2025-11-10T19:01:48,494 Created temporary directory: /tmp/pip-ephem-wheel-cache-lafrt1e2 2025-11-10T19:01:48,496 Created temporary directory: /tmp/pip-build-tracker-6d3xn3lx 2025-11-10T19:01:48,496 Initialized build tracking at /tmp/pip-build-tracker-6d3xn3lx 2025-11-10T19:01:48,497 Created build tracker: /tmp/pip-build-tracker-6d3xn3lx 2025-11-10T19:01:48,497 Entered build tracker: /tmp/pip-build-tracker-6d3xn3lx 2025-11-10T19:01:48,498 Created temporary directory: /tmp/pip-wheel-w5sxhtxy 2025-11-10T19:01:48,501 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 2025-11-10T19:01:48,503 Created temporary directory: /tmp/pip-ephem-wheel-cache-rlh4_hry 2025-11-10T19:01:48,528 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-10T19:01:48,531 2 location(s) to search for versions of cryodrgn: 2025-11-10T19:01:48,531 * https://pypi.org/simple/cryodrgn/ 2025-11-10T19:01:48,531 * https://www.piwheels.org/simple/cryodrgn/ 2025-11-10T19:01:48,532 Fetching project page and analyzing links: https://pypi.org/simple/cryodrgn/ 2025-11-10T19:01:48,533 Getting page https://pypi.org/simple/cryodrgn/ 2025-11-10T19:01:48,534 Found index url https://pypi.org/simple 2025-11-10T19:01:48,749 Fetched page https://pypi.org/simple/cryodrgn/ as application/vnd.pypi.simple.v1+json 2025-11-10T19:01:48,760 Skipping link: No binaries permitted for cryodrgn: 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https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,763 Found link https://files.pythonhosted.org/packages/24/08/8de601e5f4fe8a5177c4191c0be1848d2952dad0ef149820aadadbee2e08/cryodrgn-1.1.1.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 1.1.1 2025-11-10T19:01:48,764 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/e9/78/bdf1fd8d9394a0025206a4d1478b21170d7392e35132522c5ef87855fe73/cryodrgn-2.1.0b5-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,765 Found link https://files.pythonhosted.org/packages/68/26/6669e39abe77e36bd49d1f21f68ed04961bdd0a76f909b497c96ce78b60b/cryodrgn-2.1.0b5.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 2.1.0b5 2025-11-10T19:01:48,766 Skipping link: No binaries permitted for cryodrgn: 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2025-11-10T19:01:48,770 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/03/29/f9750c89414937c8700d9d5aa167d9ed1e3157ebb6a9971effb4bcbe8bec/cryodrgn-2.3.0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,771 Found link https://files.pythonhosted.org/packages/d2/69/c5d8c6da2da86575a985307f67f214a0f56a7f79d73492a5184170ea7036/cryodrgn-2.3.0.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 2.3.0 2025-11-10T19:01:48,772 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/08/8d/d0ff2954b5825e3b771a943b40423d57195aec5c30d4b770250ac822c7fe/cryodrgn-3.0.0b0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,772 Found link https://files.pythonhosted.org/packages/74/92/6ca0ee245ed52438a0f471cfb29de766b9822010f760da08875be946e827/cryodrgn-3.0.0b0.tar.gz (from 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https://pypi.org/simple/cryodrgn/) (requires-python:>=3.9), version: 3.4.4 2025-11-10T19:01:48,801 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/b7/88/eddacf1ad562b9ed746f062d9d4da95a3184417c03e27f473a2d22497771/cryodrgn-3.5.1-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10) 2025-11-10T19:01:48,802 Found link https://files.pythonhosted.org/packages/a1/22/8263a1c7e8fef9c7e7590b4b788a1952e4386c1eaa1b0faf647cf57c8308/cryodrgn-3.5.1.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10), version: 3.5.1 2025-11-10T19:01:48,803 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/1b/c5/b59b20d7a3670e09d36663c07312fde9375702878385139ed3358753ac59/cryodrgn-3.5.2-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10) 2025-11-10T19:01:48,804 Found link https://files.pythonhosted.org/packages/8b/b8/d392481c21db6cc1e383543965f09be40bc5e6ed451cacd03fcc45bd7379/cryodrgn-3.5.2.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10), version: 3.5.2 2025-11-10T19:01:48,805 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/c8/48/8eb8df7ec4385ecbd2a30bb39a7b36b9653953e162f61b74d95e990d8f24/cryodrgn-3.5.3-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10) 2025-11-10T19:01:48,806 Found link https://files.pythonhosted.org/packages/29/ad/0e403482ee28fb4b112c6fcd8eb29aff4f753c435ad03d685b871fb87c03/cryodrgn-3.5.3.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10), version: 3.5.3 2025-11-10T19:01:48,807 Fetching project page and analyzing links: https://www.piwheels.org/simple/cryodrgn/ 2025-11-10T19:01:48,807 Getting page https://www.piwheels.org/simple/cryodrgn/ 2025-11-10T19:01:48,809 Found index url https://www.piwheels.org/simple 2025-11-10T19:01:48,965 Fetched page https://www.piwheels.org/simple/cryodrgn/ as text/html 2025-11-10T19:01:48,972 Skipping link: No binaries permitted for cryodrgn: https://www.piwheels.org/simple/cryodrgn/cryodrgn-3.5.2-py3-none-any.whl#sha256=8cf4d2cfd750554ff4299eb72c2d9ed7fcdf5cf044d4f9638b8f9aed7f66bd83 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.10) 2025-11-10T19:01:48,973 Skipping link: No binaries permitted for cryodrgn: https://www.piwheels.org/simple/cryodrgn/cryodrgn-3.5.1-py3-none-any.whl#sha256=008b711ead8826c56e3c01d294a1d7958ebc7cbf8cfff9d4a64eb6892e393571 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.10) 2025-11-10T19:01:48,974 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.4.4-py3-none-any.whl#sha256=6ce8eadc8e7bd354fbb76c24a00fe7630579b2fbdb0c1a69bda17b8bb5ac8ea2 