2026-04-15T01:32:46,529 Created temporary directory: /tmp/pip-ephem-wheel-cache-yqhkmnhy 2026-04-15T01:32:46,531 Created temporary directory: /tmp/pip-build-tracker-svq578e0 2026-04-15T01:32:46,532 Initialized build tracking at /tmp/pip-build-tracker-svq578e0 2026-04-15T01:32:46,532 Created build tracker: /tmp/pip-build-tracker-svq578e0 2026-04-15T01:32:46,533 Entered build tracker: /tmp/pip-build-tracker-svq578e0 2026-04-15T01:32:46,534 Created temporary directory: /tmp/pip-wheel-76ppxrzz 2026-04-15T01:32:46,536 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 2026-04-15T01:32:46,539 Created temporary directory: /tmp/pip-ephem-wheel-cache-n9xz0u85 2026-04-15T01:32:46,561 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-15T01:32:46,565 2 location(s) to search for versions of topiary: 2026-04-15T01:32:46,565 * https://pypi.org/simple/topiary/ 2026-04-15T01:32:46,565 * https://www.piwheels.org/simple/topiary/ 2026-04-15T01:32:46,566 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-04-15T01:32:46,566 Getting page https://pypi.org/simple/topiary/ 2026-04-15T01:32:46,568 Found index url https://pypi.org/simple 2026-04-15T01:32:46,798 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-04-15T01:32:46,813 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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https://www.piwheels.org/simple/topiary/) 2026-04-15T01:32:47,091 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/) 2026-04-15T01:32:47,091 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/) 2026-04-15T01:32:47,091 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/) 2026-04-15T01:32:47,092 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/) 2026-04-15T01:32:47,093 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/) 2026-04-15T01:32:47,093 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/) 2026-04-15T01:32:47,094 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/) 2026-04-15T01:32:47,094 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/) 2026-04-15T01:32:47,095 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/) 2026-04-15T01:32:47,096 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/) 2026-04-15T01:32:47,096 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/) 2026-04-15T01:32:47,097 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/) 2026-04-15T01:32:47,098 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/) 2026-04-15T01:32:47,098 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/) 2026-04-15T01:32:47,099 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/) 2026-04-15T01:32:47,099 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/) 2026-04-15T01:32:47,099 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/) 2026-04-15T01:32:47,100 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/) 2026-04-15T01:32:47,100 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-15T01:32:47,101 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-15T01:32:47,128 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-15T01:32:47,148 Collecting topiary==5.6.0 2026-04-15T01:32:47,150 Created temporary directory: /tmp/pip-unpack-fb6xuwu9 2026-04-15T01:32:47,389 Downloading topiary-5.6.0.tar.gz (178 kB) 2026-04-15T01:32:47,657 Added topiary==5.6.0 from https://files.pythonhosted.org/packages/f3/89/7fe860e215fe1b79748b02b9f9069869dfd7b7f635ded3bdcf8f6f7c3255/topiary-5.6.0.tar.gz to build tracker '/tmp/pip-build-tracker-svq578e0' 2026-04-15T01:32:47,662 Created temporary directory: /tmp/pip-build-env-7eeldlj1 2026-04-15T01:32:47,667 Installing build dependencies: started 2026-04-15T01:32:47,668 Running command pip subprocess to install build dependencies 2026-04-15T01:32:48,791 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-15T01:32:49,226 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 2026-04-15T01:32:49,248 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-15T01:32:51,005 Collecting setuptools>=64 2026-04-15T01:32:51,079 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-15T01:32:54,069 Installing collected packages: setuptools 2026-04-15T01:32:57,087 Successfully installed setuptools-82.0.1 2026-04-15T01:32:57,356 Installing build dependencies: finished with status 'done' 2026-04-15T01:32:57,363 Getting requirements to build wheel: started 2026-04-15T01:32:57,364 Running command Getting requirements to build wheel 2026-04-15T01:32:58,080 /tmp/pip-build-env-7eeldlj1/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-15T01:32:58,080 !! 2026-04-15T01:32:58,081 ******************************************************************************** 2026-04-15T01:32:58,082 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-15T01:32:58,083 License :: OSI Approved :: Apache Software License 2026-04-15T01:32:58,084 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-15T01:32:58,084 ******************************************************************************** 2026-04-15T01:32:58,085 !! 