2023-11-03T15:30:13,525 Created temporary directory: /tmp/pip-build-tracker-ux95_o8t
2023-11-03T15:30:13,526 Initialized build tracking at /tmp/pip-build-tracker-ux95_o8t
2023-11-03T15:30:13,527 Created build tracker: /tmp/pip-build-tracker-ux95_o8t
2023-11-03T15:30:13,527 Entered build tracker: /tmp/pip-build-tracker-ux95_o8t
2023-11-03T15:30:13,528 Created temporary directory: /tmp/pip-wheel-x2jmw77g
2023-11-03T15:30:13,531 Created temporary directory: /tmp/pip-ephem-wheel-cache-bvf3t_di
2023-11-03T15:30:13,553 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-11-03T15:30:13,557 2 location(s) to search for versions of cryodrgn:
2023-11-03T15:30:13,557 * https://pypi.org/simple/cryodrgn/
2023-11-03T15:30:13,557 * https://www.piwheels.org/simple/cryodrgn/
2023-11-03T15:30:13,557 Fetching project page and analyzing links: https://pypi.org/simple/cryodrgn/
2023-11-03T15:30:13,558 Getting page https://pypi.org/simple/cryodrgn/
2023-11-03T15:30:13,560 Found index url https://pypi.org/simple/
2023-11-03T15:30:13,780 Fetched page https://pypi.org/simple/cryodrgn/ as application/vnd.pypi.simple.v1+json
2023-11-03T15:30:13,784   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)
2023-11-03T15:30:13,785   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
2023-11-03T15:30:13,786   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)
2023-11-03T15:30:13,787   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
2023-11-03T15:30:13,787   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)
2023-11-03T15:30:13,789   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
2023-11-03T15:30:13,789   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)
2023-11-03T15:30:13,790   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
2023-11-03T15:30:13,791   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)
2023-11-03T15:30:13,792   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
2023-11-03T15:30:13,793   Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/08/8d/d0ff2954b5825e3b771a943b40423d57195aec5c30d4b770250ac822c7fe/cryodrgn-3.0.0b0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-11-03T15:30:13,794   Found link https://files.pythonhosted.org/packages/74/92/6ca0ee245ed52438a0f471cfb29de766b9822010f760da08875be946e827/cryodrgn-3.0.0b0.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 3.0.0b0
2023-11-03T15:30:13,794   Skipping link: No binaries permitted for cryodrgn: https://files.pythonhosted.org/packages/ec/e4/6ed8adf3e7b526a69e850b7e5d1b7f6fceede2b3683b35c81944321149a7/cryodrgn-3.0.1b0-py3-none-any.whl (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-11-03T15:30:13,796   Found link https://files.pythonhosted.org/packages/9d/05/4215fddb0e1cce3525690435efa36cef19ad50c1808b1d48771ea3b7ff37/cryodrgn-3.0.1b0.tar.gz (from https://pypi.org/simple/cryodrgn/) (requires-python:>=3.7), version: 3.0.1b0
2023-11-03T15:30:13,796 Fetching project page and analyzing links: https://www.piwheels.org/simple/cryodrgn/
2023-11-03T15:30:13,797 Getting page https://www.piwheels.org/simple/cryodrgn/
2023-11-03T15:30:13,798 Found index url https://www.piwheels.org/simple/
2023-11-03T15:30:14,246 Fetched page https://www.piwheels.org/simple/cryodrgn/ as text/html
2023-11-03T15:30:14,252   Skipping link: No binaries permitted for cryodrgn: https://www.piwheels.org/simple/cryodrgn/cryodrgn-3.0.0b0-py3-none-any.whl#sha256=498fba8644092d42d124e88b81d7209e358d25ea05720b664bd44c454eb221a2 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-11-03T15:30:14,254   Skipping link: No binaries permitted for cryodrgn: https://www.piwheels.org/simple/cryodrgn/cryodrgn-2.3.0-py3-none-any.whl#sha256=d3f519ed4819eac7456ccee2c974e41070b80d0e895797cf940ea8b8ca729631 (from https://www.piwheels.org/simple/cryodrgn/) (requires-python:>=3.7)
2023-11-03T15:30:14,255   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)
2023-11-03T15:30:14,256   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)
2023-11-03T15:30:14,257   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)
2023-11-03T15:30:14,257   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)
2023-11-03T15:30:14,259 Skipping link: not a file: https://www.piwheels.org/simple/cryodrgn/
2023-11-03T15:30:14,260 Skipping link: not a file: https://pypi.org/simple/cryodrgn/
2023-11-03T15:30:14,396 Given no hashes to check 1 links for project 'cryodrgn': discarding no candidates
2023-11-03T15:30:14,958 Collecting cryodrgn==3.0.1b0
