2026-05-08T02:57:55,534 Created temporary directory: /tmp/pip-ephem-wheel-cache-tftyr2ah 2026-05-08T02:57:55,536 Created temporary directory: /tmp/pip-build-tracker-g9vismsy 2026-05-08T02:57:55,536 Initialized build tracking at /tmp/pip-build-tracker-g9vismsy 2026-05-08T02:57:55,537 Created build tracker: /tmp/pip-build-tracker-g9vismsy 2026-05-08T02:57:55,537 Entered build tracker: /tmp/pip-build-tracker-g9vismsy 2026-05-08T02:57:55,538 Created temporary directory: /tmp/pip-wheel-2x8fe7ec 2026-05-08T02:57:55,541 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/) 2026-05-08T02:57:56,195 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/) 2026-05-08T02:57:56,196 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/) 2026-05-08T02:57:56,196 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/) 2026-05-08T02:57:56,197 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/) 2026-05-08T02:57:56,198 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/) 2026-05-08T02:57:56,198 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/) 2026-05-08T02:57:56,199 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-05-08T02:57:56,199 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-05-08T02:57:56,228 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-05-08T02:57:56,248 Collecting topiary==5.11.0 2026-05-08T02:57:56,250 Created temporary directory: /tmp/pip-unpack-qreo8w0c 2026-05-08T02:57:56,397 Downloading topiary-5.11.0.tar.gz (223 kB) 2026-05-08T02:57:56,694 Added topiary==5.11.0 from https://files.pythonhosted.org/packages/fa/b5/505cd9107ba8d58f6020c6bb279fa82eeb8049cca8c7900421a5da525094/topiary-5.11.0.tar.gz to build tracker '/tmp/pip-build-tracker-g9vismsy' 2026-05-08T02:57:56,698 Created temporary directory: /tmp/pip-build-env-m0ebgfg6 2026-05-08T02:57:56,703 Installing build dependencies: started 2026-05-08T02:57:56,704 Running command pip subprocess to install build dependencies 2026-05-08T02:57:57,830 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-08T02:57:58,271 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 2026-05-08T02:57:58,293 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-08T02:58:00,081 Collecting setuptools>=64 2026-05-08T02:58:00,174 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-08T02:58:03,184 Installing collected packages: setuptools 2026-05-08T02:58:06,606 Successfully installed setuptools-82.0.1 2026-05-08T02:58:06,872 Installing build dependencies: finished with status 'done' 2026-05-08T02:58:06,883 Getting requirements to build wheel: started 2026-05-08T02:58:06,884 Running command Getting requirements to build wheel 2026-05-08T02:58:07,606 /tmp/pip-build-env-m0ebgfg6/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-08T02:58:07,606 !! 2026-05-08T02:58:07,607 ******************************************************************************** 2026-05-08T02:58:07,608 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-08T02:58:07,609 License :: OSI Approved :: Apache Software License 2026-05-08T02:58:07,610 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-08T02:58:07,611 ******************************************************************************** 2026-05-08T02:58:07,612 !! 2026-05-08T02:58:07,613 dist._finalize_license_expression() 2026-05-08T02:58:07,613 /tmp/pip-build-env-m0ebgfg6/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-08T02:58:07,614 !! 2026-05-08T02:58:07,615 ******************************************************************************** 2026-05-08T02:58:07,615 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-08T02:58:07,617 License :: OSI Approved :: Apache Software License 2026-05-08T02:58:07,618 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-08T02:58:07,618 ******************************************************************************** 2026-05-08T02:58:07,619 !! 2026-05-08T02:58:07,620 self._finalize_license_expression() 2026-05-08T02:58:07,621 running egg_info 2026-05-08T02:58:07,625 writing topiary.egg-info/PKG-INFO 2026-05-08T02:58:07,630 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-08T02:58:07,632 writing entry points to topiary.egg-info/entry_points.txt 2026-05-08T02:58:07,634 writing requirements to topiary.egg-info/requires.txt 2026-05-08T02:58:07,635 writing top-level names to topiary.egg-info/top_level.txt 2026-05-08T02:58:07,664 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-08T02:58:07,671 adding license file 'LICENSE' 2026-05-08T02:58:07,678 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-08T02:58:07,775 Getting requirements to build wheel: finished with status 'done' 2026-05-08T02:58:07,780 Created temporary directory: /tmp/pip-modern-metadata-tgua48w3 2026-05-08T02:58:07,783 Preparing metadata (pyproject.toml): started 2026-05-08T02:58:07,784 Running command Preparing metadata (pyproject.toml) 2026-05-08T02:58:08,663 /tmp/pip-build-env-m0ebgfg6/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-08T02:58:08,664 !! 