2026-04-12T22:34:36,004 Created temporary directory: /tmp/pip-ephem-wheel-cache-sstbjpzz 2026-04-12T22:34:36,006 Created temporary directory: /tmp/pip-build-tracker-90_zauyy 2026-04-12T22:34:36,007 Initialized build tracking at /tmp/pip-build-tracker-90_zauyy 2026-04-12T22:34:36,007 Created build tracker: /tmp/pip-build-tracker-90_zauyy 2026-04-12T22:34:36,008 Entered build tracker: /tmp/pip-build-tracker-90_zauyy 2026-04-12T22:34:36,009 Created temporary directory: /tmp/pip-wheel-5prt5ce9 2026-04-12T22:34:36,011 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-0.0.7-py3-none-any.whl#sha256=6e23dbd38e19c12b658a8373b501f1e929c6fd3420749dee506a82b60b190d42 (from https://www.piwheels.org/simple/topiary/) 2026-04-12T22:34:36,577 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/) 2026-04-12T22:34:36,578 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/) 2026-04-12T22:34:36,578 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/) 2026-04-12T22:34:36,579 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/) 2026-04-12T22:34:36,579 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/) 2026-04-12T22:34:36,580 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/) 2026-04-12T22:34:36,580 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/) 2026-04-12T22:34:36,581 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-12T22:34:36,582 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-12T22:34:36,608 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-12T22:34:36,628 Collecting topiary==5.0.1 2026-04-12T22:34:36,630 Created temporary directory: /tmp/pip-unpack-2umj0xwc 2026-04-12T22:34:36,858 Downloading topiary-5.0.1.tar.gz (130 kB) 2026-04-12T22:34:37,118 Added topiary==5.0.1 from https://files.pythonhosted.org/packages/a1/66/e8887661f196d2b95dc82b650d2a2311c50c39153231b6899a325fe42d98/topiary-5.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-90_zauyy' 2026-04-12T22:34:37,123 Created temporary directory: /tmp/pip-build-env-3ubobobk 2026-04-12T22:34:37,128 Installing build dependencies: started 2026-04-12T22:34:37,129 Running command pip subprocess to install build dependencies 2026-04-12T22:34:37,160 Error processing line 1 of /home/piwheels/.local/lib/python3.11/site-packages/outofcuda_hook.pth: 2026-04-12T22:34:37,199 Traceback (most recent call last): 2026-04-12T22:34:37,200 File "", line 192, in addpackage 2026-04-12T22:34:37,200 File "", line 1, in 2026-04-12T22:34:37,201 ModuleNotFoundError: No module named 'outofcuda' 2026-04-12T22:34:37,202 Remainder of file ignored 2026-04-12T22:34:38,272 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-12T22:34:38,688 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 2026-04-12T22:34:38,710 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-12T22:34:40,491 Collecting setuptools>=64 2026-04-12T22:34:40,584 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-12T22:34:43,580 Installing collected packages: setuptools 2026-04-12T22:34:46,697 Successfully installed setuptools-82.0.1 2026-04-12T22:34:46,968 Installing build dependencies: finished with status 'done' 2026-04-12T22:34:46,976 Getting requirements to build wheel: started 2026-04-12T22:34:46,977 Running command Getting requirements to build wheel 2026-04-12T22:34:47,674 /tmp/pip-build-env-3ubobobk/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T22:34:47,675 !! 2026-04-12T22:34:47,676 ******************************************************************************** 2026-04-12T22:34:47,676 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T22:34:47,677 License :: OSI Approved :: Apache Software License 2026-04-12T22:34:47,678 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T22:34:47,679 ******************************************************************************** 2026-04-12T22:34:47,680 !! 2026-04-12T22:34:47,680 dist._finalize_license_expression() 2026-04-12T22:34:47,681 /tmp/pip-build-env-3ubobobk/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T22:34:47,681 !! 2026-04-12T22:34:47,682 ******************************************************************************** 2026-04-12T22:34:47,683 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T22:34:47,684 License :: OSI Approved :: Apache Software License 2026-04-12T22:34:47,685 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T22:34:47,686 ******************************************************************************** 2026-04-12T22:34:47,687 !! 2026-04-12T22:34:47,688 self._finalize_license_expression() 2026-04-12T22:34:47,688 running egg_info 2026-04-12T22:34:47,691 writing topiary.egg-info/PKG-INFO 2026-04-12T22:34:47,695 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-12T22:34:47,698 writing entry points to topiary.egg-info/entry_points.txt 2026-04-12T22:34:47,700 writing requirements to topiary.egg-info/requires.txt 2026-04-12T22:34:47,701 writing top-level names to topiary.egg-info/top_level.txt 2026-04-12T22:34:47,728 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T22:34:47,733 adding license file 'LICENSE' 2026-04-12T22:34:47,739 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T22:34:47,836 Getting requirements to build wheel: finished with status 'done' 2026-04-12T22:34:47,840 Created temporary directory: /tmp/pip-modern-metadata-22at57fk 2026-04-12T22:34:47,842 Preparing metadata (pyproject.toml): started 2026-04-12T22:34:47,843 Running command Preparing metadata (pyproject.toml) 2026-04-12T22:34:48,485 /tmp/pip-build-env-3ubobobk/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T22:34:48,485 !! 