2023-05-13T17:15:54,072 Created temporary directory: /tmp/pip-build-tracker-zpm7i92a
2023-05-13T17:15:54,075 Initialized build tracking at /tmp/pip-build-tracker-zpm7i92a
2023-05-13T17:15:54,075 Created build tracker: /tmp/pip-build-tracker-zpm7i92a
2023-05-13T17:15:54,076 Entered build tracker: /tmp/pip-build-tracker-zpm7i92a
2023-05-13T17:15:54,077 Created temporary directory: /tmp/pip-wheel-vbbdzwwi
2023-05-13T17:15:54,085 Created temporary directory: /tmp/pip-ephem-wheel-cache-_yzd8n7t
2023-05-13T17:15:54,144 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-05-13T17:15:54,151 2 location(s) to search for versions of cryodrgn:
2023-05-13T17:15:54,151 * https://pypi.org/simple/cryodrgn/
2023-05-13T17:15:54,151 * https://www.piwheels.org/simple/cryodrgn/
2023-05-13T17:15:54,152 Fetching project page and analyzing links: https://pypi.org/simple/cryodrgn/
2023-05-13T17:15:54,153 Getting page https://pypi.org/simple/cryodrgn/
2023-05-13T17:15:54,157 Found index url https://pypi.org/simple/
2023-05-13T17:15:54,348 Fetched page https://pypi.org/simple/cryodrgn/ as application/vnd.pypi.simple.v1+json
2023-05-13T17:15:54,355   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)
2023-05-13T17:15:54,356   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
2023-05-13T17:15:54,357   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)
2023-05-13T17:15:54,359   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
2023-05-13T17:15:54,359   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)
2023-05-13T17:15:54,361   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
2023-05-13T17:15:54,361   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)
2023-05-13T17:15:54,363   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
2023-05-13T17:15:54,363   Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/03/29/f9750c89414937c8700d9d5aa167d9ed1e3157ebb6a9971effb4bcbe8bec/cryodrgn-2.3.0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-05-13T17:15:54,364   Found link https://files.pythonhosted.org/packages/d2/69/c5d8c6da2da86575a985307f67f214a0f56a7f79d73492a5184170ea7036/cryodrgn-2.3.0.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 2.3.0
2023-05-13T17:15:54,365 Fetching project page and analyzing links: https://www.piwheels.org/simple/cryodrgn/
2023-05-13T17:15:54,366 Getting page https://www.piwheels.org/simple/cryodrgn/
2023-05-13T17:15:54,369 Found index url https://www.piwheels.org/simple/
2023-05-13T17:15:54,680 Fetched page https://www.piwheels.org/simple/cryodrgn/ as text/html
2023-05-13T17:15:54,686   Skipping link: No binaries permitted for cryodrgn: https://www.piwheels.org/simple/cryodrgn/cryodrgn-2.3.0-py3-none-any.whl#sha256=f2696630939e986a4b0f727ff34abb976b704af5f9d764ecf3c30629d929fece (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-05-13T17:15:54,687   Skipping link: No binaries permitted for cryodrgn: https://www.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)
2023-05-13T17:15:54,687   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)
2023-05-13T17:15:54,688   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)
2023-05-13T17:15:54,688   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)
2023-05-13T17:15:54,689 Skipping link: not a file: https://www.piwheels.org/simple/cryodrgn/
2023-05-13T17:15:54,689 Skipping link: not a file: https://pypi.org/simple/cryodrgn/
2023-05-13T17:15:54,720 Given no hashes to check 1 links for project 'cryodrgn': discarding no candidates
2023-05-13T17:15:54,748 Collecting cryodrgn==2.3.0
2023-05-13T17:15:54,753   Created temporary directory: /tmp/pip-unpack-w4o17rla
2023-05-13T17:15:55,086   Downloading cryodrgn-2.3.0.tar.gz (31.4 MB)
2023-05-13T17:16:08,947   Added cryodrgn==2.3.0 from https://files.pythonhosted.org/packages/d2/69/c5d8c6da2da86575a985307f67f214a0f56a7f79d73492a5184170ea7036/cryodrgn-2.3.0.tar.gz to build tracker '/tmp/pip-build-tracker-zpm7i92a'
2023-05-13T17:16:08,961   Created temporary directory: /tmp/pip-build-env-jv_5rfj6