2026-05-08T02:58:08,665 ******************************************************************************** 2026-05-08T02:58:08,665 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-08T02:58:08,666 License :: OSI Approved :: Apache Software License 2026-05-08T02:58:08,668 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-08T02:58:08,668 ******************************************************************************** 2026-05-08T02:58:08,669 !! 2026-05-08T02:58:08,670 dist._finalize_license_expression() 2026-05-08T02:58:08,671 /tmp/pip-build-env-m0ebgfg6/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-08T02:58:08,671 !! 2026-05-08T02:58:08,672 ******************************************************************************** 2026-05-08T02:58:08,673 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-08T02:58:08,674 License :: OSI Approved :: Apache Software License 2026-05-08T02:58:08,676 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-08T02:58:08,676 ******************************************************************************** 2026-05-08T02:58:08,677 !! 2026-05-08T02:58:08,678 self._finalize_license_expression() 2026-05-08T02:58:08,678 running dist_info 2026-05-08T02:58:08,686 creating /tmp/pip-modern-metadata-tgua48w3/topiary.egg-info 2026-05-08T02:58:08,687 writing /tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/PKG-INFO 2026-05-08T02:58:08,691 writing dependency_links to /tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/dependency_links.txt 2026-05-08T02:58:08,693 writing entry points to /tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/entry_points.txt 2026-05-08T02:58:08,695 writing requirements to /tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/requires.txt 2026-05-08T02:58:08,696 writing top-level names to /tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/top_level.txt 2026-05-08T02:58:08,698 writing manifest file '/tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/SOURCES.txt' 2026-05-08T02:58:08,723 reading manifest file '/tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/SOURCES.txt' 2026-05-08T02:58:08,725 adding license file 'LICENSE' 2026-05-08T02:58:08,730 writing manifest file '/tmp/pip-modern-metadata-tgua48w3/topiary.egg-info/SOURCES.txt' 2026-05-08T02:58:08,732 creating '/tmp/pip-modern-metadata-tgua48w3/topiary-5.11.0.dist-info' 2026-05-08T02:58:08,861 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-08T02:58:08,868 Source in /tmp/pip-wheel-2x8fe7ec/topiary_dc87914224904e70957bf8eb3965797b has version 5.11.0, which satisfies requirement topiary==5.11.0 from https://files.pythonhosted.org/packages/fa/b5/505cd9107ba8d58f6020c6bb279fa82eeb8049cca8c7900421a5da525094/topiary-5.11.0.tar.gz 2026-05-08T02:58:08,869 Removed topiary==5.11.0 from https://files.pythonhosted.org/packages/fa/b5/505cd9107ba8d58f6020c6bb279fa82eeb8049cca8c7900421a5da525094/topiary-5.11.0.tar.gz from build tracker '/tmp/pip-build-tracker-g9vismsy' 2026-05-08T02:58:08,877 Created temporary directory: /tmp/pip-unpack-bmuwwlno 2026-05-08T02:58:08,877 Building wheels for collected packages: topiary 2026-05-08T02:58:08,884 Created temporary directory: /tmp/pip-wheel-qmxqhrt4 2026-05-08T02:58:08,885 Destination directory: /tmp/pip-wheel-qmxqhrt4 2026-05-08T02:58:08,889 Building wheel for topiary (pyproject.toml): started 2026-05-08T02:58:08,890 Running command Building wheel for topiary (pyproject.toml) 2026-05-08T02:58:09,529 /tmp/pip-build-env-m0ebgfg6/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-08T02:58:09,530 !! 2026-05-08T02:58:09,531 ******************************************************************************** 2026-05-08T02:58:09,531 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-08T02:58:09,532 License :: OSI Approved :: Apache Software License 2026-05-08T02:58:09,533 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-08T02:58:09,534 ******************************************************************************** 2026-05-08T02:58:09,535 !! 2026-05-08T02:58:09,535 dist._finalize_license_expression() 2026-05-08T02:58:09,536 /tmp/pip-build-env-m0ebgfg6/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-08T02:58:09,537 !! 2026-05-08T02:58:09,538 ******************************************************************************** 2026-05-08T02:58:09,538 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-08T02:58:09,540 License :: OSI Approved :: Apache Software License 2026-05-08T02:58:09,541 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-08T02:58:09,541 ******************************************************************************** 2026-05-08T02:58:09,543 !! 