2026-04-12T22:34:48,486 ******************************************************************************** 2026-04-12T22:34:48,487 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T22:34:48,488 License :: OSI Approved :: Apache Software License 2026-04-12T22:34:48,489 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T22:34:48,490 ******************************************************************************** 2026-04-12T22:34:48,491 !! 2026-04-12T22:34:48,492 dist._finalize_license_expression() 2026-04-12T22:34:48,493 /tmp/pip-build-env-3ubobobk/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T22:34:48,493 !! 2026-04-12T22:34:48,494 ******************************************************************************** 2026-04-12T22:34:48,495 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T22:34:48,495 License :: OSI Approved :: Apache Software License 2026-04-12T22:34:48,496 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T22:34:48,497 ******************************************************************************** 2026-04-12T22:34:48,498 !! 2026-04-12T22:34:48,498 self._finalize_license_expression() 2026-04-12T22:34:48,499 running dist_info 2026-04-12T22:34:48,507 creating /tmp/pip-modern-metadata-22at57fk/topiary.egg-info 2026-04-12T22:34:48,508 writing /tmp/pip-modern-metadata-22at57fk/topiary.egg-info/PKG-INFO 2026-04-12T22:34:48,512 writing dependency_links to /tmp/pip-modern-metadata-22at57fk/topiary.egg-info/dependency_links.txt 2026-04-12T22:34:48,514 writing entry points to /tmp/pip-modern-metadata-22at57fk/topiary.egg-info/entry_points.txt 2026-04-12T22:34:48,515 writing requirements to /tmp/pip-modern-metadata-22at57fk/topiary.egg-info/requires.txt 2026-04-12T22:34:48,516 writing top-level names to /tmp/pip-modern-metadata-22at57fk/topiary.egg-info/top_level.txt 2026-04-12T22:34:48,518 writing manifest file '/tmp/pip-modern-metadata-22at57fk/topiary.egg-info/SOURCES.txt' 2026-04-12T22:34:48,541 reading manifest file '/tmp/pip-modern-metadata-22at57fk/topiary.egg-info/SOURCES.txt' 2026-04-12T22:34:48,543 adding license file 'LICENSE' 2026-04-12T22:34:48,548 writing manifest file '/tmp/pip-modern-metadata-22at57fk/topiary.egg-info/SOURCES.txt' 2026-04-12T22:34:48,549 creating '/tmp/pip-modern-metadata-22at57fk/topiary-5.0.1.dist-info' 2026-04-12T22:34:48,672 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-12T22:34:48,678 Source in /tmp/pip-wheel-5prt5ce9/topiary_ac4a3b4f9e3a4a57b2d83cf589eb4f15 has version 5.0.1, which satisfies requirement topiary==5.0.1 from https://files.pythonhosted.org/packages/a1/66/e8887661f196d2b95dc82b650d2a2311c50c39153231b6899a325fe42d98/topiary-5.0.1.tar.gz 2026-04-12T22:34:48,679 Removed topiary==5.0.1 from https://files.pythonhosted.org/packages/a1/66/e8887661f196d2b95dc82b650d2a2311c50c39153231b6899a325fe42d98/topiary-5.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-90_zauyy' 2026-04-12T22:34:48,687 Created temporary directory: /tmp/pip-unpack-8y1ej486 2026-04-12T22:34:48,687 Building wheels for collected packages: topiary 2026-04-12T22:34:48,692 Created temporary directory: /tmp/pip-wheel-2otms652 2026-04-12T22:34:48,693 Destination directory: /tmp/pip-wheel-2otms652 2026-04-12T22:34:48,695 Building wheel for topiary (pyproject.toml): started 2026-04-12T22:34:48,696 Running command Building wheel for topiary (pyproject.toml) 2026-04-12T22:34:49,315 /tmp/pip-build-env-3ubobobk/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T22:34:49,315 !! 2026-04-12T22:34:49,316 ******************************************************************************** 2026-04-12T22:34:49,317 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T22:34:49,318 License :: OSI Approved :: Apache Software License 2026-04-12T22:34:49,319 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T22:34:49,320 ******************************************************************************** 2026-04-12T22:34:49,321 !! 2026-04-12T22:34:49,322 dist._finalize_license_expression() 2026-04-12T22:34:49,323 /tmp/pip-build-env-3ubobobk/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T22:34:49,324 !! 2026-04-12T22:34:49,325 ******************************************************************************** 2026-04-12T22:34:49,325 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T22:34:49,326 License :: OSI Approved :: Apache Software License 2026-04-12T22:34:49,327 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T22:34:49,327 ******************************************************************************** 2026-04-12T22:34:49,328 !! 