2026-04-02T16:54:45,347 Created temporary directory: /tmp/pip-ephem-wheel-cache-an_o9j8v 2026-04-02T16:54:45,348 Created temporary directory: /tmp/pip-build-tracker-rvyuv_3u 2026-04-02T16:54:45,349 Initialized build tracking at /tmp/pip-build-tracker-rvyuv_3u 2026-04-02T16:54:45,349 Created build tracker: /tmp/pip-build-tracker-rvyuv_3u 2026-04-02T16:54:45,350 Entered build tracker: /tmp/pip-build-tracker-rvyuv_3u 2026-04-02T16:54:45,351 Created temporary directory: /tmp/pip-wheel-z0nindr9 2026-04-02T16:54:45,353 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-02T16:54:45,356 Created temporary directory: /tmp/pip-ephem-wheel-cache-fclqwse9 2026-04-02T16:54:45,381 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-02T16:54:45,384 2 location(s) to search for versions of phynetpy: 2026-04-02T16:54:45,384 * https://pypi.org/simple/phynetpy/ 2026-04-02T16:54:45,384 * https://www.piwheels.org/simple/phynetpy/ 2026-04-02T16:54:45,385 Fetching project page and analyzing links: https://pypi.org/simple/phynetpy/ 2026-04-02T16:54:45,386 Getting page https://pypi.org/simple/phynetpy/ 2026-04-02T16:54:45,387 Found index url https://pypi.org/simple 2026-04-02T16:54:45,614 Fetched page https://pypi.org/simple/phynetpy/ as application/vnd.pypi.simple.v1+json 2026-04-02T16:54:45,618 Skipping link: No binaries permitted for phynetpy: https://files.pythonhosted.org/packages/ca/09/330fee700fddd31c7a667cc70c35300e3a4771a3eada01cfd210cffff202/PhyNetPy-0.0.1-py3-none-any.whl (from https://pypi.org/simple/phynetpy/) (requires-python:>=3.8) 2026-04-02T16:54:45,619 Found link https://files.pythonhosted.org/packages/07/c0/6926e821f0eda581cce14244b828941991c1224f468b0e16f77d80f63a8b/PhyNetPy-0.0.3.tar.gz (from https://pypi.org/simple/phynetpy/) (requires-python:>=3.8), version: 0.0.3 2026-04-02T16:54:45,620 Found link https://files.pythonhosted.org/packages/12/5a/4771d05caf1f35a2bed8a225f0d0e5451d92ca18b69b5f38840265b5fd66/PhyNetPy-0.0.7.tar.gz (from https://pypi.org/simple/phynetpy/) (requires-python:>=3.8), version: 0.0.7 2026-04-02T16:54:45,621 Found link https://files.pythonhosted.org/packages/ee/ed/e36b0cbe28e5be4ff209d3761fc9285e484f500538e89d8ef762cdd52f40/PhyNetPy-0.0.8.tar.gz (from https://pypi.org/simple/phynetpy/) (requires-python:>=3.8), version: 0.0.8 2026-04-02T16:54:45,621 Skipping link: No binaries permitted for phynetpy: https://files.pythonhosted.org/packages/84/cb/d3e4aae93b7b081c45816588bcee1e82c94971d3f018cd80e2dfe7cf7e25/phynetpy-0.2.0-py3-none-any.whl (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8) 2026-04-02T16:54:45,622 Found link https://files.pythonhosted.org/packages/88/ec/0566d2580987848f9e29932b915fc9666baef4250712715554f47054fea1/phynetpy-0.2.0.tar.gz (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8), version: 0.2.0 2026-04-02T16:54:45,623 Skipping link: No binaries permitted for phynetpy: https://files.pythonhosted.org/packages/dc/52/3ba4d13005377b3ed52911f887c93e88884edf45d4c40aa90c2ac56be03b/phynetpy-0.3.0-py3-none-any.whl (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8) 2026-04-02T16:54:45,624 Found link https://files.pythonhosted.org/packages/30/3e/7ce7d0f4d874356d6c081b3602feeaa88d9fa30bba6dcc92d246abb06b3e/phynetpy-0.3.0.tar.gz (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8), version: 0.3.0 2026-04-02T16:54:45,625 Skipping link: No binaries permitted for phynetpy: https://files.pythonhosted.org/packages/1e/14/4d0ab3a2cd31661cf090210d170f5f15a6e842ef810e06d19c1afd40ba64/phynetpy-0.3.1-py3-none-any.whl (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8) 