2026-05-06T16:25:45,919 Created temporary directory: /tmp/pip-ephem-wheel-cache-_feeym1a 2026-05-06T16:25:45,920 Created temporary directory: /tmp/pip-build-tracker-0dr8dpq4 2026-05-06T16:25:45,921 Initialized build tracking at /tmp/pip-build-tracker-0dr8dpq4 2026-05-06T16:25:45,921 Created build tracker: /tmp/pip-build-tracker-0dr8dpq4 2026-05-06T16:25:45,922 Entered build tracker: /tmp/pip-build-tracker-0dr8dpq4 2026-05-06T16:25:45,923 Created temporary directory: /tmp/pip-wheel-seckks2g 2026-05-06T16:25:45,925 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 2026-05-06T16:25:45,928 Created temporary directory: /tmp/pip-ephem-wheel-cache-09n7t7rh 2026-05-06T16:25:45,951 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-06T16:25:45,955 2 location(s) to search for versions of topiary: 2026-05-06T16:25:45,955 * https://pypi.org/simple/topiary/ 2026-05-06T16:25:45,955 * https://www.piwheels.org/simple/topiary/ 2026-05-06T16:25:45,956 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-05-06T16:25:45,956 Getting page https://pypi.org/simple/topiary/ 2026-05-06T16:25:45,958 Found index url https://pypi.org/simple 2026-05-06T16:25:46,184 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-05-06T16:25:46,203 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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Fetching project page and analyzing links: https://www.piwheels.org/simple/topiary/ 2026-05-06T16:25:46,291 Getting page https://www.piwheels.org/simple/topiary/ 2026-05-06T16:25:46,292 Found index url https://www.piwheels.org/simple 2026-05-06T16:25:46,464 Fetched page https://www.piwheels.org/simple/topiary/ as text/html 2026-05-06T16:25:46,482 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.10.6-py3-none-any.whl#sha256=2d1779c8170e6e40a6e5d93d2fbd639a1a38d3f4dc2487eccb07199fb5397cc9 (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T16:25:46,482 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.10.5-py3-none-any.whl#sha256=a46ce83ab3367f052c6b2da3c1e7a383b1fb356ee4a2baaaa80d464ac363a933 (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T16:25:46,483 Skipping link: No binaries permitted for topiary: 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https://www.piwheels.org/simple/topiary/topiary-5.9.0-py3-none-any.whl#sha256=94ec090d0f2805af5bdc4039e5d4b2ce2f2e3e26beb02f61f1991ad03cc43f0b (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T16:25:46,487 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.8.0-py3-none-any.whl#sha256=062f06db79fc4f0b2a47b4faf04948ff744a7c5dd7387301f8ce0ee925176ea2 (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T16:25:46,488 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.7.0-py3-none-any.whl#sha256=e7df872933c6b26a774433b8555e687898d6641f87b4b7602878d1bca941f80a (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T16:25:46,489 Skipping link: No binaries permitted for topiary: 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https://archive1.piwheels.org/simple/topiary/topiary-0.0.1-py3-none-any.whl#sha256=6743a02aee34bc7567913bbe5c15a321924d9e1cb2c15f956e4ebb9b321707f4 (from https://www.piwheels.org/simple/topiary/) 2026-05-06T16:25:46,519 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/) 2026-05-06T16:25:46,520 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-05-06T16:25:46,521 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-05-06T16:25:46,549 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-05-06T16:25:46,569 Collecting topiary==5.10.7 2026-05-06T16:25:46,571 Created temporary directory: /tmp/pip-unpack-7kx3b099 2026-05-06T16:25:46,794 Downloading topiary-5.10.7.tar.gz (221 kB) 2026-05-06T16:25:47,093 Added topiary==5.10.7 from https://files.pythonhosted.org/packages/2b/bf/7228c65faa6b5b4f4a1bad914a478aaf75384db11567cba1e6e3ab2a09c7/topiary-5.10.7.tar.gz to build tracker '/tmp/pip-build-tracker-0dr8dpq4' 2026-05-06T16:25:47,098 Created temporary directory: /tmp/pip-build-env-1y_4koaz 2026-05-06T16:25:47,102 Installing build dependencies: started 2026-05-06T16:25:47,103 Running command pip subprocess to install build dependencies 2026-05-06T16:25:48,249 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-06T16:25:48,692 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 2026-05-06T16:25:48,716 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-06T16:25:50,494 Collecting setuptools>=64 2026-05-06T16:25:50,586 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-06T16:25:53,596 Installing collected packages: setuptools 2026-05-06T16:25:56,684 Successfully installed setuptools-82.0.1 2026-05-06T16:25:56,955 Installing build dependencies: finished with status 'done' 2026-05-06T16:25:56,962 Getting requirements to build wheel: started 2026-05-06T16:25:56,964 Running command Getting requirements to build wheel 2026-05-06T16:25:57,652 /tmp/pip-build-env-1y_4koaz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T16:25:57,652 !! 