2023-03-26T04:36:12,660 Created temporary directory: /tmp/pip-ephem-wheel-cache-dw5nl6cy
2023-03-26T04:36:12,666 Created temporary directory: /tmp/pip-build-tracker-hg5y3qrf
2023-03-26T04:36:12,667 Initialized build tracking at /tmp/pip-build-tracker-hg5y3qrf
2023-03-26T04:36:12,667 Created build tracker: /tmp/pip-build-tracker-hg5y3qrf
2023-03-26T04:36:12,667 Entered build tracker: /tmp/pip-build-tracker-hg5y3qrf
2023-03-26T04:36:12,669 Created temporary directory: /tmp/pip-wheel-k5u37e4i
2023-03-26T04:36:12,684 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
2023-03-26T04:36:12,690 Created temporary directory: /tmp/pip-ephem-wheel-cache-3z8ffh9i
2023-03-26T04:36:12,750 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-26T04:36:12,756 2 location(s) to search for versions of cryodrgn:
2023-03-26T04:36:12,756 * https://pypi.org/simple/cryodrgn/
2023-03-26T04:36:12,756 * https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:36:12,758 Fetching project page and analyzing links: https://pypi.org/simple/cryodrgn/
2023-03-26T04:36:12,759 Getting page https://pypi.org/simple/cryodrgn/
2023-03-26T04:36:12,763 Found index url https://pypi.org/simple
2023-03-26T04:36:12,981 Fetched page https://pypi.org/simple/cryodrgn/ as application/vnd.pypi.simple.v1+json
2023-03-26T04:36:12,986   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)
2023-03-26T04:36:12,988   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
2023-03-26T04:36:12,989   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)
2023-03-26T04:36:12,990   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
2023-03-26T04:36:12,991   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)
2023-03-26T04:36:12,992   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
2023-03-26T04:36:12,993   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)
2023-03-26T04:36:12,994   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
2023-03-26T04:36:12,995 Fetching project page and analyzing links: https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:36:12,996 Getting page https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:36:12,998 Found index url https://www.piwheels.org/simple
2023-03-26T04:36:13,212 Fetched page https://www.piwheels.org/simple/cryodrgn/ as text/html
2023-03-26T04:36:13,216   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)
2023-03-26T04:36:13,217   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)
2023-03-26T04:36:13,217 Skipping link: not a file: https://www.piwheels.org/simple/cryodrgn/
2023-03-26T04:36:13,218 Skipping link: not a file: https://pypi.org/simple/cryodrgn/
2023-03-26T04:36:13,252 Given no hashes to check 1 links for project 'cryodrgn': discarding no candidates
2023-03-26T04:36:13,282 Collecting cryodrgn==2.2.0b0
2023-03-26T04:36:13,286   Created temporary directory: /tmp/pip-unpack-g2qaormh
2023-03-26T04:36:14,250   Downloading cryodrgn-2.2.0b0.tar.gz (31.4 MB)
2023-03-26T04:36:30,896   Added cryodrgn==2.2.0b0 from https://files.pythonhosted.org/packages/6f/19/b950e5eb7a6d3c8d122bec56e59c447d3585a660a7605112a5346816014e/cryodrgn-2.2.0b0.tar.gz to build tracker '/tmp/pip-build-tracker-hg5y3qrf'
2023-03-26T04:36:30,910   Created temporary directory: /tmp/pip-build-env-y6zg0apo
2023-03-26T04:36:30,930   Installing build dependencies: started
2023-03-26T04:36:30,933   Running command pip subprocess to install build dependencies
2023-03-26T04:36:33,721   Using pip 23.0.1 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
2023-03-26T04:36:34,966   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
2023-03-26T04:36:35,024   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-26T04:36:38,928   Collecting setuptools>=61.0
2023-03-26T04:36:39,263     Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.6.0-py3-none-any.whl (1.1 MB)
2023-03-26T04:36:40,164   Collecting setuptools_scm>=6.2
2023-03-26T04:36:40,200     Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-7.1.0-py3-none-any.whl (43 kB)
2023-03-26T04:36:40,547   Collecting tomli>=1.0.0
2023-03-26T04:36:40,580     Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB)
2023-03-26T04:36:41,555   Collecting importlib-metadata
2023-03-26T04:36:41,588     Using cached https://www.piwheels.org/simple/importlib-metadata/importlib_metadata-6.1.0-py3-none-any.whl (21 kB)
2023-03-26T04:36:41,998   Collecting packaging>=20.0
