2023-03-26T04:52:11,780 Created temporary directory: /tmp/pip-ephem-wheel-cache-wuygj76t
2023-03-26T04:52:11,785 Created temporary directory: /tmp/pip-build-tracker-w15j4bkb
2023-03-26T04:52:11,786 Initialized build tracking at /tmp/pip-build-tracker-w15j4bkb
2023-03-26T04:52:11,787 Created build tracker: /tmp/pip-build-tracker-w15j4bkb
2023-03-26T04:52:11,787 Entered build tracker: /tmp/pip-build-tracker-w15j4bkb
2023-03-26T04:52:11,788 Created temporary directory: /tmp/pip-wheel-m8i7mj8g
2023-03-26T04:52:11,798 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
2023-03-26T04:52:11,804 Created temporary directory: /tmp/pip-ephem-wheel-cache-8h07v_ye
2023-03-26T04:52:11,863 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-26T04:52:11,870 2 location(s) to search for versions of cryodrgn:
2023-03-26T04:52:11,870 * https://pypi.org/simple/cryodrgn/
2023-03-26T04:52:11,870 * https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:52:11,871 Fetching project page and analyzing links: https://pypi.org/simple/cryodrgn/
2023-03-26T04:52:11,872 Getting page https://pypi.org/simple/cryodrgn/
2023-03-26T04:52:11,875 Found index url https://pypi.org/simple
2023-03-26T04:52:11,999 Fetched page https://pypi.org/simple/cryodrgn/ as application/vnd.pypi.simple.v1+json
2023-03-26T04:52:12,005   Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/50/91/1306b78002812cfa9932e2691070f765b75d4385e4bbf559d211a4e71025/cryodrgn-1.1.1-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-03-26T04:52:12,007   Found link https://files.pythonhosted.org/packages/24/08/8de601e5f4fe8a5177c4191c0be1848d2952dad0ef149820aadadbee2e08/cryodrgn-1.1.1.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 1.1.1
2023-03-26T04:52:12,007   Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/e9/78/bdf1fd8d9394a0025206a4d1478b21170d7392e35132522c5ef87855fe73/cryodrgn-2.1.0b5-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-03-26T04:52:12,009   Found link https://files.pythonhosted.org/packages/68/26/6669e39abe77e36bd49d1f21f68ed04961bdd0a76f909b497c96ce78b60b/cryodrgn-2.1.0b5.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 2.1.0b5
2023-03-26T04:52:12,009   Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/7d/d8/dae369c30a1b908f5713f7b46f4948aed0253f9e7e124c98e6c7b15d7e57/cryodrgn-2.2.0b0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-03-26T04:52:12,011   Found link https://files.pythonhosted.org/packages/6f/19/b950e5eb7a6d3c8d122bec56e59c447d3585a660a7605112a5346816014e/cryodrgn-2.2.0b0.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 2.2.0b0
2023-03-26T04:52:12,011   Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/6d/79/97a3f0118ef0c156bf5eaf931f4a5855a5c5d27dedd04aaa0bcf57fe1f7c/cryodrgn-2.2.0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-03-26T04:52:12,013   Found link https://files.pythonhosted.org/packages/03/50/3259e1a4efc92c945d1ae88fd5765a0ba4db77f0a742fc0e0a206cd781ac/cryodrgn-2.2.0.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 2.2.0
2023-03-26T04:52:12,014 Fetching project page and analyzing links: https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:52:12,014 Getting page https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:52:12,017 Found index url https://www.piwheels.org/simple
2023-03-26T04:52:12,251 Fetched page https://www.piwheels.org/simple/cryodrgn/ as text/html
2023-03-26T04:52:12,255   Skipping link: No binaries permitted for cryodrgn: https://www.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)
2023-03-26T04:52:12,256   Skipping link: No binaries permitted for cryodrgn: https://www.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)
2023-03-26T04:52:12,256   Skipping link: No binaries permitted for cryodrgn: https://www.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)
2023-03-26T04:52:12,257 Skipping link: not a file: https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:52:12,258 Skipping link: not a file: https://pypi.org/simple/cryodrgn/
