2026-04-14T20:56:17,208 Created temporary directory: /tmp/pip-ephem-wheel-cache-ljv8bn8o 2026-04-14T20:56:17,210 Created temporary directory: /tmp/pip-build-tracker-gyzm4e35 2026-04-14T20:56:17,211 Initialized build tracking at /tmp/pip-build-tracker-gyzm4e35 2026-04-14T20:56:17,211 Created build tracker: /tmp/pip-build-tracker-gyzm4e35 2026-04-14T20:56:17,212 Entered build tracker: /tmp/pip-build-tracker-gyzm4e35 2026-04-14T20:56:17,212 Created temporary directory: /tmp/pip-wheel-ik_0ksku 2026-04-14T20:56:17,215 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://archive1.piwheels.org/simple/topiary/topiary-0.0.17-py3-none-any.whl#sha256=9caa65a5a200720510e1c38a256ba0ee4702a443d0c0f9e56724aaa16b907517 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,767 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.16-py3-none-any.whl#sha256=1cce9bca3cbb426edd71bbf7bbd1c069b0498c46d67ce549315317b0f75ab1d6 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,768 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.15-py3-none-any.whl#sha256=ca5ae7481368a4fb5d839d1ac3cab6823cbebeb2733ef0e9c6b2275854eb895f (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,768 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.14-py3-none-any.whl#sha256=48e8744f89c7f03717c8e36a17ede28b495b845c7106cb5638c216db27054fad (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,769 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.13-py3-none-any.whl#sha256=588396661f87bea8be890d90c6800ac4825d06ae7db1c50c98a1978fe9c45bd3 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,769 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.10-py3-none-any.whl#sha256=56bea0cecf1273a44cd2e51ad294714c41e0fb7d9cc0b16382709573c4ec9443 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,770 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.9-py3-none-any.whl#sha256=da4dc4334fdf5cb89b68356e11737c8dab86fd100b9c7979e95eac3dc58fbd6d (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,771 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.8-py3-none-any.whl#sha256=12b4f283d8fbedbd316649be8833a17fee852097f1e5cd8963264e6c4a2721e0 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,771 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.7-py3-none-any.whl#sha256=6e23dbd38e19c12b658a8373b501f1e929c6fd3420749dee506a82b60b190d42 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,772 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.6-py3-none-any.whl#sha256=f3b597a0744c3a7540c3ffe571b8f4fad3d2ad40ddc6198952e2aee7c96ff82c (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,773 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.5-py3-none-any.whl#sha256=52f489eb5876b619e9988ee4c2fabec4df1a087c2f67f96cbb99ece92eb57576 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,773 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.4-py3-none-any.whl#sha256=5c94fb56e54399233efc5f88a6f6cfe2914773c5b2aa67a24f6ddf6089561b3b (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,774 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.3-py3-none-any.whl#sha256=197f9da38cd367d77acaec6282f0d22aefaf1e1ab6754379f671902958348f15 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,775 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.2-py3-none-any.whl#sha256=accaff90bafe6c929aece0f65b8ccedd45839064bf361d8f69bfefd543127ec2 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,775 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.1-py3-none-any.whl#sha256=6743a02aee34bc7567913bbe5c15a321924d9e1cb2c15f956e4ebb9b321707f4 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T20:56:17,776 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/) 2026-04-14T20:56:17,776 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-14T20:56:17,777 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-14T20:56:17,804 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-14T20:56:17,824 Collecting topiary==5.5.0 2026-04-14T20:56:17,826 Created temporary directory: /tmp/pip-unpack-mfou8gsc 2026-04-14T20:56:18,161 Downloading topiary-5.5.0.tar.gz (173 kB) 2026-04-14T20:56:18,418 Added topiary==5.5.0 from https://files.pythonhosted.org/packages/4f/4f/3aafd808393293e8cbb8f76dce2a9bf46c005c0c8896fc309fbb3f34e1ee/topiary-5.5.0.tar.gz to build tracker '/tmp/pip-build-tracker-gyzm4e35' 2026-04-14T20:56:18,422 Created temporary directory: /tmp/pip-build-env-ms223xdw 2026-04-14T20:56:18,427 Installing build dependencies: started 2026-04-14T20:56:18,428 Running command pip subprocess to install build dependencies 2026-04-14T20:56:18,459 Error processing line 1 of /home/piwheels/.local/lib/python3.11/site-packages/outofcuda_hook.pth: 2026-04-14T20:56:18,502 Traceback (most recent call last): 2026-04-14T20:56:18,503 File "", line 192, in addpackage 2026-04-14T20:56:18,503 File "", line 1, in 2026-04-14T20:56:18,504 ModuleNotFoundError: No module named 'outofcuda' 2026-04-14T20:56:18,505 Remainder of file ignored 2026-04-14T20:56:19,602 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-14T20:56:20,013 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 2026-04-14T20:56:20,036 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-14T20:56:21,796 Collecting setuptools>=64 2026-04-14T20:56:21,896 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-14T20:56:24,906 Installing collected packages: setuptools 2026-04-14T20:56:28,092 Successfully installed setuptools-82.0.1 2026-04-14T20:56:28,357 Installing build dependencies: finished with status 'done' 2026-04-14T20:56:28,364 Getting requirements to build wheel: started 2026-04-14T20:56:28,366 Running command Getting requirements to build wheel 2026-04-14T20:56:29,104 /tmp/pip-build-env-ms223xdw/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T20:56:29,104 !! 