2026-04-14T17:37:43,475 Created temporary directory: /tmp/pip-ephem-wheel-cache-gmsebma1 2026-04-14T17:37:43,476 Created temporary directory: /tmp/pip-build-tracker-64rdth47 2026-04-14T17:37:43,477 Initialized build tracking at /tmp/pip-build-tracker-64rdth47 2026-04-14T17:37:43,477 Created build tracker: /tmp/pip-build-tracker-64rdth47 2026-04-14T17:37:43,478 Entered build tracker: /tmp/pip-build-tracker-64rdth47 2026-04-14T17:37:43,478 Created temporary directory: /tmp/pip-wheel-l1v_bz50 2026-04-14T17:37:43,481 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 2026-04-14T17:37:43,484 Created temporary directory: /tmp/pip-ephem-wheel-cache-9spittre 2026-04-14T17:37:43,508 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-14T17:37:43,511 2 location(s) to search for versions of topiary: 2026-04-14T17:37:43,511 * https://pypi.org/simple/topiary/ 2026-04-14T17:37:43,511 * https://www.piwheels.org/simple/topiary/ 2026-04-14T17:37:43,512 Fetching project page and analyzing links: https://pypi.org/simple/topiary/ 2026-04-14T17:37:43,513 Getting page https://pypi.org/simple/topiary/ 2026-04-14T17:37:43,514 Found index url https://pypi.org/simple 2026-04-14T17:37:43,743 Fetched page https://pypi.org/simple/topiary/ as application/vnd.pypi.simple.v1+json 2026-04-14T17:37:43,758 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) 2026-04-14T17:37:43,820 Found link https://files.pythonhosted.org/packages/a9/8a/6fe9aafba71adbf1e1392887ffb31d6301f062039efaed2321edd1b30408/topiary-5.2.0.tar.gz (from https://pypi.org/simple/topiary/) (requires-python:>=3.9), version: 5.2.0 2026-04-14T17:37:43,820 Skipping link: No binaries permitted for topiary: https://files.pythonhosted.org/packages/02/40/6505a88691b29f1e78783dc6921dd2524480cfbdcdf850d37b1be193de0a/topiary-5.4.0-py3-none-any.whl (from https://pypi.org/simple/topiary/) (requires-python:>=3.9) 2026-04-14T17:37:43,821 Found link https://files.pythonhosted.org/packages/f2/f3/b4a71bf680604fc64191ed600d88daa5eb62dcca68f9a376612d02cf4726/topiary-5.4.0.tar.gz (from https://pypi.org/simple/topiary/) (requires-python:>=3.9), version: 5.4.0 2026-04-14T17:37:43,822 Fetching project page and analyzing links: https://www.piwheels.org/simple/topiary/ 2026-04-14T17:37:43,822 Getting page https://www.piwheels.org/simple/topiary/ 2026-04-14T17:37:43,823 Found index url https://www.piwheels.org/simple 2026-04-14T17:37:43,990 Fetched page https://www.piwheels.org/simple/topiary/ as text/html 2026-04-14T17:37:44,005 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.2.0-py3-none-any.whl#sha256=dae3c176f6f432a458cdd50359c9dfa636ccd9bdb74f4f41507b7c069eed540f (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-04-14T17:37:44,006 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.1.0-py3-none-any.whl#sha256=87ce733f27cf1248d594d1bb081c678979826ff12ae413472d72ee3dec27c5c9 (from https://www.piwheels.org/simple/topiary/) (requires-python:>=3.9) 2026-04-14T17:37:44,007 Skipping link: No binaries permitted for topiary: https://www.piwheels.org/simple/topiary/topiary-5.0.1-py3-none-any.whl#sha256=0570de434f6e796f6e927c63ea685b0ff926e693b1de84f60468838985ad11cb (from https://www.piwheels.org/simple/topiary/) 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https://www.piwheels.org/simple/topiary/) 2026-04-14T17:37:44,032 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.13-py3-none-any.whl#sha256=588396661f87bea8be890d90c6800ac4825d06ae7db1c50c98a1978fe9c45bd3 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T17:37:44,033 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.10-py3-none-any.whl#sha256=56bea0cecf1273a44cd2e51ad294714c41e0fb7d9cc0b16382709573c4ec9443 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T17:37:44,034 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.9-py3-none-any.whl#sha256=da4dc4334fdf5cb89b68356e11737c8dab86fd100b9c7979e95eac3dc58fbd6d (from https://www.piwheels.org/simple/topiary/) 2026-04-14T17:37:44,034 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.8-py3-none-any.whl#sha256=12b4f283d8fbedbd316649be8833a17fee852097f1e5cd8963264e6c4a2721e0 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T17:37:44,034 Skipping link: No binaries permitted for topiary: https://archive1.piwheels.org/simple/topiary/topiary-0.0.7-py3-none-any.whl#sha256=6e23dbd38e19c12b658a8373b501f1e929c6fd3420749dee506a82b60b190d42 (from https://www.piwheels.org/simple/topiary/) 2026-04-14T17:37:44,035 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/) 2026-04-14T17:37:44,036 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/) 2026-04-14T17:37:44,036 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/) 2026-04-14T17:37:44,037 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/) 2026-04-14T17:37:44,038 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/) 2026-04-14T17:37:44,039 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/) 2026-04-14T17:37:44,039 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/) 2026-04-14T17:37:44,040 Skipping link: not a file: https://www.piwheels.org/simple/topiary/ 2026-04-14T17:37:44,040 Skipping link: not a file: https://pypi.org/simple/topiary/ 2026-04-14T17:37:44,067 Given no hashes to check 1 links for project 'topiary': discarding no candidates 2026-04-14T17:37:44,087 Collecting topiary==5.4.0 2026-04-14T17:37:44,089 Created temporary directory: /tmp/pip-unpack-luhpy2mc 2026-04-14T17:37:44,312 Downloading topiary-5.4.0.tar.gz (162 kB) 2026-04-14T17:37:44,625 Added topiary==5.4.0 from https://files.pythonhosted.org/packages/f2/f3/b4a71bf680604fc64191ed600d88daa5eb62dcca68f9a376612d02cf4726/topiary-5.4.0.tar.gz to build tracker '/tmp/pip-build-tracker-64rdth47' 2026-04-14T17:37:44,629 Created temporary directory: /tmp/pip-build-env-nl1msg7m 2026-04-14T17:37:44,634 Installing build dependencies: started 2026-04-14T17:37:44,635 Running command pip subprocess to install build dependencies 2026-04-14T17:37:45,772 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-14T17:37:46,435 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 2026-04-14T17:37:46,458 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-14T17:37:48,234 Collecting setuptools>=64 2026-04-14T17:37:48,312 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-14T17:37:51,287 Installing collected packages: setuptools 2026-04-14T17:37:54,418 Successfully installed setuptools-82.0.1 2026-04-14T17:37:54,685 Installing build dependencies: finished with status 'done' 2026-04-14T17:37:54,692 Getting requirements to build wheel: started 2026-04-14T17:37:54,694 Running command Getting requirements to build wheel 2026-04-14T17:37:55,384 /tmp/pip-build-env-nl1msg7m/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T17:37:55,384 !! 2026-04-14T17:37:55,386 ******************************************************************************** 2026-04-14T17:37:55,386 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T17:37:55,387 License :: OSI Approved :: Apache Software License 2026-04-14T17:37:55,389 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T17:37:55,389 ******************************************************************************** 2026-04-14T17:37:55,390 !! 2026-04-14T17:37:55,391 dist._finalize_license_expression() 2026-04-14T17:37:55,391 /tmp/pip-build-env-nl1msg7m/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T17:37:55,392 !! 2026-04-14T17:37:55,393 ******************************************************************************** 2026-04-14T17:37:55,394 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T17:37:55,396 License :: OSI Approved :: Apache Software License 2026-04-14T17:37:55,397 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T17:37:55,397 ******************************************************************************** 2026-04-14T17:37:55,399 !! 2026-04-14T17:37:55,399 self._finalize_license_expression() 2026-04-14T17:37:55,400 running egg_info 2026-04-14T17:37:55,405 writing topiary.egg-info/PKG-INFO 2026-04-14T17:37:55,409 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-14T17:37:55,411 writing entry points to topiary.egg-info/entry_points.txt 2026-04-14T17:37:55,413 writing requirements to topiary.egg-info/requires.txt 2026-04-14T17:37:55,414 writing top-level names to topiary.egg-info/top_level.txt 2026-04-14T17:37:55,441 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T17:37:55,447 adding license file 'LICENSE' 2026-04-14T17:37:55,453 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T17:37:55,550 Getting requirements to build wheel: finished with status 'done' 2026-04-14T17:37:55,553 Created temporary directory: /tmp/pip-modern-metadata-u9sakoy1 2026-04-14T17:37:55,555 Preparing metadata (pyproject.toml): started 2026-04-14T17:37:55,557 Running command Preparing metadata (pyproject.toml) 2026-04-14T17:37:56,230 /tmp/pip-build-env-nl1msg7m/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T17:37:56,230 !! 