2026-04-02T16:54:45,626 Found link https://files.pythonhosted.org/packages/63/4e/3bab1d32cf649a611497899fa39ec3b6f2ba6cf645dfef655ecf1415c438/phynetpy-0.3.1.tar.gz (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8), version: 0.3.1 2026-04-02T16:54:45,627 Skipping link: No binaries permitted for phynetpy: https://files.pythonhosted.org/packages/7a/7e/5f5268de54f085bbbfe97ac3b724638e7e0c87e616218c84fadb10d42151/phynetpy-0.3.2-py3-none-any.whl (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8) 2026-04-02T16:54:45,628 Found link https://files.pythonhosted.org/packages/ce/96/4a6d353b9edc53b44d59656cebf3dce2ea7307be734f16cdac73fb202312/phynetpy-0.3.2.tar.gz (from https://pypi.org/simple/phynetpy/) (requires-python:<4,>=3.8), version: 0.3.2 2026-04-02T16:54:45,629 Fetching project page and analyzing links: https://www.piwheels.org/simple/phynetpy/ 2026-04-02T16:54:45,629 Getting page https://www.piwheels.org/simple/phynetpy/ 2026-04-02T16:54:45,630 Found index url https://www.piwheels.org/simple 2026-04-02T16:54:45,805 Fetched page https://www.piwheels.org/simple/phynetpy/ as text/html 2026-04-02T16:54:45,808 Skipping link: No binaries permitted for phynetpy: https://www.piwheels.org/simple/phynetpy/phynetpy-0.3.1-py3-none-any.whl#sha256=770e9b9bd69479c461d2c229f9eb623b4580bd680076f05b38f8f88bda24553a (from https://www.piwheels.org/simple/phynetpy/) (requires-python:>=3.8, <4) 2026-04-02T16:54:45,808 Skipping link: No binaries permitted for phynetpy: https://www.piwheels.org/simple/phynetpy/phynetpy-0.3.0-py3-none-any.whl#sha256=4e1a7db7eba4f1eccdeef0eb815aae53a6960824dcdb56c26b0cace43b96967b (from https://www.piwheels.org/simple/phynetpy/) (requires-python:>=3.8, <4) 2026-04-02T16:54:45,809 Skipping link: No binaries permitted for phynetpy: https://archive1.piwheels.org/simple/phynetpy/phynetpy-0.2.0-py3-none-any.whl#sha256=5da2d5282e26d40fec52bd4989634a1459a84f87d21bde344ebaa8d1163cfa83 (from https://www.piwheels.org/simple/phynetpy/) (requires-python:>=3.8, <4) 2026-04-02T16:54:45,809 Skipping link: No binaries permitted for phynetpy: https://archive1.piwheels.org/simple/phynetpy/PhyNetPy-0.1.0-py3-none-any.whl#sha256=6e28656e552521e811ba9c1c9a7fe9b88ec882d9c1bfb898ea789ca8e45c98c7 (from https://www.piwheels.org/simple/phynetpy/) (requires-python:>=3.8) 2026-04-02T16:54:45,810 Skipping link: No binaries permitted for phynetpy: https://archive1.piwheels.org/simple/phynetpy/PhyNetPy-0.0.8-py3-none-any.whl#sha256=a2de25eda6a0d35c114a9fe90ed21157ecc2e5d5ad8c1fcd602ce24b9ffd22b3 (from https://www.piwheels.org/simple/phynetpy/) (requires-python:>=3.8) 2026-04-02T16:54:45,811 Skipping link: No binaries permitted for phynetpy: https://archive1.piwheels.org/simple/phynetpy/PhyNetPy-0.0.7-py3-none-any.whl#sha256=9b8c80272af518d16582a09c6dbf183f3c50c7bda7481812461144ccbfdb6702 (from https://www.piwheels.org/simple/phynetpy/) (requires-python:>=3.8) 2026-04-02T16:54:45,811 Skipping link: No binaries permitted for phynetpy: https://archive1.piwheels.org/simple/phynetpy/PhyNetPy-0.0.3-py3-none-any.whl#sha256=daaf000f384f301addcda39f19569d5dab0097cdd8603085af86618ab61ab0a2 (from https://www.piwheels.org/simple/phynetpy/) (requires-python:>=3.8) 2026-04-02T16:54:45,812 Skipping link: not a file: https://www.piwheels.org/simple/phynetpy/ 2026-04-02T16:54:45,813 Skipping link: not a file: https://pypi.org/simple/phynetpy/ 2026-04-02T16:54:45,832 Given no hashes to check 1 links for project 'phynetpy': discarding no candidates 2026-04-02T16:54:45,852 Collecting phynetpy==0.3.2 