2023-03-26T04:36:42,278     Using cached https://www.piwheels.org/simple/packaging/packaging-23.0-py3-none-any.whl (42 kB)
2023-03-26T04:36:42,749   Collecting typing-extensions
2023-03-26T04:36:42,798     Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.5.0-py3-none-any.whl (27 kB)
2023-03-26T04:36:43,525   Collecting zipp>=0.5
2023-03-26T04:36:43,557     Using cached https://www.piwheels.org/simple/zipp/zipp-3.15.0-py3-none-any.whl (6.8 kB)
2023-03-26T04:36:49,270   Installing collected packages: zipp, typing-extensions, tomli, setuptools, packaging, importlib-metadata, setuptools_scm
2023-03-26T04:36:54,579   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
2023-03-26T04:36:55,581   Installing build dependencies: finished with status 'done'
2023-03-26T04:36:55,592   Getting requirements to build wheel: started
2023-03-26T04:36:55,594   Running command Getting requirements to build wheel
2023-03-26T04:36:57,712   running egg_info
2023-03-26T04:36:57,726   writing cryodrgn.egg-info/PKG-INFO
2023-03-26T04:36:57,733   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-03-26T04:36:57,738   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-03-26T04:36:57,742   writing requirements to cryodrgn.egg-info/requires.txt
2023-03-26T04:36:57,744   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-03-26T04:36:57,857   /tmp/pip-build-env-y6zg0apo/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-03-26T04:36:57,857     warnings.warn(msg, _BetaConfiguration)
2023-03-26T04:36:57,858   listing git files failed - pretending there aren't any
2023-03-26T04:36:57,877   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:36:57,897   reading manifest template 'MANIFEST.in'
2023-03-26T04:36:57,902   adding license file 'LICENSE.txt'
2023-03-26T04:36:57,931   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:36:58,136   Getting requirements to build wheel: finished with status 'done'
2023-03-26T04:36:58,178   Installing backend dependencies: started
2023-03-26T04:36:58,180   Running command pip subprocess to install backend dependencies
2023-03-26T04:37:00,979   Using pip 23.0.1 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
2023-03-26T04:37:02,205   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
2023-03-26T04:37:02,262   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-26T04:37:03,153   Collecting wheel
2023-03-26T04:37:03,190     Using cached https://www.piwheels.org/simple/wheel/wheel-0.40.0-py3-none-any.whl (64 kB)
2023-03-26T04:37:07,414   Installing collected packages: wheel
2023-03-26T04:37:07,862     Creating /tmp/pip-build-env-y6zg0apo/normal/bin
2023-03-26T04:37:07,867     changing mode of /tmp/pip-build-env-y6zg0apo/normal/bin/wheel to 755
2023-03-26T04:37:07,894   Successfully installed wheel-0.40.0
2023-03-26T04:37:08,771   Installing backend dependencies: finished with status 'done'
2023-03-26T04:37:08,776   Created temporary directory: /tmp/pip-modern-metadata-8e487otw
2023-03-26T04:37:08,783   Preparing metadata (pyproject.toml): started
2023-03-26T04:37:08,785   Running command Preparing metadata (pyproject.toml)
2023-03-26T04:37:10,959   running dist_info
2023-03-26T04:37:10,975   creating /tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info
2023-03-26T04:37:10,989   writing /tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/PKG-INFO
2023-03-26T04:37:10,997   writing dependency_links to /tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/dependency_links.txt
2023-03-26T04:37:11,001   writing entry points to /tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/entry_points.txt
2023-03-26T04:37:11,004   writing requirements to /tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/requires.txt
2023-03-26T04:37:11,006   writing top-level names to /tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/top_level.txt
2023-03-26T04:37:11,009   writing manifest file '/tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:37:11,139   /tmp/pip-build-env-y6zg0apo/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-03-26T04:37:11,140     warnings.warn(msg, _BetaConfiguration)
2023-03-26T04:37:11,140   listing git files failed - pretending there aren't any
2023-03-26T04:37:11,159   reading manifest file '/tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:37:11,167   reading manifest template 'MANIFEST.in'
2023-03-26T04:37:11,172   adding license file 'LICENSE.txt'