2026-04-14T17:37:56,231 ******************************************************************************** 2026-04-14T17:37:56,232 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T17:37:56,232 License :: OSI Approved :: Apache Software License 2026-04-14T17:37:56,234 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T17:37:56,234 ******************************************************************************** 2026-04-14T17:37:56,236 !! 2026-04-14T17:37:56,236 dist._finalize_license_expression() 2026-04-14T17:37:56,237 /tmp/pip-build-env-nl1msg7m/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T17:37:56,238 !! 2026-04-14T17:37:56,239 ******************************************************************************** 2026-04-14T17:37:56,240 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T17:37:56,241 License :: OSI Approved :: Apache Software License 2026-04-14T17:37:56,243 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T17:37:56,243 ******************************************************************************** 2026-04-14T17:37:56,245 !! 2026-04-14T17:37:56,245 self._finalize_license_expression() 2026-04-14T17:37:56,246 running dist_info 2026-04-14T17:37:56,254 creating /tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info 2026-04-14T17:37:56,255 writing /tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/PKG-INFO 2026-04-14T17:37:56,259 writing dependency_links to /tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/dependency_links.txt 2026-04-14T17:37:56,261 writing entry points to /tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/entry_points.txt 2026-04-14T17:37:56,262 writing requirements to /tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/requires.txt 2026-04-14T17:37:56,264 writing top-level names to /tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/top_level.txt 2026-04-14T17:37:56,265 writing manifest file '/tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/SOURCES.txt' 2026-04-14T17:37:56,291 reading manifest file '/tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/SOURCES.txt' 2026-04-14T17:37:56,293 adding license file 'LICENSE' 2026-04-14T17:37:56,298 writing manifest file '/tmp/pip-modern-metadata-u9sakoy1/topiary.egg-info/SOURCES.txt' 2026-04-14T17:37:56,300 creating '/tmp/pip-modern-metadata-u9sakoy1/topiary-5.4.0.dist-info' 2026-04-14T17:37:56,425 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-14T17:37:56,432 Source in /tmp/pip-wheel-l1v_bz50/topiary_58343691363f40689168a6e208ec51c1 has version 5.4.0, which satisfies requirement topiary==5.4.0 from https://files.pythonhosted.org/packages/f2/f3/b4a71bf680604fc64191ed600d88daa5eb62dcca68f9a376612d02cf4726/topiary-5.4.0.tar.gz 2026-04-14T17:37:56,433 Removed topiary==5.4.0 from https://files.pythonhosted.org/packages/f2/f3/b4a71bf680604fc64191ed600d88daa5eb62dcca68f9a376612d02cf4726/topiary-5.4.0.tar.gz from build tracker '/tmp/pip-build-tracker-64rdth47' 2026-04-14T17:37:56,440 Created temporary directory: /tmp/pip-unpack-ythgxg6u 2026-04-14T17:37:56,441 Building wheels for collected packages: topiary 2026-04-14T17:37:56,446 Created temporary directory: /tmp/pip-wheel-vz1r2wj8 2026-04-14T17:37:56,446 Destination directory: /tmp/pip-wheel-vz1r2wj8 2026-04-14T17:37:56,449 Building wheel for topiary (pyproject.toml): started 2026-04-14T17:37:56,450 Running command Building wheel for topiary (pyproject.toml) 2026-04-14T17:37:57,116 /tmp/pip-build-env-nl1msg7m/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T17:37:57,116 !! 2026-04-14T17:37:57,117 ******************************************************************************** 2026-04-14T17:37:57,118 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T17:37:57,119 License :: OSI Approved :: Apache Software License 2026-04-14T17:37:57,120 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T17:37:57,120 ******************************************************************************** 2026-04-14T17:37:57,121 !! 2026-04-14T17:37:57,122 dist._finalize_license_expression() 2026-04-14T17:37:57,123 /tmp/pip-build-env-nl1msg7m/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-14T17:37:57,123 !! 