2026-05-06T16:25:57,653 ******************************************************************************** 2026-05-06T16:25:57,654 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T16:25:57,655 License :: OSI Approved :: Apache Software License 2026-05-06T16:25:57,656 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T16:25:57,657 ******************************************************************************** 2026-05-06T16:25:57,658 !! 2026-05-06T16:25:57,659 dist._finalize_license_expression() 2026-05-06T16:25:57,659 /tmp/pip-build-env-1y_4koaz/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T16:25:57,660 !! 2026-05-06T16:25:57,661 ******************************************************************************** 2026-05-06T16:25:57,662 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T16:25:57,663 License :: OSI Approved :: Apache Software License 2026-05-06T16:25:57,664 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T16:25:57,665 ******************************************************************************** 2026-05-06T16:25:57,666 !! 2026-05-06T16:25:57,667 self._finalize_license_expression() 2026-05-06T16:25:57,667 running egg_info 2026-05-06T16:25:57,671 writing topiary.egg-info/PKG-INFO 2026-05-06T16:25:57,676 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-06T16:25:57,678 writing entry points to topiary.egg-info/entry_points.txt 2026-05-06T16:25:57,680 writing requirements to topiary.egg-info/requires.txt 2026-05-06T16:25:57,681 writing top-level names to topiary.egg-info/top_level.txt 2026-05-06T16:25:57,709 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T16:25:57,716 adding license file 'LICENSE' 2026-05-06T16:25:57,722 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T16:25:57,818 Getting requirements to build wheel: finished with status 'done' 2026-05-06T16:25:57,822 Created temporary directory: /tmp/pip-modern-metadata-pikw6j5r 2026-05-06T16:25:57,825 Preparing metadata (pyproject.toml): started 2026-05-06T16:25:57,826 Running command Preparing metadata (pyproject.toml) 2026-05-06T16:25:58,475 /tmp/pip-build-env-1y_4koaz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T16:25:58,476 !! 2026-05-06T16:25:58,477 ******************************************************************************** 2026-05-06T16:25:58,477 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T16:25:58,478 License :: OSI Approved :: Apache Software License 2026-05-06T16:25:58,479 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T16:25:58,480 ******************************************************************************** 2026-05-06T16:25:58,481 !! 2026-05-06T16:25:58,481 dist._finalize_license_expression() 2026-05-06T16:25:58,482 /tmp/pip-build-env-1y_4koaz/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T16:25:58,483 !! 2026-05-06T16:25:58,484 ******************************************************************************** 2026-05-06T16:25:58,484 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T16:25:58,486 License :: OSI Approved :: Apache Software License 2026-05-06T16:25:58,487 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T16:25:58,487 ******************************************************************************** 2026-05-06T16:25:58,489 !! 2026-05-06T16:25:58,489 self._finalize_license_expression() 2026-05-06T16:25:58,490 running dist_info 2026-05-06T16:25:58,498 creating /tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info 2026-05-06T16:25:58,499 writing /tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/PKG-INFO 2026-05-06T16:25:58,503 writing dependency_links to /tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/dependency_links.txt 2026-05-06T16:25:58,505 writing entry points to /tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/entry_points.txt 2026-05-06T16:25:58,506 writing requirements to /tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/requires.txt 2026-05-06T16:25:58,507 writing top-level names to /tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/top_level.txt 2026-05-06T16:25:58,509 writing manifest file '/tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/SOURCES.txt' 2026-05-06T16:25:58,535 reading manifest file '/tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/SOURCES.txt' 2026-05-06T16:25:58,537 adding license file 'LICENSE' 2026-05-06T16:25:58,542 writing manifest file '/tmp/pip-modern-metadata-pikw6j5r/topiary.egg-info/SOURCES.txt' 2026-05-06T16:25:58,544 creating '/tmp/pip-modern-metadata-pikw6j5r/topiary-5.10.7.dist-info' 2026-05-06T16:25:58,671 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-06T16:25:58,677 Source in /tmp/pip-wheel-seckks2g/topiary_d8e38d9044ea473db347745d1b64121a has version 5.10.7, which satisfies requirement topiary==5.10.7 from https://files.pythonhosted.org/packages/2b/bf/7228c65faa6b5b4f4a1bad914a478aaf75384db11567cba1e6e3ab2a09c7/topiary-5.10.7.tar.gz 2026-05-06T16:25:58,678 Removed topiary==5.10.7 from https://files.pythonhosted.org/packages/2b/bf/7228c65faa6b5b4f4a1bad914a478aaf75384db11567cba1e6e3ab2a09c7/topiary-5.10.7.tar.gz from build tracker '/tmp/pip-build-tracker-0dr8dpq4' 2026-05-06T16:25:58,686 Created temporary directory: /tmp/pip-unpack-jtrg74mg 2026-05-06T16:25:58,687 Building wheels for collected packages: topiary 2026-05-06T16:25:58,692 Created temporary directory: /tmp/pip-wheel-_l_oms11 2026-05-06T16:25:58,692 Destination directory: /tmp/pip-wheel-_l_oms11 2026-05-06T16:25:58,694 Building wheel for topiary (pyproject.toml): started 2026-05-06T16:25:58,696 Running command Building wheel for topiary (pyproject.toml) 2026-05-06T16:25:59,331 /tmp/pip-build-env-1y_4koaz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T16:25:59,331 !! 