2026-05-06T17:25:59,111 Created temporary directory: /tmp/pip-ephem-wheel-cache-nc3xisns 2026-05-06T17:25:59,113 Created temporary directory: /tmp/pip-build-tracker-3gc5jdw3 2026-05-06T17:25:59,114 Initialized build tracking at /tmp/pip-build-tracker-3gc5jdw3 2026-05-06T17:25:59,115 Created build tracker: /tmp/pip-build-tracker-3gc5jdw3 2026-05-06T17:25:59,115 Entered build tracker: /tmp/pip-build-tracker-3gc5jdw3 2026-05-06T17:25:59,116 Created temporary directory: /tmp/pip-wheel-keu_ouf4 2026-05-06T17:25:59,119 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 2026-05-06T17:25:59,122 Created temporary directory: /tmp/pip-ephem-wheel-cache-9o5e7k59 2026-05-06T17:25:59,144 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-06T17:25:59,148 2 location(s) to search for versions of topiary: 2026-05-06T17:25:59,148 * https://pypi.org/simple/topiary/ 2026-05-06T17:25:59,148 * https://www.piwheels.org/simple/topiary/ 2026-05-06T17:25:59,148 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-05-06T17:25:59,149 Getting page https://pypi.org/simple/topiary/ 2026-05-06T17:25:59,151 Found index url https://pypi.org/simple 2026-05-06T17:25:59,305 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-05-06T17:25:59,325 Found link https://files.pythonhosted.org/packages/38/f6/60c60d77093e492c9a139a87514fa230296ca94080fec6d479f22bf5cfcd/topiary-0.0.0.tar.gz (from 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(requires-python:>=3.9) 2026-05-06T17:25:59,406 Found link https://files.pythonhosted.org/packages/54/33/00f95ffcb580dd2432682d7fc1f0b0ccafda4472e82794a16c5f75dec5a8/topiary-5.10.5.tar.gz (from https://pypi.org/simple/topiary/) (requires-python:>=3.9), version: 5.10.5 2026-05-06T17:25:59,406 Skipping link: No binaries permitted for topiary: https://files.pythonhosted.org/packages/f1/38/f058a018409822abb7a973b2262da1130cb39bee13a28d2f3926b9795374/topiary-5.10.6-py3-none-any.whl (from https://pypi.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T17:25:59,407 Found link https://files.pythonhosted.org/packages/15/38/42690947572562b575e0559dd92966cadd119d2b80b0851e991259609702/topiary-5.10.6.tar.gz (from https://pypi.org/simple/topiary/) (requires-python:>=3.9), version: 5.10.6 2026-05-06T17:25:59,408 Skipping link: No binaries permitted for topiary: 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Fetching project page and analyzing links: https://www.piwheels.org/simple/topiary/ 2026-05-06T17:25:59,412 Getting page https://www.piwheels.org/simple/topiary/ 2026-05-06T17:25:59,413 Found index url https://www.piwheels.org/simple 2026-05-06T17:25:59,591 Fetched page https://www.piwheels.org/simple/topiary/ as text/html 2026-05-06T17:25:59,609 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.10.7-py3-none-any.whl#sha256=754dfc1d8861cd497c085fb6a827410c2cf99b805952f6f8d7b546f2d443461f (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T17:25:59,610 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) 2026-05-06T17:25:59,610 Skipping link: No binaries permitted for topiary: 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https://www.piwheels.org/simple/topiary/topiary-5.9.1-py3-none-any.whl#sha256=0a4121ec262c842e9630d3057235387ce9b51ec6ef61a83940a7cbae9b8c330a (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-05-06T17:25:59,615 Skipping link: No binaries permitted for topiary: 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) 2026-05-06T17:25:59,615 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) 2026-05-06T17:25:59,616 Skipping link: No binaries permitted for topiary: 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discarding no candidates 2026-05-06T17:25:59,699 Collecting topiary==5.10.8 2026-05-06T17:25:59,701 Created temporary directory: /tmp/pip-unpack-x81d0lel 2026-05-06T17:25:59,933 Downloading topiary-5.10.8.tar.gz (221 kB) 2026-05-06T17:26:00,237 Added topiary==5.10.8 from https://files.pythonhosted.org/packages/a5/0e/6b5699c0e436716e5e2e9deae17a2d5cf08760508628b492193d7b058fee/topiary-5.10.8.tar.gz to build tracker '/tmp/pip-build-tracker-3gc5jdw3' 2026-05-06T17:26:00,241 Created temporary directory: /tmp/pip-build-env-ox5walq9 2026-05-06T17:26:00,245 Installing build dependencies: started 2026-05-06T17:26:00,246 Running command pip subprocess to install build dependencies 2026-05-06T17:26:01,360 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-05-06T17:26:01,761 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 2026-05-06T17:26:01,783 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-05-06T17:26:03,533 Collecting setuptools>=64 2026-05-06T17:26:03,610 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-05-06T17:26:06,580 Installing collected packages: setuptools 2026-05-06T17:26:09,635 Successfully installed setuptools-82.0.1 2026-05-06T17:26:09,903 Installing build dependencies: finished with status 'done' 2026-05-06T17:26:09,910 Getting requirements to build wheel: started 2026-05-06T17:26:09,912 Running command Getting requirements to build wheel 2026-05-06T17:26:10,603 /tmp/pip-build-env-ox5walq9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T17:26:10,603 !! 