2026-04-14T17:37:57,124 ******************************************************************************** 2026-04-14T17:37:57,125 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-14T17:37:57,126 License :: OSI Approved :: Apache Software License 2026-04-14T17:37:57,128 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-14T17:37:57,128 ******************************************************************************** 2026-04-14T17:37:57,130 !! 2026-04-14T17:37:57,130 self._finalize_license_expression() 2026-04-14T17:37:57,131 running bdist_wheel 2026-04-14T17:37:57,141 running build 2026-04-14T17:37:57,142 running build_py 2026-04-14T17:37:57,148 creating build/lib/topiary 2026-04-14T17:37:57,150 copying topiary/wide.py -> build/lib/topiary 2026-04-14T17:37:57,153 copying topiary/predictor.py -> build/lib/topiary 2026-04-14T17:37:57,156 copying topiary/io_lens.py -> build/lib/topiary 2026-04-14T17:37:57,158 copying topiary/__init__.py -> build/lib/topiary 2026-04-14T17:37:57,160 copying topiary/protein_fragment.py -> build/lib/topiary 2026-04-14T17:37:57,163 copying topiary/io.py -> build/lib/topiary 2026-04-14T17:37:57,165 copying topiary/sources.py -> build/lib/topiary 2026-04-14T17:37:57,168 copying topiary/sequence_helpers.py -> build/lib/topiary 2026-04-14T17:37:57,170 copying topiary/result.py -> build/lib/topiary 2026-04-14T17:37:57,173 copying topiary/io_protein_fragment.py -> build/lib/topiary 2026-04-14T17:37:57,175 copying topiary/filters.py -> build/lib/topiary 2026-04-14T17:37:57,177 copying topiary/properties.py -> build/lib/topiary 2026-04-14T17:37:57,180 copying topiary/inputs.py -> build/lib/topiary 2026-04-14T17:37:57,184 creating build/lib/tests 2026-04-14T17:37:57,185 copying tests/test_expression_integration.py -> build/lib/tests 2026-04-14T17:37:57,187 copying tests/test_effect_expression_filters.py -> build/lib/tests 2026-04-14T17:37:57,189 copying tests/test_sources.py -> build/lib/tests 2026-04-14T17:37:57,191 copying tests/test_load_stringtie_gtf_fpkm.py -> build/lib/tests 2026-04-14T17:37:57,193 copying tests/test_direct_input_regressions.py -> build/lib/tests 2026-04-14T17:37:57,195 copying tests/common.py -> build/lib/tests 2026-04-14T17:37:57,197 copying tests/test_predict_from_variants_refactor.py -> build/lib/tests 2026-04-14T17:37:57,199 copying tests/test_cli_coverage.py -> build/lib/tests 2026-04-14T17:37:57,201 copying tests/test_cli_protein_changes.py -> build/lib/tests 2026-04-14T17:37:57,203 copying tests/test_mutant_epitope_predictions_class2.py -> build/lib/tests 2026-04-14T17:37:57,205 copying tests/test_edge_case_fixtures.py -> build/lib/tests 2026-04-14T17:37:57,207 copying tests/test_frameshift_fragments.py -> build/lib/tests 2026-04-14T17:37:57,210 copying tests/test_result.py -> build/lib/tests 2026-04-14T17:37:57,212 copying tests/__init__.py -> build/lib/tests 2026-04-14T17:37:57,214 copying tests/test_sequence_helpers.py -> build/lib/tests 2026-04-14T17:37:57,216 copying tests/test_predict_from_fragments.py -> build/lib/tests 2026-04-14T17:37:57,218 copying tests/test_end_to_end.py -> build/lib/tests 2026-04-14T17:37:57,221 copying tests/data.py -> build/lib/tests 2026-04-14T17:37:57,223 copying tests/test_ranking.py -> build/lib/tests 2026-04-14T17:37:57,227 copying tests/test_inputs.py -> build/lib/tests 2026-04-14T17:37:57,229 copying tests/test_wide.py -> build/lib/tests 2026-04-14T17:37:57,232 copying tests/test_dsl_roundtrip.py -> build/lib/tests 2026-04-14T17:37:57,234 copying tests/test_epitopes_from_commandline_args.py -> build/lib/tests 2026-04-14T17:37:57,236 copying tests/test_mutant_epitope_predictions_class1.py -> build/lib/tests 2026-04-14T17:37:57,238 copying tests/test_variant_expression_filters.py -> build/lib/tests 2026-04-14T17:37:57,240 copying tests/test_io_lens.py -> build/lib/tests 2026-04-14T17:37:57,243 copying tests/test_cli_ranking.py -> build/lib/tests 2026-04-14T17:37:57,245 copying tests/test_args_outputs.py -> build/lib/tests 2026-04-14T17:37:57,247 copying tests/test_rna_helpers.py -> build/lib/tests 2026-04-14T17:37:57,249 copying tests/test_integration.py -> build/lib/tests 2026-04-14T17:37:57,251 copying tests/test_peptide_mutation_interval.py -> build/lib/tests 2026-04-14T17:37:57,253 