2025-12-23T22:55:10,906 Created temporary directory: /tmp/pip-ephem-wheel-cache-cczk1zsv 2025-12-23T22:55:10,907 Created temporary directory: /tmp/pip-build-tracker-b6nc6zyv 2025-12-23T22:55:10,908 Initialized build tracking at /tmp/pip-build-tracker-b6nc6zyv 2025-12-23T22:55:10,908 Created build tracker: /tmp/pip-build-tracker-b6nc6zyv 2025-12-23T22:55:10,909 Entered build tracker: /tmp/pip-build-tracker-b6nc6zyv 2025-12-23T22:55:10,910 Created temporary directory: /tmp/pip-wheel-um94caxz 2025-12-23T22:55:10,912 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 2025-12-23T22:55:10,915 Created temporary directory: /tmp/pip-ephem-wheel-cache-crwzt13o 2025-12-23T22:55:10,938 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-12-23T22:55:10,942 2 location(s) to search for versions of cryodrgn: 2025-12-23T22:55:10,942 * https://pypi.org/simple/cryodrgn/ 2025-12-23T22:55:10,942 * https://www.piwheels.org/simple/cryodrgn/ 2025-12-23T22:55:10,942 Fetching project page and analyzing links: https://pypi.org/simple/cryodrgn/ 2025-12-23T22:55:10,943 Getting page https://pypi.org/simple/cryodrgn/ 2025-12-23T22:55:10,945 Found index url https://pypi.org/simple 2025-12-23T22:55:11,160 Fetched page https://pypi.org/simple/cryodrgn/ as application/vnd.pypi.simple.v1+json 2025-12-23T22:55:11,170 Skipping link: No binaries permitted for cryodrgn: 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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 2025-12-23T22:55:11,212 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) 2025-12-23T22:55:11,213 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 2025-12-23T22:55:11,214 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/04/76/cdd84f24016d708011630773cb0cf7cee8554afc8d0801a7279811f94096/cryodrgn-3.5.4-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10) 2025-12-23T22:55:11,214 Found link https://files.pythonhosted.org/packages/e3/15/ffa6f7bb63dd5231b08312960b3ed93d28d30cb148aa51b17c8508dfd2f4/cryodrgn-3.5.4.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10), version: 3.5.4 2025-12-23T22:55:11,215 Fetching project page and analyzing links: https://www.piwheels.org/simple/cryodrgn/ 2025-12-23T22:55:11,216 Getting page https://www.piwheels.org/simple/cryodrgn/ 2025-12-23T22:55:11,217 Found index url https://www.piwheels.org/simple 2025-12-23T22:55:11,399 Fetched page https://www.piwheels.org/simple/cryodrgn/ as text/html 2025-12-23T22:55:11,411 Skipping link: No binaries permitted for cryodrgn: https://www.piwheels.org/simple/cryodrgn/cryodrgn-3.5.3-py3-none-any.whl#sha256=ed61d74174cf39f0b51d1b7dd04be400b134f0bdacac2785bd2bd240da78ab10 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.10) 2025-12-23T22:55:11,412 Skipping link: No binaries permitted for cryodrgn: https://archive1.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) 2025-12-23T22:55:11,412 Skipping link: No binaries permitted for cryodrgn: https://archive1.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) 2025-12-23T22:55:11,413 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) 2025-12-23T22:55:11,413 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) 2025-12-23T22:55:11,414 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) 2025-12-23T22:55:11,415 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) 2025-12-23T22:55:11,415 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) 2025-12-23T22:55:11,416 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) 2025-12-23T22:55:11,417 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) 2025-12-23T22:55:11,418 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) 2025-12-23T22:55:11,418 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) 2025-12-23T22:55:11,419 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) 2025-12-23T22:55:11,420 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) 2025-12-23T22:55:11,420 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) 2025-12-23T22:55:11,421 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) 2025-12-23T22:55:11,421 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) 2025-12-23T22:55:11,422 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) 2025-12-23T22:55:11,423 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) 2025-12-23T22:55:11,423 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) 2025-12-23T22:55:11,424 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) 2025-12-23T22:55:11,424 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) 2025-12-23T22:55:11,425 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) 2025-12-23T22:55:11,426 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) 2025-12-23T22:55:11,426 Skipping link: not a file: https://www.piwheels.org/simple/cryodrgn/ 2025-12-23T22:55:11,427 Skipping link: not a file: https://pypi.org/simple/cryodrgn/ 2025-12-23T22:55:11,447 Given no hashes to check 1 links for project 'cryodrgn': discarding no candidates 2025-12-23T22:55:11,465 Collecting cryodrgn==3.5.4 2025-12-23T22:55:11,467 Created temporary directory: /tmp/pip-unpack-6f26scnw 2025-12-23T22:55:11,690 Downloading cryodrgn-3.5.4.tar.gz (15.5 MB) 2025-12-23T22:55:16,483 Added cryodrgn==3.5.4 from https://files.pythonhosted.org/packages/e3/15/ffa6f7bb63dd5231b08312960b3ed93d28d30cb148aa51b17c8508dfd2f4/cryodrgn-3.5.4.tar.gz to build tracker '/tmp/pip-build-tracker-b6nc6zyv' 2025-12-23T22:55:16,489 Created temporary directory: /tmp/pip-build-env-ruytomll 2025-12-23T22:55:16,494 Installing build dependencies: started 2025-12-23T22:55:16,495 Running command pip subprocess to install build dependencies 2025-12-23T22:55:17,623 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-12-23T22:55:18,234 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 2025-12-23T22:55:18,257 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-12-23T22:55:19,978 Collecting setuptools>=61.0 2025-12-23T22:55:20,078 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-12-23T22:55:20,463 Collecting setuptools_scm>=6.2 2025-12-23T22:55:20,479 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-9.2.2-py3-none-any.whl (62 kB) 2025-12-23T22:55:20,664 Collecting packaging>=20 2025-12-23T22:55:20,679 Using cached https://www.piwheels.org/simple/packaging/packaging-25.0-py3-none-any.whl (66 kB) 2025-12-23T22:55:23,830 Installing collected packages: setuptools, packaging, setuptools_scm 2025-12-23T22:55:27,953 Creating /tmp/pip-build-env-ruytomll/overlay/local/bin 2025-12-23T22:55:27,955 changing mode of /tmp/pip-build-env-ruytomll/overlay/local/bin/setuptools-scm to 755 2025-12-23T22:55:27,979 Successfully installed packaging-25.0 setuptools-80.9.0 setuptools_scm-9.2.2 2025-12-23T22:55:28,263 Installing build dependencies: finished with status 'done' 2025-12-23T22:55:28,271 Getting requirements to build wheel: started 2025-12-23T22:55:28,272 Running command Getting requirements to build wheel 2025-12-23T22:55:29,071 /tmp/pip-build-env-ruytomll/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-23T22:55:29,071 !! 2025-12-23T22:55:29,073 ******************************************************************************** 2025-12-23T22:55:29,073 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-23T22:55:29,074 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-12-23T22:55:29,076 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-23T22:55:29,076 ******************************************************************************** 2025-12-23T22:55:29,077 !! 2025-12-23T22:55:29,078 dist._finalize_license_expression() 2025-12-23T22:55:29,078 /tmp/pip-build-env-ruytomll/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-23T22:55:29,079 !! 2025-12-23T22:55:29,080 ******************************************************************************** 2025-12-23T22:55:29,080 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-23T22:55:29,081 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-12-23T22:55:29,082 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-23T22:55:29,082 ******************************************************************************** 2025-12-23T22:55:29,083 !! 2025-12-23T22:55:29,084 self._finalize_license_expression() 2025-12-23T22:55:29,084 running egg_info 2025-12-23T22:55:29,091 writing cryodrgn.egg-info/PKG-INFO 2025-12-23T22:55:29,098 writing dependency_links to cryodrgn.egg-info/dependency_links.txt 2025-12-23T22:55:29,100 writing entry points to cryodrgn.egg-info/entry_points.txt 2025-12-23T22:55:29,103 writing requirements to cryodrgn.egg-info/requires.txt 2025-12-23T22:55:29,104 writing top-level names to cryodrgn.egg-info/top_level.txt 2025-12-23T22:55:29,160 listing git files failed - pretending there aren't any 2025-12-23T22:55:29,165 reading manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-12-23T22:55:29,221 reading manifest template 'MANIFEST.in' 2025-12-23T22:55:29,223 adding license file 'LICENSE.txt' 2025-12-23T22:55:29,273 writing manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-12-23T22:55:29,376 Getting requirements to build wheel: finished with status 'done' 2025-12-23T22:55:29,379 Created temporary directory: /tmp/pip-modern-metadata-0ow2jwy5 2025-12-23T22:55:29,381 Preparing metadata (pyproject.toml): started 2025-12-23T22:55:29,382 Running command Preparing metadata (pyproject.toml) 2025-12-23T22:55:30,094 /tmp/pip-build-env-ruytomll/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-23T22:55:30,095 !! 