2026-04-12T02:52:33,478 Created temporary directory: /tmp/pip-ephem-wheel-cache-0pjxyvnl 2026-04-12T02:52:33,479 Created temporary directory: /tmp/pip-build-tracker-yfsz8wez 2026-04-12T02:52:33,480 Initialized build tracking at /tmp/pip-build-tracker-yfsz8wez 2026-04-12T02:52:33,480 Created build tracker: /tmp/pip-build-tracker-yfsz8wez 2026-04-12T02:52:33,481 Entered build tracker: /tmp/pip-build-tracker-yfsz8wez 2026-04-12T02:52:33,482 Created temporary directory: /tmp/pip-wheel-q3xj780s 2026-04-12T02:52:33,484 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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version: 4.11.1 2026-04-12T02:52:33,807 Skipping link: No binaries permitted for topiary: https://files.pythonhosted.org/packages/f7/03/03419230e47f5ff77830017fabc0b0e15afaea00d7492384b88a3290d2f1/topiary-4.11.2-py3-none-any.whl (from https://pypi.org/simple/topiary/) (requires-python:>=3.9) 2026-04-12T02:52:33,807 Found link https://files.pythonhosted.org/packages/ed/07/274d4a3f7c131caa1c5eb7368b2dd8bb8e5cc6202478c91b00df2cea0d46/topiary-4.11.2.tar.gz (from https://pypi.org/simple/topiary/) (requires-python:>=3.9), version: 4.11.2 2026-04-12T02:52:33,808 Fetching project page and analyzing links: https://www.piwheels.org/simple/topiary/ 2026-04-12T02:52:33,809 Getting page https://www.piwheels.org/simple/topiary/ 2026-04-12T02:52:33,810 Found index url https://www.piwheels.org/simple 2026-04-12T02:52:34,156 Fetched page https://www.piwheels.org/simple/topiary/ as text/html 2026-04-12T02:52:34,170 Skipping link: No binaries permitted for topiary: 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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/) 2026-04-12T02:52:34,195 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/) 2026-04-12T02:52:34,196 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-12T02:52:34,197 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-12T02:52:34,223 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-12T02:52:34,242 Collecting topiary==4.11.2 2026-04-12T02:52:34,244 Created temporary directory: /tmp/pip-unpack-3aasf013 2026-04-12T02:52:34,479 Downloading topiary-4.11.2.tar.gz (116 kB) 2026-04-12T02:52:34,701 Added topiary==4.11.2 from https://files.pythonhosted.org/packages/ed/07/274d4a3f7c131caa1c5eb7368b2dd8bb8e5cc6202478c91b00df2cea0d46/topiary-4.11.2.tar.gz to build tracker '/tmp/pip-build-tracker-yfsz8wez' 2026-04-12T02:52:34,707 Created temporary directory: /tmp/pip-build-env-qz3saw6x 2026-04-12T02:52:34,711 Installing build dependencies: started 2026-04-12T02:52:34,712 Running command pip subprocess to install build dependencies 2026-04-12T02:52:35,870 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-12T02:52:36,302 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 2026-04-12T02:52:36,324 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-12T02:52:38,069 Collecting setuptools>=64 2026-04-12T02:52:38,172 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-12T02:52:41,131 Installing collected packages: setuptools 2026-04-12T02:52:44,146 Successfully installed setuptools-82.0.1 2026-04-12T02:52:44,413 Installing build dependencies: finished with status 'done' 2026-04-12T02:52:44,419 Getting requirements to build wheel: started 2026-04-12T02:52:44,420 Running command Getting requirements to build wheel 2026-04-12T02:52:45,091 /tmp/pip-build-env-qz3saw6x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T02:52:45,091 !! 2026-04-12T02:52:45,092 ******************************************************************************** 2026-04-12T02:52:45,093 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T02:52:45,094 License :: OSI Approved :: Apache Software License 2026-04-12T02:52:45,095 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T02:52:45,096 ******************************************************************************** 2026-04-12T02:52:45,097 !! 2026-04-12T02:52:45,098 dist._finalize_license_expression() 2026-04-12T02:52:45,099 /tmp/pip-build-env-qz3saw6x/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T02:52:45,099 !! 2026-04-12T02:52:45,100 ******************************************************************************** 2026-04-12T02:52:45,101 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T02:52:45,102 License :: OSI Approved :: Apache Software License 2026-04-12T02:52:45,103 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T02:52:45,104 ******************************************************************************** 2026-04-12T02:52:45,105 !! 