2023-03-26T04:52:12,291 Given no hashes to check 1 links for project 'cryodrgn': discarding no candidates
2023-03-26T04:52:12,321 Collecting cryodrgn==2.2.0
2023-03-26T04:52:12,326   Created temporary directory: /tmp/pip-unpack-rp7cbjf5
2023-03-26T04:52:12,558   Downloading cryodrgn-2.2.0.tar.gz (31.4 MB)
2023-03-26T04:52:30,341   Added cryodrgn==2.2.0 from https://files.pythonhosted.org/packages/03/50/3259e1a4efc92c945d1ae88fd5765a0ba4db77f0a742fc0e0a206cd781ac/cryodrgn-2.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-w15j4bkb'
2023-03-26T04:52:30,355   Created temporary directory: /tmp/pip-build-env-_et9j084
2023-03-26T04:52:30,375   Installing build dependencies: started
2023-03-26T04:52:30,378   Running command pip subprocess to install build dependencies
2023-03-26T04:52:33,165   Using pip 23.0.1 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
2023-03-26T04:52:34,519   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
2023-03-26T04:52:34,577   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-26T04:52:38,416   Collecting setuptools>=61.0
2023-03-26T04:52:38,696     Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.6.0-py3-none-any.whl (1.1 MB)
2023-03-26T04:52:39,654   Collecting setuptools_scm>=6.2
2023-03-26T04:52:39,720     Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-7.1.0-py3-none-any.whl (43 kB)
2023-03-26T04:52:40,221   Collecting packaging>=20.0
2023-03-26T04:52:40,259     Using cached https://www.piwheels.org/simple/packaging/packaging-23.0-py3-none-any.whl (42 kB)
2023-03-26T04:52:40,491   Collecting typing-extensions
2023-03-26T04:52:40,525     Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.5.0-py3-none-any.whl (27 kB)
2023-03-26T04:52:40,788   Collecting tomli>=1.0.0
2023-03-26T04:52:40,822     Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB)
2023-03-26T04:52:41,765   Collecting importlib-metadata
2023-03-26T04:52:41,799     Using cached https://www.piwheels.org/simple/importlib-metadata/importlib_metadata-6.1.0-py3-none-any.whl (21 kB)
2023-03-26T04:52:42,488   Collecting zipp>=0.5
2023-03-26T04:52:42,522     Using cached https://www.piwheels.org/simple/zipp/zipp-3.15.0-py3-none-any.whl (6.8 kB)
2023-03-26T04:52:49,389   Installing collected packages: zipp, typing-extensions, tomli, setuptools, packaging, importlib-metadata, setuptools_scm
2023-03-26T04:52:54,677   Successfully installed importlib-metadata-6.1.0 packaging-23.0 setuptools-67.6.0 setuptools_scm-7.1.0 tomli-2.0.1 typing-extensions-4.5.0 zipp-3.15.0
2023-03-26T04:52:55,702   Installing build dependencies: finished with status 'done'
2023-03-26T04:52:55,714   Getting requirements to build wheel: started
2023-03-26T04:52:55,716   Running command Getting requirements to build wheel
2023-03-26T04:52:57,858   running egg_info
2023-03-26T04:52:57,874   writing cryodrgn.egg-info/PKG-INFO
2023-03-26T04:52:57,881   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-03-26T04:52:57,886   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-03-26T04:52:57,891   writing requirements to cryodrgn.egg-info/requires.txt
2023-03-26T04:52:57,894   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-03-26T04:52:58,008   /tmp/pip-build-env-_et9j084/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-03-26T04:52:58,009     warnings.warn(msg, _BetaConfiguration)
2023-03-26T04:52:58,009   listing git files failed - pretending there aren't any
2023-03-26T04:52:58,030   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:52:58,051   reading manifest template 'MANIFEST.in'
2023-03-26T04:52:58,057   adding license file 'LICENSE.txt'
2023-03-26T04:52:58,087   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:52:58,292   Getting requirements to build wheel: finished with status 'done'
2023-03-26T04:52:58,334   Installing backend dependencies: started
2023-03-26T04:52:58,336   Running command pip subprocess to install backend dependencies
2023-03-26T04:53:01,124   Using pip 23.0.1 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