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.9) 2025-11-10T19:01:48,974 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.4.3-py3-none-any.whl#sha256=16ba324b6eee8de6c97fc40e0dc06a623eed747224e79f90a871e5a8f8934eab (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.12,>=3.9) 2025-11-10T19:01:48,975 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.4.2-py3-none-any.whl#sha256=6913c52d9139200123201a423a239c5fbe6441d8dd1765f118d191346bf814ce (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.12,>=3.9) 2025-11-10T19:01:48,975 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.4.1-py3-none-any.whl#sha256=9e734bf886da487b675d889b8ab3b83d6c95722c5a465b23220a2389267cd18a (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.12,>=3.9) 2025-11-10T19:01:48,976 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.4.0-py3-none-any.whl#sha256=ecbff0c320b388bc334bf4b12441a44e659edba651fc658607334371c1dbf22c (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.12,>=3.9) 2025-11-10T19:01:48,976 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.3.3-py3-none-any.whl#sha256=ff7c01a3ef9512e092ed9f9c11a163cc4a9c99f25678455ad500d4dca322f1a0 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.9) 2025-11-10T19:01:48,977 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.3.2-py3-none-any.whl#sha256=23d9324f04d89f7f6e7fcbfc4a4c90a979798fd294a840d8b07c919f6aef1817 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.9) 2025-11-10T19:01:48,978 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.3.1-py3-none-any.whl#sha256=647299cf3549465b1c2b7296e0c48b83e6208d693322dabfa10b5918d4f09358 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.9) 2025-11-10T19:01:48,978 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.3.0-py3-none-any.whl#sha256=8aae2a2c492aa891d21c236a7fbf48e454224d80748853e92d58f624f2bee91a (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.9) 2025-11-10T19:01:48,979 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.2.0b0-py3-none-any.whl#sha256=9be035b539a141bdf9a3a5e223ab2d5eac88e2e8342e4fbdf2aa106b91dd220b (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.7) 2025-11-10T19:01:48,979 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.2.0a1-py3-none-any.whl#sha256=a23e8245ce860c4122cef6f81db6fe3918ab253dab52b10afd0e4f65d9428b3e (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.7) 2025-11-10T19:01:48,980 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.2.0a0-py3-none-any.whl#sha256=ea2d2f810968f04912365abdce1cf74f011e1b5be2b671a741a705ef827f2d4a (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.7) 2025-11-10T19:01:48,980 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.1.0b0-py3-none-any.whl#sha256=929d0ff6af693745b3d438a6e7462cc2845e60d49457cd383b6b17b01778017c (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,981 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.0.1b0-py3-none-any.whl#sha256=c5aa67408ca576f776a9b8a331b966eb87343cb2d3713e29768705555e85f930 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,981 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.0.0b0-py3-none-any.whl#sha256=498fba8644092d42d124e88b81d7209e358d25ea05720b664bd44c454eb221a2 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,982 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-2.3.0-py3-none-any.whl#sha256=d3f519ed4819eac7456ccee2c974e41070b80d0e895797cf940ea8b8ca729631 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,982 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-2.2.0-py3-none-any.whl#sha256=6d705695a229d236db29c0b847f18e336bc53358ef3bc125cb158bd743f53bc9 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,983 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-2.2.0b0-py3-none-any.whl#sha256=ded8ccf2e343961488fc50ee73479e8c5a9bc61dd79a83f509f96e86c01e9306 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,983 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-2.1.0b5-py3-none-any.whl#sha256=f43221397e48ac64c02c3009e927ea1212a8ad59ed1e20421a65287c9e853652 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,984 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-1.1.1-py3-none-any.whl#sha256=b3cc3928fe1cc0f347265449cd329a61f3b7eadb9f833c26748b681c220cb4ad (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7) 2025-11-10T19:01:48,985 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-0.20.0-py3-none-any.whl#sha256=717a2f51d76e34a261789323999467e1716afd1588ee2b5ab9784100649a0453 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:<3.11,>=3.9) 2025-11-10T19:01:48,985 Skipping link: not a file: https://www.piwheels.org/simple/cryodrgn/ 2025-11-10T19:01:48,986 Skipping link: not a file: https://pypi.org/simple/cryodrgn/ 2025-11-10T19:01:49,006 Given no hashes to check 1 links for project 'cryodrgn': discarding no candidates 2025-11-10T19:01:49,024 Collecting cryodrgn==3.5.3 2025-11-10T19:01:49,027 Created temporary directory: /tmp/pip-unpack-fdjefiaf 2025-11-10T19:01:49,190 Downloading cryodrgn-3.5.3.tar.gz (15.5 MB) 2025-11-10T19:01:52,443 Added cryodrgn==3.5.3 from https://files.pythonhosted.org/packages/29/ad/0e403482ee28fb4b112c6fcd8eb29aff4f753c435ad03d685b871fb87c03/cryodrgn-3.5.3.tar.gz to build tracker '/tmp/pip-build-tracker-6d3xn3lx' 2025-11-10T19:01:52,449 Created temporary directory: /tmp/pip-build-env-tbtbysus 2025-11-10T19:01:52,454 Installing build dependencies: started 2025-11-10T19:01:52,455 