2026-05-06T17:26:10,604 ******************************************************************************** 2026-05-06T17:26:10,605 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T17:26:10,606 License :: OSI Approved :: Apache Software License 2026-05-06T17:26:10,607 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T17:26:10,608 ******************************************************************************** 2026-05-06T17:26:10,609 !! 2026-05-06T17:26:10,610 dist._finalize_license_expression() 2026-05-06T17:26:10,610 /tmp/pip-build-env-ox5walq9/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T17:26:10,611 !! 2026-05-06T17:26:10,612 ******************************************************************************** 2026-05-06T17:26:10,613 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T17:26:10,614 License :: OSI Approved :: Apache Software License 2026-05-06T17:26:10,615 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T17:26:10,616 ******************************************************************************** 2026-05-06T17:26:10,617 !! 2026-05-06T17:26:10,618 self._finalize_license_expression() 2026-05-06T17:26:10,618 running egg_info 2026-05-06T17:26:10,622 writing topiary.egg-info/PKG-INFO 2026-05-06T17:26:10,626 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-06T17:26:10,628 writing entry points to topiary.egg-info/entry_points.txt 2026-05-06T17:26:10,630 writing requirements to topiary.egg-info/requires.txt 2026-05-06T17:26:10,631 writing top-level names to topiary.egg-info/top_level.txt 2026-05-06T17:26:10,659 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T17:26:10,665 adding license file 'LICENSE' 2026-05-06T17:26:10,672 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T17:26:10,769 Getting requirements to build wheel: finished with status 'done' 2026-05-06T17:26:10,773 Created temporary directory: /tmp/pip-modern-metadata-gyzami1h 2026-05-06T17:26:10,775 Preparing metadata (pyproject.toml): started 2026-05-06T17:26:10,776 Running command Preparing metadata (pyproject.toml) 2026-05-06T17:26:11,416 /tmp/pip-build-env-ox5walq9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T17:26:11,417 !! 2026-05-06T17:26:11,418 ******************************************************************************** 2026-05-06T17:26:11,418 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T17:26:11,419 License :: OSI Approved :: Apache Software License 2026-05-06T17:26:11,420 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T17:26:11,421 ******************************************************************************** 2026-05-06T17:26:11,422 !! 2026-05-06T17:26:11,422 dist._finalize_license_expression() 2026-05-06T17:26:11,423 /tmp/pip-build-env-ox5walq9/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T17:26:11,423 !! 2026-05-06T17:26:11,424 ******************************************************************************** 2026-05-06T17:26:11,425 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T17:26:11,426 License :: OSI Approved :: Apache Software License 2026-05-06T17:26:11,427 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T17:26:11,428 ******************************************************************************** 2026-05-06T17:26:11,429 !! 