2023-03-26T04:53:02,457   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
2023-03-26T04:53:02,514   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-26T04:53:03,401   Collecting wheel
2023-03-26T04:53:03,438     Using cached https://www.piwheels.org/simple/wheel/wheel-0.40.0-py3-none-any.whl (64 kB)
2023-03-26T04:53:08,985   Installing collected packages: wheel
2023-03-26T04:53:09,455     Creating /tmp/pip-build-env-_et9j084/normal/bin
2023-03-26T04:53:09,460     changing mode of /tmp/pip-build-env-_et9j084/normal/bin/wheel to 755
2023-03-26T04:53:09,488   Successfully installed wheel-0.40.0
2023-03-26T04:53:10,373   Installing backend dependencies: finished with status 'done'
2023-03-26T04:53:10,378   Created temporary directory: /tmp/pip-modern-metadata-ive70q_v
2023-03-26T04:53:10,385   Preparing metadata (pyproject.toml): started
2023-03-26T04:53:10,387   Running command Preparing metadata (pyproject.toml)
2023-03-26T04:53:12,586   running dist_info
2023-03-26T04:53:12,602   creating /tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info
2023-03-26T04:53:12,616   writing /tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/PKG-INFO
2023-03-26T04:53:12,625   writing dependency_links to /tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/dependency_links.txt
2023-03-26T04:53:12,629   writing entry points to /tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/entry_points.txt
2023-03-26T04:53:12,633   writing requirements to /tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/requires.txt
2023-03-26T04:53:12,635   writing top-level names to /tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/top_level.txt
2023-03-26T04:53:12,637   writing manifest file '/tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:53:12,770   /tmp/pip-build-env-_et9j084/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-03-26T04:53:12,771     warnings.warn(msg, _BetaConfiguration)
2023-03-26T04:53:12,771   listing git files failed - pretending there aren't any
2023-03-26T04:53:12,791   reading manifest file '/tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:53:12,798   reading manifest template 'MANIFEST.in'
2023-03-26T04:53:12,804   adding license file 'LICENSE.txt'
2023-03-26T04:53:12,816   writing manifest file '/tmp/pip-modern-metadata-ive70q_v/cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:53:12,818   creating '/tmp/pip-modern-metadata-ive70q_v/cryodrgn-2.2.0.dist-info'
2023-03-26T04:53:13,146   Preparing metadata (pyproject.toml): finished with status 'done'
2023-03-26T04:53:13,168   Source in /tmp/pip-wheel-m8i7mj8g/cryodrgn_b64a35e6a795402b81215276895245b2 has version 2.2.0, which satisfies requirement cryodrgn==2.2.0 from https://files.pythonhosted.org/packages/03/50/3259e1a4efc92c945d1ae88fd5765a0ba4db77f0a742fc0e0a206cd781ac/cryodrgn-2.2.0.tar.gz
2023-03-26T04:53:13,170   Removed cryodrgn==2.2.0 from https://files.pythonhosted.org/packages/03/50/3259e1a4efc92c945d1ae88fd5765a0ba4db77f0a742fc0e0a206cd781ac/cryodrgn-2.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-w15j4bkb'
2023-03-26T04:53:13,190 Created temporary directory: /tmp/pip-unpack-8lc4bni8
2023-03-26T04:53:13,191 Building wheels for collected packages: cryodrgn
2023-03-26T04:53:13,200   Created temporary directory: /tmp/pip-wheel-6y1apiu6
2023-03-26T04:53:13,201   Destination directory: /tmp/pip-wheel-6y1apiu6
2023-03-26T04:53:13,206   Building wheel for cryodrgn (pyproject.toml): started
2023-03-26T04:53:13,208   Running command Building wheel for cryodrgn (pyproject.toml)
2023-03-26T04:53:15,232   running bdist_wheel
2023-03-26T04:53:15,283   running build
2023-03-26T04:53:15,283   running build_py
2023-03-26T04:53:15,302   creating build
2023-03-26T04:53:15,303   creating build/lib
2023-03-26T04:53:15,304   creating build/lib/cryodrgn
2023-03-26T04:53:15,306   copying cryodrgn/dataset.py -> build/lib/cryodrgn
2023-03-26T04:53:15,311   copying cryodrgn/__init__.py -> build/lib/cryodrgn
2023-03-26T04:53:15,314   copying cryodrgn/pose.py -> build/lib/cryodrgn
