2026-04-09T02:22:38,729 Created temporary directory: /tmp/pip-ephem-wheel-cache-3qp84fji 2026-04-09T02:22:38,731 Created temporary directory: /tmp/pip-build-tracker-e51dxreh 2026-04-09T02:22:38,732 Initialized build tracking at /tmp/pip-build-tracker-e51dxreh 2026-04-09T02:22:38,732 Created build tracker: /tmp/pip-build-tracker-e51dxreh 2026-04-09T02:22:38,733 Entered build tracker: /tmp/pip-build-tracker-e51dxreh 2026-04-09T02:22:38,733 Created temporary directory: /tmp/pip-wheel-vtyjlawn 2026-04-09T02:22:38,736 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,166 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-2.2.0-py3-none-any.whl#sha256=afb7b09b18f345de86420e8f1d61284c526a3bdcb0e352639c7383105203b2f9 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,166 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-2.1.0-py3-none-any.whl#sha256=6a54b133dc04b282ecb6254205dd09896a559c40a793a5470a1e8d77ed2244b1 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,167 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-2.0.0-py3-none-any.whl#sha256=bf376c02311efd5c80a0793be89ae4a34d82ab5397b5861dd664ce96d3e48a38 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,168 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-1.2.1-py3-none-any.whl#sha256=bc761dde043d0b6aa59153fc4cef4c3f4173d9cc2af622fc8263962c2fc21f0d (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,168 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-1.2.0-py3-none-any.whl#sha256=311e8283cb60ad0d52bad801d50774f6634e70f8998da593fb6bd3b2bc6ffa65 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,169 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.1.2-py3-none-any.whl#sha256=e7a1c96210356871a2273cd29f1899190e3ed5683d4a4572088cd945d1f5e758 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,169 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.1.0-py3-none-any.whl#sha256=46f5f6e4d2071e7711aa10d069defad14ffdf877b255780830a6cf6e42b61d5f (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,169 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.21-py3-none-any.whl#sha256=3983f7c3fbcff8c1a577833c364c6e99c1d98ac9955c3696439f59d8faa8eeda (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,170 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.20-py3-none-any.whl#sha256=3fb43551e5d6896e3e54f5a33a29922523c71c15b3849801206d04a8c4805350 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,170 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.19-py3-none-any.whl#sha256=0bdd9a0f991558f802326026fec79812c40392013a16fa27d697a9c37d0cf12c (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,171 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.18-py3-none-any.whl#sha256=9e812f2912a401afd7be2c4905413e0c158d97a57ddd49a478edb0b8d9805a28 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,172 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.17-py3-none-any.whl#sha256=9caa65a5a200720510e1c38a256ba0ee4702a443d0c0f9e56724aaa16b907517 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,172 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.16-py3-none-any.whl#sha256=1cce9bca3cbb426edd71bbf7bbd1c069b0498c46d67ce549315317b0f75ab1d6 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,173 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.15-py3-none-any.whl#sha256=ca5ae7481368a4fb5d839d1ac3cab6823cbebeb2733ef0e9c6b2275854eb895f (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,174 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.14-py3-none-any.whl#sha256=48e8744f89c7f03717c8e36a17ede28b495b845c7106cb5638c216db27054fad (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,174 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.13-py3-none-any.whl#sha256=588396661f87bea8be890d90c6800ac4825d06ae7db1c50c98a1978fe9c45bd3 (from https://www.piwheels.org/simple/topiary/) 2026-04-09T02:22:39,175 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/) 2026-04-09T02:22:39,176 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/) 2026-04-09T02:22:39,177 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/) 2026-04-09T02:22:39,178 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/) 2026-04-09T02:22:39,179 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/) 2026-04-09T02:22:39,180 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/) 2026-04-09T02:22:39,180 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/) 2026-04-09T02:22:39,181 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/) 2026-04-09T02:22:39,181 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/) 2026-04-09T02:22:39,182 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/) 2026-04-09T02:22:39,183 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/) 2026-04-09T02:22:39,183 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-09T02:22:39,184 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-09T02:22:39,209 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-09T02:22:39,229 Collecting topiary==4.3.2 