2026-04-02T16:54:45,855 Created temporary directory: /tmp/pip-unpack-2kbeso4j 2026-04-02T16:54:46,099 Downloading phynetpy-0.3.2.tar.gz (205 kB) 2026-04-02T16:54:46,302 Added phynetpy==0.3.2 from https://files.pythonhosted.org/packages/ce/96/4a6d353b9edc53b44d59656cebf3dce2ea7307be734f16cdac73fb202312/phynetpy-0.3.2.tar.gz to build tracker '/tmp/pip-build-tracker-rvyuv_3u' 2026-04-02T16:54:46,306 Created temporary directory: /tmp/pip-build-env-xc53n1ji 2026-04-02T16:54:46,311 Installing build dependencies: started 2026-04-02T16:54:46,312 Running command pip subprocess to install build dependencies 2026-04-02T16:54:47,450 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-02T16:54:47,860 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-02T16:54:47,884 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-02T16:54:49,664 Collecting setuptools>=61 2026-04-02T16:54:49,745 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-02T16:54:50,023 Collecting wheel 2026-04-02T16:54:50,040 Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB) 2026-04-02T16:54:50,226 Collecting packaging>=24.0 2026-04-02T16:54:50,245 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-04-02T16:54:53,213 Installing collected packages: setuptools, packaging, wheel 2026-04-02T16:54:56,704 Creating /tmp/pip-build-env-xc53n1ji/overlay/local/bin 2026-04-02T16:54:56,706 changing mode of /tmp/pip-build-env-xc53n1ji/overlay/local/bin/wheel to 755 2026-04-02T16:54:56,728 Successfully installed packaging-26.0 setuptools-82.0.1 wheel-0.46.3 2026-04-02T16:54:57,028 Installing build dependencies: finished with status 'done' 2026-04-02T16:54:57,034 Getting requirements to build wheel: started 2026-04-02T16:54:57,036 Running command Getting requirements to build wheel 2026-04-02T16:54:57,615 /tmp/pip-build-env-xc53n1ji/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-02T16:54:57,615 !! 2026-04-02T16:54:57,616 ******************************************************************************** 2026-04-02T16:54:57,617 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-02T16:54:57,618 License :: OSI Approved :: MIT License 2026-04-02T16:54:57,619 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-02T16:54:57,620 ******************************************************************************** 2026-04-02T16:54:57,621 !! 2026-04-02T16:54:57,622 self._finalize_license_expression() 2026-04-02T16:54:57,638 Cython not found - installing pure Python version 2026-04-02T16:54:57,639 For better performance, install Cython: pip install cython 2026-04-02T16:54:57,639 running egg_info 2026-04-02T16:54:57,645 writing phynetpy.egg-info/PKG-INFO 2026-04-02T16:54:57,650 writing dependency_links to phynetpy.egg-info/dependency_links.txt 2026-04-02T16:54:57,653 writing requirements to phynetpy.egg-info/requires.txt 2026-04-02T16:54:57,654 writing top-level names to phynetpy.egg-info/top_level.txt 2026-04-02T16:54:57,681 reading manifest file 'phynetpy.egg-info/SOURCES.txt' 2026-04-02T16:54:57,686 reading manifest template 'MANIFEST.in' 2026-04-02T16:54:57,715 no previously-included directories found matching '.venv' 2026-04-02T16:54:57,716 no previously-included directories found matching '.git' 2026-04-02T16:54:57,716 no previously-included directories found matching '.cursor' 2026-04-02T16:54:57,717 no previously-included directories found matching 'archive' 2026-04-02T16:54:57,718 no previously-included directories found matching 'build' 2026-04-02T16:54:57,719 no previously-included directories found matching 'dist' 2026-04-02T16:54:57,719 no