2025-12-23T22:55:30,096 ******************************************************************************** 2025-12-23T22:55:30,096 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-23T22:55:30,098 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-12-23T22:55:30,099 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-23T22:55:30,099 ******************************************************************************** 2025-12-23T22:55:30,100 !! 2025-12-23T22:55:30,101 dist._finalize_license_expression() 2025-12-23T22:55:30,102 /tmp/pip-build-env-ruytomll/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-23T22:55:30,102 !! 2025-12-23T22:55:30,103 ******************************************************************************** 2025-12-23T22:55:30,104 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-23T22:55:30,105 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-12-23T22:55:30,106 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-23T22:55:30,107 ******************************************************************************** 2025-12-23T22:55:30,108 !! 2025-12-23T22:55:30,109 self._finalize_license_expression() 2025-12-23T22:55:30,110 running dist_info 2025-12-23T22:55:30,123 creating /tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info 2025-12-23T22:55:30,124 writing /tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/PKG-INFO 2025-12-23T22:55:30,132 writing dependency_links to /tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/dependency_links.txt 2025-12-23T22:55:30,134 writing entry points to /tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/entry_points.txt 2025-12-23T22:55:30,137 writing requirements to /tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/requires.txt 2025-12-23T22:55:30,138 writing top-level names to /tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/top_level.txt 2025-12-23T22:55:30,140 writing manifest file '/tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/SOURCES.txt' 2025-12-23T22:55:30,191 listing git files failed - pretending there aren't any 2025-12-23T22:55:30,196 reading manifest file '/tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/SOURCES.txt' 2025-12-23T22:55:30,198 reading manifest template 'MANIFEST.in' 2025-12-23T22:55:30,199 adding license file 'LICENSE.txt' 2025-12-23T22:55:30,205 writing manifest file '/tmp/pip-modern-metadata-0ow2jwy5/cryodrgn.egg-info/SOURCES.txt' 2025-12-23T22:55:30,206 creating '/tmp/pip-modern-metadata-0ow2jwy5/cryodrgn-3.5.4.dist-info' 2025-12-23T22:55:30,344 Preparing metadata (pyproject.toml): finished with status 'done' 2025-12-23T22:55:30,350 Source in /tmp/pip-wheel-um94caxz/cryodrgn_9eb1e5503b484284a9e717b348414532 has version 3.5.4, which satisfies requirement cryodrgn==3.5.4 from https://files.pythonhosted.org/packages/e3/15/ffa6f7bb63dd5231b08312960b3ed93d28d30cb148aa51b17c8508dfd2f4/cryodrgn-3.5.4.tar.gz 2025-12-23T22:55:30,351 Removed cryodrgn==3.5.4 from https://files.pythonhosted.org/packages/e3/15/ffa6f7bb63dd5231b08312960b3ed93d28d30cb148aa51b17c8508dfd2f4/cryodrgn-3.5.4.tar.gz from build tracker '/tmp/pip-build-tracker-b6nc6zyv' 2025-12-23T22:55:30,359 Created temporary directory: /tmp/pip-unpack-r7fik4dc 2025-12-23T22:55:30,359 Building wheels for collected packages: cryodrgn 2025-12-23T22:55:30,364 Created temporary directory: /tmp/pip-wheel-gl984cmp 2025-12-23T22:55:30,364 Destination directory: /tmp/pip-wheel-gl984cmp 2025-12-23T22:55:30,367 Building wheel for cryodrgn (pyproject.toml): started 2025-12-23T22:55:30,368 Running command Building wheel for cryodrgn (pyproject.toml) 2025-12-23T22:55:31,068 /tmp/pip-build-env-ruytomll/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-23T22:55:31,068 !! 2025-12-23T22:55:31,070 ******************************************************************************** 2025-12-23T22:55:31,070 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-23T22:55:31,072 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-12-23T22:55:31,073 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-23T22:55:31,074 ******************************************************************************** 2025-12-23T22:55:31,075 !! 2025-12-23T22:55:31,075 dist._finalize_license_expression() 2025-12-23T22:55:31,076 /tmp/pip-build-env-ruytomll/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-12-23T22:55:31,076 !! 2025-12-23T22:55:31,078 ******************************************************************************** 2025-12-23T22:55:31,078 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-12-23T22:55:31,080 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-12-23T22:55:31,081 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-12-23T22:55:31,081 ******************************************************************************** 2025-12-23T22:55:31,083 !! 