2026-04-15T01:32:58,086 dist._finalize_license_expression() 2026-04-15T01:32:58,086 /tmp/pip-build-env-7eeldlj1/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-15T01:32:58,087 !! 2026-04-15T01:32:58,088 ******************************************************************************** 2026-04-15T01:32:58,088 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-15T01:32:58,089 License :: OSI Approved :: Apache Software License 2026-04-15T01:32:58,090 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-15T01:32:58,091 ******************************************************************************** 2026-04-15T01:32:58,092 !! 2026-04-15T01:32:58,092 self._finalize_license_expression() 2026-04-15T01:32:58,093 running egg_info 2026-04-15T01:32:58,100 writing topiary.egg-info/PKG-INFO 2026-04-15T01:32:58,104 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-15T01:32:58,106 writing entry points to topiary.egg-info/entry_points.txt 2026-04-15T01:32:58,107 writing requirements to topiary.egg-info/requires.txt 2026-04-15T01:32:58,109 writing top-level names to topiary.egg-info/top_level.txt 2026-04-15T01:32:58,136 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-15T01:32:58,142 adding license file 'LICENSE' 2026-04-15T01:32:58,148 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-15T01:32:58,246 Getting requirements to build wheel: finished with status 'done' 2026-04-15T01:32:58,250 Created temporary directory: /tmp/pip-modern-metadata-38cos_yr 2026-04-15T01:32:58,252 Preparing metadata (pyproject.toml): started 2026-04-15T01:32:58,253 Running command Preparing metadata (pyproject.toml) 2026-04-15T01:32:58,909 /tmp/pip-build-env-7eeldlj1/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-15T01:32:58,910 !! 2026-04-15T01:32:58,911 ******************************************************************************** 2026-04-15T01:32:58,911 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-15T01:32:58,912 License :: OSI Approved :: Apache Software License 2026-04-15T01:32:58,913 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-15T01:32:58,914 ******************************************************************************** 2026-04-15T01:32:58,915 !! 2026-04-15T01:32:58,916 dist._finalize_license_expression() 2026-04-15T01:32:58,916 /tmp/pip-build-env-7eeldlj1/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-15T01:32:58,917 !! 2026-04-15T01:32:58,918 ******************************************************************************** 2026-04-15T01:32:58,919 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-15T01:32:58,920 License :: OSI Approved :: Apache Software License 2026-04-15T01:32:58,921 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-15T01:32:58,922 ******************************************************************************** 2026-04-15T01:32:58,922 !! 2026-04-15T01:32:58,923 self._finalize_license_expression() 2026-04-15T01:32:58,923 running dist_info 2026-04-15T01:32:58,933 creating /tmp/pip-modern-metadata-38cos_yr/topiary.egg-info 2026-04-15T01:32:58,934 writing /tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/PKG-INFO 2026-04-15T01:32:58,938 writing dependency_links to /tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/dependency_links.txt 2026-04-15T01:32:58,940 writing entry points to /tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/entry_points.txt 2026-04-15T01:32:58,941 writing requirements to /tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/requires.txt 2026-04-15T01:32:58,942 writing top-level names to /tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/top_level.txt 2026-04-15T01:32:58,943 writing manifest file '/tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/SOURCES.txt' 2026-04-15T01:32:58,968 reading manifest file '/tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/SOURCES.txt' 2026-04-15T01:32:58,970 adding license file 'LICENSE' 2026-04-15T01:32:58,975 writing manifest file '/tmp/pip-modern-metadata-38cos_yr/topiary.egg-info/SOURCES.txt' 2026-04-15T01:32:58,976 creating '/tmp/pip-modern-metadata-38cos_yr/topiary-5.6.0.dist-info' 2026-04-15T01:32:59,101 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-15T01:32:59,106 Source in /tmp/pip-wheel-76ppxrzz/topiary_992a85acc5764eadac2f8ba41b074fe1 has version 5.6.0, which satisfies requirement topiary==5.6.0 from https://files.pythonhosted.org/packages/f3/89/7fe860e215fe1b79748b02b9f9069869dfd7b7f635ded3bdcf8f6f7c3255/topiary-5.6.0.tar.gz 2026-04-15T01:32:59,107 Removed topiary==5.6.0 from https://files.pythonhosted.org/packages/f3/89/7fe860e215fe1b79748b02b9f9069869dfd7b7f635ded3bdcf8f6f7c3255/topiary-5.6.0.tar.gz from build tracker '/tmp/pip-build-tracker-svq578e0' 2026-04-15T01:32:59,115 Created temporary directory: /tmp/pip-unpack-puphaimv 2026-04-15T01:32:59,116 Building wheels for collected packages: topiary 2026-04-15T01:32:59,120 Created temporary directory: /tmp/pip-wheel-vuwhq_4r 2026-04-15T01:32:59,121 Destination directory: /tmp/pip-wheel-vuwhq_4r 2026-04-15T01:32:59,123 Building wheel for topiary (pyproject.toml): started 2026-04-15T01:32:59,124 Running command Building wheel for topiary (pyproject.toml) 2026-04-15T01:32:59,739 /tmp/pip-build-env-7eeldlj1/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-15T01:32:59,739 !! 