2026-05-05T17:56:23,712 Created temporary directory: /tmp/pip-ephem-wheel-cache-e92mvb5f 2026-05-05T17:56:23,714 Created temporary directory: /tmp/pip-build-tracker-755rdti0 2026-05-05T17:56:23,714 Initialized build tracking at /tmp/pip-build-tracker-755rdti0 2026-05-05T17:56:23,715 Created build tracker: /tmp/pip-build-tracker-755rdti0 2026-05-05T17:56:23,715 Entered build tracker: /tmp/pip-build-tracker-755rdti0 2026-05-05T17:56:23,716 Created temporary directory: /tmp/pip-wheel-ei1b6zue 2026-05-05T17:56:23,719 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 2026-05-05T17:56:23,721 Created temporary directory: /tmp/pip-ephem-wheel-cache-20q3rk_k 2026-05-05T17:56:23,743 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-05T17:56:23,746 2 location(s) to search for versions of topiary: 2026-05-05T17:56:23,746 * https://pypi.org/simple/topiary/ 2026-05-05T17:56:23,746 * https://www.piwheels.org/simple/topiary/ 2026-05-05T17:56:23,747 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-05-05T17:56:23,748 Getting page https://pypi.org/simple/topiary/ 2026-05-05T17:56:23,749 Found index url https://pypi.org/simple 2026-05-05T17:56:23,984 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-05-05T17:56:24,002 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-0.0.1-py3-none-any.whl#sha256=6743a02aee34bc7567913bbe5c15a321924d9e1cb2c15f956e4ebb9b321707f4 (from https://www.piwheels.org/simple/topiary/) 2026-05-05T17:56:24,320 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/) 2026-05-05T17:56:24,321 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-05-05T17:56:24,321 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-05-05T17:56:24,348 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-05-05T17:56:24,366 Collecting topiary==5.10.3 2026-05-05T17:56:24,368 Created temporary directory: /tmp/pip-unpack-5agisaf2 2026-05-05T17:56:24,523 Downloading topiary-5.10.3.tar.gz (219 kB) 2026-05-05T17:56:24,808 Added topiary==5.10.3 from https://files.pythonhosted.org/packages/6c/7a/ddefd4c8c5f57a2c16491c57ac99843fc6e503e044b664ef30f74e694a20/topiary-5.10.3.tar.gz to build tracker '/tmp/pip-build-tracker-755rdti0' 2026-05-05T17:56:24,813 Created temporary directory: /tmp/pip-build-env-9g7h2kd0 2026-05-05T17:56:24,817 Installing build dependencies: started 2026-05-05T17:56:24,818 Running command pip subprocess to install build dependencies 2026-05-05T17:56:25,941 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-05T17:56:26,359 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 2026-05-05T17:56:26,381 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-05T17:56:28,131 Collecting setuptools>=64 2026-05-05T17:56:28,212 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-05T17:56:31,077 Installing collected packages: setuptools 2026-05-05T17:56:34,088 Successfully installed setuptools-82.0.1 2026-05-05T17:56:34,353 Installing build dependencies: finished with status 'done' 2026-05-05T17:56:34,360 Getting requirements to build wheel: started 2026-05-05T17:56:34,361 Running command Getting requirements to build wheel 2026-05-05T17:56:35,031 /tmp/pip-build-env-9g7h2kd0/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T17:56:35,032 !! 2026-05-05T17:56:35,033 ******************************************************************************** 2026-05-05T17:56:35,033 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T17:56:35,035 License :: OSI Approved :: Apache Software License 2026-05-05T17:56:35,036 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T17:56:35,036 ******************************************************************************** 2026-05-05T17:56:35,038 !! 2026-05-05T17:56:35,038 dist._finalize_license_expression() 2026-05-05T17:56:35,039 /tmp/pip-build-env-9g7h2kd0/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T17:56:35,039 !! 2026-05-05T17:56:35,040 ******************************************************************************** 2026-05-05T17:56:35,041 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T17:56:35,042 License :: OSI Approved :: Apache Software License 2026-05-05T17:56:35,043 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T17:56:35,044 ******************************************************************************** 2026-05-05T17:56:35,046 !! 