2026-04-24T01:13:25,756 Created temporary directory: /tmp/pip-ephem-wheel-cache-yrmg63rs 2026-04-24T01:13:25,758 Created temporary directory: /tmp/pip-build-tracker-_f8h8zr2 2026-04-24T01:13:25,758 Initialized build tracking at /tmp/pip-build-tracker-_f8h8zr2 2026-04-24T01:13:25,759 Created build tracker: /tmp/pip-build-tracker-_f8h8zr2 2026-04-24T01:13:25,759 Entered build tracker: /tmp/pip-build-tracker-_f8h8zr2 2026-04-24T01:13:25,760 Created temporary directory: /tmp/pip-wheel-hfdz2h7t 2026-04-24T01:13:25,763 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-24T01:13:25,765 Created temporary directory: /tmp/pip-ephem-wheel-cache-nn0muygi 2026-04-24T01:13:25,787 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-24T01:13:25,790 2 location(s) to search for versions of cryodrgn: 2026-04-24T01:13:25,790 * https://pypi.org/simple/cryodrgn/ 2026-04-24T01:13:25,790 * https://www.piwheels.org/simple/cryodrgn/ 2026-04-24T01:13:25,791 Fetching project page and analyzing links: https://pypi.org/simple/cryodrgn/ 2026-04-24T01:13:25,792 Getting page https://pypi.org/simple/cryodrgn/ 2026-04-24T01:13:25,793 Found index url https://pypi.org/simple 2026-04-24T01:13:26,024 Fetched page https://pypi.org/simple/cryodrgn/ as application/vnd.pypi.simple.v1+json 2026-04-24T01:13:26,035 Skipping link: No binaries permitted for cryodrgn: 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(requires-python:>=3.10) 2026-04-24T01:13:26,081 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 2026-04-24T01:13:26,082 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/7e/ce/43f4c0fe5d8eaf92834dca3eae5f81df32e8893fcfe6da15e28f1a5b0fdd/cryodrgn-4.2.0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10) 2026-04-24T01:13:26,083 Found link https://files.pythonhosted.org/packages/e0/a6/f88f5cce0cd14e7d8d29b793ac63670951faf571ec989cf8dbc5624aaec0/cryodrgn-4.2.0.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10), version: 4.2.0 2026-04-24T01:13:26,083 Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/c2/77/244f309391d8e9aacac46fa602616aec2fdc042fb7ca484d14027ed6b9c7/cryodrgn-4.2.1-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10) 2026-04-24T01:13:26,084 Found link https://files.pythonhosted.org/packages/16/2a/19c8882dab0f461a06d17b355fdaeb62e40b6b38fdb771297c40e59e4478/cryodrgn-4.2.1.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.10), version: 4.2.1 2026-04-24T01:13:26,085 Fetching project page and analyzing links: https://www.piwheels.org/simple/cryodrgn/ 2026-04-24T01:13:26,086 Getting page https://www.piwheels.org/simple/cryodrgn/ 2026-04-24T01:13:26,087 Found index url https://www.piwheels.org/simple 2026-04-24T01:13:26,264 Fetched page https://www.piwheels.org/simple/cryodrgn/ as text/html 2026-04-24T01:13:26,272 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-4.2.0-py3-none-any.whl#sha256=3ce1f8da3d176ae45de3e546dfba204d8cfc8c72d756e2632cff3f2ea738018d (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.10) 2026-04-24T01:13:26,273 Skipping link: No binaries permitted for cryodrgn: https://archive1.piwheels.org/simple/cryodrgn/cryodrgn-3.5.4-py3-none-any.whl#sha256=f190973fa25bd9e83d096af1b945aa45467621bd46fd466f1b5c0bddb5086646 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.10) 2026-04-24T01:13:26,274 Skipping link: No binaries permitted for cryodrgn: https://archive1.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) 2026-04-24T01:13:26,274 Skipping link: No binaries permitted for cryodrgn: 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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) 2026-04-24T01:13:26,286 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) 2026-04-24T01:13:26,286 Skipping link: not a file: https://www.piwheels.org/simple/cryodrgn/ 2026-04-24T01:13:26,287 Skipping link: not a file: https://pypi.org/simple/cryodrgn/ 2026-04-24T01:13:26,309 Given no hashes to check 1 links for project 'cryodrgn': discarding no candidates 2026-04-24T01:13:26,329 Collecting cryodrgn==4.2.1 2026-04-24T01:13:26,331 Created temporary directory: /tmp/pip-unpack-xi2j4dc0 2026-04-24T01:13:26,483 Downloading cryodrgn-4.2.1.tar.gz (18.0 MB) 2026-04-24T01:13:29,658 Added cryodrgn==4.2.1 from https://files.pythonhosted.org/packages/16/2a/19c8882dab0f461a06d17b355fdaeb62e40b6b38fdb771297c40e59e4478/cryodrgn-4.2.1.tar.gz to build tracker '/tmp/pip-build-tracker-_f8h8zr2' 2026-04-24T01:13:29,664 Created temporary directory: /tmp/pip-build-env-9g392v1q 2026-04-24T01:13:29,669 Installing build dependencies: started 2026-04-24T01:13:29,670 Running command pip subprocess to install build dependencies 2026-04-24T01:13:30,844 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-24T01:13:31,347 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-24T01:13:31,371 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-24T01:13:33,180 Collecting setuptools>=61.0 2026-04-24T01:13:33,258 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-24T01:13:33,646 Collecting setuptools_scm>=6.2 2026-04-24T01:13:33,662 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-10.0.5-py3-none-any.whl (21 kB) 2026-04-24T01:13:33,746 Collecting vcs-versioning>=1.0.0.dev0 2026-04-24T01:13:33,763 Using cached https://www.piwheels.org/simple/vcs-versioning/vcs_versioning-1.1.1-py3-none-any.whl (79 kB) 2026-04-24T01:13:33,943 Collecting packaging>=20 2026-04-24T01:13:33,960 Using cached https://www.piwheels.org/simple/packaging/packaging-26.1-py3-none-any.whl (95 kB) 2026-04-24T01:13:36,972 Installing collected packages: setuptools, packaging, vcs-versioning, setuptools_scm 2026-04-24T01:13:40,640 Creating /tmp/pip-build-env-9g392v1q/overlay/local/bin 2026-04-24T01:13:40,642 changing mode of /tmp/pip-build-env-9g392v1q/overlay/local/bin/vcs-versioning to 755 2026-04-24T01:13:40,775 changing mode of /tmp/pip-build-env-9g392v1q/overlay/local/bin/setuptools-scm to 755 2026-04-24T01:13:40,803 Successfully installed packaging-26.1 setuptools-82.0.1 setuptools_scm-10.0.5 vcs-versioning-1.1.1 2026-04-24T01:13:41,087 Installing build dependencies: finished with status 'done' 2026-04-24T01:13:41,093 Getting requirements to build wheel: started 2026-04-24T01:13:41,094 Running command Getting requirements to build wheel 2026-04-24T01:13:41,951 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-24T01:13:41,951 !! 