2023-03-26T04:53:15,318   copying cryodrgn/lattice.py -> build/lib/cryodrgn
2023-03-26T04:53:15,322   copying cryodrgn/losses.py -> build/lib/cryodrgn
2023-03-26T04:53:15,325   copying cryodrgn/fft.py -> build/lib/cryodrgn
2023-03-26T04:53:15,329   copying cryodrgn/shift_grid.py -> build/lib/cryodrgn
2023-03-26T04:53:15,332   copying cryodrgn/mrc.py -> build/lib/cryodrgn
2023-03-26T04:53:15,336   copying cryodrgn/config.py -> build/lib/cryodrgn
2023-03-26T04:53:15,340   copying cryodrgn/ctf.py -> build/lib/cryodrgn
2023-03-26T04:53:15,344   copying cryodrgn/analysis.py -> build/lib/cryodrgn
2023-03-26T04:53:15,348   copying cryodrgn/utils.py -> build/lib/cryodrgn
2023-03-26T04:53:15,352   copying cryodrgn/utils_exec.py -> build/lib/cryodrgn
2023-03-26T04:53:15,355   copying cryodrgn/lie_tools.py -> build/lib/cryodrgn
2023-03-26T04:53:15,359   copying cryodrgn/types.py -> build/lib/cryodrgn
2023-03-26T04:53:15,362   copying cryodrgn/models.py -> build/lib/cryodrgn
2023-03-26T04:53:15,368   copying cryodrgn/starfile.py -> build/lib/cryodrgn
2023-03-26T04:53:15,373   copying cryodrgn/_version.py -> build/lib/cryodrgn
2023-03-26T04:53:15,376   copying cryodrgn/shift_grid3.py -> build/lib/cryodrgn
2023-03-26T04:53:15,380   copying cryodrgn/pose_search.py -> build/lib/cryodrgn
2023-03-26T04:53:15,384   copying cryodrgn/__main__.py -> build/lib/cryodrgn
2023-03-26T04:53:15,388   copying cryodrgn/make_healpy.py -> build/lib/cryodrgn
2023-03-26T04:53:15,391   copying cryodrgn/so3_grid.py -> build/lib/cryodrgn
2023-03-26T04:53:15,395   copying cryodrgn/beta_schedule.py -> build/lib/cryodrgn
2023-03-26T04:53:15,401   creating build/lib/cryodrgn/commands
2023-03-26T04:53:15,402   copying cryodrgn/commands/downsample.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,406   copying cryodrgn/commands/preprocess.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,410   copying cryodrgn/commands/graph_traversal.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,415   copying cryodrgn/commands/eval_vol.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,419   copying cryodrgn/commands/__init__.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,423   copying cryodrgn/commands/parse_ctf_csparc.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,426   copying cryodrgn/commands/train_vae.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,432   copying cryodrgn/commands/backproject_voxel.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,436   copying cryodrgn/commands/pc_traversal.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,440   copying cryodrgn/commands/abinit_het.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,446   copying cryodrgn/commands/train_nn.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,450   copying cryodrgn/commands/parse_ctf_star.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,454   copying cryodrgn/commands/analyze_landscape.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,458   copying cryodrgn/commands/view_config.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,462   copying cryodrgn/commands/analyze.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,467   copying cryodrgn/commands/parse_pose_csparc.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,471   copying cryodrgn/commands/abinit_homo.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,476   copying cryodrgn/commands/analyze_landscape_full.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,480   copying cryodrgn/commands/eval_images.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,484   copying cryodrgn/commands/parse_pose_star.py -> build/lib/cryodrgn/commands