2026-05-06T16:25:59,332 ******************************************************************************** 2026-05-06T16:25:59,333 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T16:25:59,334 License :: OSI Approved :: Apache Software License 2026-05-06T16:25:59,335 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T16:25:59,335 ******************************************************************************** 2026-05-06T16:25:59,336 !! 2026-05-06T16:25:59,337 dist._finalize_license_expression() 2026-05-06T16:25:59,338 /tmp/pip-build-env-1y_4koaz/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T16:25:59,338 !! 2026-05-06T16:25:59,339 ******************************************************************************** 2026-05-06T16:25:59,340 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T16:25:59,341 License :: OSI Approved :: Apache Software License 2026-05-06T16:25:59,342 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T16:25:59,343 ******************************************************************************** 2026-05-06T16:25:59,344 !! 2026-05-06T16:25:59,345 self._finalize_license_expression() 2026-05-06T16:25:59,345 running bdist_wheel 2026-05-06T16:25:59,356 running build 2026-05-06T16:25:59,357 running build_py 2026-05-06T16:25:59,363 creating build/lib/topiary 2026-05-06T16:25:59,365 copying topiary/io.py -> build/lib/topiary 2026-05-06T16:25:59,368 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-06T16:25:59,370 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-06T16:25:59,373 copying topiary/result.py -> build/lib/topiary 2026-05-06T16:25:59,375 copying topiary/inputs.py -> build/lib/topiary 2026-05-06T16:25:59,378 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-06T16:25:59,380 copying topiary/__init__.py -> build/lib/topiary 2026-05-06T16:25:59,382 copying topiary/sources.py -> build/lib/topiary 2026-05-06T16:25:59,385 copying topiary/filters.py -> build/lib/topiary 2026-05-06T16:25:59,387 copying topiary/wide.py -> build/lib/topiary 2026-05-06T16:25:59,390 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-06T16:25:59,392 copying topiary/properties.py -> build/lib/topiary 2026-05-06T16:25:59,395 copying topiary/cached.py -> build/lib/topiary 2026-05-06T16:25:59,398 copying topiary/io_lens.py -> build/lib/topiary 2026-05-06T16:25:59,401 copying topiary/predictor.py -> build/lib/topiary 2026-05-06T16:25:59,406 creating build/lib/tests 2026-05-06T16:25:59,407 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-06T16:25:59,410 copying tests/test_result.py -> build/lib/tests 2026-05-06T16:25:59,412 copying tests/test_dataframe.py -> build/lib/tests 2026-05-06T16:25:59,414 copying tests/test_sources.py -> build/lib/tests 2026-05-06T16:25:59,416 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-06T16:25:59,419 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-06T16:25:59,421 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-06T16:25:59,423 copying tests/test_padding.py -> build/lib/tests 2026-05-06T16:25:59,425 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-06T16:25:59,427 copying tests/test_cli_script.py -> build/lib/tests 2026-05-06T16:25:59,429 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-06T16:25:59,431 copying tests/test_integration.py -> build/lib/tests 2026-05-06T16:25:59,433 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-06T16:25:59,435 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-06T16:25:59,438 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-06T16:25:59,440 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-06T16:25:59,441 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-06T16:25:59,443 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-06T16:25:59,445 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-06T16:25:59,448 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-06T16:25:59,450 copying tests/test_lazy_imports.py -> build/lib/tests 2026-05-06T16:25:59,452 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-06T16:25:59,455 copying tests/common.py -> build/lib/tests 2026-05-06T16:25:59,456 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-06T16:25:59,459 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-06T16:25:59,462 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-06T16:25:59,464 copying tests/__init__.py -> build/lib/tests 2026-05-06T16:25:59,466 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-06T16:25:59,469 copying tests/test_deploy_script.py -> build/lib/tests 2026-05-06T16:25:59,471 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-06T16:25:59,473 copying tests/test_wide.py -> build/lib/tests 2026-05-06T16:25:59,475 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-06T16:25:59,477 