2026-04-15T01:32:59,740 ******************************************************************************** 2026-04-15T01:32:59,741 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-15T01:32:59,742 License :: OSI Approved :: Apache Software License 2026-04-15T01:32:59,743 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-15T01:32:59,743 ******************************************************************************** 2026-04-15T01:32:59,745 !! 2026-04-15T01:32:59,745 dist._finalize_license_expression() 2026-04-15T01:32:59,746 /tmp/pip-build-env-7eeldlj1/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-15T01:32:59,747 !! 2026-04-15T01:32:59,748 ******************************************************************************** 2026-04-15T01:32:59,749 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-15T01:32:59,750 License :: OSI Approved :: Apache Software License 2026-04-15T01:32:59,751 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-15T01:32:59,752 ******************************************************************************** 2026-04-15T01:32:59,753 !! 2026-04-15T01:32:59,753 self._finalize_license_expression() 2026-04-15T01:32:59,753 running bdist_wheel 2026-04-15T01:32:59,765 running build 2026-04-15T01:32:59,765 running build_py 2026-04-15T01:32:59,771 creating build/lib/topiary 2026-04-15T01:32:59,773 copying topiary/io.py -> build/lib/topiary 2026-04-15T01:32:59,775 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-04-15T01:32:59,778 copying topiary/result.py -> build/lib/topiary 2026-04-15T01:32:59,780 copying topiary/inputs.py -> build/lib/topiary 2026-04-15T01:32:59,782 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-15T01:32:59,784 copying topiary/__init__.py -> build/lib/topiary 2026-04-15T01:32:59,786 copying topiary/sources.py -> build/lib/topiary 2026-04-15T01:32:59,788 copying topiary/filters.py -> build/lib/topiary 2026-04-15T01:32:59,791 copying topiary/wide.py -> build/lib/topiary 2026-04-15T01:32:59,793 copying topiary/protein_fragment.py -> build/lib/topiary 2026-04-15T01:32:59,795 copying topiary/properties.py -> build/lib/topiary 2026-04-15T01:32:59,798 copying topiary/cached.py -> build/lib/topiary 2026-04-15T01:32:59,800 copying topiary/io_lens.py -> build/lib/topiary 2026-04-15T01:32:59,803 copying topiary/predictor.py -> build/lib/topiary 2026-04-15T01:32:59,807 creating build/lib/tests 2026-04-15T01:32:59,808 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-15T01:32:59,811 copying tests/test_result.py -> build/lib/tests 2026-04-15T01:32:59,813 copying tests/test_dataframe.py -> build/lib/tests 2026-04-15T01:32:59,815 copying tests/test_sources.py -> build/lib/tests 2026-04-15T01:32:59,817 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-15T01:32:59,819 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-15T01:32:59,821 copying tests/test_padding.py -> build/lib/tests 2026-04-15T01:32:59,823 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-15T01:32:59,825 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-15T01:32:59,827 copying tests/test_integration.py -> build/lib/tests 2026-04-15T01:32:59,829 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-15T01:32:59,831 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-15T01:32:59,833 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-15T01:32:59,835 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-15T01:32:59,837 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-15T01:32:59,839 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-15T01:32:59,840 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-15T01:32:59,843 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-04-15T01:32:59,845 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-15T01:32:59,848 copying tests/common.py -> build/lib/tests 2026-04-15T01:32:59,849 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-04-15T01:32:59,852 copying tests/test_protein_fragment.py -> build/lib/tests 2026-04-15T01:32:59,854 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-15T01:32:59,856 copying tests/__init__.py -> build/lib/tests 2026-04-15T01:32:59,858 copying tests/test_cached_predictor.py -> build/lib/tests 2026-04-15T01:32:59,861 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-15T01:32:59,862 copying tests/test_wide.py -> build/lib/tests 2026-04-15T01:32:59,865 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-15T01:32:59,867 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-15T01:32:59,869 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-15T01:32:59,871 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-04-15T01:32:59,873 copying tests/data.py -> build/lib/tests 2026-04-15T01:32:59,875 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-15T01:32:59,877 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-15T01:32:59,879 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-15T01:32:59,881 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-15T01:32:59,882 copying tests/test_io.py -> build/lib/tests 2026-04-15T01:32:59,885 copying tests/test_inputs.py -> build/lib/tests 2026-04-15T01:32:59,887 copying tests/test_ranking.py -> build/lib/tests 2026-04-15T01:32:59,890 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-15T01:32:59,892 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-15T01:32:59,893 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-15T01:32:59,895 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-04-15T01:32:59,897 copying tests/test_io_lens.py -> build/lib/tests 2026-04-15T01:32:59,900 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-15T01:32:59,903 creating build/lib/topiary/ranking 2026-04-15T01:32:59,904 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-04-15T01:32:59,906 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-04-15T01:32:59,908 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-04-15T01:32:59,910 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-04-15T01:32:59,914 creating build/lib/topiary/cli 2026-04-15T01:32:59,915 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-15T01:32:59,917 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-15T01:32:59,919 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-15T01:32:59,920 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-15T01:32:59,922 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-15T01:32:59,924 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-15T01:32:59,926 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-15T01:32:59,928 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-15T01:32:59,930 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-15T01:32:59,933 creating build/lib/topiary/rna 2026-04-15T01:32:59,934 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-15T01:32:59,936 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-15T01:32:59,938 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-15T01:32:59,941 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-15T01:32:59,942 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-15T01:32:59,944 running egg_info 2026-04-15T01:32:59,953 writing topiary.egg-info/PKG-INFO 2026-04-15T01:32:59,957 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-15T01:32:59,958 writing entry points to topiary.egg-info/entry_points.txt 2026-04-15T01:32:59,960 writing requirements to topiary.egg-info/requires.txt 2026-04-15T01:32:59,961 writing top-level names to topiary.egg-info/top_level.txt 2026-04-15T01:32:59,976 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-15T01:32:59,982 adding license file 'LICENSE' 2026-04-15T01:32:59,988 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-15T01:33:00,004 installing to build/bdist.linux-armv7l/wheel 2026-04-15T01:33:00,005 running install 2026-04-15T01:33:00,028 running install_lib 2026-04-15T01:33:00,034 creating build/bdist.linux-armv7l/wheel 2026-04-15T01:33:00,036 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-15T01:33:00,037 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,040 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,042 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-04-15T01:33:00,043 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-15T01:33:00,046 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-15T01:33:00,048 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-15T01:33:00,050 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-15T01:33:00,053 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,055 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,057 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,060 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-15T01:33:00,061 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,063 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,065 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,066 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,068 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,070 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,071 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,073 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,076 