2026-04-13T08:30:19,592 Created temporary directory: /tmp/pip-ephem-wheel-cache-98j4sbh5 2026-04-13T08:30:19,594 Created temporary directory: /tmp/pip-build-tracker-y1ozzrg5 2026-04-13T08:30:19,594 Initialized build tracking at /tmp/pip-build-tracker-y1ozzrg5 2026-04-13T08:30:19,595 Created build tracker: /tmp/pip-build-tracker-y1ozzrg5 2026-04-13T08:30:19,595 Entered build tracker: /tmp/pip-build-tracker-y1ozzrg5 2026-04-13T08:30:19,596 Created temporary directory: /tmp/pip-wheel-fcu9m4y2 2026-04-13T08:30:19,599 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 2026-04-13T08:30:19,601 Created temporary directory: /tmp/pip-ephem-wheel-cache-fykkk316 2026-04-13T08:30:19,626 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-13T08:30:19,630 2 location(s) to search for versions of topiary: 2026-04-13T08:30:19,630 * https://pypi.org/simple/topiary/ 2026-04-13T08:30:19,630 * https://www.piwheels.org/simple/topiary/ 2026-04-13T08:30:19,630 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-04-13T08:30:19,631 Getting page https://pypi.org/simple/topiary/ 2026-04-13T08:30:19,633 Found index url https://pypi.org/simple 2026-04-13T08:30:19,865 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-04-13T08:30:19,879 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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https://www.piwheels.org/simple/topiary/) 2026-04-13T08:30:20,160 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/) 2026-04-13T08:30:20,160 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/) 2026-04-13T08:30:20,161 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/) 2026-04-13T08:30:20,161 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/) 2026-04-13T08:30:20,162 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/) 2026-04-13T08:30:20,162 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/) 2026-04-13T08:30:20,163 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-13T08:30:20,164 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-13T08:30:20,191 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-13T08:30:20,211 Collecting topiary==5.1.0 2026-04-13T08:30:20,213 Created temporary directory: /tmp/pip-unpack-trhjadhz 2026-04-13T08:30:20,363 Downloading topiary-5.1.0.tar.gz (138 kB) 2026-04-13T08:30:20,612 Added topiary==5.1.0 from https://files.pythonhosted.org/packages/85/04/5e82599a4ae9694c05af8638565cb2f7ecc93ff25893660c22fc6796be6e/topiary-5.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-y1ozzrg5' 2026-04-13T08:30:20,617 Created temporary directory: /tmp/pip-build-env-93v0_49v 2026-04-13T08:30:20,621 Installing build dependencies: started 2026-04-13T08:30:20,622 Running command pip subprocess to install build dependencies 2026-04-13T08:30:20,653 Error processing line 1 of /home/piwheels/.local/lib/python3.11/site-packages/outofcuda_hook.pth: 2026-04-13T08:30:20,693 Traceback (most recent call last): 2026-04-13T08:30:20,693 File "", line 192, in addpackage 2026-04-13T08:30:20,694 File "", line 1, in 2026-04-13T08:30:20,695 ModuleNotFoundError: No module named 'outofcuda' 2026-04-13T08:30:20,696 Remainder of file ignored 2026-04-13T08:30:21,773 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-13T08:30:22,201 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 2026-04-13T08:30:22,223 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-13T08:30:24,007 Collecting setuptools>=64 2026-04-13T08:30:24,102 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-13T08:30:27,104 Installing collected packages: setuptools 2026-04-13T08:30:30,206 Successfully installed setuptools-82.0.1 2026-04-13T08:30:30,473 Installing build dependencies: finished with status 'done' 2026-04-13T08:30:30,479 Getting requirements to build wheel: started 2026-04-13T08:30:30,480 Running command Getting requirements to build wheel 2026-04-13T08:30:31,165 /tmp/pip-build-env-93v0_49v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T08:30:31,166 !! 2026-04-13T08:30:31,167 ******************************************************************************** 2026-04-13T08:30:31,167 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T08:30:31,169 License :: OSI Approved :: Apache Software License 2026-04-13T08:30:31,170 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T08:30:31,170 ******************************************************************************** 2026-04-13T08:30:31,171 !! 