2026-05-08T02:58:09,543 self._finalize_license_expression() 2026-05-08T02:58:09,544 running bdist_wheel 2026-05-08T02:58:09,557 running build 2026-05-08T02:58:09,558 running build_py 2026-05-08T02:58:09,564 creating build/lib/topiary 2026-05-08T02:58:09,567 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-08T02:58:09,570 copying topiary/wide.py -> build/lib/topiary 2026-05-08T02:58:09,573 copying topiary/predictor.py -> build/lib/topiary 2026-05-08T02:58:09,576 copying topiary/io_lens.py -> build/lib/topiary 2026-05-08T02:58:09,578 copying topiary/__init__.py -> build/lib/topiary 2026-05-08T02:58:09,580 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-08T02:58:09,583 copying topiary/io.py -> build/lib/topiary 2026-05-08T02:58:09,585 copying topiary/sources.py -> build/lib/topiary 2026-05-08T02:58:09,588 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-08T02:58:09,590 copying topiary/cached.py -> build/lib/topiary 2026-05-08T02:58:09,593 copying topiary/result.py -> build/lib/topiary 2026-05-08T02:58:09,596 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-08T02:58:09,598 copying topiary/filters.py -> build/lib/topiary 2026-05-08T02:58:09,600 copying topiary/properties.py -> build/lib/topiary 2026-05-08T02:58:09,603 copying topiary/inputs.py -> build/lib/topiary 2026-05-08T02:58:09,606 creating build/lib/tests 2026-05-08T02:58:09,607 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-08T02:58:09,610 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-08T02:58:09,612 copying tests/test_sources.py -> build/lib/tests 2026-05-08T02:58:09,614 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-08T02:58:09,616 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-08T02:58:09,619 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-08T02:58:09,621 copying tests/common.py -> build/lib/tests 2026-05-08T02:58:09,623 copying tests/test_kind_support.py -> build/lib/tests 2026-05-08T02:58:09,625 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-08T02:58:09,628 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-08T02:58:09,630 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-08T02:58:09,633 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-08T02:58:09,634 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-08T02:58:09,637 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-08T02:58:09,640 copying tests/test_result.py -> build/lib/tests 2026-05-08T02:58:09,642 copying tests/__init__.py -> build/lib/tests 2026-05-08T02:58:09,644 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-08T02:58:09,646 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-08T02:58:09,648 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-08T02:58:09,651 copying tests/data.py -> build/lib/tests 2026-05-08T02:58:09,653 copying tests/test_ranking.py -> build/lib/tests 2026-05-08T02:58:09,658 copying tests/test_inputs.py -> build/lib/tests 2026-05-08T02:58:09,660 copying tests/test_wide.py -> build/lib/tests 2026-05-08T02:58:09,663 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-08T02:58:09,666 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-08T02:58:09,668 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-08T02:58:09,670 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-08T02:58:09,672 copying tests/test_io_lens.py -> build/lib/tests 2026-05-08T02:58:09,674 copying tests/test_cli_script.py -> build/lib/tests 2026-05-08T02:58:09,676 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-08T02:58:09,679 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-08T02:58:09,681 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-08T02:58:09,683 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-08T02:58:09,685 copying tests/test_integration.py -> build/lib/tests 2026-05-08T02:58:09,687 copying tests/test_deploy_script.py -> build/lib/tests 2026-05-08T02:58:09,690 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-08T02:58:09,691 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-08T02:58:09,693 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-08T02:58:09,696 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-08T02:58:09,699 copying tests/test_io.py -> build/lib/tests 2026-05-08T02:58:09,701 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-08T02:58:09,703 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-08T02:58:09,706 copying tests/test_padding.py -> build/lib/tests 2026-05-08T02:58:09,707 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-08T02:58:09,710 copying tests/test_lazy_imports.py -> build/lib/tests 2026-05-08T02:58:09,712 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-08T02:58:09,714 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-08T02:58:09,716 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-08T02:58:09,718 copying tests/test_dataframe.py -> build/lib/tests 2026-05-08T02:58:09,720 