2025-12-23T22:55:31,083 self._finalize_license_expression() 2025-12-23T22:55:31,084 running bdist_wheel 2025-12-23T22:55:31,102 running build 2025-12-23T22:55:31,102 running build_py 2025-12-23T22:55:31,111 creating build/lib/cryodrgn 2025-12-23T22:55:31,113 copying cryodrgn/shift_grid3.py -> build/lib/cryodrgn 2025-12-23T22:55:31,115 copying cryodrgn/lie_tools.py -> build/lib/cryodrgn 2025-12-23T22:55:31,117 copying cryodrgn/command_line.py -> build/lib/cryodrgn 2025-12-23T22:55:31,119 copying cryodrgn/_version.py -> build/lib/cryodrgn 2025-12-23T22:55:31,121 copying cryodrgn/source.py -> build/lib/cryodrgn 2025-12-23T22:55:31,124 copying cryodrgn/mrcfile.py -> build/lib/cryodrgn 2025-12-23T22:55:31,126 copying cryodrgn/beta_schedule.py -> build/lib/cryodrgn 2025-12-23T22:55:31,128 copying cryodrgn/masking.py -> build/lib/cryodrgn 2025-12-23T22:55:31,131 copying cryodrgn/dataset.py -> build/lib/cryodrgn 2025-12-23T22:55:31,133 copying cryodrgn/make_healpy.py -> build/lib/cryodrgn 2025-12-23T22:55:31,135 copying cryodrgn/models.py -> build/lib/cryodrgn 2025-12-23T22:55:31,138 copying cryodrgn/starfile.py -> build/lib/cryodrgn 2025-12-23T22:55:31,141 copying cryodrgn/pose_search.py -> build/lib/cryodrgn 2025-12-23T22:55:31,143 copying cryodrgn/shift_grid.py -> build/lib/cryodrgn 2025-12-23T22:55:31,145 copying cryodrgn/ctf.py -> build/lib/cryodrgn 2025-12-23T22:55:31,147 copying cryodrgn/analysis.py -> build/lib/cryodrgn 2025-12-23T22:55:31,150 copying cryodrgn/losses.py -> build/lib/cryodrgn 2025-12-23T22:55:31,152 copying cryodrgn/pose.py -> build/lib/cryodrgn 2025-12-23T22:55:31,154 copying cryodrgn/lattice.py -> build/lib/cryodrgn 2025-12-23T22:55:31,157 copying cryodrgn/fft.py -> build/lib/cryodrgn 2025-12-23T22:55:31,159 copying cryodrgn/config.py -> build/lib/cryodrgn 2025-12-23T22:55:31,161 copying cryodrgn/__init__.py -> build/lib/cryodrgn 2025-12-23T22:55:31,163 copying cryodrgn/so3_grid.py -> build/lib/cryodrgn 2025-12-23T22:55:31,165 copying cryodrgn/utils.py -> build/lib/cryodrgn 2025-12-23T22:55:31,169 creating build/lib/cryodrgn/commands 2025-12-23T22:55:31,170 copying cryodrgn/commands/parse_pose_star.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,172 copying cryodrgn/commands/backproject_voxel.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,174 copying cryodrgn/commands/parse_pose_csparc.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,176 copying cryodrgn/commands/parse_ctf_star.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,179 copying cryodrgn/commands/train_nn.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,182 copying cryodrgn/commands/train_vae.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,187 copying cryodrgn/commands/analyze_landscape_full.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,192 copying cryodrgn/commands/direct_traversal.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,194 copying cryodrgn/commands/pc_traversal.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,196 copying cryodrgn/commands/eval_images.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,198 copying cryodrgn/commands/filter.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,201 copying cryodrgn/commands/analyze.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,204 copying cryodrgn/commands/downsample.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,206 copying cryodrgn/commands/abinit_het.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,209 copying cryodrgn/commands/train_dec.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,212 copying cryodrgn/commands/eval_vol.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,215 copying cryodrgn/commands/abinit_homo.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,217 copying cryodrgn/commands/graph_traversal.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,220 copying cryodrgn/commands/analyze_landscape.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,223 copying cryodrgn/commands/parse_star.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,225 copying cryodrgn/commands/__init__.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,227 copying cryodrgn/commands/parse_ctf_csparc.py -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,230 creating build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,231 copying cryodrgn/commands_utils/parse_relion.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,234 copying cryodrgn/commands_utils/filter_mrcs.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,235 copying cryodrgn/commands_utils/phase_flip.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,237 copying cryodrgn/commands_utils/add_psize.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,239 copying cryodrgn/commands_utils/view_cs_header.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,241 copying cryodrgn/commands_utils/plot_classes.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,243 copying cryodrgn/commands_utils/view_mrcs.