2026-05-05T17:56:35,046 self._finalize_license_expression() 2026-05-05T17:56:35,046 running egg_info 2026-05-05T17:56:35,048 writing topiary.egg-info/PKG-INFO 2026-05-05T17:56:35,051 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-05T17:56:35,053 writing entry points to topiary.egg-info/entry_points.txt 2026-05-05T17:56:35,055 writing requirements to topiary.egg-info/requires.txt 2026-05-05T17:56:35,056 writing top-level names to topiary.egg-info/top_level.txt 2026-05-05T17:56:35,082 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T17:56:35,088 adding license file 'LICENSE' 2026-05-05T17:56:35,095 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T17:56:35,192 Getting requirements to build wheel: finished with status 'done' 2026-05-05T17:56:35,195 Created temporary directory: /tmp/pip-modern-metadata-sv3w3b9h 2026-05-05T17:56:35,197 Preparing metadata (pyproject.toml): started 2026-05-05T17:56:35,198 Running command Preparing metadata (pyproject.toml) 2026-05-05T17:56:35,828 /tmp/pip-build-env-9g7h2kd0/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T17:56:35,828 !! 2026-05-05T17:56:35,829 ******************************************************************************** 2026-05-05T17:56:35,829 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T17:56:35,830 License :: OSI Approved :: Apache Software License 2026-05-05T17:56:35,831 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T17:56:35,832 ******************************************************************************** 2026-05-05T17:56:35,833 !! 2026-05-05T17:56:35,834 dist._finalize_license_expression() 2026-05-05T17:56:35,835 /tmp/pip-build-env-9g7h2kd0/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T17:56:35,835 !! 2026-05-05T17:56:35,837 ******************************************************************************** 2026-05-05T17:56:35,837 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T17:56:35,838 License :: OSI Approved :: Apache Software License 2026-05-05T17:56:35,840 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T17:56:35,840 ******************************************************************************** 2026-05-05T17:56:35,842 !! 2026-05-05T17:56:35,842 self._finalize_license_expression() 2026-05-05T17:56:35,843 running dist_info 2026-05-05T17:56:35,851 creating /tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info 2026-05-05T17:56:35,852 writing /tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/PKG-INFO 2026-05-05T17:56:35,856 writing dependency_links to /tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/dependency_links.txt 2026-05-05T17:56:35,858 writing entry points to /tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/entry_points.txt 2026-05-05T17:56:35,859 writing requirements to /tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/requires.txt 2026-05-05T17:56:35,860 writing top-level names to /tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/top_level.txt 2026-05-05T17:56:35,862 writing manifest file '/tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/SOURCES.txt' 2026-05-05T17:56:35,886 reading manifest file '/tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/SOURCES.txt' 2026-05-05T17:56:35,888 adding license file 'LICENSE' 2026-05-05T17:56:35,894 writing manifest file '/tmp/pip-modern-metadata-sv3w3b9h/topiary.egg-info/SOURCES.txt' 2026-05-05T17:56:35,895 creating '/tmp/pip-modern-metadata-sv3w3b9h/topiary-5.10.3.dist-info' 2026-05-05T17:56:36,019 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-05T17:56:36,025 Source in /tmp/pip-wheel-ei1b6zue/topiary_b645e240a5004224ba23c88eb69453c6 has version 5.10.3, which satisfies requirement topiary==5.10.3 from https://files.pythonhosted.org/packages/6c/7a/ddefd4c8c5f57a2c16491c57ac99843fc6e503e044b664ef30f74e694a20/topiary-5.10.3.tar.gz 2026-05-05T17:56:36,026 Removed topiary==5.10.3 from https://files.pythonhosted.org/packages/6c/7a/ddefd4c8c5f57a2c16491c57ac99843fc6e503e044b664ef30f74e694a20/topiary-5.10.3.tar.gz from build tracker '/tmp/pip-build-tracker-755rdti0' 2026-05-05T17:56:36,034 Created temporary directory: /tmp/pip-unpack-9ri0lr7o 2026-05-05T17:56:36,035 Building wheels for collected packages: topiary 2026-05-05T17:56:36,039 Created temporary directory: /tmp/pip-wheel-q_fn6wkz 2026-05-05T17:56:36,040 Destination directory: /tmp/pip-wheel-q_fn6wkz 2026-05-05T17:56:36,042 Building wheel for topiary (pyproject.toml): started 2026-05-05T17:56:36,043 Running command Building wheel for topiary (pyproject.toml) 2026-05-05T17:56:36,686 /tmp/pip-build-env-9g7h2kd0/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T17:56:36,686 !! 2026-05-05T17:56:36,687 ******************************************************************************** 2026-05-05T17:56:36,688 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T17:56:36,689 License :: OSI Approved :: Apache Software License 2026-05-05T17:56:36,690 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T17:56:36,690 ******************************************************************************** 2026-05-05T17:56:36,692 !! 2026-05-05T17:56:36,692 dist._finalize_license_expression() 2026-05-05T17:56:36,693 /tmp/pip-build-env-9g7h2kd0/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-05T17:56:36,694 !! 