2026-05-06T12:24:20,429 Created temporary directory: /tmp/pip-ephem-wheel-cache-s_6b763h 2026-05-06T12:24:20,431 Created temporary directory: /tmp/pip-build-tracker-q7bd8z7o 2026-05-06T12:24:20,431 Initialized build tracking at /tmp/pip-build-tracker-q7bd8z7o 2026-05-06T12:24:20,432 Created build tracker: /tmp/pip-build-tracker-q7bd8z7o 2026-05-06T12:24:20,432 Entered build tracker: /tmp/pip-build-tracker-q7bd8z7o 2026-05-06T12:24:20,433 Created temporary directory: /tmp/pip-wheel-s_c_tp0v 2026-05-06T12:24:20,436 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 2026-05-06T12:24:20,439 Created temporary directory: /tmp/pip-ephem-wheel-cache-3wk0wu5q 2026-05-06T12:24:20,461 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-06T12:24:20,464 2 location(s) to search for versions of topiary: 2026-05-06T12:24:20,464 * https://pypi.org/simple/topiary/ 2026-05-06T12:24:20,464 * https://www.piwheels.org/simple/topiary/ 2026-05-06T12:24:20,465 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-05-06T12:24:20,466 Getting page https://pypi.org/simple/topiary/ 2026-05-06T12:24:20,467 Found index url https://pypi.org/simple 2026-05-06T12:24:20,697 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-05-06T12:24:20,717 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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discarding no candidates 2026-05-06T12:24:21,077 Collecting topiary==5.10.6 2026-05-06T12:24:21,079 Created temporary directory: /tmp/pip-unpack-dyw0xmys 2026-05-06T12:24:21,305 Downloading topiary-5.10.6.tar.gz (220 kB) 2026-05-06T12:24:21,600 Added topiary==5.10.6 from https://files.pythonhosted.org/packages/15/38/42690947572562b575e0559dd92966cadd119d2b80b0851e991259609702/topiary-5.10.6.tar.gz to build tracker '/tmp/pip-build-tracker-q7bd8z7o' 2026-05-06T12:24:21,605 Created temporary directory: /tmp/pip-build-env-tiq3kitw 2026-05-06T12:24:21,610 Installing build dependencies: started 2026-05-06T12:24:21,611 Running command pip subprocess to install build dependencies 2026-05-06T12:24:22,761 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-06T12:24:23,203 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 2026-05-06T12:24:23,225 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-06T12:24:24,988 Collecting setuptools>=64 2026-05-06T12:24:25,070 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-06T12:24:28,057 Installing collected packages: setuptools 2026-05-06T12:24:31,217 Successfully installed setuptools-82.0.1 2026-05-06T12:24:31,496 Installing build dependencies: finished with status 'done' 2026-05-06T12:24:31,506 Getting requirements to build wheel: started 2026-05-06T12:24:31,507 Running command Getting requirements to build wheel 2026-05-06T12:24:32,205 /tmp/pip-build-env-tiq3kitw/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T12:24:32,205 !! 2026-05-06T12:24:32,206 ******************************************************************************** 2026-05-06T12:24:32,207 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T12:24:32,208 License :: OSI Approved :: Apache Software License 2026-05-06T12:24:32,209 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T12:24:32,209 ******************************************************************************** 2026-05-06T12:24:32,210 !! 2026-05-06T12:24:32,211 dist._finalize_license_expression() 2026-05-06T12:24:32,211 /tmp/pip-build-env-tiq3kitw/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T12:24:32,212 !! 2026-05-06T12:24:32,213 ******************************************************************************** 2026-05-06T12:24:32,214 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T12:24:32,215 License :: OSI Approved :: Apache Software License 2026-05-06T12:24:32,216 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T12:24:32,217 ******************************************************************************** 2026-05-06T12:24:32,218 !! 2026-05-06T12:24:32,219 self._finalize_license_expression() 2026-05-06T12:24:32,220 running egg_info 2026-05-06T12:24:32,223 writing topiary.egg-info/PKG-INFO 2026-05-06T12:24:32,227 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-06T12:24:32,229 writing entry points to topiary.egg-info/entry_points.txt 2026-05-06T12:24:32,231 writing requirements to topiary.egg-info/requires.txt 2026-05-06T12:24:32,232 writing top-level names to topiary.egg-info/top_level.txt 2026-05-06T12:24:32,259 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T12:24:32,265 adding license file 'LICENSE' 2026-05-06T12:24:32,272 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T12:24:32,368 Getting requirements to build wheel: finished with status 'done' 2026-05-06T12:24:32,372 Created temporary directory: /tmp/pip-modern-metadata-kbdzocg_ 2026-05-06T12:24:32,374 Preparing metadata (pyproject.toml): started 2026-05-06T12:24:32,375 Running command Preparing metadata (pyproject.toml) 2026-05-06T12:24:33,035 /tmp/pip-build-env-tiq3kitw/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T12:24:33,036 !! 