2023-03-26T04:53:15,490   creating build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,492   copying cryodrgn/commands_utils/view_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,496   copying cryodrgn/commands_utils/translate_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,500   copying cryodrgn/commands_utils/write_cs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,503   copying cryodrgn/commands_utils/view_header.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,507   copying cryodrgn/commands_utils/__init__.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,511   copying cryodrgn/commands_utils/select_random.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,514   copying cryodrgn/commands_utils/view_cs_header.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,518   copying cryodrgn/commands_utils/phase_flip.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,521   copying cryodrgn/commands_utils/invert_contrast.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,525   copying cryodrgn/commands_utils/concat_pkls.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,528   copying cryodrgn/commands_utils/add_psize.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,532   copying cryodrgn/commands_utils/flip_hand.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,536   copying cryodrgn/commands_utils/filter_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,539   copying cryodrgn/commands_utils/filter_star.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,543   copying cryodrgn/commands_utils/write_star.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,547   copying cryodrgn/commands_utils/select_clusters.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,550   copying cryodrgn/commands_utils/filter_pkl.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:53:15,555   running egg_info
2023-03-26T04:53:15,583   writing cryodrgn.egg-info/PKG-INFO
2023-03-26T04:53:15,589   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-03-26T04:53:15,592   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-03-26T04:53:15,596   writing requirements to cryodrgn.egg-info/requires.txt
2023-03-26T04:53:15,598   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-03-26T04:53:15,685   /tmp/pip-build-env-_et9j084/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-03-26T04:53:15,686     warnings.warn(msg, _BetaConfiguration)
2023-03-26T04:53:15,686   listing git files failed - pretending there aren't any
2023-03-26T04:53:15,704   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:53:15,766   reading manifest template 'MANIFEST.in'
2023-03-26T04:53:15,770   adding license file 'LICENSE.txt'
2023-03-26T04:53:15,799   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:53:15,825   copying cryodrgn/healpy_grid.json -> build/lib/cryodrgn
2023-03-26T04:53:16,267   creating build/lib/cryodrgn/templates
2023-03-26T04:53:16,269   copying cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:53:16,275   copying cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:53:16,280   copying cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:53:16,286   copying cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:53:16,331   installing to build/bdist.linux-armv7l/wheel
2023-03-26T04:53:16,331   running install
2023-03-26T04:53:16,394   running install_lib
2023-03-26T04:53:16,409   creating build/bdist.linux-armv7l
2023-03-26T04:53:16,410   creating build/bdist.linux-armv7l/wheel
2023-03-26T04:53:16,414   creating build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,417   copying build/lib/cryodrgn/dataset.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,422   copying build/lib/cryodrgn/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,426   copying build/lib/cryodrgn/pose.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,430   copying build/lib/cryodrgn/lattice.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,435   copying build/lib/cryodrgn/losses.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,439   copying build/lib/cryodrgn/fft.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,443   copying build/lib/cryodrgn/shift_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,447   copying build/lib/cryodrgn/mrc.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,452   copying build/lib/cryodrgn/config.