2026-05-05T17:56:36,695 ******************************************************************************** 2026-05-05T17:56:36,696 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-05T17:56:36,697 License :: OSI Approved :: Apache Software License 2026-05-05T17:56:36,698 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-05T17:56:36,699 ******************************************************************************** 2026-05-05T17:56:36,700 !! 2026-05-05T17:56:36,700 self._finalize_license_expression() 2026-05-05T17:56:36,701 running bdist_wheel 2026-05-05T17:56:36,711 running build 2026-05-05T17:56:36,712 running build_py 2026-05-05T17:56:36,717 creating build/lib/topiary 2026-05-05T17:56:36,720 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-05T17:56:36,722 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-05T17:56:36,725 copying topiary/io_lens.py -> build/lib/topiary 2026-05-05T17:56:36,727 copying topiary/sources.py -> build/lib/topiary 2026-05-05T17:56:36,730 copying topiary/result.py -> build/lib/topiary 2026-05-05T17:56:36,732 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-05T17:56:36,735 copying topiary/predictor.py -> build/lib/topiary 2026-05-05T17:56:36,738 copying topiary/cached.py -> build/lib/topiary 2026-05-05T17:56:36,741 copying topiary/__init__.py -> build/lib/topiary 2026-05-05T17:56:36,743 copying topiary/properties.py -> build/lib/topiary 2026-05-05T17:56:36,745 copying topiary/wide.py -> build/lib/topiary 2026-05-05T17:56:36,747 copying topiary/filters.py -> build/lib/topiary 2026-05-05T17:56:36,750 copying topiary/inputs.py -> build/lib/topiary 2026-05-05T17:56:36,752 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-05T17:56:36,754 copying topiary/io.py -> build/lib/topiary 2026-05-05T17:56:36,758 creating build/lib/tests 2026-05-05T17:56:36,759 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-05T17:56:36,761 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-05T17:56:36,762 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-05T17:56:36,765 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-05T17:56:36,768 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-05T17:56:36,770 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-05T17:56:36,772 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-05T17:56:36,774 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-05T17:56:36,776 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-05T17:56:36,779 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-05T17:56:36,780 copying tests/test_integration.py -> build/lib/tests 2026-05-05T17:56:36,782 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-05T17:56:36,784 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-05T17:56:36,786 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-05T17:56:36,788 copying tests/test_sources.py -> build/lib/tests 2026-05-05T17:56:36,790 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-05T17:56:36,792 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-05T17:56:36,794 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-05T17:56:36,796 copying tests/test_inputs.py -> build/lib/tests 2026-05-05T17:56:36,798 copying tests/common.py -> build/lib/tests 2026-05-05T17:56:36,800 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-05T17:56:36,801 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-05T17:56:36,803 copying tests/test_cli_script.py -> build/lib/tests 2026-05-05T17:56:36,804 copying tests/test_io_lens.py -> build/lib/tests 2026-05-05T17:56:36,807 copying tests/data.py -> build/lib/tests 2026-05-05T17:56:36,808 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-05T17:56:36,810 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-05T17:56:36,812 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-05T17:56:36,814 copying tests/__init__.py -> build/lib/tests 2026-05-05T17:56:36,816 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-05T17:56:36,818 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-05T17:56:36,821 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-05T17:56:36,823 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-05T17:56:36,825 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-05T17:56:36,827 copying tests/test_dataframe.py -> build/lib/tests 2026-05-05T17:56:36,829 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-05T17:56:36,831 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-05T17:56:36,833 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-05T17:56:36,836 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-05T17:56:36,838 copying tests/test_io.py -> build/lib/tests 2026-05-05T17:56:36,840 copying tests/test_wide.py -> build/lib/tests 2026-05-05T17:56:36,843 copying tests/test_result.py -> build/lib/tests 