2026-04-09T02:22:39,231 Created temporary directory: /tmp/pip-unpack-qedozc1g 2026-04-09T02:22:39,458 Downloading topiary-4.3.2.tar.gz (59 kB) 2026-04-09T02:22:39,620 Added topiary==4.3.2 from https://files.pythonhosted.org/packages/4e/43/42cf14fecd4f5129816f90747c6594400bed574ae6c7d48354cc5115e5bf/topiary-4.3.2.tar.gz to build tracker '/tmp/pip-build-tracker-e51dxreh' 2026-04-09T02:22:39,625 Created temporary directory: /tmp/pip-build-env-ivysr_fy 2026-04-09T02:22:39,629 Installing build dependencies: started 2026-04-09T02:22:39,630 Running command pip subprocess to install build dependencies 2026-04-09T02:22:40,775 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-09T02:22:41,186 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 2026-04-09T02:22:41,209 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-09T02:22:42,972 Collecting setuptools>=64 2026-04-09T02:22:43,061 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-09T02:22:46,026 Installing collected packages: setuptools 2026-04-09T02:22:49,208 Successfully installed setuptools-82.0.1 2026-04-09T02:22:49,478 Installing build dependencies: finished with status 'done' 2026-04-09T02:22:49,484 Getting requirements to build wheel: started 2026-04-09T02:22:49,486 Running command Getting requirements to build wheel 2026-04-09T02:22:50,166 /tmp/pip-build-env-ivysr_fy/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-09T02:22:50,166 !! 2026-04-09T02:22:50,167 ******************************************************************************** 2026-04-09T02:22:50,168 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-09T02:22:50,169 License :: OSI Approved :: Apache Software License 2026-04-09T02:22:50,170 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-09T02:22:50,170 ******************************************************************************** 2026-04-09T02:22:50,172 !! 2026-04-09T02:22:50,172 dist._finalize_license_expression() 2026-04-09T02:22:50,173 /tmp/pip-build-env-ivysr_fy/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-09T02:22:50,173 !! 2026-04-09T02:22:50,174 ******************************************************************************** 2026-04-09T02:22:50,175 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-09T02:22:50,176 License :: OSI Approved :: Apache Software License 2026-04-09T02:22:50,178 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-09T02:22:50,178 ******************************************************************************** 2026-04-09T02:22:50,180 !! 2026-04-09T02:22:50,181 self._finalize_license_expression() 2026-04-09T02:22:50,181 running egg_info 2026-04-09T02:22:50,185 writing topiary.egg-info/PKG-INFO 2026-04-09T02:22:50,190 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-09T02:22:50,192 writing entry points to topiary.egg-info/entry_points.txt 2026-04-09T02:22:50,194 writing requirements to topiary.egg-info/requires.txt 2026-04-09T02:22:50,195 writing top-level names to topiary.egg-info/top_level.txt 2026-04-09T02:22:50,221 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-09T02:22:50,226 adding license file 'LICENSE' 2026-04-09T02:22:50,230 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-09T02:22:50,327 Getting requirements to build wheel: finished with status 'done' 2026-04-09T02:22:50,330 Created temporary directory: /tmp/pip-modern-metadata-fd7k781s 2026-04-09T02:22:50,333 Preparing metadata (pyproject.toml): started 2026-04-09T02:22:50,334 Running command Preparing metadata (pyproject.toml) 2026-04-09T02:22:50,973 /tmp/pip-build-env-ivysr_fy/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-09T02:22:50,973 !! 2026-04-09T02:22:50,975 ******************************************************************************** 2026-04-09T02:22:50,975 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-09T02:22:50,977 License :: OSI Approved :: Apache Software License 2026-04-09T02:22:50,978 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-09T02:22:50,978 ******************************************************************************** 2026-04-09T02:22:50,979 !! 2026-04-09T02:22:50,980 dist._finalize_license_expression() 2026-04-09T02:22:50,980 /tmp/pip-build-env-ivysr_fy/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-09T02:22:50,981 !! 2026-04-09T02:22:50,982 ******************************************************************************** 2026-04-09T02:22:50,982 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-09T02:22:50,983 License :: OSI Approved :: Apache Software License 2026-04-09T02:22:50,984 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-09T02:22:50,984 ******************************************************************************** 2026-04-09T02:22:50,985 !! 