2023-05-13T17:16:08,981   Installing build dependencies: started
2023-05-13T17:16:08,984   Running command pip subprocess to install build dependencies
2023-05-13T17:16:11,875   Using pip 23.1.2 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
2023-05-13T17:16:12,612   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-05-13T17:16:16,539   Collecting setuptools>=61.0
2023-05-13T17:16:16,814     Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.7.2-py3-none-any.whl (1.1 MB)
2023-05-13T17:16:17,678   Collecting setuptools_scm>=6.2
2023-05-13T17:16:17,713     Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-7.1.0-py3-none-any.whl (43 kB)
2023-05-13T17:16:18,595   Collecting packaging>=20.0 (from setuptools_scm>=6.2)
2023-05-13T17:16:18,656     Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB)
2023-05-13T17:16:18,906   Collecting typing-extensions (from setuptools_scm>=6.2)
2023-05-13T17:16:18,940     Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.5.0-py3-none-any.whl (27 kB)
2023-05-13T17:16:19,198   Collecting tomli>=1.0.0 (from setuptools_scm>=6.2)
2023-05-13T17:16:19,229     Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB)
2023-05-13T17:16:20,261   Collecting importlib-metadata (from setuptools_scm>=6.2)
2023-05-13T17:16:20,293     Using cached https://www.piwheels.org/simple/importlib-metadata/importlib_metadata-6.6.0-py3-none-any.whl (22 kB)
2023-05-13T17:16:20,948   Collecting zipp>=0.5 (from importlib-metadata->setuptools_scm>=6.2)
2023-05-13T17:16:20,979     Using cached https://www.piwheels.org/simple/zipp/zipp-3.15.0-py3-none-any.whl (6.8 kB)
2023-05-13T17:16:25,489   Installing collected packages: zipp, typing-extensions, tomli, setuptools, packaging, importlib-metadata, setuptools_scm
2023-05-13T17:16:31,264   Successfully installed importlib-metadata-6.6.0 packaging-23.1 setuptools-67.7.2 setuptools_scm-7.1.0 tomli-2.0.1 typing-extensions-4.5.0 zipp-3.15.0
2023-05-13T17:16:31,769   Installing build dependencies: finished with status 'done'
2023-05-13T17:16:31,780   Getting requirements to build wheel: started
2023-05-13T17:16:31,782   Running command Getting requirements to build wheel
2023-05-13T17:16:33,903   running egg_info
2023-05-13T17:16:33,916   writing cryodrgn.egg-info/PKG-INFO
2023-05-13T17:16:33,923   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-05-13T17:16:33,927   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-05-13T17:16:33,931   writing requirements to cryodrgn.egg-info/requires.txt
2023-05-13T17:16:33,933   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-05-13T17:16:34,043   /tmp/pip-build-env-jv_5rfj6/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-05-13T17:16:34,044     config = read_configuration(filepath, True, ignore_option_errors, dist)
2023-05-13T17:16:34,044   listing git files failed - pretending there aren't any
2023-05-13T17:16:34,061   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-05-13T17:16:34,081   reading manifest template 'MANIFEST.in'
2023-05-13T17:16:34,086   adding license file 'LICENSE.txt'
2023-05-13T17:16:34,115   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-05-13T17:16:34,322   Getting requirements to build wheel: finished with status 'done'
2023-05-13T17:16:34,361   Installing backend dependencies: started
2023-05-13T17:16:34,363   Running command pip subprocess to install backend dependencies
2023-05-13T17:16:37,261   Using pip 23.1.2 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
2023-05-13T17:16:37,992   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-05-13T17:16:39,902   Collecting wheel
2023-05-13T17:16:39,943     Using cached https://www.piwheels.org/simple/wheel/wheel-0.40.0-py3-none-any.whl (64 kB)
2023-05-13T17:16:43,474   Installing collected packages: wheel
2023-05-13T17:16:43,910     Creating /tmp/pip-build-env-jv_5rfj6/normal/bin
2023-05-13T17:16:43,915     changing mode of /tmp/pip-build-env-jv_5rfj6/normal/bin/wheel to 755
