2026-08-22T15:08:05,840 Created temporary directory: /tmp/pip-ephem-wheel-cache-1kie1jqw 2026-08-22T15:08:05,842 Created temporary directory: /tmp/pip-build-tracker-3y6fjpmm 2026-08-22T15:08:05,843 Initialized build tracking at /tmp/pip-build-tracker-3y6fjpmm 2026-08-22T15:08:05,844 Created build tracker: /tmp/pip-build-tracker-3y6fjpmm 2026-08-22T15:08:05,844 Entered build tracker: /tmp/pip-build-tracker-3y6fjpmm 2026-08-22T15:08:05,845 Created temporary directory: /tmp/pip-wheel-ggnd1lu_ 2026-08-22T15:08:05,848 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 2026-08-22T15:08:05,850 Created temporary directory: /tmp/pip-ephem-wheel-cache-hebr569d 2026-08-22T15:08:05,875 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-22T15:08:05,879 2 location(s) to search for versions of dendropy: 2026-08-22T15:08:05,879 * https://pypi.org/simple/dendropy/ 2026-08-22T15:08:05,879 * https://www.piwheels.org/simple/dendropy/ 2026-08-22T15:08:05,879 Fetching project page and analyzing links: https://pypi.org/simple/dendropy/ 2026-08-22T15:08:05,880 Getting page https://pypi.org/simple/dendropy/ 2026-08-22T15:08:05,882 Found index url https://pypi.org/simple 2026-08-22T15:08:06,115 Fetched page https://pypi.org/simple/dendropy/ as application/vnd.pypi.simple.v1+json 2026-08-22T15:08:06,124 Found link https://files.pythonhosted.org/packages/03/48/8379b3e170d60052da7ccf3387549af17d46808a39062fbb234df3038fa0/DendroPy-3.7.0.tar.gz (from 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2026-08-22T15:08:06,147 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 2026-08-22T15:08:06,147 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) 2026-08-22T15:08:06,148 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 2026-08-22T15:08:06,149 Skipping link: No binaries permitted for dendropy: https://files.pythonhosted.org/packages/29/3d/d93dfd44e8615b39fab0b939bc7d8030021c092bffb3cc3c50580e75fc8f/DendroPy-5.0.8-py3-none-any.whl (from 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https://files.pythonhosted.org/packages/30/ba/3b2250bb57904ab8f4bb095724b035722ed33c57ecf1fda2bc9b97bd5676/dendropy-5.0.12-py3-none-any.whl (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7) 2026-08-22T15:08:06,153 Found link https://files.pythonhosted.org/packages/83/11/b7343795581e97be7d9b85416c8d4770d9c9f5b6d29dfc96b2903d3ccaec/dendropy-5.0.12.tar.gz (from https://pypi.org/simple/dendropy/) (requires-python:>=3.7), version: 5.0.12 2026-08-22T15:08:06,154 Fetching project page and analyzing links: https://www.piwheels.org/simple/dendropy/ 2026-08-22T15:08:06,155 Getting page https://www.piwheels.org/simple/dendropy/ 2026-08-22T15:08:06,156 Found index url https://www.piwheels.org/simple 2026-08-22T15:08:06,348 Fetched page https://www.piwheels.org/simple/dendropy/ as text/html 2026-08-22T15:08:06,355 Skipping link: No binaries permitted for dendropy: 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https://www.piwheels.org/simple/dendropy/) 2026-08-22T15:08:06,362 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/) 2026-08-22T15:08:06,363 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/) 2026-08-22T15:08:06,364 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/) 2026-08-22T15:08:06,364 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/) 2026-08-22T15:08:06,365 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/) 2026-08-22T15:08:06,365 Skipping link: not a file: https://www.piwheels.org/simple/dendropy/ 2026-08-22T15:08:06,366 Skipping link: not a file: https://pypi.org/simple/dendropy/ 2026-08-22T15:08:06,388 Given no hashes to check 1 links for project 'dendropy': discarding no candidates 2026-08-22T15:08:06,406 Collecting dendropy==5.0.12 2026-08-22T15:08:06,409 Created temporary directory: /tmp/pip-unpack-qwbv3pzb 2026-08-22T15:08:06,565 Downloading dendropy-5.0.12.tar.gz (398 kB) 2026-08-22T15:08:07,009 Added dendropy==5.0.12 from https://files.pythonhosted.org/packages/83/11/b7343795581e97be7d9b85416c8d4770d9c9f5b6d29dfc96b2903d3ccaec/dendropy-5.0.12.tar.gz to build tracker '/tmp/pip-build-tracker-3y6fjpmm' 2026-08-22T15:08:07,010 Running setup.py (path:/tmp/pip-wheel-ggnd1lu_/dendropy_3b71f7b0f68b46339c26ac737a860488/setup.py) egg_info for package dendropy 2026-08-22T15:08:07,011 Created temporary directory: /tmp/pip-pip-egg-info-lrh1l2sv 2026-08-22T15:08:07,012 Preparing metadata (setup.py): started 2026-08-22T15:08:07,013 Running command python setup.py egg_info 2026-08-22T15:08:07,559 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2026-08-22T15:08:07,560 !! 2026-08-22T15:08:07,561 ******************************************************************************** 2026-08-22T15:08:07,562 Requirements should be satisfied by a PEP 517 installer. 2026-08-22T15:08:07,562 If you are using pip, you can try `pip install --use-pep517`. 2026-08-22T15:08:07,563 This deprecation is overdue, please update your project and remove deprecated 2026-08-22T15:08:07,564 calls to avoid build errors in the future. 2026-08-22T15:08:07,565 ******************************************************************************** 2026-08-22T15:08:07,566 !! 2026-08-22T15:08:07,567 dist.fetch_build_eggs(dist.setup_requires) 2026-08-22T15:08:10,414 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:288: UserWarning: Unknown distribution option: 'test_suite' 2026-08-22T15:08:10,415 warnings.warn(msg) 2026-08-22T15:08:10,416 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:288: UserWarning: Unknown distribution option: 'tests_require' 2026-08-22T15:08:10,416 warnings.warn(msg) 2026-08-22T15:08:10,477 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-22T15:08:10,478 !! 2026-08-22T15:08:10,479 ******************************************************************************** 2026-08-22T15:08:10,480 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-22T15:08:10,481 License :: OSI Approved :: BSD License 2026-08-22T15:08:10,482 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-22T15:08:10,483 ******************************************************************************** 2026-08-22T15:08:10,484 !! 