previously-included directories found matching 'tests' 2026-04-02T16:54:57,721 no previously-included directories found matching '1.1' 2026-04-02T16:54:57,721 no previously-included directories found matching 'ABC' 2026-04-02T16:54:57,722 no previously-included directories found matching 'Bayesian' 2026-04-02T16:54:57,723 no previously-included directories found matching 'DEFJ' 2026-04-02T16:54:57,724 no previously-included directories found matching 'DLLS' 2026-04-02T16:54:57,725 no previously-included directories found matching 'Guides' 2026-04-02T16:54:57,725 no previously-included directories found matching 'NexusFiles' 2026-04-02T16:54:57,726 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2026-04-02T16:54:57,727 warning: no previously-included files matching '__pycache__' found anywhere in distribution 2026-04-02T16:54:57,728 warning: no previously-included files matching '*.so' found anywhere in distribution 2026-04-02T16:54:57,729 warning: no previously-included files matching '*.c' found anywhere in distribution 2026-04-02T16:54:57,729 adding license file 'LICENSE' 2026-04-02T16:54:57,733 writing manifest file 'phynetpy.egg-info/SOURCES.txt' 2026-04-02T16:54:57,824 Getting requirements to build wheel: finished with status 'done' 2026-04-02T16:54:57,828 Created temporary directory: /tmp/pip-modern-metadata-dc7wvkhk 2026-04-02T16:54:57,830 Preparing metadata (pyproject.toml): started 2026-04-02T16:54:57,831 Running command Preparing metadata (pyproject.toml) 2026-04-02T16:54:58,381 /tmp/pip-build-env-xc53n1ji/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-02T16:54:58,381 !! 2026-04-02T16:54:58,383 ******************************************************************************** 2026-04-02T16:54:58,383 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-02T16:54:58,384 License :: OSI Approved :: MIT License 2026-04-02T16:54:58,386 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-02T16:54:58,386 ******************************************************************************** 2026-04-02T16:54:58,387 !! 2026-04-02T16:54:58,388 self._finalize_license_expression() 2026-04-02T16:54:58,405 Cython not found - installing pure Python version 2026-04-02T16:54:58,406 For better performance, install Cython: pip install cython 2026-04-02T16:54:58,406 running dist_info 2026-04-02T16:54:58,416 creating /tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info 2026-04-02T16:54:58,417 writing /tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info/PKG-INFO 2026-04-02T16:54:58,422 writing dependency_links to /tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info/dependency_links.txt 2026-04-02T16:54:58,425 writing requirements to /tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info/requires.txt 2026-04-02T16:54:58,426 writing top-level names to /tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info/top_level.txt 2026-04-02T16:54:58,428 writing manifest file '/tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info/SOURCES.txt' 2026-04-02T16:54:58,451 reading manifest file '/tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info/SOURCES.txt' 2026-04-02T16:54:58,453 reading manifest template 'MANIFEST.in' 2026-04-02T16:54:58,479 no previously-included directories found matching '.venv' 2026-04-02T16:54:58,479 no previously-included directories found matching '.git' 2026-04-02T16:54:58,480 no previously-included directories found matching '.cursor' 2026-04-02T16:54:58,481 no previously-included directories found matching 'archive' 2026-04-02T16:54:58,481 no previously-included