2026-07-12T16:35:21,923 Created temporary directory: /tmp/pip-ephem-wheel-cache-e33pmbpb 2026-07-12T16:35:21,924 Created temporary directory: /tmp/pip-build-tracker-h9z7f7bq 2026-07-12T16:35:21,925 Initialized build tracking at /tmp/pip-build-tracker-h9z7f7bq 2026-07-12T16:35:21,925 Created build tracker: /tmp/pip-build-tracker-h9z7f7bq 2026-07-12T16:35:21,926 Entered build tracker: /tmp/pip-build-tracker-h9z7f7bq 2026-07-12T16:35:21,927 Created temporary directory: /tmp/pip-wheel-z0evoo0c 2026-07-12T16:35:21,930 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 2026-07-12T16:35:21,932 Created temporary directory: /tmp/pip-ephem-wheel-cache-jp34iuvu 2026-07-12T16:35:21,953 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-12T16:35:21,957 2 location(s) to search for versions of dendropy: 2026-07-12T16:35:21,957 * https://pypi.org/simple/dendropy/ 2026-07-12T16:35:21,957 * https://www.piwheels.org/simple/dendropy/ 2026-07-12T16:35:21,958 Fetching project page and analyzing links: https://pypi.org/simple/dendropy/ 2026-07-12T16:35:21,958 Getting page https://pypi.org/simple/dendropy/ 2026-07-12T16:35:21,960 Found index url https://pypi.org/simple 2026-07-12T16:35:22,217 Fetched page https://pypi.org/simple/dendropy/ as application/vnd.pypi.simple.v1+json 2026-07-12T16:35:22,225 Found link https://files.pythonhosted.org/packages/03/48/8379b3e170d60052da7ccf3387549af17d46808a39062fbb234df3038fa0/DendroPy-3.7.0.tar.gz (from 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2026-07-12T16:35:22,247 Found link https://files.pythonhosted.org/packages/42/4b/6b300d145575ac7445e3b79b5c0c3a4ea441937278528b8dbd5b0aab42fc/DendroPy-5.0.1.tar.gz (from https://pypi.org/simple/dendropy/) (requires-python:>=3.6), version: 5.0.1 2026-07-12T16:35:22,248 Skipping link: No binaries permitted for dendropy: https://files.pythonhosted.org/packages/f9/20/95c487820aac183b540c1d9d26d5778c9975015c3505137c5c5cd230a7ee/DendroPy-5.0.7-py3-none-any.whl (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7) 2026-07-12T16:35:22,249 Found link https://files.pythonhosted.org/packages/63/35/150e49455d787ce95487b2f9fa1d9766054ac5df304eae3fc2d24eabf1f4/DendroPy-5.0.7.tar.gz (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7), version: 5.0.7 2026-07-12T16:35:22,249 Skipping link: No binaries permitted for dendropy: https://files.pythonhosted.org/packages/29/3d/d93dfd44e8615b39fab0b939bc7d8030021c092bffb3cc3c50580e75fc8f/DendroPy-5.0.8-py3-none-any.whl (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7) 2026-07-12T16:35:22,250 Found link https://files.pythonhosted.org/packages/76/e4/ea83865a284c81e58d55936578dbfaa012afd7a791a75e1105c46e928f1d/DendroPy-5.0.8.tar.gz (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7), version: 5.0.8 2026-07-12T16:35:22,251 Skipping link: No binaries permitted for dendropy: https://files.pythonhosted.org/packages/81/1d/aa89b03a4b86538a47814c4c312770135c98fc6cbf52f5e1e4a360ff4cdb/dendropy-5.0.10-py3-none-any.whl (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7) 2026-07-12T16:35:22,252 Found link https://files.pythonhosted.org/packages/d4/53/88c39ee7789e56c16be7bf0a895317a6a84b05ff18b390aaad6b8381c4f3/dendropy-5.0.10.tar.gz (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7), version: 5.0.10 2026-07-12T16:35:22,253 Fetching project page and analyzing links: https://www.piwheels.org/simple/dendropy/ 2026-07-12T16:35:22,254 Getting page https://www.piwheels.org/simple/dendropy/ 2026-07-12T16:35:22,255 Found index url https://www.piwheels.org/simple 2026-07-12T16:35:22,552 Fetched page https://www.piwheels.org/simple/dendropy/ as text/html 2026-07-12T16:35:22,558 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/dendropy-5.0.8-py3-none-any.whl#sha256=4b2177e7efdd852842ddc447290d9cd660ef9de7a55e58f91a671dd2e554c546 (from https://www.piwheels.org/simple/dendropy/) (requires-python:>=3.7) 2026-07-12T16:35:22,559 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/dendropy-5.0.7-py3-none-any.whl#sha256=58506f7f1278e140493763d4e6144d073f0a2d4eb029bd0a3adce91f534485fa (from https://www.piwheels.org/simple/dendropy/) (requires-python:>=3.7) 2026-07-12T16:35:22,559 Skipping link: No binaries permitted for dendropy: 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https://archive1.piwheels.org/simple/dendropy/DendroPy-4.6.3-py3-none-any.whl#sha256=55d64c6747ef5feb8125c6b3ba58937d2c93874d1ae798501c4b5a3d6cd56cc2 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,562 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.6.1-py3-none-any.whl#sha256=da58df7fced8722b607b168cb9ffec744a299b5ebdebb62786835351122e5236 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,562 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.6.0-py3-none-any.whl#sha256=967847ceda8c3c50c9c82bf0b17ad1cfed383857502a32878e1870fde0b9f662 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,563 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.5.2-py3-none-any.whl#sha256=7492efc1d60e0d280a9effe9093dd14da694300275c2dbc2c3cd116390521bc3 (from 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https://archive1.piwheels.org/simple/dendropy/DendroPy-4.2.0-py3-none-any.whl#sha256=b708e09e2b790f482496fd2e17b5159e212994a6d7d234771e2c9e5e208aa55e (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,565 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.1.0-py3-none-any.whl#sha256=1b13aa093d01409bfb95728a68dbff117529dc40cd5ac6fa4d4fc30756ef5357 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,566 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.0.3-py3-none-any.whl#sha256=eea9ba2017437bada349db5b12b6d9c8c6dfcbfea1832bac2a862b3c5503ceb3 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,567 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.0.2-py3-none-any.whl#sha256=81648919d17fb5fdc36f4053aff572b4a2d358a189d2462e15aab8760eb71d1a (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,567 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.0.1-py3-none-any.whl#sha256=4ba8a912afd561e3116cdfbcd6c168cafc69eec3339bfdb79858e93000402410 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,568 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.0.0-py3-none-any.whl#sha256=4687108db4e411473e5ccce4ec9a99fc10ad22b8da4c6e817154202a3e6cc0e9 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,568 Skipping link: No binaries permitted for dendropy: https://archive1.piwheels.org/simple/dendropy/DendroPy-4.0.0rc1-py3-none-any.whl#sha256=0310d7072108356c0655941033b16778503a2c6ec2d84ac1eeb88a41eb92a543 (from https://www.piwheels.org/simple/dendropy/) 