2026-08-22T15:08:10,485 self._finalize_license_expression() 2026-08-22T15:08:10,510 running egg_info 2026-08-22T15:08:10,539 creating /tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info 2026-08-22T15:08:10,540 writing /tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/PKG-INFO 2026-08-22T15:08:10,544 writing dependency_links to /tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/dependency_links.txt 2026-08-22T15:08:10,546 writing entry points to /tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/entry_points.txt 2026-08-22T15:08:10,547 writing requirements to /tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/requires.txt 2026-08-22T15:08:10,548 writing top-level names to /tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/top_level.txt 2026-08-22T15:08:10,550 writing manifest file '/tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/SOURCES.txt' 2026-08-22T15:08:10,688 reading manifest file '/tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/SOURCES.txt' 2026-08-22T15:08:10,690 reading manifest template 'MANIFEST.in' 2026-08-22T15:08:10,690 warning: no files found matching 'README.rst' 2026-08-22T15:08:10,691 warning: no files found matching 'doc/Makefile' 2026-08-22T15:08:10,692 warning: no files found matching '*' under directory 'doc/source' 2026-08-22T15:08:10,692 warning: no files found matching '*' under directory 'tests/data' 2026-08-22T15:08:10,693 warning: no previously-included files matching '.DS_Store' found anywhere in distribution 2026-08-22T15:08:10,694 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2026-08-22T15:08:10,695 warning: no previously-included files matching '.gitignore' found anywhere in distribution 2026-08-22T15:08:10,696 warning: no previously-included files matching '.gitattributes' found anywhere in distribution 2026-08-22T15:08:10,697 warning: no previously-included files matching '.idea' found anywhere in distribution 2026-08-22T15:08:10,698 warning: no previously-included files matching '__pycache__' found anywhere in distribution 2026-08-22T15:08:10,699 adding license file 'LICENSE.rst' 2026-08-22T15:08:10,699 adding license file 'NOTICES.rst' 2026-08-22T15:08:10,700 adding license file 'AUTHORS.rst' 2026-08-22T15:08:10,705 writing manifest file '/tmp/pip-pip-egg-info-lrh1l2sv/DendroPy.egg-info/SOURCES.txt' 2026-08-22T15:08:10,817 Preparing metadata (setup.py): finished with status 'done' 2026-08-22T15:08:10,822 Source in /tmp/pip-wheel-ggnd1lu_/dendropy_3b71f7b0f68b46339c26ac737a860488 has version 5.0.12, which satisfies requirement dendropy==5.0.12 from https://files.pythonhosted.org/packages/83/11/b7343795581e97be7d9b85416c8d4770d9c9f5b6d29dfc96b2903d3ccaec/dendropy-5.0.12.tar.gz 2026-08-22T15:08:10,823 Removed dendropy==5.0.12 from https://files.pythonhosted.org/packages/83/11/b7343795581e97be7d9b85416c8d4770d9c9f5b6d29dfc96b2903d3ccaec/dendropy-5.0.12.tar.gz from build tracker '/tmp/pip-build-tracker-3y6fjpmm' 2026-08-22T15:08:10,830 Created temporary directory: /tmp/pip-unpack-eylswhxx 2026-08-22T15:08:10,830 Building wheels for collected packages: dendropy 2026-08-22T15:08:10,835 Created temporary directory: /tmp/pip-wheel-54ujfdbi 2026-08-22T15:08:10,836 Building wheel for dendropy (setup.py): started 2026-08-22T15:08:10,837 Destination directory: /tmp/pip-wheel-54ujfdbi 2026-08-22T15:08:10,838 Running command python setup.py bdist_wheel 2026-08-22T15:08:11,382 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2026-08-22T15:08:11,382 !! 2026-08-22T15:08:11,383 ******************************************************************************** 2026-08-22T15:08:11,384 Requirements should be satisfied by a PEP 517 installer. 2026-08-22T15:08:11,384 If you are using pip, you can try `pip install --use-pep517`. 2026-08-22T15:08:11,386 This deprecation is overdue, please update your project and remove deprecated 2026-08-22T15:08:11,387 calls to avoid build errors in the future. 2026-08-22T15:08:11,387 ******************************************************************************** 2026-08-22T15:08:11,388 !! 2026-08-22T15:08:11,389 dist.fetch_build_eggs(dist.setup_requires) 2026-08-22T15:08:11,606 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:288: UserWarning: Unknown distribution option: 'test_suite' 2026-08-22T15:08:11,606 warnings.warn(msg) 2026-08-22T15:08:11,607 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:288: UserWarning: Unknown distribution option: 'tests_require' 2026-08-22T15:08:11,607 warnings.warn(msg) 2026-08-22T15:08:11,899 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-22T15:08:11,900 !! 2026-08-22T15:08:11,901 ******************************************************************************** 2026-08-22T15:08:11,901 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-22T15:08:11,902 License :: OSI Approved :: BSD License 2026-08-22T15:08:11,903 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-22T15:08:11,904 ******************************************************************************** 2026-08-22T15:08:11,905 !! 2026-08-22T15:08:11,905 self._finalize_license_expression() 2026-08-22T15:08:11,906 running bdist_wheel 2026-08-22T15:08:12,047 running build 2026-08-22T15:08:12,047 running build_py 2026-08-22T15:08:12,077 creating build/lib/dendropy 2026-08-22T15:08:12,079 copying src/dendropy/__init__.py -> build/lib/dendropy 2026-08-22T15:08:12,082 copying src/dendropy/__main__.py -> build/lib/dendropy 2026-08-22T15:08:12,084 creating build/lib/dendropy/interop 2026-08-22T15:08:12,086 copying src/dendropy/interop/gbif.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,088 copying src/dendropy/interop/raxml.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,091 copying src/dendropy/interop/biopython.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,093 copying src/dendropy/interop/ape.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,096 copying src/dendropy/interop/muscle.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,098 copying src/dendropy/interop/__init__.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,100 copying src/dendropy/interop/entrez.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,101 copying src/dendropy/interop/rstats.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,104 copying src/dendropy/interop/rspr.