2026-04-12T21:13:16,778 Created temporary directory: /tmp/pip-ephem-wheel-cache-kr9d6t6u 2026-04-12T21:13:16,780 Created temporary directory: /tmp/pip-build-tracker-u7lt_5wd 2026-04-12T21:13:16,781 Initialized build tracking at /tmp/pip-build-tracker-u7lt_5wd 2026-04-12T21:13:16,781 Created build tracker: /tmp/pip-build-tracker-u7lt_5wd 2026-04-12T21:13:16,781 Entered build tracker: /tmp/pip-build-tracker-u7lt_5wd 2026-04-12T21:13:16,782 Created temporary directory: /tmp/pip-wheel-61yfj4ok 2026-04-12T21:13:16,785 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://archive1.piwheels.org/simple/topiary/topiary-0.0.7-py3-none-any.whl#sha256=6e23dbd38e19c12b658a8373b501f1e929c6fd3420749dee506a82b60b190d42 (from https://www.piwheels.org/simple/topiary/) 2026-04-12T21:13:17,328 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/) 2026-04-12T21:13:17,329 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/) 2026-04-12T21:13:17,329 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/) 2026-04-12T21:13:17,330 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/) 2026-04-12T21:13:17,331 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/) 2026-04-12T21:13:17,331 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/) 2026-04-12T21:13:17,332 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/) 2026-04-12T21:13:17,332 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-12T21:13:17,333 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-12T21:13:17,359 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-12T21:13:17,379 Collecting topiary==5.0.0 2026-04-12T21:13:17,381 Created temporary directory: /tmp/pip-unpack-7alv9zmb 2026-04-12T21:13:17,606 Downloading topiary-5.0.0.tar.gz (130 kB) 2026-04-12T21:13:17,832 Added topiary==5.0.0 from https://files.pythonhosted.org/packages/7c/ab/984bf05f04602f8b951dd3132f1fef5920ef327a3a8e6b0e451aeb71990b/topiary-5.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-u7lt_5wd' 2026-04-12T21:13:17,837 Created temporary directory: /tmp/pip-build-env-pb5am9vg 2026-04-12T21:13:17,842 Installing build dependencies: started 2026-04-12T21:13:17,843 Running command pip subprocess to install build dependencies 2026-04-12T21:13:18,969 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-12T21:13:19,417 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 2026-04-12T21:13:19,439 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-12T21:13:21,196 Collecting setuptools>=64 2026-04-12T21:13:21,303 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-12T21:13:24,301 Installing collected packages: setuptools 2026-04-12T21:13:27,354 Successfully installed setuptools-82.0.1 2026-04-12T21:13:27,624 Installing build dependencies: finished with status 'done' 2026-04-12T21:13:27,630 Getting requirements to build wheel: started 2026-04-12T21:13:27,632 Running command Getting requirements to build wheel 2026-04-12T21:13:28,308 /tmp/pip-build-env-pb5am9vg/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T21:13:28,309 !! 2026-04-12T21:13:28,310 ******************************************************************************** 2026-04-12T21:13:28,311 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T21:13:28,312 License :: OSI Approved :: Apache Software License 2026-04-12T21:13:28,313 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T21:13:28,314 ******************************************************************************** 2026-04-12T21:13:28,315 !! 2026-04-12T21:13:28,316 dist._finalize_license_expression() 2026-04-12T21:13:28,316 /tmp/pip-build-env-pb5am9vg/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T21:13:28,317 !! 2026-04-12T21:13:28,317 ******************************************************************************** 2026-04-12T21:13:28,318 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T21:13:28,319 License :: OSI Approved :: Apache Software License 2026-04-12T21:13:28,320 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T21:13:28,320 ******************************************************************************** 2026-04-12T21:13:28,321 !! 2026-04-12T21:13:28,321 self._finalize_license_expression() 2026-04-12T21:13:28,322 running egg_info 2026-04-12T21:13:28,325 writing topiary.egg-info/PKG-INFO 2026-04-12T21:13:28,330 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-12T21:13:28,331 writing entry points to topiary.egg-info/entry_points.txt 2026-04-12T21:13:28,333 writing requirements to topiary.egg-info/requires.txt 2026-04-12T21:13:28,335 writing top-level names to topiary.egg-info/top_level.txt 2026-04-12T21:13:28,361 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T21:13:28,367 adding license file 'LICENSE' 2026-04-12T21:13:28,372 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T21:13:28,470 Getting requirements to build wheel: finished with status 'done' 2026-04-12T21:13:28,473 Created temporary directory: /tmp/pip-modern-metadata-fdopbub0 2026-04-12T21:13:28,475 Preparing metadata (pyproject.toml): started 2026-04-12T21:13:28,476 Running command Preparing metadata (pyproject.toml) 2026-04-12T21:13:29,335 /tmp/pip-build-env-pb5am9vg/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T21:13:29,335 !! 