2026-07-12T16:35:22,570 Skipping link: not a file: https://www.piwheels.org/simple/dendropy/ 2026-07-12T16:35:22,570 Skipping link: not a file: https://pypi.org/simple/dendropy/ 2026-07-12T16:35:22,592 Given no hashes to check 1 links for project 'dendropy': discarding no candidates 2026-07-12T16:35:22,610 Collecting dendropy==5.0.10 2026-07-12T16:35:22,612 Created temporary directory: /tmp/pip-unpack-jpf3ypua 2026-07-12T16:35:22,937 Downloading dendropy-5.0.10.tar.gz (398 kB) 2026-07-12T16:35:23,408 Added dendropy==5.0.10 from https://files.pythonhosted.org/packages/d4/53/88c39ee7789e56c16be7bf0a895317a6a84b05ff18b390aaad6b8381c4f3/dendropy-5.0.10.tar.gz to build tracker '/tmp/pip-build-tracker-h9z7f7bq' 2026-07-12T16:35:23,410 Running setup.py (path:/tmp/pip-wheel-z0evoo0c/dendropy_a62d5d62733d46d0a18e0191134ecca2/setup.py) egg_info for package dendropy 2026-07-12T16:35:23,411 Created temporary directory: /tmp/pip-pip-egg-info-z8tba48s 2026-07-12T16:35:23,411 Preparing metadata (setup.py): started 2026-07-12T16:35:23,412 Running command python setup.py egg_info 2026-07-12T16:35:24,021 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2026-07-12T16:35:24,021 !! 2026-07-12T16:35:24,022 ******************************************************************************** 2026-07-12T16:35:24,023 Requirements should be satisfied by a PEP 517 installer. 2026-07-12T16:35:24,023 If you are using pip, you can try `pip install --use-pep517`. 2026-07-12T16:35:24,025 This deprecation is overdue, please update your project and remove deprecated 2026-07-12T16:35:24,025 calls to avoid build errors in the future. 2026-07-12T16:35:24,026 ******************************************************************************** 2026-07-12T16:35:24,027 !! 2026-07-12T16:35:24,028 dist.fetch_build_eggs(dist.setup_requires) 2026-07-12T16:35:26,753 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'test_suite' 2026-07-12T16:35:26,754 warnings.warn(msg) 2026-07-12T16:35:26,754 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' 2026-07-12T16:35:26,755 warnings.warn(msg) 2026-07-12T16:35:26,814 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-07-12T16:35:26,815 !! 2026-07-12T16:35:26,816 ******************************************************************************** 2026-07-12T16:35:26,816 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-07-12T16:35:26,817 License :: OSI Approved :: BSD License 2026-07-12T16:35:26,819 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-07-12T16:35:26,819 ******************************************************************************** 2026-07-12T16:35:26,821 !! 2026-07-12T16:35:26,821 self._finalize_license_expression() 2026-07-12T16:35:26,846 running egg_info 2026-07-12T16:35:26,876 creating /tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info 2026-07-12T16:35:26,877 writing /tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/PKG-INFO 2026-07-12T16:35:26,881 writing dependency_links to /tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/dependency_links.txt 2026-07-12T16:35:26,883 writing entry points to /tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/entry_points.txt 2026-07-12T16:35:26,884 writing requirements to /tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/requires.txt 2026-07-12T16:35:26,885 writing top-level names to /tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/top_level.txt 2026-07-12T16:35:26,887 writing manifest file '/tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/SOURCES.txt' 2026-07-12T16:35:27,024 reading manifest file '/tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/SOURCES.txt' 2026-07-12T16:35:27,025 reading manifest template 'MANIFEST.in' 2026-07-12T16:35:27,026 warning: no files found matching 'README.rst' 2026-07-12T16:35:27,027 warning: no files found matching 'doc/Makefile' 2026-07-12T16:35:27,027 warning: no files found matching '*' under directory 'doc/source' 2026-07-12T16:35:27,028 warning: no files found matching '*' under directory 'tests/data' 2026-07-12T16:35:27,029 warning: no previously-included files matching '.DS_Store' found anywhere in distribution 2026-07-12T16:35:27,030 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2026-07-12T16:35:27,031 warning: no previously-included files matching '.gitignore' found anywhere in distribution 2026-07-12T16:35:27,031 warning: no previously-included files matching '.gitattributes' found anywhere in distribution 2026-07-12T16:35:27,032 warning: no previously-included files matching '.idea' found anywhere in distribution 2026-07-12T16:35:27,033 warning: no previously-included files matching '__pycache__' found anywhere in distribution 2026-07-12T16:35:27,034 adding license file 'LICENSE.rst' 2026-07-12T16:35:27,034 adding license file 'NOTICES.rst' 2026-07-12T16:35:27,035 adding license file 'AUTHORS.rst' 2026-07-12T16:35:27,040 writing manifest file '/tmp/pip-pip-egg-info-z8tba48s/DendroPy.egg-info/SOURCES.txt' 2026-07-12T16:35:27,152 Preparing metadata (setup.py): finished with status 'done' 2026-07-12T16:35:27,157 Source in /tmp/pip-wheel-z0evoo0c/dendropy_a62d5d62733d46d0a18e0191134ecca2 has version 5.0.10, which satisfies requirement dendropy==5.0.10 from https://files.pythonhosted.org/packages/d4/53/88c39ee7789e56c16be7bf0a895317a6a84b05ff18b390aaad6b8381c4f3/dendropy-5.0.10.tar.gz 2026-07-12T16:35:27,158 Removed dendropy==5.0.10 from https://files.pythonhosted.org/packages/d4/53/88c39ee7789e56c16be7bf0a895317a6a84b05ff18b390aaad6b8381c4f3/dendropy-5.0.10.tar.gz from build tracker '/tmp/pip-build-tracker-h9z7f7bq' 2026-07-12T16:35:27,165 Created temporary directory: /tmp/pip-unpack-nkjcvdhn 2026-07-12T16:35:27,165 Building wheels for collected packages: dendropy 2026-07-12T16:35:27,169 Created temporary directory: /tmp/pip-wheel-uxygbf8f 2026-07-12T16:35:27,170 Building wheel for dendropy (setup.py): started 2026-07-12T16:35:27,171 Destination directory: /tmp/pip-wheel-uxygbf8f 2026-07-12T16:35:27,172 Running command python setup.py bdist_wheel 2026-07-12T16:35:27,714 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2026-07-12T16:35:27,714 !! 2026-07-12T16:35:27,715 ******************************************************************************** 2026-07-12T16:35:27,716 Requirements should be satisfied by a PEP 517 installer. 2026-07-12T16:35:27,716 If you are using pip, you can try `pip install --use-pep517`. 2026-07-12T16:35:27,718 This deprecation is overdue, please update your project and remove deprecated 2026-07-12T16:35:27,718 calls to avoid build errors in the future. 