2026-08-31T16:20:16,909 Created temporary directory: /tmp/pip-ephem-wheel-cache-k4wofoxe 2026-08-31T16:20:16,911 Created temporary directory: /tmp/pip-build-tracker-h57yi58q 2026-08-31T16:20:16,912 Initialized build tracking at /tmp/pip-build-tracker-h57yi58q 2026-08-31T16:20:16,912 Created build tracker: /tmp/pip-build-tracker-h57yi58q 2026-08-31T16:20:16,913 Entered build tracker: /tmp/pip-build-tracker-h57yi58q 2026-08-31T16:20:16,914 Created temporary directory: /tmp/pip-wheel-fkksmpxr 2026-08-31T16:20:16,916 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 2026-08-31T16:20:16,919 Created temporary directory: /tmp/pip-ephem-wheel-cache-riahs95w 2026-08-31T16:20:16,942 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-31T16:20:16,945 2 location(s) to search for versions of topiary: 2026-08-31T16:20:16,945 * https://pypi.org/simple/topiary/ 2026-08-31T16:20:16,945 * https://www.piwheels.org/simple/topiary/ 2026-08-31T16:20:16,946 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-08-31T16:20:16,947 Getting page https://pypi.org/simple/topiary/ 2026-08-31T16:20:16,948 Found index url https://pypi.org/simple 2026-08-31T16:20:17,185 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-08-31T16:20:17,213 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/) 2026-08-31T16:20:17,606 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.10-py3-none-any.whl#sha256=56bea0cecf1273a44cd2e51ad294714c41e0fb7d9cc0b16382709573c4ec9443 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:20:17,606 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.9-py3-none-any.whl#sha256=da4dc4334fdf5cb89b68356e11737c8dab86fd100b9c7979e95eac3dc58fbd6d (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:20:17,607 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.8-py3-none-any.whl#sha256=12b4f283d8fbedbd316649be8833a17fee852097f1e5cd8963264e6c4a2721e0 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:20:17,607 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.7-py3-none-any.whl#sha256=6e23dbd38e19c12b658a8373b501f1e929c6fd3420749dee506a82b60b190d42 (from https://www.piwheels.org/simple/topiary/) 2026-08-31T16:20:17,608 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/) 2026-08-31T16:20:17,608 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/) 2026-08-31T16:20:17,609 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/) 2026-08-31T16:20:17,610 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/) 2026-08-31T16:20:17,610 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/) 2026-08-31T16:20:17,610 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/) 2026-08-31T16:20:17,611 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/) 2026-08-31T16:20:17,611 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-08-31T16:20:17,612 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-08-31T16:20:17,642 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-08-31T16:20:17,660 Collecting topiary==5.28.2 2026-08-31T16:20:17,663 Created temporary directory: /tmp/pip-unpack-40xkafpc 2026-08-31T16:20:17,819 Downloading topiary-5.28.2.tar.gz (320 kB) 2026-08-31T16:20:18,183 Added topiary==5.28.2 from https://files.pythonhosted.org/packages/8c/ed/926ad93f9eaa3a6ca9276e1c0023b9204a065b7223008e89139ea3642aae/topiary-5.28.2.tar.gz to build tracker '/tmp/pip-build-tracker-h57yi58q' 2026-08-31T16:20:18,188 Created temporary directory: /tmp/pip-build-env-i1lj06u1 2026-08-31T16:20:18,192 Installing build dependencies: started 2026-08-31T16:20:18,194 Running command pip subprocess to install build dependencies 2026-08-31T16:20:19,318 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-08-31T16:20:19,740 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 2026-08-31T16:20:19,763 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-31T16:20:21,591 Collecting setuptools>=64 2026-08-31T16:20:21,592 Obtaining dependency information for setuptools>=64 from https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata 2026-08-31T16:20:21,607 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-08-31T16:20:21,853 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-31T16:20:21,936 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-31T16:20:24,711 Installing collected packages: setuptools 2026-08-31T16:20:27,221 Successfully installed setuptools-84.0.0 2026-08-31T16:20:27,530 Installing build dependencies: finished with status 'done' 2026-08-31T16:20:27,536 Getting requirements to build wheel: started 2026-08-31T16:20:27,538 Running command Getting requirements to build wheel 2026-08-31T16:20:28,240 /tmp/pip-build-env-i1lj06u1/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:20:28,240 !! 