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,106 copying src/dendropy/interop/ete.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,108 copying src/dendropy/interop/genbank.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,111 copying src/dendropy/interop/itol.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,114 copying src/dendropy/interop/seqgen.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,116 copying src/dendropy/interop/paup.py -> build/lib/dendropy/interop 2026-08-22T15:08:12,120 creating build/lib/dendropy/application 2026-08-22T15:08:12,121 copying src/dendropy/application/dendropy_format.py -> build/lib/dendropy/application 2026-08-22T15:08:12,123 copying src/dendropy/application/sumtrees.py -> build/lib/dendropy/application 2026-08-22T15:08:12,127 copying src/dendropy/application/sumlabels.py -> build/lib/dendropy/application 2026-08-22T15:08:12,130 copying src/dendropy/application/__init__.py -> build/lib/dendropy/application 2026-08-22T15:08:12,132 creating build/lib/dendropy/utility 2026-08-22T15:08:12,133 copying src/dendropy/utility/processio.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,136 copying src/dendropy/utility/container.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,139 copying src/dendropy/utility/textprocessing.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,141 copying src/dendropy/utility/error.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,144 copying src/dendropy/utility/messaging.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,146 copying src/dendropy/utility/deprecate.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,148 copying src/dendropy/utility/constants.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,150 copying src/dendropy/utility/filesys.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,153 copying src/dendropy/utility/vcsinfo.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,155 copying src/dendropy/utility/timeprocessing.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,157 copying src/dendropy/utility/__init__.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,159 copying src/dendropy/utility/metavar.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,161 copying src/dendropy/utility/bitprocessing.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,163 copying src/dendropy/utility/urlio.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,165 copying src/dendropy/utility/terminal.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,167 copying src/dendropy/utility/debug.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,169 copying src/dendropy/utility/bibtex.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,171 copying src/dendropy/utility/cli.py -> build/lib/dendropy/utility 2026-08-22T15:08:12,174 creating build/lib/dendropy/model 2026-08-22T15:08:12,175 copying src/dendropy/model/birthdeath.py -> build/lib/dendropy/model 2026-08-22T15:08:12,179 copying src/dendropy/model/protractedspeciation.py -> build/lib/dendropy/model 2026-08-22T15:08:12,183 copying src/dendropy/model/continuous.py -> build/lib/dendropy/model 2026-08-22T15:08:12,185 copying src/dendropy/model/coalescent.py -> build/lib/dendropy/model 2026-08-22T15:08:12,188 copying src/dendropy/model/discrete.py -> build/lib/dendropy/model 2026-08-22T15:08:12,191 copying src/dendropy/model/parsimony.py -> build/lib/dendropy/model 2026-08-22T15:08:12,194 copying src/dendropy/model/multispeciescoalescent.py -> build/lib/dendropy/model 2026-08-22T15:08:12,196 copying src/dendropy/model/reconcile.py -> build/lib/dendropy/model 2026-08-22T15:08:12,199 copying src/dendropy/model/__init__.py -> build/lib/dendropy/model 2026-08-22T15:08:12,201 copying src/dendropy/model/treeshape.py -> build/lib/dendropy/model 2026-08-22T15:08:12,203 creating build/lib/dendropy/plot 2026-08-22T15:08:12,204 copying src/dendropy/plot/__init__.py -> build/lib/dendropy/plot 2026-08-22T15:08:12,206 copying src/dendropy/plot/tikzplot.py -> build/lib/dendropy/plot 2026-08-22T15:08:12,209 copying src/dendropy/plot/asciiplot.py -> build/lib/dendropy/plot 2026-08-22T15:08:12,212 creating build/lib/dendropy/calculate 2026-08-22T15:08:12,213 copying src/dendropy/calculate/phylogeneticdistance.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,217 copying src/dendropy/calculate/combinatorics.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,219 copying src/dendropy/calculate/probability.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,222 copying src/dendropy/calculate/profiledistance.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,225 copying src/dendropy/calculate/popgenstat.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,229 copying src/dendropy/calculate/statistics.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,234 copying src/dendropy/calculate/__init__.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,237 copying src/dendropy/calculate/treesum.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,240 copying src/dendropy/calculate/treescore.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,242 copying src/dendropy/calculate/treecompare.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,245 copying src/dendropy/calculate/mathfn.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,247 copying src/dendropy/calculate/treemeasure.py -> build/lib/dendropy/calculate 2026-08-22T15:08:12,250 creating build/lib/dendropy/legacy 2026-08-22T15:08:12,251 copying src/dendropy/legacy/continuous.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,253 copying src/dendropy/legacy/treecalc.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,256 copying src/dendropy/legacy/coalescent.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,258 copying src/dendropy/legacy/treemanip.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,260 copying src/dendropy/legacy/popgenstat.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,262 copying src/dendropy/legacy/reconcile.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,264 copying src/dendropy/legacy/__init__.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,266 copying src/dendropy/legacy/seqsim.