2026-07-12T16:35:27,719 ******************************************************************************** 2026-07-12T16:35:27,720 !! 2026-07-12T16:35:27,721 dist.fetch_build_eggs(dist.setup_requires) 2026-07-12T16:35:27,938 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'test_suite' 2026-07-12T16:35:27,939 warnings.warn(msg) 2026-07-12T16:35:27,939 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' 2026-07-12T16:35:27,940 warnings.warn(msg) 2026-07-12T16:35:28,231 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-07-12T16:35:28,231 !! 2026-07-12T16:35:28,232 ******************************************************************************** 2026-07-12T16:35:28,233 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-07-12T16:35:28,234 License :: OSI Approved :: BSD License 2026-07-12T16:35:28,234 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-07-12T16:35:28,235 ******************************************************************************** 2026-07-12T16:35:28,236 !! 2026-07-12T16:35:28,236 self._finalize_license_expression() 2026-07-12T16:35:28,237 running bdist_wheel 2026-07-12T16:35:28,378 running build 2026-07-12T16:35:28,378 running build_py 2026-07-12T16:35:28,411 creating build/lib/dendropy 2026-07-12T16:35:28,413 copying src/dendropy/__main__.py -> build/lib/dendropy 2026-07-12T16:35:28,415 copying src/dendropy/__init__.py -> build/lib/dendropy 2026-07-12T16:35:28,418 creating build/lib/dendropy/utility 2026-07-12T16:35:28,419 copying src/dendropy/utility/bibtex.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,421 copying src/dendropy/utility/messaging.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,424 copying src/dendropy/utility/debug.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,425 copying src/dendropy/utility/container.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,428 copying src/dendropy/utility/metavar.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,430 copying src/dendropy/utility/processio.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,432 copying src/dendropy/utility/cli.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,434 copying src/dendropy/utility/__init__.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,436 copying src/dendropy/utility/urlio.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,438 copying src/dendropy/utility/error.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,440 copying src/dendropy/utility/constants.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,442 copying src/dendropy/utility/timeprocessing.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,444 copying src/dendropy/utility/textprocessing.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,446 copying src/dendropy/utility/vcsinfo.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,448 copying src/dendropy/utility/filesys.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,451 copying src/dendropy/utility/deprecate.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,453 copying src/dendropy/utility/bitprocessing.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,455 copying src/dendropy/utility/terminal.py -> build/lib/dendropy/utility 2026-07-12T16:35:28,457 creating build/lib/dendropy/plot 2026-07-12T16:35:28,458 copying src/dendropy/plot/tikzplot.py -> build/lib/dendropy/plot 2026-07-12T16:35:28,461 copying src/dendropy/plot/asciiplot.py -> build/lib/dendropy/plot 2026-07-12T16:35:28,463 copying src/dendropy/plot/__init__.py -> build/lib/dendropy/plot 2026-07-12T16:35:28,465 creating build/lib/dendropy/interop 2026-07-12T16:35:28,466 copying src/dendropy/interop/paup.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,469 copying src/dendropy/interop/ete.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,471 copying src/dendropy/interop/rstats.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,474 copying src/dendropy/interop/seqgen.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,476 copying src/dendropy/interop/__init__.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,478 copying src/dendropy/interop/biopython.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,480 copying src/dendropy/interop/rspr.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,482 copying src/dendropy/interop/raxml.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,485 copying src/dendropy/interop/ape.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,487 copying src/dendropy/interop/muscle.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,489 copying src/dendropy/interop/entrez.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,490 copying src/dendropy/interop/itol.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,493 copying src/dendropy/interop/gbif.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,495 copying src/dendropy/interop/genbank.py -> build/lib/dendropy/interop 2026-07-12T16:35:28,498 creating build/lib/dendropy/datamodel 2026-07-12T16:35:28,499 copying src/dendropy/datamodel/treecollectionmodel.py -> build/lib/dendropy/datamodel 2026-07-12T16:35:28,504 copying src/dendropy/datamodel/datasetmodel.py -> build/lib/dendropy/datamodel 2026-07-12T16:35:28,507 copying src/dendropy/datamodel/__init__.py -> build/lib/dendropy/datamodel 2026-07-12T16:35:28,508 copying src/dendropy/datamodel/basemodel.py -> build/lib/dendropy/datamodel 2026-07-12T16:35:28,511 copying src/dendropy/datamodel/taxonmodel.py -> build/lib/dendropy/datamodel 2026-07-12T16:35:28,515 copying src/dendropy/datamodel/charmatrixmodel.py -> build/lib/dendropy/datamodel 2026-07-12T16:35:28,519 copying src/dendropy/datamodel/charstatemodel.py -> build/lib/dendropy/datamodel 2026-07-12T16:35:28,523 creating build/lib/dendropy/mathlib 2026-07-12T16:35:28,524 copying src/dendropy/mathlib/probability.py -> build/lib/dendropy/mathlib 2026-07-12T16:35:28,526 copying src/dendropy/mathlib/mathfn.py -> build/lib/dendropy/mathlib 2026-07-12T16:35:28,528 copying src/dendropy/mathlib/__init__.py -> build/lib/dendropy/mathlib 2026-07-12T16:35:28,529 copying src/dendropy/mathlib/statistics.py -> build/lib/dendropy/mathlib 2026-07-12T16:35:28,532 creating build/lib/dendropy/simulate 2026-07-12T16:35:28,533 copying src/dendropy/simulate/charsim.py -> build/lib/dendropy/simulate 2026-07-12T16:35:28,535 copying src/dendropy/simulate/__init__.py -> build/lib/dendropy/simulate 2026-07-12T16:35:28,537 copying src/dendropy/simulate/popgensim.py -> build/lib/dendropy/simulate 2026-07-12T16:35:28,539 copying src/dendropy/simulate/treesim.py -> build/lib/dendropy/simulate 2026-07-12T16:35:28,542 creating build/lib/dendropy/legacy 2026-07-12T16:35:28,543 copying src/dendropy/legacy/seqmodel.