2026-08-31T16:20:28,241 ******************************************************************************** 2026-08-31T16:20:28,241 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:20:28,242 License :: OSI Approved :: Apache Software License 2026-08-31T16:20:28,243 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:20:28,244 ******************************************************************************** 2026-08-31T16:20:28,245 !! 2026-08-31T16:20:28,245 dist._finalize_license_expression() 2026-08-31T16:20:28,246 /tmp/pip-build-env-i1lj06u1/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:20:28,246 !! 2026-08-31T16:20:28,247 ******************************************************************************** 2026-08-31T16:20:28,247 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:20:28,248 License :: OSI Approved :: Apache Software License 2026-08-31T16:20:28,249 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:20:28,250 ******************************************************************************** 2026-08-31T16:20:28,251 !! 2026-08-31T16:20:28,252 self._finalize_license_expression() 2026-08-31T16:20:28,252 running egg_info 2026-08-31T16:20:28,258 writing topiary.egg-info/PKG-INFO 2026-08-31T16:20:28,262 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-08-31T16:20:28,265 writing entry points to topiary.egg-info/entry_points.txt 2026-08-31T16:20:28,266 writing requirements to topiary.egg-info/requires.txt 2026-08-31T16:20:28,268 writing top-level names to topiary.egg-info/top_level.txt 2026-08-31T16:20:28,297 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:20:28,304 adding license file 'LICENSE' 2026-08-31T16:20:28,312 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:20:28,411 Getting requirements to build wheel: finished with status 'done' 2026-08-31T16:20:28,414 Created temporary directory: /tmp/pip-modern-metadata-2l67x4jp 2026-08-31T16:20:28,416 Preparing metadata (pyproject.toml): started 2026-08-31T16:20:28,418 Running command Preparing metadata (pyproject.toml) 2026-08-31T16:20:29,068 /tmp/pip-build-env-i1lj06u1/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:20:29,068 !! 2026-08-31T16:20:29,069 ******************************************************************************** 2026-08-31T16:20:29,070 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:20:29,071 License :: OSI Approved :: Apache Software License 2026-08-31T16:20:29,072 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:20:29,072 ******************************************************************************** 2026-08-31T16:20:29,074 !! 2026-08-31T16:20:29,074 dist._finalize_license_expression() 2026-08-31T16:20:29,075 /tmp/pip-build-env-i1lj06u1/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:20:29,076 !! 2026-08-31T16:20:29,077 ******************************************************************************** 2026-08-31T16:20:29,077 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:20:29,078 License :: OSI Approved :: Apache Software License 2026-08-31T16:20:29,079 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:20:29,080 ******************************************************************************** 2026-08-31T16:20:29,081 !! 2026-08-31T16:20:29,081 self._finalize_license_expression() 2026-08-31T16:20:29,082 running dist_info 2026-08-31T16:20:29,090 creating /tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info 2026-08-31T16:20:29,091 writing /tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/PKG-INFO 2026-08-31T16:20:29,095 writing dependency_links to /tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/dependency_links.txt 2026-08-31T16:20:29,096 writing entry points to /tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/entry_points.txt 2026-08-31T16:20:29,098 writing requirements to /tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/requires.txt 2026-08-31T16:20:29,099 writing top-level names to /tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/top_level.txt 2026-08-31T16:20:29,100 writing manifest file '/tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/SOURCES.txt' 2026-08-31T16:20:29,127 reading manifest file '/tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/SOURCES.txt' 2026-08-31T16:20:29,129 adding license file 'LICENSE' 2026-08-31T16:20:29,135 writing manifest file '/tmp/pip-modern-metadata-2l67x4jp/topiary.egg-info/SOURCES.txt' 2026-08-31T16:20:29,136 creating '/tmp/pip-modern-metadata-2l67x4jp/topiary-5.28.2.dist-info' 2026-08-31T16:20:29,261 Preparing metadata (pyproject.toml): finished with status 'done' 2026-08-31T16:20:29,268 Source in /tmp/pip-wheel-fkksmpxr/topiary_3cd0bf285a2d450cadc8448c4e611055 has version 5.28.2, which satisfies requirement topiary==5.28.2 from https://files.pythonhosted.org/packages/8c/ed/926ad93f9eaa3a6ca9276e1c0023b9204a065b7223008e89139ea3642aae/topiary-5.28.2.tar.gz 2026-08-31T16:20:29,269 Removed topiary==5.28.2 from https://files.pythonhosted.org/packages/8c/ed/926ad93f9eaa3a6ca9276e1c0023b9204a065b7223008e89139ea3642aae/topiary-5.28.2.tar.gz from build tracker '/tmp/pip-build-tracker-h57yi58q' 2026-08-31T16:20:29,277 Created temporary directory: /tmp/pip-unpack-uuxhde1q 2026-08-31T16:20:29,278 Building wheels for collected packages: topiary 2026-08-31T16:20:29,282 Created temporary directory: /tmp/pip-wheel-o2850r06 2026-08-31T16:20:29,283 Destination directory: /tmp/pip-wheel-o2850r06 2026-08-31T16:20:29,285 Building wheel for topiary (pyproject.toml): started 2026-08-31T16:20:29,286 Running command Building wheel for topiary (pyproject.toml) 2026-08-31T16:20:29,939 /tmp/pip-build-env-i1lj06u1/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:20:29,939 !! 2026-08-31T16:20:29,940 ******************************************************************************** 2026-08-31T16:20:29,941 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:20:29,943 License :: OSI Approved :: Apache Software License 2026-08-31T16:20:29,944 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:20:29,945 ******************************************************************************** 2026-08-31T16:20:29,947 !! 2026-08-31T16:20:29,948 dist._finalize_license_expression() 2026-08-31T16:20:29,949 /tmp/pip-build-env-i1lj06u1/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-31T16:20:29,950 !! 2026-08-31T16:20:29,952 ******************************************************************************** 2026-08-31T16:20:29,952 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-31T16:20:29,953 License :: OSI Approved :: Apache Software License 2026-08-31T16:20:29,954 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-31T16:20:29,954 ******************************************************************************** 2026-08-31T16:20:29,955 !! 2026-08-31T16:20:29,956 self._finalize_license_expression() 2026-08-31T16:20:29,956 running bdist_wheel 2026-08-31T16:20:29,968 running build 2026-08-31T16:20:29,969 running build_py 2026-08-31T16:20:29,976 creating build/lib/topiary 2026-08-31T16:20:29,978 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-08-31T16:20:29,980 copying topiary/__init__.py -> build/lib/topiary 2026-08-31T16:20:29,982 copying topiary/self_proteome.py -> build/lib/topiary 2026-08-31T16:20:29,985 copying topiary/inputs.py -> build/lib/topiary 2026-08-31T16:20:29,987 copying topiary/protein_fragment.py -> build/lib/topiary 2026-08-31T16:20:29,990 copying topiary/result.py -> build/lib/topiary 2026-08-31T16:20:29,993 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-08-31T16:20:29,995 copying topiary/properties.py -> build/lib/topiary 2026-08-31T16:20:29,998 copying topiary/filters.py -> build/lib/topiary 2026-08-31T16:20:30,000 copying topiary/wide.py -> build/lib/topiary 2026-08-31T16:20:30,002 copying topiary/io_lens.py -> build/lib/topiary 2026-08-31T16:20:30,005 copying topiary/sources.py -> build/lib/topiary 2026-08-31T16:20:30,007 copying topiary/predictor.py -> build/lib/topiary 2026-08-31T16:20:30,010 copying topiary/io.py -> build/lib/topiary 2026-08-31T16:20:30,013 copying topiary/cached.py -> build/lib/topiary 2026-08-31T16:20:30,018 copying topiary/io_pvacseq.py -> build/lib/topiary 2026-08-31T16:20:30,026 creating build/lib/tests 2026-08-31T16:20:30,027 copying tests/test_sort_ordering.py -> build/lib/tests 2026-08-31T16:20:30,031 copying tests/test_cli_ranking.py -> build/lib/tests 2026-08-31T16:20:30,035 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-08-31T16:20:30,036 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-08-31T16:20:30,040 copying tests/__init__.py -> build/lib/tests 2026-08-31T16:20:30,042 