Running command pip subprocess to install build dependencies 2025-11-10T19:01:53,595 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-11-10T19:01:54,202 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 2025-11-10T19:01:54,226 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-10T19:01:55,993 Collecting setuptools>=61.0 2025-11-10T19:01:56,096 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-11-10T19:01:56,497 Collecting setuptools_scm>=6.2 2025-11-10T19:01:56,515 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-9.2.2-py3-none-any.whl (62 kB) 2025-11-10T19:01:56,709 Collecting packaging>=20 2025-11-10T19:01:56,726 Using cached https://www.piwheels.org/simple/packaging/packaging-25.0-py3-none-any.whl (66 kB) 2025-11-10T19:01:59,660 Installing collected packages: setuptools, packaging, setuptools_scm 2025-11-10T19:02:03,580 Creating /tmp/pip-build-env-tbtbysus/overlay/local/bin 2025-11-10T19:02:03,582 changing mode of /tmp/pip-build-env-tbtbysus/overlay/local/bin/setuptools-scm to 755 2025-11-10T19:02:03,605 Successfully installed packaging-25.0 setuptools-80.9.0 setuptools_scm-9.2.2 2025-11-10T19:02:03,885 Installing build dependencies: finished with status 'done' 2025-11-10T19:02:03,892 Getting requirements to build wheel: started 2025-11-10T19:02:03,893 Running command Getting requirements to build wheel 2025-11-10T19:02:04,686 /tmp/pip-build-env-tbtbysus/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-11-10T19:02:04,687 !! 2025-11-10T19:02:04,688 ******************************************************************************** 2025-11-10T19:02:04,688 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-11-10T19:02:04,690 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-11-10T19:02:04,691 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-10T19:02:04,691 ******************************************************************************** 2025-11-10T19:02:04,693 !! 2025-11-10T19:02:04,693 dist._finalize_license_expression() 2025-11-10T19:02:04,694 /tmp/pip-build-env-tbtbysus/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-11-10T19:02:04,694 !! 2025-11-10T19:02:04,696 ******************************************************************************** 2025-11-10T19:02:04,696 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-11-10T19:02:04,698 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-11-10T19:02:04,699 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-10T19:02:04,699 ******************************************************************************** 2025-11-10T19:02:04,700 !! 2025-11-10T19:02:04,701 self._finalize_license_expression() 2025-11-10T19:02:04,701 running egg_info 2025-11-10T19:02:04,710 writing cryodrgn.egg-info/PKG-INFO 2025-11-10T19:02:04,717 writing dependency_links to cryodrgn.egg-info/dependency_links.txt 2025-11-10T19:02:04,719 writing entry points to cryodrgn.egg-info/entry_points.txt 2025-11-10T19:02:04,723 writing requirements to cryodrgn.egg-info/requires.txt 2025-11-10T19:02:04,724 writing top-level names to cryodrgn.egg-info/top_level.txt 2025-11-10T19:02:04,780 listing git files failed - pretending there aren't any 2025-11-10T19:02:04,785 reading manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-11-10T19:02:04,798 reading manifest template 'MANIFEST.in' 2025-11-10T19:02:04,800 adding license file 'LICENSE.txt' 2025-11-10T19:02:04,809 writing manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-11-10T19:02:04,912 Getting requirements to build wheel: finished with status 'done' 2025-11-10T19:02:04,915 Created temporary directory: /tmp/pip-modern-metadata-vhdz24e9 2025-11-10T19:02:04,918 Preparing metadata (pyproject.toml): started 2025-11-10T19:02:04,919 Running command Preparing metadata (pyproject.toml) 2025-11-10T19:02:05,674 /tmp/pip-build-env-tbtbysus/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-11-10T19:02:05,674 !! 2025-11-10T19:02:05,675 ******************************************************************************** 2025-11-10T19:02:05,676 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-11-10T19:02:05,677 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-11-10T19:02:05,678 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-10T19:02:05,679 ******************************************************************************** 2025-11-10T19:02:05,680 !! 2025-11-10T19:02:05,681 dist._finalize_license_expression() 2025-11-10T19:02:05,682 /tmp/pip-build-env-tbtbysus/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-11-10T19:02:05,682 !! 2025-11-10T19:02:05,684 ******************************************************************************** 2025-11-10T19:02:05,684 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-11-10T19:02:05,685 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-11-10T19:02:05,687 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-10T19:02:05,687 ******************************************************************************** 2025-11-10T19:02:05,688 !! 