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-08T02:58:09,722 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-08T02:58:09,725 creating build/lib/topiary/rna 2026-05-08T02:58:09,726 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-08T02:58:09,729 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-08T02:58:09,731 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-08T02:58:09,733 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-08T02:58:09,735 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-08T02:58:09,738 creating build/lib/topiary/ranking 2026-05-08T02:58:09,739 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-08T02:58:09,742 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-08T02:58:09,744 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-08T02:58:09,747 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-08T02:58:09,751 creating build/lib/topiary/cli 2026-05-08T02:58:09,752 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-08T02:58:09,754 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-08T02:58:09,757 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-08T02:58:09,759 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-08T02:58:09,761 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-08T02:58:09,763 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-08T02:58:09,765 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-08T02:58:09,767 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-08T02:58:09,769 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-08T02:58:09,772 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-08T02:58:09,774 running egg_info 2026-05-08T02:58:09,784 writing topiary.egg-info/PKG-INFO 2026-05-08T02:58:09,788 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-08T02:58:09,789 writing entry points to topiary.egg-info/entry_points.txt 2026-05-08T02:58:09,791 writing requirements to topiary.egg-info/requires.txt 2026-05-08T02:58:09,792 writing top-level names to topiary.egg-info/top_level.txt 2026-05-08T02:58:09,809 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-08T02:58:09,815 adding license file 'LICENSE' 2026-05-08T02:58:09,821 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-08T02:58:09,840 installing to build/bdist.linux-armv7l/wheel 2026-05-08T02:58:09,840 running install 2026-05-08T02:58:09,863 running install_lib 2026-05-08T02:58:09,869 creating build/bdist.linux-armv7l/wheel 2026-05-08T02:58:09,872 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-08T02:58:09,874 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-08T02:58:09,875 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-08T02:58:09,877 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-08T02:58:09,879 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-08T02:58:09,882 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-08T02:58:09,884 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-08T02:58:09,887 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-08T02:58:09,888 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-08T02:58:09,891 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-08T02:58:09,893 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-08T02:58:09,897 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-08T02:58:09,899 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,902 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,904 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,907 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,910 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,912 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,914 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,917 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,919 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,922 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,925 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,928 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,931 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-08T02:58:09,932 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,935 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,938 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,940 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,942 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,944 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,947 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,949 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,951 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,955 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-08T02:58:09,957 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,959 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,961 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-08T02:58:09,966 creating build/bdist.linux-armv7l/wheel/tests 2026-05-08T02:58:09,967 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,969 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,972 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,974 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,976 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,978 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,981 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,983 copying build/lib/tests/test_kind_support.