copying tests/test_lazy_imports.py -> build/lib/tests 2026-08-31T16:20:30,045 copying tests/test_self_proteome.py -> build/lib/tests 2026-08-31T16:20:30,048 copying tests/test_peptide_property_node.py -> build/lib/tests 2026-08-31T16:20:30,050 copying tests/test_allele_set.py -> build/lib/tests 2026-08-31T16:20:30,052 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-08-31T16:20:30,054 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-08-31T16:20:30,056 copying tests/test_protein_fragment.py -> build/lib/tests 2026-08-31T16:20:30,059 copying tests/test_cli_coverage.py -> build/lib/tests 2026-08-31T16:20:30,061 copying tests/test_kind_mhc_dependence.py -> build/lib/tests 2026-08-31T16:20:30,064 copying tests/test_group_keys.py -> build/lib/tests 2026-08-31T16:20:30,066 copying tests/common.py -> build/lib/tests 2026-08-31T16:20:30,068 copying tests/test_io_pvacseq.py -> build/lib/tests 2026-08-31T16:20:30,071 copying tests/test_allele_class.py -> build/lib/tests 2026-08-31T16:20:30,073 copying tests/test_end_to_end.py -> build/lib/tests 2026-08-31T16:20:30,075 copying tests/test_predictor_internals.py -> build/lib/tests 2026-08-31T16:20:30,077 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-08-31T16:20:30,079 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-08-31T16:20:30,082 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-08-31T16:20:30,084 copying tests/test_deploy_script.py -> build/lib/tests 2026-08-31T16:20:30,086 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-08-31T16:20:30,087 copying tests/test_scoped_filters.py -> build/lib/tests 2026-08-31T16:20:30,089 copying tests/test_canonical_methods.py -> build/lib/tests 2026-08-31T16:20:30,091 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-08-31T16:20:30,094 copying tests/test_peptide_view.py -> build/lib/tests 2026-08-31T16:20:30,097 copying tests/test_expression_integration.py -> build/lib/tests 2026-08-31T16:20:30,099 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-08-31T16:20:30,101 copying tests/test_wide.py -> build/lib/tests 2026-08-31T16:20:30,104 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-08-31T16:20:30,106 copying tests/test_dsl_polish.py -> build/lib/tests 2026-08-31T16:20:30,108 copying tests/data.py -> build/lib/tests 2026-08-31T16:20:30,110 copying tests/test_expression_loader.py -> build/lib/tests 2026-08-31T16:20:30,112 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-08-31T16:20:30,114 copying tests/test_result.py -> build/lib/tests 2026-08-31T16:20:30,117 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-08-31T16:20:30,118 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-08-31T16:20:30,120 copying tests/test_dataframe.py -> build/lib/tests 2026-08-31T16:20:30,122 copying tests/test_from_predictions.py -> build/lib/tests 2026-08-31T16:20:30,124 copying tests/test_combine_predictor_results.py -> build/lib/tests 2026-08-31T16:20:30,127 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-08-31T16:20:30,128 copying tests/test_best_allele.py -> build/lib/tests 2026-08-31T16:20:30,131 copying tests/test_inputs.py -> build/lib/tests 2026-08-31T16:20:30,133 copying tests/test_kind_support.py -> build/lib/tests 2026-08-31T16:20:30,135 copying tests/test_cli_script.py -> build/lib/tests 2026-08-31T16:20:30,137 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-08-31T16:20:30,139 copying tests/test_io_lens.py -> build/lib/tests 2026-08-31T16:20:30,141 copying tests/test_sources.py -> build/lib/tests 2026-08-31T16:20:30,143 copying tests/test_ranking.py -> build/lib/tests 2026-08-31T16:20:30,147 copying tests/test_sources_optional.py -> build/lib/tests 2026-08-31T16:20:30,149 copying tests/test_self_nearest_population.py -> build/lib/tests 2026-08-31T16:20:30,151 copying tests/test_cached_predictor.py -> build/lib/tests 2026-08-31T16:20:30,154 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-08-31T16:20:30,156 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-08-31T16:20:30,158 copying tests/test_integration.py -> build/lib/tests 2026-08-31T16:20:30,160 copying tests/test_allele_free_kinds.py -> build/lib/tests 2026-08-31T16:20:30,163 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-08-31T16:20:30,165 copying tests/test_lens_versions.py -> build/lib/tests 2026-08-31T16:20:30,167 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-08-31T16:20:30,169 copying tests/test_padding.py -> build/lib/tests 