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,545 copying src/dendropy/legacy/treecalc.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,548 copying src/dendropy/legacy/ncbi.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,550 copying src/dendropy/legacy/__init__.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,552 copying src/dendropy/legacy/popgenstat.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,555 copying src/dendropy/legacy/popgensim.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,556 copying src/dendropy/legacy/continuous.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,558 copying src/dendropy/legacy/treemanip.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,560 copying src/dendropy/legacy/seqsim.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,562 copying src/dendropy/legacy/reconcile.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,564 copying src/dendropy/legacy/treesum.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,566 copying src/dendropy/legacy/treesplit.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,569 copying src/dendropy/legacy/coalescent.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,571 copying src/dendropy/legacy/treesim.py -> build/lib/dendropy/legacy 2026-07-12T16:35:28,574 creating build/lib/dendropy/calculate 2026-07-12T16:35:28,575 copying src/dendropy/calculate/treescore.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,577 copying src/dendropy/calculate/treecompare.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,580 copying src/dendropy/calculate/treemeasure.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,582 copying src/dendropy/calculate/phylogeneticdistance.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,585 copying src/dendropy/calculate/probability.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,588 copying src/dendropy/calculate/combinatorics.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,590 copying src/dendropy/calculate/mathfn.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,591 copying src/dendropy/calculate/__init__.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,593 copying src/dendropy/calculate/popgenstat.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,595 copying src/dendropy/calculate/profiledistance.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,598 copying src/dendropy/calculate/statistics.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,600 copying src/dendropy/calculate/treesum.py -> build/lib/dendropy/calculate 2026-07-12T16:35:28,603 creating build/lib/dendropy/application 2026-07-12T16:35:28,604 copying src/dendropy/application/sumlabels.py -> build/lib/dendropy/application 2026-07-12T16:35:28,606 copying src/dendropy/application/__init__.py -> build/lib/dendropy/application 2026-07-12T16:35:28,608 copying src/dendropy/application/sumtrees.py -> build/lib/dendropy/application 2026-07-12T16:35:28,612 copying src/dendropy/application/dendropy_format.py -> build/lib/dendropy/application 2026-07-12T16:35:28,615 creating build/lib/dendropy/model 2026-07-12T16:35:28,616 copying src/dendropy/model/treeshape.py -> build/lib/dendropy/model 2026-07-12T16:35:28,618 copying src/dendropy/model/multispeciescoalescent.py -> build/lib/dendropy/model 2026-07-12T16:35:28,620 copying src/dendropy/model/protractedspeciation.py -> build/lib/dendropy/model 2026-07-12T16:35:28,624 copying src/dendropy/model/__init__.py -> build/lib/dendropy/model 2026-07-12T16:35:28,626 copying src/dendropy/model/continuous.py -> build/lib/dendropy/model 2026-07-12T16:35:28,629 copying src/dendropy/model/birthdeath.py -> build/lib/dendropy/model 2026-07-12T16:35:28,632 copying src/dendropy/model/reconcile.py -> build/lib/dendropy/model 2026-07-12T16:35:28,635 copying src/dendropy/model/discrete.py -> build/lib/dendropy/model 2026-07-12T16:35:28,637 copying src/dendropy/model/coalescent.py -> build/lib/dendropy/model 2026-07-12T16:35:28,640 copying src/dendropy/model/parsimony.py -> build/lib/dendropy/model 2026-07-12T16:35:28,643 creating build/lib/dendropy/dataio 2026-07-12T16:35:28,644 copying src/dendropy/dataio/phylipwriter.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,647 copying src/dendropy/dataio/newickwriter.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,649 copying src/dendropy/dataio/multiphylipreader.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,651 copying src/dendropy/dataio/tokenizer.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,653 copying src/dendropy/dataio/newickyielder.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,655 copying src/dendropy/dataio/nexuswriter.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,658 copying src/dendropy/dataio/nexusyielder.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,660 copying src/dendropy/dataio/nexusreader.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,664 copying src/dendropy/dataio/nexmlreader.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,667 copying src/dendropy/dataio/nexmlyielder.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,669 copying src/dendropy/dataio/__init__.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,671 copying src/dendropy/dataio/newick.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,673 copying src/dendropy/dataio/phylipreader.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,675 copying src/dendropy/dataio/newickreader.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,678 copying src/dendropy/dataio/fastawriter.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,680 copying src/dendropy/dataio/ioservice.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,682 copying src/dendropy/dataio/nexmlwriter.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,685 copying src/dendropy/dataio/nexusprocessing.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,688 copying src/dendropy/dataio/xmlprocessing.