copying tests/test_load_cufflinks_fpkm.py -> build/lib/tests 2026-04-14T17:37:57,255 copying tests/test_dsl_extensions.py -> build/lib/tests 2026-04-14T17:37:57,258 copying tests/test_io.py -> build/lib/tests 2026-04-14T17:37:57,260 copying tests/test_sources_optional.py -> build/lib/tests 2026-04-14T17:37:57,262 copying tests/test_protein_fragment.py -> build/lib/tests 2026-04-14T17:37:57,265 copying tests/test_padding.py -> build/lib/tests 2026-04-14T17:37:57,267 copying tests/test_coverage_gaps.py -> build/lib/tests 2026-04-14T17:37:57,269 copying tests/test_predictor_internals.py -> build/lib/tests 2026-04-14T17:37:57,272 copying tests/test_dsl_polish.py -> build/lib/tests 2026-04-14T17:37:57,274 copying tests/test_expression_loader.py -> build/lib/tests 2026-04-14T17:37:57,276 copying tests/test_dataframe.py -> build/lib/tests 2026-04-14T17:37:57,278 copying tests/test_contains_mutant_residues.py -> build/lib/tests 2026-04-14T17:37:57,280 copying tests/test_validation_and_edge_cases.py -> build/lib/tests 2026-04-14T17:37:57,283 creating build/lib/topiary/rna 2026-04-14T17:37:57,284 copying topiary/rna/gtf.py -> build/lib/topiary/rna 2026-04-14T17:37:57,287 copying topiary/rna/common.py -> build/lib/topiary/rna 2026-04-14T17:37:57,288 copying topiary/rna/cufflinks.py -> build/lib/topiary/rna 2026-04-14T17:37:57,291 copying topiary/rna/__init__.py -> build/lib/topiary/rna 2026-04-14T17:37:57,293 copying topiary/rna/expression_loader.py -> build/lib/topiary/rna 2026-04-14T17:37:57,296 creating build/lib/topiary/ranking 2026-04-14T17:37:57,297 copying topiary/ranking/parser.py -> build/lib/topiary/ranking 2026-04-14T17:37:57,299 copying topiary/ranking/__init__.py -> build/lib/topiary/ranking 2026-04-14T17:37:57,301 copying topiary/ranking/nodes.py -> build/lib/topiary/ranking 2026-04-14T17:37:57,305 copying topiary/ranking/apply.py -> build/lib/topiary/ranking 2026-04-14T17:37:57,307 creating build/lib/topiary/cli 2026-04-14T17:37:57,308 copying topiary/cli/rna.py -> build/lib/topiary/cli 2026-04-14T17:37:57,311 copying topiary/cli/errors.py -> build/lib/topiary/cli 2026-04-14T17:37:57,313 copying topiary/cli/__init__.py -> build/lib/topiary/cli 2026-04-14T17:37:57,315 copying topiary/cli/filtering.py -> build/lib/topiary/cli 2026-04-14T17:37:57,317 copying topiary/cli/outputs.py -> build/lib/topiary/cli 2026-04-14T17:37:57,318 copying topiary/cli/protein_changes.py -> build/lib/topiary/cli 2026-04-14T17:37:57,321 copying topiary/cli/sequence.py -> build/lib/topiary/cli 2026-04-14T17:37:57,323 copying topiary/cli/args.py -> build/lib/topiary/cli 2026-04-14T17:37:57,325 copying topiary/cli/script.py -> build/lib/topiary/cli 2026-04-14T17:37:57,327 running egg_info 2026-04-14T17:37:57,337 writing topiary.egg-info/PKG-INFO 2026-04-14T17:37:57,341 writing dependency_links to topiary.egg-info/dependency_links.txt 2026-04-14T17:37:57,342 writing entry points to topiary.egg-info/entry_points.txt 2026-04-14T17:37:57,344 writing requirements to topiary.egg-info/requires.txt 2026-04-14T17:37:57,345 writing top-level names to topiary.egg-info/top_level.txt 2026-04-14T17:37:57,360 reading manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T17:37:57,366 adding license file 'LICENSE' 2026-04-14T17:37:57,372 writing manifest file 'topiary.egg-info/SOURCES.txt' 2026-04-14T17:37:57,389 installing to build/bdist.linux-armv7l/wheel 2026-04-14T17:37:57,390 running install 2026-04-14T17:37:57,414 running install_lib 2026-04-14T17:37:57,419 creating build/bdist.linux-armv7l/wheel 2026-04-14T17:37:57,422 creating build/bdist.linux-armv7l/wheel/topiary 2026-04-14T17:37:57,423 creating build/bdist.linux-armv7l/wheel/topiary/rna 2026-04-14T17:37:57,425 copying build/lib/topiary/rna/gtf.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T17:37:57,427 copying build/lib/topiary/rna/common.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T17:37:57,429 copying build/lib/topiary/rna/cufflinks.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T17:37:57,431 copying build/lib/topiary/rna/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T17:37:57,433 copying build/lib/topiary/rna/expression_loader.py -> build/bdist.linux-armv7l/wheel/./topiary/rna 2026-04-14T17:37:57,436 creating build/bdist.linux-armv7l/wheel/topiary/ranking 2026-04-14T17:37:57,437 copying build/lib/topiary/ranking/parser.