2026-04-05T19:40:49,271 Created temporary directory: /tmp/pip-ephem-wheel-cache-t2d0x01e 2026-04-05T19:40:49,273 Created temporary directory: /tmp/pip-build-tracker-4m2_z137 2026-04-05T19:40:49,274 Initialized build tracking at /tmp/pip-build-tracker-4m2_z137 2026-04-05T19:40:49,274 Created build tracker: /tmp/pip-build-tracker-4m2_z137 2026-04-05T19:40:49,274 Entered build tracker: /tmp/pip-build-tracker-4m2_z137 2026-04-05T19:40:49,275 Created temporary directory: /tmp/pip-wheel-1lbrucll 2026-04-05T19:40:49,278 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://files.pythonhosted.org/packages/37/33/79dad79cecfc192bdbd65593c0ebf693ab7ca44aeba59f6fcda3e2933f21/isovar-0.8.2.tar.gz (from https://pypi.org/simple/isovar/), version: 0.8.2 2026-04-05T19:40:49,567 Found link https://files.pythonhosted.org/packages/8c/ab/99e3ac9a148d0acd27abf5e6d640eba635cdfdeacd876bee1bf27c0bf05f/isovar-0.8.3.tar.gz (from https://pypi.org/simple/isovar/), version: 0.8.3 2026-04-05T19:40:49,568 Found link https://files.pythonhosted.org/packages/da/ed/1f4d8fed9c2cc26b80124726bd7dd40d4f5b7e5b8afdadb8a62077bd58a1/isovar-0.8.5.tar.gz (from https://pypi.org/simple/isovar/), version: 0.8.5 2026-04-05T19:40:49,568 Found link https://files.pythonhosted.org/packages/54/91/402d3e534b4b063e6fbba41ae872627ed3e67b0ad1246f9721eb652f2237/isovar-0.9.0.tar.gz (from https://pypi.org/simple/isovar/), version: 0.9.0 2026-04-05T19:40:49,569 Found link https://files.pythonhosted.org/packages/d4/ac/f45056b97d888ecc95ce3694d270a08c9610eb45823c0ca6a907a156d7f5/isovar-1.0.0.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.0 2026-04-05T19:40:49,569 Found link https://files.pythonhosted.org/packages/92/cd/3ee3c6155d5471cdb712ccc2c59e19ebfc896ace3adbb322d26bd45dace9/isovar-1.0.1.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.1 2026-04-05T19:40:49,570 Found link https://files.pythonhosted.org/packages/77/2f/222f0d24e0baf292e4b87a9a0b1d0313668d649bbbbe3be1ede886a8e5eb/isovar-1.0.2.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.2 2026-04-05T19:40:49,571 Found link https://files.pythonhosted.org/packages/28/32/2279cf21d9d31608c4169a18e26aefd82ff9ab6d8df8df54f860f31b0601/isovar-1.0.3.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.3 2026-04-05T19:40:49,572 Found link https://files.pythonhosted.org/packages/f5/cc/8d7a6eeebae8cf6d31df23bcf5dcb5f14aad7fd4ef12790393e16426da12/isovar-1.0.4.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.4 2026-04-05T19:40:49,572 Found link https://files.pythonhosted.org/packages/e2/e3/470ea2f19176ace9ea4b19d855e025456aa529748e30c1a66e3ad1874559/isovar-1.0.5.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.5 2026-04-05T19:40:49,573 Found link https://files.pythonhosted.org/packages/0f/9f/358c17b6d0527e0b1ceb056d1b8fbb2bf0307d5181f32d4e72089bdce605/isovar-1.0.6.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.6 2026-04-05T19:40:49,573 Found link https://files.pythonhosted.org/packages/66/c1/95a0e55994915b6cbbf4bccbcafeb88b9db4838d7b934341bb97ff97b2e7/isovar-1.0.7.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.7 2026-04-05T19:40:49,574 Found link https://files.pythonhosted.org/packages/80/db/7d4cdb69c95e6a6abbfabdff6145ad18a80125d4fb72ae90510c9547712c/isovar-1.0.8.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.8 2026-04-05T19:40:49,574 Found link https://files.pythonhosted.org/packages/72/8b/5c6413f8bdede23be5e966366bb79d158d4b2ccb6465f9718f86cdb17c1b/isovar-1.0.9.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.9 2026-04-05T19:40:49,575 Found link https://files.pythonhosted.org/packages/77/93/1198731f9a82344e62c506aae7498e62ee7d66b47d9a41044449775d981a/isovar-1.0.10.tar.gz (from https://pypi.org/simple/isovar/), version: 1.0.10 2026-04-05T19:40:49,575 Found link https://files.pythonhosted.org/packages/c8/c4/bbc73d818113ef77f38866db48fef6fd04c82cdb90ec1a92415e98a7da3f/isovar-1.1.0.tar.gz (from https://pypi.org/simple/isovar/), version: 1.1.0 2026-04-05T19:40:49,576 Found link https://files.pythonhosted.org/packages/b5/1e/138d88128449d2753f828c169a45688e5d1c5b011544a83cdfa2e64af97a/isovar-1.1.1.tar.gz (from https://pypi.org/simple/isovar/), version: 1.1.1 2026-04-05T19:40:49,577 Skipping link: No binaries permitted for isovar: https://files.pythonhosted.org/packages/e5/35/3e24c2e9c31374a7d9a283598cdc15cc85082d1b59206016a8a2c09efc7c/isovar-1.3.0-py3-none-any.whl (from https://pypi.org/simple/isovar/) 2026-04-05T19:40:49,577 Found link https://files.pythonhosted.org/packages/83/be/38d44747eb1c3825a566651a8da85f85584069f1894eb7799fd2bf61a1ec/isovar-1.3.0.tar.gz (from https://pypi.org/simple/isovar/), version: 1.3.0 2026-04-05T19:40:49,578 Skipping link: No binaries permitted for isovar: https://files.pythonhosted.org/packages/2b/2e/3fbc2ce1f15635ff2d0d88fd6f730c15db30b31059de43ec8eed64fa36f9/isovar-1.4.0-py3-none-any.whl (from https://pypi.org/simple/isovar/) (requires-python:>=3.9) 2026-04-05T19:40:49,579 Found link