2026-05-12T03:24:45,687 Created temporary directory: /tmp/pip-ephem-wheel-cache-a2iyrxdw 2026-05-12T03:24:45,690 Created temporary directory: /tmp/pip-build-tracker-yz0_5bst 2026-05-12T03:24:45,690 Initialized build tracking at /tmp/pip-build-tracker-yz0_5bst 2026-05-12T03:24:45,691 Created build tracker: /tmp/pip-build-tracker-yz0_5bst 2026-05-12T03:24:45,691 Entered build tracker: /tmp/pip-build-tracker-yz0_5bst 2026-05-12T03:24:45,692 Created temporary directory: /tmp/pip-wheel-rmkr318g 2026-05-12T03:24:45,695 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://www.piwheels.org/simple/topiary/) 2026-05-12T03:24:46,307 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/) 2026-05-12T03:24:46,307 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/) 2026-05-12T03:24:46,308 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/) 2026-05-12T03:24:46,308 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/) 2026-05-12T03:24:46,309 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/) 2026-05-12T03:24:46,310 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/) 2026-05-12T03:24:46,310 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/) 2026-05-12T03:24:46,311 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/) 2026-05-12T03:24:46,312 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/) 2026-05-12T03:24:46,312 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/) 2026-05-12T03:24:46,313 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.0-py3-none-any.whl#sha256=a4de4e13dc8561c43fd350094d3cbc3267e0faacf5e65b94501ef15affdf51e6 (from https://www.piwheels.org/simple/topiary/) 2026-05-12T03:24:46,314 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-05-12T03:24:46,314 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-05-12T03:24:46,342 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-05-12T03:24:46,360 Collecting topiary==5.14.1 2026-05-12T03:24:46,363 Created temporary directory: /tmp/pip-unpack-_7a7u3nt 2026-05-12T03:24:46,592 Downloading topiary-5.14.1.tar.gz (233 kB) 2026-05-12T03:24:46,918 Added topiary==5.14.1 from https://files.pythonhosted.org/packages/cb/13/9d2055e5ff1a76fc41bc6557ffd46c2457ec8d5d6fbc161be74db8cf1b7a/topiary-5.14.1.tar.gz to build tracker '/tmp/pip-build-tracker-yz0_5bst' 2026-05-12T03:24:46,923 Created temporary directory: /tmp/pip-build-env-nwrckfn6 2026-05-12T03:24:46,928 Installing build dependencies: started 2026-05-12T03:24:46,929 Running command pip subprocess to install build dependencies 2026-05-12T03:24:48,076 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-12T03:24:48,518 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 2026-05-12T03:24:48,540 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-12T03:24:50,322 Collecting setuptools>=64 2026-05-12T03:24:50,410 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-12T03:24:53,313 Installing collected packages: setuptools 2026-05-12T03:24:56,470 Successfully installed setuptools-82.0.1 2026-05-12T03:24:56,736 Installing build dependencies: finished with status 'done' 2026-05-12T03:24:56,743 Getting requirements to build wheel: started 2026-05-12T03:24:56,744 Running command Getting requirements to build wheel 2026-05-12T03:24:57,455 /tmp/pip-build-env-nwrckfn6/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-12T03:24:57,456 !! 2026-05-12T03:24:57,457 ******************************************************************************** 2026-05-12T03:24:57,457 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-12T03:24:57,458 License :: OSI Approved :: Apache Software License 2026-05-12T03:24:57,460 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-12T03:24:57,460 ******************************************************************************** 2026-05-12T03:24:57,461 !! 2026-05-12T03:24:57,462 dist._finalize_license_expression() 2026-05-12T03:24:57,463 /tmp/pip-build-env-nwrckfn6/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-12T03:24:57,463 !! 2026-05-12T03:24:57,465 ******************************************************************************** 2026-05-12T03:24:57,465 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-12T03:24:57,466 License :: OSI Approved :: Apache Software License 2026-05-12T03:24:57,468 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-12T03:24:57,469 ******************************************************************************** 2026-05-12T03:24:57,470 !! 2026-05-12T03:24:57,471 self._finalize_license_expression() 2026-05-12T03:24:57,471 running egg_info 2026-05-12T03:24:57,475 writing topiary.egg-info/PKG-INFO 2026-05-12T03:24:57,479 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-12T03:24:57,481 writing entry points to topiary.egg-info/entry_points.txt 2026-05-12T03:24:57,483 writing requirements to topiary.egg-info/requires.txt 2026-05-12T03:24:57,484 writing top-level names to topiary.egg-info/top_level.txt 2026-05-12T03:24:57,513 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-12T03:24:57,520 adding license file 'LICENSE' 2026-05-12T03:24:57,527 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-12T03:24:57,624 Getting requirements to build wheel: finished with status 'done' 2026-05-12T03:24:57,628 Created temporary directory: /tmp/pip-modern-metadata-ty87jzzu 2026-05-12T03:24:57,630 Preparing metadata (pyproject.toml): started 2026-05-12T03:24:57,631 Running command Preparing metadata (pyproject.toml) 2026-05-12T03:24:58,282 /tmp/pip-build-env-nwrckfn6/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-12T03:24:58,283 !! 