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,690 copying src/dendropy/dataio/fastareader.py -> build/lib/dendropy/dataio 2026-07-12T16:35:28,693 creating build/lib/dendropy/utility/libexec 2026-07-12T16:35:28,694 copying src/dendropy/utility/libexec/__init__.py -> build/lib/dendropy/utility/libexec 2026-07-12T16:35:28,697 creating build/lib/dendropy/datamodel/treemodel 2026-07-12T16:35:28,698 copying src/dendropy/datamodel/treemodel/__init__.py -> build/lib/dendropy/datamodel/treemodel 2026-07-12T16:35:28,700 copying src/dendropy/datamodel/treemodel/_tree.py -> build/lib/dendropy/datamodel/treemodel 2026-07-12T16:35:28,705 copying src/dendropy/datamodel/treemodel/_bipartition.py -> build/lib/dendropy/datamodel/treemodel 2026-07-12T16:35:28,708 copying src/dendropy/datamodel/treemodel/_node.py -> build/lib/dendropy/datamodel/treemodel 2026-07-12T16:35:28,711 copying src/dendropy/datamodel/treemodel/_edge.py -> build/lib/dendropy/datamodel/treemodel 2026-07-12T16:35:28,713 running egg_info 2026-07-12T16:35:28,743 writing src/DendroPy.egg-info/PKG-INFO 2026-07-12T16:35:28,746 writing dependency_links to src/DendroPy.egg-info/dependency_links.txt 2026-07-12T16:35:28,748 writing entry points to src/DendroPy.egg-info/entry_points.txt 2026-07-12T16:35:28,750 writing requirements to src/DendroPy.egg-info/requires.txt 2026-07-12T16:35:28,751 writing top-level names to src/DendroPy.egg-info/top_level.txt 2026-07-12T16:35:28,812 reading manifest file 'src/DendroPy.egg-info/SOURCES.txt' 2026-07-12T16:35:28,820 reading manifest template 'MANIFEST.in' 2026-07-12T16:35:28,821 warning: no files found matching 'README.rst' 2026-07-12T16:35:28,822 warning: no files found matching 'doc/Makefile' 2026-07-12T16:35:28,822 warning: no files found matching '*' under directory 'doc/source' 2026-07-12T16:35:28,823 warning: no files found matching '*' under directory 'tests/data' 2026-07-12T16:35:28,824 warning: no previously-included files matching '.DS_Store' found anywhere in distribution 2026-07-12T16:35:28,825 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2026-07-12T16:35:28,826 warning: no previously-included files matching '.gitignore' found anywhere in distribution 2026-07-12T16:35:28,827 warning: no previously-included files matching '.gitattributes' found anywhere in distribution 2026-07-12T16:35:28,829 warning: no previously-included files matching '.idea' found anywhere in distribution 2026-07-12T16:35:28,830 warning: no previously-included files matching '__pycache__' found anywhere in distribution 2026-07-12T16:35:28,830 adding license file 'LICENSE.rst' 2026-07-12T16:35:28,831 adding license file 'NOTICES.rst' 2026-07-12T16:35:28,831 adding license file 'AUTHORS.rst' 2026-07-12T16:35:28,838 writing manifest file 'src/DendroPy.egg-info/SOURCES.txt' 2026-07-12T16:35:28,896 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-07-12T16:35:28,897 !! 2026-07-12T16:35:28,898 ******************************************************************************** 2026-07-12T16:35:28,899 Please avoid running ``setup.py`` directly. 2026-07-12T16:35:28,899 Instead, use pypa/build, pypa/installer or other 2026-07-12T16:35:28,900 standards-based tools. 2026-07-12T16:35:28,901 This deprecation is overdue, please update your project and remove deprecated 2026-07-12T16:35:28,901 calls to avoid build errors in the future. 2026-07-12T16:35:28,903 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-07-12T16:35:28,903 ******************************************************************************** 2026-07-12T16:35:28,904 !! 2026-07-12T16:35:28,905 self.initialize_options() 2026-07-12T16:35:28,928 installing to build/bdist.linux-armv7l/wheel 2026-07-12T16:35:28,929 running install 2026-07-12T16:35:28,952 running install_lib 2026-07-12T16:35:28,981 creating build/bdist.linux-armv7l/wheel 2026-07-12T16:35:28,983 creating build/bdist.linux-armv7l/wheel/dendropy 2026-07-12T16:35:28,984 copying build/lib/dendropy/__main__.py -> build/bdist.linux-armv7l/wheel/./dendropy 2026-07-12T16:35:28,987 creating build/bdist.linux-armv7l/wheel/dendropy/utility 2026-07-12T16:35:28,988 copying build/lib/dendropy/utility/bibtex.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:28,991 copying build/lib/dendropy/utility/messaging.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:28,993 copying build/lib/dendropy/utility/debug.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:28,994 copying build/lib/dendropy/utility/container.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:28,997 copying build/lib/dendropy/utility/metavar.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:28,999 copying build/lib/dendropy/utility/processio.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,001 copying build/lib/dendropy/utility/cli.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,004 creating build/bdist.linux-armv7l/wheel/dendropy/utility/libexec 2026-07-12T16:35:29,005 copying build/lib/dendropy/utility/libexec/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility/libexec 2026-07-12T16:35:29,007 copying build/lib/dendropy/utility/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,009 copying build/lib/dendropy/utility/urlio.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,010 copying build/lib/dendropy/utility/error.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,012 copying build/lib/dendropy/utility/constants.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,014 copying build/lib/dendropy/utility/timeprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,016 copying build/lib/dendropy/utility/textprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,019 copying build/lib/dendropy/utility/vcsinfo.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,021 copying build/lib/dendropy/utility/filesys.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,023 copying build/lib/dendropy/utility/deprecate.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,025 copying build/lib/dendropy/utility/bitprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,027 copying build/lib/dendropy/utility/terminal.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-07-12T16:35:29,030 creating build/bdist.linux-armv7l/wheel/dendropy/plot 2026-07-12T16:35:29,031 copying build/lib/dendropy/plot/tikzplot.py -> build/bdist.linux-armv7l/wheel/./dendropy/plot 2026-07-12T16:35:29,033 copying build/lib/dendropy/plot/asciiplot.py -> build/bdist.linux-armv7l/wheel/./dendropy/plot 2026-07-12T16:35:29,035 copying build/lib/dendropy/plot/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/plot 2026-07-12T16:35:29,038 creating build/bdist.linux-armv7l/wheel/dendropy/interop 2026-07-12T16:35:29,039 copying build/lib/dendropy/interop/paup.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,042 copying build/lib/dendropy/interop/ete.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,044 copying build/lib/dendropy/interop/rstats.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,046 copying build/lib/dendropy/interop/seqgen.