2023-03-26T04:37:11,185   writing manifest file '/tmp/pip-modern-metadata-8e487otw/cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:37:11,187   creating '/tmp/pip-modern-metadata-8e487otw/cryodrgn-2.2.0b0.dist-info'
2023-03-26T04:37:11,515   Preparing metadata (pyproject.toml): finished with status 'done'
2023-03-26T04:37:11,536   Source in /tmp/pip-wheel-k5u37e4i/cryodrgn_aa8110bc22b4458eb5075a80d9e05963 has version 2.2.0b0, which satisfies requirement cryodrgn==2.2.0b0 from https://files.pythonhosted.org/packages/6f/19/b950e5eb7a6d3c8d122bec56e59c447d3585a660a7605112a5346816014e/cryodrgn-2.2.0b0.tar.gz
2023-03-26T04:37:11,538   Removed cryodrgn==2.2.0b0 from https://files.pythonhosted.org/packages/6f/19/b950e5eb7a6d3c8d122bec56e59c447d3585a660a7605112a5346816014e/cryodrgn-2.2.0b0.tar.gz from build tracker '/tmp/pip-build-tracker-hg5y3qrf'
2023-03-26T04:37:11,559 Created temporary directory: /tmp/pip-unpack-2l6ant1o
2023-03-26T04:37:11,560 Building wheels for collected packages: cryodrgn
2023-03-26T04:37:11,569   Created temporary directory: /tmp/pip-wheel-4efmkzup
2023-03-26T04:37:11,570   Destination directory: /tmp/pip-wheel-4efmkzup
2023-03-26T04:37:11,575   Building wheel for cryodrgn (pyproject.toml): started
2023-03-26T04:37:11,577   Running command Building wheel for cryodrgn (pyproject.toml)
2023-03-26T04:37:13,635   running bdist_wheel
2023-03-26T04:37:13,686   running build
2023-03-26T04:37:13,687   running build_py
2023-03-26T04:37:13,705   creating build
2023-03-26T04:37:13,706   creating build/lib
2023-03-26T04:37:13,708   creating build/lib/cryodrgn
2023-03-26T04:37:13,710   copying cryodrgn/lattice.py -> build/lib/cryodrgn
2023-03-26T04:37:13,715   copying cryodrgn/shift_grid.py -> build/lib/cryodrgn
2023-03-26T04:37:13,718   copying cryodrgn/fft.py -> build/lib/cryodrgn
2023-03-26T04:37:13,722   copying cryodrgn/config.py -> build/lib/cryodrgn
2023-03-26T04:37:13,725   copying cryodrgn/utils.py -> build/lib/cryodrgn
2023-03-26T04:37:13,729   copying cryodrgn/analysis.py -> build/lib/cryodrgn
2023-03-26T04:37:13,734   copying cryodrgn/ctf.py -> build/lib/cryodrgn
2023-03-26T04:37:13,738   copying cryodrgn/__main__.py -> build/lib/cryodrgn
2023-03-26T04:37:13,742   copying cryodrgn/_version.py -> build/lib/cryodrgn
2023-03-26T04:37:13,745   copying cryodrgn/types.py -> build/lib/cryodrgn
2023-03-26T04:37:13,749   copying cryodrgn/models.py -> build/lib/cryodrgn
2023-03-26T04:37:13,755   copying cryodrgn/pose.py -> build/lib/cryodrgn
2023-03-26T04:37:13,759   copying cryodrgn/losses.py -> build/lib/cryodrgn
2023-03-26T04:37:13,763   copying cryodrgn/shift_grid3.py -> build/lib/cryodrgn
2023-03-26T04:37:13,766   copying cryodrgn/mrc.py -> build/lib/cryodrgn
2023-03-26T04:37:13,771   copying cryodrgn/lie_tools.py -> build/lib/cryodrgn
2023-03-26T04:37:13,775   copying cryodrgn/dataset.py -> build/lib/cryodrgn
2023-03-26T04:37:13,779   copying cryodrgn/make_healpy.py -> build/lib/cryodrgn
2023-03-26T04:37:13,783   copying cryodrgn/pose_search.py -> build/lib/cryodrgn
2023-03-26T04:37:13,788   copying cryodrgn/utils_exec.py -> build/lib/cryodrgn
2023-03-26T04:37:13,791   copying cryodrgn/so3_grid.py -> build/lib/cryodrgn
2023-03-26T04:37:13,795   copying cryodrgn/beta_schedule.py -> build/lib/cryodrgn
2023-03-26T04:37:13,798   copying cryodrgn/__init__.py -> build/lib/cryodrgn
2023-03-26T04:37:13,802   copying cryodrgn/starfile.py -> build/lib/cryodrgn
2023-03-26T04:37:13,810   creating build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,812   copying cryodrgn/commands_utils/add_psize.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,815   copying cryodrgn/commands_utils/select_clusters.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,819   copying cryodrgn/commands_utils/view_cs_header.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,822   copying cryodrgn/commands_utils/filter_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,826   copying cryodrgn/commands_utils/translate_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,829   copying cryodrgn/commands_utils/phase_flip.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,833   copying cryodrgn/commands_utils/flip_hand.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,836   copying cryodrgn/commands_utils/write_star.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,840   copying cryodrgn/commands_utils/write_cs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,844   copying cryodrgn/commands_utils/concat_pkls.