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,245 copying cryodrgn/commands_utils/fsc.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,247 copying cryodrgn/commands_utils/make_movies.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,250 copying cryodrgn/commands_utils/select_clusters.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,252 copying cryodrgn/commands_utils/gen_mask.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,254 copying cryodrgn/commands_utils/select_random.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,257 copying cryodrgn/commands_utils/write_cs.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,258 copying cryodrgn/commands_utils/filter_cs.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,260 copying cryodrgn/commands_utils/write_star.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,263 copying cryodrgn/commands_utils/filter_star.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,264 copying cryodrgn/commands_utils/view_header.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,266 copying cryodrgn/commands_utils/analyze_convergence.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,269 copying cryodrgn/commands_utils/filter_pkl.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,271 copying cryodrgn/commands_utils/invert_contrast.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,273 copying cryodrgn/commands_utils/plot_fsc.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,276 copying cryodrgn/commands_utils/clean.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,278 copying cryodrgn/commands_utils/concat_pkls.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,280 copying cryodrgn/commands_utils/translate_mrcs.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,282 copying cryodrgn/commands_utils/flip_hand.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,284 copying cryodrgn/commands_utils/__init__.py -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,285 running egg_info 2025-12-23T22:55:31,300 writing cryodrgn.egg-info/PKG-INFO 2025-12-23T22:55:31,307 writing dependency_links to cryodrgn.egg-info/dependency_links.txt 2025-12-23T22:55:31,308 writing entry points to cryodrgn.egg-info/entry_points.txt 2025-12-23T22:55:31,311 writing requirements to cryodrgn.egg-info/requires.txt 2025-12-23T22:55:31,312 writing top-level names to cryodrgn.egg-info/top_level.txt 2025-12-23T22:55:31,351 listing git files failed - pretending there aren't any 2025-12-23T22:55:31,355 reading manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-12-23T22:55:31,462 reading manifest template 'MANIFEST.in' 2025-12-23T22:55:31,464 adding license file 'LICENSE.txt' 2025-12-23T22:55:31,473 writing manifest file 'cryodrgn.egg-info/SOURCES.txt' 2025-12-23T22:55:31,481 copying cryodrgn/healpy_grid.json -> build/lib/cryodrgn 2025-12-23T22:55:31,661 copying cryodrgn/commands/README.md -> build/lib/cryodrgn/commands 2025-12-23T22:55:31,663 creating build/lib/cryodrgn/templates 2025-12-23T22:55:31,664 copying cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/lib/cryodrgn/templates 2025-12-23T22:55:31,668 copying cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/lib/cryodrgn/templates 2025-12-23T22:55:31,671 copying cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/lib/cryodrgn/templates 2025-12-23T22:55:31,674 copying cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/lib/cryodrgn/templates 2025-12-23T22:55:31,677 copying cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/lib/cryodrgn/templates 2025-12-23T22:55:31,681 copying cryodrgn/commands_utils/README.md -> build/lib/cryodrgn/commands_utils 2025-12-23T22:55:31,700 installing to build/bdist.linux-armv7l/wheel 2025-12-23T22:55:31,701 running install 2025-12-23T22:55:31,725 running install_lib 2025-12-23T22:55:31,733 creating build/bdist.linux-armv7l/wheel 2025-12-23T22:55:31,736 creating build/bdist.linux-armv7l/wheel/cryodrgn 2025-12-23T22:55:31,738 copying build/lib/cryodrgn/shift_grid3.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,740 copying build/lib/cryodrgn/lie_tools.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,743 copying build/lib/cryodrgn/command_line.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,745 copying build/lib/cryodrgn/_version.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,747 copying build/lib/cryodrgn/source.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,750 copying build/lib/cryodrgn/mrcfile.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,753 copying build/lib/cryodrgn/beta_schedule.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,755 copying build/lib/cryodrgn/masking.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,757 copying build/lib/cryodrgn/dataset.