2026-04-12T21:13:29,337 ******************************************************************************** 2026-04-12T21:13:29,337 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T21:13:29,338 License :: OSI Approved :: Apache Software License 2026-04-12T21:13:29,340 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T21:13:29,340 ******************************************************************************** 2026-04-12T21:13:29,342 !! 2026-04-12T21:13:29,342 dist._finalize_license_expression() 2026-04-12T21:13:29,343 /tmp/pip-build-env-pb5am9vg/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T21:13:29,343 !! 2026-04-12T21:13:29,345 ******************************************************************************** 2026-04-12T21:13:29,345 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T21:13:29,346 License :: OSI Approved :: Apache Software License 2026-04-12T21:13:29,347 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T21:13:29,348 ******************************************************************************** 2026-04-12T21:13:29,349 !! 2026-04-12T21:13:29,350 self._finalize_license_expression() 2026-04-12T21:13:29,351 running dist_info 2026-04-12T21:13:29,357 creating /tmp/pip-modern-metadata-fdopbub0/topiary.egg-info 2026-04-12T21:13:29,359 writing /tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/PKG-INFO 2026-04-12T21:13:29,363 writing dependency_links to /tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/dependency_links.txt 2026-04-12T21:13:29,364 writing entry points to /tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/entry_points.txt 2026-04-12T21:13:29,366 writing requirements to /tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/requires.txt 2026-04-12T21:13:29,367 writing top-level names to /tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/top_level.txt 2026-04-12T21:13:29,368 writing manifest file '/tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/SOURCES.txt' 2026-04-12T21:13:29,392 reading manifest file '/tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/SOURCES.txt' 2026-04-12T21:13:29,394 adding license file 'LICENSE' 2026-04-12T21:13:29,399 writing manifest file '/tmp/pip-modern-metadata-fdopbub0/topiary.egg-info/SOURCES.txt' 2026-04-12T21:13:29,400 creating '/tmp/pip-modern-metadata-fdopbub0/topiary-5.0.0.dist-info' 2026-04-12T21:13:29,525 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-12T21:13:29,531 Source in /tmp/pip-wheel-61yfj4ok/topiary_b5c8f1aaaabf4f9492b3b16d11e71ef0 has version 5.0.0, which satisfies requirement topiary==5.0.0 from https://files.pythonhosted.org/packages/7c/ab/984bf05f04602f8b951dd3132f1fef5920ef327a3a8e6b0e451aeb71990b/topiary-5.0.0.tar.gz 2026-04-12T21:13:29,532 Removed topiary==5.0.0 from https://files.pythonhosted.org/packages/7c/ab/984bf05f04602f8b951dd3132f1fef5920ef327a3a8e6b0e451aeb71990b/topiary-5.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-u7lt_5wd' 2026-04-12T21:13:29,539 Created temporary directory: /tmp/pip-unpack-ux3azv7a 2026-04-12T21:13:29,540 Building wheels for collected packages: topiary 2026-04-12T21:13:29,544 Created temporary directory: /tmp/pip-wheel-312aevca 2026-04-12T21:13:29,545 Destination directory: /tmp/pip-wheel-312aevca 2026-04-12T21:13:29,547 Building wheel for topiary (pyproject.toml): started 2026-04-12T21:13:29,548 Running command Building wheel for topiary (pyproject.toml) 2026-04-12T21:13:30,179 /tmp/pip-build-env-pb5am9vg/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T21:13:30,179 !! 2026-04-12T21:13:30,181 ******************************************************************************** 2026-04-12T21:13:30,181 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T21:13:30,182 License :: OSI Approved :: Apache Software License 2026-04-12T21:13:30,184 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T21:13:30,184 ******************************************************************************** 2026-04-12T21:13:30,186 !! 2026-04-12T21:13:30,186 dist._finalize_license_expression() 2026-04-12T21:13:30,187 /tmp/pip-build-env-pb5am9vg/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-12T21:13:30,188 !! 2026-04-12T21:13:30,189 ******************************************************************************** 2026-04-12T21:13:30,189 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-12T21:13:30,190 License :: OSI Approved :: Apache Software License 2026-04-12T21:13:30,192 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-12T21:13:30,192 ******************************************************************************** 2026-04-12T21:13:30,193 !! 