2026-04-09T02:22:50,986 self._finalize_license_expression() 2026-04-09T02:22:50,986 running dist_info 2026-04-09T02:22:50,995 creating /tmp/pip-modern-metadata-fd7k781s/topiary.egg-info 2026-04-09T02:22:50,996 writing /tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/PKG-INFO 2026-04-09T02:22:51,000 writing dependency_links to /tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/dependency_links.txt 2026-04-09T02:22:51,002 writing entry points to /tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/entry_points.txt 2026-04-09T02:22:51,004 writing requirements to /tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/requires.txt 2026-04-09T02:22:51,005 writing top-level names to /tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/top_level.txt 2026-04-09T02:22:51,006 writing manifest file '/tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/SOURCES.txt' 2026-04-09T02:22:51,029 reading manifest file '/tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/SOURCES.txt' 2026-04-09T02:22:51,030 adding license file 'LICENSE' 2026-04-09T02:22:51,034 writing manifest file '/tmp/pip-modern-metadata-fd7k781s/topiary.egg-info/SOURCES.txt' 2026-04-09T02:22:51,035 creating '/tmp/pip-modern-metadata-fd7k781s/topiary-4.3.2.dist-info' 2026-04-09T02:22:51,160 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-09T02:22:51,165 Source in /tmp/pip-wheel-vtyjlawn/topiary_a52e6f55ee364e5d838dc1b5e2e02c57 has version 4.3.2, which satisfies requirement topiary==4.3.2 from https://files.pythonhosted.org/packages/4e/43/42cf14fecd4f5129816f90747c6594400bed574ae6c7d48354cc5115e5bf/topiary-4.3.2.tar.gz 2026-04-09T02:22:51,166 Removed topiary==4.3.2 from https://files.pythonhosted.org/packages/4e/43/42cf14fecd4f5129816f90747c6594400bed574ae6c7d48354cc5115e5bf/topiary-4.3.2.tar.gz from build tracker '/tmp/pip-build-tracker-e51dxreh' 2026-04-09T02:22:51,173 Created temporary directory: /tmp/pip-unpack-df_x6guv 2026-04-09T02:22:51,174 Building wheels for collected packages: topiary 2026-04-09T02:22:51,178 Created temporary directory: /tmp/pip-wheel-tqmm5bmc 2026-04-09T02:22:51,179 Destination directory: /tmp/pip-wheel-tqmm5bmc 2026-04-09T02:22:51,181 Building wheel for topiary (pyproject.toml): started 2026-04-09T02:22:51,182 Running command Building wheel for topiary (pyproject.toml) 2026-04-09T02:22:51,816 /tmp/pip-build-env-ivysr_fy/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-09T02:22:51,816 !! 2026-04-09T02:22:51,817 ******************************************************************************** 2026-04-09T02:22:51,818 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-09T02:22:51,819 License :: OSI Approved :: Apache Software License 2026-04-09T02:22:51,821 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-09T02:22:51,821 ******************************************************************************** 2026-04-09T02:22:51,822 !! 2026-04-09T02:22:51,822 dist._finalize_license_expression() 2026-04-09T02:22:51,823 /tmp/pip-build-env-ivysr_fy/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-09T02:22:51,824 !! 2026-04-09T02:22:51,824 ******************************************************************************** 2026-04-09T02:22:51,825 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-09T02:22:51,826 License :: OSI Approved :: Apache Software License 2026-04-09T02:22:51,827 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-09T02:22:51,827 ******************************************************************************** 2026-04-09T02:22:51,828 !! 2026-04-09T02:22:51,829 self._finalize_license_expression() 2026-04-09T02:22:51,829 running bdist_wheel 2026-04-09T02:22:51,842 running build 2026-04-09T02:22:51,842 running build_py 2026-04-09T02:22:51,849 creating build/lib/topiary 2026-04-09T02:22:51,851 copying topiary/ranking.py -> build/lib/topiary 2026-04-09T02:22:51,854 copying topiary/__init__.py -> build/lib/topiary 2026-04-09T02:22:51,856 copying topiary/sources.py -> build/lib/topiary 2026-04-09T02:22:51,858 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-09T02:22:51,860 copying topiary/inputs.py -> build/lib/topiary 2026-04-09T02:22:51,863 copying topiary/predictor.py -> build/lib/topiary 2026-04-09T02:22:51,865 copying topiary/filters.py -> build/lib/topiary 2026-04-09T02:22:51,869 creating build/lib/tests 2026-04-09T02:22:51,870 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-09T02:22:51,872 copying tests/test_integration.py -> build/lib/tests 2026-04-09T02:22:51,873 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-09T02:22:51,875 copying tests/test_ranking.py -> build/lib/tests 2026-04-09T02:22:51,878 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-09T02:22:51,880 copying tests/__init__.py -> build/lib/tests 2026-04-09T02:22:51,882 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-09T02:22:51,884 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-09T02:22:51,885 copying tests/test_inputs.py -> build/lib/tests 2026-04-09T02:22:51,888 copying tests/test_sources.py -> build/lib/tests 2026-04-09T02:22:51,890 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-09T02:22:51,892 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-09T02:22:51,894 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-09T02:22:51,896 copying tests/test_padding.py -> build/lib/tests 2026-04-09T02:22:51,897 copying tests/data.py -> build/lib/tests 2026-04-09T02:22:51,899 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-09T02:22:51,901 copying tests/test_dataframe.py -> build/lib/tests 2026-04-09T02:22:51,903 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-09T02:22:51,905 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-09T02:22:51,907 copying tests/common.py -> build/lib/tests 2026-04-09T02:22:51,909 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-09T02:22:51,911 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-09T02:22:51,913 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-09T02:22:51,915 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-09T02:22:51,918 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-09T02:22:51,920 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-09T02:22:51,922 creating build/lib/topiary/cli 2026-04-09T02:22:51,923 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-09T02:22:51,925 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-09T02:22:51,926 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-09T02:22:51,928 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-09T02:22:51,930 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-09T02:22:51,932 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-09T02:22:51,934 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-09T02:22:51,936 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-09T02:22:51,938 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-09T02:22:51,941 creating build/lib/topiary/rna 2026-04-09T02:22:51,942 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-09T02:22:51,943 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-09T02:22:51,946 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-09T02:22:51,947 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-09T02:22:51,949 running egg_info 2026-04-09T02:22:51,958 writing topiary.egg-info/PKG-INFO 2026-04-09T02:22:51,962 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-09T02:22:51,963 writing entry points to topiary.egg-info/entry_points.txt 2026-04-09T02:22:51,965 writing requirements to topiary.egg-info/requires.txt 2026-04-09T02:22:51,966 writing top-level names to topiary.egg-info/top_level.txt 2026-04-09T02:22:51,979 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-09T02:22:51,983 adding license file 'LICENSE' 2026-04-09T02:22:51,988 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-09T02:22:52,002 installing to build/bdist.linux-armv7l/wheel 2026-04-09T02:22:52,003 running install 2026-04-09T02:22:52,027 running install_lib 2026-04-09T02:22:52,032 creating build/bdist.linux-armv7l/wheel 2026-04-09T02:22:52,034 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-09T02:22:52,035 copying build/lib/topiary/ranking.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-09T02:22:52,038 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-09T02:22:52,040 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-09T02:22:52,042 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-09T02:22:52,044 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-09T02:22:52,045 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,047 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,049 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,051 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,053 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,055 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,057 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,058 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,061 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-09T02:22:52,063 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-09T02:22:52,064 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-09T02:22:52,066 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-09T02:22:52,069 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-09T02:22:52,070 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-09T02:22:52,072 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-09T02:22:52,074 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-09T02:22:52,077 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-09T02:22:52,080 creating build/bdist.linux-armv7l/wheel/tests 2026-04-09T02:22:52,081 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,083 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,084 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,086 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,089 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,091 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,092 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,094 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,096 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,098 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,100 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,102 