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,760 copying build/lib/cryodrgn/make_healpy.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,762 copying build/lib/cryodrgn/models.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,766 creating build/bdist.linux-armv7l/wheel/cryodrgn/commands 2025-12-23T22:55:31,768 copying build/lib/cryodrgn/commands/parse_pose_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,770 copying build/lib/cryodrgn/commands/backproject_voxel.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,773 copying build/lib/cryodrgn/commands/parse_pose_csparc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,775 copying build/lib/cryodrgn/commands/parse_ctf_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,777 copying build/lib/cryodrgn/commands/train_nn.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,780 copying build/lib/cryodrgn/commands/train_vae.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,783 copying build/lib/cryodrgn/commands/analyze_landscape_full.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,786 copying build/lib/cryodrgn/commands/direct_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,788 copying build/lib/cryodrgn/commands/pc_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,790 copying build/lib/cryodrgn/commands/eval_images.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,792 copying build/lib/cryodrgn/commands/filter.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,795 copying build/lib/cryodrgn/commands/analyze.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,798 copying build/lib/cryodrgn/commands/README.md -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,801 copying build/lib/cryodrgn/commands/downsample.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,803 copying build/lib/cryodrgn/commands/abinit_het.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,807 copying build/lib/cryodrgn/commands/train_dec.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,809 copying build/lib/cryodrgn/commands/eval_vol.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,812 copying build/lib/cryodrgn/commands/abinit_homo.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,815 copying build/lib/cryodrgn/commands/graph_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,818 copying build/lib/cryodrgn/commands/analyze_landscape.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,820 copying build/lib/cryodrgn/commands/parse_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,823 copying build/lib/cryodrgn/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,824 copying build/lib/cryodrgn/commands/parse_ctf_csparc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2025-12-23T22:55:31,827 copying build/lib/cryodrgn/healpy_grid.json -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:31,996 copying build/lib/cryodrgn/starfile.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,000 copying build/lib/cryodrgn/pose_search.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,003 creating build/bdist.linux-armv7l/wheel/cryodrgn/templates 2025-12-23T22:55:32,005 copying build/lib/cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-12-23T22:55:32,008 copying build/lib/cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-12-23T22:55:32,012 copying build/lib/cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-12-23T22:55:32,016 copying build/lib/cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-12-23T22:55:32,019 copying build/lib/cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2025-12-23T22:55:32,023 copying build/lib/cryodrgn/shift_grid.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,026 copying build/lib/cryodrgn/ctf.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,029 copying build/lib/cryodrgn/analysis.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,033 copying build/lib/cryodrgn/losses.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,035 copying build/lib/cryodrgn/pose.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,039 copying build/lib/cryodrgn/lattice.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,041 copying build/lib/cryodrgn/fft.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,044 copying build/lib/cryodrgn/config.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,046 copying build/lib/cryodrgn/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,049 creating build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils 2025-12-23T22:55:32,050 copying build/lib/cryodrgn/commands_utils/parse_relion.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,053 copying build/lib/cryodrgn/commands_utils/filter_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,056 copying build/lib/cryodrgn/commands_utils/phase_flip.