2026-04-13T08:30:31,172 dist._finalize_license_expression() 2026-04-13T08:30:31,174 /tmp/pip-build-env-93v0_49v/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T08:30:31,175 !! 2026-04-13T08:30:31,177 ******************************************************************************** 2026-04-13T08:30:31,177 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T08:30:31,178 License :: OSI Approved :: Apache Software License 2026-04-13T08:30:31,180 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T08:30:31,180 ******************************************************************************** 2026-04-13T08:30:31,181 !! 2026-04-13T08:30:31,182 self._finalize_license_expression() 2026-04-13T08:30:31,185 running egg_info 2026-04-13T08:30:31,191 writing topiary.egg-info/PKG-INFO 2026-04-13T08:30:31,196 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-13T08:30:31,198 writing entry points to topiary.egg-info/entry_points.txt 2026-04-13T08:30:31,200 writing requirements to topiary.egg-info/requires.txt 2026-04-13T08:30:31,202 writing top-level names to topiary.egg-info/top_level.txt 2026-04-13T08:30:31,228 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T08:30:31,234 adding license file 'LICENSE' 2026-04-13T08:30:31,240 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T08:30:31,337 Getting requirements to build wheel: finished with status 'done' 2026-04-13T08:30:31,341 Created temporary directory: /tmp/pip-modern-metadata-qix6_3nj 2026-04-13T08:30:31,343 Preparing metadata (pyproject.toml): started 2026-04-13T08:30:31,344 Running command Preparing metadata (pyproject.toml) 2026-04-13T08:30:31,983 /tmp/pip-build-env-93v0_49v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T08:30:31,984 !! 2026-04-13T08:30:31,985 ******************************************************************************** 2026-04-13T08:30:31,985 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T08:30:31,986 License :: OSI Approved :: Apache Software License 2026-04-13T08:30:31,987 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T08:30:31,988 ******************************************************************************** 2026-04-13T08:30:31,988 !! 2026-04-13T08:30:31,989 dist._finalize_license_expression() 2026-04-13T08:30:31,989 /tmp/pip-build-env-93v0_49v/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T08:30:31,990 !! 2026-04-13T08:30:31,991 ******************************************************************************** 2026-04-13T08:30:31,991 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T08:30:31,992 License :: OSI Approved :: Apache Software License 2026-04-13T08:30:31,993 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T08:30:31,994 ******************************************************************************** 2026-04-13T08:30:31,995 !! 2026-04-13T08:30:31,995 self._finalize_license_expression() 2026-04-13T08:30:31,996 running dist_info 2026-04-13T08:30:32,006 creating /tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info 2026-04-13T08:30:32,007 writing /tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/PKG-INFO 2026-04-13T08:30:32,012 writing dependency_links to /tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/dependency_links.txt 2026-04-13T08:30:32,013 writing entry points to /tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/entry_points.txt 2026-04-13T08:30:32,015 writing requirements to /tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/requires.txt 2026-04-13T08:30:32,016 writing top-level names to /tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/top_level.txt 2026-04-13T08:30:32,017 writing manifest file '/tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/SOURCES.txt' 2026-04-13T08:30:32,041 reading manifest file '/tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/SOURCES.txt' 2026-04-13T08:30:32,043 adding license file 'LICENSE' 2026-04-13T08:30:32,048 writing manifest file '/tmp/pip-modern-metadata-qix6_3nj/topiary.egg-info/SOURCES.txt' 2026-04-13T08:30:32,049 creating '/tmp/pip-modern-metadata-qix6_3nj/topiary-5.1.0.dist-info' 2026-04-13T08:30:32,175 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-13T08:30:32,181 Source in /tmp/pip-wheel-fcu9m4y2/topiary_7445efb94304469c9fe3dea8a0cb7bbf has version 5.1.0, which satisfies requirement topiary==5.1.0 from https://files.pythonhosted.org/packages/85/04/5e82599a4ae9694c05af8638565cb2f7ecc93ff25893660c22fc6796be6e/topiary-5.1.0.tar.gz 2026-04-13T08:30:32,182 Removed topiary==5.1.0 from https://files.pythonhosted.org/packages/85/04/5e82599a4ae9694c05af8638565cb2f7ecc93ff25893660c22fc6796be6e/topiary-5.