt 2026-05-09T03:47:36,832 writing requirements to /tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/requires.txt 2026-05-09T03:47:36,833 writing top-level names to /tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/top_level.txt 2026-05-09T03:47:36,834 writing manifest file '/tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/SOURCES.txt' 2026-05-09T03:47:36,859 reading manifest file '/tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/SOURCES.txt' 2026-05-09T03:47:36,861 adding license file 'LICENSE' 2026-05-09T03:47:36,866 writing manifest file '/tmp/pip-modern-metadata-kvo_wyh5/topiary.egg-info/SOURCES.txt' 2026-05-09T03:47:36,867 creating '/tmp/pip-modern-metadata-kvo_wyh5/topiary-5.12.0.dist-info' 2026-05-09T03:47:36,995 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-09T03:47:37,002 Source in /tmp/pip-wheel-dhi85yzf/topiary_1e54b4162c274a79b1d4ec67c255d7bd has version 5.12.0, which satisfies requirement topiary==5.12.0 from https://files.pythonhosted.org/packages/f8/b4/023a32e2dbe29176e05aac6b437d722f07ac5412efa25afe37df47012fdf/topiary-5.12.0.tar.gz 2026-05-09T03:47:37,003 Removed topiary==5.12.0 from https://files.pythonhosted.org/packages/f8/b4/023a32e2dbe29176e05aac6b437d722f07ac5412efa25afe37df47012fdf/topiary-5.12.0.tar.gz from build tracker '/tmp/pip-build-tracker-ep7ygech' 2026-05-09T03:47:37,011 Created temporary directory: /tmp/pip-unpack-hjn_5u66 2026-05-09T03:47:37,012 Building wheels for collected packages: topiary 2026-05-09T03:47:37,017 Created temporary directory: /tmp/pip-wheel-ljry931o 2026-05-09T03:47:37,017 Destination directory: /tmp/pip-wheel-ljry931o 2026-05-09T03:47:37,020 Building wheel for topiary (pyproject.toml): started 2026-05-09T03:47:37,021 Running command Building wheel for topiary (pyproject.toml) 2026-05-09T03:47:37,659 /tmp/pip-build-env-oso9y7lo/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-09T03:47:37,659 !! 2026-05-09T03:47:37,660 ******************************************************************************** 2026-05-09T03:47:37,661 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-09T03:47:37,662 License :: OSI Approved :: Apache Software License 2026-05-09T03:47:37,663 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-09T03:47:37,664 ******************************************************************************** 2026-05-09T03:47:37,665 !! 2026-05-09T03:47:37,666 dist._finalize_license_expression() 2026-05-09T03:47:37,667 /tmp/pip-build-env-oso9y7lo/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-09T03:47:37,667 !! 2026-05-09T03:47:37,669 ******************************************************************************** 2026-05-09T03:47:37,669 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-09T03:47:37,670 License :: OSI Approved :: Apache Software License 2026-05-09T03:47:37,672 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-09T03:47:37,672 ******************************************************************************** 2026-05-09T03:47:37,673 !! 2026-05-09T03:47:37,674 self._finalize_license_expression() 2026-05-09T03:47:37,674 running bdist_wheel 2026-05-09T03:47:37,684 running build 2026-05-09T03:47:37,685 running build_py 2026-05-09T03:47:37,691 creating build/lib/topiary 2026-05-09T03:47:37,694 copying topiary/filters.py -> build/lib/topiary 2026-05-09T03:47:37,696 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-09T03:47:37,699 copying topiary/io.py -> build/lib/topiary 2026-05-09T03:47:37,701 copying topiary/properties.py -> build/lib/topiary 2026-05-09T03:47:37,704 copying topiary/wide.py -> build/lib/topiary 2026-05-09T03:47:37,706 copying topiary/inputs.py -> build/lib/topiary 2026-05-09T03:47:37,708 copying topiary/io_lens.py -> build/lib/topiary 2026-05-09T03:47:37,711 copying topiary/result.py -> build/lib/topiary 2026-05-09T03:47:37,713 copying topiary/predictor.py -> build/lib/topiary 2026-05-09T03:47:37,717 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-09T03:47:37,719 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-09T03:47:37,721 copying topiary/cached.py -> build/lib/topiary 2026-05-09T03:47:37,725 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-09T03:47:37,727 copying topiary/__init__.py -> build/lib/topiary 2026-05-09T03:47:37,729 copying topiary/sources.py -> build/lib/topiary 2026-05-09T03:47:37,733 creating build/lib/tests 2026-05-09T03:47:37,734 copying tests/test_padding.py -> build/lib/tests 2026-05-09T03:47:37,736 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-09T03:47:37,738 copying tests/test_lazy_imports.py -> build/lib/tests 2026-05-09T03:47:37,740 copying tests/test_io_lens.py -> build/lib/tests 2026-05-09T03:47:37,742 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-09T03:47:37,744 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-09T03:47:37,747 copying tests/test_cli_script.py -> build/lib/tests 2026-05-09T03:47:37,749 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-09T03:47:37,752 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-09T03:47:37,753 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-09T03:47:37,755 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-09T03:47:37,757 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-09T03:47:37,759 copying tests/test_kind_support.py -> build/lib/tests 2026-05-09T03:47:37,761 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-09T03:47:37,764 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-09T03:47:37,766 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-09T03:47:37,768 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-09T03:47:37,770 