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,058 copying build/lib/cryodrgn/commands_utils/add_psize.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,061 copying build/lib/cryodrgn/commands_utils/view_cs_header.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,063 copying build/lib/cryodrgn/commands_utils/plot_classes.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,066 copying build/lib/cryodrgn/commands_utils/view_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,068 copying build/lib/cryodrgn/commands_utils/fsc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,071 copying build/lib/cryodrgn/commands_utils/make_movies.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,074 copying build/lib/cryodrgn/commands_utils/select_clusters.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,076 copying build/lib/cryodrgn/commands_utils/gen_mask.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,078 copying build/lib/cryodrgn/commands_utils/README.md -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,080 copying build/lib/cryodrgn/commands_utils/select_random.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,082 copying build/lib/cryodrgn/commands_utils/write_cs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,085 copying build/lib/cryodrgn/commands_utils/filter_cs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,087 copying build/lib/cryodrgn/commands_utils/write_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,089 copying build/lib/cryodrgn/commands_utils/filter_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,092 copying build/lib/cryodrgn/commands_utils/view_header.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,094 copying build/lib/cryodrgn/commands_utils/analyze_convergence.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,097 copying build/lib/cryodrgn/commands_utils/filter_pkl.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,100 copying build/lib/cryodrgn/commands_utils/invert_contrast.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,102 copying build/lib/cryodrgn/commands_utils/plot_fsc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,105 copying build/lib/cryodrgn/commands_utils/clean.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,108 copying build/lib/cryodrgn/commands_utils/concat_pkls.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,110 copying build/lib/cryodrgn/commands_utils/translate_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,112 copying build/lib/cryodrgn/commands_utils/flip_hand.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,115 copying build/lib/cryodrgn/commands_utils/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2025-12-23T22:55:32,117 copying build/lib/cryodrgn/so3_grid.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,119 copying build/lib/cryodrgn/utils.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2025-12-23T22:55:32,121 running install_egg_info 2025-12-23T22:55:32,129 Copying cryodrgn.egg-info to build/bdist.linux-armv7l/wheel/./cryodrgn-3.5.4-py3.11.egg-info 2025-12-23T22:55:32,145 running install_scripts 2025-12-23T22:55:32,161 creating build/bdist.linux-armv7l/wheel/cryodrgn-3.5.4.dist-info/WHEEL 2025-12-23T22:55:32,164 creating '/tmp/pip-wheel-gl984cmp/.tmp-8bxwjydp/cryodrgn-3.5.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-12-23T22:55:32,167 adding 'cryodrgn/__init__.py' 2025-12-23T22:55:32,169 adding 'cryodrgn/_version.py' 2025-12-23T22:55:32,172 adding 'cryodrgn/analysis.py' 2025-12-23T22:55:32,174 adding 'cryodrgn/beta_schedule.py' 2025-12-23T22:55:32,176 adding 'cryodrgn/command_line.py' 2025-12-23T22:55:32,178 adding 'cryodrgn/config.py' 2025-12-23T22:55:32,180 adding 'cryodrgn/ctf.py' 2025-12-23T22:55:32,183 adding 'cryodrgn/dataset.py' 2025-12-23T22:55:32,185 adding 'cryodrgn/fft.py' 2025-12-23T22:55:32,955 adding 'cryodrgn/healpy_grid.json' 2025-12-23T22:55:33,021 adding 'cryodrgn/lattice.py' 2025-12-23T22:55:33,023 adding 'cryodrgn/lie_tools.py' 2025-12-23T22:55:33,025 adding 'cryodrgn/losses.py' 2025-12-23T22:55:33,026 adding 'cryodrgn/make_healpy.py' 2025-12-23T22:55:33,028 adding 'cryodrgn/masking.py' 2025-12-23T22:55:33,033 adding 'cryodrgn/models.py' 2025-12-23T22:55:33,035 adding 'cryodrgn/mrcfile.py' 2025-12-23T22:55:33,037 adding 'cryodrgn/pose.py' 2025-12-23T22:55:33,040 adding 'cryodrgn/pose_search.py' 2025-12-23T22:55:33,042 adding 'cryodrgn/shift_grid.py' 2025-12-23T22:55:33,043 adding 'cryodrgn/shift_grid3.py' 2025-12-23T22:55:33,045 adding 'cryodrgn/so3_grid.py' 2025-12-23T22:55:33,049 adding 'cryodrgn/source.py' 2025-12-23T22:55:33,051 adding 'cryodrgn/starfile.py' 2025-12-23T22:55:33,054 adding 'cryodrgn/utils.py' 2025-12-23T22:55:33,056 adding 'cryodrgn/commands/README.md' 2025-12-23T22:55:33,057 adding 'cryodrgn/commands/__init__.py' 2025-12-23T22:55:33,062 