2026-08-31T16:20:30,171 copying tests/test_args_outputs.py -> build/lib/tests 2026-08-31T16:20:30,173 copying tests/test_io.py -> build/lib/tests 2026-08-31T16:20:30,175 copying tests/test_rna_helpers.py -> build/lib/tests 2026-08-31T16:20:30,177 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-08-31T16:20:30,180 copying tests/test_lens_multi_version.py -> build/lib/tests 2026-08-31T16:20:30,183 creating build/lib/topiary/ranking 2026-08-31T16:20:30,184 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-08-31T16:20:30,187 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-08-31T16:20:30,189 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-08-31T16:20:30,191 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-08-31T16:20:30,195 creating build/lib/topiary/cli 2026-08-31T16:20:30,196 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-08-31T16:20:30,198 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-08-31T16:20:30,200 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-08-31T16:20:30,202 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-08-31T16:20:30,205 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-08-31T16:20:30,206 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-08-31T16:20:30,209 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-08-31T16:20:30,211 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-08-31T16:20:30,213 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-08-31T16:20:30,215 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-08-31T16:20:30,217 creating build/lib/topiary/rna 2026-08-31T16:20:30,218 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-08-31T16:20:30,220 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-08-31T16:20:30,222 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-08-31T16:20:30,224 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-08-31T16:20:30,226 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-08-31T16:20:30,228 running egg_info 2026-08-31T16:20:30,237 writing topiary.egg-info/PKG-INFO 2026-08-31T16:20:30,241 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-08-31T16:20:30,242 writing entry points to topiary.egg-info/entry_points.txt 2026-08-31T16:20:30,244 writing requirements to topiary.egg-info/requires.txt 2026-08-31T16:20:30,245 writing top-level names to topiary.egg-info/top_level.txt 2026-08-31T16:20:30,262 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:20:30,270 adding license file 'LICENSE' 2026-08-31T16:20:30,277 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-08-31T16:20:30,296 installing to build/bdist.linux-armv7l/wheel 2026-08-31T16:20:30,296 running install 2026-08-31T16:20:30,318 running install_lib 2026-08-31T16:20:30,324 creating build/bdist.linux-armv7l/wheel 2026-08-31T16:20:30,327 creating build/bdist.linux-armv7l/wheel/topiary 2026-08-31T16:20:30,328 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,330 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,332 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,335 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,338 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-08-31T16:20:30,339 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:20:30,342 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:20:30,344 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:20:30,347 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-08-31T16:20:30,351 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,354 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,357 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,359 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,362 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,364 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,367 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,369 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,372 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,375 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,377 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,381 copying build/lib/topiary/io_pvacseq.