2023-05-13T17:16:43,940   Successfully installed wheel-0.40.0
2023-05-13T17:16:44,325   Installing backend dependencies: finished with status 'done'
2023-05-13T17:16:44,330   Created temporary directory: /tmp/pip-modern-metadata-rwntdvqm
2023-05-13T17:16:44,337   Preparing metadata (pyproject.toml): started
2023-05-13T17:16:44,339   Running command Preparing metadata (pyproject.toml)
2023-05-13T17:16:46,507   running dist_info
2023-05-13T17:16:46,523   creating /tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info
2023-05-13T17:16:46,537   writing /tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/PKG-INFO
2023-05-13T17:16:46,544   writing dependency_links to /tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/dependency_links.txt
2023-05-13T17:16:46,549   writing entry points to /tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/entry_points.txt
2023-05-13T17:16:46,608   writing requirements to /tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/requires.txt
2023-05-13T17:16:46,610   writing top-level names to /tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/top_level.txt
2023-05-13T17:16:46,613   writing manifest file '/tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/SOURCES.txt'
2023-05-13T17:16:46,743   /tmp/pip-build-env-jv_5rfj6/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-05-13T17:16:46,743     config = read_configuration(filepath, True, ignore_option_errors, dist)
2023-05-13T17:16:46,743   listing git files failed - pretending there aren't any
2023-05-13T17:16:46,762   reading manifest file '/tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/SOURCES.txt'
2023-05-13T17:16:46,769   reading manifest template 'MANIFEST.in'
2023-05-13T17:16:46,775   adding license file 'LICENSE.txt'
2023-05-13T17:16:46,787   writing manifest file '/tmp/pip-modern-metadata-rwntdvqm/cryodrgn.egg-info/SOURCES.txt'
2023-05-13T17:16:46,789   creating '/tmp/pip-modern-metadata-rwntdvqm/cryodrgn-2.3.0.dist-info'
2023-05-13T17:16:47,124   Preparing metadata (pyproject.toml): finished with status 'done'
2023-05-13T17:16:47,144   Source in /tmp/pip-wheel-vbbdzwwi/cryodrgn_a7083dcd068e49c49e3c4cf717df52a7 has version 2.3.0, which satisfies requirement cryodrgn==2.3.0 from https://files.pythonhosted.org/packages/d2/69/c5d8c6da2da86575a985307f67f214a0f56a7f79d73492a5184170ea7036/cryodrgn-2.3.0.tar.gz
2023-05-13T17:16:47,146   Removed cryodrgn==2.3.0 from https://files.pythonhosted.org/packages/d2/69/c5d8c6da2da86575a985307f67f214a0f56a7f79d73492a5184170ea7036/cryodrgn-2.3.0.tar.gz from build tracker '/tmp/pip-build-tracker-zpm7i92a'
2023-05-13T17:16:47,167 Created temporary directory: /tmp/pip-unpack-9iii3x75
2023-05-13T17:16:47,168 Building wheels for collected packages: cryodrgn
2023-05-13T17:16:47,177   Created temporary directory: /tmp/pip-wheel-v0xr2xmh
2023-05-13T17:16:47,177   Destination directory: /tmp/pip-wheel-v0xr2xmh
2023-05-13T17:16:47,182   Building wheel for cryodrgn (pyproject.toml): started
2023-05-13T17:16:47,184   Running command Building wheel for cryodrgn (pyproject.toml)
2023-05-13T17:16:49,236   running bdist_wheel
2023-05-13T17:16:49,286   running build
2023-05-13T17:16:49,287   running build_py
2023-05-13T17:16:49,305   creating build
2023-05-13T17:16:49,306   creating build/lib
2023-05-13T17:16:49,307   creating build/lib/cryodrgn
2023-05-13T17:16:49,309   copying cryodrgn/ctf.py -> build/lib/cryodrgn
2023-05-13T17:16:49,314   copying cryodrgn/losses.py -> build/lib/cryodrgn
2023-05-13T17:16:49,317   copying cryodrgn/shift_grid3.py -> build/lib/cryodrgn
2023-05-13T17:16:49,320   copying cryodrgn/utils.py -> build/lib/cryodrgn
2023-05-13T17:16:49,324   copying cryodrgn/config.py -> build/lib/cryodrgn
2023-05-13T17:16:49,327   copying cryodrgn/lattice.py -> build/lib/cryodrgn
2023-05-13T17:16:49,331   copying cryodrgn/mrc.py -> build/lib/cryodrgn
2023-05-13T17:16:49,336   copying cryodrgn/make_healpy.py -> build/lib/cryodrgn
2023-05-13T17:16:49,339   copying cryodrgn/beta_schedule.py -> build/lib/cryodrgn