https://files.pythonhosted.org/packages/3f/f1/f4adc10fc650b60cc01f1d3101df6edde5169ec141a72dd60f32cc7eb938/isovar-1.4.0.tar.gz (from https://pypi.org/simple/isovar/) (requires-python:>=3.9), version: 1.4.0 2026-04-05T19:40:49,580 Fetching project page and analyzing links: https://www.piwheels.org/simple/isovar/ 2026-04-05T19:40:49,581 Getting page https://www.piwheels.org/simple/isovar/ 2026-04-05T19:40:49,582 Found index url https://www.piwheels.org/simple 2026-04-05T19:40:49,762 Fetched page 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2026-04-05T19:40:49,777 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-1.0.6-py3-none-any.whl#sha256=2cf10195495be17f3094bccee7f9fc49a571ec1830838e565ed37812a73ffb1a (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,778 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-1.0.5-py3-none-any.whl#sha256=b28c73d0a66e50d7043c64f9389ae3fac6592ae97520029bb35d8a13a414afb9 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,778 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-1.0.4-py3-none-any.whl#sha256=13750d5398c04a7136974d3cc64c421bcacdc06979233b9c35ad0bed72f5de5c (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,779 Skipping link: No binaries permitted for isovar: 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2026-04-05T19:40:49,781 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.9.0-py3-none-any.whl#sha256=93e6c5d78217229ba1fc17fcdba4933e7288a0b5fac47499530543be8d926114 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,782 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.8.5-py3-none-any.whl#sha256=3e040cc19ffb8f5b6563713d12135d20ff3f72aefbc3f682defced21cd6490f1 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,782 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.8.3-py3-none-any.whl#sha256=ab5cf46ee8ef34af6041b12b2ac7c1b502105b0070267f1dd164eae803bda79a (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,783 Skipping link: No binaries permitted for isovar: 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2026-04-05T19:40:49,785 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.7.4-py3-none-any.whl#sha256=a28a28dbc4bc797ba85dddf7fc3f5629eadef4e10779400418df5559ea25d31f (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,785 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.7.3-py3-none-any.whl#sha256=19bb9ea17e75b529ec6d27a10e85691e0e89225c5f47f82656c4e75414504bb3 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,786 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.7.2-py3-none-any.whl#sha256=05fdf6bedb1e653eb76f280196726c2bf133a786d271509ee2ea3453d8df0c58 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,786 Skipping link: No binaries permitted for isovar: 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2026-04-05T19:40:49,789 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.5.2-py3-none-any.whl#sha256=c3a0efab34c6879d8e0c15b80481b591c5ea319601fee4147e28a109ca338c1e (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,789 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.5.0-py3-none-any.whl#sha256=83ba7764960fac3b11d56deee3d616800d6833d1c57f7418d852a04e4f0e93e7 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,790 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.4.0-py3-none-any.whl#sha256=9cfc7274f39f4f218d25eaaaa6ba235cf6a7b457dcc3997ca42322a8fe84bf17 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,790 Skipping link: No binaries permitted for isovar: 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2026-04-05T19:40:49,793 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.2.0-py3-none-any.whl#sha256=ab7b0e6349d9a2c4802489d7cc7a867b23e3c2972f66283839629ac8f858cbce (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,793 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.1.5-py3-none-any.whl#sha256=ba9438ba3b8c2a1e59345d0c9fbfb207ded65feaf93b8d4dbf0972c7de89035c (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,794 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.1.3-py3-none-any.whl#sha256=c266801b0b080abcaf155870dfcd593ca904b27565767a27067326c819f0b15c (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,794 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.1.0-py3-none-any.whl#sha256=272454342ccc3da1af19007ad496e6d33165a4482470cef97f1e1bd4a898aee8 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,795 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.0.6-py3-none-any.whl#sha256=04d869c163e51c11ed2d2bb125bffaf7e0c89cb17d906bcbc52914d1fa888e72 (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,795 Skipping link: No binaries permitted for isovar: https://archive1.piwheels.org/simple/isovar/isovar-0.0.5-py3-none-any.whl#sha256=57d3b95575aae8439f0aaa54ce12c1cb00b1bcb2e4fec582550cb0484903bcbc (from https://www.piwheels.org/simple/isovar/) 2026-04-05T19:40:49,796 Skipping link: not a file: https://www.piwheels.org/simple/isovar/ 2026-04-05T19:40:49,796 Skipping link: not a file: https://pypi.org/simple/isovar/ 2026-04-05T19:40:49,822 Given no hashes