2026-04-24T01:13:41,952 ******************************************************************************** 2026-04-24T01:13:41,952 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-24T01:13:41,953 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-04-24T01:13:41,954 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-24T01:13:41,955 ******************************************************************************** 2026-04-24T01:13:41,956 !! 2026-04-24T01:13:41,957 dist._finalize_license_expression() 2026-04-24T01:13:41,958 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-24T01:13:41,959 !! 2026-04-24T01:13:41,960 ******************************************************************************** 2026-04-24T01:13:41,960 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-24T01:13:41,962 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-04-24T01:13:41,963 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-24T01:13:41,963 ******************************************************************************** 2026-04-24T01:13:41,965 !! 2026-04-24T01:13:41,965 self._finalize_license_expression() 2026-04-24T01:13:41,966 running egg_info 2026-04-24T01:13:41,974 writing cryodrgn.egg-info/PKG-INFO 2026-04-24T01:13:41,980 writing dependency_links to cryodrgn.egg-info/dependency_links.txt 2026-04-24T01:13:41,982 writing entry points to cryodrgn.egg-info/entry_points.txt 2026-04-24T01:13:41,985 writing requirements to cryodrgn.egg-info/requires.txt 2026-04-24T01:13:41,986 writing top-level names to cryodrgn.egg-info/top_level.txt 2026-04-24T01:13:42,036 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. 2026-04-24T01:13:42,037 return get_active_overrides().subprocess_timeout 2026-04-24T01:13:42,046 listing git files failed - pretending there aren't any 2026-04-24T01:13:42,052 reading manifest file 'cryodrgn.egg-info/SOURCES.txt' 2026-04-24T01:13:42,067 reading manifest template 'MANIFEST.in' 2026-04-24T01:13:42,069 adding license file 'LICENSE.txt' 2026-04-24T01:13:42,080 writing manifest file 'cryodrgn.egg-info/SOURCES.txt' 2026-04-24T01:13:42,186 Getting requirements to build wheel: finished with status 'done' 2026-04-24T01:13:42,189 Created temporary directory: /tmp/pip-modern-metadata-wib2yvdp 2026-04-24T01:13:42,191 Preparing metadata (pyproject.toml): started 2026-04-24T01:13:42,193 Running command Preparing metadata (pyproject.toml) 2026-04-24T01:13:42,952 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-24T01:13:42,952 !! 2026-04-24T01:13:42,953 ******************************************************************************** 2026-04-24T01:13:42,954 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-24T01:13:42,955 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-04-24T01:13:42,955 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-24T01:13:42,956 ******************************************************************************** 2026-04-24T01:13:42,957 !! 2026-04-24T01:13:42,957 dist._finalize_license_expression() 2026-04-24T01:13:42,958 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-24T01:13:42,958 !! 2026-04-24T01:13:42,959 ******************************************************************************** 2026-04-24T01:13:42,960 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-24T01:13:42,961 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-04-24T01:13:42,962 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-24T01:13:42,963 ******************************************************************************** 2026-04-24T01:13:42,964 !! 2026-04-24T01:13:42,965 self._finalize_license_expression() 2026-04-24T01:13:42,966 running dist_info 2026-04-24T01:13:42,980 creating /tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info 2026-04-24T01:13:42,981 writing /tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/PKG-INFO 2026-04-24T01:13:42,987 writing dependency_links to /tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/dependency_links.txt 2026-04-24T01:13:42,989 writing entry points to /tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/entry_points.txt 2026-04-24T01:13:42,992 writing requirements to /tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/requires.txt 2026-04-24T01:13:42,993 writing top-level names to /tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/top_level.txt 2026-04-24T01:13:42,994 writing manifest file '/tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/SOURCES.txt' 2026-04-24T01:13:43,039 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. 2026-04-24T01:13:43,039 return get_active_overrides().subprocess_timeout 2026-04-24T01:13:43,046 listing git files failed - pretending there aren't any 2026-04-24T01:13:43,051 reading manifest file '/tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/SOURCES.txt' 2026-04-24T01:13:43,053 reading manifest template 'MANIFEST.in' 2026-04-24T01:13:43,054 adding license file 'LICENSE.txt' 2026-04-24T01:13:43,061 writing manifest file '/tmp/pip-modern-metadata-wib2yvdp/cryodrgn.egg-info/SOURCES.txt' 2026-04-24T01:13:43,063 creating '/tmp/pip-modern-metadata-wib2yvdp/cryodrgn-4.2.1.dist-info' 2026-04-24T01:13:43,202 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-24T01:13:43,208 Source in /tmp/pip-wheel-hfdz2h7t/cryodrgn_a03a5a2f24f2458ebc7abaf2ab1711d8 has version 4.2.1, which satisfies requirement cryodrgn==4.2.1 from https://files.pythonhosted.org/packages/16/2a/19c8882dab0f461a06d17b355fdaeb62e40b6b38fdb771297c40e59e4478/cryodrgn-4.2.1.tar.gz 2026-04-24T01:13:43,209 Removed cryodrgn==4.2.1 from https://files.pythonhosted.org/packages/16/2a/19c8882dab0f461a06d17b355fdaeb62e40b6b38fdb771297c40e59e4478/cryodrgn-4.2.1.tar.gz from build tracker '/tmp/pip-build-tracker-_f8h8zr2' 2026-04-24T01:13:43,216 Created temporary directory: /tmp/pip-unpack-pj8yzw9e 2026-04-24T01:13:43,217 Building wheels for collected packages: cryodrgn 2026-04-24T01:13:43,221 Created temporary directory: /tmp/pip-wheel-x72liaz0 2026-04-24T01:13:43,222 Destination directory: /tmp/pip-wheel-x72liaz0 2026-04-24T01:13:43,224 Building wheel for cryodrgn (pyproject.toml): started 2026-04-24T01:13:43,225 Running command Building wheel for cryodrgn (pyproject.toml) 2026-04-24T01:13:43,959 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-24T01:13:43,960 !! 