2026-04-12T02:52:45,105 self._finalize_license_expression() 2026-04-12T02:52:45,106 running egg_info 2026-04-12T02:52:45,110 writing topiary.egg-info/PKG-INFO 2026-04-12T02:52:45,114 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-12T02:52:45,116 writing entry points to topiary.egg-info/entry_points.txt 2026-04-12T02:52:45,117 writing requirements to topiary.egg-info/requires.txt 2026-04-12T02:52:45,118 writing top-level names to topiary.egg-info/top_level.txt 2026-04-12T02:52:45,144 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T02:52:45,149 adding license file 'LICENSE' 2026-04-12T02:52:45,155 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T02:52:45,252 Getting requirements to build wheel: finished with status 'done' 2026-04-12T02:52:45,255 Created temporary directory: /tmp/pip-modern-metadata-2fqc88v8 2026-04-12T02:52:45,257 Preparing metadata (pyproject.toml): started 2026-04-12T02:52:45,258 Running command Preparing metadata (pyproject.toml) 2026-04-12T02:52:45,891 /tmp/pip-build-env-qz3saw6x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T02:52:45,891 !! 2026-04-12T02:52:45,892 ******************************************************************************** 2026-04-12T02:52:45,893 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T02:52:45,894 License :: OSI Approved :: Apache Software License 2026-04-12T02:52:45,894 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T02:52:45,895 ******************************************************************************** 2026-04-12T02:52:45,896 !! 2026-04-12T02:52:45,896 dist._finalize_license_expression() 2026-04-12T02:52:45,897 /tmp/pip-build-env-qz3saw6x/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T02:52:45,897 !! 2026-04-12T02:52:45,899 ******************************************************************************** 2026-04-12T02:52:45,899 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T02:52:45,900 License :: OSI Approved :: Apache Software License 2026-04-12T02:52:45,901 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T02:52:45,902 ******************************************************************************** 2026-04-12T02:52:45,903 !! 2026-04-12T02:52:45,903 self._finalize_license_expression() 2026-04-12T02:52:45,904 running dist_info 2026-04-12T02:52:45,913 creating /tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info 2026-04-12T02:52:45,914 writing /tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/PKG-INFO 2026-04-12T02:52:45,918 writing dependency_links to /tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/dependency_links.txt 2026-04-12T02:52:45,920 writing entry points to /tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/entry_points.txt 2026-04-12T02:52:45,921 writing requirements to /tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/requires.txt 2026-04-12T02:52:45,922 writing top-level names to /tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/top_level.txt 2026-04-12T02:52:45,924 writing manifest file '/tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/SOURCES.txt' 2026-04-12T02:52:45,946 reading manifest file '/tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/SOURCES.txt' 2026-04-12T02:52:45,948 adding license file 'LICENSE' 2026-04-12T02:52:45,953 writing manifest file '/tmp/pip-modern-metadata-2fqc88v8/topiary.egg-info/SOURCES.txt' 2026-04-12T02:52:45,954 creating '/tmp/pip-modern-metadata-2fqc88v8/topiary-4.11.2.dist-info' 2026-04-12T02:52:46,077 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-12T02:52:46,083 Source in /tmp/pip-wheel-q3xj780s/topiary_0a74f3a3fbd14cfaa53fef47ec3777f3 has version 4.11.2, which satisfies requirement topiary==4.11.2 from https://files.pythonhosted.org/packages/ed/07/274d4a3f7c131caa1c5eb7368b2dd8bb8e5cc6202478c91b00df2cea0d46/topiary-4.11.2.tar.gz 2026-04-12T02:52:46,084 Removed topiary==4.11.2 from https://files.pythonhosted.org/packages/ed/07/274d4a3f7c131caa1c5eb7368b2dd8bb8e5cc6202478c91b00df2cea0d46/topiary-4.11.2.tar.gz from build tracker '/tmp/pip-build-tracker-yfsz8wez' 2026-04-12T02:52:46,092 Created temporary directory: /tmp/pip-unpack-os2jvchp 2026-04-12T02:52:46,092 Building wheels for collected packages: topiary 2026-04-12T02:52:46,097 Created temporary directory: /tmp/pip-wheel-eqyczukk 2026-04-12T02:52:46,098 Destination directory: /tmp/pip-wheel-eqyczukk 2026-04-12T02:52:46,100 Building wheel for topiary (pyproject.toml): started 2026-04-12T02:52:46,101 Running command Building wheel for topiary (pyproject.toml) 2026-04-12T02:52:46,759 /tmp/pip-build-env-qz3saw6x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T02:52:46,759 !! 2026-04-12T02:52:46,760 ******************************************************************************** 2026-04-12T02:52:46,761 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T02:52:46,762 License :: OSI Approved :: Apache Software License 2026-04-12T02:52:46,763 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T02:52:46,763 ******************************************************************************** 2026-04-12T02:52:46,764 !! 2026-04-12T02:52:46,764 dist._finalize_license_expression() 2026-04-12T02:52:46,765 /tmp/pip-build-env-qz3saw6x/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T02:52:46,765 !! 