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-15T01:33:00,079 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-15T01:33:00,080 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-15T01:33:00,082 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-15T01:33:00,084 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-15T01:33:00,086 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-15T01:33:00,088 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-15T01:33:00,090 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,091 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,094 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,096 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,098 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,101 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,103 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,106 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,108 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-15T01:33:00,112 creating build/bdist.linux-armv7l/wheel/tests 2026-04-15T01:33:00,113 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,115 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,118 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,120 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,122 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,124 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,125 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,127 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,129 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,131 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,133 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,135 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,137 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,139 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,141 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,142 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,144 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,147 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,149 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,151 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,153 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,155 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,158 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,160 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,161 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,164 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,166 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,168 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,170 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,172 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,174 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,176 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,178 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,181 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,182 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,184 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,186 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,188 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,190 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,194 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,195 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,197 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,199 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,201 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,203 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-15T01:33:00,206 running install_egg_info 2026-04-15T01:33:00,211 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.6.0-py3.11.egg-info 2026-04-15T01:33:00,222 running install_scripts 2026-04-15T01:33:00,234 creating build/bdist.linux-armv7l/wheel/topiary-5.6.0.dist-info/WHEEL 2026-04-15T01:33:00,237 creating '/tmp/pip-wheel-vuwhq_4r/.tmp-1z_9_jjp/topiary-5.6.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-15T01:33:00,240 adding 'tests/__init__.py' 2026-04-15T01:33:00,241 adding 'tests/common.py' 2026-04-15T01:33:00,242 adding 'tests/data.py' 2026-04-15T01:33:00,243 adding 'tests/test_args_outputs.py' 2026-04-15T01:33:00,247 adding 'tests/test_cached_predictor.py' 2026-04-15T01:33:00,249 adding 'tests/test_cli_coverage.py' 2026-04-15T01:33:00,250 adding 'tests/test_cli_protein_changes.py' 2026-04-15T01:33:00,252 adding 'tests/test_cli_ranking.py' 2026-04-15T01:33:00,253 adding 'tests/test_contains_mutant_residues.py' 2026-04-15T01:33:00,255 adding 'tests/test_coverage_gaps.py' 2026-04-15T01:33:00,256 adding 'tests/test_dataframe.py' 2026-04-15T01:33:00,258 adding 'tests/test_direct_input_regressions.py' 2026-04-15T01:33:00,260 adding 