2026-08-27T21:52:45,707 Created temporary directory: /tmp/pip-ephem-wheel-cache-mlnzj6rp 2026-08-27T21:52:45,709 Created temporary directory: /tmp/pip-build-tracker-e7nygoww 2026-08-27T21:52:45,710 Initialized build tracking at /tmp/pip-build-tracker-e7nygoww 2026-08-27T21:52:45,710 Created build tracker: /tmp/pip-build-tracker-e7nygoww 2026-08-27T21:52:45,711 Entered build tracker: /tmp/pip-build-tracker-e7nygoww 2026-08-27T21:52:45,712 Created temporary directory: /tmp/pip-wheel-i3dhnttc 2026-08-27T21:52:45,714 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 2026-08-27T21:52:45,717 Created temporary directory: /tmp/pip-ephem-wheel-cache-fp1lo56k 2026-08-27T21:52:45,739 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-27T21:52:45,743 2 location(s) to search for versions of topiary: 2026-08-27T21:52:45,743 * https://pypi.org/simple/topiary/ 2026-08-27T21:52:45,743 * https://www.piwheels.org/simple/topiary/ 2026-08-27T21:52:45,743 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-08-27T21:52:45,744 Getting page https://pypi.org/simple/topiary/ 2026-08-27T21:52:45,746 Found index url https://pypi.org/simple 2026-08-27T21:52:45,980 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-08-27T21:52:46,004 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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https://archive1.piwheels.org/simple/topiary/topiary-0.0.0-py3-none-any.whl#sha256=a4de4e13dc8561c43fd350094d3cbc3267e0faacf5e65b94501ef15affdf51e6 (from https://www.piwheels.org/simple/topiary/) 2026-08-27T21:52:46,375 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-08-27T21:52:46,376 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-08-27T21:52:46,405 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-08-27T21:52:46,423 Collecting topiary==5.20.1 2026-08-27T21:52:46,425 Created temporary directory: /tmp/pip-unpack-7fwgij2_ 2026-08-27T21:52:46,651 Downloading topiary-5.20.1.tar.gz (289 kB) 2026-08-27T21:52:46,979 Added topiary==5.20.1 from https://files.pythonhosted.org/packages/9c/61/e99c98fbd236e0f96cf36b33ce48d60023f8605cd241aceb154c2f024a9c/topiary-5.20.1.tar.gz to build tracker '/tmp/pip-build-tracker-e7nygoww' 2026-08-27T21:52:46,984 Created temporary directory: /tmp/pip-build-env-1zll5g5n 2026-08-27T21:52:46,988 Installing build dependencies: started 2026-08-27T21:52:46,989 Running command pip subprocess to install build dependencies 2026-08-27T21:52:48,127 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-08-27T21:52:48,559 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 2026-08-27T21:52:48,582 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-27T21:52:50,389 Collecting setuptools>=64 2026-08-27T21:52:50,390 Obtaining dependency information for setuptools>=64 from https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata 2026-08-27T21:52:50,406 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-08-27T21:52:50,653 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-27T21:52:50,738 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-27T21:52:53,494 Installing collected packages: setuptools 2026-08-27T21:52:55,847 Successfully installed setuptools-84.0.0 2026-08-27T21:52:56,116 Installing build dependencies: finished with status 'done' 2026-08-27T21:52:56,124 Getting requirements to build wheel: started 2026-08-27T21:52:56,125 Running command Getting requirements to build wheel 2026-08-27T21:52:56,866 /tmp/pip-build-env-1zll5g5n/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T21:52:56,866 !! 2026-08-27T21:52:56,868 ******************************************************************************** 2026-08-27T21:52:56,868 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T21:52:56,870 License :: OSI Approved :: Apache Software License 2026-08-27T21:52:56,871 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T21:52:56,871 ******************************************************************************** 2026-08-27T21:52:56,873 !! 2026-08-27T21:52:56,873 dist._finalize_license_expression() 2026-08-27T21:52:56,874 /tmp/pip-build-env-1zll5g5n/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T21:52:56,874 !! 2026-08-27T21:52:56,875 ******************************************************************************** 2026-08-27T21:52:56,876 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T21:52:56,877 License :: OSI Approved :: Apache Software License 2026-08-27T21:52:56,878 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T21:52:56,879 ******************************************************************************** 2026-08-27T21:52:56,881 !! 