2023-05-13T17:16:49,342   copying cryodrgn/types.py -> build/lib/cryodrgn
2023-05-13T17:16:49,346   copying cryodrgn/shift_grid.py -> build/lib/cryodrgn
2023-05-13T17:16:49,349   copying cryodrgn/pose_search.py -> build/lib/cryodrgn
2023-05-13T17:16:49,353   copying cryodrgn/lie_tools.py -> build/lib/cryodrgn
2023-05-13T17:16:49,357   copying cryodrgn/__init__.py -> build/lib/cryodrgn
2023-05-13T17:16:49,361   copying cryodrgn/pose.py -> build/lib/cryodrgn
2023-05-13T17:16:49,364   copying cryodrgn/utils_exec.py -> build/lib/cryodrgn
2023-05-13T17:16:49,368   copying cryodrgn/fft.py -> build/lib/cryodrgn
2023-05-13T17:16:49,371   copying cryodrgn/so3_grid.py -> build/lib/cryodrgn
2023-05-13T17:16:49,375   copying cryodrgn/models.py -> build/lib/cryodrgn
2023-05-13T17:16:49,380   copying cryodrgn/_version.py -> build/lib/cryodrgn
2023-05-13T17:16:49,384   copying cryodrgn/starfile.py -> build/lib/cryodrgn
2023-05-13T17:16:49,388   copying cryodrgn/__main__.py -> build/lib/cryodrgn
2023-05-13T17:16:49,391   copying cryodrgn/dataset.py -> build/lib/cryodrgn
2023-05-13T17:16:49,395   copying cryodrgn/analysis.py -> build/lib/cryodrgn
2023-05-13T17:16:49,404   creating build/lib/cryodrgn/commands
2023-05-13T17:16:49,406   copying cryodrgn/commands/view_config.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,410   copying cryodrgn/commands/analyze_landscape_full.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,415   copying cryodrgn/commands/pc_traversal.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,419   copying cryodrgn/commands/preprocess.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,424   copying cryodrgn/commands/downsample.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,428   copying cryodrgn/commands/parse_ctf_csparc.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,432   copying cryodrgn/commands/eval_images.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,437   copying cryodrgn/commands/parse_ctf_star.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,441   copying cryodrgn/commands/backproject_voxel.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,446   copying cryodrgn/commands/__init__.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,450   copying cryodrgn/commands/parse_pose_csparc.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,454   copying cryodrgn/commands/abinit_homo.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,460   copying cryodrgn/commands/train_vae.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,466   copying cryodrgn/commands/graph_traversal.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,471   copying cryodrgn/commands/eval_vol.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,476   copying cryodrgn/commands/analyze_landscape.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,481   copying cryodrgn/commands/abinit_het.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,512   copying cryodrgn/commands/analyze.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,517   copying cryodrgn/commands/train_nn.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,522   copying cryodrgn/commands/parse_pose_star.py -> build/lib/cryodrgn/commands
2023-05-13T17:16:49,529   creating build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,531   copying cryodrgn/commands_utils/write_star.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,536   copying cryodrgn/commands_utils/write_cs.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,540   copying cryodrgn/commands_utils/filter_pkl.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,544   copying cryodrgn/commands_utils/filter_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,548   copying cryodrgn/commands_utils/view_cs_header.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,552   copying cryodrgn/commands_utils/flip_hand.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,556   copying cryodrgn/commands_utils/select_random.