2026-05-06T12:24:33,037 ******************************************************************************** 2026-05-06T12:24:33,038 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T12:24:33,039 License :: OSI Approved :: Apache Software License 2026-05-06T12:24:33,041 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T12:24:33,042 ******************************************************************************** 2026-05-06T12:24:33,043 !! 2026-05-06T12:24:33,043 dist._finalize_license_expression() 2026-05-06T12:24:33,047 /tmp/pip-build-env-tiq3kitw/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T12:24:33,048 !! 2026-05-06T12:24:33,049 ******************************************************************************** 2026-05-06T12:24:33,050 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T12:24:33,051 License :: OSI Approved :: Apache Software License 2026-05-06T12:24:33,052 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T12:24:33,052 ******************************************************************************** 2026-05-06T12:24:33,054 !! 2026-05-06T12:24:33,054 self._finalize_license_expression() 2026-05-06T12:24:33,059 running dist_info 2026-05-06T12:24:33,070 creating /tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info 2026-05-06T12:24:33,071 writing /tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/PKG-INFO 2026-05-06T12:24:33,075 writing dependency_links to /tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/dependency_links.txt 2026-05-06T12:24:33,077 writing entry points to /tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/entry_points.txt 2026-05-06T12:24:33,079 writing requirements to /tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/requires.txt 2026-05-06T12:24:33,081 writing top-level names to /tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/top_level.txt 2026-05-06T12:24:33,082 writing manifest file '/tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/SOURCES.txt' 2026-05-06T12:24:33,107 reading manifest file '/tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/SOURCES.txt' 2026-05-06T12:24:33,109 adding license file 'LICENSE' 2026-05-06T12:24:33,115 writing manifest file '/tmp/pip-modern-metadata-kbdzocg_/topiary.egg-info/SOURCES.txt' 2026-05-06T12:24:33,117 creating '/tmp/pip-modern-metadata-kbdzocg_/topiary-5.10.6.dist-info' 2026-05-06T12:24:33,240 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-06T12:24:33,246 Source in /tmp/pip-wheel-s_c_tp0v/topiary_5ff9c4cc774e4e21a40d5d80e29ed5f1 has version 5.10.6, which satisfies requirement topiary==5.10.6 from https://files.pythonhosted.org/packages/15/38/42690947572562b575e0559dd92966cadd119d2b80b0851e991259609702/topiary-5.10.6.tar.gz 2026-05-06T12:24:33,247 Removed topiary==5.10.6 from https://files.pythonhosted.org/packages/15/38/42690947572562b575e0559dd92966cadd119d2b80b0851e991259609702/topiary-5.10.6.tar.gz from build tracker '/tmp/pip-build-tracker-q7bd8z7o' 2026-05-06T12:24:33,256 Created temporary directory: /tmp/pip-unpack-g5ajn61j 2026-05-06T12:24:33,256 Building wheels for collected packages: topiary 2026-05-06T12:24:33,261 Created temporary directory: /tmp/pip-wheel-n86f3en6 2026-05-06T12:24:33,261 Destination directory: /tmp/pip-wheel-n86f3en6 2026-05-06T12:24:33,264 Building wheel for topiary (pyproject.toml): started 2026-05-06T12:24:33,265 Running command Building wheel for topiary (pyproject.toml) 2026-05-06T12:24:33,883 /tmp/pip-build-env-tiq3kitw/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T12:24:33,883 !! 2026-05-06T12:24:33,884 ******************************************************************************** 2026-05-06T12:24:33,885 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T12:24:33,886 License :: OSI Approved :: Apache Software License 2026-05-06T12:24:33,887 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T12:24:33,888 ******************************************************************************** 2026-05-06T12:24:33,889 !! 2026-05-06T12:24:33,890 dist._finalize_license_expression() 2026-05-06T12:24:33,890 /tmp/pip-build-env-tiq3kitw/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T12:24:33,891 !! 2026-05-06T12:24:33,892 ******************************************************************************** 2026-05-06T12:24:33,892 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T12:24:33,893 License :: OSI Approved :: Apache Software License 2026-05-06T12:24:33,894 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T12:24:33,895 ******************************************************************************** 2026-05-06T12:24:33,896 !! 