2026-08-27T21:52:56,881 self._finalize_license_expression() 2026-08-27T21:52:56,882 running egg_info 2026-08-27T21:52:56,886 writing topiary.egg-info/PKG-INFO 2026-08-27T21:52:56,890 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-08-27T21:52:56,892 writing entry points to topiary.egg-info/entry_points.txt 2026-08-27T21:52:56,894 writing requirements to topiary.egg-info/requires.txt 2026-08-27T21:52:56,895 writing top-level names to topiary.egg-info/top_level.txt 2026-08-27T21:52:56,925 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-27T21:52:56,931 adding license file 'LICENSE' 2026-08-27T21:52:56,938 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-27T21:52:57,037 Getting requirements to build wheel: finished with status 'done' 2026-08-27T21:52:57,040 Created temporary directory: /tmp/pip-modern-metadata-qmqmfa_0 2026-08-27T21:52:57,043 Preparing metadata (pyproject.toml): started 2026-08-27T21:52:57,044 Running command Preparing metadata (pyproject.toml) 2026-08-27T21:52:57,733 /tmp/pip-build-env-1zll5g5n/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T21:52:57,733 !! 2026-08-27T21:52:57,734 ******************************************************************************** 2026-08-27T21:52:57,735 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T21:52:57,736 License :: OSI Approved :: Apache Software License 2026-08-27T21:52:57,737 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T21:52:57,737 ******************************************************************************** 2026-08-27T21:52:57,738 !! 2026-08-27T21:52:57,739 dist._finalize_license_expression() 2026-08-27T21:52:57,739 /tmp/pip-build-env-1zll5g5n/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T21:52:57,740 !! 2026-08-27T21:52:57,741 ******************************************************************************** 2026-08-27T21:52:57,742 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T21:52:57,743 License :: OSI Approved :: Apache Software License 2026-08-27T21:52:57,744 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T21:52:57,745 ******************************************************************************** 2026-08-27T21:52:57,746 !! 2026-08-27T21:52:57,747 self._finalize_license_expression() 2026-08-27T21:52:57,747 running dist_info 2026-08-27T21:52:57,755 creating /tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info 2026-08-27T21:52:57,756 writing /tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/PKG-INFO 2026-08-27T21:52:57,761 writing dependency_links to /tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/dependency_links.txt 2026-08-27T21:52:57,762 writing entry points to /tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/entry_points.txt 2026-08-27T21:52:57,764 writing requirements to /tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/requires.txt 2026-08-27T21:52:57,765 writing top-level names to /tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/top_level.txt 2026-08-27T21:52:57,767 writing manifest file '/tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/SOURCES.txt' 2026-08-27T21:52:57,794 reading manifest file '/tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/SOURCES.txt' 2026-08-27T21:52:57,796 adding license file 'LICENSE' 2026-08-27T21:52:57,801 writing manifest file '/tmp/pip-modern-metadata-qmqmfa_0/topiary.egg-info/SOURCES.txt' 2026-08-27T21:52:57,802 creating '/tmp/pip-modern-metadata-qmqmfa_0/topiary-5.20.1.dist-info' 2026-08-27T21:52:57,930 Preparing metadata (pyproject.toml): finished with status 'done' 2026-08-27T21:52:57,937 Source in /tmp/pip-wheel-i3dhnttc/topiary_2f348e540ad047feb9cbaa64b46b2b15 has version 5.20.1, which satisfies requirement topiary==5.20.1 from https://files.pythonhosted.org/packages/9c/61/e99c98fbd236e0f96cf36b33ce48d60023f8605cd241aceb154c2f024a9c/topiary-5.20.1.tar.gz 2026-08-27T21:52:57,938 Removed topiary==5.20.1 from https://files.pythonhosted.org/packages/9c/61/e99c98fbd236e0f96cf36b33ce48d60023f8605cd241aceb154c2f024a9c/topiary-5.20.1.tar.gz from build tracker '/tmp/pip-build-tracker-e7nygoww' 2026-08-27T21:52:57,946 Created temporary directory: /tmp/pip-unpack-aqk42d6r 2026-08-27T21:52:57,946 Building wheels for collected packages: topiary 2026-08-27T21:52:57,951 Created temporary directory: /tmp/pip-wheel-ace_1ltw 2026-08-27T21:52:57,952 Destination directory: /tmp/pip-wheel-ace_1ltw 2026-08-27T21:52:57,954 Building wheel for topiary (pyproject.toml): started 2026-08-27T21:52:57,955 Running command Building wheel for topiary (pyproject.toml) 2026-08-27T21:52:58,626 /tmp/pip-build-env-1zll5g5n/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T21:52:58,626 !! 