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,560   copying cryodrgn/commands_utils/phase_flip.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,564   copying cryodrgn/commands_utils/translate_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,568   copying cryodrgn/commands_utils/invert_contrast.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,572   copying cryodrgn/commands_utils/filter_star.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,576   copying cryodrgn/commands_utils/__init__.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,579   copying cryodrgn/commands_utils/concat_pkls.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,583   copying cryodrgn/commands_utils/view_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,587   copying cryodrgn/commands_utils/select_clusters.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,591   copying cryodrgn/commands_utils/add_psize.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,595   copying cryodrgn/commands_utils/view_header.py -> build/lib/cryodrgn/commands_utils
2023-05-13T17:16:49,598   running egg_info
2023-05-13T17:16:49,626   writing cryodrgn.egg-info/PKG-INFO
2023-05-13T17:16:49,633   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-05-13T17:16:49,638   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-05-13T17:16:49,641   writing requirements to cryodrgn.egg-info/requires.txt
2023-05-13T17:16:49,644   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-05-13T17:16:49,728   /tmp/pip-build-env-jv_5rfj6/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-05-13T17:16:49,729     config = read_configuration(filepath, True, ignore_option_errors, dist)
2023-05-13T17:16:49,729   listing git files failed - pretending there aren't any
2023-05-13T17:16:49,747   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-05-13T17:16:49,803   reading manifest template 'MANIFEST.in'
2023-05-13T17:16:49,807   adding license file 'LICENSE.txt'
2023-05-13T17:16:49,837   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-05-13T17:16:49,862   copying cryodrgn/healpy_grid.json -> build/lib/cryodrgn
2023-05-13T17:16:50,279   creating build/lib/cryodrgn/templates
2023-05-13T17:16:50,281   copying cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/lib/cryodrgn/templates
2023-05-13T17:16:50,286   copying cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/lib/cryodrgn/templates
2023-05-13T17:16:50,291   copying cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/lib/cryodrgn/templates
2023-05-13T17:16:50,296   copying cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/lib/cryodrgn/templates
2023-05-13T17:16:50,342   installing to build/bdist.linux-armv7l/wheel
2023-05-13T17:16:50,342   running install
2023-05-13T17:16:50,404   running install_lib
2023-05-13T17:16:50,419   creating build/bdist.linux-armv7l
2023-05-13T17:16:50,420   creating build/bdist.linux-armv7l/wheel
2023-05-13T17:16:50,424   creating build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,427   creating build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-05-13T17:16:50,429   copying build/lib/cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-05-13T17:16:50,435   copying build/lib/cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-05-13T17:16:50,441   copying build/lib/cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-05-13T17:16:50,445   copying build/lib/cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-05-13T17:16:50,450   copying build/lib/cryodrgn/ctf.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,454   copying build/lib/cryodrgn/losses.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,459   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,461   copying build/lib/cryodrgn/commands/view_config.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,465   copying build/lib/cryodrgn/commands/analyze_landscape_full.