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T17:37:57,440 copying build/lib/topiary/ranking/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T17:37:57,442 copying build/lib/topiary/ranking/nodes.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T17:37:57,445 copying build/lib/topiary/ranking/apply.py -> build/bdist.linux-armv7l/wheel/./topiary/ranking 2026-04-14T17:37:57,447 copying build/lib/topiary/wide.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,450 copying build/lib/topiary/predictor.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,453 copying build/lib/topiary/io_lens.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,456 copying build/lib/topiary/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,458 copying build/lib/topiary/protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,460 copying build/lib/topiary/io.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,463 copying build/lib/topiary/sources.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,465 copying build/lib/topiary/sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,467 copying build/lib/topiary/result.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,470 copying build/lib/topiary/io_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,473 creating build/bdist.linux-armv7l/wheel/topiary/cli 2026-04-14T17:37:57,474 copying build/lib/topiary/cli/rna.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,476 copying build/lib/topiary/cli/errors.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,478 copying build/lib/topiary/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,480 copying build/lib/topiary/cli/filtering.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,482 copying build/lib/topiary/cli/outputs.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,484 copying build/lib/topiary/cli/protein_changes.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,486 copying build/lib/topiary/cli/sequence.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,488 copying build/lib/topiary/cli/args.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,491 copying build/lib/topiary/cli/script.py -> build/bdist.linux-armv7l/wheel/./topiary/cli 2026-04-14T17:37:57,494 copying build/lib/topiary/filters.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,496 copying build/lib/topiary/properties.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,498 copying build/lib/topiary/inputs.py -> build/bdist.linux-armv7l/wheel/./topiary 2026-04-14T17:37:57,502 creating build/bdist.linux-armv7l/wheel/tests 2026-04-14T17:37:57,503 copying build/lib/tests/test_expression_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,505 copying build/lib/tests/test_effect_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,507 copying build/lib/tests/test_sources.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,509 copying build/lib/tests/test_load_stringtie_gtf_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,511 copying build/lib/tests/test_direct_input_regressions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,513 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,515 copying build/lib/tests/test_predict_from_variants_refactor.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,518 copying build/lib/tests/test_cli_coverage.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,520 copying build/lib/tests/test_cli_protein_changes.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,522 copying build/lib/tests/test_mutant_epitope_predictions_class2.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,524 copying build/lib/tests/test_edge_case_fixtures.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,526 copying build/lib/tests/test_frameshift_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,529 copying build/lib/tests/test_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,531 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,533 copying build/lib/tests/test_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,535 copying build/lib/tests/test_predict_from_fragments.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,537 copying build/lib/tests/test_end_to_end.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,540 copying build/lib/tests/data.