2026-08-27T21:52:58,627 ******************************************************************************** 2026-08-27T21:52:58,628 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T21:52:58,629 License :: OSI Approved :: Apache Software License 2026-08-27T21:52:58,630 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T21:52:58,630 ******************************************************************************** 2026-08-27T21:52:58,631 !! 2026-08-27T21:52:58,632 dist._finalize_license_expression() 2026-08-27T21:52:58,632 /tmp/pip-build-env-1zll5g5n/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T21:52:58,633 !! 2026-08-27T21:52:58,634 ******************************************************************************** 2026-08-27T21:52:58,634 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T21:52:58,635 License :: OSI Approved :: Apache Software License 2026-08-27T21:52:58,637 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T21:52:58,637 ******************************************************************************** 2026-08-27T21:52:58,638 !! 2026-08-27T21:52:58,639 self._finalize_license_expression() 2026-08-27T21:52:58,639 running bdist_wheel 2026-08-27T21:52:58,651 running build 2026-08-27T21:52:58,651 running build_py 2026-08-27T21:52:58,658 creating build/lib/topiary 2026-08-27T21:52:58,660 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-08-27T21:52:58,663 copying topiary/__init__.py -> build/lib/topiary 2026-08-27T21:52:58,665 copying topiary/self_proteome.py -> build/lib/topiary 2026-08-27T21:52:58,668 copying topiary/inputs.py -> build/lib/topiary 2026-08-27T21:52:58,670 copying topiary/protein_fragment.py -> build/lib/topiary 2026-08-27T21:52:58,673 copying topiary/result.py -> build/lib/topiary 2026-08-27T21:52:58,676 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-08-27T21:52:58,678 copying topiary/properties.py -> build/lib/topiary 2026-08-27T21:52:58,681 copying topiary/filters.py -> build/lib/topiary 2026-08-27T21:52:58,683 copying topiary/wide.py -> build/lib/topiary 2026-08-27T21:52:58,686 copying topiary/io_lens.py -> build/lib/topiary 2026-08-27T21:52:58,689 copying topiary/sources.py -> build/lib/topiary 2026-08-27T21:52:58,692 copying topiary/predictor.py -> build/lib/topiary 2026-08-27T21:52:58,696 copying topiary/io.py -> build/lib/topiary 2026-08-27T21:52:58,698 copying topiary/cached.py -> build/lib/topiary 2026-08-27T21:52:58,702 copying topiary/io_pvacseq.py -> build/lib/topiary 2026-08-27T21:52:58,706 creating build/lib/tests 2026-08-27T21:52:58,707 copying tests/test_cli_ranking.py -> build/lib/tests 2026-08-27T21:52:58,710 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-08-27T21:52:58,712 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-08-27T21:52:58,715 copying tests/__init__.py -> build/lib/tests 2026-08-27T21:52:58,717 copying tests/test_lazy_imports.py -> build/lib/tests 2026-08-27T21:52:58,718 copying tests/test_self_proteome.py -> build/lib/tests 2026-08-27T21:52:58,721 copying tests/test_peptide_property_node.py -> build/lib/tests 2026-08-27T21:52:58,723 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-08-27T21:52:58,725 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-08-27T21:52:58,727 copying tests/test_protein_fragment.py -> build/lib/tests 2026-08-27T21:52:58,730 copying tests/test_cli_coverage.py -> build/lib/tests 2026-08-27T21:52:58,732 copying tests/test_group_keys.py -> build/lib/tests 2026-08-27T21:52:58,735 copying tests/common.py -> build/lib/tests 2026-08-27T21:52:58,737 copying tests/test_io_pvacseq.py -> build/lib/tests 2026-08-27T21:52:58,739 copying tests/test_end_to_end.py -> build/lib/tests 2026-08-27T21:52:58,742 copying tests/test_predictor_internals.py -> build/lib/tests 2026-08-27T21:52:58,744 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-08-27T21:52:58,746 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-08-27T21:52:58,749 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-08-27T21:52:58,751 copying tests/test_deploy_script.py -> build/lib/tests 2026-08-27T21:52:58,753 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-08-27T21:52:58,755 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-08-27T21:52:58,757 copying tests/test_peptide_view.py -> build/lib/tests 2026-08-27T21:52:58,760 copying tests/test_expression_integration.py -> build/lib/tests 2026-08-27T21:52:58,762 