2023-11-03T15:30:15,078   Created temporary directory: /tmp/pip-unpack-dz3j7xfw
2023-11-03T15:30:15,539   Downloading cryodrgn-3.0.1b0.tar.gz (35.7 MB)
2023-11-03T15:30:24,636   Added cryodrgn==3.0.1b0 from https://files.pythonhosted.org/packages/9d/05/4215fddb0e1cce3525690435efa36cef19ad50c1808b1d48771ea3b7ff37/cryodrgn-3.0.1b0.tar.gz to build tracker '/tmp/pip-build-tracker-ux95_o8t'
2023-11-03T15:30:24,642   Created temporary directory: /tmp/pip-build-env-3wmslkzx
2023-11-03T15:30:24,647   Installing build dependencies: started
2023-11-03T15:30:24,649   Running command pip subprocess to install build dependencies
2023-11-03T15:30:26,837   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-11-03T15:30:27,381   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-11-03T15:30:29,036   Collecting setuptools>=61.0
2023-11-03T15:30:29,104     Using cached https://www.piwheels.org/simple/setuptools/setuptools-68.2.2-py3-none-any.whl (807 kB)
2023-11-03T15:30:29,441   Collecting setuptools_scm>=6.2
2023-11-03T15:30:29,459     Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-8.0.4-py3-none-any.whl (42 kB)
2023-11-03T15:30:29,802   Collecting packaging>=20 (from setuptools_scm>=6.2)
2023-11-03T15:30:29,818     Using cached https://www.piwheels.org/simple/packaging/packaging-23.2-py3-none-any.whl (53 kB)
2023-11-03T15:30:29,932   Collecting typing-extensions (from setuptools_scm>=6.2)
2023-11-03T15:30:29,957     Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.8.0-py3-none-any.whl (31 kB)
2023-11-03T15:30:32,425   Installing collected packages: typing-extensions, setuptools, packaging, setuptools_scm
2023-11-03T15:30:35,108   Successfully installed packaging-23.2 setuptools-68.2.2 setuptools_scm-8.0.4 typing-extensions-4.8.0

2023-11-03T15:30:35,377   [notice] A new release of pip is available: 23.2.1 -> 23.3.1
2023-11-03T15:30:35,378   [notice] To update, run: python3 -m pip install --upgrade pip
2023-11-03T15:30:35,655   Installing build dependencies: finished with status 'done'
2023-11-03T15:30:35,658   Getting requirements to build wheel: started
2023-11-03T15:30:35,659   Running command Getting requirements to build wheel
2023-11-03T15:30:36,724   running egg_info
2023-11-03T15:30:36,730   writing cryodrgn.egg-info/PKG-INFO
2023-11-03T15:30:36,737   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-11-03T15:30:36,739   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-11-03T15:30:36,742   writing requirements to cryodrgn.egg-info/requires.txt
2023-11-03T15:30:36,743   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-11-03T15:30:36,785   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-11-03T15:30:36,788   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-11-03T15:30:36,796   reading manifest template 'MANIFEST.in'
2023-11-03T15:30:36,797   adding license file 'LICENSE.txt'
2023-11-03T15:30:36,808   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-11-03T15:30:36,926   Getting requirements to build wheel: finished with status 'done'
2023-11-03T15:30:36,937   Installing backend dependencies: started
2023-11-03T15:30:36,938   Running command pip subprocess to install backend dependencies
2023-11-03T15:30:38,116   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-11-03T15:30:38,617   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-11-03T15:30:39,170   Collecting wheel
2023-11-03T15:30:39,199     Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.3-py3-none-any.whl (65 kB)
2023-11-03T15:30:42,357   Installing collected packages: wheel
2023-11-03T15:30:42,651     Creating /tmp/pip-build-env-3wmslkzx/normal/local/bin
2023-11-03T15:30:42,654     changing mode of /tmp/pip-build-env-3wmslkzx/normal/local/bin/wheel to 755
2023-11-03T15:30:42,669   Successfully installed wheel-0.41.3

2023-11-03T15:30:42,947   [notice] A new release of pip is available: 23.2.1 -> 23.3.1
2023-11-03T15:30:42,947   [notice] To update, run: python3 -m pip install --upgrade pip
2023-11-03T15:30:43,173   Installing backend dependencies: finished with status 'done'
2023-11-03T15:30:43,175   Created temporary directory: /tmp/pip-modern-metadata-nbtqyzho
2023-11-03T15:30:43,177   Preparing metadata (pyproject.toml): started
2023-11-03T15:30:43,179   Running command Preparing metadata (pyproject.toml)
2023-11-03T15:30:44,104   running dist_info
2023-11-03T15:30:44,110   creating /tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info