2026-04-24T01:13:43,961 ******************************************************************************** 2026-04-24T01:13:43,961 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-24T01:13:43,962 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-04-24T01:13:43,963 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-24T01:13:43,964 ******************************************************************************** 2026-04-24T01:13:43,965 !! 2026-04-24T01:13:43,966 dist._finalize_license_expression() 2026-04-24T01:13:43,966 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-24T01:13:43,967 !! 2026-04-24T01:13:43,968 ******************************************************************************** 2026-04-24T01:13:43,969 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-24T01:13:43,970 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2026-04-24T01:13:43,972 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-24T01:13:43,972 ******************************************************************************** 2026-04-24T01:13:43,973 !! 2026-04-24T01:13:43,974 self._finalize_license_expression() 2026-04-24T01:13:43,974 running bdist_wheel 2026-04-24T01:13:43,995 running build 2026-04-24T01:13:43,995 running build_py 2026-04-24T01:13:43,998 creating build/lib/cryodrgn 2026-04-24T01:13:44,000 copying cryodrgn/command_line.py -> build/lib/cryodrgn 2026-04-24T01:13:44,003 copying cryodrgn/lie_tools.py -> build/lib/cryodrgn 2026-04-24T01:13:44,005 copying cryodrgn/analysis_drgnai.py -> build/lib/cryodrgn 2026-04-24T01:13:44,008 copying cryodrgn/lattice.py -> build/lib/cryodrgn 2026-04-24T01:13:44,010 copying cryodrgn/losses.py -> build/lib/cryodrgn 2026-04-24T01:13:44,012 copying cryodrgn/pose_search.py -> build/lib/cryodrgn 2026-04-24T01:13:44,015 copying cryodrgn/models_ai.py -> build/lib/cryodrgn 2026-04-24T01:13:44,018 copying cryodrgn/make_healpy.py -> build/lib/cryodrgn 2026-04-24T01:13:44,020 copying cryodrgn/masking.py -> build/lib/cryodrgn 2026-04-24T01:13:44,022 copying cryodrgn/pose_search_ai.py -> build/lib/cryodrgn 2026-04-24T01:13:44,025 copying cryodrgn/shift_grid3.py -> build/lib/cryodrgn 2026-04-24T01:13:44,027 copying cryodrgn/fft.py -> build/lib/cryodrgn 2026-04-24T01:13:44,029 copying cryodrgn/ctf.py -> build/lib/cryodrgn 2026-04-24T01:13:44,031 copying cryodrgn/metrics.py -> build/lib/cryodrgn 2026-04-24T01:13:44,033 copying cryodrgn/shift_grid.py -> build/lib/cryodrgn 2026-04-24T01:13:44,035 copying cryodrgn/source.py -> build/lib/cryodrgn 2026-04-24T01:13:44,037 copying cryodrgn/starfile.py -> build/lib/cryodrgn 2026-04-24T01:13:44,040 copying cryodrgn/beta_schedule.py -> build/lib/cryodrgn 2026-04-24T01:13:44,042 copying cryodrgn/utils.py -> build/lib/cryodrgn 2026-04-24T01:13:44,044 copying cryodrgn/_version.py -> build/lib/cryodrgn 2026-04-24T01:13:44,046 copying cryodrgn/config.py -> build/lib/cryodrgn 2026-04-24T01:13:44,048 copying cryodrgn/analysis.py -> build/lib/cryodrgn 2026-04-24T01:13:44,050 copying cryodrgn/pose.py -> build/lib/cryodrgn 2026-04-24T01:13:44,052 copying cryodrgn/so3_grid.py -> build/lib/cryodrgn 2026-04-24T01:13:44,055 copying cryodrgn/dataset.py -> build/lib/cryodrgn 2026-04-24T01:13:44,057 copying cryodrgn/models.py -> build/lib/cryodrgn 2026-04-24T01:13:44,060 copying cryodrgn/__init__.py -> build/lib/cryodrgn 2026-04-24T01:13:44,062 copying cryodrgn/mrcfile.py -> build/lib/cryodrgn 2026-04-24T01:13:44,065 creating build/lib/cryodrgn/commands 2026-04-24T01:13:44,067 copying cryodrgn/commands/parse_ctf_csparc.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,069 copying cryodrgn/commands/analyze_landscape_full.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,072 copying cryodrgn/commands/parse_pose_star.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,073 copying cryodrgn/commands/backproject_voxel.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,076 copying cryodrgn/commands/abinit.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,080 copying cryodrgn/commands/train_vae.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,083 copying cryodrgn/commands/dashboard.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,085 copying cryodrgn/commands/parse_pose_csparc.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,087 copying cryodrgn/commands/analyze.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,090 copying cryodrgn/commands/pc_traversal.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,092 copying cryodrgn/commands/train_nn.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,094 copying cryodrgn/commands/graph_traversal.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,097 copying cryodrgn/commands/abinit_het_old.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,100 copying cryodrgn/commands/eval_images.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,102 copying cryodrgn/commands/filter.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,105 copying cryodrgn/commands/direct_traversal.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,107 copying cryodrgn/commands/analyze_landscape.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,110 copying cryodrgn/commands/parse_star.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,112 copying cryodrgn/commands/eval_vol.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,114 copying cryodrgn/commands/abinit_homo_old.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,117 copying cryodrgn/commands/downsample.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,119 copying cryodrgn/commands/train_dec.