2026-05-05T23:41:19,085 Created temporary directory: /tmp/pip-ephem-wheel-cache-qza_mmi2 2026-05-05T23:41:19,087 Created temporary directory: /tmp/pip-build-tracker-dla7_0sf 2026-05-05T23:41:19,087 Initialized build tracking at /tmp/pip-build-tracker-dla7_0sf 2026-05-05T23:41:19,088 Created build tracker: /tmp/pip-build-tracker-dla7_0sf 2026-05-05T23:41:19,088 Entered build tracker: /tmp/pip-build-tracker-dla7_0sf 2026-05-05T23:41:19,089 Created temporary directory: /tmp/pip-wheel-ln7m4gop 2026-05-05T23:41:19,092 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 2026-05-05T23:41:19,094 Created temporary directory: /tmp/pip-ephem-wheel-cache-83129hnj 2026-05-05T23:41:19,117 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-05T23:41:19,120 2 location(s) to search for versions of topiary: 2026-05-05T23:41:19,120 * https://pypi.org/simple/topiary/ 2026-05-05T23:41:19,120 * https://www.piwheels.org/simple/topiary/ 2026-05-05T23:41:19,121 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-05-05T23:41:19,122 Getting page https://pypi.org/simple/topiary/ 2026-05-05T23:41:19,123 Found index url https://pypi.org/simple 2026-05-05T23:41:19,348 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-05-05T23:41:19,367 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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(requires-python:>=3.9) 2026-05-05T23:41:19,451 Found link https://files.pythonhosted.org/packages/54/33/00f95ffcb580dd2432682d7fc1f0b0ccafda4472e82794a16c5f75dec5a8/topiary-5.10.5.tar.gz (from https://pypi.org/simple/topiary/) (requires-python:>=3.9), version: 5.10.5 2026-05-05T23:41:19,452 Fetching project page and analyzing links: https://www.piwheels.org/simple/topiary/ 2026-05-05T23:41:19,453 Getting page https://www.piwheels.org/simple/topiary/ 2026-05-05T23:41:19,454 Found index url https://www.piwheels.org/simple 2026-05-05T23:41:19,630 Fetched page https://www.piwheels.org/simple/topiary/ as text/html 2026-05-05T23:41:19,648 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.10.4-py3-none-any.whl#sha256=a6a56f5f46cf0168a81839f5805284f98c016133e8a6256ff3bd04b5cc0013b9 (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-05T23:41:19,648 Skipping link: No binaries permitted for topiary: 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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/) 2026-05-05T23:41:19,686 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-05-05T23:41:19,687 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-05-05T23:41:19,716 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-05-05T23:41:19,736 Collecting topiary==5.10.5 2026-05-05T23:41:19,738 Created temporary directory: /tmp/pip-unpack-bt7ar6k3 2026-05-05T23:41:19,961 Downloading topiary-5.10.5.tar.gz (220 kB) 2026-05-05T23:41:20,261 Added topiary==5.10.5 from https://files.pythonhosted.org/packages/54/33/00f95ffcb580dd2432682d7fc1f0b0ccafda4472e82794a16c5f75dec5a8/topiary-5.10.5.tar.gz to build tracker '/tmp/pip-build-tracker-dla7_0sf' 2026-05-05T23:41:20,266 Created temporary directory: /tmp/pip-build-env-exz94wxp 2026-05-05T23:41:20,271 Installing build dependencies: started 2026-05-05T23:41:20,272 Running command pip subprocess to install build dependencies 2026-05-05T23:41:21,407 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-05T23:41:22,040 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 2026-05-05T23:41:22,065 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-05T23:41:23,829 Collecting setuptools>=64 2026-05-05T23:41:23,931 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-05T23:41:26,917 Installing collected packages: setuptools 2026-05-05T23:41:30,056 Successfully installed setuptools-82.0.1 2026-05-05T23:41:30,346 Installing build dependencies: finished with status 'done' 2026-05-05T23:41:30,353 Getting requirements to build wheel: started 2026-05-05T23:41:30,354 Running command Getting requirements to build wheel 2026-05-05T23:41:31,039 /tmp/pip-build-env-exz94wxp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T23:41:31,039 !! 2026-05-05T23:41:31,041 ******************************************************************************** 2026-05-05T23:41:31,041 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T23:41:31,042 License :: OSI Approved :: Apache Software License 2026-05-05T23:41:31,043 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T23:41:31,043 ******************************************************************************** 2026-05-05T23:41:31,044 !! 2026-05-05T23:41:31,045 dist._finalize_license_expression() 2026-05-05T23:41:31,046 /tmp/pip-build-env-exz94wxp/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T23:41:31,046 !! 2026-05-05T23:41:31,047 ******************************************************************************** 2026-05-05T23:41:31,047 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T23:41:31,048 License :: OSI Approved :: Apache Software License 2026-05-05T23:41:31,049 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T23:41:31,050 ******************************************************************************** 2026-05-05T23:41:31,051 !! 