2026-04-13T21:13:55,816 Created temporary directory: /tmp/pip-ephem-wheel-cache-xr792zgi 2026-04-13T21:13:55,817 Created temporary directory: /tmp/pip-build-tracker-9atn1agn 2026-04-13T21:13:55,818 Initialized build tracking at /tmp/pip-build-tracker-9atn1agn 2026-04-13T21:13:55,818 Created build tracker: /tmp/pip-build-tracker-9atn1agn 2026-04-13T21:13:55,819 Entered build tracker: /tmp/pip-build-tracker-9atn1agn 2026-04-13T21:13:55,820 Created temporary directory: /tmp/pip-wheel-1thkuztb 2026-04-13T21:13:55,822 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 2026-04-13T21:13:55,825 Created temporary directory: /tmp/pip-ephem-wheel-cache-rq33sr45 2026-04-13T21:13:55,846 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-13T21:13:55,850 2 location(s) to search for versions of topiary: 2026-04-13T21:13:55,850 * https://pypi.org/simple/topiary/ 2026-04-13T21:13:55,850 * https://www.piwheels.org/simple/topiary/ 2026-04-13T21:13:55,851 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-04-13T21:13:55,851 Getting page https://pypi.org/simple/topiary/ 2026-04-13T21:13:55,853 Found index url https://pypi.org/simple 2026-04-13T21:13:56,085 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-04-13T21:13:56,100 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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https://archive1.piwheels.org/simple/topiary/topiary-0.0.9-py3-none-any.whl#sha256=da4dc4334fdf5cb89b68356e11737c8dab86fd100b9c7979e95eac3dc58fbd6d (from https://www.piwheels.org/simple/topiary/) 2026-04-13T21:13:56,382 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/) 2026-04-13T21:13:56,382 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/) 2026-04-13T21:13:56,382 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.6-py3-none-any.whl#sha256=f3b597a0744c3a7540c3ffe571b8f4fad3d2ad40ddc6198952e2aee7c96ff82c (from https://www.piwheels.org/simple/topiary/) 2026-04-13T21:13:56,383 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/) 2026-04-13T21:13:56,384 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/) 2026-04-13T21:13:56,384 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/) 2026-04-13T21:13:56,385 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/) 2026-04-13T21:13:56,386 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/) 2026-04-13T21:13:56,386 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/) 2026-04-13T21:13:56,387 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-13T21:13:56,387 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-13T21:13:56,414 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-13T21:13:56,434 Collecting topiary==5.2.0 2026-04-13T21:13:56,436 Created temporary directory: /tmp/pip-unpack-y8035zim 2026-04-13T21:13:56,665 Downloading topiary-5.2.0.tar.gz (152 kB) 2026-04-13T21:13:56,917 Added topiary==5.2.0 from https://files.pythonhosted.org/packages/a9/8a/6fe9aafba71adbf1e1392887ffb31d6301f062039efaed2321edd1b30408/topiary-5.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-9atn1agn' 2026-04-13T21:13:56,922 Created temporary directory: /tmp/pip-build-env-tbt76equ 2026-04-13T21:13:56,926 Installing build dependencies: started 2026-04-13T21:13:56,927 Running command pip subprocess to install build dependencies 2026-04-13T21:13:58,069 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-13T21:13:58,507 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 2026-04-13T21:13:58,530 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-13T21:14:00,294 Collecting setuptools>=64 2026-04-13T21:14:00,384 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-13T21:14:03,342 Installing collected packages: setuptools 2026-04-13T21:14:06,366 Successfully installed setuptools-82.0.1 2026-04-13T21:14:06,634 Installing build dependencies: finished with status 'done' 2026-04-13T21:14:06,640 Getting requirements to build wheel: started 2026-04-13T21:14:06,641 Running command Getting requirements to build wheel 2026-04-13T21:14:07,335 /tmp/pip-build-env-tbt76equ/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T21:14:07,335 !! 2026-04-13T21:14:07,337 ******************************************************************************** 2026-04-13T21:14:07,337 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T21:14:07,338 License :: OSI Approved :: Apache Software License 2026-04-13T21:14:07,340 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T21:14:07,340 ******************************************************************************** 2026-04-13T21:14:07,341 !! 2026-04-13T21:14:07,342 dist._finalize_license_expression() 2026-04-13T21:14:07,342 /tmp/pip-build-env-tbt76equ/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T21:14:07,343 !! 