2026-04-14T20:56:29,105 ******************************************************************************** 2026-04-14T20:56:29,106 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T20:56:29,107 License :: OSI Approved :: Apache Software License 2026-04-14T20:56:29,108 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T20:56:29,108 ******************************************************************************** 2026-04-14T20:56:29,109 !! 2026-04-14T20:56:29,110 dist._finalize_license_expression() 2026-04-14T20:56:29,110 /tmp/pip-build-env-ms223xdw/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T20:56:29,111 !! 2026-04-14T20:56:29,112 ******************************************************************************** 2026-04-14T20:56:29,112 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T20:56:29,113 License :: OSI Approved :: Apache Software License 2026-04-14T20:56:29,114 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T20:56:29,114 ******************************************************************************** 2026-04-14T20:56:29,115 !! 2026-04-14T20:56:29,116 self._finalize_license_expression() 2026-04-14T20:56:29,117 running egg_info 2026-04-14T20:56:29,123 writing topiary.egg-info/PKG-INFO 2026-04-14T20:56:29,127 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-14T20:56:29,128 writing entry points to topiary.egg-info/entry_points.txt 2026-04-14T20:56:29,130 writing requirements to topiary.egg-info/requires.txt 2026-04-14T20:56:29,131 writing top-level names to topiary.egg-info/top_level.txt 2026-04-14T20:56:29,159 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T20:56:29,165 adding license file 'LICENSE' 2026-04-14T20:56:29,171 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T20:56:29,268 Getting requirements to build wheel: finished with status 'done' 2026-04-14T20:56:29,272 Created temporary directory: /tmp/pip-modern-metadata-y5iq8s4e 2026-04-14T20:56:29,274 Preparing metadata (pyproject.toml): started 2026-04-14T20:56:29,275 Running command Preparing metadata (pyproject.toml) 2026-04-14T20:56:29,926 /tmp/pip-build-env-ms223xdw/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T20:56:29,926 !! 2026-04-14T20:56:29,927 ******************************************************************************** 2026-04-14T20:56:29,928 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T20:56:29,929 License :: OSI Approved :: Apache Software License 2026-04-14T20:56:29,931 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T20:56:29,931 ******************************************************************************** 2026-04-14T20:56:29,933 !! 2026-04-14T20:56:29,933 dist._finalize_license_expression() 2026-04-14T20:56:29,934 /tmp/pip-build-env-ms223xdw/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T20:56:29,934 !! 2026-04-14T20:56:29,936 ******************************************************************************** 2026-04-14T20:56:29,936 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T20:56:29,938 License :: OSI Approved :: Apache Software License 2026-04-14T20:56:29,939 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T20:56:29,940 ******************************************************************************** 2026-04-14T20:56:29,941 !! 2026-04-14T20:56:29,942 self._finalize_license_expression() 2026-04-14T20:56:29,942 running dist_info 2026-04-14T20:56:29,951 creating /tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info 2026-04-14T20:56:29,952 writing /tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/PKG-INFO 2026-04-14T20:56:29,957 writing dependency_links to /tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/dependency_links.txt 2026-04-14T20:56:29,959 writing entry points to /tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/entry_points.txt 2026-04-14T20:56:29,961 writing requirements to /tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/requires.txt 2026-04-14T20:56:29,963 writing top-level names to /tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/top_level.txt 2026-04-14T20:56:29,964 writing manifest file '/tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/SOURCES.txt' 2026-04-14T20:56:29,990 reading manifest file '/tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/SOURCES.txt' 2026-04-14T20:56:29,992 adding license file 