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-08-27T21:52:58,765 copying tests/test_wide.py -> build/lib/tests 2026-08-27T21:52:58,768 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-08-27T21:52:58,770 copying tests/test_dsl_polish.py -> build/lib/tests 2026-08-27T21:52:58,773 copying tests/data.py -> build/lib/tests 2026-08-27T21:52:58,775 copying tests/test_expression_loader.py -> build/lib/tests 2026-08-27T21:52:58,777 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-08-27T21:52:58,779 copying tests/test_result.py -> build/lib/tests 2026-08-27T21:52:58,782 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-08-27T21:52:58,784 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-08-27T21:52:58,786 copying tests/test_dataframe.py -> build/lib/tests 2026-08-27T21:52:58,788 copying tests/test_combine_predictor_results.py -> build/lib/tests 2026-08-27T21:52:58,791 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-08-27T21:52:58,793 copying tests/test_best_allele.py -> build/lib/tests 2026-08-27T21:52:58,796 copying tests/test_inputs.py -> build/lib/tests 2026-08-27T21:52:58,798 copying tests/test_kind_support.py -> build/lib/tests 2026-08-27T21:52:58,801 copying tests/test_cli_script.py -> build/lib/tests 2026-08-27T21:52:58,803 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-08-27T21:52:58,805 copying tests/test_io_lens.py -> build/lib/tests 2026-08-27T21:52:58,808 copying tests/test_sources.py -> build/lib/tests 2026-08-27T21:52:58,810 copying tests/test_ranking.py -> build/lib/tests 2026-08-27T21:52:58,815 copying tests/test_sources_optional.py -> build/lib/tests 2026-08-27T21:52:58,817 copying tests/test_cached_predictor.py -> build/lib/tests 2026-08-27T21:52:58,820 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-08-27T21:52:58,822 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-08-27T21:52:58,825 copying tests/test_integration.py -> build/lib/tests 2026-08-27T21:52:58,827 copying tests/test_allele_free_kinds.py -> build/lib/tests 2026-08-27T21:52:58,830 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-08-27T21:52:58,832 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-08-27T21:52:58,834 copying tests/test_padding.py -> build/lib/tests 2026-08-27T21:52:58,835 copying tests/test_args_outputs.py -> build/lib/tests 2026-08-27T21:52:58,837 copying tests/test_io.py -> build/lib/tests 2026-08-27T21:52:58,840 copying tests/test_rna_helpers.py -> build/lib/tests 2026-08-27T21:52:58,842 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-08-27T21:52:58,845 creating build/lib/topiary/ranking 2026-08-27T21:52:58,846 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-08-27T21:52:58,849 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-08-27T21:52:58,851 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-08-27T21:52:58,854 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-08-27T21:52:58,858 creating build/lib/topiary/cli 2026-08-27T21:52:58,859 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-08-27T21:52:58,861 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-08-27T21:52:58,863 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-08-27T21:52:58,866 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-08-27T21:52:58,869 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-08-27T21:52:58,870 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-08-27T21:52:58,873 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-08-27T21:52:58,875 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-08-27T21:52:58,877 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-08-27T21:52:58,880 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-08-27T21:52:58,882 creating build/lib/topiary/rna 2026-08-27T21:52:58,883 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-08-27T21:52:58,885 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-08-27T21:52:58,888 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-08-27T21:52:58,890 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-08-27T21:52:58,892 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-08-27T21:52:58,894 running egg_info 2026-08-27T21:52:58,903 writing topiary.egg-info/PKG-INFO 2026-08-27T21:52:58,907 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-08-27T21:52:58,909 writing entry points to topiary.egg-info/entry_points.txt 2026-08-27T21:52:58,910 writing requirements to topiary.egg-info/requires.txt 2026-08-27T21:52:58,911 writing top-level names to topiary.egg-info/top_level.txt 2026-08-27T21:52:58,929 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-27T21:52:58,935 