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-y1ozzrg5' 2026-04-13T08:30:32,190 Created temporary directory: /tmp/pip-unpack-e3b09gch 2026-04-13T08:30:32,190 Building wheels for collected packages: topiary 2026-04-13T08:30:32,194 Created temporary directory: /tmp/pip-wheel-h5stmykm 2026-04-13T08:30:32,195 Destination directory: /tmp/pip-wheel-h5stmykm 2026-04-13T08:30:32,197 Building wheel for topiary (pyproject.toml): started 2026-04-13T08:30:32,198 Running command Building wheel for topiary (pyproject.toml) 2026-04-13T08:30:32,847 /tmp/pip-build-env-93v0_49v/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T08:30:32,847 !! 2026-04-13T08:30:32,848 ******************************************************************************** 2026-04-13T08:30:32,849 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T08:30:32,850 License :: OSI Approved :: Apache Software License 2026-04-13T08:30:32,851 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T08:30:32,851 ******************************************************************************** 2026-04-13T08:30:32,852 !! 2026-04-13T08:30:32,853 dist._finalize_license_expression() 2026-04-13T08:30:32,853 /tmp/pip-build-env-93v0_49v/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T08:30:32,854 !! 2026-04-13T08:30:32,855 ******************************************************************************** 2026-04-13T08:30:32,855 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T08:30:32,856 License :: OSI Approved :: Apache Software License 2026-04-13T08:30:32,857 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T08:30:32,857 ******************************************************************************** 2026-04-13T08:30:32,858 !! 2026-04-13T08:30:32,859 self._finalize_license_expression() 2026-04-13T08:30:32,859 running bdist_wheel 2026-04-13T08:30:32,872 running build 2026-04-13T08:30:32,872 running build_py 2026-04-13T08:30:32,879 creating build/lib/tests 2026-04-13T08:30:32,881 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-13T08:30:32,883 copying tests/data.py -> build/lib/tests 2026-04-13T08:30:32,885 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-13T08:30:32,887 copying tests/test_ranking.py -> build/lib/tests 2026-04-13T08:30:32,890 copying tests/__init__.py -> build/lib/tests 2026-04-13T08:30:32,892 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-13T08:30:32,894 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-13T08:30:32,896 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-13T08:30:32,898 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-13T08:30:32,901 copying tests/test_wide.py -> build/lib/tests 2026-04-13T08:30:32,903 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-13T08:30:32,905 copying tests/test_io_lens.py -> build/lib/tests 2026-04-13T08:30:32,908 copying tests/test_integration.py -> build/lib/tests 2026-04-13T08:30:32,909 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-13T08:30:32,911 copying tests/test_sources.py -> build/lib/tests 2026-04-13T08:30:32,913 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-13T08:30:32,916 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-13T08:30:32,918 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-13T08:30:32,919 copying tests/test_io.py -> build/lib/tests 2026-04-13T08:30:32,922 copying tests/test_result.py -> build/lib/tests 2026-04-13T08:30:32,925 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-13T08:30:32,926 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-13T08:30:32,928 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-13T08:30:32,930 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-13T08:30:32,932 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-13T08:30:32,935 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-13T08:30:32,937 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-13T08:30:32,939 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-13T08:30:32,942 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-13T08:30:32,944 copying tests/test_dataframe.py -> build/lib/tests 2026-04-13T08:30:32,945 copying tests/test_padding.py -> build/lib/tests 2026-04-13T08:30:32,947 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-13T08:30:32,949 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-13T08:30:32,952 copying tests/test_inputs.py -> build/lib/tests 2026-04-13T08:30:32,954 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-13T08:30:32,956 