2026-04-12T02:52:46,767 ******************************************************************************** 2026-04-12T02:52:46,767 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T02:52:46,768 License :: OSI Approved :: Apache Software License 2026-04-12T02:52:46,769 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T02:52:46,770 ******************************************************************************** 2026-04-12T02:52:46,771 !! 2026-04-12T02:52:46,772 self._finalize_license_expression() 2026-04-12T02:52:46,773 running bdist_wheel 2026-04-12T02:52:46,785 running build 2026-04-12T02:52:46,786 running build_py 2026-04-12T02:52:46,792 creating build/lib/topiary 2026-04-12T02:52:46,794 copying topiary/io.py -> build/lib/topiary 2026-04-12T02:52:46,796 copying topiary/inputs.py -> build/lib/topiary 2026-04-12T02:52:46,799 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-12T02:52:46,801 copying topiary/ranking.py -> build/lib/topiary 2026-04-12T02:52:46,807 copying topiary/__init__.py -> build/lib/topiary 2026-04-12T02:52:46,809 copying topiary/sources.py -> build/lib/topiary 2026-04-12T02:52:46,811 copying topiary/filters.py -> build/lib/topiary 2026-04-12T02:52:46,813 copying topiary/wide.py -> build/lib/topiary 2026-04-12T02:52:46,816 copying topiary/properties.py -> build/lib/topiary 2026-04-12T02:52:46,818 copying topiary/predictor.py -> build/lib/topiary 2026-04-12T02:52:46,822 creating build/lib/tests 2026-04-12T02:52:46,823 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-12T02:52:46,826 copying tests/test_dataframe.py -> build/lib/tests 2026-04-12T02:52:46,828 copying tests/test_sources.py -> build/lib/tests 2026-04-12T02:52:46,830 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-12T02:52:46,832 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-12T02:52:46,834 copying tests/test_padding.py -> build/lib/tests 2026-04-12T02:52:46,836 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-12T02:52:46,838 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-12T02:52:46,840 copying tests/test_integration.py -> build/lib/tests 2026-04-12T02:52:46,842 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-12T02:52:46,844 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-12T02:52:46,846 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-12T02:52:46,849 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-12T02:52:46,850 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-12T02:52:46,852 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-12T02:52:46,854 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-12T02:52:46,856 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-12T02:52:46,859 copying tests/common.py -> build/lib/tests 2026-04-12T02:52:46,860 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-12T02:52:46,862 copying tests/__init__.py -> build/lib/tests 2026-04-12T02:52:46,864 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-12T02:52:46,865 copying tests/test_wide.py -> build/lib/tests 2026-04-12T02:52:46,868 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-12T02:52:46,870 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-12T02:52:46,872 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-12T02:52:46,874 copying tests/data.py -> build/lib/tests 2026-04-12T02:52:46,875 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-12T02:52:46,878 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-12T02:52:46,879 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-12T02:52:46,881 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-12T02:52:46,883 copying tests/test_io.py -> build/lib/tests 2026-04-12T02:52:46,886 copying tests/test_inputs.py -> build/lib/tests 2026-04-12T02:52:46,888 copying tests/test_ranking.py -> build/lib/tests 2026-04-12T02:52:46,892 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-12T02:52:46,894 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-12T02:52:46,895 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-12T02:52:46,897 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-12T02:52:46,901 creating build/lib/topiary/cli 2026-04-12T02:52:46,902 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-12T02:52:46,904 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-12T02:52:46,906 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-12T02:52:46,908 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-12T02:52:46,910 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-12T02:52:46,912 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-12T02:52:46,913 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-12T02:52:46,916 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-12T02:52:46,919 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-12T02:52:46,922 creating build/lib/topiary/rna 2026-04-12T02:52:46,923 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-12T02:52:46,926 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-12T02:52:46,927 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-12T02:52:46,930 