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,122 copying cryodrgn/commands/__init__.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,123 copying cryodrgn/commands/parse_ctf_star.py -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,126 creating build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,128 copying cryodrgn/commands_utils/phase_flip.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,130 copying cryodrgn/commands_utils/gen_mask.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,131 copying cryodrgn/commands_utils/plot_classes.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,134 copying cryodrgn/commands_utils/invert_contrast.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,136 copying cryodrgn/commands_utils/view_mrcs.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,138 copying cryodrgn/commands_utils/flip_hand.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,139 copying cryodrgn/commands_utils/concat_pkls.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,141 copying cryodrgn/commands_utils/make_movies.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,143 copying cryodrgn/commands_utils/add_psize.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,145 copying cryodrgn/commands_utils/write_star.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,147 copying cryodrgn/commands_utils/filter_pkl.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,149 copying cryodrgn/commands_utils/select_clusters.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,151 copying cryodrgn/commands_utils/parse_relion.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,153 copying cryodrgn/commands_utils/filter_cs.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,155 copying cryodrgn/commands_utils/filter_mrcs.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,157 copying cryodrgn/commands_utils/translate_mrcs.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,159 copying cryodrgn/commands_utils/view_cs_header.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,161 copying cryodrgn/commands_utils/view_header.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,162 copying cryodrgn/commands_utils/filter_star.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,164 copying cryodrgn/commands_utils/plot_fsc.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,167 copying cryodrgn/commands_utils/fsc.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,169 copying cryodrgn/commands_utils/write_cs.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,171 copying cryodrgn/commands_utils/__init__.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,173 copying cryodrgn/commands_utils/select_random.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,175 copying cryodrgn/commands_utils/analyze_convergence.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,178 copying cryodrgn/commands_utils/clean.py -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,181 creating build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,182 copying cryodrgn/dashboard/data.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,185 copying cryodrgn/dashboard/app.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,188 copying cryodrgn/dashboard/plots.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,191 copying cryodrgn/dashboard/trajectory.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,194 copying cryodrgn/dashboard/command_builder_cli_help.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,195 copying cryodrgn/dashboard/context.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,198 copying cryodrgn/dashboard/mpl_style.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,200 copying cryodrgn/dashboard/bench_plot_interfaces.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,203 copying cryodrgn/dashboard/preload.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,205 copying cryodrgn/dashboard/command_builder_data.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,208 copying cryodrgn/dashboard/explorer_volumes.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,210 copying cryodrgn/dashboard/__init__.py -> build/lib/cryodrgn/dashboard 2026-04-24T01:13:44,213 running egg_info 2026-04-24T01:13:44,226 writing cryodrgn.egg-info/PKG-INFO 2026-04-24T01:13:44,231 writing dependency_links to cryodrgn.egg-info/dependency_links.txt 2026-04-24T01:13:44,233 writing entry points to cryodrgn.egg-info/entry_points.txt 2026-04-24T01:13:44,236 writing requirements to cryodrgn.egg-info/requires.txt 2026-04-24T01:13:44,237 writing top-level names to cryodrgn.egg-info/top_level.txt 2026-04-24T01:13:44,274 /tmp/pip-build-env-9g392v1q/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. 2026-04-24T01:13:44,275 return get_active_overrides().subprocess_timeout 2026-04-24T01:13:44,281 listing git files failed - pretending there aren't any 2026-04-24T01:13:44,285 reading manifest file 'cryodrgn.egg-info/SOURCES.txt' 2026-04-24T01:13:44,299 reading manifest template 'MANIFEST.in' 2026-04-24T01:13:44,301 adding license file 'LICENSE.txt' 2026-04-24T01:13:44,312 writing manifest file 'cryodrgn.egg-info/SOURCES.txt' 2026-04-24T01:13:44,323 copying cryodrgn/healpy_grid.json -> build/lib/cryodrgn 2026-04-24T01:13:44,487 copying cryodrgn/commands/README.md -> build/lib/cryodrgn/commands 2026-04-24T01:13:44,490 copying cryodrgn/commands_utils/README.md -> build/lib/cryodrgn/commands_utils 2026-04-24T01:13:44,492 creating build/lib/cryodrgn/templates 2026-04-24T01:13:44,493 copying cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/lib/cryodrgn/templates 2026-04-24T01:13:44,496 copying cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/lib/cryodrgn/templates 2026-04-24T01:13:44,499 copying cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/lib/cryodrgn/templates 2026-04-24T01:13:44,502 copying cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/lib/cryodrgn/templates 2026-04-24T01:13:44,505 copying cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/lib/cryodrgn/templates 2026-04-24T01:13:44,508 creating build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,509 copying cryodrgn/dashboard/templates/latent_3d.