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-06T16:25:59,479 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-06T16:25:59,481 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-06T16:25:59,484 copying tests/data.py -> build/lib/tests 2026-05-06T16:25:59,486 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-06T16:25:59,488 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-06T16:25:59,490 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-06T16:25:59,492 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-06T16:25:59,494 copying tests/test_io.py -> build/lib/tests 2026-05-06T16:25:59,497 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-06T16:25:59,499 copying tests/test_inputs.py -> build/lib/tests 2026-05-06T16:25:59,501 copying tests/test_ranking.py -> build/lib/tests 2026-05-06T16:25:59,505 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-06T16:25:59,507 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-06T16:25:59,509 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-06T16:25:59,511 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-06T16:25:59,514 copying tests/test_io_lens.py -> build/lib/tests 2026-05-06T16:25:59,516 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-06T16:25:59,519 creating build/lib/topiary/ranking 2026-05-06T16:25:59,520 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-06T16:25:59,523 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-06T16:25:59,525 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-06T16:25:59,528 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-06T16:25:59,532 creating build/lib/topiary/cli 2026-05-06T16:25:59,533 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-06T16:25:59,535 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-06T16:25:59,537 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-06T16:25:59,539 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-06T16:25:59,541 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-06T16:25:59,543 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-06T16:25:59,545 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-06T16:25:59,547 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-06T16:25:59,549 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-06T16:25:59,552 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-06T16:25:59,555 creating build/lib/topiary/rna 2026-05-06T16:25:59,556 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-06T16:25:59,558 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-06T16:25:59,560 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-06T16:25:59,562 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-06T16:25:59,564 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-06T16:25:59,566 running egg_info 2026-05-06T16:25:59,575 writing topiary.egg-info/PKG-INFO 2026-05-06T16:25:59,579 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-06T16:25:59,581 writing entry points to topiary.egg-info/entry_points.txt 2026-05-06T16:25:59,582 writing requirements to topiary.egg-info/requires.txt 2026-05-06T16:25:59,583 writing top-level names to topiary.egg-info/top_level.txt 2026-05-06T16:25:59,600 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T16:25:59,606 adding license file 'LICENSE' 2026-05-06T16:25:59,612 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T16:25:59,629 installing to build/bdist.linux-armv7l/wheel 2026-05-06T16:25:59,630 running install 2026-05-06T16:25:59,653 running install_lib 2026-05-06T16:25:59,659 creating build/bdist.linux-armv7l/wheel 2026-05-06T16:25:59,661 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-06T16:25:59,662 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,665 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,668 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,670 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-06T16:25:59,671 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T16:25:59,674 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T16:25:59,676 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T16:25:59,679 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T16:25:59,682 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,684 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,687 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,690 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-06T16:25:59,691 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,693 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,696 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,697 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,699 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,701 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,703 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,706 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,709 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,711 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T16:25:59,714 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-06T16:25:59,715 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T16:25:59,718 