'LICENSE' 2026-04-14T20:56:29,997 writing manifest file '/tmp/pip-modern-metadata-y5iq8s4e/topiary.egg-info/SOURCES.txt' 2026-04-14T20:56:29,998 creating '/tmp/pip-modern-metadata-y5iq8s4e/topiary-5.5.0.dist-info' 2026-04-14T20:56:30,126 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-14T20:56:30,132 Source in /tmp/pip-wheel-ik_0ksku/topiary_7249b4429374410daafc46a6a8d92b20 has version 5.5.0, which satisfies requirement topiary==5.5.0 from https://files.pythonhosted.org/packages/4f/4f/3aafd808393293e8cbb8f76dce2a9bf46c005c0c8896fc309fbb3f34e1ee/topiary-5.5.0.tar.gz 2026-04-14T20:56:30,133 Removed topiary==5.5.0 from https://files.pythonhosted.org/packages/4f/4f/3aafd808393293e8cbb8f76dce2a9bf46c005c0c8896fc309fbb3f34e1ee/topiary-5.5.0.tar.gz from build tracker '/tmp/pip-build-tracker-gyzm4e35' 2026-04-14T20:56:30,141 Created temporary directory: /tmp/pip-unpack-khtepklx 2026-04-14T20:56:30,141 Building wheels for collected packages: topiary 2026-04-14T20:56:30,146 Created temporary directory: /tmp/pip-wheel-nzv3frj3 2026-04-14T20:56:30,146 Destination directory: /tmp/pip-wheel-nzv3frj3 2026-04-14T20:56:30,148 Building wheel for topiary (pyproject.toml): started 2026-04-14T20:56:30,149 Running command Building wheel for topiary (pyproject.toml) 2026-04-14T20:56:30,764 /tmp/pip-build-env-ms223xdw/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T20:56:30,764 !! 2026-04-14T20:56:30,765 ******************************************************************************** 2026-04-14T20:56:30,766 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T20:56:30,767 License :: OSI Approved :: Apache Software License 2026-04-14T20:56:30,768 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T20:56:30,769 ******************************************************************************** 2026-04-14T20:56:30,770 !! 2026-04-14T20:56:30,771 dist._finalize_license_expression() 2026-04-14T20:56:30,771 /tmp/pip-build-env-ms223xdw/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T20:56:30,772 !! 2026-04-14T20:56:30,773 ******************************************************************************** 2026-04-14T20:56:30,774 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T20:56:30,775 License :: OSI Approved :: Apache Software License 2026-04-14T20:56:30,776 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T20:56:30,777 ******************************************************************************** 2026-04-14T20:56:30,778 !! 2026-04-14T20:56:30,779 self._finalize_license_expression() 2026-04-14T20:56:30,779 running bdist_wheel 2026-04-14T20:56:30,789 running build 2026-04-14T20:56:30,790 running build_py 2026-04-14T20:56:30,796 creating build/lib/tests 2026-04-14T20:56:30,798 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-14T20:56:30,800 copying tests/data.py -> build/lib/tests 2026-04-14T20:56:30,802 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-14T20:56:30,804 copying tests/test_ranking.py -> build/lib/tests 2026-04-14T20:56:30,807 copying tests/__init__.py -> build/lib/tests 2026-04-14T20:56:30,809 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-14T20:56:30,811 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-14T20:56:30,813 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-14T20:56:30,815 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-14T20:56:30,817 copying tests/test_wide.py -> build/lib/tests 2026-04-14T20:56:30,819 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-14T20:56:30,821 copying tests/test_io_lens.py -> build/lib/tests 2026-04-14T20:56:30,823 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-04-14T20:56:30,826 copying tests/test_integration.py -> build/lib/tests 2026-04-14T20:56:30,828 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-14T20:56:30,829 copying tests/test_sources.py -> build/lib/tests 2026-04-14T20:56:30,831 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-14T20:56:30,833 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-14T20:56:30,835 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-14T20:56:30,837 copying tests/test_io.py -> build/lib/tests 2026-04-14T20:56:30,839 copying tests/test_result.py -> build/lib/tests 2026-04-14T20:56:30,842 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-14T20:56:30,844 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-14T20:56:30,845 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-14T20:56:30,847 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-14T20:56:30,849 copying tests/test_protein_fragment.py -> build/lib/tests 2026-04-14T20:56:30,852 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-14T20:56:30,854 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-14T20:56:30,856 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-14T20:56:30,858 copying tests/test_cached_predictor.py -> build/lib/tests 2026-04-14T20:56:30,861 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-14T20:56:30,863 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-14T20:56:30,864 copying tests/test_dataframe.py -> build/lib/tests 