2023-11-03T15:30:44,115   writing /tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/PKG-INFO
2023-11-03T15:30:44,123   writing dependency_links to /tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/dependency_links.txt
2023-11-03T15:30:44,125   writing entry points to /tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/entry_points.txt
2023-11-03T15:30:44,128   writing requirements to /tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/requires.txt
2023-11-03T15:30:44,129   writing top-level names to /tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/top_level.txt
2023-11-03T15:30:44,131   writing manifest file '/tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/SOURCES.txt'
2023-11-03T15:30:44,184   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-11-03T15:30:44,187   reading manifest file '/tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/SOURCES.txt'
2023-11-03T15:30:44,189   reading manifest template 'MANIFEST.in'
2023-11-03T15:30:44,191   adding license file 'LICENSE.txt'
2023-11-03T15:30:44,196   writing manifest file '/tmp/pip-modern-metadata-nbtqyzho/cryodrgn.egg-info/SOURCES.txt'
2023-11-03T15:30:44,197   creating '/tmp/pip-modern-metadata-nbtqyzho/cryodrgn-3.0.1b0.dist-info'
2023-11-03T15:30:44,366   Preparing metadata (pyproject.toml): finished with status 'done'
2023-11-03T15:30:44,371   Source in /tmp/pip-wheel-x2jmw77g/cryodrgn_b58827b344bb427aa7b9e3e55036743c has version 3.0.1b0, which satisfies requirement cryodrgn==3.0.1b0 from https://files.pythonhosted.org/packages/9d/05/4215fddb0e1cce3525690435efa36cef19ad50c1808b1d48771ea3b7ff37/cryodrgn-3.0.1b0.tar.gz
2023-11-03T15:30:44,372   Removed cryodrgn==3.0.1b0 from https://files.pythonhosted.org/packages/9d/05/4215fddb0e1cce3525690435efa36cef19ad50c1808b1d48771ea3b7ff37/cryodrgn-3.0.1b0.tar.gz from build tracker '/tmp/pip-build-tracker-ux95_o8t'
2023-11-03T15:30:44,381 Created temporary directory: /tmp/pip-unpack-dx_e8ey1
2023-11-03T15:30:44,382 Created temporary directory: /tmp/pip-unpack-fhqx_fir
2023-11-03T15:30:44,424 Building wheels for collected packages: cryodrgn
2023-11-03T15:30:44,428   Created temporary directory: /tmp/pip-wheel-jm1xx92e
2023-11-03T15:30:44,429   Destination directory: /tmp/pip-wheel-jm1xx92e
2023-11-03T15:30:44,431   Building wheel for cryodrgn (pyproject.toml): started
2023-11-03T15:30:44,433   Running command Building wheel for cryodrgn (pyproject.toml)
2023-11-03T15:30:45,494   running bdist_wheel
2023-11-03T15:30:45,517   running build
2023-11-03T15:30:45,517   running build_py
2023-11-03T15:30:45,524   creating build
2023-11-03T15:30:45,524   creating build/lib
2023-11-03T15:30:45,525   creating build/lib/cryodrgn
2023-11-03T15:30:45,527   copying cryodrgn/__init__.py -> build/lib/cryodrgn
2023-11-03T15:30:45,529   copying cryodrgn/analysis.py -> build/lib/cryodrgn
2023-11-03T15:30:45,531   copying cryodrgn/fft.py -> build/lib/cryodrgn
2023-11-03T15:30:45,534   copying cryodrgn/mrc.py -> build/lib/cryodrgn
2023-11-03T15:30:45,536   copying cryodrgn/models.py -> build/lib/cryodrgn
2023-11-03T15:30:45,541   copying cryodrgn/lattice.py -> build/lib/cryodrgn
2023-11-03T15:30:45,544   copying cryodrgn/ctf.py -> build/lib/cryodrgn
2023-11-03T15:30:45,546   copying cryodrgn/lie_tools.py -> build/lib/cryodrgn
2023-11-03T15:30:45,548   copying cryodrgn/utils.py -> build/lib/cryodrgn
2023-11-03T15:30:45,550   copying cryodrgn/_version.py -> build/lib/cryodrgn
2023-11-03T15:30:45,552   copying cryodrgn/pose_search.py -> build/lib/cryodrgn
2023-11-03T15:30:45,554   copying cryodrgn/utils_exec.py -> build/lib/cryodrgn
2023-11-03T15:30:45,556   copying cryodrgn/dataset.py -> build/lib/cryodrgn
2023-11-03T15:30:45,559   copying cryodrgn/config.py -> build/lib/cryodrgn
2023-11-03T15:30:45,562   copying cryodrgn/losses.py -> build/lib/cryodrgn
2023-11-03T15:30:45,564   copying cryodrgn/so3_grid.py -> build/lib/cryodrgn
2023-11-03T15:30:45,567   copying cryodrgn/make_healpy.py -> build/lib/cryodrgn
2023-11-03T15:30:45,570   copying cryodrgn/__main__.py -> build/lib/cryodrgn
2023-11-03T15:30:45,572   copying cryodrgn/shift_grid.py -> build/lib/cryodrgn
2023-11-03T15:30:45,574   copying cryodrgn/shift_grid3.py -> build/lib/cryodrgn
2023-11-03T15:30:45,577   copying cryodrgn/source.py -> build/lib/cryodrgn
2023-11-03T15:30:45,579   copying cryodrgn/beta_schedule.py -> build/lib/cryodrgn
2023-11-03T15:30:45,581   copying cryodrgn/pose.py -> build/lib/cryodrgn