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,049 copying build/lib/dendropy/interop/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,050 copying build/lib/dendropy/interop/biopython.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,052 copying build/lib/dendropy/interop/rspr.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,054 copying build/lib/dendropy/interop/raxml.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,057 copying build/lib/dendropy/interop/ape.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,060 copying build/lib/dendropy/interop/muscle.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,062 copying build/lib/dendropy/interop/entrez.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,063 copying build/lib/dendropy/interop/itol.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,066 copying build/lib/dendropy/interop/gbif.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,068 copying build/lib/dendropy/interop/genbank.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-07-12T16:35:29,072 creating build/bdist.linux-armv7l/wheel/dendropy/datamodel 2026-07-12T16:35:29,073 copying build/lib/dendropy/datamodel/treecollectionmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-07-12T16:35:29,078 copying build/lib/dendropy/datamodel/datasetmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-07-12T16:35:29,081 copying build/lib/dendropy/datamodel/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-07-12T16:35:29,083 copying build/lib/dendropy/datamodel/basemodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-07-12T16:35:29,086 copying build/lib/dendropy/datamodel/taxonmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-07-12T16:35:29,091 creating build/bdist.linux-armv7l/wheel/dendropy/datamodel/treemodel 2026-07-12T16:35:29,092 copying build/lib/dendropy/datamodel/treemodel/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-07-12T16:35:29,094 copying build/lib/dendropy/datamodel/treemodel/_tree.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-07-12T16:35:29,099 copying build/lib/dendropy/datamodel/treemodel/_bipartition.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-07-12T16:35:29,102 copying build/lib/dendropy/datamodel/treemodel/_node.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-07-12T16:35:29,106 copying build/lib/dendropy/datamodel/treemodel/_edge.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-07-12T16:35:29,109 copying build/lib/dendropy/datamodel/charmatrixmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-07-12T16:35:29,150 copying build/lib/dendropy/datamodel/charstatemodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-07-12T16:35:29,154 creating build/bdist.linux-armv7l/wheel/dendropy/mathlib 2026-07-12T16:35:29,156 copying build/lib/dendropy/mathlib/probability.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-07-12T16:35:29,158 copying build/lib/dendropy/mathlib/mathfn.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-07-12T16:35:29,160 copying build/lib/dendropy/mathlib/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-07-12T16:35:29,162 copying build/lib/dendropy/mathlib/statistics.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-07-12T16:35:29,164 copying build/lib/dendropy/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy 2026-07-12T16:35:29,167 creating build/bdist.linux-armv7l/wheel/dendropy/simulate 2026-07-12T16:35:29,169 copying build/lib/dendropy/simulate/charsim.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-07-12T16:35:29,171 copying build/lib/dendropy/simulate/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-07-12T16:35:29,173 copying build/lib/dendropy/simulate/popgensim.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-07-12T16:35:29,176 copying build/lib/dendropy/simulate/treesim.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-07-12T16:35:29,179 creating build/bdist.linux-armv7l/wheel/dendropy/legacy 2026-07-12T16:35:29,180 copying build/lib/dendropy/legacy/seqmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,182 copying build/lib/dendropy/legacy/treecalc.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,185 copying build/lib/dendropy/legacy/ncbi.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,187 copying build/lib/dendropy/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,189 copying build/lib/dendropy/legacy/popgenstat.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,192 copying build/lib/dendropy/legacy/popgensim.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,194 copying build/lib/dendropy/legacy/continuous.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,196 copying build/lib/dendropy/legacy/treemanip.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,198 copying build/lib/dendropy/legacy/seqsim.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,201 copying build/lib/dendropy/legacy/reconcile.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,203 copying build/lib/dendropy/legacy/treesum.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,205 copying build/lib/dendropy/legacy/treesplit.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,207 copying build/lib/dendropy/legacy/coalescent.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,210 copying build/lib/dendropy/legacy/treesim.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-07-12T16:35:29,213 creating build/bdist.linux-armv7l/wheel/dendropy/calculate 2026-07-12T16:35:29,214 copying build/lib/dendropy/calculate/treescore.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,216 copying build/lib/dendropy/calculate/treecompare.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,220 copying build/lib/dendropy/calculate/treemeasure.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,222 copying build/lib/dendropy/calculate/phylogeneticdistance.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,226 copying build/lib/dendropy/calculate/probability.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,229 copying build/lib/dendropy/calculate/combinatorics.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,231 copying build/lib/dendropy/calculate/mathfn.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,233 copying build/lib/dendropy/calculate/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,235 copying build/lib/dendropy/calculate/popgenstat.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,238 copying build/lib/dendropy/calculate/profiledistance.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,241 copying build/lib/dendropy/calculate/statistics.