copying tests/test_result.py -> build/lib/tests 2026-05-09T03:47:37,773 copying tests/test_io.py -> build/lib/tests 2026-05-09T03:47:37,776 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-09T03:47:37,778 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-09T03:47:37,781 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-09T03:47:37,783 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-09T03:47:37,785 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-09T03:47:37,788 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-09T03:47:37,790 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-09T03:47:37,793 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-09T03:47:37,795 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-09T03:47:37,797 copying tests/data.py -> build/lib/tests 2026-05-09T03:47:37,799 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-09T03:47:37,801 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-09T03:47:37,804 copying tests/test_inputs.py -> build/lib/tests 2026-05-09T03:47:37,806 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-09T03:47:37,808 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-09T03:47:37,811 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-09T03:47:37,813 copying tests/common.py -> build/lib/tests 2026-05-09T03:47:37,815 copying tests/test_sources.py -> build/lib/tests 2026-05-09T03:47:37,817 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-09T03:47:37,819 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-09T03:47:37,822 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-09T03:47:37,824 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-09T03:47:37,827 copying tests/test_dataframe.py -> build/lib/tests 2026-05-09T03:47:37,828 copying tests/test_ranking.py -> build/lib/tests 2026-05-09T03:47:37,832 copying tests/test_deploy_script.py -> build/lib/tests 2026-05-09T03:47:37,834 copying tests/test_integration.py -> build/lib/tests 2026-05-09T03:47:37,836 copying tests/__init__.py -> build/lib/tests 2026-05-09T03:47:37,838 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-09T03:47:37,840 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-09T03:47:37,843 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-09T03:47:37,845 copying tests/test_wide.py -> build/lib/tests 2026-05-09T03:47:37,847 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-09T03:47:37,850 creating build/lib/topiary/ranking 2026-05-09T03:47:37,851 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-09T03:47:37,854 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-09T03:47:37,856 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-09T03:47:37,860 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-09T03:47:37,863 creating build/lib/topiary/rna 2026-05-09T03:47:37,864 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-09T03:47:37,866 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-09T03:47:37,868 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-09T03:47:37,870 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-09T03:47:37,873 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-09T03:47:37,875 creating build/lib/topiary/cli 2026-05-09T03:47:37,876 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-09T03:47:37,878 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-09T03:47:37,881 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-09T03:47:37,883 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-09T03:47:37,885 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-09T03:47:37,888 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-09T03:47:37,890 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-09T03:47:37,893 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-09T03:47:37,895 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-09T03:47:37,896 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-09T03:47:37,898 running egg_info 2026-05-09T03:47:37,908 writing topiary.egg-info/PKG-INFO 2026-05-09T03:47:37,912 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-09T03:47:37,913 writing entry points to topiary.egg-info/entry_points.txt 2026-05-09T03:47:37,915 writing requirements to topiary.egg-info/requires.txt 2026-05-09T03:47:37,916 writing top-level names to topiary.egg-info/top_level.txt 2026-05-09T03:47:37,932 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-09T03:47:37,939 adding license file 'LICENSE' 2026-05-09T03:47:37,945 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-09T03:47:37,963 installing to build/bdist.linux-armv7l/wheel 2026-05-09T03:47:37,963 running install 2026-05-09T03:47:37,987 running install_lib 2026-05-09T03:47:37,993 creating build/bdist.linux-armv7l/wheel 2026-05-09T03:47:37,995 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-09T03:47:37,997 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:37,999 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,002 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,004 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,006 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,009 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,011 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-09T03:47:38,012 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-09T03:47:38,015 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-09T03:47:38,018 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-09T03:47:38,021 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-09T03:47:38,023 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-09T03:47:38,024 