2026-05-05T23:41:31,052 self._finalize_license_expression() 2026-05-05T23:41:31,052 running egg_info 2026-05-05T23:41:31,056 writing topiary.egg-info/PKG-INFO 2026-05-05T23:41:31,060 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-05T23:41:31,061 writing entry points to topiary.egg-info/entry_points.txt 2026-05-05T23:41:31,063 writing requirements to topiary.egg-info/requires.txt 2026-05-05T23:41:31,064 writing top-level names to topiary.egg-info/top_level.txt 2026-05-05T23:41:31,091 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T23:41:31,097 adding license file 'LICENSE' 2026-05-05T23:41:31,104 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T23:41:31,200 Getting requirements to build wheel: finished with status 'done' 2026-05-05T23:41:31,204 Created temporary directory: /tmp/pip-modern-metadata-di4knsag 2026-05-05T23:41:31,206 Preparing metadata (pyproject.toml): started 2026-05-05T23:41:31,207 Running command Preparing metadata (pyproject.toml) 2026-05-05T23:41:31,878 /tmp/pip-build-env-exz94wxp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T23:41:31,879 !! 2026-05-05T23:41:31,880 ******************************************************************************** 2026-05-05T23:41:31,881 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T23:41:31,882 License :: OSI Approved :: Apache Software License 2026-05-05T23:41:31,884 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T23:41:31,885 ******************************************************************************** 2026-05-05T23:41:31,886 !! 2026-05-05T23:41:31,887 dist._finalize_license_expression() 2026-05-05T23:41:31,888 /tmp/pip-build-env-exz94wxp/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T23:41:31,889 !! 2026-05-05T23:41:31,890 ******************************************************************************** 2026-05-05T23:41:31,891 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T23:41:31,893 License :: OSI Approved :: Apache Software License 2026-05-05T23:41:31,894 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T23:41:31,895 ******************************************************************************** 2026-05-05T23:41:31,895 !! 2026-05-05T23:41:31,896 self._finalize_license_expression() 2026-05-05T23:41:31,896 running dist_info 2026-05-05T23:41:31,902 creating /tmp/pip-modern-metadata-di4knsag/topiary.egg-info 2026-05-05T23:41:31,903 writing /tmp/pip-modern-metadata-di4knsag/topiary.egg-info/PKG-INFO 2026-05-05T23:41:31,907 writing dependency_links to /tmp/pip-modern-metadata-di4knsag/topiary.egg-info/dependency_links.txt 2026-05-05T23:41:31,909 writing entry points to /tmp/pip-modern-metadata-di4knsag/topiary.egg-info/entry_points.txt 2026-05-05T23:41:31,910 writing requirements to /tmp/pip-modern-metadata-di4knsag/topiary.egg-info/requires.txt 2026-05-05T23:41:31,911 writing top-level names to /tmp/pip-modern-metadata-di4knsag/topiary.egg-info/top_level.txt 2026-05-05T23:41:31,913 writing manifest file '/tmp/pip-modern-metadata-di4knsag/topiary.egg-info/SOURCES.txt' 2026-05-05T23:41:31,938 reading manifest file '/tmp/pip-modern-metadata-di4knsag/topiary.egg-info/SOURCES.txt' 2026-05-05T23:41:31,940 adding license file 'LICENSE' 2026-05-05T23:41:31,945 writing manifest file '/tmp/pip-modern-metadata-di4knsag/topiary.egg-info/SOURCES.txt' 2026-05-05T23:41:31,947 creating '/tmp/pip-modern-metadata-di4knsag/topiary-5.10.5.dist-info' 2026-05-05T23:41:32,073 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-05T23:41:32,079 Source in /tmp/pip-wheel-ln7m4gop/topiary_9ec437cd67214d22af0870714c7c7a19 has version 5.10.5, which satisfies requirement topiary==5.10.5 from https://files.pythonhosted.org/packages/54/33/00f95ffcb580dd2432682d7fc1f0b0ccafda4472e82794a16c5f75dec5a8/topiary-5.10.5.tar.gz 2026-05-05T23:41:32,080 Removed topiary==5.10.5 from https://files.pythonhosted.org/packages/54/33/00f95ffcb580dd2432682d7fc1f0b0ccafda4472e82794a16c5f75dec5a8/topiary-5.10.5.tar.gz from build tracker '/tmp/pip-build-tracker-dla7_0sf' 2026-05-05T23:41:32,089 Created temporary directory: /tmp/pip-unpack-rctbi99v 2026-05-05T23:41:32,089 Building wheels for collected packages: topiary 2026-05-05T23:41:32,094 Created temporary directory: /tmp/pip-wheel-gvnafb1m 2026-05-05T23:41:32,094 Destination directory: /tmp/pip-wheel-gvnafb1m 2026-05-05T23:41:32,097 Building wheel for topiary (pyproject.toml): started 2026-05-05T23:41:32,098 Running command Building wheel for topiary (pyproject.toml) 2026-05-05T23:41:32,752 /tmp/pip-build-env-exz94wxp/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T23:41:32,752 !! 