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,469   copying build/lib/cryodrgn/commands/pc_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,472   copying build/lib/cryodrgn/commands/preprocess.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,476   copying build/lib/cryodrgn/commands/downsample.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,480   copying build/lib/cryodrgn/commands/parse_ctf_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,484   copying build/lib/cryodrgn/commands/eval_images.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,488   copying build/lib/cryodrgn/commands/parse_ctf_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,491   copying build/lib/cryodrgn/commands/backproject_voxel.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,496   copying build/lib/cryodrgn/commands/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,499   copying build/lib/cryodrgn/commands/parse_pose_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,502   copying build/lib/cryodrgn/commands/abinit_homo.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,507   copying build/lib/cryodrgn/commands/train_vae.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,513   copying build/lib/cryodrgn/commands/graph_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,517   copying build/lib/cryodrgn/commands/eval_vol.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,521   copying build/lib/cryodrgn/commands/analyze_landscape.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,526   copying build/lib/cryodrgn/commands/abinit_het.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,531   copying build/lib/cryodrgn/commands/analyze.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,536   copying build/lib/cryodrgn/commands/train_nn.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,541   copying build/lib/cryodrgn/commands/parse_pose_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-05-13T17:16:50,545   copying build/lib/cryodrgn/shift_grid3.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,549   copying build/lib/cryodrgn/utils.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,552   copying build/lib/cryodrgn/config.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,556   copying build/lib/cryodrgn/lattice.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,561   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,563   copying build/lib/cryodrgn/commands_utils/write_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,567   copying build/lib/cryodrgn/commands_utils/write_cs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,571   copying build/lib/cryodrgn/commands_utils/filter_pkl.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,574   copying build/lib/cryodrgn/commands_utils/filter_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,578   copying build/lib/cryodrgn/commands_utils/view_cs_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,581   copying build/lib/cryodrgn/commands_utils/flip_hand.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,584   copying build/lib/cryodrgn/commands_utils/select_random.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,588   copying build/lib/cryodrgn/commands_utils/phase_flip.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,591   copying build/lib/cryodrgn/commands_utils/translate_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,595   copying build/lib/cryodrgn/commands_utils/invert_contrast.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,598   copying build/lib/cryodrgn/commands_utils/filter_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,601   copying build/lib/cryodrgn/commands_utils/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,604   copying build/lib/cryodrgn/commands_utils/concat_pkls.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,608   copying build/lib/cryodrgn/commands_utils/view_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,611   copying build/lib/cryodrgn/commands_utils/select_clusters.