2026-04-14T20:56:30,866 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-04-14T20:56:30,869 copying tests/test_padding.py -> build/lib/tests 2026-04-14T20:56:30,870 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-14T20:56:30,873 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-14T20:56:30,875 copying tests/test_inputs.py -> build/lib/tests 2026-04-14T20:56:30,877 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-14T20:56:30,879 copying tests/common.py -> build/lib/tests 2026-04-14T20:56:30,881 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-04-14T20:56:30,884 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-14T20:56:30,886 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-14T20:56:30,888 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-14T20:56:30,890 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-04-14T20:56:30,893 creating build/lib/topiary 2026-04-14T20:56:30,894 copying topiary/inputs.py -> build/lib/topiary 2026-04-14T20:56:30,897 copying topiary/wide.py -> build/lib/topiary 2026-04-14T20:56:30,899 copying topiary/result.py -> build/lib/topiary 2026-04-14T20:56:30,901 copying topiary/__init__.py -> build/lib/topiary 2026-04-14T20:56:30,903 copying topiary/protein_fragment.py -> build/lib/topiary 2026-04-14T20:56:30,905 copying topiary/filters.py -> build/lib/topiary 2026-04-14T20:56:30,907 copying topiary/sources.py -> build/lib/topiary 2026-04-14T20:56:30,910 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-04-14T20:56:30,912 copying topiary/cached.py -> build/lib/topiary 2026-04-14T20:56:30,915 copying topiary/io.py -> build/lib/topiary 2026-04-14T20:56:30,917 copying topiary/predictor.py -> build/lib/topiary 2026-04-14T20:56:30,920 copying topiary/io_lens.py -> build/lib/topiary 2026-04-14T20:56:30,922 copying topiary/properties.py -> build/lib/topiary 2026-04-14T20:56:30,924 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-14T20:56:30,927 creating build/lib/topiary/ranking 2026-04-14T20:56:30,928 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-04-14T20:56:30,930 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-04-14T20:56:30,932 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-04-14T20:56:30,935 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-04-14T20:56:30,938 creating build/lib/topiary/cli 2026-04-14T20:56:30,939 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-14T20:56:30,941 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-14T20:56:30,943 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-14T20:56:30,945 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-14T20:56:30,947 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-14T20:56:30,949 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-14T20:56:30,951 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-14T20:56:30,953 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-14T20:56:30,955 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-14T20:56:30,958 creating build/lib/topiary/rna 2026-04-14T20:56:30,959 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-14T20:56:30,961 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-14T20:56:30,963 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-14T20:56:30,965 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-14T20:56:30,967 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-14T20:56:30,969 running egg_info 2026-04-14T20:56:30,979 writing topiary.egg-info/PKG-INFO 2026-04-14T20:56:30,983 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-14T20:56:30,984 writing entry points to topiary.egg-info/entry_points.txt 2026-04-14T20:56:30,985 writing requirements to topiary.egg-info/requires.txt 2026-04-14T20:56:30,986 writing top-level names to topiary.egg-info/top_level.txt 2026-04-14T20:56:31,002 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T20:56:31,008 adding license file 'LICENSE' 2026-04-14T20:56:31,014 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T20:56:31,032 installing to build/bdist.linux-armv7l/wheel 2026-04-14T20:56:31,033 running install 2026-04-14T20:56:31,057 running install_lib 2026-04-14T20:56:31,063 creating build/bdist.linux-armv7l/wheel 2026-04-14T20:56:31,066 creating build/bdist.linux-armv7l/wheel/tests 2026-04-14T20:56:31,067 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,069 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,071 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,073 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,077 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,079 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,081 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,084 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,086 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,090 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,092 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,094 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,097 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,100 