to check 1 links for project 'isovar': discarding no candidates 2026-04-05T19:40:49,841 Collecting isovar==1.4.0 2026-04-05T19:40:49,844 Created temporary directory: /tmp/pip-unpack-jfxfprov 2026-04-05T19:40:50,073 Downloading isovar-1.4.0.tar.gz (100 kB) 2026-04-05T19:40:50,331 Added isovar==1.4.0 from https://files.pythonhosted.org/packages/3f/f1/f4adc10fc650b60cc01f1d3101df6edde5169ec141a72dd60f32cc7eb938/isovar-1.4.0.tar.gz to build tracker '/tmp/pip-build-tracker-4m2_z137' 2026-04-05T19:40:50,333 Running setup.py (path:/tmp/pip-wheel-1lbrucll/isovar_c8fcae5b6e68414e87914cb816d9015e/setup.py) egg_info for package isovar 2026-04-05T19:40:50,334 Created temporary directory: /tmp/pip-pip-egg-info-agi8onek 2026-04-05T19:40:50,334 Preparing metadata (setup.py): started 2026-04-05T19:40:50,335 Running command python setup.py egg_info 2026-04-05T19:40:51,248 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-05T19:40:51,249 !! 2026-04-05T19:40:51,250 ******************************************************************************** 2026-04-05T19:40:51,250 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-05T19:40:51,252 License :: OSI Approved :: Apache Software License 2026-04-05T19:40:51,253 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-05T19:40:51,253 ******************************************************************************** 2026-04-05T19:40:51,255 !! 2026-04-05T19:40:51,255 self._finalize_license_expression() 2026-04-05T19:40:51,279 running egg_info 2026-04-05T19:40:51,306 creating /tmp/pip-pip-egg-info-agi8onek/isovar.egg-info 2026-04-05T19:40:51,307 writing /tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/PKG-INFO 2026-04-05T19:40:51,311 writing dependency_links to /tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/dependency_links.txt 2026-04-05T19:40:51,313 writing entry points to /tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/entry_points.txt 2026-04-05T19:40:51,315 writing requirements to /tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/requires.txt 2026-04-05T19:40:51,316 writing top-level names to /tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/top_level.txt 2026-04-05T19:40:51,317 writing manifest file '/tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/SOURCES.txt' 2026-04-05T19:40:51,414 reading manifest file '/tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/SOURCES.txt' 2026-04-05T19:40:51,416 adding license file 'LICENSE' 2026-04-05T19:40:51,421 writing manifest file '/tmp/pip-pip-egg-info-agi8onek/isovar.egg-info/SOURCES.txt' 2026-04-05T19:40:51,528 Preparing metadata (setup.py): finished with status 'done' 2026-04-05T19:40:51,533 Source in /tmp/pip-wheel-1lbrucll/isovar_c8fcae5b6e68414e87914cb816d9015e has version 1.4.0, which satisfies requirement isovar==1.4.0 from https://files.pythonhosted.org/packages/3f/f1/f4adc10fc650b60cc01f1d3101df6edde5169ec141a72dd60f32cc7eb938/isovar-1.4.0.tar.gz 2026-04-05T19:40:51,534 Removed isovar==1.4.0 from https://files.pythonhosted.org/packages/3f/f1/f4adc10fc650b60cc01f1d3101df6edde5169ec141a72dd60f32cc7eb938/isovar-1.4.0.tar.gz from build tracker '/tmp/pip-build-tracker-4m2_z137' 2026-04-05T19:40:51,543 Created temporary directory: /tmp/pip-unpack-lygw_93s 2026-04-05T19:40:51,543 Building wheels for collected packages: isovar 2026-04-05T19:40:51,556 Created temporary directory: /tmp/pip-wheel-csx50wx6 2026-04-05T19:40:51,557 Building wheel for isovar (setup.py): started 2026-04-05T19:40:51,558 Destination directory: /tmp/pip-wheel-csx50wx6 2026-04-05T19:40:51,559 Running command python setup.py bdist_wheel 2026-04-05T19:40:52,414 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-05T19:40:52,415 !! 2026-04-05T19:40:52,416 ******************************************************************************** 2026-04-05T19:40:52,416 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-05T19:40:52,417 License :: OSI Approved :: Apache Software License 2026-04-05T19:40:52,419 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-05T19:40:52,419 ******************************************************************************** 2026-04-05T19:40:52,420 !! 2026-04-05T19:40:52,421 self._finalize_license_expression() 2026-04-05T19:40:52,422 running bdist_wheel 2026-04-05T19:40:52,557 running build 2026-04-05T19:40:52,558 running build_py 2026-04-05T19:40:52,591 creating build/lib/tests 2026-04-05T19:40:52,594 copying tests/test_genetic_code.py -> build/lib/tests 2026-04-05T19:40:52,596 copying tests/test_isovar_result.py -> build/lib/tests 2026-04-05T19:40:52,598 copying tests/test_translation.py -> build/lib/tests 2026-04-05T19:40:52,600 copying tests/test_filtering.py -> build/lib/tests 2026-04-05T19:40:52,602 copying tests/__init__.py -> build/lib/tests 2026-04-05T19:40:52,604 copying tests/test_assembly.py -> build/lib/tests 2026-04-05T19:40:52,607 copying tests/test_variant_helpers.py -> build/lib/tests 2026-04-05T19:40:52,609 copying tests/test_locus_reads.py -> build/lib/tests 