2026-05-06T12:24:33,896 self._finalize_license_expression() 2026-05-06T12:24:33,897 running bdist_wheel 2026-05-06T12:24:33,911 running build 2026-05-06T12:24:33,911 running build_py 2026-05-06T12:24:33,918 creating build/lib/topiary 2026-05-06T12:24:33,920 copying topiary/io.py -> build/lib/topiary 2026-05-06T12:24:33,923 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-06T12:24:33,926 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-06T12:24:33,928 copying topiary/result.py -> build/lib/topiary 2026-05-06T12:24:33,931 copying topiary/inputs.py -> build/lib/topiary 2026-05-06T12:24:33,933 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-06T12:24:33,936 copying topiary/__init__.py -> build/lib/topiary 2026-05-06T12:24:33,937 copying topiary/sources.py -> build/lib/topiary 2026-05-06T12:24:33,940 copying topiary/filters.py -> build/lib/topiary 2026-05-06T12:24:33,942 copying topiary/wide.py -> build/lib/topiary 2026-05-06T12:24:33,945 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-06T12:24:33,947 copying topiary/properties.py -> build/lib/topiary 2026-05-06T12:24:33,950 copying topiary/cached.py -> build/lib/topiary 2026-05-06T12:24:33,953 copying topiary/io_lens.py -> build/lib/topiary 2026-05-06T12:24:33,956 copying topiary/predictor.py -> build/lib/topiary 2026-05-06T12:24:33,960 creating build/lib/tests 2026-05-06T12:24:33,961 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-06T12:24:33,964 copying tests/test_result.py -> build/lib/tests 2026-05-06T12:24:33,967 copying tests/test_dataframe.py -> build/lib/tests 2026-05-06T12:24:33,969 copying tests/test_sources.py -> build/lib/tests 2026-05-06T12:24:33,971 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-06T12:24:33,974 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-06T12:24:33,977 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-06T12:24:33,979 copying tests/test_padding.py -> build/lib/tests 2026-05-06T12:24:33,981 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-06T12:24:33,984 copying tests/test_cli_script.py -> build/lib/tests 2026-05-06T12:24:33,986 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-06T12:24:33,988 copying tests/test_integration.py -> build/lib/tests 2026-05-06T12:24:33,990 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-06T12:24:33,992 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-06T12:24:33,995 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-06T12:24:33,997 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-06T12:24:33,999 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-06T12:24:34,001 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-06T12:24:34,003 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-06T12:24:34,006 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-06T12:24:34,008 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-06T12:24:34,011 copying tests/common.py -> build/lib/tests 2026-05-06T12:24:34,013 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-06T12:24:34,015 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-06T12:24:34,017 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-06T12:24:34,020 copying tests/__init__.py -> build/lib/tests 2026-05-06T12:24:34,021 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-06T12:24:34,024 copying tests/test_deploy_script.py -> build/lib/tests 2026-05-06T12:24:34,026 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-06T12:24:34,028 copying tests/test_wide.py -> build/lib/tests 2026-05-06T12:24:34,030 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-06T12:24:34,032 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-06T12:24:34,034 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-06T12:24:34,036 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-06T12:24:34,038 copying tests/data.py -> build/lib/tests 2026-05-06T12:24:34,040 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-06T12:24:34,042 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-06T12:24:34,044 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-06T12:24:34,046 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-06T12:24:34,048 copying tests/test_io.py -> build/lib/tests 2026-05-06T12:24:34,050 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-06T12:24:34,053 copying tests/test_inputs.py -> build/lib/tests 2026-05-06T12:24:34,055 copying tests/test_ranking.py -> build/lib/tests 2026-05-06T12:24:34,059 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-06T12:24:34,061 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-06T12:24:34,063 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-06T12:24:34,065 