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,615   copying build/lib/cryodrgn/commands_utils/add_psize.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,618   copying build/lib/cryodrgn/commands_utils/view_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-05-13T17:16:50,621   copying build/lib/cryodrgn/mrc.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,626   copying build/lib/cryodrgn/make_healpy.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,629   copying build/lib/cryodrgn/beta_schedule.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,632   copying build/lib/cryodrgn/types.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,636   copying build/lib/cryodrgn/shift_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:50,639   copying build/lib/cryodrgn/healpy_grid.json -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,057   copying build/lib/cryodrgn/pose_search.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,061   copying build/lib/cryodrgn/lie_tools.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,065   copying build/lib/cryodrgn/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,069   copying build/lib/cryodrgn/pose.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,073   copying build/lib/cryodrgn/utils_exec.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,076   copying build/lib/cryodrgn/fft.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,080   copying build/lib/cryodrgn/so3_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,083   copying build/lib/cryodrgn/models.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,089   copying build/lib/cryodrgn/_version.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,093   copying build/lib/cryodrgn/starfile.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,097   copying build/lib/cryodrgn/__main__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,101   copying build/lib/cryodrgn/dataset.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,105   copying build/lib/cryodrgn/analysis.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-05-13T17:16:51,110   running install_egg_info
2023-05-13T17:16:51,126   Copying cryodrgn.egg-info to build/bdist.linux-armv7l/wheel/cryodrgn-2.3.0-py3.7.egg-info
2023-05-13T17:16:51,157   running install_scripts
2023-05-13T17:16:51,222   creating build/bdist.linux-armv7l/wheel/cryodrgn-2.3.0.dist-info/WHEEL
2023-05-13T17:16:51,227   creating '/tmp/pip-wheel-v0xr2xmh/.tmp-__7r_gym/cryodrgn-2.3.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-05-13T17:16:51,233   adding 'cryodrgn/__init__.py'
2023-05-13T17:16:51,235   adding 'cryodrgn/__main__.py'
2023-05-13T17:16:51,238   adding 'cryodrgn/_version.py'
2023-05-13T17:16:51,244   adding 'cryodrgn/analysis.py'
2023-05-13T17:16:51,247   adding 'cryodrgn/beta_schedule.py'
2023-05-13T17:16:51,249   adding 'cryodrgn/config.py'
2023-05-13T17:16:51,252   adding 'cryodrgn/ctf.py'
2023-05-13T17:16:51,258   adding 'cryodrgn/dataset.py'
2023-05-13T17:16:51,260   adding 'cryodrgn/fft.py'
2023-05-13T17:16:53,198   adding 'cryodrgn/healpy_grid.json'
2023-05-13T17:16:53,407   adding 'cryodrgn/lattice.py'
2023-05-13T17:16:53,411   adding 'cryodrgn/lie_tools.py'
2023-05-13T17:16:53,414   adding 'cryodrgn/losses.py'
2023-05-13T17:16:53,416   adding 'cryodrgn/make_healpy.py'
2023-05-13T17:16:53,426   adding 'cryodrgn/models.py'
2023-05-13T17:16:53,430   adding 'cryodrgn/mrc.py'
2023-05-13T17:16:53,434   adding 'cryodrgn/pose.py'
2023-05-13T17:16:53,439   adding 'cryodrgn/pose_search.py'
2023-05-13T17:16:53,442   adding 'cryodrgn/shift_grid.py'
2023-05-13T17:16:53,445   adding 'cryodrgn/shift_grid3.py'
2023-05-13T17:16:53,448   adding 'cryodrgn/so3_grid.py'
2023-05-13T17:16:53,451   adding 'cryodrgn/starfile.py'
2023-05-13T17:16:53,454   adding 'cryodrgn/types.py'
2023-05-13T17:16:53,457   adding 'cryodrgn/utils.py'
2023-05-13T17:16:53,460   adding 'cryodrgn/utils_exec.py'
2023-05-13T17:16:53,464   adding 'cryodrgn/commands/__init__.py'