2026-05-05T23:41:32,753 ******************************************************************************** 2026-05-05T23:41:32,754 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T23:41:32,755 License :: OSI Approved :: Apache Software License 2026-05-05T23:41:32,757 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T23:41:32,757 ******************************************************************************** 2026-05-05T23:41:32,759 !! 2026-05-05T23:41:32,759 dist._finalize_license_expression() 2026-05-05T23:41:32,760 /tmp/pip-build-env-exz94wxp/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T23:41:32,761 !! 2026-05-05T23:41:32,762 ******************************************************************************** 2026-05-05T23:41:32,763 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T23:41:32,765 License :: OSI Approved :: Apache Software License 2026-05-05T23:41:32,765 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T23:41:32,766 ******************************************************************************** 2026-05-05T23:41:32,767 !! 2026-05-05T23:41:32,768 self._finalize_license_expression() 2026-05-05T23:41:32,768 running bdist_wheel 2026-05-05T23:41:32,777 running build 2026-05-05T23:41:32,778 running build_py 2026-05-05T23:41:32,784 creating build/lib/topiary 2026-05-05T23:41:32,786 copying topiary/properties.py -> build/lib/topiary 2026-05-05T23:41:32,789 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-05T23:41:32,792 copying topiary/__init__.py -> build/lib/topiary 2026-05-05T23:41:32,794 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-05T23:41:32,796 copying topiary/result.py -> build/lib/topiary 2026-05-05T23:41:32,799 copying topiary/sources.py -> build/lib/topiary 2026-05-05T23:41:32,801 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-05T23:41:32,803 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-05T23:41:32,806 copying topiary/io.py -> build/lib/topiary 2026-05-05T23:41:32,808 copying topiary/wide.py -> build/lib/topiary 2026-05-05T23:41:32,810 copying topiary/io_lens.py -> build/lib/topiary 2026-05-05T23:41:32,812 copying topiary/inputs.py -> build/lib/topiary 2026-05-05T23:41:32,815 copying topiary/cached.py -> build/lib/topiary 2026-05-05T23:41:32,818 copying topiary/predictor.py -> build/lib/topiary 2026-05-05T23:41:32,820 copying topiary/filters.py -> build/lib/topiary 2026-05-05T23:41:32,824 creating build/lib/tests 2026-05-05T23:41:32,825 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-05T23:41:32,827 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-05T23:41:32,830 copying tests/test_integration.py -> build/lib/tests 2026-05-05T23:41:32,832 copying tests/test_io.py -> build/lib/tests 2026-05-05T23:41:32,834 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-05T23:41:32,836 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-05T23:41:32,839 copying tests/test_ranking.py -> build/lib/tests 2026-05-05T23:41:32,844 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-05T23:41:32,846 copying tests/__init__.py -> build/lib/tests 2026-05-05T23:41:32,848 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-05T23:41:32,850 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-05T23:41:32,852 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-05T23:41:32,854 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-05T23:41:32,856 copying tests/test_inputs.py -> build/lib/tests 2026-05-05T23:41:32,859 copying tests/test_sources.py -> build/lib/tests 2026-05-05T23:41:32,861 copying tests/test_wide.py -> build/lib/tests 2026-05-05T23:41:32,863 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-05T23:41:32,865 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-05T23:41:32,867 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-05T23:41:32,870 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-05T23:41:32,872 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-05T23:41:32,874 copying tests/test_padding.py -> build/lib/tests 2026-05-05T23:41:32,876 copying tests/data.py -> build/lib/tests 2026-05-05T23:41:32,878 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-05T23:41:32,880 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-05T23:41:32,883 copying tests/test_dataframe.py -> build/lib/tests 2026-05-05T23:41:32,885 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-05T23:41:32,887 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-05T23:41:32,890 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-05T23:41:32,892 copying tests/common.py -> build/lib/tests 2026-05-05T23:41:32,893 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-05T23:41:32,896 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-05T23:41:32,898 copying tests/test_result.py -> build/lib/tests 2026-05-05T23:41:32,901 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-05T23:41:32,903 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-05T23:41:32,905 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-05T23:41:32,908 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-05T23:41:32,910 