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,268 copying src/dendropy/legacy/ncbi.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,270 copying src/dendropy/legacy/popgensim.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,272 copying src/dendropy/legacy/seqmodel.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,274 copying src/dendropy/legacy/treesim.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,276 copying src/dendropy/legacy/treesum.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,278 copying src/dendropy/legacy/treesplit.py -> build/lib/dendropy/legacy 2026-08-22T15:08:12,281 creating build/lib/dendropy/mathlib 2026-08-22T15:08:12,282 copying src/dendropy/mathlib/probability.py -> build/lib/dendropy/mathlib 2026-08-22T15:08:12,284 copying src/dendropy/mathlib/statistics.py -> build/lib/dendropy/mathlib 2026-08-22T15:08:12,286 copying src/dendropy/mathlib/__init__.py -> build/lib/dendropy/mathlib 2026-08-22T15:08:12,288 copying src/dendropy/mathlib/mathfn.py -> build/lib/dendropy/mathlib 2026-08-22T15:08:12,290 creating build/lib/dendropy/dataio 2026-08-22T15:08:12,291 copying src/dendropy/dataio/multiphylipreader.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,293 copying src/dendropy/dataio/nexuswriter.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,296 copying src/dendropy/dataio/newick.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,298 copying src/dendropy/dataio/newickreader.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,301 copying src/dendropy/dataio/phylipreader.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,303 copying src/dendropy/dataio/fastawriter.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,305 copying src/dendropy/dataio/nexusreader.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,308 copying src/dendropy/dataio/newickyielder.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,310 copying src/dendropy/dataio/phylipwriter.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,313 copying src/dendropy/dataio/nexmlwriter.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,316 copying src/dendropy/dataio/nexmlyielder.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,318 copying src/dendropy/dataio/tokenizer.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,320 copying src/dendropy/dataio/nexusprocessing.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,323 copying src/dendropy/dataio/ioservice.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,325 copying src/dendropy/dataio/newickwriter.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,328 copying src/dendropy/dataio/__init__.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,331 copying src/dendropy/dataio/xmlprocessing.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,333 copying src/dendropy/dataio/nexusyielder.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,335 copying src/dendropy/dataio/fastareader.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,337 copying src/dendropy/dataio/nexmlreader.py -> build/lib/dendropy/dataio 2026-08-22T15:08:12,341 creating build/lib/dendropy/datamodel 2026-08-22T15:08:12,342 copying src/dendropy/datamodel/basemodel.py -> build/lib/dendropy/datamodel 2026-08-22T15:08:12,345 copying src/dendropy/datamodel/taxonmodel.py -> build/lib/dendropy/datamodel 2026-08-22T15:08:12,348 copying src/dendropy/datamodel/charstatemodel.py -> build/lib/dendropy/datamodel 2026-08-22T15:08:12,351 copying src/dendropy/datamodel/datasetmodel.py -> build/lib/dendropy/datamodel 2026-08-22T15:08:12,354 copying src/dendropy/datamodel/__init__.py -> build/lib/dendropy/datamodel 2026-08-22T15:08:12,355 copying src/dendropy/datamodel/treecollectionmodel.py -> build/lib/dendropy/datamodel 2026-08-22T15:08:12,359 copying src/dendropy/datamodel/charmatrixmodel.py -> build/lib/dendropy/datamodel 2026-08-22T15:08:12,363 creating build/lib/dendropy/simulate 2026-08-22T15:08:12,364 copying src/dendropy/simulate/charsim.py -> build/lib/dendropy/simulate 2026-08-22T15:08:12,366 copying src/dendropy/simulate/__init__.py -> build/lib/dendropy/simulate 2026-08-22T15:08:12,368 copying src/dendropy/simulate/popgensim.py -> build/lib/dendropy/simulate 2026-08-22T15:08:12,371 copying src/dendropy/simulate/treesim.py -> build/lib/dendropy/simulate 2026-08-22T15:08:12,374 creating build/lib/dendropy/utility/libexec 2026-08-22T15:08:12,375 copying src/dendropy/utility/libexec/__init__.py -> build/lib/dendropy/utility/libexec 2026-08-22T15:08:12,378 creating build/lib/dendropy/datamodel/treemodel 2026-08-22T15:08:12,379 copying src/dendropy/datamodel/treemodel/_edge.py -> build/lib/dendropy/datamodel/treemodel 2026-08-22T15:08:12,382 copying src/dendropy/datamodel/treemodel/__init__.py -> build/lib/dendropy/datamodel/treemodel 2026-08-22T15:08:12,384 copying src/dendropy/datamodel/treemodel/_node.py -> build/lib/dendropy/datamodel/treemodel 2026-08-22T15:08:12,388 copying src/dendropy/datamodel/treemodel/_bipartition.py -> build/lib/dendropy/datamodel/treemodel 2026-08-22T15:08:12,391 copying src/dendropy/datamodel/treemodel/_tree.py -> build/lib/dendropy/datamodel/treemodel 2026-08-22T15:08:12,396 running egg_info 2026-08-22T15:08:12,427 writing src/DendroPy.egg-info/PKG-INFO 2026-08-22T15:08:12,430 writing dependency_links to src/DendroPy.egg-info/dependency_links.txt 2026-08-22T15:08:12,433 writing entry points to src/DendroPy.egg-info/entry_points.txt 2026-08-22T15:08:12,434 writing requirements to src/DendroPy.egg-info/requires.txt 2026-08-22T15:08:12,436 writing top-level names to src/DendroPy.egg-info/top_level.txt 2026-08-22T15:08:12,498 reading manifest file 'src/DendroPy.egg-info/SOURCES.txt' 2026-08-22T15:08:12,506 reading manifest template 'MANIFEST.in' 2026-08-22T15:08:12,507 warning: no files found matching 'README.rst' 2026-08-22T15:08:12,508 warning: no files found matching 'doc/Makefile' 2026-08-22T15:08:12,508 warning: no files found matching '*' under directory 'doc/source' 2026-08-22T15:08:12,509 warning: no files found matching '*' under directory 'tests/data' 2026-08-22T15:08:12,510 warning: no previously-included files matching '.DS_Store' found anywhere in distribution 2026-08-22T15:08:12,512 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2026-08-22T15:08:12,513 warning: no previously-included files matching '.gitignore' found anywhere in distribution 2026-08-22T15:08:12,514 warning: no previously-included files matching '.gitattributes' found anywhere in distribution 2026-08-22T15:08:12,515 warning: no previously-included files matching '.idea' found anywhere in distribution 2026-08-22T15:08:12,517 warning: no previously-included files matching '__pycache__' found anywhere in distribution 2026-08-22T15:08:12,517 adding license file 'LICENSE.rst' 2026-08-22T15:08:12,518 adding license file 'NOTICES.rst' 2026-08-22T15:08:12,519 adding license file 'AUTHORS.rst' 2026-08-22T15:08:12,525 writing manifest file 'src/DendroPy.egg-info/SOURCES.txt' 2026-08-22T15:08:12,590 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-08-22T15:08:12,591 !! 