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,847   copying cryodrgn/commands_utils/select_random.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,851   copying cryodrgn/commands_utils/filter_star.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,854   copying cryodrgn/commands_utils/invert_contrast.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,858   copying cryodrgn/commands_utils/filter_pkl.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,861   copying cryodrgn/commands_utils/__init__.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,864   copying cryodrgn/commands_utils/view_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,868   copying cryodrgn/commands_utils/view_header.py -> build/lib/cryodrgn/commands_utils
2023-03-26T04:37:13,874   creating build/lib/cryodrgn/commands
2023-03-26T04:37:13,876   copying cryodrgn/commands/parse_ctf_star.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,879   copying cryodrgn/commands/train_nn.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,884   copying cryodrgn/commands/analyze_landscape_full.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,888   copying cryodrgn/commands/abinit_het.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,894   copying cryodrgn/commands/parse_pose_star.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,898   copying cryodrgn/commands/parse_ctf_csparc.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,901   copying cryodrgn/commands/graph_traversal.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,905   copying cryodrgn/commands/downsample.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,910   copying cryodrgn/commands/backproject_voxel.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,914   copying cryodrgn/commands/analyze.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,918   copying cryodrgn/commands/pc_traversal.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,922   copying cryodrgn/commands/preprocess.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,926   copying cryodrgn/commands/abinit_homo.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,931   copying cryodrgn/commands/eval_vol.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,935   copying cryodrgn/commands/train_vae.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,940   copying cryodrgn/commands/parse_pose_csparc.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,944   copying cryodrgn/commands/view_config.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,947   copying cryodrgn/commands/analyze_landscape.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,952   copying cryodrgn/commands/eval_images.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,957   copying cryodrgn/commands/__init__.py -> build/lib/cryodrgn/commands
2023-03-26T04:37:13,959   running egg_info
2023-03-26T04:37:13,987   writing cryodrgn.egg-info/PKG-INFO
2023-03-26T04:37:13,993   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-03-26T04:37:13,997   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-03-26T04:37:14,000   writing requirements to cryodrgn.egg-info/requires.txt
2023-03-26T04:37:14,002   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-03-26T04:37:14,089   /tmp/pip-build-env-y6zg0apo/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
2023-03-26T04:37:14,090     warnings.warn(msg, _BetaConfiguration)
2023-03-26T04:37:14,090   listing git files failed - pretending there aren't any
2023-03-26T04:37:14,109   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:37:14,168   reading manifest template 'MANIFEST.in'
2023-03-26T04:37:14,173   adding license file 'LICENSE.txt'
2023-03-26T04:37:14,202   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-03-26T04:37:14,227   copying cryodrgn/healpy_grid.json -> build/lib/cryodrgn
2023-03-26T04:37:14,642   creating build/lib/cryodrgn/templates
2023-03-26T04:37:14,644   copying cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:37:14,649   copying cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:37:14,655   copying cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:37:14,662   copying cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/lib/cryodrgn/templates
2023-03-26T04:37:14,709   installing to build/bdist.linux-armv7l/wheel