adding license file 'LICENSE' 2026-08-27T21:52:58,942 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-27T21:52:58,960 installing to build/bdist.linux-armv7l/wheel 2026-08-27T21:52:58,961 running install 2026-08-27T21:52:58,983 running install_lib 2026-08-27T21:52:58,988 creating build/bdist.linux-armv7l/wheel 2026-08-27T21:52:58,991 creating build/bdist.linux-armv7l/wheel/topiary 2026-08-27T21:52:58,992 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:58,995 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:58,997 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:58,999 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,002 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-08-27T21:52:59,004 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-27T21:52:59,006 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-27T21:52:59,008 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-27T21:52:59,011 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-27T21:52:59,015 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,018 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,021 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,023 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,026 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,028 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,031 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,033 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,036 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,039 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,041 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,044 copying build/lib/topiary/io_pvacseq.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-27T21:52:59,048 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-08-27T21:52:59,049 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,051 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,053 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,055 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,057 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,059 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,062 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,064 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,066 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,069 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-27T21:52:59,072 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-08-27T21:52:59,073 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-27T21:52:59,075 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-27T21:52:59,077 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-27T21:52:59,079 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-27T21:52:59,082 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-27T21:52:59,086 creating build/bdist.linux-armv7l/wheel/tests 2026-08-27T21:52:59,087 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,090 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,092 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,095 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,097 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,099 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,102 copying build/lib/tests/test_peptide_property_node.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,104 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,106 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,108 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,111 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,114 copying build/lib/tests/test_group_keys.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,117 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,119 copying build/lib/tests/test_io_pvacseq.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,121 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,124 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,126 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,128 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,131 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,133 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,135 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,137 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,140 copying build/lib/tests/test_peptide_view.