2026-04-05T19:40:52,611 copying tests/test_effect_prediction.py -> build/lib/tests 2026-04-05T19:40:52,612 copying tests/test_gather_variant_reads_wgs.py -> build/lib/tests 2026-04-05T19:40:52,614 copying tests/testing_helpers.py -> build/lib/tests 2026-04-05T19:40:52,616 copying tests/test_common.py -> build/lib/tests 2026-04-05T19:40:52,618 copying tests/test_read_helpers.py -> build/lib/tests 2026-04-05T19:40:52,620 copying tests/test_dna_helpers.py -> build/lib/tests 2026-04-05T19:40:52,621 copying tests/test_value_object.py -> build/lib/tests 2026-04-05T19:40:52,623 copying tests/test_somatic_variant_with_0_supporting_rna_reads.py -> build/lib/tests 2026-04-05T19:40:52,625 copying tests/test_allele_counts.py -> build/lib/tests 2026-04-05T19:40:52,627 copying tests/test_reference_contexts.py -> build/lib/tests 2026-04-05T19:40:52,629 copying tests/test_dataframe_builder.py -> build/lib/tests 2026-04-05T19:40:52,630 copying tests/mock_objects.py -> build/lib/tests 2026-04-05T19:40:52,633 copying tests/test_variant_orf.py -> build/lib/tests 2026-04-05T19:40:52,635 copying tests/common.py -> build/lib/tests 2026-04-05T19:40:52,637 copying tests/genomes_for_testing.py -> build/lib/tests 2026-04-05T19:40:52,639 copying tests/test_argparser_helpers.py -> build/lib/tests 2026-04-05T19:40:52,641 copying tests/test_mutant_amino_acids_in_protein_sequence.py -> build/lib/tests 2026-04-05T19:40:52,643 copying tests/test_reference_coding_sequence_key.py -> build/lib/tests 2026-04-05T19:40:52,645 copying tests/test_variant_sequences.py -> build/lib/tests 2026-04-05T19:40:52,647 copying tests/test_somatic_variant_with_2_supporting_rna_reads.py -> build/lib/tests 2026-04-05T19:40:52,649 copying tests/test_reference_sequence_key.py -> build/lib/tests 2026-04-05T19:40:52,652 copying tests/test_cli.py -> build/lib/tests 2026-04-05T19:40:52,653 copying tests/test_protein_sequences.py -> build/lib/tests 2026-04-05T19:40:52,656 copying tests/test_variant_reads_with_dummy_samfile.py -> build/lib/tests 2026-04-05T19:40:52,658 copying tests/test_main.py -> build/lib/tests 2026-04-05T19:40:52,660 copying tests/test_allele_reads.py -> build/lib/tests 2026-04-05T19:40:52,661 copying tests/test_alignment_score.py -> build/lib/tests 2026-04-05T19:40:52,665 creating build/lib/isovar 2026-04-05T19:40:52,666 copying isovar/variant_sequence.py -> build/lib/isovar 2026-04-05T19:40:52,669 copying isovar/protein_sequence.py -> build/lib/isovar 2026-04-05T19:40:52,671 copying isovar/effect_prediction.py -> build/lib/isovar 2026-04-05T19:40:52,673 copying isovar/__init__.py -> build/lib/isovar 2026-04-05T19:40:52,675 copying isovar/allele_read_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,677 copying isovar/translation.py -> build/lib/isovar 2026-04-05T19:40:52,679 copying isovar/reference_coding_sequence_key.py -> build/lib/isovar 2026-04-05T19:40:52,681 copying isovar/reference_context_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,683 copying isovar/translation_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,686 copying isovar/reference_context.py -> build/lib/isovar 2026-04-05T19:40:52,687 copying isovar/value_object.py -> build/lib/isovar 2026-04-05T19:40:52,689 copying isovar/read_collector.py -> build/lib/isovar 2026-04-05T19:40:52,692 copying isovar/variant_sequence_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,694 copying isovar/variant_orf_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,696 copying isovar/reference_sequence_key.py -> build/lib/isovar 2026-04-05T19:40:52,699 copying isovar/variant_sequence_creator.py -> build/lib/isovar 2026-04-05T19:40:52,701 copying isovar/dataframe_builder.py -> build/lib/isovar 2026-04-05T19:40:52,703 copying isovar/variant_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,706 copying isovar/alignment_score.py -> build/lib/isovar 2026-04-05T19:40:52,708 copying isovar/isovar_result.py -> build/lib/isovar 2026-04-05T19:40:52,712 copying isovar/string_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,714 copying isovar/main.py -> build/lib/isovar 2026-04-05T19:40:52,717 copying isovar/filtering.py -> build/lib/isovar 2026-04-05T19:40:52,719 copying isovar/protein_sequence_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,721 copying isovar/common.py -> build/lib/isovar 2026-04-05T19:40:52,723 copying isovar/genetic_code.py -> build/lib/isovar 2026-04-05T19:40:52,726 copying isovar/phasing.py -> build/lib/isovar 2026-04-05T19:40:52,728 copying isovar/variant_orf.py -> build/lib/isovar 2026-04-05T19:40:52,730 copying isovar/translation_key.py -> build/lib/isovar 2026-04-05T19:40:52,733 copying isovar/read_evidence.py -> build/lib/isovar 2026-04-05T19:40:52,735 copying isovar/dataframe_helpers.py -> build/lib/isovar 2026-04-05T19:40:52,737 copying isovar/dna.py -> build/lib/isovar 2026-04-05T19:40:52,739 copying isovar/allele_read.py -> build/lib/isovar 2026-04-05T19:40:52,741 copying isovar/assembly.py -> build/lib/isovar 2026-04-05T19:40:52,743 