2023-05-13T17:16:53,473   adding 'cryodrgn/commands/abinit_het.py'
2023-05-13T17:16:53,481   adding 'cryodrgn/commands/abinit_homo.py'
2023-05-13T17:16:53,485   adding 'cryodrgn/commands/analyze.py'
2023-05-13T17:16:53,491   adding 'cryodrgn/commands/analyze_landscape.py'
2023-05-13T17:16:53,496   adding 'cryodrgn/commands/analyze_landscape_full.py'
2023-05-13T17:16:53,500   adding 'cryodrgn/commands/backproject_voxel.py'
2023-05-13T17:16:53,503   adding 'cryodrgn/commands/downsample.py'
2023-05-13T17:16:53,508   adding 'cryodrgn/commands/eval_images.py'
2023-05-13T17:16:53,511   adding 'cryodrgn/commands/eval_vol.py'
2023-05-13T17:16:53,515   adding 'cryodrgn/commands/graph_traversal.py'
2023-05-13T17:16:53,518   adding 'cryodrgn/commands/parse_ctf_csparc.py'
2023-05-13T17:16:53,521   adding 'cryodrgn/commands/parse_ctf_star.py'
2023-05-13T17:16:53,524   adding 'cryodrgn/commands/parse_pose_csparc.py'
2023-05-13T17:16:53,527   adding 'cryodrgn/commands/parse_pose_star.py'
2023-05-13T17:16:53,530   adding 'cryodrgn/commands/pc_traversal.py'
2023-05-13T17:16:53,534   adding 'cryodrgn/commands/preprocess.py'
2023-05-13T17:16:53,539   adding 'cryodrgn/commands/train_nn.py'
2023-05-13T17:16:53,548   adding 'cryodrgn/commands/train_vae.py'
2023-05-13T17:16:53,551   adding 'cryodrgn/commands/view_config.py'
2023-05-13T17:16:53,555   adding 'cryodrgn/commands_utils/__init__.py'
2023-05-13T17:16:53,557   adding 'cryodrgn/commands_utils/add_psize.py'
2023-05-13T17:16:53,560   adding 'cryodrgn/commands_utils/concat_pkls.py'
2023-05-13T17:16:53,562   adding 'cryodrgn/commands_utils/filter_mrcs.py'
2023-05-13T17:16:53,565   adding 'cryodrgn/commands_utils/filter_pkl.py'
2023-05-13T17:16:53,567   adding 'cryodrgn/commands_utils/filter_star.py'
2023-05-13T17:16:53,569   adding 'cryodrgn/commands_utils/flip_hand.py'
2023-05-13T17:16:53,572   adding 'cryodrgn/commands_utils/invert_contrast.py'
2023-05-13T17:16:53,575   adding 'cryodrgn/commands_utils/phase_flip.py'
2023-05-13T17:16:53,577   adding 'cryodrgn/commands_utils/select_clusters.py'
2023-05-13T17:16:53,580   adding 'cryodrgn/commands_utils/select_random.py'
2023-05-13T17:16:53,583   adding 'cryodrgn/commands_utils/translate_mrcs.py'
2023-05-13T17:16:53,585   adding 'cryodrgn/commands_utils/view_cs_header.py'
2023-05-13T17:16:53,588   adding 'cryodrgn/commands_utils/view_header.py'
2023-05-13T17:16:53,590   adding 'cryodrgn/commands_utils/view_mrcs.py'
2023-05-13T17:16:53,593   adding 'cryodrgn/commands_utils/write_cs.py'
2023-05-13T17:16:53,596   adding 'cryodrgn/commands_utils/write_star.py'
2023-05-13T17:16:53,601   adding 'cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb'
2023-05-13T17:16:53,605   adding 'cryodrgn/templates/cryoDRGN_figures_template.ipynb'
2023-05-13T17:16:53,611   adding 'cryodrgn/templates/cryoDRGN_filtering_template.ipynb'
2023-05-13T17:16:53,617   adding 'cryodrgn/templates/cryoDRGN_viz_template.ipynb'
2023-05-13T17:16:53,634   adding 'cryodrgn-2.3.0.dist-info/LICENSE.txt'
2023-05-13T17:16:53,645   adding 'cryodrgn-2.3.0.dist-info/METADATA'
2023-05-13T17:16:53,648   adding 'cryodrgn-2.3.0.dist-info/WHEEL'
2023-05-13T17:16:53,650   adding 'cryodrgn-2.3.0.dist-info/entry_points.txt'
2023-05-13T17:16:53,652   adding 'cryodrgn-2.3.0.dist-info/top_level.txt'
2023-05-13T17:16:53,656   adding 'cryodrgn-2.3.0.dist-info/RECORD'
2023-05-13T17:16:53,705   removing build/bdist.linux-armv7l/wheel
2023-05-13T17:16:53,964   Building wheel for cryodrgn (pyproject.toml): finished with status 'done'
2023-05-13T17:16:54,040   Created wheel for cryodrgn: filename=cryodrgn-2.3.0-py3-none-any.whl size=1131755 sha256=d3f519ed4819eac7456ccee2c974e41070b80d0e895797cf940ea8b8ca729631
2023-05-13T17:16:54,042   Stored in directory: /tmp/pip-ephem-wheel-cache-_yzd8n7t/wheels/3b/09/10/f4ad6a2ddae718e71b1c706aea05e406a4cc177faa4c589c25
2023-05-13T17:16:54,087 Successfully built cryodrgn
2023-05-13T17:16:54,181 Removed build tracker: '/tmp/pip-build-tracker-zpm7i92a'