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,456   copying build/lib/cryodrgn/ctf.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,460   copying build/lib/cryodrgn/analysis.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,466   copying build/lib/cryodrgn/utils.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,470   copying build/lib/cryodrgn/utils_exec.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,474   copying build/lib/cryodrgn/lie_tools.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,478   copying build/lib/cryodrgn/types.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,482   copying build/lib/cryodrgn/models.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,488   copying build/lib/cryodrgn/starfile.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,494   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,496   copying build/lib/cryodrgn/commands/downsample.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,500   copying build/lib/cryodrgn/commands/preprocess.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,505   copying build/lib/cryodrgn/commands/graph_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,509   copying build/lib/cryodrgn/commands/eval_vol.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,513   copying build/lib/cryodrgn/commands/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,516   copying build/lib/cryodrgn/commands/parse_ctf_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,520   copying build/lib/cryodrgn/commands/train_vae.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,525   copying build/lib/cryodrgn/commands/backproject_voxel.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,529   copying build/lib/cryodrgn/commands/pc_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,533   copying build/lib/cryodrgn/commands/abinit_het.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,539   copying build/lib/cryodrgn/commands/train_nn.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,544   copying build/lib/cryodrgn/commands/parse_ctf_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,547   copying build/lib/cryodrgn/commands/analyze_landscape.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,553   copying build/lib/cryodrgn/commands/view_config.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,557   copying build/lib/cryodrgn/commands/analyze.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,562   copying build/lib/cryodrgn/commands/parse_pose_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,566   copying build/lib/cryodrgn/commands/abinit_homo.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,572   copying build/lib/cryodrgn/commands/analyze_landscape_full.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,578   copying build/lib/cryodrgn/commands/eval_images.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,583   copying build/lib/cryodrgn/commands/parse_pose_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:53:16,588   copying build/lib/cryodrgn/_version.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,592   copying build/lib/cryodrgn/shift_grid3.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:16,598   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,600   copying build/lib/cryodrgn/commands_utils/view_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,604   copying build/lib/cryodrgn/commands_utils/translate_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,609   copying build/lib/cryodrgn/commands_utils/write_cs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,613   copying build/lib/cryodrgn/commands_utils/view_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,617   copying build/lib/cryodrgn/commands_utils/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,621   copying build/lib/cryodrgn/commands_utils/select_random.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,625   copying build/lib/cryodrgn/commands_utils/view_cs_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,629   copying build/lib/cryodrgn/commands_utils/phase_flip.