directories found matching 'build' 2026-04-02T16:54:58,482 no previously-included directories found matching 'dist' 2026-04-02T16:54:58,482 no previously-included directories found matching 'tests' 2026-04-02T16:54:58,483 no previously-included directories found matching 'phynetpy.egg-info' 2026-04-02T16:54:58,484 no previously-included directories found matching '1.1' 2026-04-02T16:54:58,485 no previously-included directories found matching 'ABC' 2026-04-02T16:54:58,485 no previously-included directories found matching 'Bayesian' 2026-04-02T16:54:58,486 no previously-included directories found matching 'DEFJ' 2026-04-02T16:54:58,487 no previously-included directories found matching 'DLLS' 2026-04-02T16:54:58,487 no previously-included directories found matching 'Guides' 2026-04-02T16:54:58,488 no previously-included directories found matching 'NexusFiles' 2026-04-02T16:54:58,488 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2026-04-02T16:54:58,489 warning: no previously-included files matching '__pycache__' found anywhere in distribution 2026-04-02T16:54:58,489 warning: no previously-included files matching '*.so' found anywhere in distribution 2026-04-02T16:54:58,489 warning: no previously-included files matching '*.c' found anywhere in distribution 2026-04-02T16:54:58,490 adding license file 'LICENSE' 2026-04-02T16:54:58,492 writing manifest file '/tmp/pip-modern-metadata-dc7wvkhk/phynetpy.egg-info/SOURCES.txt' 2026-04-02T16:54:58,493 creating '/tmp/pip-modern-metadata-dc7wvkhk/phynetpy-0.3.2.dist-info' 2026-04-02T16:54:58,616 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-02T16:54:58,621 Source in /tmp/pip-wheel-z0nindr9/phynetpy_1dcdd33f96d742d09e41d28fbb8d03f6 has version 0.3.2, which satisfies requirement phynetpy==0.3.2 from https://files.pythonhosted.org/packages/ce/96/4a6d353b9edc53b44d59656cebf3dce2ea7307be734f16cdac73fb202312/phynetpy-0.3.2.tar.gz 2026-04-02T16:54:58,622 Removed phynetpy==0.3.2 from https://files.pythonhosted.org/packages/ce/96/4a6d353b9edc53b44d59656cebf3dce2ea7307be734f16cdac73fb202312/phynetpy-0.3.2.tar.gz from build tracker '/tmp/pip-build-tracker-rvyuv_3u' 2026-04-02T16:54:58,627 Created temporary directory: /tmp/pip-unpack-rb1j42ne 2026-04-02T16:54:58,628 Building wheels for collected packages: phynetpy 2026-04-02T16:54:58,633 Created temporary directory: /tmp/pip-wheel-ersa6les 2026-04-02T16:54:58,633 Destination directory: /tmp/pip-wheel-ersa6les 2026-04-02T16:54:58,636 Building wheel for phynetpy (pyproject.toml): started 2026-04-02T16:54:58,637 Running command Building wheel for phynetpy (pyproject.toml) 2026-04-02T16:54:59,177 /tmp/pip-build-env-xc53n1ji/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-02T16:54:59,177 !! 2026-04-02T16:54:59,179 ******************************************************************************** 2026-04-02T16:54:59,179 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-02T16:54:59,180 License :: OSI Approved :: MIT License 2026-04-02T16:54:59,182 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-02T16:54:59,182 ******************************************************************************** 2026-04-02T16:54:59,183 !! 