2023-03-26T04:37:14,709   running install
2023-03-26T04:37:14,770   running install_lib
2023-03-26T04:37:14,785   creating build/bdist.linux-armv7l
2023-03-26T04:37:14,786   creating build/bdist.linux-armv7l/wheel
2023-03-26T04:37:14,791   creating build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:14,793   copying build/lib/cryodrgn/lattice.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:14,798   copying build/lib/cryodrgn/shift_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:14,802   copying build/lib/cryodrgn/fft.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:14,806   copying build/lib/cryodrgn/config.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:14,811   creating build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:37:14,813   copying build/lib/cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:37:14,818   copying build/lib/cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:37:14,824   copying build/lib/cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:37:14,829   copying build/lib/cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-03-26T04:37:14,834   copying build/lib/cryodrgn/healpy_grid.json -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,247   copying build/lib/cryodrgn/utils.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,251   copying build/lib/cryodrgn/analysis.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,256   copying build/lib/cryodrgn/ctf.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,260   copying build/lib/cryodrgn/__main__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,264   copying build/lib/cryodrgn/_version.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,268   copying build/lib/cryodrgn/types.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,271   copying build/lib/cryodrgn/models.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,277   copying build/lib/cryodrgn/pose.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,281   copying build/lib/cryodrgn/losses.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,285   copying build/lib/cryodrgn/shift_grid3.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,289   copying build/lib/cryodrgn/mrc.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,293   copying build/lib/cryodrgn/lie_tools.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,298   copying build/lib/cryodrgn/dataset.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,303   copying build/lib/cryodrgn/make_healpy.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,307   copying build/lib/cryodrgn/pose_search.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,312   copying build/lib/cryodrgn/utils_exec.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,318   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,320   copying build/lib/cryodrgn/commands_utils/add_psize.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,325   copying build/lib/cryodrgn/commands_utils/select_clusters.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,329   copying build/lib/cryodrgn/commands_utils/view_cs_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,333   copying build/lib/cryodrgn/commands_utils/filter_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,337   copying build/lib/cryodrgn/commands_utils/translate_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,342   copying build/lib/cryodrgn/commands_utils/phase_flip.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,346   copying build/lib/cryodrgn/commands_utils/flip_hand.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,350   copying build/lib/cryodrgn/commands_utils/write_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,355   copying build/lib/cryodrgn/commands_utils/write_cs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,359   copying build/lib/cryodrgn/commands_utils/concat_pkls.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,363   copying build/lib/cryodrgn/commands_utils/select_random.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,367   copying build/lib/cryodrgn/commands_utils/filter_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,370   copying build/lib/cryodrgn/commands_utils/invert_contrast.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,374   copying build/lib/cryodrgn/commands_utils/filter_pkl.