2026-05-12T03:24:58,284 ******************************************************************************** 2026-05-12T03:24:58,284 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-12T03:24:58,285 License :: OSI Approved :: Apache Software License 2026-05-12T03:24:58,286 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-12T03:24:58,287 ******************************************************************************** 2026-05-12T03:24:58,288 !! 2026-05-12T03:24:58,289 dist._finalize_license_expression() 2026-05-12T03:24:58,289 /tmp/pip-build-env-nwrckfn6/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-12T03:24:58,290 !! 2026-05-12T03:24:58,291 ******************************************************************************** 2026-05-12T03:24:58,292 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-12T03:24:58,293 License :: OSI Approved :: Apache Software License 2026-05-12T03:24:58,294 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-12T03:24:58,295 ******************************************************************************** 2026-05-12T03:24:58,296 !! 2026-05-12T03:24:58,296 self._finalize_license_expression() 2026-05-12T03:24:58,297 running dist_info 2026-05-12T03:24:58,305 creating /tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info 2026-05-12T03:24:58,306 writing /tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/PKG-INFO 2026-05-12T03:24:58,310 writing dependency_links to /tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/dependency_links.txt 2026-05-12T03:24:58,312 writing entry points to /tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/entry_points.txt 2026-05-12T03:24:58,314 writing requirements to /tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/requires.txt 2026-05-12T03:24:58,315 writing top-level names to /tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/top_level.txt 2026-05-12T03:24:58,316 writing manifest file '/tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/SOURCES.txt' 2026-05-12T03:24:58,341 reading manifest file '/tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/SOURCES.txt' 2026-05-12T03:24:58,343 adding license file 'LICENSE' 2026-05-12T03:24:58,349 writing manifest file '/tmp/pip-modern-metadata-ty87jzzu/topiary.egg-info/SOURCES.txt' 2026-05-12T03:24:58,350 creating '/tmp/pip-modern-metadata-ty87jzzu/topiary-5.14.1.dist-info' 2026-05-12T03:24:58,477 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-12T03:24:58,483 Source in /tmp/pip-wheel-rmkr318g/topiary_a5afc4429c6a47ed860e455d268a567c has version 5.14.1, which satisfies requirement topiary==5.14.1 from https://files.pythonhosted.org/packages/cb/13/9d2055e5ff1a76fc41bc6557ffd46c2457ec8d5d6fbc161be74db8cf1b7a/topiary-5.14.1.tar.gz 2026-05-12T03:24:58,484 Removed topiary==5.14.1 from https://files.pythonhosted.org/packages/cb/13/9d2055e5ff1a76fc41bc6557ffd46c2457ec8d5d6fbc161be74db8cf1b7a/topiary-5.14.1.tar.gz from build tracker '/tmp/pip-build-tracker-yz0_5bst' 2026-05-12T03:24:58,493 Created temporary directory: /tmp/pip-unpack-gmlbhvnf 2026-05-12T03:24:58,493 Building wheels for collected packages: topiary 2026-05-12T03:24:58,498 Created temporary directory: /tmp/pip-wheel-zxm671nh 2026-05-12T03:24:58,498 Destination directory: /tmp/pip-wheel-zxm671nh 2026-05-12T03:24:58,500 Building wheel for topiary (pyproject.toml): started 2026-05-12T03:24:58,502 Running command Building wheel for topiary (pyproject.toml) 2026-05-12T03:24:59,146 /tmp/pip-build-env-nwrckfn6/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-12T03:24:59,146 !! 2026-05-12T03:24:59,147 ******************************************************************************** 2026-05-12T03:24:59,148 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-12T03:24:59,149 License :: OSI Approved :: Apache Software License 2026-05-12T03:24:59,150 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-12T03:24:59,150 ******************************************************************************** 2026-05-12T03:24:59,151 !! 2026-05-12T03:24:59,152 dist._finalize_license_expression() 2026-05-12T03:24:59,152 /tmp/pip-build-env-nwrckfn6/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-12T03:24:59,153 !! 2026-05-12T03:24:59,154 ******************************************************************************** 2026-05-12T03:24:59,155 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-12T03:24:59,156 License :: OSI Approved :: Apache Software License 2026-05-12T03:24:59,157 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-12T03:24:59,158 ******************************************************************************** 2026-05-12T03:24:59,159 !! 