2026-04-02T16:54:59,184 self._finalize_license_expression() 2026-04-02T16:54:59,202 Cython not found - installing pure Python version 2026-04-02T16:54:59,202 For better performance, install Cython: pip install cython 2026-04-02T16:54:59,203 running bdist_wheel 2026-04-02T16:54:59,230 running build 2026-04-02T16:54:59,230 running build_py 2026-04-02T16:54:59,240 creating build/lib/phynetpy 2026-04-02T16:54:59,242 copying src/MetropolisHastings.py -> build/lib/phynetpy 2026-04-02T16:54:59,245 copying src/State.py -> build/lib/phynetpy 2026-04-02T16:54:59,247 copying src/BiMarkers.py -> build/lib/phynetpy 2026-04-02T16:54:59,251 copying src/GeneTrees.py -> build/lib/phynetpy 2026-04-02T16:54:59,254 copying src/Infer_MP_Allop.py -> build/lib/phynetpy 2026-04-02T16:54:59,256 copying src/ModelMove.py -> build/lib/phynetpy 2026-04-02T16:54:59,259 copying src/__init__.py -> build/lib/phynetpy 2026-04-02T16:54:59,261 copying src/Validation.py -> build/lib/phynetpy 2026-04-02T16:54:59,264 copying src/Visitor.py -> build/lib/phynetpy 2026-04-02T16:54:59,266 copying src/Phylo.py -> build/lib/phynetpy 2026-04-02T16:54:59,268 copying src/Sync.py -> build/lib/phynetpy 2026-04-02T16:54:59,270 copying src/IO.py -> build/lib/phynetpy 2026-04-02T16:54:59,273 copying src/SNPSimulator.py -> build/lib/phynetpy 2026-04-02T16:54:59,276 copying src/ModelFactory.py -> build/lib/phynetpy 2026-04-02T16:54:59,278 copying src/MPL.py -> build/lib/phynetpy 2026-04-02T16:54:59,281 copying src/MSA.py -> build/lib/phynetpy 2026-04-02T16:54:59,284 copying src/Alphabet.py -> build/lib/phynetpy 2026-04-02T16:54:59,286 copying src/PhyloNet.py -> build/lib/phynetpy 2026-04-02T16:54:59,288 copying src/GraphUtils.py -> build/lib/phynetpy 2026-04-02T16:54:59,292 copying src/Matrix.py -> build/lib/phynetpy 2026-04-02T16:54:59,294 copying src/NetworkMoves.py -> build/lib/phynetpy 2026-04-02T16:54:59,297 copying src/ModelGraph.py -> build/lib/phynetpy 2026-04-02T16:54:59,300 copying src/Logger.py -> build/lib/phynetpy 2026-04-02T16:54:59,302 copying src/Newick.py -> build/lib/phynetpy 2026-04-02T16:54:59,304 copying src/Traversal.py -> build/lib/phynetpy 2026-04-02T16:54:59,306 copying src/BirthDeath.py -> build/lib/phynetpy 2026-04-02T16:54:59,309 copying src/Strategy.py -> build/lib/phynetpy 2026-04-02T16:54:59,311 copying src/graph_core.py -> build/lib/phynetpy 2026-04-02T16:54:59,313 copying src/Executor.py -> build/lib/phynetpy 2026-04-02T16:54:59,315 copying src/Network.py -> build/lib/phynetpy 2026-04-02T16:54:59,320 copying src/GTR.py -> build/lib/phynetpy 2026-04-02T16:54:59,337 installing to build/bdist.linux-armv7l/wheel 2026-04-02T16:54:59,338 running install 2026-04-02T16:54:59,361 running install_lib 2026-04-02T16:54:59,370 creating build/bdist.linux-armv7l/wheel 2026-04-02T16:54:59,372 creating build/bdist.linux-armv7l/wheel/phynetpy 2026-04-02T16:54:59,374 copying build/lib/phynetpy/MetropolisHastings.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,377 copying build/lib/phynetpy/State.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,379 copying build/lib/phynetpy/BiMarkers.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,382 copying build/lib/phynetpy/GeneTrees.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,386 copying build/lib/phynetpy/Infer_MP_Allop.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,389 copying build/lib/phynetpy/ModelMove.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,392 copying build/lib/phynetpy/__init__.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,394 copying build/lib/phynetpy/Validation.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,397 copying build/lib/phynetpy/Visitor.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,399 copying build/lib/phynetpy/Phylo.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,401 copying build/lib/phynetpy/Sync.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,403 copying build/lib/phynetpy/IO.