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-12T02:52:46,932 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-12T02:52:46,934 running egg_info 2026-04-12T02:52:46,944 writing topiary.egg-info/PKG-INFO 2026-04-12T02:52:46,947 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-12T02:52:46,949 writing entry points to topiary.egg-info/entry_points.txt 2026-04-12T02:52:46,950 writing requirements to topiary.egg-info/requires.txt 2026-04-12T02:52:46,951 writing top-level names to topiary.egg-info/top_level.txt 2026-04-12T02:52:46,965 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T02:52:46,970 adding license file 'LICENSE' 2026-04-12T02:52:46,976 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T02:52:46,991 installing to build/bdist.linux-armv7l/wheel 2026-04-12T02:52:46,992 running install 2026-04-12T02:52:47,015 running install_lib 2026-04-12T02:52:47,021 creating build/bdist.linux-armv7l/wheel 2026-04-12T02:52:47,023 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-12T02:52:47,024 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,026 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,028 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,031 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-12T02:52:47,032 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,034 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,036 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,038 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,039 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,041 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,043 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,045 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,047 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T02:52:47,050 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-12T02:52:47,051 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T02:52:47,054 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T02:52:47,055 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T02:52:47,058 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T02:52:47,060 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T02:52:47,062 copying build/lib/topiary/ranking.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,065 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,067 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,069 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,072 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,074 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,076 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T02:52:47,080 creating build/bdist.linux-armv7l/wheel/tests 2026-04-12T02:52:47,081 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,083 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,085 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,087 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,089 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,091 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,093 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,095 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,097 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,100 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,102 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,104 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,106 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,107 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,109 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,111 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,113 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,115 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,117 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,119 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,121 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,123 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,125 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,127 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,129 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,131 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,133 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,135 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,137 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,139 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,141 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,143 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,145 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,149 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,151 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,152 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,154 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T02:52:47,157 running install_egg_info 2026-04-12T02:52:47,162 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-4.11.2-py3.11.egg-info 2026-04-12T02:52:47,173 running install_scripts 2026-04-12T02:52:47,186 creating build/bdist.linux-armv7l/wheel/topiary-4.11.2.dist-info/WHEEL 2026-04-12T02:52:47,189 creating '/tmp/pip-wheel-eqyczukk/.tmp-jts8gumk/topiary-4.11.