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T16:25:59,719 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T16:25:59,722 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T16:25:59,723 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T16:25:59,725 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,727 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,730 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,732 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,734 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,737 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,740 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,742 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,745 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T16:25:59,749 creating build/bdist.linux-armv7l/wheel/tests 2026-05-06T16:25:59,750 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,753 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,756 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,758 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,760 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,763 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,765 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,767 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,769 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,772 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,774 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,776 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,778 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,780 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,782 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,784 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,786 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,788 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,790 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,792 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,795 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,796 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,799 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,801 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,803 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,806 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,808 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,810 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,813 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,815 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,817 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,819 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,822 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,824 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,826 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,828 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,830 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,832 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,834 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,836 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,838 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,841 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,844 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,846 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,852 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,854 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,857 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,859 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,862 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,865 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T16:25:59,867 running install_egg_info 2026-05-06T16:25:59,872 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.10.7-py3.11.egg-info 2026-05-06T16:25:59,885 running install_scripts 2026-05-06T16:25:59,899 creating build/bdist.linux-armv7l/wheel/topiary-5.10.7.dist-info/WHEEL 2026-05-06T16:25:59,902 creating '/tmp/pip-wheel-_l_oms11/.tmp-uon80tdg/topiary-5.10.7-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-06T16:25:59,905 adding 'tests/__init__.py' 2026-05-06T16:25:59,907 adding 'tests/common.py' 2026-05-06T16:25:59,908 adding 'tests/data.py' 2026-05-06T16:25:59,909 adding 'tests/test_args_outputs.py' 2026-05-06T16:25:59,914 adding 'tests/test_cached_predictor.py' 2026-05-06T16:25:59,916 adding 'tests/test_cli_cached_predictor.py' 2026-05-06T16:25:59,917 adding 'tests/test_cli_coverage.py' 2026-05-06T16:25:59,919 adding 'tests/test_cli_protein_changes.py' 2026-05-06T16:25:59,921 adding 'tests/test_cli_ranking.py' 2026-05-06T16:25:59,922 adding 'tests/test_cli_script.py' 2026-05-06T16:25:59,924 adding 'tests/test_contains_mutant_residues.py' 2026-05-06T16:25:59,925 adding 'tests/test_coverage_gaps.py' 2026-05-06T16:25:59,927 adding 'tests/test_dataframe.py' 2026-05-06T16:25:59,928 adding 'tests/test_deploy_script.py' 2026-05-06T16:25:59,929 adding 'tests/test_direct_input_regressions.py' 2026-05-06T16:25:59,932 