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-06T12:24:34,067 copying tests/test_io_lens.py -> build/lib/tests 2026-05-06T12:24:34,070 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-06T12:24:34,073 creating build/lib/topiary/ranking 2026-05-06T12:24:34,074 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-06T12:24:34,077 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-06T12:24:34,078 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-06T12:24:34,081 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-06T12:24:34,084 creating build/lib/topiary/cli 2026-05-06T12:24:34,085 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-06T12:24:34,088 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-06T12:24:34,090 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-06T12:24:34,092 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-06T12:24:34,094 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-06T12:24:34,096 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-06T12:24:34,098 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-06T12:24:34,100 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-06T12:24:34,102 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-06T12:24:34,105 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-06T12:24:34,108 creating build/lib/topiary/rna 2026-05-06T12:24:34,109 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-06T12:24:34,112 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-06T12:24:34,114 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-06T12:24:34,116 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-06T12:24:34,118 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-06T12:24:34,120 running egg_info 2026-05-06T12:24:34,129 writing topiary.egg-info/PKG-INFO 2026-05-06T12:24:34,133 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-06T12:24:34,134 writing entry points to topiary.egg-info/entry_points.txt 2026-05-06T12:24:34,136 writing requirements to topiary.egg-info/requires.txt 2026-05-06T12:24:34,137 writing top-level names to topiary.egg-info/top_level.txt 2026-05-06T12:24:34,153 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T12:24:34,159 adding license file 'LICENSE' 2026-05-06T12:24:34,165 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T12:24:34,182 installing to build/bdist.linux-armv7l/wheel 2026-05-06T12:24:34,183 running install 2026-05-06T12:24:34,206 running install_lib 2026-05-06T12:24:34,211 creating build/bdist.linux-armv7l/wheel 2026-05-06T12:24:34,213 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-06T12:24:34,215 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,217 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,220 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,223 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-06T12:24:34,224 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T12:24:34,226 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T12:24:34,228 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T12:24:34,230 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T12:24:34,234 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,236 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,239 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,242 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-06T12:24:34,243 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,245 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,247 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,249 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,251 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,253 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,255 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,257 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,259 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,262 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T12:24:34,265 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-06T12:24:34,266 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T12:24:34,268 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T12:24:34,270 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T12:24:34,273 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T12:24:34,275 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T12:24:34,277 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,279 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,281 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,284 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,286 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,289 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,292 