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,407 copying build/lib/phynetpy/SNPSimulator.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,411 copying build/lib/phynetpy/ModelFactory.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,414 copying build/lib/phynetpy/MPL.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,417 copying build/lib/phynetpy/MSA.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,420 copying build/lib/phynetpy/Alphabet.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,422 copying build/lib/phynetpy/PhyloNet.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,424 copying build/lib/phynetpy/GraphUtils.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,428 copying build/lib/phynetpy/Matrix.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,431 copying build/lib/phynetpy/NetworkMoves.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,434 copying build/lib/phynetpy/ModelGraph.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,436 copying build/lib/phynetpy/Logger.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,438 copying build/lib/phynetpy/Newick.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,440 copying build/lib/phynetpy/Traversal.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,443 copying build/lib/phynetpy/BirthDeath.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,446 copying build/lib/phynetpy/Strategy.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,447 copying build/lib/phynetpy/graph_core.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,449 copying build/lib/phynetpy/Executor.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,454 copying build/lib/phynetpy/Network.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,468 copying build/lib/phynetpy/GTR.py -> build/bdist.linux-armv7l/wheel/./phynetpy 2026-04-02T16:54:59,471 running install_egg_info 2026-04-02T16:54:59,490 running egg_info 2026-04-02T16:54:59,496 writing phynetpy.egg-info/PKG-INFO 2026-04-02T16:54:59,500 writing dependency_links to phynetpy.egg-info/dependency_links.txt 2026-04-02T16:54:59,503 writing requirements to phynetpy.egg-info/requires.txt 2026-04-02T16:54:59,504 writing top-level names to phynetpy.egg-info/top_level.txt 2026-04-02T16:54:59,513 reading manifest file 'phynetpy.egg-info/SOURCES.txt' 2026-04-02T16:54:59,517 reading manifest template 'MANIFEST.in' 2026-04-02T16:54:59,544 no previously-included directories found matching '.venv' 2026-04-02T16:54:59,545 no previously-included directories found matching '.git' 2026-04-02T16:54:59,545 no previously-included directories found matching '.cursor' 2026-04-02T16:54:59,546 no previously-included directories found matching 'archive' 2026-04-02T16:54:59,547 no previously-included directories found matching 'build' 2026-04-02T16:54:59,548 no previously-included directories found matching 'dist' 2026-04-02T16:54:59,548 no previously-included directories found matching 'tests' 2026-04-02T16:54:59,550 no previously-included directories found matching '1.1' 2026-04-02T16:54:59,550 no previously-included directories found matching 'ABC' 2026-04-02T16:54:59,551 no previously-included directories found matching 'Bayesian' 2026-04-02T16:54:59,552 no previously-included directories found matching 'DEFJ' 2026-04-02T16:54:59,553 no previously-included directories found matching 'DLLS' 2026-04-02T16:54:59,553 no previously-included directories found matching 'Guides' 2026-04-02T16:54:59,554 no previously-included directories found matching 'NexusFiles' 2026-04-02T16:54:59,555 