2023-11-03T15:30:45,583   copying cryodrgn/starfile.py -> build/lib/cryodrgn
2023-11-03T15:30:45,586   creating build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,587   copying cryodrgn/commands_utils/__init__.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,589   copying cryodrgn/commands_utils/filter_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,591   copying cryodrgn/commands_utils/view_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,593   copying cryodrgn/commands_utils/view_header.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,595   copying cryodrgn/commands_utils/write_star.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,597   copying cryodrgn/commands_utils/flip_hand.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,598   copying cryodrgn/commands_utils/phase_flip.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,600   copying cryodrgn/commands_utils/invert_contrast.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,601   copying cryodrgn/commands_utils/concat_pkls.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,603   copying cryodrgn/commands_utils/translate_mrcs.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,605   copying cryodrgn/commands_utils/view_cs_header.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,606   copying cryodrgn/commands_utils/write_cs.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,608   copying cryodrgn/commands_utils/select_random.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,610   copying cryodrgn/commands_utils/add_psize.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,612   copying cryodrgn/commands_utils/filter_star.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,614   copying cryodrgn/commands_utils/filter_pkl.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,616   copying cryodrgn/commands_utils/select_clusters.py -> build/lib/cryodrgn/commands_utils
2023-11-03T15:30:45,618   creating build/lib/cryodrgn/commands
2023-11-03T15:30:45,619   copying cryodrgn/commands/__init__.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,621   copying cryodrgn/commands/abinit_homo.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,623   copying cryodrgn/commands/abinit_het.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,626   copying cryodrgn/commands/train_nn.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,629   copying cryodrgn/commands/analyze.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,633   copying cryodrgn/commands/view_config.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,635   copying cryodrgn/commands/parse_pose_star.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,637   copying cryodrgn/commands/eval_vol.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,639   copying cryodrgn/commands/preprocess.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,641   copying cryodrgn/commands/train_vae.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,644   copying cryodrgn/commands/direct_traversal.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,646   copying cryodrgn/commands/parse_ctf_csparc.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,648   copying cryodrgn/commands/backproject_voxel.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,651   copying cryodrgn/commands/graph_traversal.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,654   copying cryodrgn/commands/analyze_landscape.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,657   copying cryodrgn/commands/parse_pose_csparc.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,658   copying cryodrgn/commands/eval_images.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,660   copying cryodrgn/commands/analyze_landscape_full.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,663   copying cryodrgn/commands/parse_ctf_star.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,664   copying cryodrgn/commands/downsample.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,667   copying cryodrgn/commands/pc_traversal.py -> build/lib/cryodrgn/commands
2023-11-03T15:30:45,668   running egg_info
2023-11-03T15:30:45,674   writing cryodrgn.egg-info/PKG-INFO
2023-11-03T15:30:45,682   writing dependency_links to cryodrgn.egg-info/dependency_links.txt
2023-11-03T15:30:45,684   writing entry points to cryodrgn.egg-info/entry_points.txt
2023-11-03T15:30:45,686   writing requirements to cryodrgn.egg-info/requires.txt