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,296 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,298 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T12:24:34,303 creating build/bdist.linux-armv7l/wheel/tests 2026-05-06T12:24:34,304 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,307 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,310 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,312 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,314 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,317 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,319 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,321 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,323 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,325 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,327 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,330 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,332 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,334 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,336 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,338 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,340 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,342 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,344 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,346 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,349 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,351 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,353 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,356 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,359 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,361 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,363 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,366 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,367 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,369 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,372 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,374 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,376 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,377 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,380 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,382 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,385 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,386 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,388 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,390 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,393 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,395 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,398 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,402 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,404 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,406 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,407 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,410 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,413 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T12:24:34,415 running install_egg_info 2026-05-06T12:24:34,420 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.10.6-py3.11.egg-info 2026-05-06T12:24:34,433 running install_scripts 2026-05-06T12:24:34,447 creating build/bdist.linux-armv7l/wheel/topiary-5.10.6.dist-info/WHEEL 2026-05-06T12:24:34,450 creating '/tmp/pip-wheel-n86f3en6/.tmp-dbzx1mp2/topiary-5.10.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-06T12:24:34,453 adding 'tests/__init__.py' 2026-05-06T12:24:34,454 adding 'tests/common.py' 2026-05-06T12:24:34,456 adding 'tests/data.py' 2026-05-06T12:24:34,457 adding 'tests/test_args_outputs.py' 2026-05-06T12:24:34,462 adding 'tests/test_cached_predictor.py' 2026-05-06T12:24:34,465 adding 'tests/test_cli_cached_predictor.py' 2026-05-06T12:24:34,466 adding 'tests/test_cli_coverage.py' 2026-05-06T12:24:34,468 adding 'tests/test_cli_protein_changes.py' 2026-05-06T12:24:34,471 adding 'tests/test_cli_ranking.py' 2026-05-06T12:24:34,473 adding 'tests/test_cli_script.py' 2026-05-06T12:24:34,475 adding 'tests/test_contains_mutant_residues.py' 2026-05-06T12:24:34,478 adding 'tests/test_coverage_gaps.py' 2026-05-06T12:24:34,480 adding 'tests/test_dataframe.py' 2026-05-06T12:24:34,482 adding 'tests/test_deploy_script.py' 2026-05-06T12:24:34,484 adding 'tests/test_direct_input_regressions.py' 2026-05-06T12:24:34,488 adding 'tests/test_dsl_extensions.py' 2026-05-06T12:24:34,491 adding 'tests/test_dsl_polish.py' 2026-05-06T12:24:34,495 adding 'tests/test_dsl_roundtrip.py' 2026-05-06T12:24:34,497 adding 'tests/test_edge_case_fixtures.py' 2026-05-06T12:24:34,499 adding 'tests/test_effect_expression_filters.py' 2026-05-06T12:24:34,501 