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,143 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,145 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,148 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,151 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,154 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,157 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,159 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,161 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,164 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,167 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,170 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,172 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,174 copying build/lib/tests/test_combine_predictor_results.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,177 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,180 copying build/lib/tests/test_best_allele.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,182 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,185 copying build/lib/tests/test_kind_support.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,188 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,191 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,194 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,197 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,199 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,204 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,206 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,210 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,213 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,216 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,219 copying build/lib/tests/test_allele_free_kinds.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,221 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,224 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,226 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,228 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,231 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,234 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,236 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-27T21:52:59,239 running install_egg_info 2026-08-27T21:52:59,245 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.20.1-py3.11.egg-info 2026-08-27T21:52:59,260 running install_scripts 2026-08-27T21:52:59,278 creating build/bdist.linux-armv7l/wheel/topiary-5.20.1.dist-info/WHEEL 2026-08-27T21:52:59,282 creating '/tmp/pip-wheel-ace_1ltw/.tmp-5ivdxc4v/topiary-5.20.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-08-27T21:52:59,289 adding 'tests/__init__.py' 2026-08-27T21:52:59,290 adding 'tests/common.py' 2026-08-27T21:52:59,293 adding 'tests/data.py' 2026-08-27T21:52:59,296 adding 'tests/test_allele_free_kinds.py' 2026-08-27T21:52:59,298 adding 'tests/test_args_outputs.py' 2026-08-27T21:52:59,301 adding 'tests/test_best_allele.py' 2026-08-27T21:52:59,306 adding 'tests/test_cached_predictor.py' 2026-08-27T21:52:59,309 adding 'tests/test_cli_cached_predictor.py' 2026-08-27T21:52:59,310 adding 'tests/test_cli_coverage.py' 2026-08-27T21:52:59,312 adding 'tests/test_cli_protein_changes.py' 2026-08-27T21:52:59,314 adding 'tests/test_cli_ranking.py' 2026-08-27T21:52:59,316 adding 'tests/test_cli_script.py' 2026-08-27T21:52:59,319 adding 'tests/test_combine_predictor_results.py' 2026-08-27T21:52:59,321 adding 'tests/test_contains_mutant_residues.py' 2026-08-27T21:52:59,323 adding 'tests/test_coverage_gaps.py' 2026-08-27T21:52:59,325 adding 'tests/test_dataframe.py' 2026-08-27T21:52:59,327 adding 'tests/test_deploy_script.py' 2026-08-27T21:52:59,328 adding 'tests/test_direct_input_regressions.py' 2026-08-27T21:52:59,332 adding 'tests/test_dsl_extensions.py' 2026-08-27T21:52:59,334 adding 'tests/test_dsl_polish.py' 2026-08-27T21:52:59,337 adding 'tests/test_dsl_roundtrip.py' 2026-08-27T21:52:59,339 adding 'tests/test_edge_case_fixtures.py' 2026-08-27T21:52:59,341 adding 'tests/test_effect_expression_filters.py' 2026-08-27T21:52:59,343 adding 'tests/test_end_to_end.py' 2026-08-27T21:52:59,345 adding 'tests/test_epitopes_from_commandline_args.py' 2026-08-27T21:52:59,347 adding 'tests/test_expression_integration.py' 2026-08-27T21:52:59,348 adding 'tests/test_expression_loader.py' 2026-08-27T21:52:59,351 adding 'tests/test_frameshift_fragments.py' 2026-08-27T21:52:59,354 adding 'tests/test_group_keys.py' 2026-08-27T21:52:59,356 adding 'tests/test_inputs.py' 2026-08-27T21:52:59,358 adding 'tests/test_integration.py' 2026-08-27T21:52:59,361 adding 'tests/test_io.py' 2026-08-27T21:52:59,363 adding 'tests/test_io_lens.py' 2026-08-27T21:52:59,366 adding 