2026-05-12T03:24:59,160 self._finalize_license_expression() 2026-05-12T03:24:59,161 running bdist_wheel 2026-05-12T03:24:59,172 running build 2026-05-12T03:24:59,173 running build_py 2026-05-12T03:24:59,179 creating build/lib/topiary 2026-05-12T03:24:59,182 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-12T03:24:59,184 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-12T03:24:59,187 copying topiary/io_lens.py -> build/lib/topiary 2026-05-12T03:24:59,190 copying topiary/sources.py -> build/lib/topiary 2026-05-12T03:24:59,192 copying topiary/result.py -> build/lib/topiary 2026-05-12T03:24:59,195 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-12T03:24:59,198 copying topiary/predictor.py -> build/lib/topiary 2026-05-12T03:24:59,201 copying topiary/cached.py -> build/lib/topiary 2026-05-12T03:24:59,204 copying topiary/__init__.py -> build/lib/topiary 2026-05-12T03:24:59,205 copying topiary/properties.py -> build/lib/topiary 2026-05-12T03:24:59,208 copying topiary/wide.py -> build/lib/topiary 2026-05-12T03:24:59,211 copying topiary/filters.py -> build/lib/topiary 2026-05-12T03:24:59,213 copying topiary/inputs.py -> build/lib/topiary 2026-05-12T03:24:59,215 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-12T03:24:59,218 copying topiary/io.py -> build/lib/topiary 2026-05-12T03:24:59,222 creating build/lib/tests 2026-05-12T03:24:59,223 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-12T03:24:59,225 copying tests/test_deploy_script.py -> build/lib/tests 2026-05-12T03:24:59,227 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-12T03:24:59,229 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-12T03:24:59,232 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-12T03:24:59,236 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-12T03:24:59,238 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-12T03:24:59,240 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-12T03:24:59,242 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-12T03:24:59,245 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-12T03:24:59,248 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-12T03:24:59,250 copying tests/test_integration.py -> build/lib/tests 2026-05-12T03:24:59,252 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-12T03:24:59,254 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-12T03:24:59,257 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-12T03:24:59,259 copying tests/test_sources.py -> build/lib/tests 2026-05-12T03:24:59,261 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-12T03:24:59,263 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-12T03:24:59,266 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-12T03:24:59,268 copying tests/test_inputs.py -> build/lib/tests 2026-05-12T03:24:59,270 copying tests/common.py -> build/lib/tests 2026-05-12T03:24:59,272 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-12T03:24:59,274 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-12T03:24:59,276 copying tests/test_peptide_property_node.py -> build/lib/tests 2026-05-12T03:24:59,279 copying tests/test_cli_script.py -> build/lib/tests 2026-05-12T03:24:59,281 copying tests/test_io_lens.py -> build/lib/tests 2026-05-12T03:24:59,283 copying tests/data.py -> build/lib/tests 2026-05-12T03:24:59,285 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-12T03:24:59,287 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-12T03:24:59,290 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-12T03:24:59,292 copying tests/__init__.py -> build/lib/tests 2026-05-12T03:24:59,293 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-12T03:24:59,296 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-12T03:24:59,299 copying tests/test_kind_support.py -> build/lib/tests 2026-05-12T03:24:59,302 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-12T03:24:59,304 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-12T03:24:59,306 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-12T03:24:59,309 copying tests/test_dataframe.py -> build/lib/tests 2026-05-12T03:24:59,311 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-12T03:24:59,313 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-12T03:24:59,315 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-12T03:24:59,318 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-12T03:24:59,320 copying tests/test_io.py -> build/lib/tests 2026-05-12T03:24:59,323 copying tests/test_wide.py -> build/lib/tests 2026-05-12T03:24:59,326 copying tests/test_result.py -> build/lib/tests 2026-05-12T03:24:59,328 copying tests/test_lazy_imports.py -> build/lib/tests 2026-05-12T03:24:59,330 copying tests/test_ranking.py -> build/lib/tests 2026-05-12T03:24:59,335 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-12T03:24:59,337 