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,985 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,988 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,990 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,992 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,994 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,996 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:09,999 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,002 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,003 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,005 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,008 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,011 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,013 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,018 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,021 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,023 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,026 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,028 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,030 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,032 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,035 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,037 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,042 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,044 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,047 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,049 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,051 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,053 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,055 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,057 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,061 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,064 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,067 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,069 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,072 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,073 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,076 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,078 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,081 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,083 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,086 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,088 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,090 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-08T02:58:10,092 running install_egg_info 2026-05-08T02:58:10,097 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.11.0-py3.11.egg-info 2026-05-08T02:58:10,115 running install_scripts 2026-05-08T02:58:10,140 creating build/bdist.linux-armv7l/wheel/topiary-5.11.0.dist-info/WHEEL 2026-05-08T02:58:10,144 creating '/tmp/pip-wheel-qmxqhrt4/.tmp-xfxeojn1/topiary-5.11.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-08T02:58:10,147 adding 'tests/__init__.py' 2026-05-08T02:58:10,149 adding 'tests/common.py' 2026-05-08T02:58:10,150 adding 'tests/data.py' 2026-05-08T02:58:10,151 adding 'tests/test_args_outputs.py' 2026-05-08T02:58:10,156 adding 'tests/test_cached_predictor.py' 2026-05-08T02:58:10,158 adding 'tests/test_cli_cached_predictor.py' 2026-05-08T02:58:10,160 adding 'tests/test_cli_coverage.py' 2026-05-08T02:58:10,161 adding 'tests/test_cli_protein_changes.py' 2026-05-08T02:58:10,163 adding 'tests/test_cli_ranking.py' 2026-05-08T02:58:10,164 adding 'tests/test_cli_script.py' 2026-05-08T02:58:10,165 adding 'tests/test_contains_mutant_residues.py' 2026-05-08T02:58:10,167 adding 'tests/test_coverage_gaps.py' 2026-05-08T02:58:10,169 adding 'tests/test_dataframe.py' 2026-05-08T02:58:10,170 adding 'tests/test_deploy_script.py' 2026-05-08T02:58:10,171 adding 'tests/test_direct_input_regressions.py' 2026-05-08T02:58:10,174 adding 'tests/test_dsl_extensions.py' 2026-05-08T02:58:10,175 adding 'tests/test_dsl_polish.py' 2026-05-08T02:58:10,178 adding 'tests/test_dsl_roundtrip.py' 2026-05-08T02:58:10,180 adding 'tests/test_edge_case_fixtures.py' 2026-05-08T02:58:10,181 adding 'tests/test_effect_expression_filters.py' 2026-05-08T02:58:10,183 adding 'tests/test_end_to_end.py' 