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-05T23:41:32,913 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-05T23:41:32,915 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-05T23:41:32,917 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-05T23:41:32,919 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-05T23:41:32,921 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-05T23:41:32,924 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-05T23:41:32,926 copying tests/test_cli_script.py -> build/lib/tests 2026-05-05T23:41:32,928 copying tests/test_io_lens.py -> build/lib/tests 2026-05-05T23:41:32,930 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-05T23:41:32,932 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-05T23:41:32,936 copying tests/test_deploy_script.py -> build/lib/tests 2026-05-05T23:41:32,938 creating build/lib/topiary/ranking 2026-05-05T23:41:32,939 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-05T23:41:32,943 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-05T23:41:32,946 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-05T23:41:32,949 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-05T23:41:32,955 creating build/lib/topiary/cli 2026-05-05T23:41:32,957 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-05T23:41:32,960 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-05T23:41:32,963 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-05T23:41:32,965 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-05T23:41:32,967 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-05T23:41:32,970 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-05T23:41:32,971 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-05T23:41:32,973 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-05T23:41:32,975 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-05T23:41:32,978 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-05T23:41:32,981 creating build/lib/topiary/rna 2026-05-05T23:41:32,982 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-05T23:41:32,984 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-05T23:41:32,986 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-05T23:41:32,988 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-05T23:41:32,990 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-05T23:41:32,992 running egg_info 2026-05-05T23:41:33,003 writing topiary.egg-info/PKG-INFO 2026-05-05T23:41:33,006 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-05T23:41:33,008 writing entry points to topiary.egg-info/entry_points.txt 2026-05-05T23:41:33,009 writing requirements to topiary.egg-info/requires.txt 2026-05-05T23:41:33,011 writing top-level names to topiary.egg-info/top_level.txt 2026-05-05T23:41:33,027 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T23:41:33,033 adding license file 'LICENSE' 2026-05-05T23:41:33,039 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T23:41:33,057 installing to build/bdist.linux-armv7l/wheel 2026-05-05T23:41:33,057 running install 2026-05-05T23:41:33,080 running install_lib 2026-05-05T23:41:33,085 creating build/bdist.linux-armv7l/wheel 2026-05-05T23:41:33,088 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-05T23:41:33,089 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,092 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-05T23:41:33,093 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T23:41:33,096 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T23:41:33,098 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T23:41:33,100 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T23:41:33,103 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,105 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,107 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,110 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,112 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,115 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,118 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-05T23:41:33,119 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,121 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,123 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,125 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,128 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,130 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,132 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,134 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,136 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,138 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T23:41:33,140 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,143 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,145 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,147 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,150 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-05T23:41:33,151 