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-08-31T16:20:30,384 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-08-31T16:20:30,385 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,387 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,389 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,391 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,394 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,396 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,398 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,401 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,403 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,405 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-08-31T16:20:30,408 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-08-31T16:20:30,409 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:20:30,411 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:20:30,413 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:20:30,415 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:20:30,418 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-08-31T16:20:30,422 creating build/bdist.linux-armv7l/wheel/tests 2026-08-31T16:20:30,423 copying build/lib/tests/test_sort_ordering.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,425 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,428 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,430 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,433 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,434 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,436 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,439 copying build/lib/tests/test_peptide_property_node.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,441 copying build/lib/tests/test_allele_set.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,444 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,446 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,448 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,451 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,453 copying build/lib/tests/test_kind_mhc_dependence.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,456 copying build/lib/tests/test_group_keys.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,459 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,461 copying build/lib/tests/test_io_pvacseq.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,464 copying build/lib/tests/test_allele_class.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,467 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,469 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,471 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,473 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,476 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,478 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,480 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,482 copying build/lib/tests/test_scoped_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,485 copying build/lib/tests/test_canonical_methods.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,487 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,491 copying build/lib/tests/test_peptide_view.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,496 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,498 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,501 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,504 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,508 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,510 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,512 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,514 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,517 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,519 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,521 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,523 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,525 copying build/lib/tests/test_from_predictions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,528 copying build/lib/tests/test_combine_predictor_results.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,530 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,532 copying build/lib/tests/test_best_allele.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,535 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,537 copying build/lib/tests/test_kind_support.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,540 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,542 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,544 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,547 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,549 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,552 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,554 copying build/lib/tests/test_self_nearest_population.