copying tests/common.py -> build/lib/tests 2026-04-13T08:30:32,958 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-04-13T08:30:32,960 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-13T08:30:32,962 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-13T08:30:32,964 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-13T08:30:32,967 creating build/lib/topiary 2026-04-13T08:30:32,968 copying topiary/inputs.py -> build/lib/topiary 2026-04-13T08:30:32,970 copying topiary/wide.py -> build/lib/topiary 2026-04-13T08:30:32,973 copying topiary/result.py -> build/lib/topiary 2026-04-13T08:30:32,975 copying topiary/__init__.py -> build/lib/topiary 2026-04-13T08:30:32,976 copying topiary/filters.py -> build/lib/topiary 2026-04-13T08:30:32,979 copying topiary/sources.py -> build/lib/topiary 2026-04-13T08:30:32,981 copying topiary/io.py -> build/lib/topiary 2026-04-13T08:30:32,983 copying topiary/predictor.py -> build/lib/topiary 2026-04-13T08:30:32,986 copying topiary/io_lens.py -> build/lib/topiary 2026-04-13T08:30:32,988 copying topiary/properties.py -> build/lib/topiary 2026-04-13T08:30:32,990 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-13T08:30:32,993 creating build/lib/topiary/ranking 2026-04-13T08:30:32,994 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-04-13T08:30:32,996 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-04-13T08:30:32,998 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-04-13T08:30:33,001 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-04-13T08:30:33,004 creating build/lib/topiary/cli 2026-04-13T08:30:33,005 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-13T08:30:33,007 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-13T08:30:33,009 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-13T08:30:33,011 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-13T08:30:33,013 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-13T08:30:33,015 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-13T08:30:33,016 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-13T08:30:33,019 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-13T08:30:33,021 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-13T08:30:33,024 creating build/lib/topiary/rna 2026-04-13T08:30:33,025 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-13T08:30:33,027 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-13T08:30:33,029 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-13T08:30:33,031 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-13T08:30:33,033 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-13T08:30:33,035 running egg_info 2026-04-13T08:30:33,044 writing topiary.egg-info/PKG-INFO 2026-04-13T08:30:33,048 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-13T08:30:33,049 writing entry points to topiary.egg-info/entry_points.txt 2026-04-13T08:30:33,050 writing requirements to topiary.egg-info/requires.txt 2026-04-13T08:30:33,051 writing top-level names to topiary.egg-info/top_level.txt 2026-04-13T08:30:33,066 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T08:30:33,072 adding license file 'LICENSE' 2026-04-13T08:30:33,077 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T08:30:33,094 installing to build/bdist.linux-armv7l/wheel 2026-04-13T08:30:33,094 running install 2026-04-13T08:30:33,117 running install_lib 2026-04-13T08:30:33,123 creating build/bdist.linux-armv7l/wheel 2026-04-13T08:30:33,125 creating build/bdist.linux-armv7l/wheel/tests 2026-04-13T08:30:33,126 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,128 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,130 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,131 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,135 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,137 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,138 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,141 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,142 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,145 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,147 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,149 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,151 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,153 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,155 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,157 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,159 