2026-05-06T17:26:11,430 self._finalize_license_expression() 2026-05-06T17:26:11,430 running dist_info 2026-05-06T17:26:11,439 creating /tmp/pip-modern-metadata-gyzami1h/topiary.egg-info 2026-05-06T17:26:11,440 writing /tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/PKG-INFO 2026-05-06T17:26:11,444 writing dependency_links to /tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/dependency_links.txt 2026-05-06T17:26:11,446 writing entry points to /tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/entry_points.txt 2026-05-06T17:26:11,448 writing requirements to /tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/requires.txt 2026-05-06T17:26:11,449 writing top-level names to /tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/top_level.txt 2026-05-06T17:26:11,450 writing manifest file '/tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/SOURCES.txt' 2026-05-06T17:26:11,475 reading manifest file '/tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/SOURCES.txt' 2026-05-06T17:26:11,477 adding license file 'LICENSE' 2026-05-06T17:26:11,483 writing manifest file '/tmp/pip-modern-metadata-gyzami1h/topiary.egg-info/SOURCES.txt' 2026-05-06T17:26:11,484 creating '/tmp/pip-modern-metadata-gyzami1h/topiary-5.10.8.dist-info' 2026-05-06T17:26:11,609 Preparing metadata (pyproject.toml): finished with status 'done' 2026-05-06T17:26:11,616 Source in /tmp/pip-wheel-keu_ouf4/topiary_6b7559a45f1248c886695ce45f832d4a has version 5.10.8, which satisfies requirement topiary==5.10.8 from https://files.pythonhosted.org/packages/a5/0e/6b5699c0e436716e5e2e9deae17a2d5cf08760508628b492193d7b058fee/topiary-5.10.8.tar.gz 2026-05-06T17:26:11,617 Removed topiary==5.10.8 from https://files.pythonhosted.org/packages/a5/0e/6b5699c0e436716e5e2e9deae17a2d5cf08760508628b492193d7b058fee/topiary-5.10.8.tar.gz from build tracker '/tmp/pip-build-tracker-3gc5jdw3' 2026-05-06T17:26:11,625 Created temporary directory: /tmp/pip-unpack-lf_o9bhi 2026-05-06T17:26:11,625 Building wheels for collected packages: topiary 2026-05-06T17:26:11,630 Created temporary directory: /tmp/pip-wheel-adanqagm 2026-05-06T17:26:11,630 Destination directory: /tmp/pip-wheel-adanqagm 2026-05-06T17:26:11,633 Building wheel for topiary (pyproject.toml): started 2026-05-06T17:26:11,634 Running command Building wheel for topiary (pyproject.toml) 2026-05-06T17:26:12,256 /tmp/pip-build-env-ox5walq9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T17:26:12,257 !! 2026-05-06T17:26:12,258 ******************************************************************************** 2026-05-06T17:26:12,258 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T17:26:12,259 License :: OSI Approved :: Apache Software License 2026-05-06T17:26:12,260 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T17:26:12,261 ******************************************************************************** 2026-05-06T17:26:12,262 !! 2026-05-06T17:26:12,262 dist._finalize_license_expression() 2026-05-06T17:26:12,263 /tmp/pip-build-env-ox5walq9/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-05-06T17:26:12,264 !! 2026-05-06T17:26:12,265 ******************************************************************************** 2026-05-06T17:26:12,266 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-05-06T17:26:12,267 License :: OSI Approved :: Apache Software License 2026-05-06T17:26:12,268 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-05-06T17:26:12,269 ******************************************************************************** 2026-05-06T17:26:12,270 !! 2026-05-06T17:26:12,271 self._finalize_license_expression() 2026-05-06T17:26:12,271 running bdist_wheel 2026-05-06T17:26:12,284 running build 2026-05-06T17:26:12,285 running build_py 2026-05-06T17:26:12,291 creating build/lib/topiary 2026-05-06T17:26:12,293 copying topiary/properties.py -> build/lib/topiary 2026-05-06T17:26:12,297 copying topiary/self_proteome.py -> build/lib/topiary 2026-05-06T17:26:12,300 copying topiary/__init__.py -> build/lib/topiary 2026-05-06T17:26:12,302 copying topiary/protein_fragment.py -> build/lib/topiary 2026-05-06T17:26:12,304 copying topiary/result.py -> build/lib/topiary 2026-05-06T17:26:12,307 copying topiary/sources.py -> build/lib/topiary 2026-05-06T17:26:12,309 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-05-06T17:26:12,311 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-05-06T17:26:12,313 copying topiary/io.py -> build/lib/topiary 2026-05-06T17:26:12,316 copying topiary/wide.py -> build/lib/topiary 2026-05-06T17:26:12,318 copying topiary/io_lens.py -> build/lib/topiary 2026-05-06T17:26:12,321 copying topiary/inputs.py -> build/lib/topiary 2026-05-06T17:26:12,324 copying topiary/cached.py -> build/lib/topiary 2026-05-06T17:26:12,327 copying topiary/predictor.py -> build/lib/topiary 2026-05-06T17:26:12,330 copying topiary/filters.py -> build/lib/topiary 2026-05-06T17:26:12,334 creating build/lib/tests 2026-05-06T17:26:12,335 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-05-06T17:26:12,337 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-05-06T17:26:12,340 copying tests/test_integration.py -> build/lib/tests 2026-05-06T17:26:12,342 copying tests/test_io.py -> build/lib/tests 2026-05-06T17:26:12,344 copying tests/test_args_outputs.py -> build/lib/tests 2026-05-06T17:26:12,346 copying tests/test_self_proteome.py -> build/lib/tests 2026-05-06T17:26:12,349 copying tests/test_ranking.py -> build/lib/tests 2026-05-06T17:26:12,353 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-05-06T17:26:12,355 copying tests/__init__.py -> build/lib/tests 2026-05-06T17:26:12,357 copying tests/test_dsl_polish.py -> build/lib/tests 2026-05-06T17:26:12,359 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-05-06T17:26:12,361 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-05-06T17:26:12,363 copying tests/test_cli_cached_predictor.py -> build/lib/tests 2026-05-06T17:26:12,366 copying tests/test_inputs.py -> build/lib/tests 2026-05-06T17:26:12,369 copying tests/test_lazy_imports.py -> build/lib/tests 2026-05-06T17:26:12,371 copying tests/test_sources.py -> build/lib/tests 2026-05-06T17:26:12,373 copying tests/test_wide.py -> build/lib/tests 2026-05-06T17:26:12,376 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-05-06T17:26:12,377 copying tests/test_cli_coverage.py -> build/lib/tests 2026-05-06T17:26:12,380 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-05-06T17:26:12,383 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-05-06T17:26:12,385 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-05-06T17:26:12,386 copying tests/test_padding.py -> build/lib/tests 2026-05-06T17:26:12,388 copying tests/data.py -> build/lib/tests 2026-05-06T17:26:12,390 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-05-06T17:26:12,392 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-05-06T17:26:12,395 copying tests/test_dataframe.py -> build/lib/tests 2026-05-06T17:26:12,397 copying tests/test_end_to_end.py -> build/lib/tests 2026-05-06T17:26:12,400 copying tests/test_predictor_internals.py -> build/lib/tests 2026-05-06T17:26:12,402 copying tests/test_sources_optional.py -> build/lib/tests 2026-05-06T17:26:12,404 copying tests/common.py -> build/lib/tests 2026-05-06T17:26:12,406 copying tests/test_cli_ranking.py -> build/lib/tests 2026-05-06T17:26:12,409 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-05-06T17:26:12,411 copying tests/test_result.py -> build/lib/tests 2026-05-06T17:26:12,414 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-05-06T17:26:12,416 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-05-06T17:26:12,418 copying tests/test_protein_fragment.py -> build/lib/tests 2026-05-06T17:26:12,421 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-05-06T17:26:12,424 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-05-06T17:26:12,426 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-05-06T17:26:12,428 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-05-06T17:26:12,430 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-05-06T17:26:12,433 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-05-06T17:26:12,435 copying tests/test_expression_integration.py -> build/lib/tests 2026-05-06T17:26:12,437 copying tests/test_rna_helpers.py -> build/lib/tests 2026-05-06T17:26:12,439 copying tests/test_cli_script.py -> build/lib/tests 2026-05-06T17:26:12,441 copying tests/test_io_lens.py -> build/lib/tests 2026-05-06T17:26:12,444 copying tests/test_expression_loader.py -> build/lib/tests 2026-05-06T17:26:12,446 copying tests/test_cached_predictor.py -> build/lib/tests 2026-05-06T17:26:12,450 copying tests/test_deploy_script.py -> build/lib/tests 2026-05-06T17:26:12,452 creating build/lib/topiary/ranking 2026-05-06T17:26:12,453 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-05-06T17:26:12,456 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-05-06T17:26:12,458 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-05-06T17:26:12,460 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-05-06T17:26:12,464 creating build/lib/topiary/cli 2026-05-06T17:26:12,465 copying topiary/cli/cached_predictor.py -> build/lib/topiary/cli 2026-05-06T17:26:12,467 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-05-06T17:26:12,469 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-05-06T17:26:12,471 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-05-06T17:26:12,473 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-05-06T17:26:12,476 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-05-06T17:26:12,477 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-05-06T17:26:12,479 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-05-06T17:26:12,481 