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,542 copying build/lib/tests/test_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,545 copying build/lib/tests/test_inputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,548 copying build/lib/tests/test_wide.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,550 copying build/lib/tests/test_dsl_roundtrip.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,553 copying build/lib/tests/test_epitopes_from_commandline_args.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,555 copying build/lib/tests/test_mutant_epitope_predictions_class1.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,556 copying build/lib/tests/test_variant_expression_filters.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,558 copying build/lib/tests/test_io_lens.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,561 copying build/lib/tests/test_cli_ranking.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,563 copying build/lib/tests/test_args_outputs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,565 copying build/lib/tests/test_rna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,567 copying build/lib/tests/test_integration.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,569 copying build/lib/tests/test_peptide_mutation_interval.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,571 copying build/lib/tests/test_load_cufflinks_fpkm.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,573 copying build/lib/tests/test_dsl_extensions.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,575 copying build/lib/tests/test_io.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,578 copying build/lib/tests/test_sources_optional.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,580 copying build/lib/tests/test_protein_fragment.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,582 copying build/lib/tests/test_padding.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,584 copying build/lib/tests/test_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,586 copying build/lib/tests/test_predictor_internals.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,588 copying build/lib/tests/test_dsl_polish.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,591 copying build/lib/tests/test_expression_loader.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,593 copying build/lib/tests/test_dataframe.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,595 copying build/lib/tests/test_contains_mutant_residues.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,597 copying build/lib/tests/test_validation_and_edge_cases.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-14T17:37:57,599 running install_egg_info 2026-04-14T17:37:57,604 Copying topiary.egg-info to build/bdist.linux-armv7l/wheel/./topiary-5.4.0-py3.11.egg-info 2026-04-14T17:37:57,616 running install_scripts 2026-04-14T17:37:57,629 creating build/bdist.linux-armv7l/wheel/topiary-5.4.0.dist-info/WHEEL 2026-04-14T17:37:57,632 creating '/tmp/pip-wheel-vz1r2wj8/.tmp-lwct64jc/topiary-5.4.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-14T17:37:57,635 adding 'tests/__init__.py' 2026-04-14T17:37:57,636 adding 'tests/common.py' 2026-04-14T17:37:57,638 adding 'tests/data.py' 2026-04-14T17:37:57,639 adding 'tests/test_args_outputs.py' 2026-04-14T17:37:57,641 adding 'tests/test_cli_coverage.py' 2026-04-14T17:37:57,642 adding 'tests/test_cli_protein_changes.py' 2026-04-14T17:37:57,644 adding 'tests/test_cli_ranking.py' 2026-04-14T17:37:57,645 adding 'tests/test_contains_mutant_residues.py' 2026-04-14T17:37:57,647 adding 'tests/test_coverage_gaps.py' 2026-04-14T17:37:57,648 adding 'tests/test_dataframe.py' 2026-04-14T17:37:57,650 adding 'tests/test_direct_input_regressions.py' 2026-04-14T17:37:57,652 adding 'tests/test_dsl_extensions.py' 2026-04-14T17:37:57,654 adding 'tests/test_dsl_polish.py' 2026-04-14T17:37:57,657 adding 'tests/test_dsl_roundtrip.py' 2026-04-14T17:37:57,658 adding 'tests/test_edge_case_fixtures.py' 2026-04-14T17:37:57,659 adding 'tests/test_effect_expression_filters.py' 2026-04-14T17:37:57,661 adding 'tests/test_end_to_end.py' 2026-04-14T17:37:57,662 adding 'tests/test_epitopes_from_commandline_args.py' 2026-04-14T17:37:57,663 adding 'tests/test_expression_integration.py' 2026-04-14T17:37:57,665 adding 