2026-04-13T21:14:07,344 ******************************************************************************** 2026-04-13T21:14:07,345 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T21:14:07,346 License :: OSI Approved :: Apache Software License 2026-04-13T21:14:07,347 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T21:14:07,348 ******************************************************************************** 2026-04-13T21:14:07,349 !! 2026-04-13T21:14:07,350 self._finalize_license_expression() 2026-04-13T21:14:07,350 running egg_info 2026-04-13T21:14:07,355 writing topiary.egg-info/PKG-INFO 2026-04-13T21:14:07,359 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-13T21:14:07,361 writing entry points to topiary.egg-info/entry_points.txt 2026-04-13T21:14:07,363 writing requirements to topiary.egg-info/requires.txt 2026-04-13T21:14:07,364 writing top-level names to topiary.egg-info/top_level.txt 2026-04-13T21:14:07,391 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T21:14:07,397 adding license file 'LICENSE' 2026-04-13T21:14:07,403 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T21:14:07,500 Getting requirements to build wheel: finished with status 'done' 2026-04-13T21:14:07,504 Created temporary directory: /tmp/pip-modern-metadata-6stz59ir 2026-04-13T21:14:07,506 Preparing metadata (pyproject.toml): started 2026-04-13T21:14:07,507 Running command Preparing metadata (pyproject.toml) 2026-04-13T21:14:08,150 /tmp/pip-build-env-tbt76equ/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T21:14:08,150 !! 2026-04-13T21:14:08,151 ******************************************************************************** 2026-04-13T21:14:08,152 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T21:14:08,153 License :: OSI Approved :: Apache Software License 2026-04-13T21:14:08,153 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T21:14:08,154 ******************************************************************************** 2026-04-13T21:14:08,155 !! 2026-04-13T21:14:08,155 dist._finalize_license_expression() 2026-04-13T21:14:08,156 /tmp/pip-build-env-tbt76equ/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T21:14:08,156 !! 2026-04-13T21:14:08,158 ******************************************************************************** 2026-04-13T21:14:08,158 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T21:14:08,159 License :: OSI Approved :: Apache Software License 2026-04-13T21:14:08,160 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T21:14:08,161 ******************************************************************************** 2026-04-13T21:14:08,162 !! 2026-04-13T21:14:08,162 self._finalize_license_expression() 2026-04-13T21:14:08,163 running dist_info 2026-04-13T21:14:08,172 creating /tmp/pip-modern-metadata-6stz59ir/topiary.egg-info 2026-04-13T21:14:08,173 writing /tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/PKG-INFO 2026-04-13T21:14:08,177 writing dependency_links to /tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/dependency_links.txt 2026-04-13T21:14:08,179 writing entry points to /tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/entry_points.txt 2026-04-13T21:14:08,180 writing requirements to /tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/requires.txt 2026-04-13T21:14:08,181 writing top-level names to /tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/top_level.txt 2026-04-13T21:14:08,183 writing manifest file '/tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/SOURCES.txt' 2026-04-13T21:14:08,207 reading manifest file '/tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/SOURCES.txt' 2026-04-13T21:14:08,209 adding license file 'LICENSE' 2026-04-13T21:14:08,214 writing manifest file '/tmp/pip-modern-metadata-6stz59ir/topiary.egg-info/SOURCES.txt' 2026-04-13T21:14:08,215 creating '/tmp/pip-modern-metadata-6stz59ir/topiary-5.2.0.dist-info' 2026-04-13T21:14:08,342 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-13T21:14:08,348 Source in /tmp/pip-wheel-1thkuztb/topiary_e2b985ff2241452f9e46e14d24a1d332 has version 5.2.0, which satisfies requirement topiary==5.2.0 from https://files.pythonhosted.org/packages/a9/8a/6fe9aafba71adbf1e1392887ffb31d6301f062039efaed2321edd1b30408/topiary-5.2.0.tar.gz 2026-04-13T21:14:08,349 Removed topiary==5.2.0 from https://files.pythonhosted.org/packages/a9/8a/6fe9aafba71adbf1e1392887ffb31d6301f062039efaed2321edd1b30408/topiary-5.