2023-11-03T15:30:45,687   writing top-level names to cryodrgn.egg-info/top_level.txt
2023-11-03T15:30:45,720   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2023-11-03T15:30:45,723   reading manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-11-03T15:30:45,754   reading manifest template 'MANIFEST.in'
2023-11-03T15:30:45,756   adding license file 'LICENSE.txt'
2023-11-03T15:30:45,766   writing manifest file 'cryodrgn.egg-info/SOURCES.txt'
2023-11-03T15:30:45,774   copying cryodrgn/healpy_grid.json -> build/lib/cryodrgn
2023-11-03T15:30:46,016   creating build/lib/cryodrgn/templates
2023-11-03T15:30:46,018   copying cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/lib/cryodrgn/templates
2023-11-03T15:30:46,022   copying cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/lib/cryodrgn/templates
2023-11-03T15:30:46,025   copying cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/lib/cryodrgn/templates
2023-11-03T15:30:46,029   copying cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/lib/cryodrgn/templates
2023-11-03T15:30:46,034   copying cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/lib/cryodrgn/templates
2023-11-03T15:30:46,050   installing to build/bdist.linux-armv7l/wheel
2023-11-03T15:30:46,051   running install
2023-11-03T15:30:46,074   running install_lib
2023-11-03T15:30:46,080   creating build/bdist.linux-armv7l
2023-11-03T15:30:46,080   creating build/bdist.linux-armv7l/wheel
2023-11-03T15:30:46,083   creating build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,084   copying build/lib/cryodrgn/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,086   copying build/lib/cryodrgn/analysis.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,089   creating build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-11-03T15:30:46,090   copying build/lib/cryodrgn/templates/cryoDRGN_figures_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-11-03T15:30:46,093   copying build/lib/cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-11-03T15:30:46,095   copying build/lib/cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-11-03T15:30:46,098   copying build/lib/cryodrgn/templates/cryoDRGN_viz_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-11-03T15:30:46,100   copying build/lib/cryodrgn/templates/cryoDRGN_filtering_template.ipynb -> build/bdist.linux-armv7l/wheel/cryodrgn/templates
2023-11-03T15:30:46,103   copying build/lib/cryodrgn/fft.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,106   copying build/lib/cryodrgn/healpy_grid.json -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,286   copying build/lib/cryodrgn/mrc.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,289   copying build/lib/cryodrgn/models.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,292   copying build/lib/cryodrgn/lattice.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,295   copying build/lib/cryodrgn/ctf.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,297   copying build/lib/cryodrgn/lie_tools.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,456   copying build/lib/cryodrgn/utils.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:46,464   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:46,466   copying build/lib/cryodrgn/commands_utils/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:46,469   copying build/lib/cryodrgn/commands_utils/filter_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,275   copying build/lib/cryodrgn/commands_utils/view_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,434   copying build/lib/cryodrgn/commands_utils/view_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,606   copying build/lib/cryodrgn/commands_utils/write_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,610   copying build/lib/cryodrgn/commands_utils/flip_hand.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,618   copying build/lib/cryodrgn/commands_utils/phase_flip.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,622   copying build/lib/cryodrgn/commands_utils/invert_contrast.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,626   copying build/lib/cryodrgn/commands_utils/concat_pkls.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,630   copying build/lib/cryodrgn/commands_utils/translate_mrcs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,633   copying build/lib/cryodrgn/commands_utils/view_cs_header.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,637   copying build/lib/cryodrgn/commands_utils/write_cs.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,640   copying build/lib/cryodrgn/commands_utils/select_random.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,644   copying build/lib/cryodrgn/commands_utils/add_psize.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,647   copying build/lib/cryodrgn/commands_utils/filter_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,651   copying build/lib/cryodrgn/commands_utils/filter_pkl.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,654   copying build/lib/cryodrgn/commands_utils/select_clusters.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands_utils