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T23:41:33,154 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T23:41:33,156 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T23:41:33,158 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T23:41:33,160 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T23:41:33,163 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,165 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,168 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,171 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T23:41:33,175 creating build/bdist.linux-armv7l/wheel/tests 2026-05-05T23:41:33,175 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,177 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,180 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,182 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,185 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,186 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,189 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,193 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,195 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,196 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,199 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,200 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,202 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,205 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,207 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,209 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,211 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,213 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,216 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,218 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,220 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,222 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,223 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,225 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,227 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,230 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,232 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,234 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,237 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,238 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,240 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,244 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,247 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,252 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,256 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,259 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,264 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,268 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,272 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,275 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,278 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,282 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,285 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,289 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,292 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,295 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,298 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,301 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,305 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T23:41:33,307 running install_egg_info 2026-05-05T23:41:33,315 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.10.5-py3.11.egg-info 2026-05-05T23:41:33,332 running install_scripts 2026-05-05T23:41:33,348 creating build/bdist.linux-armv7l/wheel/topiary-5.10.5.dist-info/WHEEL 2026-05-05T23:41:33,351 creating '/tmp/pip-wheel-gvnafb1m/.tmp-yaxdsqy8/topiary-5.10.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-05T23:41:33,354 adding 'tests/__init__.py' 2026-05-05T23:41:33,356 adding 'tests/common.py' 2026-05-05T23:41:33,357 adding 'tests/data.py' 2026-05-05T23:41:33,358 adding 'tests/test_args_outputs.py' 2026-05-05T23:41:33,363 adding 'tests/test_cached_predictor.py' 2026-05-05T23:41:33,365 adding 'tests/test_cli_cached_predictor.py' 2026-05-05T23:41:33,367 adding 'tests/test_cli_coverage.py' 2026-05-05T23:41:33,368 adding 'tests/test_cli_protein_changes.py' 2026-05-05T23:41:33,370 adding 'tests/test_cli_ranking.py' 2026-05-05T23:41:33,371 adding 'tests/test_cli_script.py' 2026-05-05T23:41:33,373 adding 'tests/test_contains_mutant_residues.py' 2026-05-05T23:41:33,375 adding 'tests/test_coverage_gaps.py' 2026-05-05T23:41:33,376 adding 'tests/test_dataframe.py' 2026-05-05T23:41:33,377 adding 'tests/test_deploy_script.py' 2026-05-05T23:41:33,379 adding 'tests/test_direct_input_regressions.py' 2026-05-05T23:41:33,381 adding 'tests/test_dsl_extensions.py' 2026-05-05T23:41:33,383 adding 'tests/test_dsl_polish.py' 2026-05-05T23:41:33,386 