2026-08-22T15:08:12,592 ******************************************************************************** 2026-08-22T15:08:12,593 Please avoid running ``setup.py`` directly. 2026-08-22T15:08:12,593 Instead, use pypa/build, pypa/installer or other 2026-08-22T15:08:12,594 standards-based tools. 2026-08-22T15:08:12,595 This deprecation is overdue, please update your project and remove deprecated 2026-08-22T15:08:12,595 calls to avoid build errors in the future. 2026-08-22T15:08:12,596 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-08-22T15:08:12,596 ******************************************************************************** 2026-08-22T15:08:12,597 !! 2026-08-22T15:08:12,598 self.initialize_options() 2026-08-22T15:08:12,621 installing to build/bdist.linux-armv7l/wheel 2026-08-22T15:08:12,621 running install 2026-08-22T15:08:12,644 running install_lib 2026-08-22T15:08:12,674 creating build/bdist.linux-armv7l/wheel 2026-08-22T15:08:12,676 creating build/bdist.linux-armv7l/wheel/dendropy 2026-08-22T15:08:12,678 creating build/bdist.linux-armv7l/wheel/dendropy/interop 2026-08-22T15:08:12,679 copying build/lib/dendropy/interop/gbif.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,682 copying build/lib/dendropy/interop/raxml.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,685 copying build/lib/dendropy/interop/biopython.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,687 copying build/lib/dendropy/interop/ape.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,689 copying build/lib/dendropy/interop/muscle.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,691 copying build/lib/dendropy/interop/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,694 copying build/lib/dendropy/interop/entrez.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,696 copying build/lib/dendropy/interop/rstats.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,699 copying build/lib/dendropy/interop/rspr.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,702 copying build/lib/dendropy/interop/ete.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,704 copying build/lib/dendropy/interop/genbank.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,707 copying build/lib/dendropy/interop/itol.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,711 copying build/lib/dendropy/interop/seqgen.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,713 copying build/lib/dendropy/interop/paup.py -> build/bdist.linux-armv7l/wheel/./dendropy/interop 2026-08-22T15:08:12,718 creating build/bdist.linux-armv7l/wheel/dendropy/application 2026-08-22T15:08:12,719 copying build/lib/dendropy/application/dendropy_format.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-08-22T15:08:12,722 copying build/lib/dendropy/application/sumtrees.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-08-22T15:08:12,727 copying build/lib/dendropy/application/sumlabels.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-08-22T15:08:12,730 copying build/lib/dendropy/application/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/application 2026-08-22T15:08:12,732 creating build/bdist.linux-armv7l/wheel/dendropy/utility 2026-08-22T15:08:12,734 copying build/lib/dendropy/utility/processio.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,736 copying build/lib/dendropy/utility/container.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,740 copying build/lib/dendropy/utility/textprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,743 copying build/lib/dendropy/utility/error.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,746 creating build/bdist.linux-armv7l/wheel/dendropy/utility/libexec 2026-08-22T15:08:12,747 copying build/lib/dendropy/utility/libexec/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility/libexec 2026-08-22T15:08:12,750 copying build/lib/dendropy/utility/messaging.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,753 copying build/lib/dendropy/utility/deprecate.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,755 copying build/lib/dendropy/utility/constants.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,757 copying build/lib/dendropy/utility/filesys.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,760 copying build/lib/dendropy/utility/vcsinfo.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,763 copying build/lib/dendropy/utility/timeprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,765 copying build/lib/dendropy/utility/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,767 copying build/lib/dendropy/utility/metavar.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,769 copying build/lib/dendropy/utility/bitprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,771 copying build/lib/dendropy/utility/urlio.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,773 copying build/lib/dendropy/utility/terminal.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,776 copying build/lib/dendropy/utility/debug.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,778 copying build/lib/dendropy/utility/bibtex.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,781 copying build/lib/dendropy/utility/cli.py -> build/bdist.linux-armv7l/wheel/./dendropy/utility 2026-08-22T15:08:12,784 copying build/lib/dendropy/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy 2026-08-22T15:08:12,787 creating build/bdist.linux-armv7l/wheel/dendropy/model 2026-08-22T15:08:12,788 copying build/lib/dendropy/model/birthdeath.