2025-11-10T19:02:05,689 self._finalize_license_expression() 2025-11-10T19:02:05,690 running dist_info 2025-11-10T19:02:05,705 creating /tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info 2025-11-10T19:02:05,706 writing /tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/PKG-INFO 2025-11-10T19:02:05,713 writing dependency_links to /tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/dependency_links.txt 2025-11-10T19:02:05,715 writing entry points to /tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/entry_points.txt 2025-11-10T19:02:05,718 writing requirements to /tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/requires.txt 2025-11-10T19:02:05,720 writing top-level names to /tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/top_level.txt 2025-11-10T19:02:05,721 writing manifest file '/tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/SOURCES.txt' 2025-11-10T19:02:05,771 listing git files failed - pretending there aren't any 2025-11-10T19:02:05,776 reading manifest file '/tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/SOURCES.txt' 2025-11-10T19:02:05,778 reading manifest template 'MANIFEST.in' 2025-11-10T19:02:05,779 adding license file 'LICENSE.txt' 2025-11-10T19:02:05,785 writing manifest file '/tmp/pip-modern-metadata-vhdz24e9/cryodrgn.egg-info/SOURCES.txt' 2025-11-10T19:02:05,786 creating '/tmp/pip-modern-metadata-vhdz24e9/cryodrgn-3.5.3.dist-info' 2025-11-10T19:02:05,924 Preparing metadata (pyproject.toml): finished with status 'done' 2025-11-10T19:02:05,930 Source in /tmp/pip-wheel-w5sxhtxy/cryodrgn_37bede2cb6f84b5f928b469dfe4477b5 has version 3.5.3, which satisfies requirement cryodrgn==3.5.3 from https://files.pythonhosted.org/packages/29/ad/0e403482ee28fb4b112c6fcd8eb29aff4f753c435ad03d685b871fb87c03/cryodrgn-3.5.3.tar.gz 2025-11-10T19:02:05,931 Removed cryodrgn==3.5.3 from https://files.pythonhosted.org/packages/29/ad/0e403482ee28fb4b112c6fcd8eb29aff4f753c435ad03d685b871fb87c03/cryodrgn-3.5.3.tar.gz from build tracker '/tmp/pip-build-tracker-6d3xn3lx' 2025-11-10T19:02:05,939 Created temporary directory: /tmp/pip-unpack-k9w5notv 2025-11-10T19:02:05,939 Building wheels for collected packages: cryodrgn 2025-11-10T19:02:05,944 Created temporary directory: /tmp/pip-wheel-pnxfldw_ 2025-11-10T19:02:05,944 Destination directory: /tmp/pip-wheel-pnxfldw_ 2025-11-10T19:02:05,946 Building wheel for cryodrgn (pyproject.toml): started 2025-11-10T19:02:05,948 Running command Building wheel for cryodrgn (pyproject.toml) 2025-11-10T19:02:06,707 /tmp/pip-build-env-tbtbysus/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-11-10T19:02:06,707 !! 2025-11-10T19:02:06,708 ******************************************************************************** 2025-11-10T19:02:06,709 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-11-10T19:02:06,710 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-11-10T19:02:06,711 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-10T19:02:06,712 ******************************************************************************** 2025-11-10T19:02:06,713 !! 2025-11-10T19:02:06,714 dist._finalize_license_expression() 2025-11-10T19:02:06,714 /tmp/pip-build-env-tbtbysus/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-11-10T19:02:06,715 !! 2025-11-10T19:02:06,716 ******************************************************************************** 2025-11-10T19:02:06,716 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-11-10T19:02:06,718 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-11-10T19:02:06,719 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-11-10T19:02:06,720 ******************************************************************************** 2025-11-10T19:02:06,721 !! 2025-11-10T19:02:06,721 self._finalize_license_expression() 2025-11-10T19:02:06,722 running bdist_wheel 2025-11-10T19:02:06,741 running build 2025-11-10T19:02:06,741 running build_py 2025-11-10T19:02:06,750 creating build/lib/cryodrgn 2025-11-10T19:02:06,752 copying cryodrgn/make_healpy.py -> build/lib/cryodrgn 2025-11-10T19:02:06,754 copying cryodrgn/fft.py -> build/lib/cryodrgn 2025-11-10T19:02:06,756 copying cryodrgn/source.py -> build/lib/cryodrgn 2025-11-10T19:02:06,759 copying cryodrgn/command_line.py -> build/lib/cryodrgn 2025-11-10T19:02:06,762 copying cryodrgn/ctf.py -> build/lib/cryodrgn 2025-11-10T19:02:06,764 copying cryodrgn/so3_grid.py -> build/lib/cryodrgn 2025-11-10T19:02:06,766 copying cryodrgn/_version.py -> build/lib/cryodrgn 2025-11-10T19:02:06,768 copying cryodrgn/shift_grid.py -> build/lib/cryodrgn 2025-11-10T19:02:06,770 copying cryodrgn/config.py -> build/lib/cryodrgn 2025-11-10T19:02:06,772 copying cryodrgn/starfile.py -> build/lib/cryodrgn 2025-11-10T19:02:06,774 copying cryodrgn/masking.py -> build/lib/cryodrgn 2025-11-10T19:02:06,776 copying cryodrgn/lattice.py -> build/lib/cryodrgn 2025-11-10T19:02:06,779 copying cryodrgn/pose.py -> build/lib/cryodrgn 2025-11-10T19:02:06,781 copying cryodrgn/pose_search.py -> build/lib/cryodrgn 2025-11-10T19:02:06,783 copying cryodrgn/beta_schedule.py -> build/lib/cryodrgn 2025-11-10T19:02:06,785 copying cryodrgn/losses.py -> build/lib/cryodrgn 2025-11-10T19:02:06,787 copying cryodrgn/models.py -> build/lib/cryodrgn 2025-11-10T19:02:06,790 copying cryodrgn/utils.py -> build/lib/cryodrgn 2025-11-10T19:02:06,792 copying cryodrgn/analysis.py -> build/lib/cryodrgn 2025-11-10T19:02:06,795 copying cryodrgn/shift_grid3.py -> build/lib/cryodrgn 2025-11-10T19:02:06,797 copying cryodrgn/mrcfile.py -> build/lib/cryodrgn 2025-11-10T19:02:06,799 copying cryodrgn/__init__.py -> build/lib/cryodrgn 2025-11-10T19:02:06,801 copying cryodrgn/lie_tools.py -> build/lib/cryodrgn 2025-11-10T19:02:06,803 copying cryodrgn/dataset.py -> build/lib/cryodrgn 2025-11-10T19:02:06,807 creating build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,808 copying cryodrgn/commands_utils/add_psize.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,810 copying cryodrgn/commands_utils/filter_star.