adding 'tests/test_dsl_roundtrip.py' 2026-05-05T23:41:33,388 adding 'tests/test_edge_case_fixtures.py' 2026-05-05T23:41:33,389 adding 'tests/test_effect_expression_filters.py' 2026-05-05T23:41:33,391 adding 'tests/test_end_to_end.py' 2026-05-05T23:41:33,392 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-05T23:41:33,394 adding 'tests/test_expression_integration.py' 2026-05-05T23:41:33,395 adding 'tests/test_expression_loader.py' 2026-05-05T23:41:33,398 adding 'tests/test_frameshift_fragments.py' 2026-05-05T23:41:33,400 adding 'tests/test_inputs.py' 2026-05-05T23:41:33,401 adding 'tests/test_integration.py' 2026-05-05T23:41:33,403 adding 'tests/test_io.py' 2026-05-05T23:41:33,405 adding 'tests/test_io_lens.py' 2026-05-05T23:41:33,407 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-05T23:41:33,408 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-05T23:41:33,409 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-05T23:41:33,411 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-05T23:41:33,412 adding 'tests/test_padding.py' 2026-05-05T23:41:33,413 adding 'tests/test_peptide_mutation_interval.py' 2026-05-05T23:41:33,416 adding 'tests/test_predict_from_fragments.py' 2026-05-05T23:41:33,418 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-05T23:41:33,420 adding 'tests/test_predictor_internals.py' 2026-05-05T23:41:33,422 adding 'tests/test_protein_fragment.py' 2026-05-05T23:41:33,431 adding 'tests/test_ranking.py' 2026-05-05T23:41:33,434 adding 'tests/test_result.py' 2026-05-05T23:41:33,436 adding 'tests/test_rna_helpers.py' 2026-05-05T23:41:33,438 adding 'tests/test_self_proteome.py' 2026-05-05T23:41:33,440 adding 'tests/test_sequence_helpers.py' 2026-05-05T23:41:33,441 adding 'tests/test_sources.py' 2026-05-05T23:41:33,442 adding 'tests/test_sources_optional.py' 2026-05-05T23:41:33,444 adding 'tests/test_validation_and_edge_cases.py' 2026-05-05T23:41:33,445 adding 'tests/test_variant_expression_filters.py' 2026-05-05T23:41:33,447 adding 'tests/test_wide.py' 2026-05-05T23:41:33,449 adding 'topiary/__init__.py' 2026-05-05T23:41:33,455 adding 'topiary/cached.py' 2026-05-05T23:41:33,457 adding 'topiary/filters.py' 2026-05-05T23:41:33,459 adding 'topiary/inputs.py' 2026-05-05T23:41:33,460 adding 'topiary/io.py' 2026-05-05T23:41:33,462 adding 'topiary/io_lens.py' 2026-05-05T23:41:33,464 adding 'topiary/io_protein_fragment.py' 2026-05-05T23:41:33,469 adding 'topiary/predictor.py' 2026-05-05T23:41:33,472 adding 'topiary/properties.py' 2026-05-05T23:41:33,474 adding 'topiary/protein_fragment.py' 2026-05-05T23:41:33,476 adding 'topiary/result.py' 2026-05-05T23:41:33,480 adding 'topiary/self_proteome.py' 2026-05-05T23:41:33,482 adding 'topiary/sequence_helpers.py' 2026-05-05T23:41:33,484 adding 'topiary/sources.py' 2026-05-05T23:41:33,486 adding 'topiary/wide.py' 2026-05-05T23:41:33,488 adding 'topiary/cli/__init__.py' 2026-05-05T23:41:33,491 adding 'topiary/cli/args.py' 2026-05-05T23:41:33,493 adding 'topiary/cli/cached_predictor.py' 2026-05-05T23:41:33,494 adding 'topiary/cli/errors.py' 2026-05-05T23:41:33,496 adding 'topiary/cli/filtering.py' 2026-05-05T23:41:33,498 adding 'topiary/cli/outputs.py' 2026-05-05T23:41:33,499 adding 'topiary/cli/protein_changes.py' 2026-05-05T23:41:33,501 adding 'topiary/cli/rna.py' 2026-05-05T23:41:33,502 adding 'topiary/cli/script.py' 2026-05-05T23:41:33,504 adding 'topiary/cli/sequence.py' 2026-05-05T23:41:33,506 adding 'topiary/ranking/__init__.py' 2026-05-05T23:41:33,508 adding 'topiary/ranking/apply.py' 2026-05-05T23:41:33,514 adding 'topiary/ranking/nodes.py' 2026-05-05T23:41:33,517 adding 'topiary/ranking/parser.py' 2026-05-05T23:41:33,519 adding 'topiary/rna/__init__.py' 2026-05-05T23:41:33,521 adding 'topiary/rna/common.py' 2026-05-05T23:41:33,522 adding 'topiary/rna/cufflinks.py' 2026-05-05T23:41:33,524 adding 'topiary/rna/expression_loader.py' 2026-05-05T23:41:33,526 adding 'topiary/rna/gtf.py' 2026-05-05T23:41:33,529 adding 'topiary-5.10.5.dist-info/licenses/LICENSE' 2026-05-05T23:41:33,533 adding 'topiary-5.10.5.dist-info/METADATA' 2026-05-05T23:41:33,534 adding 'topiary-5.10.5.dist-info/WHEEL' 2026-05-05T23:41:33,535 adding 'topiary-5.10.5.dist-info/entry_points.txt' 2026-05-05T23:41:33,536 adding 'topiary-5.10.5.dist-info/top_level.txt' 2026-05-05T23:41:33,538 adding 'topiary-5.10.5.dist-info/RECORD' 2026-05-05T23:41:33,542 removing build/bdist.linux-armv7l/wheel 2026-05-05T23:41:33,662 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-05T23:41:33,672 Created wheel for topiary: filename=topiary-5.10.5-py3-none-any.whl size=246924 sha256=a46ce83ab3367f052c6b2da3c1e7a383b1fb356ee4a2baaaa80d464ac363a933 2026-05-05T23:41:33,674 Stored in directory: /tmp/pip-ephem-wheel-cache-83129hnj/wheels/ee/aa/41/5a65583018c2f043e1d723beb2a7c81af2c123fa2ad6a42936 2026-05-05T23:41:33,691 Successfully built topiary 2026-05-05T23:41:33,703 Removed build tracker: '/tmp/pip-build-tracker-dla7_0sf'