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,244 copying build/lib/dendropy/calculate/treesum.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-07-12T16:35:29,248 creating build/bdist.linux-armv7l/wheel/dendropy/application 2026-07-12T16:35:29,249 copying build/lib/dendropy/application/sumlabels.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-07-12T16:35:29,252 copying build/lib/dendropy/application/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-07-12T16:35:29,254 copying build/lib/dendropy/application/sumtrees.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-07-12T16:35:29,260 copying build/lib/dendropy/application/dendropy_format.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-07-12T16:35:29,263 creating build/bdist.linux-armv7l/wheel/dendropy/model 2026-07-12T16:35:29,264 copying build/lib/dendropy/model/treeshape.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,266 copying build/lib/dendropy/model/multispeciescoalescent.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,269 copying build/lib/dendropy/model/protractedspeciation.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,273 copying build/lib/dendropy/model/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,275 copying build/lib/dendropy/model/continuous.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,278 copying build/lib/dendropy/model/birthdeath.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,282 copying build/lib/dendropy/model/reconcile.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,285 copying build/lib/dendropy/model/discrete.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,288 copying build/lib/dendropy/model/coalescent.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,292 copying build/lib/dendropy/model/parsimony.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-07-12T16:35:29,295 creating build/bdist.linux-armv7l/wheel/dendropy/dataio 2026-07-12T16:35:29,297 copying build/lib/dendropy/dataio/phylipwriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,300 copying build/lib/dendropy/dataio/newickwriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,302 copying build/lib/dendropy/dataio/multiphylipreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,304 copying build/lib/dendropy/dataio/tokenizer.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,306 copying build/lib/dendropy/dataio/newickyielder.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,308 copying build/lib/dendropy/dataio/nexuswriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,311 copying build/lib/dendropy/dataio/nexusyielder.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,313 copying build/lib/dendropy/dataio/nexusreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,316 copying build/lib/dendropy/dataio/nexmlreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,319 copying build/lib/dendropy/dataio/nexmlyielder.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,321 copying build/lib/dendropy/dataio/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,323 copying build/lib/dendropy/dataio/newick.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,325 copying build/lib/dendropy/dataio/phylipreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,327 copying build/lib/dendropy/dataio/newickreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,330 copying build/lib/dendropy/dataio/fastawriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,332 copying build/lib/dendropy/dataio/ioservice.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,335 copying build/lib/dendropy/dataio/nexmlwriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,337 copying build/lib/dendropy/dataio/nexusprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,340 copying build/lib/dendropy/dataio/xmlprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,342 copying build/lib/dendropy/dataio/fastareader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-07-12T16:35:29,344 running install_egg_info 2026-07-12T16:35:29,376 Copying src/DendroPy.egg-info to build/bdist.linux-armv7l/wheel/./DendroPy-5.0.10-py3.11.egg-info 2026-07-12T16:35:29,389 running install_scripts 2026-07-12T16:35:29,405 creating build/bdist.linux-armv7l/wheel/dendropy-5.0.10.dist-info/WHEEL 2026-07-12T16:35:29,408 creating '/tmp/pip-wheel-uxygbf8f/dendropy-5.0.10-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-12T16:35:29,411 adding 'dendropy/__init__.py' 2026-07-12T16:35:29,412 adding 'dendropy/__main__.py' 2026-07-12T16:35:29,414 adding 'dendropy/application/__init__.py' 2026-07-12T16:35:29,415 adding 'dendropy/application/dendropy_format.py' 2026-07-12T16:35:29,417 adding 'dendropy/application/sumlabels.py' 2026-07-12T16:35:29,428 adding 'dendropy/application/sumtrees.py' 2026-07-12T16:35:29,430 adding 'dendropy/calculate/__init__.py' 2026-07-12T16:35:29,432 adding 'dendropy/calculate/combinatorics.py' 2026-07-12T16:35:29,433 adding 'dendropy/calculate/mathfn.py' 2026-07-12T16:35:29,439 adding 'dendropy/calculate/phylogeneticdistance.py' 2026-07-12T16:35:29,442 adding 'dendropy/calculate/popgenstat.py' 2026-07-12T16:35:29,444 adding 'dendropy/calculate/probability.py' 2026-07-12T16:35:29,446 adding 'dendropy/calculate/profiledistance.py' 2026-07-12T16:35:29,449 adding 'dendropy/calculate/statistics.py' 2026-07-12T16:35:29,453 adding 'dendropy/calculate/treecompare.py' 2026-07-12T16:35:29,455 adding 'dendropy/calculate/treemeasure.py' 2026-07-12T16:35:29,456 adding 'dendropy/calculate/treescore.py' 2026-07-12T16:35:29,459 adding 'dendropy/calculate/treesum.py' 2026-07-12T16:35:29,461 adding 'dendropy/dataio/__init__.py' 2026-07-12T16:35:29,462 adding 'dendropy/dataio/fastareader.py' 2026-07-12T16:35:29,464 adding 'dendropy/dataio/fastawriter.py' 2026-07-12T16:35:29,466 adding 'dendropy/dataio/ioservice.py' 2026-07-12T16:35:29,468 adding 'dendropy/dataio/multiphylipreader.py' 2026-07-12T16:35:29,469 adding 'dendropy/dataio/newick.py' 2026-07-12T16:35:29,472 adding 'dendropy/dataio/newickreader.py' 2026-07-12T16:35:29,475 adding 'dendropy/dataio/newickwriter.py' 2026-07-12T16:35:29,477 adding 'dendropy/dataio/newickyielder.py' 2026-07-12T16:35:29,481 adding 'dendropy/dataio/nexmlreader.py' 2026-07-12T16:35:29,485 adding 'dendropy/dataio/nexmlwriter.py' 2026-07-12T16:35:29,486 adding 'dendropy/dataio/nexmlyielder.py' 2026-07-12T16:35:29,489 adding 'dendropy/dataio/nexusprocessing.py' 2026-07-12T16:35:29,495 adding 'dendropy/dataio/nexusreader.py' 2026-07-12T16:35:29,499 adding 'dendropy/dataio/nexuswriter.py' 2026-07-12T16:35:29,501 adding 'dendropy/dataio/nexusyielder.py' 