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-09T03:47:38,027 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-09T03:47:38,029 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-09T03:47:38,031 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-09T03:47:38,034 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-09T03:47:38,035 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,038 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,041 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,043 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,046 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,048 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,051 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,054 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-09T03:47:38,056 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,058 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,060 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,062 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,064 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,067 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,069 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,072 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,074 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,076 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-09T03:47:38,077 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,079 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-09T03:47:38,083 creating build/bdist.linux-armv7l/wheel/tests 2026-05-09T03:47:38,084 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,086 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,088 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,089 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,092 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,093 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,096 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,097 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,100 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,102 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,104 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,106 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,108 copying build/lib/tests/test_kind_support.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,110 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,112 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,114 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,116 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,118 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,121 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,123 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,125 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,128 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,130 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,131 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,134 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,136 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,138 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,140 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,143 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,144 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,147 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,149 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,151 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,153 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,155 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,158 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,159 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,161 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,163 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,165 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,167 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,169 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,171 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,174 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,176 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,178 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,179 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,182 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,184 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,185 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,188 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-09T03:47:38,189 running install_egg_info 2026-05-09T03:47:38,194 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.12.0-py3.11.egg-info 2026-05-09T03:47:38,206 running install_scripts 2026-05-09T03:47:38,218 creating build/bdist.linux-armv7l/wheel/topiary-5.12.0.dist-info/WHEEL 2026-05-09T03:47:38,220 creating '/tmp/pip-wheel-ljry931o/.tmp-8omocvhi/topiary-5.12.