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-05-06T17:26:12,484 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-05-06T17:26:12,486 creating build/lib/topiary/rna 2026-05-06T17:26:12,487 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-05-06T17:26:12,489 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-05-06T17:26:12,491 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-05-06T17:26:12,493 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-05-06T17:26:12,495 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-05-06T17:26:12,497 running egg_info 2026-05-06T17:26:12,507 writing topiary.egg-info/PKG-INFO 2026-05-06T17:26:12,511 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-05-06T17:26:12,512 writing entry points to topiary.egg-info/entry_points.txt 2026-05-06T17:26:12,514 writing requirements to topiary.egg-info/requires.txt 2026-05-06T17:26:12,515 writing top-level names to topiary.egg-info/top_level.txt 2026-05-06T17:26:12,532 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T17:26:12,538 adding license file 'LICENSE' 2026-05-06T17:26:12,544 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-05-06T17:26:12,562 installing to build/bdist.linux-armv7l/wheel 2026-05-06T17:26:12,562 running install 2026-05-06T17:26:12,586 running install_lib 2026-05-06T17:26:12,591 creating build/bdist.linux-armv7l/wheel 2026-05-06T17:26:12,594 creating build/bdist.linux-armv7l/wheel/topiary 2026-05-06T17:26:12,595 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,598 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-05-06T17:26:12,600 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T17:26:12,602 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T17:26:12,604 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T17:26:12,607 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-05-06T17:26:12,610 copying build/lib/topiary/self_proteome.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,612 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,614 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,617 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,620 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,622 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,625 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-05-06T17:26:12,626 copying build/lib/topiary/cli/cached_predictor.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,628 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,631 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,633 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,635 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,637 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,639 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,641 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,643 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,646 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-05-06T17:26:12,648 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,650 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,652 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,654 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,657 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-05-06T17:26:12,658 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T17:26:12,660 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T17:26:12,663 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T17:26:12,664 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T17:26:12,666 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-05-06T17:26:12,669 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,671 copying build/lib/topiary/cached.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,675 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,677 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-05-06T17:26:12,681 creating build/bdist.linux-armv7l/wheel/tests 2026-05-06T17:26:12,682 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,684 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,687 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,689 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,691 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,693 copying build/lib/tests/test_self_proteome.