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-12T03:24:59,339 copying tests/test_best_allele.py -> build/lib/tests 2026-05-12T03:24:59,342 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-12T03:24:59,345 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-12T03:24:59,347 copying tests/test_padding.py -> build/lib/tests 2026-05-12T03:24:59,350 creating build/lib/topiary/cli 2026-05-12T03:24:59,352 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-12T03:24:59,354 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-12T03:24:59,356 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-12T03:24:59,359 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-12T03:24:59,361 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-12T03:24:59,362 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-12T03:24:59,364 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-12T03:24:59,367 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-12T03:24:59,369 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-12T03:24:59,371 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-12T03:24:59,374 creating build/lib/topiary/rna 2026-05-12T03:24:59,375 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-12T03:24:59,378 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-12T03:24:59,380 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-12T03:24:59,382 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-12T03:24:59,384 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-12T03:24:59,387 creating build/lib/topiary/ranking 2026-05-12T03:24:59,388 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-12T03:24:59,390 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-12T03:24:59,393 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-12T03:24:59,395 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-12T03:24:59,399 running egg_info 2026-05-12T03:24:59,409 writing topiary.egg-info/PKG-INFO 2026-05-12T03:24:59,413 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-12T03:24:59,415 writing entry points to topiary.egg-info/entry_points.txt 2026-05-12T03:24:59,416 writing requirements to topiary.egg-info/requires.txt 2026-05-12T03:24:59,417 writing top-level names to topiary.egg-info/top_level.txt 2026-05-12T03:24:59,434 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-12T03:24:59,441 adding license file 'LICENSE' 2026-05-12T03:24:59,448 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-12T03:24:59,466 installing to build/bdist.linux-armv7l/wheel 2026-05-12T03:24:59,467 running install 2026-05-12T03:24:59,490 running install_lib 2026-05-12T03:24:59,497 creating build/bdist.linux-armv7l/wheel 2026-05-12T03:24:59,500 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-12T03:24:59,502 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-12T03:24:59,503 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,505 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,508 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,511 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,513 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,515 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,517 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,519 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,522 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,524 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-12T03:24:59,526 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,528 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,531 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-12T03:24:59,533 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-12T03:24:59,535 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-12T03:24:59,537 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-12T03:24:59,539 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-12T03:24:59,541 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-12T03:24:59,543 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,546 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,548 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,551 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,554 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,558 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,562 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,564 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-12T03:24:59,565 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-12T03:24:59,568 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-12T03:24:59,571 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-12T03:24:59,573 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-12T03:24:59,577 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,581 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,584 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,586 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,589 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,591 