copying isovar/default_parameters.py -> build/lib/isovar 2026-04-05T19:40:52,746 copying isovar/protein_sequence_creator.py -> build/lib/isovar 2026-04-05T19:40:52,749 copying isovar/logging.py -> build/lib/isovar 2026-04-05T19:40:52,751 copying isovar/locus_read.py -> build/lib/isovar 2026-04-05T19:40:52,754 creating build/lib/isovar/cli 2026-04-05T19:40:52,756 copying isovar/cli/isovar_allele_reads.py -> build/lib/isovar/cli 2026-04-05T19:40:52,758 copying isovar/cli/__init__.py -> build/lib/isovar/cli 2026-04-05T19:40:52,761 copying isovar/cli/main_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,763 copying isovar/cli/isovar_variant_sequences.py -> build/lib/isovar/cli 2026-04-05T19:40:52,765 copying isovar/cli/rna_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,767 copying isovar/cli/isovar_reference_contexts.py -> build/lib/isovar/cli 2026-04-05T19:40:52,769 copying isovar/cli/isovar_translations.py -> build/lib/isovar/cli 2026-04-05T19:40:52,771 copying isovar/cli/filter_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,774 copying isovar/cli/isovar_allele_counts.py -> build/lib/isovar/cli 2026-04-05T19:40:52,776 copying isovar/cli/isovar_main.py -> build/lib/isovar/cli 2026-04-05T19:40:52,778 copying isovar/cli/variant_sequences_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,780 copying isovar/cli/isovar_variant_reads.py -> build/lib/isovar/cli 2026-04-05T19:40:52,782 copying isovar/cli/translation_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,784 copying isovar/cli/isovar_protein_sequences.py -> build/lib/isovar/cli 2026-04-05T19:40:52,786 copying isovar/cli/reference_context_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,788 copying isovar/cli/output_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,791 copying isovar/cli/protein_sequence_args.py -> build/lib/isovar/cli 2026-04-05T19:40:52,795 copying isovar/logging.conf -> build/lib/isovar 2026-04-05T19:40:52,828 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-04-05T19:40:52,829 !! 2026-04-05T19:40:52,830 ******************************************************************************** 2026-04-05T19:40:52,830 Please avoid running ``setup.py`` directly. 2026-04-05T19:40:52,831 Instead, use pypa/build, pypa/installer or other 2026-04-05T19:40:52,831 standards-based tools. 2026-04-05T19:40:52,833 This deprecation is overdue, please update your project and remove deprecated 2026-04-05T19:40:52,833 calls to avoid build errors in the future. 2026-04-05T19:40:52,834 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-04-05T19:40:52,835 ******************************************************************************** 2026-04-05T19:40:52,836 !! 2026-04-05T19:40:52,837 self.initialize_options() 2026-04-05T19:40:52,861 installing to build/bdist.linux-armv7l/wheel 2026-04-05T19:40:52,861 running install 2026-04-05T19:40:52,885 running install_lib 2026-04-05T19:40:52,913 creating build/bdist.linux-armv7l/wheel 2026-04-05T19:40:52,916 creating build/bdist.linux-armv7l/wheel/tests 2026-04-05T19:40:52,918 copying build/lib/tests/test_genetic_code.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,921 copying build/lib/tests/test_isovar_result.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,923 copying build/lib/tests/test_translation.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,925 copying build/lib/tests/test_filtering.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,927 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,929 copying build/lib/tests/test_assembly.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,932 copying build/lib/tests/test_variant_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,934 copying build/lib/tests/test_locus_reads.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,937 copying build/lib/tests/test_effect_prediction.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,939 copying build/lib/tests/test_gather_variant_reads_wgs.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,941 copying build/lib/tests/testing_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,943 copying build/lib/tests/test_common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,944 copying build/lib/tests/test_read_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,946 copying build/lib/tests/test_dna_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,948 copying build/lib/tests/test_value_object.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,950 copying build/lib/tests/test_somatic_variant_with_0_supporting_rna_reads.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,952 copying build/lib/tests/test_allele_counts.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,954 copying build/lib/tests/test_reference_contexts.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,957 copying build/lib/tests/test_dataframe_builder.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,959 copying build/lib/tests/mock_objects.