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,696 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,700 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,702 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,703 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,706 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,708 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,709 copying build/lib/tests/test_cli_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,712 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,714 copying build/lib/tests/test_lazy_imports.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,716 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,718 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,720 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,722 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,724 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,727 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,729 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,731 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,732 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,734 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,736 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,739 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,741 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,743 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,746 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,747 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,749 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,751 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,754 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,756 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,759 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,761 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,764 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,766 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,769 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,771 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,773 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,775 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,777 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,780 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,781 copying build/lib/tests/test_cli_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,783 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,786 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,788 copying build/lib/tests/test_cached_predictor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,792 copying build/lib/tests/test_deploy_script.py -> build/bdist.linux-armv7l/wheel/./tests 2026-05-06T17:26:12,793 running install_egg_info 2026-05-06T17:26:12,798 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.10.8-py3.11.egg-info 2026-05-06T17:26:12,810 running install_scripts 2026-05-06T17:26:12,824 creating build/bdist.linux-armv7l/wheel/topiary-5.10.8.dist-info/WHEEL 2026-05-06T17:26:12,827 creating '/tmp/pip-wheel-adanqagm/.tmp-wyv4qlxs/topiary-5.10.8-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-05-06T17:26:12,830 adding 'tests/__init__.py' 2026-05-06T17:26:12,831 adding 'tests/common.py' 2026-05-06T17:26:12,833 adding 'tests/data.py' 2026-05-06T17:26:12,834 adding 'tests/test_args_outputs.py' 2026-05-06T17:26:12,838 adding 'tests/test_cached_predictor.py' 2026-05-06T17:26:12,841 adding 'tests/test_cli_cached_predictor.py' 2026-05-06T17:26:12,843 adding 'tests/test_cli_coverage.py' 2026-05-06T17:26:12,844 adding 'tests/test_cli_protein_changes.py' 2026-05-06T17:26:12,846 adding 'tests/test_cli_ranking.py' 2026-05-06T17:26:12,847 adding 'tests/test_cli_script.py' 2026-05-06T17:26:12,849 adding 'tests/test_contains_mutant_residues.py' 2026-05-06T17:26:12,851 adding 'tests/test_coverage_gaps.py' 2026-05-06T17:26:12,852 adding 'tests/test_dataframe.py' 2026-05-06T17:26:12,853 adding 'tests/test_deploy_script.py' 2026-05-06T17:26:12,854 adding 'tests/test_direct_input_regressions.py' 2026-05-06T17:26:12,857 adding 'tests/test_dsl_extensions.py' 2026-05-06T17:26:12,859 adding 'tests/test_dsl_polish.py' 2026-05-06T17:26:12,861 adding 'tests/test_dsl_roundtrip.py' 2026-05-06T17:26:12,863 adding 'tests/test_edge_case_fixtures.py' 2026-05-06T17:26:12,864 adding 'tests/test_effect_expression_filters.py' 2026-05-06T17:26:12,866 adding 'tests/test_end_to_end.py' 2026-05-06T17:26:12,867 adding 'tests/test_epitopes_from_commandline_args.py' 2026-05-06T17:26:12,869 adding 'tests/test_expression_integration.py' 2026-05-06T17:26:12,870 adding 'tests/test_expression_loader.py' 2026-05-06T17:26:12,873 adding 