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-9atn1agn' 2026-04-13T21:14:08,357 Created temporary directory: /tmp/pip-unpack-c2ymwh0l 2026-04-13T21:14:08,358 Building wheels for collected packages: topiary 2026-04-13T21:14:08,362 Created temporary directory: /tmp/pip-wheel-br3wcksc 2026-04-13T21:14:08,363 Destination directory: /tmp/pip-wheel-br3wcksc 2026-04-13T21:14:08,364 Building wheel for topiary (pyproject.toml): started 2026-04-13T21:14:08,366 Running command Building wheel for topiary (pyproject.toml) 2026-04-13T21:14:09,011 /tmp/pip-build-env-tbt76equ/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T21:14:09,011 !! 2026-04-13T21:14:09,012 ******************************************************************************** 2026-04-13T21:14:09,012 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T21:14:09,013 License :: OSI Approved :: Apache Software License 2026-04-13T21:14:09,014 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T21:14:09,015 ******************************************************************************** 2026-04-13T21:14:09,016 !! 2026-04-13T21:14:09,016 dist._finalize_license_expression() 2026-04-13T21:14:09,017 /tmp/pip-build-env-tbt76equ/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-13T21:14:09,017 !! 2026-04-13T21:14:09,019 ******************************************************************************** 2026-04-13T21:14:09,019 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-13T21:14:09,020 License :: OSI Approved :: Apache Software License 2026-04-13T21:14:09,021 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-13T21:14:09,022 ******************************************************************************** 2026-04-13T21:14:09,023 !! 2026-04-13T21:14:09,023 self._finalize_license_expression() 2026-04-13T21:14:09,024 running bdist_wheel 2026-04-13T21:14:09,037 running build 2026-04-13T21:14:09,037 running build_py 2026-04-13T21:14:09,043 creating build/lib/topiary 2026-04-13T21:14:09,046 copying topiary/wide.py -> build/lib/topiary 2026-04-13T21:14:09,048 copying topiary/predictor.py -> build/lib/topiary 2026-04-13T21:14:09,051 copying topiary/antigen.py -> build/lib/topiary 2026-04-13T21:14:09,054 copying topiary/io_lens.py -> build/lib/topiary 2026-04-13T21:14:09,056 copying topiary/__init__.py -> build/lib/topiary 2026-04-13T21:14:09,058 copying topiary/io.py -> build/lib/topiary 2026-04-13T21:14:09,060 copying topiary/sources.py -> build/lib/topiary 2026-04-13T21:14:09,063 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-13T21:14:09,065 copying topiary/result.py -> build/lib/topiary 2026-04-13T21:14:09,068 copying topiary/io_antigen.py -> build/lib/topiary 2026-04-13T21:14:09,070 copying topiary/filters.py -> build/lib/topiary 2026-04-13T21:14:09,072 copying topiary/properties.py -> build/lib/topiary 2026-04-13T21:14:09,075 copying topiary/inputs.py -> build/lib/topiary 2026-04-13T21:14:09,079 creating build/lib/tests 2026-04-13T21:14:09,080 copying tests/test_antigen.py -> build/lib/tests 2026-04-13T21:14:09,082 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-13T21:14:09,085 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-13T21:14:09,087 copying tests/test_sources.py -> build/lib/tests 2026-04-13T21:14:09,089 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-13T21:14:09,091 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-13T21:14:09,093 copying tests/common.py -> build/lib/tests 2026-04-13T21:14:09,095 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-13T21:14:09,097 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-13T21:14:09,099 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-13T21:14:09,101 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-13T21:14:09,103 copying tests/test_result.py -> build/lib/tests 2026-04-13T21:14:09,106 copying tests/__init__.py -> build/lib/tests 2026-04-13T21:14:09,108 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-13T21:14:09,109 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-13T21:14:09,112 copying tests/data.py -> build/lib/tests 2026-04-13T21:14:09,114 copying tests/test_ranking.py -> build/lib/tests 2026-04-13T21:14:09,117 copying tests/test_inputs.py -> build/lib/tests 2026-04-13T21:14:09,119 copying tests/test_wide.py -> build/lib/tests 2026-04-13T21:14:09,122 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-04-13T21:14:09,124 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-13T21:14:09,126 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-13T21:14:09,128 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-13T21:14:09,130 copying tests/test_io_lens.py -> build/lib/tests 2026-04-13T21:14:09,133 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-13T21:14:09,135 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-13T21:14:09,137 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-13T21:14:09,139 