2026-04-12T21:13:30,194 self._finalize_license_expression() 2026-04-12T21:13:30,195 running bdist_wheel 2026-04-12T21:13:30,205 running build 2026-04-12T21:13:30,205 running build_py 2026-04-12T21:13:30,211 creating build/lib/topiary 2026-04-12T21:13:30,213 copying topiary/wide.py -> build/lib/topiary 2026-04-12T21:13:30,216 copying topiary/predictor.py -> build/lib/topiary 2026-04-12T21:13:30,219 copying topiary/__init__.py -> build/lib/topiary 2026-04-12T21:13:30,221 copying topiary/io.py -> build/lib/topiary 2026-04-12T21:13:30,223 copying topiary/sources.py -> build/lib/topiary 2026-04-12T21:13:30,226 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-12T21:13:30,228 copying topiary/result.py -> build/lib/topiary 2026-04-12T21:13:30,230 copying topiary/filters.py -> build/lib/topiary 2026-04-12T21:13:30,233 copying topiary/properties.py -> build/lib/topiary 2026-04-12T21:13:30,235 copying topiary/inputs.py -> build/lib/topiary 2026-04-12T21:13:30,239 creating build/lib/tests 2026-04-12T21:13:30,240 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-12T21:13:30,242 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-12T21:13:30,244 copying tests/test_sources.py -> build/lib/tests 2026-04-12T21:13:30,246 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-12T21:13:30,248 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-12T21:13:30,250 copying tests/common.py -> build/lib/tests 2026-04-12T21:13:30,251 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-12T21:13:30,254 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-12T21:13:30,256 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-12T21:13:30,258 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-12T21:13:30,260 copying tests/test_result.py -> build/lib/tests 2026-04-12T21:13:30,262 copying tests/__init__.py -> build/lib/tests 2026-04-12T21:13:30,264 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-12T21:13:30,266 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-12T21:13:30,268 copying tests/data.py -> build/lib/tests 2026-04-12T21:13:30,270 copying tests/test_ranking.py -> build/lib/tests 2026-04-12T21:13:30,273 copying tests/test_inputs.py -> build/lib/tests 2026-04-12T21:13:30,276 copying tests/test_wide.py -> build/lib/tests 2026-04-12T21:13:30,278 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-04-12T21:13:30,281 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-12T21:13:30,283 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-12T21:13:30,285 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-12T21:13:30,287 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-12T21:13:30,290 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-12T21:13:30,291 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-12T21:13:30,293 copying tests/test_integration.py -> build/lib/tests 2026-04-12T21:13:30,295 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-12T21:13:30,297 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-12T21:13:30,299 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-12T21:13:30,302 copying tests/test_io.py -> build/lib/tests 2026-04-12T21:13:30,304 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-12T21:13:30,306 copying tests/test_padding.py -> build/lib/tests 2026-04-12T21:13:30,308 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-12T21:13:30,311 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-12T21:13:30,313 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-12T21:13:30,315 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-12T21:13:30,318 copying tests/test_dataframe.py -> build/lib/tests 2026-04-12T21:13:30,320 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-12T21:13:30,321 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-12T21:13:30,325 creating build/lib/topiary/rna 2026-04-12T21:13:30,326 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-12T21:13:30,328 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-12T21:13:30,330 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-12T21:13:30,332 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-12T21:13:30,334 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-12T21:13:30,337 creating build/lib/topiary/ranking 2026-04-12T21:13:30,338 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-04-12T21:13:30,341 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-04-12T21:13:30,343 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-04-12T21:13:30,346 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-04-12T21:13:30,348 creating build/lib/topiary/cli 2026-04-12T21:13:30,349 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-12T21:13:30,352 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-12T21:13:30,353 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-12T21:13:30,355 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-12T21:13:30,357 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-12T21:13:30,359 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-12T21:13:30,362 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-12T21:13:30,363 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-12T21:13:30,366 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-12T21:13:30,368 running egg_info 2026-04-12T21:13:30,377 writing topiary.egg-info/PKG-INFO 2026-04-12T21:13:30,381 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-12T21:13:30,383 writing entry points to topiary.egg-info/entry_points.txt 2026-04-12T21:13:30,384 writing requirements to topiary.egg-info/requires.txt 2026-04-12T21:13:30,386 writing