2026-05-05T17:56:36,845 copying tests/test_ranking.py -> build/lib/tests 2026-05-05T17:56:36,849 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-05T17:56:36,851 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-05T17:56:36,853 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-05T17:56:36,856 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-05T17:56:36,858 copying tests/test_padding.py -> build/lib/tests 2026-05-05T17:56:36,860 creating build/lib/topiary/cli 2026-05-05T17:56:36,861 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-05T17:56:36,863 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-05T17:56:36,866 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-05T17:56:36,868 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-05T17:56:36,870 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-05T17:56:36,871 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-05T17:56:36,873 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-05T17:56:36,875 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-05T17:56:36,877 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-05T17:56:36,879 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-05T17:56:36,882 creating build/lib/topiary/rna 2026-05-05T17:56:36,883 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-05T17:56:36,885 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-05T17:56:36,887 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-05T17:56:36,889 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-05T17:56:36,890 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-05T17:56:36,893 creating build/lib/topiary/ranking 2026-05-05T17:56:36,893 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-05T17:56:36,895 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-05T17:56:36,898 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-05T17:56:36,900 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-05T17:56:36,902 running egg_info 2026-05-05T17:56:36,912 writing topiary.egg-info/PKG-INFO 2026-05-05T17:56:36,915 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-05T17:56:36,917 writing entry points to topiary.egg-info/entry_points.txt 2026-05-05T17:56:36,918 writing requirements to topiary.egg-info/requires.txt 2026-05-05T17:56:36,920 writing top-level names to topiary.egg-info/top_level.txt 2026-05-05T17:56:36,935 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T17:56:36,942 adding license file 'LICENSE' 2026-05-05T17:56:36,948 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-05T17:56:36,966 installing to build/bdist.linux-armv7l/wheel 2026-05-05T17:56:36,966 running install 2026-05-05T17:56:36,990 running install_lib 2026-05-05T17:56:36,996 creating build/bdist.linux-armv7l/wheel 2026-05-05T17:56:36,998 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-05T17:56:37,000 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-05T17:56:37,002 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,004 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,007 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,010 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,012 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,014 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,016 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,019 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,021 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,023 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-05T17:56:37,026 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,029 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,032 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-05T17:56:37,033 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T17:56:37,036 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T17:56:37,038 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T17:56:37,041 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T17:56:37,043 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-05T17:56:37,045 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,048 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,050 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,053 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,055 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,058 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,062 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,064 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-05T17:56:37,066 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T17:56:37,069 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T17:56:37,072 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T17:56:37,074 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-05T17:56:37,077 