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,161 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,163 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,165 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,168 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,169 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,171 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,173 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,175 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,177 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,180 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,182 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,184 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,185 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,187 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,189 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,191 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,193 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,195 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,197 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,199 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,202 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,204 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,206 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T08:30:33,209 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-13T08:30:33,210 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,213 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,215 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,217 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,220 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-04-13T08:30:33,221 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T08:30:33,222 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T08:30:33,225 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T08:30:33,228 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T08:30:33,230 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,232 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,235 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-13T08:30:33,236 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,238 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,240 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,242 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,244 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,246 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,247 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,250 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,252 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T08:30:33,254 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,257 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,260 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-13T08:30:33,261 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T08:30:33,263 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T08:30:33,265 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T08:30:33,267 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T08:30:33,269 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T08:30:33,271 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,273 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,275 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T08:30:33,277 running install_egg_info 2026-04-13T08:30:33,282 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.1.0-py3.11.egg-info 2026-04-13T08:30:33,293 running install_scripts 2026-04-13T08:30:33,306 creating build/bdist.linux-armv7l/wheel/topiary-5.1.0.dist-info/WHEEL 2026-04-13T08:30:33,308 creating '/tmp/pip-wheel-h5stmykm/.tmp-h7wcjjz_/topiary-5.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-13T08:30:33,311 adding 'tests/__init__.py' 2026-04-13T08:30:33,312 adding 'tests/common.py' 2026-04-13T08:30:33,314 adding 'tests/data.py' 2026-04-13T08:30:33,315 adding 'tests/test_args_outputs.py' 2026-04-13T08:30:33,316 adding 'tests/test_cli_coverage.py' 2026-04-13T08:30:33,318 adding 'tests/test_cli_protein_changes.py' 2026-04-13T08:30:33,320 adding 'tests/test_cli_ranking.py' 2026-04-13T08:30:33,321 adding 'tests/test_contains_mutant_residues.py' 2026-04-13T08:30:33,323 adding 'tests/test_coverage_gaps.py' 2026-04-13T08:30:33,324 adding 'tests/test_dataframe.py' 2026-04-13T08:30:33,325 adding 'tests/test_direct_input_regressions.py' 2026-04-13T08:30:33,328 adding 'tests/test_dsl_extensions.py' 2026-04-13T08:30:33,330 adding 'tests/test_dsl_polish.py' 2026-04-13T08:30:33,333 adding 'tests/test_dsl_roundtrip.py' 2026-04-13T08:30:33,334 adding 'tests/test_edge_case_fixtures.py' 2026-04-13T08:30:33,335 adding 'tests/test_effect_expression_filters.py' 2026-04-13T08:30:33,337 adding 'tests/test_end_to_end.py' 2026-04-13T08:30:33,338 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-13T08:30:33,340 adding 'tests/test_expression_integration.py' 2026-04-13T08:30:33,341 adding 'tests/test_expression_loader.py' 2026-04-13T08:30:33,343 adding 'tests/test_inputs.py' 2026-04-13T08:30:33,344 adding 'tests/test_integration.py' 2026-04-13T08:30:33,346 adding 'tests/test_io.py' 2026-04-13T08:30:33,348 adding 'tests/test_io_lens.py' 2026-04-13T08:30:33,350 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-13T08:30:33,351 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-13T08:30:33,352 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-13T08:30:33,353 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-13T08:30:33,355 adding 'tests/test_padding.py' 2026-04-13T08:30:33,356 adding 'tests/test_peptide_mutation_interval.py' 2026-04-13T08:30:33,357 adding 'tests/test_predictor_internals.py' 2026-04-13T08:30:33,364 adding 'tests/test_ranking.py' 2026-04-13T08:30:33,367 adding 'tests/test_result.py' 2026-04-13T08:30:33,368 adding 'tests/test_rna_helpers.py' 2026-04-13T08:30:33,369 adding 'tests/test_sequence_helpers.py' 2026-04-13T08:30:33,371 adding 'tests/test_sources.py' 2026-04-13T08:30:33,372 adding 'tests/test_sources_optional.py' 2026-04-13T08:30:33,374 adding 'tests/test_validation_and_edge_cases.py' 2026-04-13T08:30:33,375 adding 'tests/test_variant_expression_filters.py' 2026-04-13T08:30:33,377 adding 'tests/test_wide.py' 2026-04-13T08:30:33,379 adding 'topiary/__init__.py' 2026-04-13T08:30:33,380 adding 'topiary/filters.py' 2026-04-13T08:30:33,382 adding 'topiary/inputs.py' 2026-04-13T08:30:33,384 adding 'topiary/io.py' 2026-04-13T08:30:33,386 adding 'topiary/io_lens.py' 2026-04-13T08:30:33,389 adding 'topiary/predictor.py' 2026-04-13T08:30:33,391 adding 'topiary/properties.py' 2026-04-13T08:30:33,393 adding 'topiary/result.py' 2026-04-13T08:30:33,395 adding 'topiary/sequence_helpers.py' 2026-04-13T08:30:33,397 adding 'topiary/sources.py' 2026-04-13T08:30:33,399 adding 'topiary/wide.py' 2026-04-13T08:30:33,400 adding 'topiary/cli/__init__.py' 2026-04-13T08:30:33,403 adding 'topiary/cli/args.py' 2026-04-13T08:30:33,404 adding 'topiary/cli/errors.py' 2026-04-13T08:30:33,405 adding 'topiary/cli/filtering.py' 2026-04-13T08:30:33,407 adding 'topiary/cli/outputs.py' 2026-04-13T08:30:33,408 adding 'topiary/cli/protein_changes.py' 2026-04-13T08:30:33,409 adding 'topiary/cli/rna.py' 2026-04-13T08:30:33,410 adding 'topiary/cli/script.py' 2026-04-13T08:30:33,411 adding 'topiary/cli/sequence.py' 2026-04-13T08:30:33,413 adding 'topiary/ranking/__init__.py' 2026-04-13T08:30:33,415 adding 'topiary/ranking/apply.py' 2026-04-13T08:30:33,420 adding 'topiary/ranking/nodes.py' 2026-04-13T08:30:33,422 adding 'topiary/ranking/parser.py' 2026-04-13T08:30:33,424 adding 'topiary/rna/__init__.py' 2026-04-13T08:30:33,425 adding 'topiary/rna/common.py' 2026-04-13T08:30:33,427 adding 'topiary/rna/cufflinks.py' 2026-04-13T08:30:33,429 adding 'topiary/rna/expression_loader.py' 2026-04-13T08:30:33,430 adding 'topiary/rna/gtf.py' 2026-04-13T08:30:33,433 adding 'topiary-5.1.0.dist-info/licenses/LICENSE' 2026-04-13T08:30:33,436 adding 'topiary-5.1.0.dist-info/METADATA' 2026-04-13T08:30:33,437 adding 'topiary-5.1.0.dist-info/WHEEL' 2026-04-13T08:30:33,438 adding 'topiary-5.1.0.dist-info/entry_points.txt' 2026-04-13T08:30:33,439 adding 'topiary-5.1.0.dist-info/top_level.txt' 2026-04-13T08:30:33,440 adding 'topiary-5.1.0.dist-info/RECORD' 2026-04-13T08:30:33,444 removing build/bdist.linux-armv7l/wheel 2026-04-13T08:30:33,560 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-13T08:30:33,569 Created wheel for topiary: filename=topiary-5.1.0-py3-none-any.whl size=159710 sha256=87ce733f27cf1248d594d1bb081c678979826ff12ae413472d72ee3dec27c5c9 2026-04-13T08:30:33,570 Stored in directory: /tmp/pip-ephem-wheel-cache-fykkk316/wheels/12/e3/0f/04d02df20431f24afbf7f528a96dcc9370db393af9f6029545 2026-04-13T08:30:33,586 Successfully built topiary 2026-04-13T08:30:33,595 Removed build tracker: '/tmp/pip-build-tracker-y1ozzrg5'