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-12T03:24:59,595 creating build/bdist.linux-armv7l/wheel/tests 2026-05-12T03:24:59,596 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,598 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,600 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,602 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,605 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,608 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,611 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,613 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,615 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,618 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,621 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,623 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,624 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,627 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,629 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,632 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,634 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,636 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,638 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,640 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,643 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,645 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,647 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,649 copying build/lib/tests/test_peptide_property_node.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,651 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,653 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,656 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,658 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,659 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,662 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,664 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,665 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,668 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,672 copying build/lib/tests/test_kind_support.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,674 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,676 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,678 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,681 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,683 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,685 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,688 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,690 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,692 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,695 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,698 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,701 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,703 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,708 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,710 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,712 copying build/lib/tests/test_best_allele.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,714 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,717 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,719 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-12T03:24:59,721 running install_egg_info 2026-05-12T03:24:59,726 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.14.1-py3.11.egg-info 2026-05-12T03:24:59,738 running install_scripts 2026-05-12T03:24:59,751 creating build/bdist.linux-armv7l/wheel/topiary-5.14.1.dist-info/WHEEL 2026-05-12T03:24:59,754 creating '/tmp/pip-wheel-zxm671nh/.tmp-flacs460/topiary-5.14.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-12T03:24:59,757 adding 'tests/__init__.py' 2026-05-12T03:24:59,758 adding 'tests/common.py' 2026-05-12T03:24:59,760 adding 'tests/data.py' 2026-05-12T03:24:59,761 adding 'tests/test_args_outputs.py' 2026-05-12T03:24:59,763 adding 'tests/test_best_allele.py' 2026-05-12T03:24:59,768 adding 'tests/test_cached_predictor.py' 2026-05-12T03:24:59,770 adding 'tests/test_cli_cached_predictor.py' 2026-05-12T03:24:59,772 adding 'tests/test_cli_coverage.py' 2026-05-12T03:24:59,773 adding 'tests/test_cli_protein_changes.py' 2026-05-12T03:24:59,775 adding 'tests/test_cli_ranking.py' 2026-05-12T03:24:59,777 adding 'tests/test_cli_script.py' 2026-05-12T03:24:59,778 adding 'tests/test_contains_mutant_residues.py' 2026-05-12T03:24:59,780 adding 'tests/test_coverage_gaps.py' 2026-05-12T03:24:59,781 adding 'tests/test_dataframe.py' 2026-05-12T03:24:59,782 adding 'tests/test_deploy_script.py' 2026-05-12T03:24:59,784 adding 'tests/test_direct_input_regressions.py' 2026-05-12T03:24:59,786 adding 'tests/test_dsl_extensions.py' 2026-05-12T03:24:59,788 adding 'tests/test_dsl_polish.py' 2026-05-12T03:24:59,791 adding 'tests/test_dsl_roundtrip.py' 2026-05-12T03:24:59,792 adding 'tests/test_edge_case_fixtures.py' 2026-05-12T03:24:59,794 