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,080 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,083 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,085 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,088 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,091 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-05T17:56:37,095 creating build/bdist.linux-armv7l/wheel/tests 2026-05-05T17:56:37,096 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,098 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,101 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,104 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,107 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,109 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,112 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,114 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,118 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,120 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,123 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,125 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,128 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,130 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,133 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,135 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,137 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,140 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,142 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,145 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,147 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,149 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,152 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,154 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,156 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,159 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,161 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,163 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,165 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,167 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,170 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,173 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,175 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,178 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,181 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,185 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,189 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,194 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,198 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,201 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,205 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,209 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,213 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,218 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,221 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,223 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,227 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,231 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-05T17:56:37,233 running install_egg_info 2026-05-05T17:56:37,241 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.10.3-py3.11.egg-info 2026-05-05T17:56:37,257 running install_scripts 2026-05-05T17:56:37,279 creating build/bdist.linux-armv7l/wheel/topiary-5.10.3.dist-info/WHEEL 2026-05-05T17:56:37,283 creating '/tmp/pip-wheel-q_fn6wkz/.tmp-zhwoos8f/topiary-5.10.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-05T17:56:37,287 adding 'tests/__init__.py' 2026-05-05T17:56:37,289 adding 'tests/common.py' 2026-05-05T17:56:37,291 adding 'tests/data.py' 2026-05-05T17:56:37,292 adding 'tests/test_args_outputs.py' 2026-05-05T17:56:37,298 adding 'tests/test_cached_predictor.py' 2026-05-05T17:56:37,301 adding 'tests/test_cli_cached_predictor.py' 2026-05-05T17:56:37,303 adding 'tests/test_cli_coverage.py' 2026-05-05T17:56:37,305 adding 'tests/test_cli_protein_changes.py' 2026-05-05T17:56:37,308 adding 'tests/test_cli_ranking.py' 2026-05-05T17:56:37,310 adding 'tests/test_cli_script.py' 2026-05-05T17:56:37,312 adding 'tests/test_contains_mutant_residues.py' 2026-05-05T17:56:37,314 adding 'tests/test_coverage_gaps.py' 2026-05-05T17:56:37,316 adding 'tests/test_dataframe.py' 2026-05-05T17:56:37,317 adding 'tests/test_direct_input_regressions.py' 2026-05-05T17:56:37,320 adding 'tests/test_dsl_extensions.py' 2026-05-05T17:56:37,322 adding 'tests/test_dsl_polish.py' 2026-05-05T17:56:37,326 adding 'tests/test_dsl_roundtrip.py' 2026-05-05T17:56:37,328 adding 'tests/test_edge_case_fixtures.py' 2026-05-05T17:56:37,329 adding 'tests/test_effect_expression_filters.py' 