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,812 copying cryodrgn/commands_utils/plot_classes.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,815 copying cryodrgn/commands_utils/clean.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,818 copying cryodrgn/commands_utils/write_cs.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,820 copying cryodrgn/commands_utils/select_random.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,822 copying cryodrgn/commands_utils/write_star.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,824 copying cryodrgn/commands_utils/filter_cs.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,826 copying cryodrgn/commands_utils/make_movies.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,828 copying cryodrgn/commands_utils/fsc.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,831 copying cryodrgn/commands_utils/gen_mask.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,833 copying cryodrgn/commands_utils/plot_fsc.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,835 copying cryodrgn/commands_utils/invert_contrast.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,837 copying cryodrgn/commands_utils/view_mrcs.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,839 copying cryodrgn/commands_utils/concat_pkls.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,841 copying cryodrgn/commands_utils/filter_pkl.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,843 copying cryodrgn/commands_utils/select_clusters.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,845 copying cryodrgn/commands_utils/parse_relion.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,848 copying cryodrgn/commands_utils/__init__.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,849 copying cryodrgn/commands_utils/phase_flip.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,851 copying cryodrgn/commands_utils/flip_hand.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,853 copying cryodrgn/commands_utils/translate_mrcs.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,855 copying cryodrgn/commands_utils/analyze_convergence.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,859 copying cryodrgn/commands_utils/view_header.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,861 copying cryodrgn/commands_utils/filter_mrcs.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,863 copying cryodrgn/commands_utils/view_cs_header.py -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:06,865 creating build/lib/cryodrgn/commands 2025-11-10T19:02:06,866 copying cryodrgn/commands/abinit_homo.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,869 copying cryodrgn/commands/train_vae.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,872 copying cryodrgn/commands/analyze_landscape_full.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,875 copying cryodrgn/commands/direct_traversal.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,877 copying cryodrgn/commands/graph_traversal.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,879 copying cryodrgn/commands/parse_ctf_csparc.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,881 copying cryodrgn/commands/abinit_het.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,884 copying cryodrgn/commands/filter.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,887 copying cryodrgn/commands/analyze_landscape.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,889 copying cryodrgn/commands/downsample.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,892 copying cryodrgn/commands/pc_traversal.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,894 copying cryodrgn/commands/analyze.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,896 copying cryodrgn/commands/parse_ctf_star.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,898 copying cryodrgn/commands/parse_star.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,900 copying cryodrgn/commands/backproject_voxel.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,903 copying cryodrgn/commands/parse_pose_csparc.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,905 copying cryodrgn/commands/eval_vol.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,907 copying cryodrgn/commands/train_nn.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,910 copying cryodrgn/commands/train_dec.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,912 copying cryodrgn/commands/__init__.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,914 copying cryodrgn/commands/eval_images.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,917 copying cryodrgn/commands/parse_pose_star.py -> build/lib/cryodrgn/commands 2025-11-10T19:02:06,919 running egg_info 2025-11-10T19:02:06,933 writing cryodrgn.egg-info/PKG-INFO 2025-11-10T19:02:06,940 writing dependency_links to cryodrgn.egg-info/dependency_links.txt 2025-11-10T19:02:06,942 writing entry points to cryodrgn.egg-info/entry_points.txt 2025-11-10T19:02:06,945 writing requirements to cryodrgn.egg-info/requires.txt 2025-11-10T19:02:06,946 writing top-level names to cryodrgn.egg-info/top_level.txt 2025-11-10T19:02:06,986 listing git files failed - pretending there aren't any 2025-11-10T19:02:06,990 reading manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-11-10T19:02:07,002 reading manifest template 'MANIFEST.in' 2025-11-10T19:02:07,003 adding license file 'LICENSE.txt' 2025-11-10T19:02:07,013 writing manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-11-10T19:02:07,020 copying cryodrgn/healpy_grid.json -> build/lib/cryodrgn 2025-11-10T19:02:07,492 creating build/lib/cryodrgn/templates 2025-11-10T19:02:07,493 copying cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/lib/cryodrgn/templates 2025-11-10T19:02:07,497 copying cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/lib/cryodrgn/templates 2025-11-10T19:02:07,500 copying cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/lib/cryodrgn/templates 2025-11-10T19:02:07,502 copying cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/lib/cryodrgn/templates 2025-11-10T19:02:07,505 copying cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/lib/cryodrgn/templates 2025-11-10T19:02:07,508 copying cryodrgn/commands_utils/README.md -> build/lib/cryodrgn/commands_utils 2025-11-10T19:02:07,511 copying cryodrgn/commands/README.md -> build/lib/cryodrgn/commands 2025-11-10T19:02:07,529 installing to build/bdist.linux-armv7l/wheel 2025-11-10T19:02:07,530 running install 2025-11-10T19:02:07,553 running install_lib 2025-11-10T19:02:07,561 creating build/bdist.linux-armv7l/wheel 2025-11-10T19:02:07,564 creating build/bdist.linux-armv7l/wheel/cryodrgn 2025-11-10T19:02:07,565 creating build/bdist.linux-armv7l/wheel/cryodrgn/templates 2025-11-10T19:02:07,566 copying build/lib/cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-11-10T19:02:07,569 copying build/lib/cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-11-10T19:02:07,571 copying build/lib/cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-11-10T19:02:07,574 copying build/lib/cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-11-10T19:02:07,576 copying build/lib/cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-11-10T19:02:07,579 copying build/lib/cryodrgn/make_healpy.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,581 creating build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils 2025-11-10T19:02:07,583 copying build/lib/cryodrgn/commands_utils/add_psize.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,584 copying build/lib/cryodrgn/commands_utils/filter_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,586 copying build/lib/cryodrgn/commands_utils/plot_classes.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,588 copying build/lib/cryodrgn/commands_utils/clean.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,591 copying build/lib/cryodrgn/commands_utils/write_cs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,592 copying build/lib/cryodrgn/commands_utils/select_random.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,594 copying build/lib/cryodrgn/commands_utils/write_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,596 copying build/lib/cryodrgn/commands_utils/filter_cs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,598 copying build/lib/cryodrgn/commands_utils/make_movies.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,600 copying build/lib/cryodrgn/commands_utils/fsc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,603 copying build/lib/cryodrgn/commands_utils/gen_mask.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,605 copying build/lib/cryodrgn/commands_utils/plot_fsc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,607 copying build/lib/cryodrgn/commands_utils/invert_contrast.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,609 copying build/lib/cryodrgn/commands_utils/view_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,611 copying build/lib/cryodrgn/commands_utils/concat_pkls.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,613 copying build/lib/cryodrgn/commands_utils/filter_pkl.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,614 copying build/lib/cryodrgn/commands_utils/select_clusters.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,616 copying build/lib/cryodrgn/commands_utils/parse_relion.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,619 copying build/lib/cryodrgn/commands_utils/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,620 copying build/lib/cryodrgn/commands_utils/phase_flip.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,622 copying build/lib/cryodrgn/commands_utils/flip_hand.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,624 copying build/lib/cryodrgn/commands_utils/README.md -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,626 copying build/lib/cryodrgn/commands_utils/translate_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,627 copying build/lib/cryodrgn/commands_utils/analyze_convergence.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,630 copying build/lib/cryodrgn/commands_utils/view_header.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,632 copying build/lib/cryodrgn/commands_utils/filter_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,634 copying build/lib/cryodrgn/commands_utils/view_cs_header.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-11-10T19:02:07,635 copying build/lib/cryodrgn/fft.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,637 copying build/lib/cryodrgn/source.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,640 copying build/lib/cryodrgn/command_line.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,642 copying build/lib/cryodrgn/ctf.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,644 copying build/lib/cryodrgn/so3_grid.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,646 copying build/lib/cryodrgn/_version.