adding 'tests/test_dsl_extensions.py' 2026-05-06T16:25:59,934 adding 'tests/test_dsl_polish.py' 2026-05-06T16:25:59,937 adding 'tests/test_dsl_roundtrip.py' 2026-05-06T16:25:59,938 adding 'tests/test_edge_case_fixtures.py' 2026-05-06T16:25:59,940 adding 'tests/test_effect_expression_filters.py' 2026-05-06T16:25:59,941 adding 'tests/test_end_to_end.py' 2026-05-06T16:25:59,943 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-06T16:25:59,944 adding 'tests/test_expression_integration.py' 2026-05-06T16:25:59,945 adding 'tests/test_expression_loader.py' 2026-05-06T16:25:59,948 adding 'tests/test_frameshift_fragments.py' 2026-05-06T16:25:59,950 adding 'tests/test_inputs.py' 2026-05-06T16:25:59,951 adding 'tests/test_integration.py' 2026-05-06T16:25:59,953 adding 'tests/test_io.py' 2026-05-06T16:25:59,955 adding 'tests/test_io_lens.py' 2026-05-06T16:25:59,957 adding 'tests/test_lazy_imports.py' 2026-05-06T16:25:59,958 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-06T16:25:59,959 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-06T16:25:59,961 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-06T16:25:59,962 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-06T16:25:59,964 adding 'tests/test_padding.py' 2026-05-06T16:25:59,965 adding 'tests/test_peptide_mutation_interval.py' 2026-05-06T16:25:59,968 adding 'tests/test_predict_from_fragments.py' 2026-05-06T16:25:59,970 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-06T16:25:59,972 adding 'tests/test_predictor_internals.py' 2026-05-06T16:25:59,974 adding 'tests/test_protein_fragment.py' 2026-05-06T16:25:59,983 adding 'tests/test_ranking.py' 2026-05-06T16:25:59,986 adding 'tests/test_result.py' 2026-05-06T16:25:59,987 adding 'tests/test_rna_helpers.py' 2026-05-06T16:25:59,990 adding 'tests/test_self_proteome.py' 2026-05-06T16:25:59,991 adding 'tests/test_sequence_helpers.py' 2026-05-06T16:25:59,993 adding 'tests/test_sources.py' 2026-05-06T16:25:59,994 adding 'tests/test_sources_optional.py' 2026-05-06T16:25:59,996 adding 'tests/test_validation_and_edge_cases.py' 2026-05-06T16:25:59,997 adding 'tests/test_variant_expression_filters.py' 2026-05-06T16:26:00,000 adding 'tests/test_wide.py' 2026-05-06T16:26:00,002 adding 'topiary/__init__.py' 2026-05-06T16:26:00,008 adding 'topiary/cached.py' 2026-05-06T16:26:00,009 adding 'topiary/filters.py' 2026-05-06T16:26:00,011 adding 'topiary/inputs.py' 2026-05-06T16:26:00,013 adding 'topiary/io.py' 2026-05-06T16:26:00,015 adding 'topiary/io_lens.py' 2026-05-06T16:26:00,016 adding 'topiary/io_protein_fragment.py' 2026-05-06T16:26:00,021 adding 'topiary/predictor.py' 2026-05-06T16:26:00,024 adding 'topiary/properties.py' 2026-05-06T16:26:00,026 adding 'topiary/protein_fragment.py' 2026-05-06T16:26:00,029 adding 'topiary/result.py' 2026-05-06T16:26:00,033 adding 'topiary/self_proteome.py' 2026-05-06T16:26:00,034 adding 'topiary/sequence_helpers.py' 2026-05-06T16:26:00,036 adding 'topiary/sources.py' 2026-05-06T16:26:00,038 adding 'topiary/wide.py' 2026-05-06T16:26:00,040 adding 'topiary/cli/__init__.py' 2026-05-06T16:26:00,043 adding 'topiary/cli/args.py' 2026-05-06T16:26:00,045 adding 'topiary/cli/cached_predictor.py' 2026-05-06T16:26:00,047 adding 'topiary/cli/errors.py' 2026-05-06T16:26:00,048 adding 'topiary/cli/filtering.py' 2026-05-06T16:26:00,049 adding 'topiary/cli/outputs.py' 2026-05-06T16:26:00,051 adding 'topiary/cli/protein_changes.py' 2026-05-06T16:26:00,052 adding 'topiary/cli/rna.py' 2026-05-06T16:26:00,054 adding 'topiary/cli/script.py' 2026-05-06T16:26:00,055 adding 'topiary/cli/sequence.py' 2026-05-06T16:26:00,057 adding 'topiary/ranking/__init__.py' 2026-05-06T16:26:00,058 adding 'topiary/ranking/apply.py' 2026-05-06T16:26:00,065 adding 'topiary/ranking/nodes.py' 2026-05-06T16:26:00,068 adding 'topiary/ranking/parser.py' 2026-05-06T16:26:00,070 adding 'topiary/rna/__init__.py' 2026-05-06T16:26:00,071 adding 'topiary/rna/common.py' 2026-05-06T16:26:00,073 adding 'topiary/rna/cufflinks.py' 2026-05-06T16:26:00,075 adding 'topiary/rna/expression_loader.py' 2026-05-06T16:26:00,076 adding 'topiary/rna/gtf.py' 2026-05-06T16:26:00,079 adding 'topiary-5.10.7.dist-info/licenses/LICENSE' 2026-05-06T16:26:00,082 adding 'topiary-5.10.7.dist-info/METADATA' 2026-05-06T16:26:00,084 adding 'topiary-5.10.7.dist-info/WHEEL' 2026-05-06T16:26:00,085 adding 'topiary-5.10.7.dist-info/entry_points.txt' 2026-05-06T16:26:00,086 adding 'topiary-5.10.7.dist-info/top_level.txt' 2026-05-06T16:26:00,087 adding 'topiary-5.10.7.dist-info/RECORD' 2026-05-06T16:26:00,092 removing build/bdist.linux-armv7l/wheel 2026-05-06T16:26:00,208 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-06T16:26:00,217 Created wheel for topiary: filename=topiary-5.10.7-py3-none-any.whl size=248775 sha256=754dfc1d8861cd497c085fb6a827410c2cf99b805952f6f8d7b546f2d443461f 2026-05-06T16:26:00,218 Stored in directory: /tmp/pip-ephem-wheel-cache-09n7t7rh/wheels/77/99/5a/d4b7cd138ac1931b7493ecd2a31cce32a0a47a7bb4c7aa047d 2026-05-06T16:26:00,235 Successfully built topiary 2026-05-06T16:26:00,246 Removed build tracker: '/tmp/pip-build-tracker-0dr8dpq4'