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,512 copying cryodrgn/dashboard/templates/scatter_explorer.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,515 copying cryodrgn/dashboard/templates/pair_grid.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,518 copying cryodrgn/dashboard/templates/index.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,521 copying cryodrgn/dashboard/templates/pair_grid_need_more_cols.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,523 copying cryodrgn/dashboard/templates/trajectory_creator.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,527 copying cryodrgn/dashboard/templates/no_images.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,529 copying cryodrgn/dashboard/templates/base.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,532 copying cryodrgn/dashboard/templates/command_builder.html -> build/lib/cryodrgn/dashboard/templates 2026-04-24T01:13:44,535 creating build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,536 copying cryodrgn/dashboard/static/cryodrgn_logo.png -> build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,560 copying cryodrgn/dashboard/static/thumb_viewer.png -> build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,565 copying cryodrgn/dashboard/static/thumb_command_builder.png -> build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,568 copying cryodrgn/dashboard/static/thumb_pair.png -> build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,572 copying cryodrgn/dashboard/static/thumb_3d.png -> build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,576 copying cryodrgn/dashboard/static/favicon.png -> build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,595 copying cryodrgn/dashboard/static/thumb_trajectory.png -> build/lib/cryodrgn/dashboard/static 2026-04-24T01:13:44,624 installing to build/bdist.linux-armv7l/wheel 2026-04-24T01:13:44,625 running install 2026-04-24T01:13:44,649 running install_lib 2026-04-24T01:13:44,657 creating build/bdist.linux-armv7l/wheel 2026-04-24T01:13:44,660 creating build/bdist.linux-armv7l/wheel/cryodrgn 2026-04-24T01:13:44,662 copying build/lib/cryodrgn/command_line.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,664 copying build/lib/cryodrgn/lie_tools.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,667 copying build/lib/cryodrgn/analysis_drgnai.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,670 copying build/lib/cryodrgn/lattice.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,673 copying build/lib/cryodrgn/losses.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,675 copying build/lib/cryodrgn/pose_search.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,678 copying build/lib/cryodrgn/models_ai.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,681 copying build/lib/cryodrgn/make_healpy.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,683 copying build/lib/cryodrgn/masking.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,686 copying build/lib/cryodrgn/pose_search_ai.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,689 copying build/lib/cryodrgn/shift_grid3.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,692 creating build/bdist.linux-armv7l/wheel/cryodrgn/commands 2026-04-24T01:13:44,693 copying build/lib/cryodrgn/commands/parse_ctf_csparc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,696 copying build/lib/cryodrgn/commands/analyze_landscape_full.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,699 copying build/lib/cryodrgn/commands/parse_pose_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,701 copying build/lib/cryodrgn/commands/backproject_voxel.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,704 copying build/lib/cryodrgn/commands/README.md -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,706 copying build/lib/cryodrgn/commands/abinit.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,710 copying build/lib/cryodrgn/commands/train_vae.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,713 copying build/lib/cryodrgn/commands/dashboard.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,716 copying build/lib/cryodrgn/commands/parse_pose_csparc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,718 copying build/lib/cryodrgn/commands/analyze.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,721 copying build/lib/cryodrgn/commands/pc_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,723 copying build/lib/cryodrgn/commands/train_nn.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,726 copying build/lib/cryodrgn/commands/graph_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,729 copying build/lib/cryodrgn/commands/abinit_het_old.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,732 copying build/lib/cryodrgn/commands/eval_images.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,735 copying build/lib/cryodrgn/commands/filter.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,738 copying build/lib/cryodrgn/commands/direct_traversal.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,740 copying build/lib/cryodrgn/commands/analyze_landscape.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,743 copying build/lib/cryodrgn/commands/parse_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,745 copying build/lib/cryodrgn/commands/eval_vol.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,748 copying build/lib/cryodrgn/commands/abinit_homo_old.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,751 copying build/lib/cryodrgn/commands/downsample.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,754 copying build/lib/cryodrgn/commands/train_dec.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,757 copying build/lib/cryodrgn/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,759 copying build/lib/cryodrgn/commands/parse_ctf_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands 2026-04-24T01:13:44,761 copying build/lib/cryodrgn/fft.