'tests/test_dsl_extensions.py' 2026-04-15T01:33:00,262 adding 'tests/test_dsl_polish.py' 2026-04-15T01:33:00,265 adding 'tests/test_dsl_roundtrip.py' 2026-04-15T01:33:00,266 adding 'tests/test_edge_case_fixtures.py' 2026-04-15T01:33:00,267 adding 'tests/test_effect_expression_filters.py' 2026-04-15T01:33:00,269 adding 'tests/test_end_to_end.py' 2026-04-15T01:33:00,270 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-15T01:33:00,272 adding 'tests/test_expression_integration.py' 2026-04-15T01:33:00,273 adding 'tests/test_expression_loader.py' 2026-04-15T01:33:00,276 adding 'tests/test_frameshift_fragments.py' 2026-04-15T01:33:00,277 adding 'tests/test_inputs.py' 2026-04-15T01:33:00,279 adding 'tests/test_integration.py' 2026-04-15T01:33:00,281 adding 'tests/test_io.py' 2026-04-15T01:33:00,283 adding 'tests/test_io_lens.py' 2026-04-15T01:33:00,284 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-15T01:33:00,286 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-15T01:33:00,287 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-15T01:33:00,288 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-15T01:33:00,290 adding 'tests/test_padding.py' 2026-04-15T01:33:00,291 adding 'tests/test_peptide_mutation_interval.py' 2026-04-15T01:33:00,293 adding 'tests/test_predict_from_fragments.py' 2026-04-15T01:33:00,295 adding 'tests/test_predict_from_variants_refactor.py' 2026-04-15T01:33:00,296 adding 'tests/test_predictor_internals.py' 2026-04-15T01:33:00,299 adding 'tests/test_protein_fragment.py' 2026-04-15T01:33:00,306 adding 'tests/test_ranking.py' 2026-04-15T01:33:00,308 adding 'tests/test_result.py' 2026-04-15T01:33:00,310 adding 'tests/test_rna_helpers.py' 2026-04-15T01:33:00,311 adding 'tests/test_sequence_helpers.py' 2026-04-15T01:33:00,313 adding 'tests/test_sources.py' 2026-04-15T01:33:00,314 adding 'tests/test_sources_optional.py' 2026-04-15T01:33:00,316 adding 'tests/test_validation_and_edge_cases.py' 2026-04-15T01:33:00,317 adding 'tests/test_variant_expression_filters.py' 2026-04-15T01:33:00,319 adding 'tests/test_wide.py' 2026-04-15T01:33:00,321 adding 'topiary/__init__.py' 2026-04-15T01:33:00,325 adding 'topiary/cached.py' 2026-04-15T01:33:00,327 adding 'topiary/filters.py' 2026-04-15T01:33:00,329 adding 'topiary/inputs.py' 2026-04-15T01:33:00,330 adding 'topiary/io.py' 2026-04-15T01:33:00,332 adding 'topiary/io_lens.py' 2026-04-15T01:33:00,334 adding 'topiary/io_protein_fragment.py' 2026-04-15T01:33:00,338 adding 'topiary/predictor.py' 2026-04-15T01:33:00,340 adding 'topiary/properties.py' 2026-04-15T01:33:00,343 adding 'topiary/protein_fragment.py' 2026-04-15T01:33:00,345 adding 'topiary/result.py' 2026-04-15T01:33:00,346 adding 'topiary/sequence_helpers.py' 2026-04-15T01:33:00,348 adding 'topiary/sources.py' 2026-04-15T01:33:00,350 adding 'topiary/wide.py' 2026-04-15T01:33:00,352 adding 'topiary/cli/__init__.py' 2026-04-15T01:33:00,354 adding 'topiary/cli/args.py' 2026-04-15T01:33:00,356 adding 'topiary/cli/errors.py' 2026-04-15T01:33:00,357 adding 'topiary/cli/filtering.py' 2026-04-15T01:33:00,359 adding 'topiary/cli/outputs.py' 2026-04-15T01:33:00,360 adding 'topiary/cli/protein_changes.py' 2026-04-15T01:33:00,362 adding 'topiary/cli/rna.py' 2026-04-15T01:33:00,363 adding 'topiary/cli/script.py' 2026-04-15T01:33:00,364 adding 'topiary/cli/sequence.py' 2026-04-15T01:33:00,366 adding 'topiary/ranking/__init__.py' 2026-04-15T01:33:00,367 adding 'topiary/ranking/apply.py' 2026-04-15T01:33:00,373 adding 'topiary/ranking/nodes.py' 2026-04-15T01:33:00,375 adding 'topiary/ranking/parser.py' 2026-04-15T01:33:00,377 adding 'topiary/rna/__init__.py' 2026-04-15T01:33:00,378 adding 'topiary/rna/common.py' 2026-04-15T01:33:00,380 adding 'topiary/rna/cufflinks.py' 2026-04-15T01:33:00,382 adding 'topiary/rna/expression_loader.py' 2026-04-15T01:33:00,383 adding 'topiary/rna/gtf.py' 2026-04-15T01:33:00,387 adding 'topiary-5.6.0.dist-info/licenses/LICENSE' 2026-04-15T01:33:00,390 adding 'topiary-5.6.0.dist-info/METADATA' 2026-04-15T01:33:00,391 adding 'topiary-5.6.0.dist-info/WHEEL' 2026-04-15T01:33:00,392 adding 'topiary-5.6.0.dist-info/entry_points.txt' 2026-04-15T01:33:00,392 adding 'topiary-5.6.0.dist-info/top_level.txt' 2026-04-15T01:33:00,394 adding 'topiary-5.6.0.dist-info/RECORD' 2026-04-15T01:33:00,398 removing build/bdist.linux-armv7l/wheel 2026-04-15T01:33:00,513 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-15T01:33:00,522 Created wheel for topiary: filename=topiary-5.6.0-py3-none-any.whl size=203190 sha256=58913ecb381c105b1cdb32319e3ee965c7a210d0cb08a439db6812d08d978157 2026-04-15T01:33:00,523 Stored in directory: /tmp/pip-ephem-wheel-cache-n9xz0u85/wheels/a4/e0/58/6a92837da6a15193add55d82f0a44725f12f1966647a3e0920 2026-04-15T01:33:00,540 Successfully built topiary 2026-04-15T01:33:00,549 Removed build tracker: '/tmp/pip-build-tracker-svq578e0'