2026-05-05T17:56:37,331 adding 'tests/test_end_to_end.py' 2026-05-05T17:56:37,333 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-05T17:56:37,335 adding 'tests/test_expression_integration.py' 2026-05-05T17:56:37,337 adding 'tests/test_expression_loader.py' 2026-05-05T17:56:37,340 adding 'tests/test_frameshift_fragments.py' 2026-05-05T17:56:37,343 adding 'tests/test_inputs.py' 2026-05-05T17:56:37,344 adding 'tests/test_integration.py' 2026-05-05T17:56:37,347 adding 'tests/test_io.py' 2026-05-05T17:56:37,351 adding 'tests/test_io_lens.py' 2026-05-05T17:56:37,353 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-05T17:56:37,355 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-05T17:56:37,356 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-05T17:56:37,358 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-05T17:56:37,360 adding 'tests/test_padding.py' 2026-05-05T17:56:37,361 adding 'tests/test_peptide_mutation_interval.py' 2026-05-05T17:56:37,364 adding 'tests/test_predict_from_fragments.py' 2026-05-05T17:56:37,367 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-05T17:56:37,369 adding 'tests/test_predictor_internals.py' 2026-05-05T17:56:37,371 adding 'tests/test_protein_fragment.py' 2026-05-05T17:56:37,381 adding 'tests/test_ranking.py' 2026-05-05T17:56:37,385 adding 'tests/test_result.py' 2026-05-05T17:56:37,386 adding 'tests/test_rna_helpers.py' 2026-05-05T17:56:37,390 adding 'tests/test_self_proteome.py' 2026-05-05T17:56:37,391 adding 'tests/test_sequence_helpers.py' 2026-05-05T17:56:37,393 adding 'tests/test_sources.py' 2026-05-05T17:56:37,395 adding 'tests/test_sources_optional.py' 2026-05-05T17:56:37,397 adding 'tests/test_validation_and_edge_cases.py' 2026-05-05T17:56:37,399 adding 'tests/test_variant_expression_filters.py' 2026-05-05T17:56:37,401 adding 'tests/test_wide.py' 2026-05-05T17:56:37,403 adding 'topiary/__init__.py' 2026-05-05T17:56:37,409 adding 'topiary/cached.py' 2026-05-05T17:56:37,411 adding 'topiary/filters.py' 2026-05-05T17:56:37,414 adding 'topiary/inputs.py' 2026-05-05T17:56:37,416 adding 'topiary/io.py' 2026-05-05T17:56:37,418 adding 'topiary/io_lens.py' 2026-05-05T17:56:37,420 adding 'topiary/io_protein_fragment.py' 2026-05-05T17:56:37,426 adding 'topiary/predictor.py' 2026-05-05T17:56:37,428 adding 'topiary/properties.py' 2026-05-05T17:56:37,430 adding 'topiary/protein_fragment.py' 2026-05-05T17:56:37,433 adding 'topiary/result.py' 2026-05-05T17:56:37,437 adding 'topiary/self_proteome.py' 2026-05-05T17:56:37,438 adding 'topiary/sequence_helpers.py' 2026-05-05T17:56:37,440 adding 'topiary/sources.py' 2026-05-05T17:56:37,442 adding 'topiary/wide.py' 2026-05-05T17:56:37,443 adding 'topiary/cli/__init__.py' 2026-05-05T17:56:37,446 adding 'topiary/cli/args.py' 2026-05-05T17:56:37,448 adding 'topiary/cli/cached_predictor.py' 2026-05-05T17:56:37,449 adding 'topiary/cli/errors.py' 2026-05-05T17:56:37,451 adding 'topiary/cli/filtering.py' 2026-05-05T17:56:37,452 adding 'topiary/cli/outputs.py' 2026-05-05T17:56:37,454 adding 'topiary/cli/protein_changes.py' 2026-05-05T17:56:37,455 adding 'topiary/cli/rna.py' 2026-05-05T17:56:37,456 adding 'topiary/cli/script.py' 2026-05-05T17:56:37,458 adding 'topiary/cli/sequence.py' 2026-05-05T17:56:37,460 adding 'topiary/ranking/__init__.py' 2026-05-05T17:56:37,461 adding 'topiary/ranking/apply.py' 2026-05-05T17:56:37,468 adding 'topiary/ranking/nodes.py' 2026-05-05T17:56:37,471 adding 'topiary/ranking/parser.py' 2026-05-05T17:56:37,473 adding 'topiary/rna/__init__.py' 2026-05-05T17:56:37,474 adding 'topiary/rna/common.py' 2026-05-05T17:56:37,476 adding 'topiary/rna/cufflinks.py' 2026-05-05T17:56:37,477 adding 'topiary/rna/expression_loader.py' 2026-05-05T17:56:37,479 adding 'topiary/rna/gtf.py' 2026-05-05T17:56:37,482 adding 'topiary-5.10.3.dist-info/licenses/LICENSE' 2026-05-05T17:56:37,485 adding 'topiary-5.10.3.dist-info/METADATA' 2026-05-05T17:56:37,487 adding 'topiary-5.10.3.dist-info/WHEEL' 2026-05-05T17:56:37,487 adding 'topiary-5.10.3.dist-info/entry_points.txt' 2026-05-05T17:56:37,488 adding 'topiary-5.10.3.dist-info/top_level.txt' 2026-05-05T17:56:37,490 adding 'topiary-5.10.3.dist-info/RECORD' 2026-05-05T17:56:37,494 removing build/bdist.linux-armv7l/wheel 2026-05-05T17:56:37,610 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-05T17:56:37,620 Created wheel for topiary: filename=topiary-5.10.3-py3-none-any.whl size=246211 sha256=513f060557ecf806ae8a36414ffaa892a337790cac530e820fa3af7570264434 2026-05-05T17:56:37,621 Stored in directory: /tmp/pip-ephem-wheel-cache-20q3rk_k/wheels/23/8f/e6/1ed57b1cecdf16b5842d197715d8a65f0889a12f10152e56ac 2026-05-05T17:56:37,638 Successfully built topiary 2026-05-05T17:56:37,649 Removed build tracker: '/tmp/pip-build-tracker-755rdti0'