2026-07-12T16:35:29,503 adding 'dendropy/dataio/phylipreader.py' 2026-07-12T16:35:29,505 adding 'dendropy/dataio/phylipwriter.py' 2026-07-12T16:35:29,506 adding 'dendropy/dataio/tokenizer.py' 2026-07-12T16:35:29,508 adding 'dendropy/dataio/xmlprocessing.py' 2026-07-12T16:35:29,510 adding 'dendropy/datamodel/__init__.py' 2026-07-12T16:35:29,516 adding 'dendropy/datamodel/basemodel.py' 2026-07-12T16:35:29,525 adding 'dendropy/datamodel/charmatrixmodel.py' 2026-07-12T16:35:29,531 adding 'dendropy/datamodel/charstatemodel.py' 2026-07-12T16:35:29,534 adding 'dendropy/datamodel/datasetmodel.py' 2026-07-12T16:35:29,543 adding 'dendropy/datamodel/taxonmodel.py' 2026-07-12T16:35:29,556 adding 'dendropy/datamodel/treecollectionmodel.py' 2026-07-12T16:35:29,559 adding 'dendropy/datamodel/treemodel/__init__.py' 2026-07-12T16:35:29,562 adding 'dendropy/datamodel/treemodel/_bipartition.py' 2026-07-12T16:35:29,564 adding 'dendropy/datamodel/treemodel/_edge.py' 2026-07-12T16:35:29,570 adding 'dendropy/datamodel/treemodel/_node.py' 2026-07-12T16:35:29,588 adding 'dendropy/datamodel/treemodel/_tree.py' 2026-07-12T16:35:29,591 adding 'dendropy/interop/__init__.py' 2026-07-12T16:35:29,593 adding 'dendropy/interop/ape.py' 2026-07-12T16:35:29,594 adding 'dendropy/interop/biopython.py' 2026-07-12T16:35:29,595 adding 'dendropy/interop/entrez.py' 2026-07-12T16:35:29,597 adding 'dendropy/interop/ete.py' 2026-07-12T16:35:29,599 adding 'dendropy/interop/gbif.py' 2026-07-12T16:35:29,602 adding 'dendropy/interop/genbank.py' 2026-07-12T16:35:29,604 adding 'dendropy/interop/itol.py' 2026-07-12T16:35:29,605 adding 'dendropy/interop/muscle.py' 2026-07-12T16:35:29,609 adding 'dendropy/interop/paup.py' 2026-07-12T16:35:29,614 adding 'dendropy/interop/raxml.py' 2026-07-12T16:35:29,615 adding 'dendropy/interop/rspr.py' 2026-07-12T16:35:29,617 adding 'dendropy/interop/rstats.py' 2026-07-12T16:35:29,619 adding 'dendropy/interop/seqgen.py' 2026-07-12T16:35:29,620 adding 'dendropy/legacy/__init__.py' 2026-07-12T16:35:29,622 adding 'dendropy/legacy/coalescent.py' 2026-07-12T16:35:29,623 adding 'dendropy/legacy/continuous.py' 2026-07-12T16:35:29,625 adding 'dendropy/legacy/ncbi.py' 2026-07-12T16:35:29,626 adding 'dendropy/legacy/popgensim.py' 2026-07-12T16:35:29,628 adding 'dendropy/legacy/popgenstat.py' 2026-07-12T16:35:29,629 adding 'dendropy/legacy/reconcile.py' 2026-07-12T16:35:29,630 adding 'dendropy/legacy/seqmodel.py' 2026-07-12T16:35:29,631 adding 'dendropy/legacy/seqsim.py' 2026-07-12T16:35:29,633 adding 'dendropy/legacy/treecalc.py' 2026-07-12T16:35:29,634 adding 'dendropy/legacy/treemanip.py' 2026-07-12T16:35:29,635 adding 'dendropy/legacy/treesim.py' 2026-07-12T16:35:29,637 adding 'dendropy/legacy/treesplit.py' 2026-07-12T16:35:29,638 adding 'dendropy/legacy/treesum.py' 2026-07-12T16:35:29,640 adding 'dendropy/mathlib/__init__.py' 2026-07-12T16:35:29,641 adding 'dendropy/mathlib/mathfn.py' 2026-07-12T16:35:29,643 adding 'dendropy/mathlib/probability.py' 2026-07-12T16:35:29,644 adding 'dendropy/mathlib/statistics.py' 2026-07-12T16:35:29,645 adding 'dendropy/model/__init__.py' 2026-07-12T16:35:29,653 adding 'dendropy/model/birthdeath.py' 2026-07-12T16:35:29,658 adding 'dendropy/model/coalescent.py' 2026-07-12T16:35:29,661 adding 'dendropy/model/continuous.py' 2026-07-12T16:35:29,663 adding 'dendropy/model/discrete.py' 2026-07-12T16:35:29,665 adding 'dendropy/model/multispeciescoalescent.py' 2026-07-12T16:35:29,668 adding 'dendropy/model/parsimony.py' 2026-07-12T16:35:29,672 adding 'dendropy/model/protractedspeciation.py' 2026-07-12T16:35:29,676 adding 'dendropy/model/reconcile.py' 2026-07-12T16:35:29,677 adding 'dendropy/model/treeshape.py' 2026-07-12T16:35:29,679 adding 'dendropy/plot/__init__.py' 2026-07-12T16:35:29,681 adding 'dendropy/plot/asciiplot.py' 2026-07-12T16:35:29,682 adding 'dendropy/plot/tikzplot.py' 2026-07-12T16:35:29,684 adding 'dendropy/simulate/__init__.py' 2026-07-12T16:35:29,685 adding 'dendropy/simulate/charsim.py' 2026-07-12T16:35:29,687 adding 'dendropy/simulate/popgensim.py' 2026-07-12T16:35:29,689 adding 'dendropy/simulate/treesim.py' 2026-07-12T16:35:29,691 adding 'dendropy/utility/__init__.py' 2026-07-12T16:35:29,693 adding 'dendropy/utility/bibtex.py' 2026-07-12T16:35:29,694 adding 'dendropy/utility/bitprocessing.py' 2026-07-12T16:35:29,696 adding 'dendropy/utility/cli.py' 2026-07-12T16:35:29,697 adding 'dendropy/utility/constants.py' 2026-07-12T16:35:29,702 adding 'dendropy/utility/container.py' 2026-07-12T16:35:29,704 adding 'dendropy/utility/debug.py' 2026-07-12T16:35:29,705 adding 'dendropy/utility/deprecate.py' 2026-07-12T16:35:29,707 adding 'dendropy/utility/error.py' 2026-07-12T16:35:29,709 adding 'dendropy/utility/filesys.py' 2026-07-12T16:35:29,710 adding 'dendropy/utility/messaging.py' 2026-07-12T16:35:29,712 adding 'dendropy/utility/metavar.py' 2026-07-12T16:35:29,713 adding 'dendropy/utility/processio.py' 2026-07-12T16:35:29,714 adding 'dendropy/utility/terminal.py' 2026-07-12T16:35:29,716 adding 'dendropy/utility/textprocessing.py' 2026-07-12T16:35:29,717 adding 'dendropy/utility/timeprocessing.py' 2026-07-12T16:35:29,718 adding 'dendropy/utility/urlio.py' 2026-07-12T16:35:29,720 adding 'dendropy/utility/vcsinfo.py' 2026-07-12T16:35:29,721 adding 'dendropy/utility/libexec/__init__.py' 2026-07-12T16:35:29,724 adding 'dendropy-5.0.10.dist-info/licenses/AUTHORS.rst' 2026-07-12T16:35:29,725 adding 'dendropy-5.0.10.dist-info/licenses/LICENSE.rst' 2026-07-12T16:35:29,726 adding 'dendropy-5.0.10.dist-info/licenses/NOTICES.rst' 2026-07-12T16:35:29,728 adding 'dendropy-5.0.10.dist-info/METADATA' 2026-07-12T16:35:29,729 adding 'dendropy-5.0.10.dist-info/WHEEL' 2026-07-12T16:35:29,729 adding 'dendropy-5.0.10.dist-info/entry_points.txt' 2026-07-12T16:35:29,730 adding 'dendropy-5.0.10.dist-info/top_level.txt' 2026-07-12T16:35:29,731 adding 'dendropy-5.0.10.dist-info/zip-safe' 2026-07-12T16:35:29,733 adding 'dendropy-5.0.10.dist-info/RECORD' 2026-07-12T16:35:29,741 removing build/bdist.linux-armv7l/wheel 2026-07-12T16:35:29,882 Building wheel for dendropy (setup.py): finished with status 'done' 2026-07-12T16:35:29,890 Created wheel for dendropy: filename=dendropy-5.0.10-py3-none-any.whl size=465248 sha256=f67e8f017135978518ae0a7ebc71e27e3607e2d20de88036dfb878bfcf86e78a 2026-07-12T16:35:29,891 Stored in directory: /tmp/pip-ephem-wheel-cache-jp34iuvu/wheels/94/ac/9d/e11ea07041200e9b0ccd919e80a1c125f16bbba3fb427366fb 2026-07-12T16:35:29,907 Successfully built dendropy 2026-07-12T16:35:29,927 Removed build tracker: '/tmp/pip-build-tracker-h9z7f7bq'