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,793 copying build/lib/dendropy/model/protractedspeciation.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,796 copying build/lib/dendropy/model/continuous.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,799 copying build/lib/dendropy/model/coalescent.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,802 copying build/lib/dendropy/model/discrete.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,804 copying build/lib/dendropy/model/parsimony.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,807 copying build/lib/dendropy/model/multispeciescoalescent.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,809 copying build/lib/dendropy/model/reconcile.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,812 copying build/lib/dendropy/model/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,814 copying build/lib/dendropy/model/treeshape.py -> build/bdist.linux-armv7l/wheel/./dendropy/model 2026-08-22T15:08:12,816 creating build/bdist.linux-armv7l/wheel/dendropy/plot 2026-08-22T15:08:12,817 copying build/lib/dendropy/plot/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/plot 2026-08-22T15:08:12,819 copying build/lib/dendropy/plot/tikzplot.py -> build/bdist.linux-armv7l/wheel/./dendropy/plot 2026-08-22T15:08:12,821 copying build/lib/dendropy/plot/asciiplot.py -> build/bdist.linux-armv7l/wheel/./dendropy/plot 2026-08-22T15:08:12,823 copying build/lib/dendropy/__main__.py -> build/bdist.linux-armv7l/wheel/./dendropy 2026-08-22T15:08:12,826 creating build/bdist.linux-armv7l/wheel/dendropy/calculate 2026-08-22T15:08:12,827 copying build/lib/dendropy/calculate/phylogeneticdistance.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,830 copying build/lib/dendropy/calculate/combinatorics.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,832 copying build/lib/dendropy/calculate/probability.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,835 copying build/lib/dendropy/calculate/profiledistance.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,837 copying build/lib/dendropy/calculate/popgenstat.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,839 copying build/lib/dendropy/calculate/statistics.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,842 copying build/lib/dendropy/calculate/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,843 copying build/lib/dendropy/calculate/treesum.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,846 copying build/lib/dendropy/calculate/treescore.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,848 copying build/lib/dendropy/calculate/treecompare.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,850 copying build/lib/dendropy/calculate/mathfn.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,852 copying build/lib/dendropy/calculate/treemeasure.py -> build/bdist.linux-armv7l/wheel/./dendropy/calculate 2026-08-22T15:08:12,855 creating build/bdist.linux-armv7l/wheel/dendropy/legacy 2026-08-22T15:08:12,856 copying build/lib/dendropy/legacy/continuous.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,858 copying build/lib/dendropy/legacy/treecalc.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,860 copying build/lib/dendropy/legacy/coalescent.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,862 copying build/lib/dendropy/legacy/treemanip.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,864 copying build/lib/dendropy/legacy/popgenstat.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,867 copying build/lib/dendropy/legacy/reconcile.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,868 copying build/lib/dendropy/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,870 copying build/lib/dendropy/legacy/seqsim.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,872 copying build/lib/dendropy/legacy/ncbi.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,875 copying build/lib/dendropy/legacy/popgensim.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,876 copying build/lib/dendropy/legacy/seqmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,878 copying build/lib/dendropy/legacy/treesim.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,880 copying build/lib/dendropy/legacy/treesum.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,882 copying build/lib/dendropy/legacy/treesplit.py -> build/bdist.linux-armv7l/wheel/./dendropy/legacy 2026-08-22T15:08:12,885 creating build/bdist.linux-armv7l/wheel/dendropy/mathlib 2026-08-22T15:08:12,886 copying build/lib/dendropy/mathlib/probability.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-08-22T15:08:12,888 copying build/lib/dendropy/mathlib/statistics.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-08-22T15:08:12,890 copying build/lib/dendropy/mathlib/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-08-22T15:08:12,892 copying build/lib/dendropy/mathlib/mathfn.py -> build/bdist.linux-armv7l/wheel/./dendropy/mathlib 2026-08-22T15:08:12,894 creating build/bdist.linux-armv7l/wheel/dendropy/dataio 2026-08-22T15:08:12,895 copying build/lib/dendropy/dataio/multiphylipreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,897 copying build/lib/dendropy/dataio/nexuswriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,900 copying build/lib/dendropy/dataio/newick.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,902 copying build/lib/dendropy/dataio/newickreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,904 copying build/lib/dendropy/dataio/phylipreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,907 copying build/lib/dendropy/dataio/fastawriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,909 copying build/lib/dendropy/dataio/nexusreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,912 copying build/lib/dendropy/dataio/newickyielder.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,914 copying build/lib/dendropy/dataio/phylipwriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,916 copying build/lib/dendropy/dataio/nexmlwriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,919 copying build/lib/dendropy/dataio/nexmlyielder.