2026-04-12T22:34:49,329 self._finalize_license_expression() 2026-04-12T22:34:49,329 running bdist_wheel 2026-04-12T22:34:49,341 running build 2026-04-12T22:34:49,342 running build_py 2026-04-12T22:34:49,349 creating build/lib/tests 2026-04-12T22:34:49,351 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-12T22:34:49,353 copying tests/data.py -> build/lib/tests 2026-04-12T22:34:49,355 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-12T22:34:49,356 copying tests/test_ranking.py -> build/lib/tests 2026-04-12T22:34:49,360 copying tests/__init__.py -> build/lib/tests 2026-04-12T22:34:49,361 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-12T22:34:49,363 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-12T22:34:49,365 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-12T22:34:49,367 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-12T22:34:49,370 copying tests/test_wide.py -> build/lib/tests 2026-04-12T22:34:49,372 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-12T22:34:49,374 copying tests/test_integration.py -> build/lib/tests 2026-04-12T22:34:49,376 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-12T22:34:49,377 copying tests/test_sources.py -> build/lib/tests 2026-04-12T22:34:49,379 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-12T22:34:49,381 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-12T22:34:49,383 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-12T22:34:49,385 copying tests/test_io.py -> build/lib/tests 2026-04-12T22:34:49,387 copying tests/test_result.py -> build/lib/tests 2026-04-12T22:34:49,390 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-12T22:34:49,391 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-12T22:34:49,393 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-12T22:34:49,395 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-12T22:34:49,397 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-12T22:34:49,399 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-12T22:34:49,402 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-12T22:34:49,404 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-12T22:34:49,406 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-12T22:34:49,408 copying tests/test_dataframe.py -> build/lib/tests 2026-04-12T22:34:49,410 copying tests/test_padding.py -> build/lib/tests 2026-04-12T22:34:49,412 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-12T22:34:49,415 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-12T22:34:49,417 copying tests/test_inputs.py -> build/lib/tests 2026-04-12T22:34:49,420 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-12T22:34:49,422 copying tests/common.py -> build/lib/tests 2026-04-12T22:34:49,424 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-04-12T22:34:49,427 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-12T22:34:49,429 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-12T22:34:49,431 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-12T22:34:49,434 creating build/lib/topiary 2026-04-12T22:34:49,435 copying topiary/inputs.py -> build/lib/topiary 2026-04-12T22:34:49,438 copying topiary/wide.py -> build/lib/topiary 2026-04-12T22:34:49,440 copying topiary/result.py -> build/lib/topiary 2026-04-12T22:34:49,443 copying topiary/__init__.py -> build/lib/topiary 2026-04-12T22:34:49,444 copying topiary/filters.py -> build/lib/topiary 2026-04-12T22:34:49,447 copying topiary/sources.py -> build/lib/topiary 2026-04-12T22:34:49,449 copying topiary/io.py -> build/lib/topiary 2026-04-12T22:34:49,451 copying topiary/predictor.py -> build/lib/topiary 2026-04-12T22:34:49,454 copying topiary/properties.py -> build/lib/topiary 2026-04-12T22:34:49,456 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-12T22:34:49,459 creating build/lib/topiary/ranking 2026-04-12T22:34:49,460 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-04-12T22:34:49,462 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-04-12T22:34:49,464 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-04-12T22:34:49,467 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-04-12T22:34:49,471 creating build/lib/topiary/cli 2026-04-12T22:34:49,472 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-12T22:34:49,474 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-12T22:34:49,476 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-12T22:34:49,478 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-12T22:34:49,480 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-12T22:34:49,482 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-12T22:34:49,484 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-12T22:34:49,487 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-12T22:34:49,489 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-12T22:34:49,492 creating build/lib/topiary/rna 2026-04-12T22:34:49,493 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-12T22:34:49,496 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-12T22:34:49,498 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-12T22:34:49,500 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-12T22:34:49,502 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-12T22:34:49,504 running egg_info 2026-04-12T22:34:49,514 writing topiary.egg-info/PKG-INFO 2026-04-12T22:34:49,518 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-12T22:34:49,519 writing entry points to