top-level names to topiary.egg-info/top_level.txt 2026-04-12T21:13:30,401 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T21:13:30,406 adding license file 'LICENSE' 2026-04-12T21:13:30,412 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-12T21:13:30,429 installing to build/bdist.linux-armv7l/wheel 2026-04-12T21:13:30,430 running install 2026-04-12T21:13:30,453 running install_lib 2026-04-12T21:13:30,459 creating build/bdist.linux-armv7l/wheel 2026-04-12T21:13:30,461 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-12T21:13:30,463 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-12T21:13:30,465 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T21:13:30,467 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T21:13:30,470 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T21:13:30,472 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T21:13:30,474 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-12T21:13:30,478 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-04-12T21:13:30,479 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T21:13:30,482 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T21:13:30,485 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T21:13:30,488 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-12T21:13:30,491 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,493 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,496 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,499 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,501 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,503 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,506 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,509 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-12T21:13:30,510 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,512 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,514 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,516 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,517 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,519 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,522 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,523 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,526 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-12T21:13:30,528 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,530 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,532 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-12T21:13:30,536 creating build/bdist.linux-armv7l/wheel/tests 2026-04-12T21:13:30,537 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,539 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,541 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,543 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,545 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,547 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,549 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,551 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,553 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,555 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,557 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,560 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,561 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,563 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,565 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,567 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,571 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,573 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,576 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,579 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,580 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,582 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,584 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,587 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,589 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,591 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,592 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,594 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,596 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,599 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,601 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,603 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,605 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,608 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,610 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,613 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,616 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,618 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,620 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-12T21:13:30,622 running install_egg_info 2026-04-12T21:13:30,627 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.0.0-py3.11.egg-info 2026-04-12T21:13:30,640 running install_scripts 2026-04-12T21:13:30,653 creating build/bdist.linux-armv7l/wheel/topiary-5.0.0.dist-info/WHEEL 2026-04-12T21:13:30,656 creating '/tmp/pip-wheel-312aevca/.tmp-svxigvgp/topiary-5.