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,377   copying build/lib/cryodrgn/commands_utils/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,380   copying build/lib/cryodrgn/commands_utils/view_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,384   copying build/lib/cryodrgn/commands_utils/view_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-03-26T04:37:15,387   copying build/lib/cryodrgn/so3_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,391   copying build/lib/cryodrgn/beta_schedule.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,396   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,397   copying build/lib/cryodrgn/commands/parse_ctf_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,401   copying build/lib/cryodrgn/commands/train_nn.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,406   copying build/lib/cryodrgn/commands/analyze_landscape_full.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,410   copying build/lib/cryodrgn/commands/abinit_het.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,416   copying build/lib/cryodrgn/commands/parse_pose_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,420   copying build/lib/cryodrgn/commands/parse_ctf_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,424   copying build/lib/cryodrgn/commands/graph_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,428   copying build/lib/cryodrgn/commands/downsample.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,432   copying build/lib/cryodrgn/commands/backproject_voxel.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,437   copying build/lib/cryodrgn/commands/analyze.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,442   copying build/lib/cryodrgn/commands/pc_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,445   copying build/lib/cryodrgn/commands/preprocess.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,450   copying build/lib/cryodrgn/commands/abinit_homo.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,455   copying build/lib/cryodrgn/commands/eval_vol.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,459   copying build/lib/cryodrgn/commands/train_vae.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,465   copying build/lib/cryodrgn/commands/parse_pose_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,468   copying build/lib/cryodrgn/commands/view_config.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,472   copying build/lib/cryodrgn/commands/analyze_landscape.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,477   copying build/lib/cryodrgn/commands/eval_images.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,482   copying build/lib/cryodrgn/commands/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-03-26T04:37:15,485   copying build/lib/cryodrgn/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,489   copying build/lib/cryodrgn/starfile.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-03-26T04:37:15,493   running install_egg_info
2023-03-26T04:37:15,507   Copying cryodrgn.egg-info to build/bdist.linux-armv7l/wheel/cryodrgn-2.2.0b0-py3.7.egg-info
2023-03-26T04:37:15,538   running install_scripts
2023-03-26T04:37:15,601   creating build/bdist.linux-armv7l/wheel/cryodrgn-2.2.0b0.dist-info/WHEEL
2023-03-26T04:37:15,606   creating '/tmp/pip-wheel-4efmkzup/.tmp-6ws5hgm6/cryodrgn-2.2.0b0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-03-26T04:37:15,612   adding 'cryodrgn/__init__.py'
2023-03-26T04:37:15,615   adding 'cryodrgn/__main__.py'
2023-03-26T04:37:15,617   adding 'cryodrgn/_version.py'
2023-03-26T04:37:15,624   adding 'cryodrgn/analysis.py'
2023-03-26T04:37:15,626   adding 'cryodrgn/beta_schedule.py'
2023-03-26T04:37:15,629   adding 'cryodrgn/config.py'
2023-03-26T04:37:15,632   adding 'cryodrgn/ctf.py'
2023-03-26T04:37:15,637   adding 'cryodrgn/dataset.py'
2023-03-26T04:37:15,640   adding 'cryodrgn/fft.py'
2023-03-26T04:37:17,582   adding 'cryodrgn/healpy_grid.json'
2023-03-26T04:37:17,791   adding 'cryodrgn/lattice.py'
2023-03-26T04:37:17,795   adding 'cryodrgn/lie_tools.py'
2023-03-26T04:37:17,798   adding 'cryodrgn/losses.py'
2023-03-26T04:37:17,800   adding 'cryodrgn/make_healpy.py'
2023-03-26T04:37:17,810   adding 'cryodrgn/models.py'
2023-03-26T04:37:17,815   adding 'cryodrgn/mrc.py'
2023-03-26T04:37:17,818   adding 'cryodrgn/pose.py'
2023-03-26T04:37:17,824   adding 'cryodrgn/pose_search.py'
2023-03-26T04:37:17,826   adding 'cryodrgn/shift_grid.py'