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,633   copying build/lib/cryodrgn/commands_utils/invert_contrast.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,637   copying build/lib/cryodrgn/commands_utils/concat_pkls.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,641   copying build/lib/cryodrgn/commands_utils/add_psize.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,644   copying build/lib/cryodrgn/commands_utils/flip_hand.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,648   copying build/lib/cryodrgn/commands_utils/filter_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,652   copying build/lib/cryodrgn/commands_utils/filter_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,655   copying build/lib/cryodrgn/commands_utils/write_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,659   copying build/lib/cryodrgn/commands_utils/select_clusters.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,663   copying build/lib/cryodrgn/commands_utils/filter_pkl.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:53:16,667   copying build/lib/cryodrgn/healpy_grid.json -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:17,184   copying build/lib/cryodrgn/pose_search.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:17,189   copying build/lib/cryodrgn/__main__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:17,195   creating build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:53:17,197   copying build/lib/cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:53:17,202   copying build/lib/cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:53:17,208   copying build/lib/cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:53:17,213   copying build/lib/cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:53:17,217   copying build/lib/cryodrgn/make_healpy.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:17,221   copying build/lib/cryodrgn/so3_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:17,226   copying build/lib/cryodrgn/beta_schedule.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:53:17,228   running install_egg_info
2023-03-26T04:53:17,243   Copying cryodrgn.egg-info to build/bdist.linux-armv7l/wheel/cryodrgn-2.2.0-py3.7.egg-info
2023-03-26T04:53:17,274   running install_scripts
2023-03-26T04:53:17,336   creating build/bdist.linux-armv7l/wheel/cryodrgn-2.2.0.dist-info/WHEEL
2023-03-26T04:53:17,342   creating '/tmp/pip-wheel-6y1apiu6/.tmp-oc584wfq/cryodrgn-2.2.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-03-26T04:53:17,348   adding 'cryodrgn/__init__.py'
2023-03-26T04:53:17,351   adding 'cryodrgn/__main__.py'
2023-03-26T04:53:17,353   adding 'cryodrgn/_version.py'
2023-03-26T04:53:17,360   adding 'cryodrgn/analysis.py'
2023-03-26T04:53:17,363   adding 'cryodrgn/beta_schedule.py'
2023-03-26T04:53:17,365   adding 'cryodrgn/config.py'
2023-03-26T04:53:17,369   adding 'cryodrgn/ctf.py'
2023-03-26T04:53:17,373   adding 'cryodrgn/dataset.py'
2023-03-26T04:53:17,376   adding 'cryodrgn/fft.py'
2023-03-26T04:53:19,333   adding 'cryodrgn/healpy_grid.json'
2023-03-26T04:53:19,542   adding 'cryodrgn/lattice.py'
2023-03-26T04:53:19,546   adding 'cryodrgn/lie_tools.py'
2023-03-26T04:53:19,549   adding 'cryodrgn/losses.py'
2023-03-26T04:53:19,552   adding 'cryodrgn/make_healpy.py'
2023-03-26T04:53:19,561   adding 'cryodrgn/models.py'
2023-03-26T04:53:19,566   adding 'cryodrgn/mrc.py'
2023-03-26T04:53:19,570   adding 'cryodrgn/pose.py'
2023-03-26T04:53:19,575   adding 'cryodrgn/pose_search.py'
2023-03-26T04:53:19,578   adding 'cryodrgn/shift_grid.py'
2023-03-26T04:53:19,581   adding 'cryodrgn/shift_grid3.py'
2023-03-26T04:53:19,584   adding 'cryodrgn/so3_grid.py'
2023-03-26T04:53:19,588   adding 'cryodrgn/starfile.py'
2023-03-26T04:53:19,591   adding 'cryodrgn/types.py'
2023-03-26T04:53:19,594   adding 'cryodrgn/utils.py'
2023-03-26T04:53:19,597   adding 'cryodrgn/utils_exec.py'