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,102 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,105 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,107 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,109 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,112 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,114 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,117 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,120 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,122 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,125 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,127 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,130 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,132 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,135 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,137 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,140 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,143 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,145 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,147 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,149 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,152 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,154 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,157 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,160 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,163 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,166 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,168 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,171 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,174 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,176 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,179 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T20:56:31,183 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-14T20:56:31,184 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,187 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,190 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,192 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,195 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,198 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-04-14T20:56:31,199 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T20:56:31,202 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T20:56:31,204 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T20:56:31,208 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T20:56:31,211 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,213 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,215 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,218 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-14T20:56:31,219 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,221 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,223 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,225 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,226 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,228 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,230 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,232 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,234 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T20:56:31,237 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,240 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,242 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,246 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-14T20:56:31,247 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T20:56:31,249 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T20:56:31,251 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T20:56:31,253 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T20:56:31,256 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T20:56:31,258 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,260 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,262 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T20:56:31,264 running install_egg_info 2026-04-14T20:56:31,269 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.5.0-py3.11.egg-info 2026-04-14T20:56:31,281 running install_scripts 2026-04-14T20:56:31,294 creating build/bdist.linux-armv7l/wheel/topiary-5.5.0.dist-info/WHEEL 2026-04-14T20:56:31,297 creating '/tmp/pip-wheel-nzv3frj3/.tmp-kell0ylg/topiary-5.5.