copying tests/test_integration.py -> build/lib/tests 2026-04-13T21:14:09,141 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-13T21:14:09,143 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-13T21:14:09,145 copying tests/test_predict_from_antigens.py -> build/lib/tests 2026-04-13T21:14:09,147 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-13T21:14:09,150 copying tests/test_io.py -> build/lib/tests 2026-04-13T21:14:09,153 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-13T21:14:09,154 copying tests/test_padding.py -> build/lib/tests 2026-04-13T21:14:09,156 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-13T21:14:09,159 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-13T21:14:09,161 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-13T21:14:09,164 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-13T21:14:09,166 copying tests/test_dataframe.py -> build/lib/tests 2026-04-13T21:14:09,168 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-13T21:14:09,170 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-13T21:14:09,173 creating build/lib/topiary/rna 2026-04-13T21:14:09,174 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-13T21:14:09,176 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-13T21:14:09,178 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-13T21:14:09,180 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-13T21:14:09,182 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-13T21:14:09,185 creating build/lib/topiary/ranking 2026-04-13T21:14:09,186 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-04-13T21:14:09,189 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-04-13T21:14:09,191 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-04-13T21:14:09,195 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-04-13T21:14:09,198 creating build/lib/topiary/cli 2026-04-13T21:14:09,199 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-13T21:14:09,201 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-13T21:14:09,203 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-13T21:14:09,205 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-13T21:14:09,207 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-13T21:14:09,209 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-13T21:14:09,211 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-13T21:14:09,213 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-13T21:14:09,216 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-13T21:14:09,218 running egg_info 2026-04-13T21:14:09,227 writing topiary.egg-info/PKG-INFO 2026-04-13T21:14:09,231 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-13T21:14:09,232 writing entry points to topiary.egg-info/entry_points.txt 2026-04-13T21:14:09,234 writing requirements to topiary.egg-info/requires.txt 2026-04-13T21:14:09,235 writing top-level names to topiary.egg-info/top_level.txt 2026-04-13T21:14:09,251 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T21:14:09,256 adding license file 'LICENSE' 2026-04-13T21:14:09,262 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-13T21:14:09,279 installing to build/bdist.linux-armv7l/wheel 2026-04-13T21:14:09,280 running install 2026-04-13T21:14:09,304 running install_lib 2026-04-13T21:14:09,310 creating build/bdist.linux-armv7l/wheel 2026-04-13T21:14:09,312 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-13T21:14:09,314 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-13T21:14:09,315 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T21:14:09,317 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T21:14:09,319 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T21:14:09,321 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T21:14:09,323 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-13T21:14:09,325 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-04-13T21:14:09,326 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T21:14:09,329 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T21:14:09,331 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T21:14:09,334 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-13T21:14:09,336 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,338 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,341 copying build/lib/topiary/antigen.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,344 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,346 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,348 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,350 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,353 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,355 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,357 copying build/lib/topiary/io_antigen.