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,961 copying build/lib/tests/test_variant_orf.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,964 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,966 copying build/lib/tests/genomes_for_testing.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,969 copying build/lib/tests/test_argparser_helpers.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,971 copying build/lib/tests/test_mutant_amino_acids_in_protein_sequence.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,973 copying build/lib/tests/test_reference_coding_sequence_key.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,976 copying build/lib/tests/test_variant_sequences.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,979 copying build/lib/tests/test_somatic_variant_with_2_supporting_rna_reads.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,981 copying build/lib/tests/test_reference_sequence_key.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,984 copying build/lib/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,986 copying build/lib/tests/test_protein_sequences.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,988 copying build/lib/tests/test_variant_reads_with_dummy_samfile.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,990 copying build/lib/tests/test_main.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,992 copying build/lib/tests/test_allele_reads.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,994 copying build/lib/tests/test_alignment_score.py -> build/bdist.linux-armv7l/wheel/./tests 2026-04-05T19:40:52,997 creating build/bdist.linux-armv7l/wheel/isovar 2026-04-05T19:40:52,998 copying build/lib/isovar/variant_sequence.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,001 copying build/lib/isovar/protein_sequence.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,004 copying build/lib/isovar/effect_prediction.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,006 copying build/lib/isovar/__init__.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,007 copying build/lib/isovar/allele_read_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,009 copying build/lib/isovar/translation.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,011 copying build/lib/isovar/reference_coding_sequence_key.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,014 copying build/lib/isovar/reference_context_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,015 copying build/lib/isovar/translation_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,018 copying build/lib/isovar/reference_context.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,019 copying build/lib/isovar/value_object.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,021 copying build/lib/isovar/read_collector.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,024 copying build/lib/isovar/variant_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,026 copying build/lib/isovar/variant_orf_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,028 copying build/lib/isovar/reference_sequence_key.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,031 creating build/bdist.linux-armv7l/wheel/isovar/cli 2026-04-05T19:40:53,032 copying build/lib/isovar/cli/isovar_allele_reads.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,034 copying build/lib/isovar/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,035 copying build/lib/isovar/cli/main_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,037 copying build/lib/isovar/cli/isovar_variant_sequences.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,039 copying build/lib/isovar/cli/rna_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,041 copying build/lib/isovar/cli/isovar_reference_contexts.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,043 copying build/lib/isovar/cli/isovar_translations.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,045 copying build/lib/isovar/cli/filter_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,047 copying build/lib/isovar/cli/isovar_allele_counts.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,049 copying build/lib/isovar/cli/isovar_main.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,050 copying build/lib/isovar/cli/variant_sequences_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,052 copying build/lib/isovar/cli/isovar_variant_reads.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,054 copying build/lib/isovar/cli/translation_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,056 copying build/lib/isovar/cli/isovar_protein_sequences.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,057 copying build/lib/isovar/cli/reference_context_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,059 copying build/lib/isovar/cli/output_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,061 copying build/lib/isovar/cli/protein_sequence_args.py -> build/bdist.linux-armv7l/wheel/./isovar/cli 2026-04-05T19:40:53,063 copying build/lib/isovar/variant_sequence_creator.