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,763 copying build/lib/cryodrgn/ctf.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,766 copying build/lib/cryodrgn/metrics.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,769 creating build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils 2026-04-24T01:13:44,771 copying build/lib/cryodrgn/commands_utils/phase_flip.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,773 copying build/lib/cryodrgn/commands_utils/gen_mask.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,775 copying build/lib/cryodrgn/commands_utils/plot_classes.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,778 copying build/lib/cryodrgn/commands_utils/invert_contrast.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,780 copying build/lib/cryodrgn/commands_utils/README.md -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,782 copying build/lib/cryodrgn/commands_utils/view_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,784 copying build/lib/cryodrgn/commands_utils/flip_hand.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,786 copying build/lib/cryodrgn/commands_utils/concat_pkls.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,788 copying build/lib/cryodrgn/commands_utils/make_movies.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,791 copying build/lib/cryodrgn/commands_utils/add_psize.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,794 copying build/lib/cryodrgn/commands_utils/write_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,796 copying build/lib/cryodrgn/commands_utils/filter_pkl.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,799 copying build/lib/cryodrgn/commands_utils/select_clusters.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,801 copying build/lib/cryodrgn/commands_utils/parse_relion.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,804 copying build/lib/cryodrgn/commands_utils/filter_cs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,806 copying build/lib/cryodrgn/commands_utils/filter_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,808 copying build/lib/cryodrgn/commands_utils/translate_mrcs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,811 copying build/lib/cryodrgn/commands_utils/view_cs_header.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,813 copying build/lib/cryodrgn/commands_utils/view_header.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,815 copying build/lib/cryodrgn/commands_utils/filter_star.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,817 copying build/lib/cryodrgn/commands_utils/plot_fsc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,820 copying build/lib/cryodrgn/commands_utils/fsc.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,823 copying build/lib/cryodrgn/commands_utils/write_cs.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,825 copying build/lib/cryodrgn/commands_utils/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,827 copying build/lib/cryodrgn/commands_utils/select_random.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,829 copying build/lib/cryodrgn/commands_utils/analyze_convergence.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,832 copying build/lib/cryodrgn/commands_utils/clean.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/commands_utils 2026-04-24T01:13:44,835 copying build/lib/cryodrgn/shift_grid.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,837 copying build/lib/cryodrgn/source.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,839 copying build/lib/cryodrgn/starfile.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,842 copying build/lib/cryodrgn/beta_schedule.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,843 copying build/lib/cryodrgn/utils.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,846 copying build/lib/cryodrgn/_version.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,848 copying build/lib/cryodrgn/config.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,850 copying build/lib/cryodrgn/analysis.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:44,853 copying build/lib/cryodrgn/healpy_grid.json -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:45,005 copying build/lib/cryodrgn/pose.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:45,007 copying build/lib/cryodrgn/so3_grid.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:45,010 copying build/lib/cryodrgn/dataset.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:45,013 creating build/bdist.linux-armv7l/wheel/cryodrgn/templates 2026-04-24T01:13:45,014 copying build/lib/cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2026-04-24T01:13:45,017 copying build/lib/cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2026-04-24T01:13:45,019 copying build/lib/cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2026-04-24T01:13:45,022 copying build/lib/cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2026-04-24T01:13:45,025 copying build/lib/cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/./cryodrgn/templates 2026-04-24T01:13:45,027 copying build/lib/cryodrgn/models.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:45,031 creating build/bdist.linux-armv7l/wheel/cryodrgn/dashboard 2026-04-24T01:13:45,032 copying build/lib/cryodrgn/dashboard/data.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,034 copying build/lib/cryodrgn/dashboard/app.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,037 copying build/lib/cryodrgn/dashboard/plots.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,040 copying build/lib/cryodrgn/dashboard/trajectory.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,043 copying build/lib/cryodrgn/dashboard/command_builder_cli_help.