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-14T20:56:31,300 adding 'tests/__init__.py' 2026-04-14T20:56:31,301 adding 'tests/common.py' 2026-04-14T20:56:31,303 adding 'tests/data.py' 2026-04-14T20:56:31,304 adding 'tests/test_args_outputs.py' 2026-04-14T20:56:31,307 adding 'tests/test_cached_predictor.py' 2026-04-14T20:56:31,309 adding 'tests/test_cli_coverage.py' 2026-04-14T20:56:31,310 adding 'tests/test_cli_protein_changes.py' 2026-04-14T20:56:31,312 adding 'tests/test_cli_ranking.py' 2026-04-14T20:56:31,313 adding 'tests/test_contains_mutant_residues.py' 2026-04-14T20:56:31,315 adding 'tests/test_coverage_gaps.py' 2026-04-14T20:56:31,316 adding 'tests/test_dataframe.py' 2026-04-14T20:56:31,318 adding 'tests/test_direct_input_regressions.py' 2026-04-14T20:56:31,320 adding 'tests/test_dsl_extensions.py' 2026-04-14T20:56:31,322 adding 'tests/test_dsl_polish.py' 2026-04-14T20:56:31,325 adding 'tests/test_dsl_roundtrip.py' 2026-04-14T20:56:31,327 adding 'tests/test_edge_case_fixtures.py' 2026-04-14T20:56:31,328 adding 'tests/test_effect_expression_filters.py' 2026-04-14T20:56:31,330 adding 'tests/test_end_to_end.py' 2026-04-14T20:56:31,331 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-14T20:56:31,333 adding 'tests/test_expression_integration.py' 2026-04-14T20:56:31,334 adding 'tests/test_expression_loader.py' 2026-04-14T20:56:31,337 adding 'tests/test_frameshift_fragments.py' 2026-04-14T20:56:31,339 adding 'tests/test_inputs.py' 2026-04-14T20:56:31,340 adding 'tests/test_integration.py' 2026-04-14T20:56:31,342 adding 'tests/test_io.py' 2026-04-14T20:56:31,344 adding 'tests/test_io_lens.py' 2026-04-14T20:56:31,346 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-14T20:56:31,347 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-14T20:56:31,348 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-14T20:56:31,349 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-14T20:56:31,351 adding 'tests/test_padding.py' 2026-04-14T20:56:31,352 adding 'tests/test_peptide_mutation_interval.py' 2026-04-14T20:56:31,354 adding 'tests/test_predict_from_fragments.py' 2026-04-14T20:56:31,356 adding 'tests/test_predict_from_variants_refactor.py' 2026-04-14T20:56:31,358 adding 'tests/test_predictor_internals.py' 2026-04-14T20:56:31,360 adding 'tests/test_protein_fragment.py' 2026-04-14T20:56:31,366 adding 'tests/test_ranking.py' 2026-04-14T20:56:31,369 adding 'tests/test_result.py' 2026-04-14T20:56:31,371 adding 'tests/test_rna_helpers.py' 2026-04-14T20:56:31,372 adding 'tests/test_sequence_helpers.py' 2026-04-14T20:56:31,373 adding 'tests/test_sources.py' 2026-04-14T20:56:31,374 adding 'tests/test_sources_optional.py' 2026-04-14T20:56:31,376 adding 'tests/test_validation_and_edge_cases.py' 2026-04-14T20:56:31,378 adding 'tests/test_variant_expression_filters.py' 2026-04-14T20:56:31,380 adding 'tests/test_wide.py' 2026-04-14T20:56:31,382 adding 'topiary/__init__.py' 2026-04-14T20:56:31,385 adding 'topiary/cached.py' 2026-04-14T20:56:31,386 adding 'topiary/filters.py' 2026-04-14T20:56:31,388 adding 'topiary/inputs.py' 2026-04-14T20:56:31,390 adding 'topiary/io.py' 2026-04-14T20:56:31,392 adding 'topiary/io_lens.py' 2026-04-14T20:56:31,393 adding 'topiary/io_protein_fragment.py' 2026-04-14T20:56:31,397 adding 'topiary/predictor.py' 2026-04-14T20:56:31,399 adding 'topiary/properties.py' 2026-04-14T20:56:31,402 adding 'topiary/protein_fragment.py' 2026-04-14T20:56:31,404 adding 'topiary/result.py' 2026-04-14T20:56:31,405 adding 'topiary/sequence_helpers.py' 2026-04-14T20:56:31,407 adding 'topiary/sources.py' 2026-04-14T20:56:31,409 adding 'topiary/wide.py' 2026-04-14T20:56:31,411 adding 'topiary/cli/__init__.py' 2026-04-14T20:56:31,413 adding 'topiary/cli/args.py' 2026-04-14T20:56:31,414 adding 'topiary/cli/errors.py' 2026-04-14T20:56:31,416 adding 'topiary/cli/filtering.py' 2026-04-14T20:56:31,417 adding 'topiary/cli/outputs.py' 2026-04-14T20:56:31,418 adding 'topiary/cli/protein_changes.py' 2026-04-14T20:56:31,420 adding 'topiary/cli/rna.py' 2026-04-14T20:56:31,421 adding 'topiary/cli/script.py' 2026-04-14T20:56:31,422 adding 'topiary/cli/sequence.py' 2026-04-14T20:56:31,424 adding 'topiary/ranking/__init__.py' 2026-04-14T20:56:31,426 adding 'topiary/ranking/apply.py' 2026-04-14T20:56:31,431 adding 'topiary/ranking/nodes.py' 2026-04-14T20:56:31,433 adding 'topiary/ranking/parser.py' 2026-04-14T20:56:31,435 adding 'topiary/rna/__init__.py' 2026-04-14T20:56:31,436 adding 'topiary/rna/common.py' 2026-04-14T20:56:31,438 adding 'topiary/rna/cufflinks.py' 2026-04-14T20:56:31,440 adding 'topiary/rna/expression_loader.py' 2026-04-14T20:56:31,441 adding 'topiary/rna/gtf.py' 2026-04-14T20:56:31,445 adding 'topiary-5.5.0.dist-info/licenses/LICENSE' 2026-04-14T20:56:31,448 adding 'topiary-5.5.0.dist-info/METADATA' 2026-04-14T20:56:31,449 adding 'topiary-5.5.0.dist-info/WHEEL' 2026-04-14T20:56:31,450 adding 'topiary-5.5.0.dist-info/entry_points.txt' 2026-04-14T20:56:31,451 adding 'topiary-5.5.0.dist-info/top_level.txt' 2026-04-14T20:56:31,452 adding 'topiary-5.5.0.dist-info/RECORD' 2026-04-14T20:56:31,456 removing build/bdist.linux-armv7l/wheel 2026-04-14T20:56:31,572 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-14T20:56:31,581 Created wheel for topiary: filename=topiary-5.5.0-py3-none-any.whl size=197599 sha256=a4bdff51577b78e93795f8c7a0b4fdbbac99aaa96f58e1eb14ca081bb9b44b2d 2026-04-14T20:56:31,582 Stored in directory: /tmp/pip-ephem-wheel-cache-_njwq8us/wheels/81/60/54/264d8c7413546a6e2274cf0f1460bcba7fc1ff28b1a8fc3f05 2026-04-14T20:56:31,599 Successfully built topiary 2026-04-14T20:56:31,607 Removed build tracker: '/tmp/pip-build-tracker-gyzm4e35'