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-09T03:47:38,223 adding 'tests/__init__.py' 2026-05-09T03:47:38,225 adding 'tests/common.py' 2026-05-09T03:47:38,226 adding 'tests/data.py' 2026-05-09T03:47:38,227 adding 'tests/test_args_outputs.py' 2026-05-09T03:47:38,232 adding 'tests/test_cached_predictor.py' 2026-05-09T03:47:38,234 adding 'tests/test_cli_cached_predictor.py' 2026-05-09T03:47:38,235 adding 'tests/test_cli_coverage.py' 2026-05-09T03:47:38,237 adding 'tests/test_cli_protein_changes.py' 2026-05-09T03:47:38,239 adding 'tests/test_cli_ranking.py' 2026-05-09T03:47:38,240 adding 'tests/test_cli_script.py' 2026-05-09T03:47:38,241 adding 'tests/test_contains_mutant_residues.py' 2026-05-09T03:47:38,243 adding 'tests/test_coverage_gaps.py' 2026-05-09T03:47:38,245 adding 'tests/test_dataframe.py' 2026-05-09T03:47:38,246 adding 'tests/test_deploy_script.py' 2026-05-09T03:47:38,247 adding 'tests/test_direct_input_regressions.py' 2026-05-09T03:47:38,250 adding 'tests/test_dsl_extensions.py' 2026-05-09T03:47:38,252 adding 'tests/test_dsl_polish.py' 2026-05-09T03:47:38,254 adding 'tests/test_dsl_roundtrip.py' 2026-05-09T03:47:38,256 adding 'tests/test_edge_case_fixtures.py' 2026-05-09T03:47:38,257 adding 'tests/test_effect_expression_filters.py' 2026-05-09T03:47:38,259 adding 'tests/test_end_to_end.py' 2026-05-09T03:47:38,260 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-09T03:47:38,262 adding 'tests/test_expression_integration.py' 2026-05-09T03:47:38,263 adding 'tests/test_expression_loader.py' 2026-05-09T03:47:38,266 adding 'tests/test_frameshift_fragments.py' 2026-05-09T03:47:38,268 adding 'tests/test_inputs.py' 2026-05-09T03:47:38,269 adding 'tests/test_integration.py' 2026-05-09T03:47:38,271 adding 'tests/test_io.py' 2026-05-09T03:47:38,273 adding 'tests/test_io_lens.py' 2026-05-09T03:47:38,275 adding 'tests/test_kind_support.py' 2026-05-09T03:47:38,276 adding 'tests/test_lazy_imports.py' 2026-05-09T03:47:38,277 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-09T03:47:38,278 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-09T03:47:38,280 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-09T03:47:38,281 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-09T03:47:38,282 adding 'tests/test_padding.py' 2026-05-09T03:47:38,283 adding 'tests/test_peptide_mutation_interval.py' 2026-05-09T03:47:38,286 adding 'tests/test_predict_from_fragments.py' 2026-05-09T03:47:38,289 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-09T03:47:38,290 adding 'tests/test_predictor_internals.py' 2026-05-09T03:47:38,292 adding 'tests/test_protein_fragment.py' 2026-05-09T03:47:38,302 adding 'tests/test_ranking.py' 2026-05-09T03:47:38,305 adding 'tests/test_result.py' 2026-05-09T03:47:38,306 adding 'tests/test_rna_helpers.py' 2026-05-09T03:47:38,309 adding 'tests/test_self_proteome.py' 2026-05-09T03:47:38,310 adding 'tests/test_sequence_helpers.py' 2026-05-09T03:47:38,311 adding 'tests/test_sources.py' 2026-05-09T03:47:38,313 adding 'tests/test_sources_optional.py' 2026-05-09T03:47:38,315 adding 'tests/test_validation_and_edge_cases.py' 2026-05-09T03:47:38,316 adding 'tests/test_variant_expression_filters.py' 2026-05-09T03:47:38,318 adding 'tests/test_wide.py' 2026-05-09T03:47:38,320 adding 'topiary/__init__.py' 2026-05-09T03:47:38,326 adding 'topiary/cached.py' 2026-05-09T03:47:38,328 adding 'topiary/filters.py' 2026-05-09T03:47:38,329 adding 'topiary/inputs.py' 2026-05-09T03:47:38,331 adding 'topiary/io.py' 2026-05-09T03:47:38,333 adding 'topiary/io_lens.py' 2026-05-09T03:47:38,335 adding 'topiary/io_protein_fragment.py' 2026-05-09T03:47:38,340 adding 'topiary/predictor.py' 2026-05-09T03:47:38,342 adding 'topiary/properties.py' 2026-05-09T03:47:38,344 adding 'topiary/protein_fragment.py' 2026-05-09T03:47:38,347 adding 'topiary/result.py' 2026-05-09T03:47:38,351 adding 'topiary/self_proteome.py' 2026-05-09T03:47:38,352 adding 'topiary/sequence_helpers.py' 2026-05-09T03:47:38,354 adding 'topiary/sources.py' 2026-05-09T03:47:38,356 adding 'topiary/wide.py' 2026-05-09T03:47:38,358 adding 'topiary/cli/__init__.py' 2026-05-09T03:47:38,361 adding 'topiary/cli/args.py' 2026-05-09T03:47:38,363 adding 'topiary/cli/cached_predictor.py' 2026-05-09T03:47:38,364 adding 'topiary/cli/errors.py' 2026-05-09T03:47:38,366 adding 'topiary/cli/filtering.py' 2026-05-09T03:47:38,367 adding 'topiary/cli/outputs.py' 2026-05-09T03:47:38,369 adding 'topiary/cli/protein_changes.py' 2026-05-09T03:47:38,370 adding 'topiary/cli/rna.py' 2026-05-09T03:47:38,372 adding 'topiary/cli/script.py' 2026-05-09T03:47:38,373 adding 'topiary/cli/sequence.py' 2026-05-09T03:47:38,375 adding 'topiary/ranking/__init__.py' 2026-05-09T03:47:38,376 adding 'topiary/ranking/apply.py' 2026-05-09T03:47:38,383 adding 'topiary/ranking/nodes.py' 2026-05-09T03:47:38,386 adding 'topiary/ranking/parser.py' 2026-05-09T03:47:38,388 adding 'topiary/rna/__init__.py' 2026-05-09T03:47:38,389 adding 'topiary/rna/common.py' 2026-05-09T03:47:38,391 adding 'topiary/rna/cufflinks.py' 2026-05-09T03:47:38,393 adding 'topiary/rna/expression_loader.py' 2026-05-09T03:47:38,394 adding 'topiary/rna/gtf.py' 2026-05-09T03:47:38,398 adding 'topiary-5.12.0.dist-info/licenses/LICENSE' 2026-05-09T03:47:38,401 adding 'topiary-5.12.0.dist-info/METADATA' 2026-05-09T03:47:38,402 adding 'topiary-5.12.0.dist-info/WHEEL' 2026-05-09T03:47:38,403 adding 'topiary-5.12.0.dist-info/entry_points.txt' 2026-05-09T03:47:38,404 adding 'topiary-5.12.0.dist-info/top_level.txt' 2026-05-09T03:47:38,405 adding 'topiary-5.12.0.dist-info/RECORD' 2026-05-09T03:47:38,410 removing build/bdist.linux-armv7l/wheel 2026-05-09T03:47:38,528 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-09T03:47:38,538 Created wheel for topiary: filename=topiary-5.12.0-py3-none-any.whl size=251547 sha256=7b96d1e1ca9842c876431911009d77bad7dd8571cf23ae35def43aea0d78496d 2026-05-09T03:47:38,539 Stored in directory: /tmp/pip-ephem-wheel-cache-dc2n_gxy/wheels/45/cb/92/b363212d102cb99d029e6ffa1dd0f989b5ed53dcc3d65f18b9 2026-05-09T03:47:38,557 Successfully built topiary 2026-05-09T03:47:38,569 Removed build tracker: '/tmp/pip-build-tracker-ep7ygech'