topiary.egg-info/entry_points.txt 2026-04-12T22:34:49,521 writing requirements to topiary.egg-info/requires.txt 2026-04-12T22:34:49,522 writing top-level names to topiary.egg-info/top_level.txt 2026-04-12T22:34:49,537 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T22:34:49,543 adding license file 'LICENSE' 2026-04-12T22:34:49,548 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T22:34:49,566 installing to build/bdist.linux-armv7l/wheel 2026-04-12T22:34:49,566 running install 2026-04-12T22:34:49,589 running install_lib 2026-04-12T22:34:49,595 creating build/bdist.linux-armv7l/wheel 2026-04-12T22:34:49,598 creating build/bdist.linux-armv7l/wheel/tests 2026-04-12T22:34:49,599 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,601 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,604 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,606 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,609 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,611 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,613 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,616 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,618 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,621 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,623 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,625 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,627 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,630 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,632 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,634 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,636 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,638 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,641 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,644 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,646 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,648 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,650 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,652 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,655 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,657 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,659 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,661 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,664 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,666 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,668 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,670 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,673 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,675 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,678 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,680 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,682 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,685 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,687 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T22:34:49,691 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-12T22:34:49,692 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,694 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,697 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,700 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,702 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-04-12T22:34:49,703 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T22:34:49,706 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T22:34:49,708 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T22:34:49,711 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T22:34:49,714 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,716 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,720 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-12T22:34:49,721 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,723 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,725 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,727 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,730 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,732 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,734 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,737 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,739 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T22:34:49,742 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,744 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,747 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-12T22:34:49,749 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T22:34:49,751 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T22:34:49,753 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T22:34:49,755 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T22:34:49,758 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T22:34:49,760 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,763 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T22:34:49,765 running install_egg_info 2026-04-12T22:34:49,770 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.0.1-py3.11.egg-info 2026-04-12T22:34:49,784 running install_scripts 2026-04-12T22:34:49,799 creating build/bdist.linux-armv7l/wheel/topiary-5.0.1.dist-info/WHEEL 2026-04-12T22:34:49,801 creating '/tmp/pip-wheel-2otms652/.tmp-nfhe63bq/topiary-5.