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-12T02:52:47,191 adding 'tests/__init__.py' 2026-04-12T02:52:47,192 adding 'tests/common.py' 2026-04-12T02:52:47,194 adding 'tests/data.py' 2026-04-12T02:52:47,195 adding 'tests/test_args_outputs.py' 2026-04-12T02:52:47,197 adding 'tests/test_cli_coverage.py' 2026-04-12T02:52:47,198 adding 'tests/test_cli_protein_changes.py' 2026-04-12T02:52:47,200 adding 'tests/test_cli_ranking.py' 2026-04-12T02:52:47,201 adding 'tests/test_contains_mutant_residues.py' 2026-04-12T02:52:47,203 adding 'tests/test_coverage_gaps.py' 2026-04-12T02:52:47,204 adding 'tests/test_dataframe.py' 2026-04-12T02:52:47,205 adding 'tests/test_direct_input_regressions.py' 2026-04-12T02:52:47,208 adding 'tests/test_dsl_extensions.py' 2026-04-12T02:52:47,209 adding 'tests/test_dsl_polish.py' 2026-04-12T02:52:47,211 adding 'tests/test_edge_case_fixtures.py' 2026-04-12T02:52:47,212 adding 'tests/test_effect_expression_filters.py' 2026-04-12T02:52:47,213 adding 'tests/test_end_to_end.py' 2026-04-12T02:52:47,215 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-12T02:52:47,216 adding 'tests/test_expression_integration.py' 2026-04-12T02:52:47,217 adding 'tests/test_expression_loader.py' 2026-04-12T02:52:47,219 adding 'tests/test_inputs.py' 2026-04-12T02:52:47,220 adding 'tests/test_integration.py' 2026-04-12T02:52:47,222 adding 'tests/test_io.py' 2026-04-12T02:52:47,224 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-12T02:52:47,225 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-12T02:52:47,226 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-12T02:52:47,228 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-12T02:52:47,229 adding 'tests/test_padding.py' 2026-04-12T02:52:47,230 adding 'tests/test_peptide_mutation_interval.py' 2026-04-12T02:52:47,231 adding 'tests/test_predictor_internals.py' 2026-04-12T02:52:47,238 adding 'tests/test_ranking.py' 2026-04-12T02:52:47,239 adding 'tests/test_rna_helpers.py' 2026-04-12T02:52:47,241 adding 'tests/test_sequence_helpers.py' 2026-04-12T02:52:47,242 adding 'tests/test_sources.py' 2026-04-12T02:52:47,243 adding 'tests/test_sources_optional.py' 2026-04-12T02:52:47,245 adding 'tests/test_validation_and_edge_cases.py' 2026-04-12T02:52:47,246 adding 'tests/test_variant_expression_filters.py' 2026-04-12T02:52:47,248 adding 'tests/test_wide.py' 2026-04-12T02:52:47,250 adding 'topiary/__init__.py' 2026-04-12T02:52:47,252 adding 'topiary/filters.py' 2026-04-12T02:52:47,253 adding 'topiary/inputs.py' 2026-04-12T02:52:47,255 adding 'topiary/io.py' 2026-04-12T02:52:47,258 adding 'topiary/predictor.py' 2026-04-12T02:52:47,260 adding 'topiary/properties.py' 2026-04-12T02:52:47,268 adding 'topiary/ranking.py' 2026-04-12T02:52:47,270 adding 'topiary/sequence_helpers.py' 2026-04-12T02:52:47,272 adding 'topiary/sources.py' 2026-04-12T02:52:47,274 adding 'topiary/wide.py' 2026-04-12T02:52:47,276 adding 'topiary/cli/__init__.py' 2026-04-12T02:52:47,278 adding 'topiary/cli/args.py' 2026-04-12T02:52:47,279 adding 'topiary/cli/errors.py' 2026-04-12T02:52:47,281 adding 'topiary/cli/filtering.py' 2026-04-12T02:52:47,282 adding 'topiary/cli/outputs.py' 2026-04-12T02:52:47,284 adding 'topiary/cli/protein_changes.py' 2026-04-12T02:52:47,285 adding 'topiary/cli/rna.py' 2026-04-12T02:52:47,287 adding 'topiary/cli/script.py' 2026-04-12T02:52:47,288 adding 'topiary/cli/sequence.py' 2026-04-12T02:52:47,290 adding 'topiary/rna/__init__.py' 2026-04-12T02:52:47,291 adding 'topiary/rna/common.py' 2026-04-12T02:52:47,293 adding 'topiary/rna/cufflinks.py' 2026-04-12T02:52:47,295 adding 'topiary/rna/expression_loader.py' 2026-04-12T02:52:47,296 adding 'topiary/rna/gtf.py' 2026-04-12T02:52:47,300 adding 'topiary-4.11.2.dist-info/licenses/LICENSE' 2026-04-12T02:52:47,302 adding 'topiary-4.11.2.dist-info/METADATA' 2026-04-12T02:52:47,303 adding 'topiary-4.11.2.dist-info/WHEEL' 2026-04-12T02:52:47,304 adding 'topiary-4.11.2.dist-info/entry_points.txt' 2026-04-12T02:52:47,305 adding 'topiary-4.11.2.dist-info/top_level.txt' 2026-04-12T02:52:47,307 adding 'topiary-4.11.2.dist-info/RECORD' 2026-04-12T02:52:47,310 removing build/bdist.linux-armv7l/wheel 2026-04-12T02:52:47,423 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-12T02:52:47,431 Created wheel for topiary: filename=topiary-4.11.2-py3-none-any.whl size=133729 sha256=0aa2a79e03f91b1b0636edb0b44384b8dab3c370421430154d1e249d1e0d223b 2026-04-12T02:52:47,432 Stored in directory: /tmp/pip-ephem-wheel-cache-qftv71wi/wheels/6c/e0/0e/57e21ea8f168d2cf1ac9ede960ca3c7428d6c303db914331b9 2026-04-12T02:52:47,448 Successfully built topiary 2026-04-12T02:52:47,454 Removed build tracker: '/tmp/pip-build-tracker-yfsz8wez'