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,648 copying build/lib/cryodrgn/shift_grid.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,651 creating build/bdist.linux-armv7l/wheel/cryodrgn/commands 2025-11-10T19:02:07,652 copying build/lib/cryodrgn/commands/abinit_homo.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,654 copying build/lib/cryodrgn/commands/train_vae.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,657 copying build/lib/cryodrgn/commands/analyze_landscape_full.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,659 copying build/lib/cryodrgn/commands/direct_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,661 copying build/lib/cryodrgn/commands/graph_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,664 copying build/lib/cryodrgn/commands/parse_ctf_csparc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,666 copying build/lib/cryodrgn/commands/abinit_het.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,669 copying build/lib/cryodrgn/commands/filter.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,672 copying build/lib/cryodrgn/commands/analyze_landscape.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,674 copying build/lib/cryodrgn/commands/downsample.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,677 copying build/lib/cryodrgn/commands/pc_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,679 copying build/lib/cryodrgn/commands/analyze.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,681 copying build/lib/cryodrgn/commands/parse_ctf_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,683 copying build/lib/cryodrgn/commands/parse_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,685 copying build/lib/cryodrgn/commands/backproject_voxel.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,688 copying build/lib/cryodrgn/commands/parse_pose_csparc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,689 copying build/lib/cryodrgn/commands/eval_vol.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,692 copying build/lib/cryodrgn/commands/train_nn.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,694 copying build/lib/cryodrgn/commands/train_dec.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,697 copying build/lib/cryodrgn/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,698 copying build/lib/cryodrgn/commands/eval_images.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,700 copying build/lib/cryodrgn/commands/README.md -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,702 copying build/lib/cryodrgn/commands/parse_pose_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-11-10T19:02:07,704 copying build/lib/cryodrgn/config.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,706 copying build/lib/cryodrgn/starfile.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,708 copying build/lib/cryodrgn/masking.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,710 copying build/lib/cryodrgn/lattice.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,712 copying build/lib/cryodrgn/pose.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,714 copying build/lib/cryodrgn/pose_search.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,717 copying build/lib/cryodrgn/beta_schedule.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,719 copying build/lib/cryodrgn/losses.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,721 copying build/lib/cryodrgn/models.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,724 copying build/lib/cryodrgn/utils.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,726 copying build/lib/cryodrgn/analysis.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:07,940 copying build/lib/cryodrgn/healpy_grid.json -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:08,135 copying build/lib/cryodrgn/shift_grid3.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:08,137 copying build/lib/cryodrgn/mrcfile.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:08,140 copying build/lib/cryodrgn/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:08,142 copying build/lib/cryodrgn/lie_tools.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:08,144 copying build/lib/cryodrgn/dataset.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-11-10T19:02:08,146 running install_egg_info 2025-11-10T19:02:08,153 Copying cryodrgn.egg-info to build/bdist.linux-armv7l/wheel/./cryodrgn-3.5.3-py3.11.egg-info 2025-11-10T19:02:08,168 running install_scripts 2025-11-10T19:02:08,181 creating build/bdist.linux-armv7l/wheel/cryodrgn-3.5.3.dist-info/WHEEL 2025-11-10T19:02:08,184 creating '/tmp/pip-wheel-pnxfldw_/.tmp-dq0ohvk1/cryodrgn-3.5.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-10T19:02:08,187 adding 'cryodrgn/__init__.py' 2025-11-10T19:02:08,189 adding 'cryodrgn/_version.py' 2025-11-10T19:02:08,191 adding 'cryodrgn/analysis.py' 2025-11-10T19:02:08,193 adding 'cryodrgn/beta_schedule.py' 2025-11-10T19:02:08,194 adding 'cryodrgn/command_line.py' 2025-11-10T19:02:08,196 adding 'cryodrgn/config.py' 2025-11-10T19:02:08,198 adding 'cryodrgn/ctf.py' 2025-11-10T19:02:08,200 adding 'cryodrgn/dataset.py' 2025-11-10T19:02:08,202 adding 'cryodrgn/fft.py' 2025-11-10T19:02:08,967 adding 'cryodrgn/healpy_grid.json' 2025-11-10T19:02:09,033 adding 'cryodrgn/lattice.py' 2025-11-10T19:02:09,034 adding 'cryodrgn/lie_tools.py' 2025-11-10T19:02:09,036 adding 'cryodrgn/losses.py' 2025-11-10T19:02:09,037 adding 'cryodrgn/make_healpy.py' 2025-11-10T19:02:09,039 adding 'cryodrgn/masking.py' 