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-12T21:13:30,659 adding 'tests/__init__.py' 2026-04-12T21:13:30,660 adding 'tests/common.py' 2026-04-12T21:13:30,662 adding 'tests/data.py' 2026-04-12T21:13:30,663 adding 'tests/test_args_outputs.py' 2026-04-12T21:13:30,665 adding 'tests/test_cli_coverage.py' 2026-04-12T21:13:30,666 adding 'tests/test_cli_protein_changes.py' 2026-04-12T21:13:30,668 adding 'tests/test_cli_ranking.py' 2026-04-12T21:13:30,670 adding 'tests/test_contains_mutant_residues.py' 2026-04-12T21:13:30,672 adding 'tests/test_coverage_gaps.py' 2026-04-12T21:13:30,673 adding 'tests/test_dataframe.py' 2026-04-12T21:13:30,674 adding 'tests/test_direct_input_regressions.py' 2026-04-12T21:13:30,677 adding 'tests/test_dsl_extensions.py' 2026-04-12T21:13:30,679 adding 'tests/test_dsl_polish.py' 2026-04-12T21:13:30,681 adding 'tests/test_dsl_roundtrip.py' 2026-04-12T21:13:30,683 adding 'tests/test_edge_case_fixtures.py' 2026-04-12T21:13:30,684 adding 'tests/test_effect_expression_filters.py' 2026-04-12T21:13:30,686 adding 'tests/test_end_to_end.py' 2026-04-12T21:13:30,687 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-12T21:13:30,689 adding 'tests/test_expression_integration.py' 2026-04-12T21:13:30,690 adding 'tests/test_expression_loader.py' 2026-04-12T21:13:30,692 adding 'tests/test_inputs.py' 2026-04-12T21:13:30,693 adding 'tests/test_integration.py' 2026-04-12T21:13:30,695 adding 'tests/test_io.py' 2026-04-12T21:13:30,697 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-12T21:13:30,698 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-12T21:13:30,699 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-12T21:13:30,701 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-12T21:13:30,702 adding 'tests/test_padding.py' 2026-04-12T21:13:30,703 adding 'tests/test_peptide_mutation_interval.py' 2026-04-12T21:13:30,704 adding 'tests/test_predictor_internals.py' 2026-04-12T21:13:30,711 adding 'tests/test_ranking.py' 2026-04-12T21:13:30,714 adding 'tests/test_result.py' 2026-04-12T21:13:30,715 adding 'tests/test_rna_helpers.py' 2026-04-12T21:13:30,717 adding 'tests/test_sequence_helpers.py' 2026-04-12T21:13:30,718 adding 'tests/test_sources.py' 2026-04-12T21:13:30,720 adding 'tests/test_sources_optional.py' 2026-04-12T21:13:30,721 adding 'tests/test_validation_and_edge_cases.py' 2026-04-12T21:13:30,723 adding 'tests/test_variant_expression_filters.py' 2026-04-12T21:13:30,725 adding 'tests/test_wide.py' 2026-04-12T21:13:30,727 adding 'topiary/__init__.py' 2026-04-12T21:13:30,729 adding 'topiary/filters.py' 2026-04-12T21:13:30,730 adding 'topiary/inputs.py' 2026-04-12T21:13:30,732 adding 'topiary/io.py' 2026-04-12T21:13:30,735 adding 'topiary/predictor.py' 2026-04-12T21:13:30,737 adding 'topiary/properties.py' 2026-04-12T21:13:30,740 adding 'topiary/result.py' 2026-04-12T21:13:30,741 adding 'topiary/sequence_helpers.py' 2026-04-12T21:13:30,743 adding 'topiary/sources.py' 2026-04-12T21:13:30,745 adding 'topiary/wide.py' 2026-04-12T21:13:30,747 adding 'topiary/cli/__init__.py' 2026-04-12T21:13:30,749 adding 'topiary/cli/args.py' 2026-04-12T21:13:30,751 adding 'topiary/cli/errors.py' 2026-04-12T21:13:30,752 adding 'topiary/cli/filtering.py' 2026-04-12T21:13:30,753 adding 'topiary/cli/outputs.py' 2026-04-12T21:13:30,755 adding 'topiary/cli/protein_changes.py' 2026-04-12T21:13:30,756 adding 'topiary/cli/rna.py' 2026-04-12T21:13:30,758 adding 'topiary/cli/script.py' 2026-04-12T21:13:30,759 adding 'topiary/cli/sequence.py' 2026-04-12T21:13:30,761 adding 'topiary/ranking/__init__.py' 2026-04-12T21:13:30,762 adding 'topiary/ranking/apply.py' 2026-04-12T21:13:30,767 adding 'topiary/ranking/nodes.py' 2026-04-12T21:13:30,770 adding 'topiary/ranking/parser.py' 2026-04-12T21:13:30,771 adding 'topiary/rna/__init__.py' 2026-04-12T21:13:30,773 adding 'topiary/rna/common.py' 2026-04-12T21:13:30,774 adding 'topiary/rna/cufflinks.py' 2026-04-12T21:13:30,776 adding 'topiary/rna/expression_loader.py' 2026-04-12T21:13:30,778 adding 'topiary/rna/gtf.py' 2026-04-12T21:13:30,781 adding 'topiary-5.0.0.dist-info/licenses/LICENSE' 2026-04-12T21:13:30,784 adding 'topiary-5.0.0.dist-info/METADATA' 2026-04-12T21:13:30,785 adding 'topiary-5.0.0.dist-info/WHEEL' 2026-04-12T21:13:30,786 adding 'topiary-5.0.0.dist-info/entry_points.txt' 2026-04-12T21:13:30,787 adding 'topiary-5.0.0.dist-info/top_level.txt' 2026-04-12T21:13:30,788 adding 'topiary-5.0.0.dist-info/RECORD' 2026-04-12T21:13:30,791 removing build/bdist.linux-armv7l/wheel 2026-04-12T21:13:30,905 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-12T21:13:30,913 Created wheel for topiary: filename=topiary-5.0.0-py3-none-any.whl size=150383 sha256=9e8f43d65576ac914c20b849c577c84970cdbae00c03f4aa8968786d610c1165 2026-04-12T21:13:30,915 Stored in directory: /tmp/pip-ephem-wheel-cache-j07xe_4p/wheels/60/24/83/942f304b2dbb3997ed72b7906050afc3a93465d993c1d30cf4 2026-04-12T21:13:30,931 Successfully built topiary 2026-04-12T21:13:30,940 Removed build tracker: '/tmp/pip-build-tracker-u7lt_5wd'