2023-03-26T04:37:17,829   adding 'cryodrgn/shift_grid3.py'
2023-03-26T04:37:17,832   adding 'cryodrgn/so3_grid.py'
2023-03-26T04:37:17,836   adding 'cryodrgn/starfile.py'
2023-03-26T04:37:17,839   adding 'cryodrgn/types.py'
2023-03-26T04:37:17,842   adding 'cryodrgn/utils.py'
2023-03-26T04:37:17,845   adding 'cryodrgn/utils_exec.py'
2023-03-26T04:37:17,849   adding 'cryodrgn/commands/__init__.py'
2023-03-26T04:37:17,859   adding 'cryodrgn/commands/abinit_het.py'
2023-03-26T04:37:17,866   adding 'cryodrgn/commands/abinit_homo.py'
2023-03-26T04:37:17,871   adding 'cryodrgn/commands/analyze.py'
2023-03-26T04:37:17,877   adding 'cryodrgn/commands/analyze_landscape.py'
2023-03-26T04:37:17,881   adding 'cryodrgn/commands/analyze_landscape_full.py'
2023-03-26T04:37:17,885   adding 'cryodrgn/commands/backproject_voxel.py'
2023-03-26T04:37:17,889   adding 'cryodrgn/commands/downsample.py'
2023-03-26T04:37:17,894   adding 'cryodrgn/commands/eval_images.py'
2023-03-26T04:37:17,897   adding 'cryodrgn/commands/eval_vol.py'
2023-03-26T04:37:17,901   adding 'cryodrgn/commands/graph_traversal.py'
2023-03-26T04:37:17,904   adding 'cryodrgn/commands/parse_ctf_csparc.py'
2023-03-26T04:37:17,907   adding 'cryodrgn/commands/parse_ctf_star.py'
2023-03-26T04:37:17,910   adding 'cryodrgn/commands/parse_pose_csparc.py'
2023-03-26T04:37:17,913   adding 'cryodrgn/commands/parse_pose_star.py'
2023-03-26T04:37:17,916   adding 'cryodrgn/commands/pc_traversal.py'
2023-03-26T04:37:17,920   adding 'cryodrgn/commands/preprocess.py'
2023-03-26T04:37:17,926   adding 'cryodrgn/commands/train_nn.py'
2023-03-26T04:37:17,934   adding 'cryodrgn/commands/train_vae.py'
2023-03-26T04:37:17,938   adding 'cryodrgn/commands/view_config.py'
2023-03-26T04:37:17,942   adding 'cryodrgn/commands_utils/__init__.py'
2023-03-26T04:37:17,944   adding 'cryodrgn/commands_utils/add_psize.py'
2023-03-26T04:37:17,947   adding 'cryodrgn/commands_utils/concat_pkls.py'
2023-03-26T04:37:17,949   adding 'cryodrgn/commands_utils/filter_mrcs.py'
2023-03-26T04:37:17,952   adding 'cryodrgn/commands_utils/filter_pkl.py'
2023-03-26T04:37:17,955   adding 'cryodrgn/commands_utils/filter_star.py'
2023-03-26T04:37:17,957   adding 'cryodrgn/commands_utils/flip_hand.py'
2023-03-26T04:37:17,960   adding 'cryodrgn/commands_utils/invert_contrast.py'
2023-03-26T04:37:17,962   adding 'cryodrgn/commands_utils/phase_flip.py'
2023-03-26T04:37:17,965   adding 'cryodrgn/commands_utils/select_clusters.py'
2023-03-26T04:37:17,968   adding 'cryodrgn/commands_utils/select_random.py'
2023-03-26T04:37:17,971   adding 'cryodrgn/commands_utils/translate_mrcs.py'
2023-03-26T04:37:17,973   adding 'cryodrgn/commands_utils/view_cs_header.py'
2023-03-26T04:37:17,976   adding 'cryodrgn/commands_utils/view_header.py'
2023-03-26T04:37:17,978   adding 'cryodrgn/commands_utils/view_mrcs.py'
2023-03-26T04:37:17,982   adding 'cryodrgn/commands_utils/write_cs.py'
2023-03-26T04:37:17,985   adding 'cryodrgn/commands_utils/write_star.py'
2023-03-26T04:37:17,990   adding 'cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb'
2023-03-26T04:37:17,994   adding 'cryodrgn/templates/cryoDRGN_figures_template.ipynb'
2023-03-26T04:37:18,000   adding 'cryodrgn/templates/cryoDRGN_filtering_template.ipynb'
2023-03-26T04:37:18,006   adding 'cryodrgn/templates/cryoDRGN_viz_template.ipynb'
2023-03-26T04:37:18,023   adding 'cryodrgn-2.2.0b0.dist-info/LICENSE.txt'
2023-03-26T04:37:18,035   adding 'cryodrgn-2.2.0b0.dist-info/METADATA'
2023-03-26T04:37:18,037   adding 'cryodrgn-2.2.0b0.dist-info/WHEEL'
2023-03-26T04:37:18,039   adding 'cryodrgn-2.2.0b0.dist-info/entry_points.txt'
2023-03-26T04:37:18,041   adding 'cryodrgn-2.2.0b0.dist-info/top_level.txt'
2023-03-26T04:37:18,045   adding 'cryodrgn-2.2.0b0.dist-info/RECORD'
2023-03-26T04:37:18,092   removing build/bdist.linux-armv7l/wheel
2023-03-26T04:37:18,352   Building wheel for cryodrgn (pyproject.toml): finished with status 'done'
2023-03-26T04:37:18,433   Created wheel for cryodrgn: filename=cryodrgn-2.2.0b0-py3-none-any.whl size=1129896 sha256=ded8ccf2e343961488fc50ee73479e8c5a9bc61dd79a83f509f96e86c01e9306
2023-03-26T04:37:18,436   Stored in directory: /tmp/pip-ephem-wheel-cache-3z8ffh9i/wheels/66/25/36/8554657ba4f8da12d0fab6b5ec8ba592a93b92082a20681cee
2023-03-26T04:37:18,480 Successfully built cryodrgn
2023-03-26T04:37:18,564 Removed build tracker: '/tmp/pip-build-tracker-hg5y3qrf'