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,921 copying build/lib/dendropy/dataio/tokenizer.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,923 copying build/lib/dendropy/dataio/nexusprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,925 copying build/lib/dendropy/dataio/ioservice.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,928 copying build/lib/dendropy/dataio/newickwriter.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,930 copying build/lib/dendropy/dataio/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,932 copying build/lib/dendropy/dataio/xmlprocessing.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,935 copying build/lib/dendropy/dataio/nexusyielder.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,937 copying build/lib/dendropy/dataio/fastareader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,939 copying build/lib/dendropy/dataio/nexmlreader.py -> build/bdist.linux-armv7l/wheel/./dendropy/dataio 2026-08-22T15:08:12,943 creating build/bdist.linux-armv7l/wheel/dendropy/datamodel 2026-08-22T15:08:12,944 copying build/lib/dendropy/datamodel/basemodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-08-22T15:08:12,947 copying build/lib/dendropy/datamodel/taxonmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-08-22T15:08:12,951 copying build/lib/dendropy/datamodel/charstatemodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-08-22T15:08:12,954 copying build/lib/dendropy/datamodel/datasetmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-08-22T15:08:12,957 copying build/lib/dendropy/datamodel/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-08-22T15:08:12,959 creating build/bdist.linux-armv7l/wheel/dendropy/datamodel/treemodel 2026-08-22T15:08:12,961 copying build/lib/dendropy/datamodel/treemodel/_edge.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-08-22T15:08:12,963 copying build/lib/dendropy/datamodel/treemodel/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-08-22T15:08:12,965 copying build/lib/dendropy/datamodel/treemodel/_node.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-08-22T15:08:12,969 copying build/lib/dendropy/datamodel/treemodel/_bipartition.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-08-22T15:08:12,971 copying build/lib/dendropy/datamodel/treemodel/_tree.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel/treemodel 2026-08-22T15:08:12,978 copying build/lib/dendropy/datamodel/treecollectionmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-08-22T15:08:12,982 copying build/lib/dendropy/datamodel/charmatrixmodel.py -> build/bdist.linux-armv7l/wheel/./dendropy/datamodel 2026-08-22T15:08:12,986 creating build/bdist.linux-armv7l/wheel/dendropy/simulate 2026-08-22T15:08:12,987 copying build/lib/dendropy/simulate/charsim.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-08-22T15:08:12,988 copying build/lib/dendropy/simulate/__init__.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-08-22T15:08:12,990 copying build/lib/dendropy/simulate/popgensim.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-08-22T15:08:12,992 copying build/lib/dendropy/simulate/treesim.py -> build/bdist.linux-armv7l/wheel/./dendropy/simulate 2026-08-22T15:08:12,994 running install_egg_info 2026-08-22T15:08:13,024 Copying src/DendroPy.egg-info to build/bdist.linux-armv7l/wheel/./DendroPy-5.0.12-py3.11.egg-info 2026-08-22T15:08:13,038 running install_scripts 2026-08-22T15:08:13,056 creating build/bdist.linux-armv7l/wheel/dendropy-5.0.12.dist-info/WHEEL 2026-08-22T15:08:13,058 creating '/tmp/pip-wheel-54ujfdbi/dendropy-5.0.12-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-08-22T15:08:13,061 adding 'dendropy/__init__.py' 2026-08-22T15:08:13,062 adding 'dendropy/__main__.py' 2026-08-22T15:08:13,064 adding 'dendropy/application/__init__.py' 2026-08-22T15:08:13,066 adding 'dendropy/application/dendropy_format.py' 2026-08-22T15:08:13,068 adding 'dendropy/application/sumlabels.py' 2026-08-22T15:08:13,078 adding 'dendropy/application/sumtrees.py' 2026-08-22T15:08:13,081 adding 'dendropy/calculate/__init__.py' 2026-08-22T15:08:13,082 adding 'dendropy/calculate/combinatorics.py' 2026-08-22T15:08:13,084 adding 'dendropy/calculate/mathfn.py' 2026-08-22T15:08:13,090 adding 'dendropy/calculate/phylogeneticdistance.py' 2026-08-22T15:08:13,092 adding 'dendropy/calculate/popgenstat.py' 2026-08-22T15:08:13,094 adding 'dendropy/calculate/probability.py' 2026-08-22T15:08:13,097 adding 'dendropy/calculate/profiledistance.py' 2026-08-22T15:08:13,099 adding 'dendropy/calculate/statistics.py' 2026-08-22T15:08:13,103 adding 'dendropy/calculate/treecompare.py' 2026-08-22T15:08:13,105 adding 'dendropy/calculate/treemeasure.py' 2026-08-22T15:08:13,106 adding 'dendropy/calculate/treescore.py' 2026-08-22T15:08:13,108 adding 'dendropy/calculate/treesum.py' 2026-08-22T15:08:13,111 adding 'dendropy/dataio/__init__.py' 2026-08-22T15:08:13,112 adding 'dendropy/dataio/fastareader.py' 2026-08-22T15:08:13,113 adding 'dendropy/dataio/fastawriter.py' 2026-08-22T15:08:13,116 adding 'dendropy/dataio/ioservice.py' 2026-08-22T15:08:13,118 adding 'dendropy/dataio/multiphylipreader.py' 2026-08-22T15:08:13,119 adding 'dendropy/dataio/newick.py' 2026-08-22T15:08:13,122 adding 'dendropy/dataio/newickreader.py' 2026-08-22T15:08:13,125 adding 'dendropy/dataio/newickwriter.py' 2026-08-22T15:08:13,127 adding 'dendropy/dataio/newickyielder.py' 2026-08-22T15:08:13,131 adding 'dendropy/dataio/nexmlreader.py' 2026-08-22T15:08:13,135 adding 'dendropy/dataio/nexmlwriter.py' 2026-08-22T15:08:13,136 adding 'dendropy/dataio/nexmlyielder.py' 2026-08-22T15:08:13,139 adding 'dendropy/dataio/nexusprocessing.py' 2026-08-22T15:08:13,145 adding 'dendropy/dataio/nexusreader.py' 2026-08-22T15:08:13,149 adding 'dendropy/dataio/nexuswriter.py' 2026-08-22T15:08:13,151 adding 'dendropy/dataio/nexusyielder.py' 2026-08-22T15:08:13,153 adding 'dendropy/dataio/phylipreader.py' 2026-08-22T15:08:13,155 adding 'dendropy/dataio/phylipwriter.py' 2026-08-22T15:08:13,156 adding 'dendropy/dataio/tokenizer.py' 2026-08-22T15:08:13,158 adding 'dendropy/dataio/xmlprocessing.py' 2026-08-22T15:08:13,160 adding 'dendropy/datamodel/__init__.py' 2026-08-22T15:08:13,165 adding 