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,104 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,107 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,108 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,110 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,112 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,114 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,116 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,118 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,119 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,121 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,124 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,126 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,129 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,130 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-09T02:22:52,132 running install_egg_info 2026-04-09T02:22:52,137 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-4.3.2-py3.11.egg-info 2026-04-09T02:22:52,149 running install_scripts 2026-04-09T02:22:52,161 creating build/bdist.linux-armv7l/wheel/topiary-4.3.2.dist-info/WHEEL 2026-04-09T02:22:52,164 creating '/tmp/pip-wheel-tqmm5bmc/.tmp-upunno4k/topiary-4.3.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-09T02:22:52,167 adding 'tests/__init__.py' 2026-04-09T02:22:52,168 adding 'tests/common.py' 2026-04-09T02:22:52,169 adding 'tests/data.py' 2026-04-09T02:22:52,171 adding 'tests/test_args_outputs.py' 2026-04-09T02:22:52,172 adding 'tests/test_cli_protein_changes.py' 2026-04-09T02:22:52,173 adding 'tests/test_contains_mutant_residues.py' 2026-04-09T02:22:52,175 adding 'tests/test_coverage_gaps.py' 2026-04-09T02:22:52,176 adding 'tests/test_dataframe.py' 2026-04-09T02:22:52,177 adding 'tests/test_direct_input_regressions.py' 2026-04-09T02:22:52,179 adding 'tests/test_effect_expression_filters.py' 2026-04-09T02:22:52,180 adding 'tests/test_end_to_end.py' 2026-04-09T02:22:52,182 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-09T02:22:52,183 adding 'tests/test_inputs.py' 2026-04-09T02:22:52,184 adding 'tests/test_integration.py' 2026-04-09T02:22:52,186 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-09T02:22:52,187 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-09T02:22:52,188 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-09T02:22:52,189 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-09T02:22:52,191 adding 'tests/test_padding.py' 2026-04-09T02:22:52,192 adding 'tests/test_peptide_mutation_interval.py' 2026-04-09T02:22:52,194 adding 'tests/test_ranking.py' 2026-04-09T02:22:52,195 adding 'tests/test_rna_helpers.py' 2026-04-09T02:22:52,197 adding 'tests/test_sources.py' 2026-04-09T02:22:52,198 adding 'tests/test_sources_optional.py' 2026-04-09T02:22:52,200 adding 'tests/test_validation_and_edge_cases.py' 2026-04-09T02:22:52,201 adding 'tests/test_variant_expression_filters.py' 2026-04-09T02:22:52,203 adding 'topiary/__init__.py' 2026-04-09T02:22:52,204 adding 'topiary/filters.py' 2026-04-09T02:22:52,206 adding 'topiary/inputs.py' 2026-04-09T02:22:52,209 adding 'topiary/predictor.py' 2026-04-09T02:22:52,212 adding 'topiary/ranking.py' 2026-04-09T02:22:52,213 adding 'topiary/sequence_helpers.py' 2026-04-09T02:22:52,215 adding 'topiary/sources.py' 2026-04-09T02:22:52,217 adding 'topiary/cli/__init__.py' 2026-04-09T02:22:52,219 adding 'topiary/cli/args.py' 2026-04-09T02:22:52,221 adding 'topiary/cli/errors.py' 2026-04-09T02:22:52,222 adding 'topiary/cli/filtering.py' 2026-04-09T02:22:52,223 adding 'topiary/cli/outputs.py' 2026-04-09T02:22:52,225 adding 'topiary/cli/protein_changes.py' 2026-04-09T02:22:52,226 adding 'topiary/cli/rna.py' 2026-04-09T02:22:52,228 adding 'topiary/cli/script.py' 2026-04-09T02:22:52,229 adding 'topiary/cli/sequence.py' 2026-04-09T02:22:52,231 adding 'topiary/rna/__init__.py' 2026-04-09T02:22:52,232 adding 'topiary/rna/common.py' 2026-04-09T02:22:52,234 adding 'topiary/rna/cufflinks.py' 2026-04-09T02:22:52,235 adding 'topiary/rna/gtf.py' 2026-04-09T02:22:52,239 adding 'topiary-4.3.2.dist-info/licenses/LICENSE' 2026-04-09T02:22:52,241 adding 'topiary-4.3.2.dist-info/METADATA' 2026-04-09T02:22:52,242 adding 'topiary-4.3.2.dist-info/WHEEL' 2026-04-09T02:22:52,243 adding 'topiary-4.3.2.dist-info/entry_points.txt' 2026-04-09T02:22:52,244 adding 'topiary-4.3.2.dist-info/top_level.txt' 2026-04-09T02:22:52,245 adding 'topiary-4.3.2.dist-info/RECORD' 2026-04-09T02:22:52,248 removing build/bdist.linux-armv7l/wheel 2026-04-09T02:22:52,357 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-09T02:22:52,364 Created wheel for topiary: filename=topiary-4.3.2-py3-none-any.whl size=74299 sha256=8f63e71936c3b02f002347a85c852e16fd02a920c2d6c8788ade523951cb02b7 2026-04-09T02:22:52,365 Stored in directory: /tmp/pip-ephem-wheel-cache-om6algny/wheels/ba/f0/87/c94a34e3c5006e0bc6d4334016b1dcf603d5dbfdee7dbe356a 2026-04-09T02:22:52,378 Successfully built topiary 2026-04-09T02:22:52,384 Removed build tracker: '/tmp/pip-build-tracker-e51dxreh'