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,066 copying build/lib/isovar/dataframe_builder.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,068 copying build/lib/isovar/variant_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,071 copying build/lib/isovar/alignment_score.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,072 copying build/lib/isovar/isovar_result.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,075 copying build/lib/isovar/string_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,077 copying build/lib/isovar/main.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,079 copying build/lib/isovar/filtering.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,082 copying build/lib/isovar/protein_sequence_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,084 copying build/lib/isovar/common.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,086 copying build/lib/isovar/genetic_code.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,088 copying build/lib/isovar/phasing.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,090 copying build/lib/isovar/variant_orf.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,093 copying build/lib/isovar/translation_key.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,095 copying build/lib/isovar/read_evidence.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,097 copying build/lib/isovar/dataframe_helpers.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,099 copying build/lib/isovar/dna.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,101 copying build/lib/isovar/allele_read.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,103 copying build/lib/isovar/assembly.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,106 copying build/lib/isovar/default_parameters.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,108 copying build/lib/isovar/protein_sequence_creator.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,112 copying build/lib/isovar/logging.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,114 copying build/lib/isovar/logging.conf -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,116 copying build/lib/isovar/locus_read.py -> build/bdist.linux-armv7l/wheel/./isovar 2026-04-05T19:40:53,118 running install_egg_info 2026-04-05T19:40:53,153 running egg_info 2026-04-05T19:40:53,181 writing isovar.egg-info/PKG-INFO 2026-04-05T19:40:53,185 writing dependency_links to isovar.egg-info/dependency_links.txt 2026-04-05T19:40:53,187 writing entry points to isovar.egg-info/entry_points.txt 2026-04-05T19:40:53,188 writing requirements to isovar.egg-info/requires.txt 2026-04-05T19:40:53,189 writing top-level names to isovar.egg-info/top_level.txt 2026-04-05T19:40:53,226 reading manifest file 'isovar.egg-info/SOURCES.txt' 2026-04-05T19:40:53,233 adding license file 'LICENSE' 2026-04-05T19:40:53,239 writing manifest file 'isovar.egg-info/SOURCES.txt' 2026-04-05T19:40:53,241 Copying isovar.egg-info to build/bdist.linux-armv7l/wheel/./isovar-1.4.0-py3.11.egg-info 2026-04-05T19:40:53,259 running install_scripts 2026-04-05T19:40:53,279 creating build/bdist.linux-armv7l/wheel/isovar-1.4.0.dist-info/WHEEL 2026-04-05T19:40:53,282 creating '/tmp/pip-wheel-csx50wx6/isovar-1.4.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-05T19:40:53,285 adding 'isovar/__init__.py' 2026-04-05T19:40:53,286 adding 'isovar/alignment_score.py' 2026-04-05T19:40:53,288 adding 'isovar/allele_read.py' 2026-04-05T19:40:53,290 adding 'isovar/allele_read_helpers.py' 2026-04-05T19:40:53,292 adding 'isovar/assembly.py' 2026-04-05T19:40:53,293 adding 'isovar/common.py' 2026-04-05T19:40:53,295 adding 'isovar/dataframe_builder.py' 2026-04-05T19:40:53,297 adding 'isovar/dataframe_helpers.py' 2026-04-05T19:40:53,299 adding 'isovar/default_parameters.py' 2026-04-05T19:40:53,300 adding 'isovar/dna.py' 2026-04-05T19:40:53,302 adding 'isovar/effect_prediction.py' 2026-04-05T19:40:53,304 adding 'isovar/filtering.py' 2026-04-05T19:40:53,306 adding 'isovar/genetic_code.py' 2026-04-05T19:40:53,309 adding 'isovar/isovar_result.py' 2026-04-05T19:40:53,311 adding 'isovar/locus_read.py' 2026-04-05T19:40:53,313 adding 'isovar/logging.conf' 2026-04-05T19:40:53,314 adding 'isovar/logging.py' 2026-04-05T19:40:53,316 adding 'isovar/main.py' 2026-04-05T19:40:53,318 adding 'isovar/phasing.py' 2026-04-05T19:40:53,320 adding 'isovar/protein_sequence.py' 2026-04-05T19:40:53,323 adding 'isovar/protein_sequence_creator.py' 2026-04-05T19:40:53,324 adding 'isovar/protein_sequence_helpers.py' 2026-04-05T19:40:53,327 adding 'isovar/read_collector.py' 2026-04-05T19:40:53,329 adding 'isovar/read_evidence.py' 2026-04-05T19:40:53,331 adding 'isovar/reference_coding_sequence_key.py' 2026-04-05T19:40:53,332 adding 'isovar/reference_context.py' 2026-04-05T19:40:53,333 adding 'isovar/reference_context_helpers.py' 2026-04-05T19:40:53,335 adding 'isovar/reference_sequence_key.py' 2026-04-05T19:40:53,336 