'tests/test_frameshift_fragments.py' 2026-05-06T17:26:12,875 adding 'tests/test_inputs.py' 2026-05-06T17:26:12,876 adding 'tests/test_integration.py' 2026-05-06T17:26:12,878 adding 'tests/test_io.py' 2026-05-06T17:26:12,880 adding 'tests/test_io_lens.py' 2026-05-06T17:26:12,881 adding 'tests/test_lazy_imports.py' 2026-05-06T17:26:12,883 adding 'tests/test_load_cufflinks_fpkm.py' 2026-05-06T17:26:12,884 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-05-06T17:26:12,885 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-05-06T17:26:12,887 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-05-06T17:26:12,888 adding 'tests/test_padding.py' 2026-05-06T17:26:12,889 adding 'tests/test_peptide_mutation_interval.py' 2026-05-06T17:26:12,892 adding 'tests/test_predict_from_fragments.py' 2026-05-06T17:26:12,894 adding 'tests/test_predict_from_variants_refactor.py' 2026-05-06T17:26:12,896 adding 'tests/test_predictor_internals.py' 2026-05-06T17:26:12,898 adding 'tests/test_protein_fragment.py' 2026-05-06T17:26:12,907 adding 'tests/test_ranking.py' 2026-05-06T17:26:12,910 adding 'tests/test_result.py' 2026-05-06T17:26:12,912 adding 'tests/test_rna_helpers.py' 2026-05-06T17:26:12,914 adding 'tests/test_self_proteome.py' 2026-05-06T17:26:12,916 adding 'tests/test_sequence_helpers.py' 2026-05-06T17:26:12,917 adding 'tests/test_sources.py' 2026-05-06T17:26:12,918 adding 'tests/test_sources_optional.py' 2026-05-06T17:26:12,920 adding 'tests/test_validation_and_edge_cases.py' 2026-05-06T17:26:12,922 adding 'tests/test_variant_expression_filters.py' 2026-05-06T17:26:12,924 adding 'tests/test_wide.py' 2026-05-06T17:26:12,926 adding 'topiary/__init__.py' 2026-05-06T17:26:12,932 adding 'topiary/cached.py' 2026-05-06T17:26:12,934 adding 'topiary/filters.py' 2026-05-06T17:26:12,935 adding 'topiary/inputs.py' 2026-05-06T17:26:12,937 adding 'topiary/io.py' 2026-05-06T17:26:12,939 adding 'topiary/io_lens.py' 2026-05-06T17:26:12,941 adding 'topiary/io_protein_fragment.py' 2026-05-06T17:26:12,946 adding 'topiary/predictor.py' 2026-05-06T17:26:12,949 adding 'topiary/properties.py' 2026-05-06T17:26:12,951 adding 'topiary/protein_fragment.py' 2026-05-06T17:26:12,953 adding 'topiary/result.py' 2026-05-06T17:26:12,957 adding 'topiary/self_proteome.py' 2026-05-06T17:26:12,959 adding 'topiary/sequence_helpers.py' 2026-05-06T17:26:12,961 adding 'topiary/sources.py' 2026-05-06T17:26:12,963 adding 'topiary/wide.py' 2026-05-06T17:26:12,964 adding 'topiary/cli/__init__.py' 2026-05-06T17:26:12,967 adding 'topiary/cli/args.py' 2026-05-06T17:26:12,969 adding 'topiary/cli/cached_predictor.py' 2026-05-06T17:26:12,970 adding 'topiary/cli/errors.py' 2026-05-06T17:26:12,972 adding 'topiary/cli/filtering.py' 2026-05-06T17:26:12,973 adding 'topiary/cli/outputs.py' 2026-05-06T17:26:12,975 adding 'topiary/cli/protein_changes.py' 2026-05-06T17:26:12,976 adding 'topiary/cli/rna.py' 2026-05-06T17:26:12,977 adding 'topiary/cli/script.py' 2026-05-06T17:26:12,979 adding 'topiary/cli/sequence.py' 2026-05-06T17:26:12,980 adding 'topiary/ranking/__init__.py' 2026-05-06T17:26:12,982 adding 'topiary/ranking/apply.py' 2026-05-06T17:26:12,988 adding 'topiary/ranking/nodes.py' 2026-05-06T17:26:12,992 adding 'topiary/ranking/parser.py' 2026-05-06T17:26:12,994 adding 'topiary/rna/__init__.py' 2026-05-06T17:26:12,995 adding 'topiary/rna/common.py' 2026-05-06T17:26:12,997 adding 'topiary/rna/cufflinks.py' 2026-05-06T17:26:12,999 adding 'topiary/rna/expression_loader.py' 2026-05-06T17:26:13,000 adding 'topiary/rna/gtf.py' 2026-05-06T17:26:13,003 adding 'topiary-5.10.8.dist-info/licenses/LICENSE' 2026-05-06T17:26:13,007 adding 'topiary-5.10.8.dist-info/METADATA' 2026-05-06T17:26:13,008 adding 'topiary-5.10.8.dist-info/WHEEL' 2026-05-06T17:26:13,009 adding 'topiary-5.10.8.dist-info/entry_points.txt' 2026-05-06T17:26:13,010 adding 'topiary-5.10.8.dist-info/top_level.txt' 2026-05-06T17:26:13,011 adding 'topiary-5.10.8.dist-info/RECORD' 2026-05-06T17:26:13,016 removing build/bdist.linux-armv7l/wheel 2026-05-06T17:26:13,135 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-05-06T17:26:13,145 Created wheel for topiary: filename=topiary-5.10.8-py3-none-any.whl size=248154 sha256=865e483dec323a79b52f19e6640254214bf6d88962a91b152d1a95b6280b486f 2026-05-06T17:26:13,146 Stored in directory: /tmp/pip-ephem-wheel-cache-9o5e7k59/wheels/2b/8a/d8/2e5f477fd3d94976f986f84030c8b69223593d04c6eddf94a2 2026-05-06T17:26:13,164 Successfully built topiary 2026-05-06T17:26:13,173 Removed build tracker: '/tmp/pip-build-tracker-3gc5jdw3'