adding 'tests/test_effect_expression_filters.py' 2026-05-12T03:24:59,795 adding 'tests/test_end_to_end.py' 2026-05-12T03:24:59,797 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-12T03:24:59,798 adding 'tests/test_expression_integration.py' 2026-05-12T03:24:59,800 adding 'tests/test_expression_loader.py' 2026-05-12T03:24:59,803 adding 'tests/test_frameshift_fragments.py' 2026-05-12T03:24:59,804 adding 'tests/test_inputs.py' 2026-05-12T03:24:59,806 adding 'tests/test_integration.py' 2026-05-12T03:24:59,808 adding 'tests/test_io.py' 2026-05-12T03:24:59,810 adding 'tests/test_io_lens.py' 2026-05-12T03:24:59,812 adding 'tests/test_kind_support.py' 2026-05-12T03:24:59,813 adding 'tests/test_lazy_imports.py' 2026-05-12T03:24:59,814 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-12T03:24:59,816 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-12T03:24:59,817 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-12T03:24:59,818 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-12T03:24:59,820 adding 'tests/test_padding.py' 2026-05-12T03:24:59,821 adding 'tests/test_peptide_mutation_interval.py' 2026-05-12T03:24:59,823 adding 'tests/test_peptide_property_node.py' 2026-05-12T03:24:59,825 adding 'tests/test_predict_from_fragments.py' 2026-05-12T03:24:59,828 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-12T03:24:59,829 adding 'tests/test_predictor_internals.py' 2026-05-12T03:24:59,831 adding 'tests/test_protein_fragment.py' 2026-05-12T03:24:59,841 adding 'tests/test_ranking.py' 2026-05-12T03:24:59,844 adding 'tests/test_result.py' 2026-05-12T03:24:59,845 adding 'tests/test_rna_helpers.py' 2026-05-12T03:24:59,848 adding 'tests/test_self_proteome.py' 2026-05-12T03:24:59,849 adding 'tests/test_sequence_helpers.py' 2026-05-12T03:24:59,851 adding 'tests/test_sources.py' 2026-05-12T03:24:59,852 adding 'tests/test_sources_optional.py' 2026-05-12T03:24:59,854 adding 'tests/test_validation_and_edge_cases.py' 2026-05-12T03:24:59,855 adding 'tests/test_variant_expression_filters.py' 2026-05-12T03:24:59,857 adding 'tests/test_wide.py' 2026-05-12T03:24:59,860 adding 'topiary/__init__.py' 2026-05-12T03:24:59,866 adding 'topiary/cached.py' 2026-05-12T03:24:59,868 adding 'topiary/filters.py' 2026-05-12T03:24:59,870 adding 'topiary/inputs.py' 2026-05-12T03:24:59,871 adding 'topiary/io.py' 2026-05-12T03:24:59,873 adding 'topiary/io_lens.py' 2026-05-12T03:24:59,875 adding 'topiary/io_protein_fragment.py' 2026-05-12T03:24:59,880 adding 'topiary/predictor.py' 2026-05-12T03:24:59,883 adding 'topiary/properties.py' 2026-05-12T03:24:59,885 adding 'topiary/protein_fragment.py' 2026-05-12T03:24:59,887 adding 'topiary/result.py' 2026-05-12T03:24:59,892 adding 'topiary/self_proteome.py' 2026-05-12T03:24:59,893 adding 'topiary/sequence_helpers.py' 2026-05-12T03:24:59,895 adding 'topiary/sources.py' 2026-05-12T03:24:59,897 adding 'topiary/wide.py' 2026-05-12T03:24:59,899 adding 'topiary/cli/__init__.py' 2026-05-12T03:24:59,902 adding 'topiary/cli/args.py' 2026-05-12T03:24:59,904 adding 'topiary/cli/cached_predictor.py' 2026-05-12T03:24:59,905 adding 'topiary/cli/errors.py' 2026-05-12T03:24:59,907 adding 'topiary/cli/filtering.py' 2026-05-12T03:24:59,908 adding 'topiary/cli/outputs.py' 2026-05-12T03:24:59,910 adding 'topiary/cli/protein_changes.py' 2026-05-12T03:24:59,911 adding 'topiary/cli/rna.py' 2026-05-12T03:24:59,912 adding 'topiary/cli/script.py' 2026-05-12T03:24:59,914 adding 'topiary/cli/sequence.py' 2026-05-12T03:24:59,916 adding 'topiary/ranking/__init__.py' 2026-05-12T03:24:59,918 adding 'topiary/ranking/apply.py' 2026-05-12T03:24:59,926 adding 'topiary/ranking/nodes.py' 2026-05-12T03:24:59,929 adding 'topiary/ranking/parser.py' 2026-05-12T03:24:59,931 adding 'topiary/rna/__init__.py' 2026-05-12T03:24:59,932 adding 'topiary/rna/common.py' 2026-05-12T03:24:59,934 adding 'topiary/rna/cufflinks.py' 2026-05-12T03:24:59,936 adding 'topiary/rna/expression_loader.py' 2026-05-12T03:24:59,938 adding 'topiary/rna/gtf.py' 2026-05-12T03:24:59,941 adding 'topiary-5.14.1.dist-info/licenses/LICENSE' 2026-05-12T03:24:59,944 adding 'topiary-5.14.1.dist-info/METADATA' 2026-05-12T03:24:59,946 adding 'topiary-5.14.1.dist-info/WHEEL' 2026-05-12T03:24:59,947 adding 'topiary-5.14.1.dist-info/entry_points.txt' 2026-05-12T03:24:59,948 adding 'topiary-5.14.1.dist-info/top_level.txt' 2026-05-12T03:24:59,949 adding 'topiary-5.14.1.dist-info/RECORD' 2026-05-12T03:24:59,954 removing build/bdist.linux-armv7l/wheel 2026-05-12T03:25:00,075 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-12T03:25:00,086 Created wheel for topiary: filename=topiary-5.14.1-py3-none-any.whl size=262425 sha256=24055ab69510225d5730c2c37481f7fdc310956cf29fe18a39391d46504ff29c 2026-05-12T03:25:00,088 Stored in directory: /tmp/pip-ephem-wheel-cache-yvpt1qx_/wheels/d5/16/b0/7ac6fe3a45df83042d0a7e0a6cbe41f7b3dc665a5f094aed73 2026-05-12T03:25:00,106 Successfully built topiary 2026-05-12T03:25:00,119 Removed build tracker: '/tmp/pip-build-tracker-yz0_5bst'