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,360 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-13T21:14:09,361 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,363 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,365 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,367 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,368 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,370 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,373 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,374 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,377 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-13T21:14:09,378 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,380 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,383 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-13T21:14:09,386 creating build/bdist.linux-armv7l/wheel/tests 2026-04-13T21:14:09,387 copying build/lib/tests/test_antigen.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,389 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,392 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,393 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,395 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,397 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,399 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,401 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,403 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,405 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,407 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,409 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,411 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,413 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,415 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,417 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,419 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,422 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,424 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,427 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,430 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,431 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,433 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,435 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,437 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,440 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,441 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,443 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,445 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,448 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,449 copying build/lib/tests/test_predict_from_antigens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,452 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,454 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,456 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,458 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,459 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,462 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,464 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,466 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,468 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,470 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,471 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-13T21:14:09,473 running install_egg_info 2026-04-13T21:14:09,478 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.2.0-py3.11.egg-info 2026-04-13T21:14:09,491 running install_scripts 2026-04-13T21:14:09,504 creating build/bdist.linux-armv7l/wheel/topiary-5.2.0.dist-info/WHEEL 2026-04-13T21:14:09,507 creating '/tmp/pip-wheel-br3wcksc/.tmp-n5eupaed/topiary-5.2.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-13T21:14:09,510 adding 'tests/__init__.py' 2026-04-13T21:14:09,512 adding 'tests/common.py' 2026-04-13T21:14:09,513 adding 'tests/data.py' 2026-04-13T21:14:09,515 adding 'tests/test_antigen.py' 2026-04-13T21:14:09,517 adding 'tests/test_args_outputs.py' 2026-04-13T21:14:09,519 adding 'tests/test_cli_coverage.py' 2026-04-13T21:14:09,520 adding 'tests/test_cli_protein_changes.py' 2026-04-13T21:14:09,522 adding 'tests/test_cli_ranking.py' 2026-04-13T21:14:09,523 adding 'tests/test_contains_mutant_residues.py' 2026-04-13T21:14:09,525 adding 'tests/test_coverage_gaps.py' 2026-04-13T21:14:09,527 adding 'tests/test_dataframe.py' 2026-04-13T21:14:09,528 adding 