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,046 creating build/bdist.linux-armv7l/wheel/cryodrgn/dashboard/static 2026-04-24T01:13:45,047 copying build/lib/cryodrgn/dashboard/static/cryodrgn_logo.png -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/static 2026-04-24T01:13:45,065 copying build/lib/cryodrgn/dashboard/static/thumb_viewer.png -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/static 2026-04-24T01:13:45,069 copying build/lib/cryodrgn/dashboard/static/thumb_command_builder.png -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/static 2026-04-24T01:13:45,072 copying build/lib/cryodrgn/dashboard/static/thumb_pair.png -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/static 2026-04-24T01:13:45,076 copying build/lib/cryodrgn/dashboard/static/thumb_3d.png -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/static 2026-04-24T01:13:45,080 copying build/lib/cryodrgn/dashboard/static/favicon.png -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/static 2026-04-24T01:13:45,099 copying build/lib/cryodrgn/dashboard/static/thumb_trajectory.png -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/static 2026-04-24T01:13:45,103 copying build/lib/cryodrgn/dashboard/context.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,105 copying build/lib/cryodrgn/dashboard/mpl_style.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,107 copying build/lib/cryodrgn/dashboard/bench_plot_interfaces.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,109 copying build/lib/cryodrgn/dashboard/preload.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,112 creating build/bdist.linux-armv7l/wheel/cryodrgn/dashboard/templates 2026-04-24T01:13:45,113 copying build/lib/cryodrgn/dashboard/templates/latent_3d.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,115 copying build/lib/cryodrgn/dashboard/templates/scatter_explorer.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,118 copying build/lib/cryodrgn/dashboard/templates/pair_grid.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,121 copying build/lib/cryodrgn/dashboard/templates/index.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,124 copying build/lib/cryodrgn/dashboard/templates/pair_grid_need_more_cols.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,125 copying build/lib/cryodrgn/dashboard/templates/trajectory_creator.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,129 copying build/lib/cryodrgn/dashboard/templates/no_images.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,130 copying build/lib/cryodrgn/dashboard/templates/base.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,133 copying build/lib/cryodrgn/dashboard/templates/command_builder.html -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard/templates 2026-04-24T01:13:45,136 copying build/lib/cryodrgn/dashboard/command_builder_data.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,138 copying build/lib/cryodrgn/dashboard/explorer_volumes.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,141 copying build/lib/cryodrgn/dashboard/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn/dashboard 2026-04-24T01:13:45,143 copying build/lib/cryodrgn/__init__.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:45,146 copying build/lib/cryodrgn/mrcfile.py -> build/bdist.linux-armv7l/wheel/./cryodrgn 2026-04-24T01:13:45,148 running install_egg_info 2026-04-24T01:13:45,155 Copying cryodrgn.egg-info to build/bdist.linux-armv7l/wheel/./cryodrgn-4.2.1-py3.11.egg-info 2026-04-24T01:13:45,169 running install_scripts 2026-04-24T01:13:45,183 creating build/bdist.linux-armv7l/wheel/cryodrgn-4.2.1.dist-info/WHEEL 2026-04-24T01:13:45,186 creating '/tmp/pip-wheel-x72liaz0/.tmp-dbu1mc4l/cryodrgn-4.2.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-24T01:13:45,188 adding 'cryodrgn/__init__.py' 2026-04-24T01:13:45,190 adding 'cryodrgn/_version.py' 2026-04-24T01:13:45,194 adding 'cryodrgn/analysis.py' 2026-04-24T01:13:45,197 adding 'cryodrgn/analysis_drgnai.py' 2026-04-24T01:13:45,198 adding 'cryodrgn/beta_schedule.py' 2026-04-24T01:13:45,200 adding 'cryodrgn/command_line.py' 2026-04-24T01:13:45,202 adding 'cryodrgn/config.py' 2026-04-24T01:13:45,204 adding 'cryodrgn/ctf.py' 2026-04-24T01:13:45,207 adding 'cryodrgn/dataset.py' 2026-04-24T01:13:45,209 adding 'cryodrgn/fft.py' 2026-04-24T01:13:45,976 adding 'cryodrgn/healpy_grid.json' 2026-04-24T01:13:46,041 adding 'cryodrgn/lattice.py' 2026-04-24T01:13:46,043 adding 'cryodrgn/lie_tools.py' 2026-04-24T01:13:46,045 adding 'cryodrgn/losses.py' 2026-04-24T01:13:46,046 adding 'cryodrgn/make_healpy.py' 2026-04-24T01:13:46,047 adding 'cryodrgn/masking.py' 2026-04-24T01:13:46,049 adding 'cryodrgn/metrics.py' 2026-04-24T01:13:46,053 adding 'cryodrgn/models.py' 2026-04-24T01:13:46,057 adding 'cryodrgn/models_ai.py' 2026-04-24T01:13:46,059 adding 'cryodrgn/mrcfile.py' 2026-04-24T01:13:46,061 adding 'cryodrgn/pose.py' 2026-04-24T01:13:46,063 adding 'cryodrgn/pose_search.py' 2026-04-24T01:13:46,066 adding 'cryodrgn/pose_search_ai.py' 2026-04-24T01:13:46,068 adding 'cryodrgn/shift_grid.py' 2026-04-24T01:13:46,069 adding 'cryodrgn/shift_grid3.py' 2026-04-24T01:13:46,071 adding 'cryodrgn/so3_grid.py' 2026-04-24T01:13:46,074 adding 'cryodrgn/source.py' 2026-04-24T01:13:46,076 adding 'cryodrgn/starfile.py' 2026-04-24T01:13:46,078 adding 'cryodrgn/utils.py' 2026-04-24T01:13:46,080 adding 'cryodrgn/commands/README.md' 2026-04-24T01:13:46,081 adding 'cryodrgn/commands/__init__.py' 2026-04-24T01:13:46,087 adding 'cryodrgn/commands/abinit.py' 2026-04-24T01:13:46,092 adding 'cryodrgn/commands/abinit_het_old.py' 2026-04-24T01:13:46,095 adding 'cryodrgn/commands/abinit_homo_old.py' 2026-04-24T01:13:46,098 adding 'cryodrgn/commands/analyze.py' 2026-04-24T01:13:46,100 adding 'cryodrgn/commands/analyze_landscape.py' 2026-04-24T01:13:46,103 adding 'cryodrgn/commands/analyze_landscape_full.py' 2026-04-24T01:13:46,106 adding 'cryodrgn/commands/backproject_voxel.py' 2026-04-24T01:13:46,108 adding 'cryodrgn/commands/dashboard.py' 2026-04-24T01:13:46,109 adding 'cryodrgn/commands/direct_traversal.py' 2026-04-24T01:13:46,111 adding 'cryodrgn/commands/downsample.py' 2026-04-24T01:13:46,113 adding 'cryodrgn/commands/eval_images.py' 2026-04-24T01:13:46,115 adding 'cryodrgn/commands/eval_vol.py' 2026-04-24T01:13:46,118 adding 'cryodrgn/commands/filter.py' 2026-04-24T01:13:46,120 adding 'cryodrgn/commands/graph_traversal.py' 