'tests/test_io_pvacseq.py' 2026-08-27T21:52:59,369 adding 'tests/test_kind_support.py' 2026-08-27T21:52:59,370 adding 'tests/test_lazy_imports.py' 2026-08-27T21:52:59,372 adding 'tests/test_load_cufflinks_fpkm.py' 2026-08-27T21:52:59,373 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-08-27T21:52:59,375 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-08-27T21:52:59,376 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-08-27T21:52:59,378 adding 'tests/test_padding.py' 2026-08-27T21:52:59,379 adding 'tests/test_peptide_mutation_interval.py' 2026-08-27T21:52:59,381 adding 'tests/test_peptide_property_node.py' 2026-08-27T21:52:59,384 adding 'tests/test_peptide_view.py' 2026-08-27T21:52:59,387 adding 'tests/test_predict_from_fragments.py' 2026-08-27T21:52:59,390 adding 'tests/test_predict_from_variants_refactor.py' 2026-08-27T21:52:59,392 adding 'tests/test_predictor_internals.py' 2026-08-27T21:52:59,394 adding 'tests/test_protein_fragment.py' 2026-08-27T21:52:59,403 adding 'tests/test_ranking.py' 2026-08-27T21:52:59,407 adding 'tests/test_result.py' 2026-08-27T21:52:59,408 adding 'tests/test_rna_helpers.py' 2026-08-27T21:52:59,411 adding 'tests/test_self_proteome.py' 2026-08-27T21:52:59,412 adding 'tests/test_sequence_helpers.py' 2026-08-27T21:52:59,413 adding 'tests/test_sources.py' 2026-08-27T21:52:59,415 adding 'tests/test_sources_optional.py' 2026-08-27T21:52:59,417 adding 'tests/test_validation_and_edge_cases.py' 2026-08-27T21:52:59,418 adding 'tests/test_variant_expression_filters.py' 2026-08-27T21:52:59,420 adding 'tests/test_wide.py' 2026-08-27T21:52:59,422 adding 'topiary/__init__.py' 2026-08-27T21:52:59,428 adding 'topiary/cached.py' 2026-08-27T21:52:59,430 adding 'topiary/filters.py' 2026-08-27T21:52:59,432 adding 'topiary/inputs.py' 2026-08-27T21:52:59,434 adding 'topiary/io.py' 2026-08-27T21:52:59,436 adding 'topiary/io_lens.py' 2026-08-27T21:52:59,437 adding 'topiary/io_protein_fragment.py' 2026-08-27T21:52:59,440 adding 'topiary/io_pvacseq.py' 2026-08-27T21:52:59,446 adding 'topiary/predictor.py' 2026-08-27T21:52:59,449 adding 'topiary/properties.py' 2026-08-27T21:52:59,451 adding 'topiary/protein_fragment.py' 2026-08-27T21:52:59,455 adding 'topiary/result.py' 2026-08-27T21:52:59,459 adding 'topiary/self_proteome.py' 2026-08-27T21:52:59,461 adding 'topiary/sequence_helpers.py' 2026-08-27T21:52:59,464 adding 'topiary/sources.py' 2026-08-27T21:52:59,466 adding 'topiary/wide.py' 2026-08-27T21:52:59,468 adding 'topiary/cli/__init__.py' 2026-08-27T21:52:59,471 adding 'topiary/cli/args.py' 2026-08-27T21:52:59,473 adding 'topiary/cli/cached_predictor.py' 2026-08-27T21:52:59,474 adding 'topiary/cli/errors.py' 2026-08-27T21:52:59,476 adding 'topiary/cli/filtering.py' 2026-08-27T21:52:59,477 adding 'topiary/cli/outputs.py' 2026-08-27T21:52:59,479 adding 'topiary/cli/protein_changes.py' 2026-08-27T21:52:59,480 adding 'topiary/cli/rna.py' 2026-08-27T21:52:59,482 adding 'topiary/cli/script.py' 2026-08-27T21:52:59,483 adding 'topiary/cli/sequence.py' 2026-08-27T21:52:59,485 adding 'topiary/ranking/__init__.py' 2026-08-27T21:52:59,488 adding 'topiary/ranking/apply.py' 2026-08-27T21:52:59,500 adding 'topiary/ranking/nodes.py' 2026-08-27T21:52:59,504 adding 'topiary/ranking/parser.py' 2026-08-27T21:52:59,506 adding 'topiary/rna/__init__.py' 2026-08-27T21:52:59,507 adding 'topiary/rna/common.py' 2026-08-27T21:52:59,509 adding 'topiary/rna/cufflinks.py' 2026-08-27T21:52:59,511 adding 'topiary/rna/expression_loader.py' 2026-08-27T21:52:59,512 adding 'topiary/rna/gtf.py' 2026-08-27T21:52:59,516 adding 'topiary-5.20.1.dist-info/licenses/LICENSE' 2026-08-27T21:52:59,520 adding 'topiary-5.20.1.dist-info/METADATA' 2026-08-27T21:52:59,521 adding 'topiary-5.20.1.dist-info/WHEEL' 2026-08-27T21:52:59,522 adding 'topiary-5.20.1.dist-info/entry_points.txt' 2026-08-27T21:52:59,523 adding 'topiary-5.20.1.dist-info/top_level.txt' 2026-08-27T21:52:59,524 adding 'topiary-5.20.1.dist-info/RECORD' 2026-08-27T21:52:59,530 removing build/bdist.linux-armv7l/wheel 2026-08-27T21:52:59,656 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-08-27T21:52:59,669 Created wheel for topiary: filename=topiary-5.20.1-py3-none-any.whl size=321601 sha256=e3eaab54e89685ad3afd94ac2a93979fe553f3377b7a71c330f02355fa56f8ca 2026-08-27T21:52:59,670 Stored in directory: /tmp/pip-ephem-wheel-cache-fp1lo56k/wheels/34/6c/38/6cc1d2fcea093c505d9747274b50b747ff13ed081bfcaa77ff 2026-08-27T21:52:59,689 Successfully built topiary 2026-08-27T21:52:59,700 Removed build tracker: '/tmp/pip-build-tracker-e7nygoww'