'dendropy/datamodel/basemodel.py' 2026-08-22T15:08:13,175 adding 'dendropy/datamodel/charmatrixmodel.py' 2026-08-22T15:08:13,180 adding 'dendropy/datamodel/charstatemodel.py' 2026-08-22T15:08:13,183 adding 'dendropy/datamodel/datasetmodel.py' 2026-08-22T15:08:13,192 adding 'dendropy/datamodel/taxonmodel.py' 2026-08-22T15:08:13,205 adding 'dendropy/datamodel/treecollectionmodel.py' 2026-08-22T15:08:13,208 adding 'dendropy/datamodel/treemodel/__init__.py' 2026-08-22T15:08:13,211 adding 'dendropy/datamodel/treemodel/_bipartition.py' 2026-08-22T15:08:13,213 adding 'dendropy/datamodel/treemodel/_edge.py' 2026-08-22T15:08:13,219 adding 'dendropy/datamodel/treemodel/_node.py' 2026-08-22T15:08:13,237 adding 'dendropy/datamodel/treemodel/_tree.py' 2026-08-22T15:08:13,240 adding 'dendropy/interop/__init__.py' 2026-08-22T15:08:13,242 adding 'dendropy/interop/ape.py' 2026-08-22T15:08:13,243 adding 'dendropy/interop/biopython.py' 2026-08-22T15:08:13,245 adding 'dendropy/interop/entrez.py' 2026-08-22T15:08:13,246 adding 'dendropy/interop/ete.py' 2026-08-22T15:08:13,248 adding 'dendropy/interop/gbif.py' 2026-08-22T15:08:13,252 adding 'dendropy/interop/genbank.py' 2026-08-22T15:08:13,254 adding 'dendropy/interop/itol.py' 2026-08-22T15:08:13,256 adding 'dendropy/interop/muscle.py' 2026-08-22T15:08:13,260 adding 'dendropy/interop/paup.py' 2026-08-22T15:08:13,264 adding 'dendropy/interop/raxml.py' 2026-08-22T15:08:13,266 adding 'dendropy/interop/rspr.py' 2026-08-22T15:08:13,267 adding 'dendropy/interop/rstats.py' 2026-08-22T15:08:13,269 adding 'dendropy/interop/seqgen.py' 2026-08-22T15:08:13,271 adding 'dendropy/legacy/__init__.py' 2026-08-22T15:08:13,272 adding 'dendropy/legacy/coalescent.py' 2026-08-22T15:08:13,274 adding 'dendropy/legacy/continuous.py' 2026-08-22T15:08:13,276 adding 'dendropy/legacy/ncbi.py' 2026-08-22T15:08:13,277 adding 'dendropy/legacy/popgensim.py' 2026-08-22T15:08:13,278 adding 'dendropy/legacy/popgenstat.py' 2026-08-22T15:08:13,279 adding 'dendropy/legacy/reconcile.py' 2026-08-22T15:08:13,281 adding 'dendropy/legacy/seqmodel.py' 2026-08-22T15:08:13,282 adding 'dendropy/legacy/seqsim.py' 2026-08-22T15:08:13,284 adding 'dendropy/legacy/treecalc.py' 2026-08-22T15:08:13,285 adding 'dendropy/legacy/treemanip.py' 2026-08-22T15:08:13,286 adding 'dendropy/legacy/treesim.py' 2026-08-22T15:08:13,288 adding 'dendropy/legacy/treesplit.py' 2026-08-22T15:08:13,289 adding 'dendropy/legacy/treesum.py' 2026-08-22T15:08:13,291 adding 'dendropy/mathlib/__init__.py' 2026-08-22T15:08:13,292 adding 'dendropy/mathlib/mathfn.py' 2026-08-22T15:08:13,293 adding 'dendropy/mathlib/probability.py' 2026-08-22T15:08:13,295 adding 'dendropy/mathlib/statistics.py' 2026-08-22T15:08:13,296 adding 'dendropy/model/__init__.py' 2026-08-22T15:08:13,304 adding 'dendropy/model/birthdeath.py' 2026-08-22T15:08:13,309 adding 'dendropy/model/coalescent.py' 2026-08-22T15:08:13,312 adding 'dendropy/model/continuous.py' 2026-08-22T15:08:13,315 adding 'dendropy/model/discrete.py' 2026-08-22T15:08:13,317 adding 'dendropy/model/multispeciescoalescent.py' 2026-08-22T15:08:13,319 adding 'dendropy/model/parsimony.py' 2026-08-22T15:08:13,324 adding 'dendropy/model/protractedspeciation.py' 2026-08-22T15:08:13,328 adding 'dendropy/model/reconcile.py' 2026-08-22T15:08:13,329 adding 'dendropy/model/treeshape.py' 2026-08-22T15:08:13,331 adding 'dendropy/plot/__init__.py' 2026-08-22T15:08:13,333 adding 'dendropy/plot/asciiplot.py' 2026-08-22T15:08:13,334 adding 'dendropy/plot/tikzplot.py' 2026-08-22T15:08:13,336 adding 'dendropy/simulate/__init__.py' 2026-08-22T15:08:13,338 adding 'dendropy/simulate/charsim.py' 2026-08-22T15:08:13,340 adding 'dendropy/simulate/popgensim.py' 2026-08-22T15:08:13,342 adding 'dendropy/simulate/treesim.py' 2026-08-22T15:08:13,344 adding 'dendropy/utility/__init__.py' 2026-08-22T15:08:13,346 adding 'dendropy/utility/bibtex.py' 2026-08-22T15:08:13,348 adding 'dendropy/utility/bitprocessing.py' 2026-08-22T15:08:13,349 adding 'dendropy/utility/cli.py' 2026-08-22T15:08:13,351 adding 'dendropy/utility/constants.py' 2026-08-22T15:08:13,356 adding 'dendropy/utility/container.py' 2026-08-22T15:08:13,358 adding 'dendropy/utility/debug.py' 2026-08-22T15:08:13,359 adding 'dendropy/utility/deprecate.py' 2026-08-22T15:08:13,360 adding 'dendropy/utility/error.py' 2026-08-22T15:08:13,362 adding 'dendropy/utility/filesys.py' 2026-08-22T15:08:13,364 adding 'dendropy/utility/messaging.py' 2026-08-22T15:08:13,365 adding 'dendropy/utility/metavar.py' 2026-08-22T15:08:13,366 adding 'dendropy/utility/processio.py' 2026-08-22T15:08:13,368 adding 'dendropy/utility/terminal.py' 2026-08-22T15:08:13,369 adding 'dendropy/utility/textprocessing.py' 2026-08-22T15:08:13,370 adding 'dendropy/utility/timeprocessing.py' 2026-08-22T15:08:13,372 adding 'dendropy/utility/urlio.py' 2026-08-22T15:08:13,373 adding 'dendropy/utility/vcsinfo.py' 2026-08-22T15:08:13,375 adding 'dendropy/utility/libexec/__init__.py' 2026-08-22T15:08:13,378 adding 'dendropy-5.0.12.dist-info/licenses/AUTHORS.rst' 2026-08-22T15:08:13,379 adding 'dendropy-5.0.12.dist-info/licenses/LICENSE.rst' 2026-08-22T15:08:13,380 adding 'dendropy-5.0.12.dist-info/licenses/NOTICES.rst' 2026-08-22T15:08:13,382 adding 'dendropy-5.0.12.dist-info/METADATA' 2026-08-22T15:08:13,383 adding 'dendropy-5.0.12.dist-info/WHEEL' 2026-08-22T15:08:13,383 adding 'dendropy-5.0.12.dist-info/entry_points.txt' 2026-08-22T15:08:13,384 adding 'dendropy-5.0.12.dist-info/top_level.txt' 2026-08-22T15:08:13,385 adding 'dendropy-5.0.12.dist-info/zip-safe' 2026-08-22T15:08:13,387 adding 'dendropy-5.0.12.dist-info/RECORD' 2026-08-22T15:08:13,395 removing build/bdist.linux-armv7l/wheel 2026-08-22T15:08:13,540 Building wheel for dendropy (setup.py): finished with status 'done' 2026-08-22T15:08:13,547 Created wheel for dendropy: filename=dendropy-5.0.12-py3-none-any.whl size=465565 sha256=4029fed83f7cdf3b795f40e863f4ee75b67ae20a1c430e7ed4f94236de2b8c71 2026-08-22T15:08:13,549 Stored in directory: /tmp/pip-ephem-wheel-cache-hebr569d/wheels/79/39/c4/0fd20c94a1e2d0ebe281b574568e41f3b112d724cd1a205bc5 2026-08-22T15:08:13,564 Successfully built dendropy 2026-08-22T15:08:13,578 Removed build tracker: '/tmp/pip-build-tracker-3y6fjpmm'