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-12T22:34:49,804 adding 'tests/__init__.py' 2026-04-12T22:34:49,806 adding 'tests/common.py' 2026-04-12T22:34:49,807 adding 'tests/data.py' 2026-04-12T22:34:49,809 adding 'tests/test_args_outputs.py' 2026-04-12T22:34:49,810 adding 'tests/test_cli_coverage.py' 2026-04-12T22:34:49,812 adding 'tests/test_cli_protein_changes.py' 2026-04-12T22:34:49,813 adding 'tests/test_cli_ranking.py' 2026-04-12T22:34:49,815 adding 'tests/test_contains_mutant_residues.py' 2026-04-12T22:34:49,817 adding 'tests/test_coverage_gaps.py' 2026-04-12T22:34:49,818 adding 'tests/test_dataframe.py' 2026-04-12T22:34:49,819 adding 'tests/test_direct_input_regressions.py' 2026-04-12T22:34:49,822 adding 'tests/test_dsl_extensions.py' 2026-04-12T22:34:49,824 adding 'tests/test_dsl_polish.py' 2026-04-12T22:34:49,826 adding 'tests/test_dsl_roundtrip.py' 2026-04-12T22:34:49,828 adding 'tests/test_edge_case_fixtures.py' 2026-04-12T22:34:49,829 adding 'tests/test_effect_expression_filters.py' 2026-04-12T22:34:49,831 adding 'tests/test_end_to_end.py' 2026-04-12T22:34:49,832 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-12T22:34:49,834 adding 'tests/test_expression_integration.py' 2026-04-12T22:34:49,836 adding 'tests/test_expression_loader.py' 2026-04-12T22:34:49,837 adding 'tests/test_inputs.py' 2026-04-12T22:34:49,839 adding 'tests/test_integration.py' 2026-04-12T22:34:49,841 adding 'tests/test_io.py' 2026-04-12T22:34:49,842 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-12T22:34:49,843 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-12T22:34:49,845 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-12T22:34:49,846 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-12T22:34:49,847 adding 'tests/test_padding.py' 2026-04-12T22:34:49,849 adding 'tests/test_peptide_mutation_interval.py' 2026-04-12T22:34:49,850 adding 'tests/test_predictor_internals.py' 2026-04-12T22:34:49,857 adding 'tests/test_ranking.py' 2026-04-12T22:34:49,859 adding 'tests/test_result.py' 2026-04-12T22:34:49,861 adding 'tests/test_rna_helpers.py' 2026-04-12T22:34:49,862 adding 'tests/test_sequence_helpers.py' 2026-04-12T22:34:49,863 adding 'tests/test_sources.py' 2026-04-12T22:34:49,865 adding 'tests/test_sources_optional.py' 2026-04-12T22:34:49,867 adding 'tests/test_validation_and_edge_cases.py' 2026-04-12T22:34:49,868 adding 'tests/test_variant_expression_filters.py' 2026-04-12T22:34:49,870 adding 'tests/test_wide.py' 2026-04-12T22:34:49,872 adding 'topiary/__init__.py' 2026-04-12T22:34:49,873 adding 'topiary/filters.py' 2026-04-12T22:34:49,875 adding 'topiary/inputs.py' 2026-04-12T22:34:49,877 adding 'topiary/io.py' 2026-04-12T22:34:49,880 adding 'topiary/predictor.py' 2026-04-12T22:34:49,882 adding 'topiary/properties.py' 2026-04-12T22:34:49,884 adding 'topiary/result.py' 2026-04-12T22:34:49,886 adding 'topiary/sequence_helpers.py' 2026-04-12T22:34:49,888 adding 'topiary/sources.py' 2026-04-12T22:34:49,890 adding 'topiary/wide.py' 2026-04-12T22:34:49,892 adding 'topiary/cli/__init__.py' 2026-04-12T22:34:49,895 adding 'topiary/cli/args.py' 2026-04-12T22:34:49,896 adding 'topiary/cli/errors.py' 2026-04-12T22:34:49,898 adding 'topiary/cli/filtering.py' 2026-04-12T22:34:49,899 adding 'topiary/cli/outputs.py' 2026-04-12T22:34:49,901 adding 'topiary/cli/protein_changes.py' 2026-04-12T22:34:49,902 adding 'topiary/cli/rna.py' 2026-04-12T22:34:49,904 adding 'topiary/cli/script.py' 2026-04-12T22:34:49,905 adding 'topiary/cli/sequence.py' 2026-04-12T22:34:49,907 adding 'topiary/ranking/__init__.py' 2026-04-12T22:34:49,908 adding 'topiary/ranking/apply.py' 2026-04-12T22:34:49,913 adding 'topiary/ranking/nodes.py' 2026-04-12T22:34:49,916 adding 'topiary/ranking/parser.py' 2026-04-12T22:34:49,918 adding 'topiary/rna/__init__.py' 2026-04-12T22:34:49,919 adding 'topiary/rna/common.py' 2026-04-12T22:34:49,921 adding 'topiary/rna/cufflinks.py' 2026-04-12T22:34:49,923 adding 'topiary/rna/expression_loader.py' 2026-04-12T22:34:49,925 adding 'topiary/rna/gtf.py' 2026-04-12T22:34:49,928 adding 'topiary-5.0.1.dist-info/licenses/LICENSE' 2026-04-12T22:34:49,931 adding 'topiary-5.0.1.dist-info/METADATA' 2026-04-12T22:34:49,932 adding 'topiary-5.0.1.dist-info/WHEEL' 2026-04-12T22:34:49,933 adding 'topiary-5.0.1.dist-info/entry_points.txt' 2026-04-12T22:34:49,934 adding 'topiary-5.0.1.dist-info/top_level.txt' 2026-04-12T22:34:49,936 adding 'topiary-5.0.1.dist-info/RECORD' 2026-04-12T22:34:49,939 removing build/bdist.linux-armv7l/wheel 2026-04-12T22:34:50,059 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-12T22:34:50,065 Created wheel for topiary: filename=topiary-5.0.1-py3-none-any.whl size=150861 sha256=0570de434f6e796f6e927c63ea685b0ff926e693b1de84f60468838985ad11cb 2026-04-12T22:34:50,066 Stored in directory: /tmp/pip-ephem-wheel-cache-km1jdr9a/wheels/16/e7/3e/6cd0b6c6e7ee82a6f2bc235e79baab672f6f08a220fe44a2c3 2026-04-12T22:34:50,082 Successfully built topiary 2026-04-12T22:34:50,089 Removed build tracker: '/tmp/pip-build-tracker-90_zauyy'