'tests/test_direct_input_regressions.py' 2026-04-13T21:14:09,530 adding 'tests/test_dsl_extensions.py' 2026-04-13T21:14:09,532 adding 'tests/test_dsl_polish.py' 2026-04-13T21:14:09,535 adding 'tests/test_dsl_roundtrip.py' 2026-04-13T21:14:09,537 adding 'tests/test_edge_case_fixtures.py' 2026-04-13T21:14:09,538 adding 'tests/test_effect_expression_filters.py' 2026-04-13T21:14:09,540 adding 'tests/test_end_to_end.py' 2026-04-13T21:14:09,541 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-13T21:14:09,543 adding 'tests/test_expression_integration.py' 2026-04-13T21:14:09,544 adding 'tests/test_expression_loader.py' 2026-04-13T21:14:09,546 adding 'tests/test_inputs.py' 2026-04-13T21:14:09,547 adding 'tests/test_integration.py' 2026-04-13T21:14:09,549 adding 'tests/test_io.py' 2026-04-13T21:14:09,551 adding 'tests/test_io_lens.py' 2026-04-13T21:14:09,553 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-13T21:14:09,554 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-13T21:14:09,555 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-13T21:14:09,557 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-13T21:14:09,558 adding 'tests/test_padding.py' 2026-04-13T21:14:09,559 adding 'tests/test_peptide_mutation_interval.py' 2026-04-13T21:14:09,561 adding 'tests/test_predict_from_antigens.py' 2026-04-13T21:14:09,563 adding 'tests/test_predictor_internals.py' 2026-04-13T21:14:09,570 adding 'tests/test_ranking.py' 2026-04-13T21:14:09,573 adding 'tests/test_result.py' 2026-04-13T21:14:09,574 adding 'tests/test_rna_helpers.py' 2026-04-13T21:14:09,575 adding 'tests/test_sequence_helpers.py' 2026-04-13T21:14:09,577 adding 'tests/test_sources.py' 2026-04-13T21:14:09,578 adding 'tests/test_sources_optional.py' 2026-04-13T21:14:09,580 adding 'tests/test_validation_and_edge_cases.py' 2026-04-13T21:14:09,581 adding 'tests/test_variant_expression_filters.py' 2026-04-13T21:14:09,583 adding 'tests/test_wide.py' 2026-04-13T21:14:09,585 adding 'topiary/__init__.py' 2026-04-13T21:14:09,588 adding 'topiary/antigen.py' 2026-04-13T21:14:09,589 adding 'topiary/filters.py' 2026-04-13T21:14:09,591 adding 'topiary/inputs.py' 2026-04-13T21:14:09,593 adding 'topiary/io.py' 2026-04-13T21:14:09,595 adding 'topiary/io_antigen.py' 2026-04-13T21:14:09,597 adding 'topiary/io_lens.py' 2026-04-13T21:14:09,600 adding 'topiary/predictor.py' 2026-04-13T21:14:09,603 adding 'topiary/properties.py' 2026-04-13T21:14:09,605 adding 'topiary/result.py' 2026-04-13T21:14:09,607 adding 'topiary/sequence_helpers.py' 2026-04-13T21:14:09,608 adding 'topiary/sources.py' 2026-04-13T21:14:09,610 adding 'topiary/wide.py' 2026-04-13T21:14:09,612 adding 'topiary/cli/__init__.py' 2026-04-13T21:14:09,615 adding 'topiary/cli/args.py' 2026-04-13T21:14:09,616 adding 'topiary/cli/errors.py' 2026-04-13T21:14:09,617 adding 'topiary/cli/filtering.py' 2026-04-13T21:14:09,619 adding 'topiary/cli/outputs.py' 2026-04-13T21:14:09,620 adding 'topiary/cli/protein_changes.py' 2026-04-13T21:14:09,622 adding 'topiary/cli/rna.py' 2026-04-13T21:14:09,623 adding 'topiary/cli/script.py' 2026-04-13T21:14:09,624 adding 'topiary/cli/sequence.py' 2026-04-13T21:14:09,627 adding 'topiary/ranking/__init__.py' 2026-04-13T21:14:09,628 adding 'topiary/ranking/apply.py' 2026-04-13T21:14:09,634 adding 'topiary/ranking/nodes.py' 2026-04-13T21:14:09,636 adding 'topiary/ranking/parser.py' 2026-04-13T21:14:09,638 adding 'topiary/rna/__init__.py' 2026-04-13T21:14:09,639 adding 'topiary/rna/common.py' 2026-04-13T21:14:09,641 adding 'topiary/rna/cufflinks.py' 2026-04-13T21:14:09,643 adding 'topiary/rna/expression_loader.py' 2026-04-13T21:14:09,644 adding 'topiary/rna/gtf.py' 2026-04-13T21:14:09,648 adding 'topiary-5.2.0.dist-info/licenses/LICENSE' 2026-04-13T21:14:09,651 adding 'topiary-5.2.0.dist-info/METADATA' 2026-04-13T21:14:09,652 adding 'topiary-5.2.0.dist-info/WHEEL' 2026-04-13T21:14:09,653 adding 'topiary-5.2.0.dist-info/entry_points.txt' 2026-04-13T21:14:09,654 adding 'topiary-5.2.0.dist-info/top_level.txt' 2026-04-13T21:14:09,656 adding 'topiary-5.2.0.dist-info/RECORD' 2026-04-13T21:14:09,660 removing build/bdist.linux-armv7l/wheel 2026-04-13T21:14:09,776 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-13T21:14:09,785 Created wheel for topiary: filename=topiary-5.2.0-py3-none-any.whl size=174966 sha256=dae3c176f6f432a458cdd50359c9dfa636ccd9bdb74f4f41507b7c069eed540f 2026-04-13T21:14:09,786 Stored in directory: /tmp/pip-ephem-wheel-cache-rq33sr45/wheels/c5/63/5a/0533ebeccbf51c13e5a3700916b02b9f3fa790236700739dda 2026-04-13T21:14:09,803 Successfully built topiary 2026-04-13T21:14:09,812 Removed build tracker: '/tmp/pip-build-tracker-9atn1agn'