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,557 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,560 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,561 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,564 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,566 copying build/lib/tests/test_allele_free_kinds.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,568 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,570 copying build/lib/tests/test_lens_versions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,572 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,574 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,575 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,577 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,580 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,581 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,584 copying build/lib/tests/test_lens_multi_version.py -> build/bdist.linux-armv7l/wheel/./tests 2026-08-31T16:20:30,586 running install_egg_info 2026-08-31T16:20:30,591 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.28.2-py3.11.egg-info 2026-08-31T16:20:30,603 running install_scripts 2026-08-31T16:20:30,616 creating build/bdist.linux-armv7l/wheel/topiary-5.28.2.dist-info/WHEEL 2026-08-31T16:20:30,619 creating '/tmp/pip-wheel-o2850r06/.tmp-bf9vi9z8/topiary-5.28.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-08-31T16:20:30,623 adding 'tests/__init__.py' 2026-08-31T16:20:30,624 adding 'tests/common.py' 2026-08-31T16:20:30,625 adding 'tests/data.py' 2026-08-31T16:20:30,627 adding 'tests/test_allele_class.py' 2026-08-31T16:20:30,629 adding 'tests/test_allele_free_kinds.py' 2026-08-31T16:20:30,631 adding 'tests/test_allele_set.py' 2026-08-31T16:20:30,632 adding 'tests/test_args_outputs.py' 2026-08-31T16:20:30,635 adding 'tests/test_best_allele.py' 2026-08-31T16:20:30,639 adding 'tests/test_cached_predictor.py' 2026-08-31T16:20:30,641 adding 'tests/test_canonical_methods.py' 2026-08-31T16:20:30,643 adding 'tests/test_cli_cached_predictor.py' 2026-08-31T16:20:30,644 adding 'tests/test_cli_coverage.py' 2026-08-31T16:20:30,646 adding 'tests/test_cli_protein_changes.py' 2026-08-31T16:20:30,648 adding 'tests/test_cli_ranking.py' 2026-08-31T16:20:30,649 adding 'tests/test_cli_script.py' 2026-08-31T16:20:30,652 adding 'tests/test_combine_predictor_results.py' 2026-08-31T16:20:30,653 adding 'tests/test_contains_mutant_residues.py' 2026-08-31T16:20:30,656 adding 'tests/test_coverage_gaps.py' 2026-08-31T16:20:30,657 adding 'tests/test_dataframe.py' 2026-08-31T16:20:30,658 adding 'tests/test_deploy_script.py' 2026-08-31T16:20:30,659 adding 'tests/test_direct_input_regressions.py' 2026-08-31T16:20:30,662 adding 'tests/test_dsl_extensions.py' 2026-08-31T16:20:30,664 adding 'tests/test_dsl_polish.py' 2026-08-31T16:20:30,667 adding 'tests/test_dsl_roundtrip.py' 2026-08-31T16:20:30,669 adding 'tests/test_edge_case_fixtures.py' 2026-08-31T16:20:30,670 adding 'tests/test_effect_expression_filters.py' 2026-08-31T16:20:30,671 adding 'tests/test_end_to_end.py' 2026-08-31T16:20:30,673 adding 'tests/test_epitopes_from_commandline_args.py' 2026-08-31T16:20:30,674 adding 'tests/test_expression_integration.py' 2026-08-31T16:20:30,675 adding 'tests/test_expression_loader.py' 2026-08-31T16:20:30,679 adding 'tests/test_frameshift_fragments.py' 2026-08-31T16:20:30,682 adding 'tests/test_from_predictions.py' 2026-08-31T16:20:30,685 adding 'tests/test_group_keys.py' 2026-08-31T16:20:30,687 adding 'tests/test_inputs.py' 2026-08-31T16:20:30,689 adding 'tests/test_integration.py' 2026-08-31T16:20:30,692 adding 'tests/test_io.py' 2026-08-31T16:20:30,695 adding 'tests/test_io_lens.py' 2026-08-31T16:20:30,699 adding 'tests/test_io_pvacseq.py' 2026-08-31T16:20:30,701 adding 'tests/test_kind_mhc_dependence.py' 2026-08-31T16:20:30,704 adding 'tests/test_kind_support.py' 2026-08-31T16:20:30,705 adding 'tests/test_lazy_imports.py' 2026-08-31T16:20:30,708 adding 'tests/test_lens_multi_version.py' 2026-08-31T16:20:30,710 adding 'tests/test_lens_versions.py' 2026-08-31T16:20:30,711 adding 'tests/test_load_cufflinks_fpkm.py' 2026-08-31T16:20:30,713 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-08-31T16:20:30,715 