adding 'isovar/string_helpers.py' 2026-04-05T19:40:53,338 adding 'isovar/translation.py' 2026-04-05T19:40:53,339 adding 'isovar/translation_helpers.py' 2026-04-05T19:40:53,341 adding 'isovar/translation_key.py' 2026-04-05T19:40:53,342 adding 'isovar/value_object.py' 2026-04-05T19:40:53,344 adding 'isovar/variant_helpers.py' 2026-04-05T19:40:53,346 adding 'isovar/variant_orf.py' 2026-04-05T19:40:53,347 adding 'isovar/variant_orf_helpers.py' 2026-04-05T19:40:53,349 adding 'isovar/variant_sequence.py' 2026-04-05T19:40:53,351 adding 'isovar/variant_sequence_creator.py' 2026-04-05T19:40:53,352 adding 'isovar/variant_sequence_helpers.py' 2026-04-05T19:40:53,355 adding 'isovar/cli/__init__.py' 2026-04-05T19:40:53,356 adding 'isovar/cli/filter_args.py' 2026-04-05T19:40:53,358 adding 'isovar/cli/isovar_allele_counts.py' 2026-04-05T19:40:53,359 adding 'isovar/cli/isovar_allele_reads.py' 2026-04-05T19:40:53,360 adding 'isovar/cli/isovar_main.py' 2026-04-05T19:40:53,362 adding 'isovar/cli/isovar_protein_sequences.py' 2026-04-05T19:40:53,363 adding 'isovar/cli/isovar_reference_contexts.py' 2026-04-05T19:40:53,365 adding 'isovar/cli/isovar_translations.py' 2026-04-05T19:40:53,366 adding 'isovar/cli/isovar_variant_reads.py' 2026-04-05T19:40:53,368 adding 'isovar/cli/isovar_variant_sequences.py' 2026-04-05T19:40:53,369 adding 'isovar/cli/main_args.py' 2026-04-05T19:40:53,370 adding 'isovar/cli/output_args.py' 2026-04-05T19:40:53,372 adding 'isovar/cli/protein_sequence_args.py' 2026-04-05T19:40:53,374 adding 'isovar/cli/reference_context_args.py' 2026-04-05T19:40:53,375 adding 'isovar/cli/rna_args.py' 2026-04-05T19:40:53,377 adding 'isovar/cli/translation_args.py' 2026-04-05T19:40:53,378 adding 'isovar/cli/variant_sequences_args.py' 2026-04-05T19:40:53,382 adding 'isovar-1.4.0.dist-info/licenses/LICENSE' 2026-04-05T19:40:53,384 adding 'tests/__init__.py' 2026-04-05T19:40:53,386 adding 'tests/common.py' 2026-04-05T19:40:53,387 adding 'tests/genomes_for_testing.py' 2026-04-05T19:40:53,388 adding 'tests/mock_objects.py' 2026-04-05T19:40:53,390 adding 'tests/test_alignment_score.py' 2026-04-05T19:40:53,391 adding 'tests/test_allele_counts.py' 2026-04-05T19:40:53,392 adding 'tests/test_allele_reads.py' 2026-04-05T19:40:53,394 adding 'tests/test_argparser_helpers.py' 2026-04-05T19:40:53,395 adding 'tests/test_assembly.py' 2026-04-05T19:40:53,397 adding 'tests/test_cli.py' 2026-04-05T19:40:53,398 adding 'tests/test_common.py' 2026-04-05T19:40:53,399 adding 'tests/test_dataframe_builder.py' 2026-04-05T19:40:53,400 adding 'tests/test_dna_helpers.py' 2026-04-05T19:40:53,402 adding 'tests/test_effect_prediction.py' 2026-04-05T19:40:53,403 adding 'tests/test_filtering.py' 2026-04-05T19:40:53,404 adding 'tests/test_gather_variant_reads_wgs.py' 2026-04-05T19:40:53,406 adding 'tests/test_genetic_code.py' 2026-04-05T19:40:53,407 adding 'tests/test_isovar_result.py' 2026-04-05T19:40:53,409 adding 'tests/test_locus_reads.py' 2026-04-05T19:40:53,410 adding 'tests/test_main.py' 2026-04-05T19:40:53,411 adding 'tests/test_mutant_amino_acids_in_protein_sequence.py' 2026-04-05T19:40:53,413 adding 'tests/test_protein_sequences.py' 2026-04-05T19:40:53,414 adding 'tests/test_read_helpers.py' 2026-04-05T19:40:53,416 adding 'tests/test_reference_coding_sequence_key.py' 2026-04-05T19:40:53,417 adding 'tests/test_reference_contexts.py' 2026-04-05T19:40:53,419 adding 'tests/test_reference_sequence_key.py' 2026-04-05T19:40:53,420 adding 'tests/test_somatic_variant_with_0_supporting_rna_reads.py' 2026-04-05T19:40:53,421 adding 'tests/test_somatic_variant_with_2_supporting_rna_reads.py' 2026-04-05T19:40:53,422 adding 'tests/test_translation.py' 2026-04-05T19:40:53,424 adding 'tests/test_value_object.py' 2026-04-05T19:40:53,425 adding 'tests/test_variant_helpers.py' 2026-04-05T19:40:53,427 adding 'tests/test_variant_orf.py' 2026-04-05T19:40:53,428 adding 'tests/test_variant_reads_with_dummy_samfile.py' 2026-04-05T19:40:53,430 adding 'tests/test_variant_sequences.py' 2026-04-05T19:40:53,431 adding 'tests/testing_helpers.py' 2026-04-05T19:40:53,434 adding 'isovar-1.4.0.dist-info/METADATA' 2026-04-05T19:40:53,435 adding 'isovar-1.4.0.dist-info/WHEEL' 2026-04-05T19:40:53,436 adding 'isovar-1.4.0.dist-info/entry_points.txt' 2026-04-05T19:40:53,437 adding 'isovar-1.4.0.dist-info/top_level.txt' 2026-04-05T19:40:53,438 adding 'isovar-1.4.0.dist-info/RECORD' 2026-04-05T19:40:53,442 removing build/bdist.linux-armv7l/wheel 2026-04-05T19:40:53,572 Building wheel for isovar (setup.py): finished with status 'done' 2026-04-05T19:40:53,576 Created wheel for isovar: filename=isovar-1.4.0-py3-none-any.whl size=152584 sha256=8acc93c516812e2418dcf1ba3b271fae9fecadd186ce4428444805ed6fe40215 2026-04-05T19:40:53,577 Stored in directory: /tmp/pip-ephem-wheel-cache-edf8sivd/wheels/43/51/3f/2e7692fe34ca7ca895f2ae8ea9cffccfd3533f1bf0183525b3 2026-04-05T19:40:53,593 Successfully built isovar 2026-04-05T19:40:53,601 Removed build tracker: '/tmp/pip-build-tracker-4m2_z137'