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2026-04-02T16:54:59,556 warning: no previously-included files matching '__pycache__' found anywhere in distribution 2026-04-02T16:54:59,557 warning: no previously-included files matching '*.so' found anywhere in distribution 2026-04-02T16:54:59,558 warning: no previously-included files matching '*.c' found anywhere in distribution 2026-04-02T16:54:59,559 adding license file 'LICENSE' 2026-04-02T16:54:59,562 writing manifest file 'phynetpy.egg-info/SOURCES.txt' 2026-04-02T16:54:59,564 Copying phynetpy.egg-info to build/bdist.linux-armv7l/wheel/./phynetpy-0.3.2-py3.11.egg-info 2026-04-02T16:54:59,573 running install_scripts 2026-04-02T16:54:59,582 creating build/bdist.linux-armv7l/wheel/phynetpy-0.3.2.dist-info/WHEEL 2026-04-02T16:54:59,585 creating '/tmp/pip-wheel-ersa6les/.tmp-5qoty81h/phynetpy-0.3.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-02T16:54:59,588 adding 'phynetpy/Alphabet.py' 2026-04-02T16:54:59,597 adding 'phynetpy/BiMarkers.py' 2026-04-02T16:54:59,601 adding 'phynetpy/BirthDeath.py' 2026-04-02T16:54:59,606 adding 'phynetpy/Executor.py' 2026-04-02T16:54:59,609 adding 'phynetpy/GTR.py' 2026-04-02T16:54:59,613 adding 'phynetpy/GeneTrees.py' 2026-04-02T16:54:59,622 adding 'phynetpy/GraphUtils.py' 2026-04-02T16:54:59,630 adding 'phynetpy/IO.py' 2026-04-02T16:54:59,634 adding 'phynetpy/Infer_MP_Allop.py' 2026-04-02T16:54:59,636 adding 'phynetpy/Logger.py' 2026-04-02T16:54:59,640 adding 'phynetpy/MPL.py' 2026-04-02T16:54:59,644 adding 'phynetpy/MSA.py' 2026-04-02T16:54:59,646 adding 'phynetpy/Matrix.py' 2026-04-02T16:54:59,649 adding 'phynetpy/MetropolisHastings.py' 2026-04-02T16:54:59,651 adding 'phynetpy/ModelFactory.py' 2026-04-02T16:54:59,653 adding 'phynetpy/ModelGraph.py' 2026-04-02T16:54:59,657 adding 'phynetpy/ModelMove.py' 2026-04-02T16:54:59,675 adding 'phynetpy/Network.py' 2026-04-02T16:54:59,679 adding 'phynetpy/NetworkMoves.py' 2026-04-02T16:54:59,682 adding 'phynetpy/Newick.py' 2026-04-02T16:54:59,683 adding 'phynetpy/Phylo.py' 2026-04-02T16:54:59,684 adding 'phynetpy/PhyloNet.py' 2026-04-02T16:54:59,688 adding 'phynetpy/SNPSimulator.py' 2026-04-02T16:54:59,690 adding 'phynetpy/State.py' 2026-04-02T16:54:59,691 adding 'phynetpy/Strategy.py' 2026-04-02T16:54:59,693 adding 'phynetpy/Sync.py' 2026-04-02T16:54:59,695 adding 'phynetpy/Traversal.py' 2026-04-02T16:54:59,701 adding 'phynetpy/Validation.py' 2026-04-02T16:54:59,703 adding 'phynetpy/Visitor.py' 2026-04-02T16:54:59,705 adding 'phynetpy/__init__.py' 2026-04-02T16:54:59,706 adding 'phynetpy/graph_core.py' 2026-04-02T16:54:59,709 adding 'phynetpy-0.3.2.dist-info/licenses/LICENSE' 2026-04-02T16:54:59,710 adding 'phynetpy-0.3.2.dist-info/METADATA' 2026-04-02T16:54:59,711 adding 'phynetpy-0.3.2.dist-info/WHEEL' 2026-04-02T16:54:59,712 adding 'phynetpy-0.3.2.dist-info/top_level.txt' 2026-04-02T16:54:59,713 adding 'phynetpy-0.3.2.dist-info/RECORD' 2026-04-02T16:54:59,717 removing build/bdist.linux-armv7l/wheel 2026-04-02T16:54:59,821 Building wheel for phynetpy (pyproject.toml): finished with status 'done' 2026-04-02T16:54:59,831 Created wheel for phynetpy: filename=phynetpy-0.3.2-py3-none-any.whl size=212887 sha256=ba8042b6f83249df5f08c62b9bbfb5c87a84e6001ef758b50dd009bb9a49e50b 2026-04-02T16:54:59,833 Stored in directory: /tmp/pip-ephem-wheel-cache-fclqwse9/wheels/3e/02/5f/55b621ad3e4193f7a0548e39d885efae455c08f7c473eb26e3 2026-04-02T16:54:59,844 Successfully built phynetpy 2026-04-02T16:54:59,855 Removed build tracker: '/tmp/pip-build-tracker-rvyuv_3u'