2026-05-08T02:58:10,184 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-08T02:58:10,186 adding 'tests/test_expression_integration.py' 2026-05-08T02:58:10,187 adding 'tests/test_expression_loader.py' 2026-05-08T02:58:10,190 adding 'tests/test_frameshift_fragments.py' 2026-05-08T02:58:10,192 adding 'tests/test_inputs.py' 2026-05-08T02:58:10,193 adding 'tests/test_integration.py' 2026-05-08T02:58:10,195 adding 'tests/test_io.py' 2026-05-08T02:58:10,197 adding 'tests/test_io_lens.py' 2026-05-08T02:58:10,199 adding 'tests/test_kind_support.py' 2026-05-08T02:58:10,200 adding 'tests/test_lazy_imports.py' 2026-05-08T02:58:10,202 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-08T02:58:10,203 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-08T02:58:10,204 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-08T02:58:10,205 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-08T02:58:10,206 adding 'tests/test_padding.py' 2026-05-08T02:58:10,208 adding 'tests/test_peptide_mutation_interval.py' 2026-05-08T02:58:10,210 adding 'tests/test_predict_from_fragments.py' 2026-05-08T02:58:10,213 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-08T02:58:10,214 adding 'tests/test_predictor_internals.py' 2026-05-08T02:58:10,216 adding 'tests/test_protein_fragment.py' 2026-05-08T02:58:10,226 adding 'tests/test_ranking.py' 2026-05-08T02:58:10,229 adding 'tests/test_result.py' 2026-05-08T02:58:10,230 adding 'tests/test_rna_helpers.py' 2026-05-08T02:58:10,233 adding 'tests/test_self_proteome.py' 2026-05-08T02:58:10,234 adding 'tests/test_sequence_helpers.py' 2026-05-08T02:58:10,236 adding 'tests/test_sources.py' 2026-05-08T02:58:10,237 adding 'tests/test_sources_optional.py' 2026-05-08T02:58:10,239 adding 'tests/test_validation_and_edge_cases.py' 2026-05-08T02:58:10,240 adding 'tests/test_variant_expression_filters.py' 2026-05-08T02:58:10,242 adding 'tests/test_wide.py' 2026-05-08T02:58:10,245 adding 'topiary/__init__.py' 2026-05-08T02:58:10,251 adding 'topiary/cached.py' 2026-05-08T02:58:10,253 adding 'topiary/filters.py' 2026-05-08T02:58:10,254 adding 'topiary/inputs.py' 2026-05-08T02:58:10,256 adding 'topiary/io.py' 2026-05-08T02:58:10,258 adding 'topiary/io_lens.py' 2026-05-08T02:58:10,260 adding 'topiary/io_protein_fragment.py' 2026-05-08T02:58:10,265 adding 'topiary/predictor.py' 2026-05-08T02:58:10,267 adding 'topiary/properties.py' 2026-05-08T02:58:10,270 adding 'topiary/protein_fragment.py' 2026-05-08T02:58:10,272 adding 'topiary/result.py' 2026-05-08T02:58:10,276 adding 'topiary/self_proteome.py' 2026-05-08T02:58:10,277 adding 'topiary/sequence_helpers.py' 2026-05-08T02:58:10,279 adding 'topiary/sources.py' 2026-05-08T02:58:10,281 adding 'topiary/wide.py' 2026-05-08T02:58:10,283 adding 'topiary/cli/__init__.py' 2026-05-08T02:58:10,286 adding 'topiary/cli/args.py' 2026-05-08T02:58:10,288 adding 'topiary/cli/cached_predictor.py' 2026-05-08T02:58:10,289 adding 'topiary/cli/errors.py' 2026-05-08T02:58:10,291 adding 'topiary/cli/filtering.py' 2026-05-08T02:58:10,292 adding 'topiary/cli/outputs.py' 2026-05-08T02:58:10,294 adding 'topiary/cli/protein_changes.py' 2026-05-08T02:58:10,296 adding 'topiary/cli/rna.py' 2026-05-08T02:58:10,298 adding 'topiary/cli/script.py' 2026-05-08T02:58:10,300 adding 'topiary/cli/sequence.py' 2026-05-08T02:58:10,303 adding 'topiary/ranking/__init__.py' 2026-05-08T02:58:10,306 adding 'topiary/ranking/apply.py' 2026-05-08T02:58:10,313 adding 'topiary/ranking/nodes.py' 2026-05-08T02:58:10,316 adding 'topiary/ranking/parser.py' 2026-05-08T02:58:10,317 adding 'topiary/rna/__init__.py' 2026-05-08T02:58:10,319 adding 'topiary/rna/common.py' 2026-05-08T02:58:10,321 adding 'topiary/rna/cufflinks.py' 2026-05-08T02:58:10,323 adding 'topiary/rna/expression_loader.py' 2026-05-08T02:58:10,324 adding 'topiary/rna/gtf.py' 2026-05-08T02:58:10,328 adding 'topiary-5.11.0.dist-info/licenses/LICENSE' 2026-05-08T02:58:10,331 adding 'topiary-5.11.0.dist-info/METADATA' 2026-05-08T02:58:10,332 adding 'topiary-5.11.0.dist-info/WHEEL' 2026-05-08T02:58:10,333 adding 'topiary-5.11.0.dist-info/entry_points.txt' 2026-05-08T02:58:10,334 adding 'topiary-5.11.0.dist-info/top_level.txt' 2026-05-08T02:58:10,335 adding 'topiary-5.11.0.dist-info/RECORD' 2026-05-08T02:58:10,340 removing build/bdist.linux-armv7l/wheel 2026-05-08T02:58:10,462 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-08T02:58:10,479 Created wheel for topiary: filename=topiary-5.11.0-py3-none-any.whl size=251368 sha256=90f10c8721d8b933af021a1dfb745e8278f94724157cad79abeada9e7492b374 2026-05-08T02:58:10,480 Stored in directory: /tmp/pip-ephem-wheel-cache-szg1d9jk/wheels/c0/94/bc/d6e6fd77594ba306ed719df1a9911c37d7bad560eb52ee143b 2026-05-08T02:58:10,499 Successfully built topiary 2026-05-08T02:58:10,511 Removed build tracker: '/tmp/pip-build-tracker-g9vismsy'