adding 'tests/test_end_to_end.py' 2026-05-06T12:24:34,503 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-06T12:24:34,505 adding 'tests/test_expression_integration.py' 2026-05-06T12:24:34,507 adding 'tests/test_expression_loader.py' 2026-05-06T12:24:34,511 adding 'tests/test_frameshift_fragments.py' 2026-05-06T12:24:34,513 adding 'tests/test_inputs.py' 2026-05-06T12:24:34,515 adding 'tests/test_integration.py' 2026-05-06T12:24:34,518 adding 'tests/test_io.py' 2026-05-06T12:24:34,521 adding 'tests/test_io_lens.py' 2026-05-06T12:24:34,523 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-06T12:24:34,525 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-06T12:24:34,527 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-06T12:24:34,528 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-06T12:24:34,530 adding 'tests/test_padding.py' 2026-05-06T12:24:34,532 adding 'tests/test_peptide_mutation_interval.py' 2026-05-06T12:24:34,536 adding 'tests/test_predict_from_fragments.py' 2026-05-06T12:24:34,539 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-06T12:24:34,541 adding 'tests/test_predictor_internals.py' 2026-05-06T12:24:34,544 adding 'tests/test_protein_fragment.py' 2026-05-06T12:24:34,559 adding 'tests/test_ranking.py' 2026-05-06T12:24:34,564 adding 'tests/test_result.py' 2026-05-06T12:24:34,566 adding 'tests/test_rna_helpers.py' 2026-05-06T12:24:34,569 adding 'tests/test_self_proteome.py' 2026-05-06T12:24:34,571 adding 'tests/test_sequence_helpers.py' 2026-05-06T12:24:34,572 adding 'tests/test_sources.py' 2026-05-06T12:24:34,573 adding 'tests/test_sources_optional.py' 2026-05-06T12:24:34,575 adding 'tests/test_validation_and_edge_cases.py' 2026-05-06T12:24:34,576 adding 'tests/test_variant_expression_filters.py' 2026-05-06T12:24:34,578 adding 'tests/test_wide.py' 2026-05-06T12:24:34,580 adding 'topiary/__init__.py' 2026-05-06T12:24:34,586 adding 'topiary/cached.py' 2026-05-06T12:24:34,588 adding 'topiary/filters.py' 2026-05-06T12:24:34,590 adding 'topiary/inputs.py' 2026-05-06T12:24:34,591 adding 'topiary/io.py' 2026-05-06T12:24:34,594 adding 'topiary/io_lens.py' 2026-05-06T12:24:34,595 adding 'topiary/io_protein_fragment.py' 2026-05-06T12:24:34,600 adding 'topiary/predictor.py' 2026-05-06T12:24:34,602 adding 'topiary/properties.py' 2026-05-06T12:24:34,605 adding 'topiary/protein_fragment.py' 2026-05-06T12:24:34,607 adding 'topiary/result.py' 2026-05-06T12:24:34,611 adding 'topiary/self_proteome.py' 2026-05-06T12:24:34,613 adding 'topiary/sequence_helpers.py' 2026-05-06T12:24:34,615 adding 'topiary/sources.py' 2026-05-06T12:24:34,617 adding 'topiary/wide.py' 2026-05-06T12:24:34,619 adding 'topiary/cli/__init__.py' 2026-05-06T12:24:34,622 adding 'topiary/cli/args.py' 2026-05-06T12:24:34,624 adding 'topiary/cli/cached_predictor.py' 2026-05-06T12:24:34,625 adding 'topiary/cli/errors.py' 2026-05-06T12:24:34,626 adding 'topiary/cli/filtering.py' 2026-05-06T12:24:34,628 adding 'topiary/cli/outputs.py' 2026-05-06T12:24:34,630 adding 'topiary/cli/protein_changes.py' 2026-05-06T12:24:34,632 adding 'topiary/cli/rna.py' 2026-05-06T12:24:34,633 adding 'topiary/cli/script.py' 2026-05-06T12:24:34,635 adding 'topiary/cli/sequence.py' 2026-05-06T12:24:34,637 adding 'topiary/ranking/__init__.py' 2026-05-06T12:24:34,639 adding 'topiary/ranking/apply.py' 2026-05-06T12:24:34,645 adding 'topiary/ranking/nodes.py' 2026-05-06T12:24:34,648 adding 'topiary/ranking/parser.py' 2026-05-06T12:24:34,650 adding 'topiary/rna/__init__.py' 2026-05-06T12:24:34,651 adding 'topiary/rna/common.py' 2026-05-06T12:24:34,653 adding 'topiary/rna/cufflinks.py' 2026-05-06T12:24:34,655 adding 'topiary/rna/expression_loader.py' 2026-05-06T12:24:34,656 adding 'topiary/rna/gtf.py' 2026-05-06T12:24:34,660 adding 'topiary-5.10.6.dist-info/licenses/LICENSE' 2026-05-06T12:24:34,662 adding 'topiary-5.10.6.dist-info/METADATA' 2026-05-06T12:24:34,664 adding 'topiary-5.10.6.dist-info/WHEEL' 2026-05-06T12:24:34,665 adding 'topiary-5.10.6.dist-info/entry_points.txt' 2026-05-06T12:24:34,665 adding 'topiary-5.10.6.dist-info/top_level.txt' 2026-05-06T12:24:34,667 adding 'topiary-5.10.6.dist-info/RECORD' 2026-05-06T12:24:34,672 removing build/bdist.linux-armv7l/wheel 2026-05-06T12:24:34,792 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-06T12:24:34,802 Created wheel for topiary: filename=topiary-5.10.6-py3-none-any.whl size=247569 sha256=2d1779c8170e6e40a6e5d93d2fbd639a1a38d3f4dc2487eccb07199fb5397cc9 2026-05-06T12:24:34,803 Stored in directory: /tmp/pip-ephem-wheel-cache-3wk0wu5q/wheels/56/ee/e6/5004e2b91e5c2238ffba36956b2ec0c55e021a5d44bbd9fd98 2026-05-06T12:24:34,821 Successfully built topiary 2026-05-06T12:24:34,832 Removed build tracker: '/tmp/pip-build-tracker-q7bd8z7o'