2023-03-26T04:53:19,601   adding 'cryodrgn/commands/__init__.py'
2023-03-26T04:53:19,611   adding 'cryodrgn/commands/abinit_het.py'
2023-03-26T04:53:19,618   adding 'cryodrgn/commands/abinit_homo.py'
2023-03-26T04:53:19,623   adding 'cryodrgn/commands/analyze.py'
2023-03-26T04:53:19,629   adding 'cryodrgn/commands/analyze_landscape.py'
2023-03-26T04:53:19,634   adding 'cryodrgn/commands/analyze_landscape_full.py'
2023-03-26T04:53:19,638   adding 'cryodrgn/commands/backproject_voxel.py'
2023-03-26T04:53:19,641   adding 'cryodrgn/commands/downsample.py'
2023-03-26T04:53:19,646   adding 'cryodrgn/commands/eval_images.py'
2023-03-26T04:53:19,650   adding 'cryodrgn/commands/eval_vol.py'
2023-03-26T04:53:19,653   adding 'cryodrgn/commands/graph_traversal.py'
2023-03-26T04:53:19,657   adding 'cryodrgn/commands/parse_ctf_csparc.py'
2023-03-26T04:53:19,660   adding 'cryodrgn/commands/parse_ctf_star.py'
2023-03-26T04:53:19,663   adding 'cryodrgn/commands/parse_pose_csparc.py'
2023-03-26T04:53:19,666   adding 'cryodrgn/commands/parse_pose_star.py'
2023-03-26T04:53:19,669   adding 'cryodrgn/commands/pc_traversal.py'
2023-03-26T04:53:19,672   adding 'cryodrgn/commands/preprocess.py'
2023-03-26T04:53:19,678   adding 'cryodrgn/commands/train_nn.py'
2023-03-26T04:53:19,687   adding 'cryodrgn/commands/train_vae.py'
2023-03-26T04:53:19,690   adding 'cryodrgn/commands/view_config.py'
2023-03-26T04:53:19,694   adding 'cryodrgn/commands_utils/__init__.py'
2023-03-26T04:53:19,697   adding 'cryodrgn/commands_utils/add_psize.py'
2023-03-26T04:53:19,700   adding 'cryodrgn/commands_utils/concat_pkls.py'
2023-03-26T04:53:19,702   adding 'cryodrgn/commands_utils/filter_mrcs.py'
2023-03-26T04:53:19,705   adding 'cryodrgn/commands_utils/filter_pkl.py'
2023-03-26T04:53:19,708   adding 'cryodrgn/commands_utils/filter_star.py'
2023-03-26T04:53:19,710   adding 'cryodrgn/commands_utils/flip_hand.py'
2023-03-26T04:53:19,713   adding 'cryodrgn/commands_utils/invert_contrast.py'
2023-03-26T04:53:19,716   adding 'cryodrgn/commands_utils/phase_flip.py'
2023-03-26T04:53:19,718   adding 'cryodrgn/commands_utils/select_clusters.py'
2023-03-26T04:53:19,721   adding 'cryodrgn/commands_utils/select_random.py'
2023-03-26T04:53:19,724   adding 'cryodrgn/commands_utils/translate_mrcs.py'
2023-03-26T04:53:19,727   adding 'cryodrgn/commands_utils/view_cs_header.py'
2023-03-26T04:53:19,729   adding 'cryodrgn/commands_utils/view_header.py'
2023-03-26T04:53:19,732   adding 'cryodrgn/commands_utils/view_mrcs.py'
2023-03-26T04:53:19,735   adding 'cryodrgn/commands_utils/write_cs.py'
2023-03-26T04:53:19,738   adding 'cryodrgn/commands_utils/write_star.py'
2023-03-26T04:53:19,743   adding 'cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb'
2023-03-26T04:53:19,747   adding 'cryodrgn/templates/cryoDRGN_figures_template.ipynb'
2023-03-26T04:53:19,755   adding 'cryodrgn/templates/cryoDRGN_filtering_template.ipynb'
2023-03-26T04:53:19,760   adding 'cryodrgn/templates/cryoDRGN_viz_template.ipynb'
2023-03-26T04:53:19,778   adding 'cryodrgn-2.2.0.dist-info/LICENSE.txt'
2023-03-26T04:53:19,789   adding 'cryodrgn-2.2.0.dist-info/METADATA'
2023-03-26T04:53:19,792   adding 'cryodrgn-2.2.0.dist-info/WHEEL'
2023-03-26T04:53:19,794   adding 'cryodrgn-2.2.0.dist-info/entry_points.txt'
2023-03-26T04:53:19,796   adding 'cryodrgn-2.2.0.dist-info/top_level.txt'
2023-03-26T04:53:19,800   adding 'cryodrgn-2.2.0.dist-info/RECORD'
2023-03-26T04:53:19,848   removing build/bdist.linux-armv7l/wheel
2023-03-26T04:53:20,100   Building wheel for cryodrgn (pyproject.toml): finished with status 'done'
2023-03-26T04:53:20,184   Created wheel for cryodrgn: filename=cryodrgn-2.2.0-py3-none-any.whl size=1129870 sha256=6d705695a229d236db29c0b847f18e336bc53358ef3bc125cb158bd743f53bc9
2023-03-26T04:53:20,186   Stored in directory: /tmp/pip-ephem-wheel-cache-8h07v_ye/wheels/1d/3f/76/5dc4b43c051fc22550c0f78fd525b0d84be687e06245d9867b
2023-03-26T04:53:20,231 Successfully built cryodrgn
2023-03-26T04:53:20,334 Removed build tracker: '/tmp/pip-build-tracker-w15j4bkb'