2025-11-10T19:02:09,043 adding 'cryodrgn/models.py' 2025-11-10T19:02:09,045 adding 'cryodrgn/mrcfile.py' 2025-11-10T19:02:09,046 adding 'cryodrgn/pose.py' 2025-11-10T19:02:09,049 adding 'cryodrgn/pose_search.py' 2025-11-10T19:02:09,050 adding 'cryodrgn/shift_grid.py' 2025-11-10T19:02:09,051 adding 'cryodrgn/shift_grid3.py' 2025-11-10T19:02:09,053 adding 'cryodrgn/so3_grid.py' 2025-11-10T19:02:09,056 adding 'cryodrgn/source.py' 2025-11-10T19:02:09,058 adding 'cryodrgn/starfile.py' 2025-11-10T19:02:09,060 adding 'cryodrgn/utils.py' 2025-11-10T19:02:09,062 adding 'cryodrgn/commands/README.md' 2025-11-10T19:02:09,063 adding 'cryodrgn/commands/__init__.py' 2025-11-10T19:02:09,067 adding 'cryodrgn/commands/abinit_het.py' 2025-11-10T19:02:09,070 adding 'cryodrgn/commands/abinit_homo.py' 2025-11-10T19:02:09,073 adding 'cryodrgn/commands/analyze.py' 2025-11-10T19:02:09,076 adding 'cryodrgn/commands/analyze_landscape.py' 2025-11-10T19:02:09,078 adding 'cryodrgn/commands/analyze_landscape_full.py' 2025-11-10T19:02:09,081 adding 'cryodrgn/commands/backproject_voxel.py' 2025-11-10T19:02:09,082 adding 'cryodrgn/commands/direct_traversal.py' 2025-11-10T19:02:09,084 adding 'cryodrgn/commands/downsample.py' 2025-11-10T19:02:09,087 adding 'cryodrgn/commands/eval_images.py' 2025-11-10T19:02:09,089 adding 'cryodrgn/commands/eval_vol.py' 2025-11-10T19:02:09,091 adding 'cryodrgn/commands/filter.py' 2025-11-10T19:02:09,093 adding 'cryodrgn/commands/graph_traversal.py' 2025-11-10T19:02:09,095 adding 'cryodrgn/commands/parse_ctf_csparc.py' 2025-11-10T19:02:09,096 adding 'cryodrgn/commands/parse_ctf_star.py' 2025-11-10T19:02:09,097 adding 'cryodrgn/commands/parse_pose_csparc.py' 2025-11-10T19:02:09,099 adding 'cryodrgn/commands/parse_pose_star.py' 2025-11-10T19:02:09,100 adding 'cryodrgn/commands/parse_star.py' 2025-11-10T19:02:09,101 adding 'cryodrgn/commands/pc_traversal.py' 2025-11-10T19:02:09,104 adding 'cryodrgn/commands/train_dec.py' 2025-11-10T19:02:09,107 adding 'cryodrgn/commands/train_nn.py' 2025-11-10T19:02:09,111 adding 'cryodrgn/commands/train_vae.py' 2025-11-10T19:02:09,113 adding 'cryodrgn/commands_utils/README.md' 2025-11-10T19:02:09,114 adding 'cryodrgn/commands_utils/__init__.py' 2025-11-10T19:02:09,116 adding 'cryodrgn/commands_utils/add_psize.py' 2025-11-10T19:02:09,121 adding 'cryodrgn/commands_utils/analyze_convergence.py' 2025-11-10T19:02:09,123 adding 'cryodrgn/commands_utils/clean.py' 2025-11-10T19:02:09,125 adding 'cryodrgn/commands_utils/concat_pkls.py' 2025-11-10T19:02:09,126 adding 'cryodrgn/commands_utils/filter_cs.py' 2025-11-10T19:02:09,128 adding 'cryodrgn/commands_utils/filter_mrcs.py' 2025-11-10T19:02:09,129 adding 'cryodrgn/commands_utils/filter_pkl.py' 2025-11-10T19:02:09,130 adding 'cryodrgn/commands_utils/filter_star.py' 2025-11-10T19:02:09,132 adding 'cryodrgn/commands_utils/flip_hand.py' 2025-11-10T19:02:09,134 adding 'cryodrgn/commands_utils/fsc.py' 2025-11-10T19:02:09,135 adding 'cryodrgn/commands_utils/gen_mask.py' 2025-11-10T19:02:09,137 adding 'cryodrgn/commands_utils/invert_contrast.py' 2025-11-10T19:02:09,138 adding 'cryodrgn/commands_utils/make_movies.py' 2025-11-10T19:02:09,141 adding 'cryodrgn/commands_utils/parse_relion.py' 2025-11-10T19:02:09,142 adding 'cryodrgn/commands_utils/phase_flip.py' 2025-11-10T19:02:09,144 adding 'cryodrgn/commands_utils/plot_classes.py' 2025-11-10T19:02:09,145 adding 'cryodrgn/commands_utils/plot_fsc.py' 2025-11-10T19:02:09,147 adding 'cryodrgn/commands_utils/select_clusters.py' 2025-11-10T19:02:09,148 adding 'cryodrgn/commands_utils/select_random.py' 2025-11-10T19:02:09,149 adding 'cryodrgn/commands_utils/translate_mrcs.py' 2025-11-10T19:02:09,151 adding 'cryodrgn/commands_utils/view_cs_header.py' 2025-11-10T19:02:09,152 adding 'cryodrgn/commands_utils/view_header.py' 2025-11-10T19:02:09,153 adding 'cryodrgn/commands_utils/view_mrcs.py' 2025-11-10T19:02:09,154 adding 'cryodrgn/commands_utils/write_cs.py' 2025-11-10T19:02:09,156 adding 'cryodrgn/commands_utils/write_star.py' 2025-11-10T19:02:09,160 adding 'cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb' 2025-11-10T19:02:09,162 adding 'cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb' 2025-11-10T19:02:09,164 adding 'cryodrgn/templates/cryoDRGN_figures_template.ipynb' 2025-11-10T19:02:09,167 adding 'cryodrgn/templates/cryoDRGN_filtering_template.ipynb' 2025-11-10T19:02:09,170 adding 'cryodrgn/templates/cryoDRGN_viz_template.ipynb' 2025-11-10T19:02:09,177 adding 'cryodrgn-3.5.3.dist-info/licenses/LICENSE.txt' 2025-11-10T19:02:09,181 adding 'cryodrgn-3.5.3.dist-info/METADATA' 2025-11-10T19:02:09,182 adding 'cryodrgn-3.5.3.dist-info/WHEEL' 2025-11-10T19:02:09,183 adding 'cryodrgn-3.5.3.dist-info/entry_points.txt' 2025-11-10T19:02:09,184 adding 'cryodrgn-3.5.3.dist-info/top_level.txt' 2025-11-10T19:02:09,186 adding 'cryodrgn-3.5.3.dist-info/RECORD' 2025-11-10T19:02:09,199 removing build/bdist.linux-armv7l/wheel 2025-11-10T19:02:09,326 Building wheel for cryodrgn (pyproject.toml): finished with status 'done' 2025-11-10T19:02:09,358 Created wheel for cryodrgn: filename=cryodrgn-3.5.3-py3-none-any.whl size=1216113 sha256=ed61d74174cf39f0b51d1b7dd04be400b134f0bdacac2785bd2bd240da78ab10 2025-11-10T19:02:09,359 Stored in directory: /tmp/pip-ephem-wheel-cache-rlh4_hry/wheels/7b/35/7e/f08615caec80e22f28f9fb098ddc458b10b3fe064d4133a54f 2025-11-10T19:02:09,377 Successfully built cryodrgn 2025-11-10T19:02:09,406 Removed build tracker: '/tmp/pip-build-tracker-6d3xn3lx'