'tests/test_expression_loader.py' 2026-04-14T17:37:57,667 adding 'tests/test_frameshift_fragments.py' 2026-04-14T17:37:57,669 adding 'tests/test_inputs.py' 2026-04-14T17:37:57,670 adding 'tests/test_integration.py' 2026-04-14T17:37:57,672 adding 'tests/test_io.py' 2026-04-14T17:37:57,674 adding 'tests/test_io_lens.py' 2026-04-14T17:37:57,676 adding 'tests/test_load_cufflinks_fpkm.py' 2026-04-14T17:37:57,677 adding 'tests/test_load_stringtie_gtf_fpkm.py' 2026-04-14T17:37:57,679 adding 'tests/test_mutant_epitope_predictions_class1.py' 2026-04-14T17:37:57,680 adding 'tests/test_mutant_epitope_predictions_class2.py' 2026-04-14T17:37:57,681 adding 'tests/test_padding.py' 2026-04-14T17:37:57,682 adding 'tests/test_peptide_mutation_interval.py' 2026-04-14T17:37:57,684 adding 'tests/test_predict_from_fragments.py' 2026-04-14T17:37:57,687 adding 'tests/test_predict_from_variants_refactor.py' 2026-04-14T17:37:57,688 adding 'tests/test_predictor_internals.py' 2026-04-14T17:37:57,690 adding 'tests/test_protein_fragment.py' 2026-04-14T17:37:57,697 adding 'tests/test_ranking.py' 2026-04-14T17:37:57,700 adding 'tests/test_result.py' 2026-04-14T17:37:57,701 adding 'tests/test_rna_helpers.py' 2026-04-14T17:37:57,702 adding 'tests/test_sequence_helpers.py' 2026-04-14T17:37:57,704 adding 'tests/test_sources.py' 2026-04-14T17:37:57,705 adding 'tests/test_sources_optional.py' 2026-04-14T17:37:57,707 adding 'tests/test_validation_and_edge_cases.py' 2026-04-14T17:37:57,709 adding 'tests/test_variant_expression_filters.py' 2026-04-14T17:37:57,710 adding 'tests/test_wide.py' 2026-04-14T17:37:57,713 adding 'topiary/__init__.py' 2026-04-14T17:37:57,714 adding 'topiary/filters.py' 2026-04-14T17:37:57,716 adding 'topiary/inputs.py' 2026-04-14T17:37:57,718 adding 'topiary/io.py' 2026-04-14T17:37:57,720 adding 'topiary/io_lens.py' 2026-04-14T17:37:57,721 adding 'topiary/io_protein_fragment.py' 2026-04-14T17:37:57,725 adding 'topiary/predictor.py' 2026-04-14T17:37:57,728 adding 'topiary/properties.py' 2026-04-14T17:37:57,730 adding 'topiary/protein_fragment.py' 2026-04-14T17:37:57,732 adding 'topiary/result.py' 2026-04-14T17:37:57,734 adding 'topiary/sequence_helpers.py' 2026-04-14T17:37:57,736 adding 'topiary/sources.py' 2026-04-14T17:37:57,738 adding 'topiary/wide.py' 2026-04-14T17:37:57,740 adding 'topiary/cli/__init__.py' 2026-04-14T17:37:57,743 adding 'topiary/cli/args.py' 2026-04-14T17:37:57,744 adding 'topiary/cli/errors.py' 2026-04-14T17:37:57,745 adding 'topiary/cli/filtering.py' 2026-04-14T17:37:57,747 adding 'topiary/cli/outputs.py' 2026-04-14T17:37:57,748 adding 'topiary/cli/protein_changes.py' 2026-04-14T17:37:57,750 adding 'topiary/cli/rna.py' 2026-04-14T17:37:57,751 adding 'topiary/cli/script.py' 2026-04-14T17:37:57,753 adding 'topiary/cli/sequence.py' 2026-04-14T17:37:57,755 adding 'topiary/ranking/__init__.py' 2026-04-14T17:37:57,756 adding 'topiary/ranking/apply.py' 2026-04-14T17:37:57,762 adding 'topiary/ranking/nodes.py' 2026-04-14T17:37:57,764 adding 'topiary/ranking/parser.py' 2026-04-14T17:37:57,766 adding 'topiary/rna/__init__.py' 2026-04-14T17:37:57,768 adding 'topiary/rna/common.py' 2026-04-14T17:37:57,769 adding 'topiary/rna/cufflinks.py' 2026-04-14T17:37:57,771 adding 'topiary/rna/expression_loader.py' 2026-04-14T17:37:57,773 adding 'topiary/rna/gtf.py' 2026-04-14T17:37:57,776 adding 'topiary-5.4.0.dist-info/licenses/LICENSE' 2026-04-14T17:37:57,779 adding 'topiary-5.4.0.dist-info/METADATA' 2026-04-14T17:37:57,780 adding 'topiary-5.4.0.dist-info/WHEEL' 2026-04-14T17:37:57,781 adding 'topiary-5.4.0.dist-info/entry_points.txt' 2026-04-14T17:37:57,782 adding 'topiary-5.4.0.dist-info/top_level.txt' 2026-04-14T17:37:57,784 adding 'topiary-5.4.0.dist-info/RECORD' 2026-04-14T17:37:57,787 removing build/bdist.linux-armv7l/wheel 2026-04-14T17:37:57,904 Building wheel for topiary (pyproject.toml): finished with status 'done' 2026-04-14T17:37:57,914 Created wheel for topiary: filename=topiary-5.4.0-py3-none-any.whl size=186730 sha256=c6ada9dae9e95c5422e2b926a6b0909fed4cc7e12a8cbed90a506141d690a436 2026-04-14T17:37:57,915 Stored in directory: /tmp/pip-ephem-wheel-cache-9spittre/wheels/a1/cb/c7/ad95f5eab4f95d87eba7a6dc9e98cab38f66a81b4dd268cb8a 2026-04-14T17:37:57,932 Successfully built topiary 2026-04-14T17:37:57,940 Removed build tracker: '/tmp/pip-build-tracker-64rdth47'