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-08-31T16:20:30,716 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-08-31T16:20:30,718 adding 'tests/test_padding.py' 2026-08-31T16:20:30,719 adding 'tests/test_peptide_mutation_interval.py' 2026-08-31T16:20:30,721 adding 'tests/test_peptide_property_node.py' 2026-08-31T16:20:30,726 adding 'tests/test_peptide_view.py' 2026-08-31T16:20:30,730 adding 'tests/test_predict_from_fragments.py' 2026-08-31T16:20:30,733 adding 'tests/test_predict_from_variants_refactor.py' 2026-08-31T16:20:30,736 adding 'tests/test_predictor_internals.py' 2026-08-31T16:20:30,739 adding 'tests/test_protein_fragment.py' 2026-08-31T16:20:30,752 adding 'tests/test_ranking.py' 2026-08-31T16:20:30,757 adding 'tests/test_result.py' 2026-08-31T16:20:30,758 adding 'tests/test_rna_helpers.py' 2026-08-31T16:20:30,760 adding 'tests/test_scoped_filters.py' 2026-08-31T16:20:30,762 adding 'tests/test_self_nearest_population.py' 2026-08-31T16:20:30,766 adding 'tests/test_self_proteome.py' 2026-08-31T16:20:30,768 adding 'tests/test_sequence_helpers.py' 2026-08-31T16:20:30,770 adding 'tests/test_sort_ordering.py' 2026-08-31T16:20:30,771 adding 'tests/test_sources.py' 2026-08-31T16:20:30,773 adding 'tests/test_sources_optional.py' 2026-08-31T16:20:30,776 adding 'tests/test_validation_and_edge_cases.py' 2026-08-31T16:20:30,778 adding 'tests/test_variant_expression_filters.py' 2026-08-31T16:20:30,780 adding 'tests/test_wide.py' 2026-08-31T16:20:30,782 adding 'topiary/__init__.py' 2026-08-31T16:20:30,788 adding 'topiary/cached.py' 2026-08-31T16:20:30,790 adding 'topiary/filters.py' 2026-08-31T16:20:30,791 adding 'topiary/inputs.py' 2026-08-31T16:20:30,793 adding 'topiary/io.py' 2026-08-31T16:20:30,796 adding 'topiary/io_lens.py' 2026-08-31T16:20:30,798 adding 'topiary/io_protein_fragment.py' 2026-08-31T16:20:30,801 adding 'topiary/io_pvacseq.py' 2026-08-31T16:20:30,809 adding 'topiary/predictor.py' 2026-08-31T16:20:30,811 adding 'topiary/properties.py' 2026-08-31T16:20:30,814 adding 'topiary/protein_fragment.py' 2026-08-31T16:20:30,818 adding 'topiary/result.py' 2026-08-31T16:20:30,822 adding 'topiary/self_proteome.py' 2026-08-31T16:20:30,824 adding 'topiary/sequence_helpers.py' 2026-08-31T16:20:30,825 adding 'topiary/sources.py' 2026-08-31T16:20:30,828 adding 'topiary/wide.py' 2026-08-31T16:20:30,830 adding 'topiary/cli/__init__.py' 2026-08-31T16:20:30,832 adding 'topiary/cli/args.py' 2026-08-31T16:20:30,835 adding 'topiary/cli/cached_predictor.py' 2026-08-31T16:20:30,836 adding 'topiary/cli/errors.py' 2026-08-31T16:20:30,837 adding 'topiary/cli/filtering.py' 2026-08-31T16:20:30,839 adding 'topiary/cli/outputs.py' 2026-08-31T16:20:30,840 adding 'topiary/cli/protein_changes.py' 2026-08-31T16:20:30,841 adding 'topiary/cli/rna.py' 2026-08-31T16:20:30,843 adding 'topiary/cli/script.py' 2026-08-31T16:20:30,844 adding 'topiary/cli/sequence.py' 2026-08-31T16:20:30,846 adding 'topiary/ranking/__init__.py' 2026-08-31T16:20:30,848 adding 'topiary/ranking/apply.py' 2026-08-31T16:20:30,863 adding 'topiary/ranking/nodes.py' 2026-08-31T16:20:30,867 adding 'topiary/ranking/parser.py' 2026-08-31T16:20:30,869 adding 'topiary/rna/__init__.py' 2026-08-31T16:20:30,870 adding 'topiary/rna/common.py' 2026-08-31T16:20:30,871 adding 'topiary/rna/cufflinks.py' 2026-08-31T16:20:30,873 adding 'topiary/rna/expression_loader.py' 2026-08-31T16:20:30,875 adding 'topiary/rna/gtf.py' 2026-08-31T16:20:30,878 adding 'topiary-5.28.2.dist-info/licenses/LICENSE' 2026-08-31T16:20:30,881 adding 'topiary-5.28.2.dist-info/METADATA' 2026-08-31T16:20:30,882 adding 'topiary-5.28.2.dist-info/WHEEL' 2026-08-31T16:20:30,883 adding 'topiary-5.28.2.dist-info/entry_points.txt' 2026-08-31T16:20:30,884 adding 'topiary-5.28.2.dist-info/top_level.txt' 2026-08-31T16:20:30,886 adding 'topiary-5.28.2.dist-info/RECORD' 2026-08-31T16:20:30,892 removing build/bdist.linux-armv7l/wheel 2026-08-31T16:20:31,017 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-08-31T16:20:31,035 Created wheel for topiary: filename=topiary-5.28.2-py3-none-any.whl size=357808 sha256=704676abb52a8cbaec52caca4ec79dcd610234390395cd0c428afc64fe520ff8 2026-08-31T16:20:31,036 Stored in directory: /tmp/pip-ephem-wheel-cache-riahs95w/wheels/9d/0e/6c/e97be44242962db7454c8d4bde96272860986feb8a070fb4b3 2026-08-31T16:20:31,054 Successfully built topiary 2026-08-31T16:20:31,076 Removed build tracker: '/tmp/pip-build-tracker-h57yi58q'