adding 'cryodrgn/commands/abinit_het.py' 2025-12-23T22:55:33,066 adding 'cryodrgn/commands/abinit_homo.py' 2025-12-23T22:55:33,069 adding 'cryodrgn/commands/analyze.py' 2025-12-23T22:55:33,072 adding 'cryodrgn/commands/analyze_landscape.py' 2025-12-23T22:55:33,075 adding 'cryodrgn/commands/analyze_landscape_full.py' 2025-12-23T22:55:33,078 adding 'cryodrgn/commands/backproject_voxel.py' 2025-12-23T22:55:33,080 adding 'cryodrgn/commands/direct_traversal.py' 2025-12-23T22:55:33,082 adding 'cryodrgn/commands/downsample.py' 2025-12-23T22:55:33,085 adding 'cryodrgn/commands/eval_images.py' 2025-12-23T22:55:33,087 adding 'cryodrgn/commands/eval_vol.py' 2025-12-23T22:55:33,090 adding 'cryodrgn/commands/filter.py' 2025-12-23T22:55:33,093 adding 'cryodrgn/commands/graph_traversal.py' 2025-12-23T22:55:33,094 adding 'cryodrgn/commands/parse_ctf_csparc.py' 2025-12-23T22:55:33,096 adding 'cryodrgn/commands/parse_ctf_star.py' 2025-12-23T22:55:33,098 adding 'cryodrgn/commands/parse_pose_csparc.py' 2025-12-23T22:55:33,100 adding 'cryodrgn/commands/parse_pose_star.py' 2025-12-23T22:55:33,101 adding 'cryodrgn/commands/parse_star.py' 2025-12-23T22:55:33,103 adding 'cryodrgn/commands/pc_traversal.py' 2025-12-23T22:55:33,106 adding 'cryodrgn/commands/train_dec.py' 2025-12-23T22:55:33,109 adding 'cryodrgn/commands/train_nn.py' 2025-12-23T22:55:33,114 adding 'cryodrgn/commands/train_vae.py' 2025-12-23T22:55:33,116 adding 'cryodrgn/commands_utils/README.md' 2025-12-23T22:55:33,118 adding 'cryodrgn/commands_utils/__init__.py' 2025-12-23T22:55:33,119 adding 'cryodrgn/commands_utils/add_psize.py' 2025-12-23T22:55:33,125 adding 'cryodrgn/commands_utils/analyze_convergence.py' 2025-12-23T22:55:33,127 adding 'cryodrgn/commands_utils/clean.py' 2025-12-23T22:55:33,129 adding 'cryodrgn/commands_utils/concat_pkls.py' 2025-12-23T22:55:33,130 adding 'cryodrgn/commands_utils/filter_cs.py' 2025-12-23T22:55:33,132 adding 'cryodrgn/commands_utils/filter_mrcs.py' 2025-12-23T22:55:33,134 adding 'cryodrgn/commands_utils/filter_pkl.py' 2025-12-23T22:55:33,135 adding 'cryodrgn/commands_utils/filter_star.py' 2025-12-23T22:55:33,137 adding 'cryodrgn/commands_utils/flip_hand.py' 2025-12-23T22:55:33,140 adding 'cryodrgn/commands_utils/fsc.py' 2025-12-23T22:55:33,141 adding 'cryodrgn/commands_utils/gen_mask.py' 2025-12-23T22:55:33,143 adding 'cryodrgn/commands_utils/invert_contrast.py' 2025-12-23T22:55:33,145 adding 'cryodrgn/commands_utils/make_movies.py' 2025-12-23T22:55:33,148 adding 'cryodrgn/commands_utils/parse_relion.py' 2025-12-23T22:55:33,149 adding 'cryodrgn/commands_utils/phase_flip.py' 2025-12-23T22:55:33,152 adding 'cryodrgn/commands_utils/plot_classes.py' 2025-12-23T22:55:33,153 adding 'cryodrgn/commands_utils/plot_fsc.py' 2025-12-23T22:55:33,155 adding 'cryodrgn/commands_utils/select_clusters.py' 2025-12-23T22:55:33,157 adding 'cryodrgn/commands_utils/select_random.py' 2025-12-23T22:55:33,158 adding 'cryodrgn/commands_utils/translate_mrcs.py' 2025-12-23T22:55:33,160 adding 'cryodrgn/commands_utils/view_cs_header.py' 2025-12-23T22:55:33,161 adding 'cryodrgn/commands_utils/view_header.py' 2025-12-23T22:55:33,163 adding 'cryodrgn/commands_utils/view_mrcs.py' 2025-12-23T22:55:33,165 adding 'cryodrgn/commands_utils/write_cs.py' 2025-12-23T22:55:33,167 adding 'cryodrgn/commands_utils/write_star.py' 2025-12-23T22:55:33,170 adding 'cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb' 2025-12-23T22:55:33,172 adding 'cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb' 2025-12-23T22:55:33,175 adding 'cryodrgn/templates/cryoDRGN_figures_template.ipynb' 2025-12-23T22:55:33,178 adding 'cryodrgn/templates/cryoDRGN_filtering_template.ipynb' 2025-12-23T22:55:33,181 adding 'cryodrgn/templates/cryoDRGN_viz_template.ipynb' 2025-12-23T22:55:33,189 adding 'cryodrgn-3.5.4.dist-info/licenses/LICENSE.txt' 2025-12-23T22:55:33,193 adding 'cryodrgn-3.5.4.dist-info/METADATA' 2025-12-23T22:55:33,195 adding 'cryodrgn-3.5.4.dist-info/WHEEL' 2025-12-23T22:55:33,196 adding 'cryodrgn-3.5.4.dist-info/entry_points.txt' 2025-12-23T22:55:33,198 adding 'cryodrgn-3.5.4.dist-info/top_level.txt' 2025-12-23T22:55:33,200 adding 'cryodrgn-3.5.4.dist-info/RECORD' 2025-12-23T22:55:33,216 removing build/bdist.linux-armv7l/wheel 2025-12-23T22:55:33,341 Building wheel for cryodrgn (pyproject.toml): finished with status 'done' 2025-12-23T22:55:33,379 Created wheel for cryodrgn: filename=cryodrgn-3.5.4-py3-none-any.whl size=1216322 sha256=f190973fa25bd9e83d096af1b945aa45467621bd46fd466f1b5c0bddb5086646 2025-12-23T22:55:33,381 Stored in directory: /tmp/pip-ephem-wheel-cache-crwzt13o/wheels/cc/cb/a6/49f0796d8c6b106cf8600ff220b25c08a8591df3d6ea3bf2f0 2025-12-23T22:55:33,402 Successfully built cryodrgn 2025-12-23T22:55:33,441 Removed build tracker: '/tmp/pip-build-tracker-b6nc6zyv'