2026-04-24T01:13:46,121 adding 'cryodrgn/commands/parse_ctf_csparc.py' 2026-04-24T01:13:46,122 adding 'cryodrgn/commands/parse_ctf_star.py' 2026-04-24T01:13:46,124 adding 'cryodrgn/commands/parse_pose_csparc.py' 2026-04-24T01:13:46,125 adding 'cryodrgn/commands/parse_pose_star.py' 2026-04-24T01:13:46,127 adding 'cryodrgn/commands/parse_star.py' 2026-04-24T01:13:46,128 adding 'cryodrgn/commands/pc_traversal.py' 2026-04-24T01:13:46,131 adding 'cryodrgn/commands/train_dec.py' 2026-04-24T01:13:46,133 adding 'cryodrgn/commands/train_nn.py' 2026-04-24T01:13:46,137 adding 'cryodrgn/commands/train_vae.py' 2026-04-24T01:13:46,139 adding 'cryodrgn/commands_utils/README.md' 2026-04-24T01:13:46,140 adding 'cryodrgn/commands_utils/__init__.py' 2026-04-24T01:13:46,142 adding 'cryodrgn/commands_utils/add_psize.py' 2026-04-24T01:13:46,147 adding 'cryodrgn/commands_utils/analyze_convergence.py' 2026-04-24T01:13:46,149 adding 'cryodrgn/commands_utils/clean.py' 2026-04-24T01:13:46,150 adding 'cryodrgn/commands_utils/concat_pkls.py' 2026-04-24T01:13:46,151 adding 'cryodrgn/commands_utils/filter_cs.py' 2026-04-24T01:13:46,153 adding 'cryodrgn/commands_utils/filter_mrcs.py' 2026-04-24T01:13:46,154 adding 'cryodrgn/commands_utils/filter_pkl.py' 2026-04-24T01:13:46,155 adding 'cryodrgn/commands_utils/filter_star.py' 2026-04-24T01:13:46,157 adding 'cryodrgn/commands_utils/flip_hand.py' 2026-04-24T01:13:46,159 adding 'cryodrgn/commands_utils/fsc.py' 2026-04-24T01:13:46,160 adding 'cryodrgn/commands_utils/gen_mask.py' 2026-04-24T01:13:46,162 adding 'cryodrgn/commands_utils/invert_contrast.py' 2026-04-24T01:13:46,163 adding 'cryodrgn/commands_utils/make_movies.py' 2026-04-24T01:13:46,166 adding 'cryodrgn/commands_utils/parse_relion.py' 2026-04-24T01:13:46,167 adding 'cryodrgn/commands_utils/phase_flip.py' 2026-04-24T01:13:46,169 adding 'cryodrgn/commands_utils/plot_classes.py' 2026-04-24T01:13:46,170 adding 'cryodrgn/commands_utils/plot_fsc.py' 2026-04-24T01:13:46,172 adding 'cryodrgn/commands_utils/select_clusters.py' 2026-04-24T01:13:46,173 adding 'cryodrgn/commands_utils/select_random.py' 2026-04-24T01:13:46,174 adding 'cryodrgn/commands_utils/translate_mrcs.py' 2026-04-24T01:13:46,176 adding 'cryodrgn/commands_utils/view_cs_header.py' 2026-04-24T01:13:46,177 adding 'cryodrgn/commands_utils/view_header.py' 2026-04-24T01:13:46,178 adding 'cryodrgn/commands_utils/view_mrcs.py' 2026-04-24T01:13:46,179 adding 'cryodrgn/commands_utils/write_cs.py' 2026-04-24T01:13:46,181 adding 'cryodrgn/commands_utils/write_star.py' 2026-04-24T01:13:46,183 adding 'cryodrgn/dashboard/__init__.py' 2026-04-24T01:13:46,187 adding 'cryodrgn/dashboard/app.py' 2026-04-24T01:13:46,188 adding 'cryodrgn/dashboard/bench_plot_interfaces.py' 2026-04-24T01:13:46,190 adding 'cryodrgn/dashboard/command_builder_cli_help.py' 2026-04-24T01:13:46,192 adding 'cryodrgn/dashboard/command_builder_data.py' 2026-04-24T01:13:46,195 adding 'cryodrgn/dashboard/context.py' 2026-04-24T01:13:46,196 adding 'cryodrgn/dashboard/data.py' 2026-04-24T01:13:46,199 adding 'cryodrgn/dashboard/explorer_volumes.py' 2026-04-24T01:13:46,200 adding 'cryodrgn/dashboard/mpl_style.py' 2026-04-24T01:13:46,204 adding 'cryodrgn/dashboard/plots.py' 2026-04-24T01:13:46,206 adding 'cryodrgn/dashboard/preload.py' 2026-04-24T01:13:46,209 adding 'cryodrgn/dashboard/trajectory.py' 2026-04-24T01:13:46,320 adding 'cryodrgn/dashboard/static/cryodrgn_logo.png' 2026-04-24T01:13:46,436 adding 'cryodrgn/dashboard/static/favicon.png' 2026-04-24T01:13:46,450 adding 'cryodrgn/dashboard/static/thumb_3d.png' 2026-04-24T01:13:46,454 adding 'cryodrgn/dashboard/static/thumb_command_builder.png' 2026-04-24T01:13:46,463 adding 'cryodrgn/dashboard/static/thumb_pair.png' 2026-04-24T01:13:46,473 adding 'cryodrgn/dashboard/static/thumb_trajectory.png' 2026-04-24T01:13:46,488 adding 'cryodrgn/dashboard/static/thumb_viewer.png' 2026-04-24T01:13:46,492 adding 'cryodrgn/dashboard/templates/base.html' 2026-04-24T01:13:46,495 adding 'cryodrgn/dashboard/templates/command_builder.html' 2026-04-24T01:13:46,497 adding 'cryodrgn/dashboard/templates/index.html' 2026-04-24T01:13:46,499 adding 'cryodrgn/dashboard/templates/latent_3d.html' 2026-04-24T01:13:46,501 adding 'cryodrgn/dashboard/templates/no_images.html' 2026-04-24T01:13:46,504 adding 'cryodrgn/dashboard/templates/pair_grid.html' 2026-04-24T01:13:46,505 adding 'cryodrgn/dashboard/templates/pair_grid_need_more_cols.html' 2026-04-24T01:13:46,514 adding 'cryodrgn/dashboard/templates/scatter_explorer.html' 2026-04-24T01:13:46,522 adding 'cryodrgn/dashboard/templates/trajectory_creator.html' 2026-04-24T01:13:46,526 adding 'cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb' 2026-04-24T01:13:46,528 adding 'cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb' 2026-04-24T01:13:46,530 adding 'cryodrgn/templates/cryoDRGN_figures_template.ipynb' 2026-04-24T01:13:46,533 adding 'cryodrgn/templates/cryoDRGN_filtering_template.ipynb' 2026-04-24T01:13:46,535 adding 'cryodrgn/templates/cryoDRGN_viz_template.ipynb' 2026-04-24T01:13:46,543 adding 'cryodrgn-4.2.1.dist-info/licenses/LICENSE.txt' 2026-04-24T01:13:46,547 adding 'cryodrgn-4.2.1.dist-info/METADATA' 2026-04-24T01:13:46,548 adding 'cryodrgn-4.2.1.dist-info/WHEEL' 2026-04-24T01:13:46,549 adding 'cryodrgn-4.2.1.dist-info/entry_points.txt' 2026-04-24T01:13:46,551 adding 'cryodrgn-4.2.1.dist-info/top_level.txt' 2026-04-24T01:13:46,553 adding 'cryodrgn-4.2.1.dist-info/RECORD' 2026-04-24T01:13:46,606 removing build/bdist.linux-armv7l/wheel 2026-04-24T01:13:46,749 Building wheel for cryodrgn (pyproject.toml): finished with status 'done' 2026-04-24T01:13:46,830 Created wheel for cryodrgn: filename=cryodrgn-4.2.1-py3-none-any.whl size=3737885 sha256=380572553ecc18de647c6be286e502d34060095af5bd57bea72c6a3426650620 2026-04-24T01:13:46,831 Stored in directory: /tmp/pip-ephem-wheel-cache-nn0muygi/wheels/5c/e6/8d/4b952d13ccd6706f3bf70307c1b26bd009a45b160555fba0c0 2026-04-24T01:13:46,854 Successfully built cryodrgn 2026-04-24T01:13:46,945 Removed build tracker: '/tmp/pip-build-tracker-_f8h8zr2'