2023-11-03T15:30:47,659   creating build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,662   copying build/lib/cryodrgn/commands/__init__.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,665   copying build/lib/cryodrgn/commands/abinit_homo.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,671   copying build/lib/cryodrgn/commands/abinit_het.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,676   copying build/lib/cryodrgn/commands/train_nn.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,680   copying build/lib/cryodrgn/commands/analyze.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,685   copying build/lib/cryodrgn/commands/view_config.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,688   copying build/lib/cryodrgn/commands/parse_pose_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,692   copying build/lib/cryodrgn/commands/eval_vol.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,696   copying build/lib/cryodrgn/commands/preprocess.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,699   copying build/lib/cryodrgn/commands/train_vae.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,704   copying build/lib/cryodrgn/commands/direct_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,707   copying build/lib/cryodrgn/commands/parse_ctf_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,711   copying build/lib/cryodrgn/commands/backproject_voxel.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,715   copying build/lib/cryodrgn/commands/graph_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,719   copying build/lib/cryodrgn/commands/analyze_landscape.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,723   copying build/lib/cryodrgn/commands/parse_pose_csparc.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,726   copying build/lib/cryodrgn/commands/eval_images.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,730   copying build/lib/cryodrgn/commands/analyze_landscape_full.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,733   copying build/lib/cryodrgn/commands/parse_ctf_star.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,736   copying build/lib/cryodrgn/commands/downsample.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,741   copying build/lib/cryodrgn/commands/pc_traversal.py -> build/bdist.linux-armv7l/wheel/cryodrgn/commands
2023-11-03T15:30:47,744   copying build/lib/cryodrgn/_version.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:47,747   copying build/lib/cryodrgn/pose_search.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:47,751   copying build/lib/cryodrgn/utils_exec.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:47,754   copying build/lib/cryodrgn/dataset.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,353   copying build/lib/cryodrgn/config.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,357   copying build/lib/cryodrgn/losses.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,361   copying build/lib/cryodrgn/so3_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,366   copying build/lib/cryodrgn/make_healpy.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,369   copying build/lib/cryodrgn/__main__.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,373   copying build/lib/cryodrgn/shift_grid.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,377   copying build/lib/cryodrgn/shift_grid3.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,381   copying build/lib/cryodrgn/source.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,386   copying build/lib/cryodrgn/beta_schedule.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,389   copying build/lib/cryodrgn/pose.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,393   copying build/lib/cryodrgn/starfile.py -> build/bdist.linux-armv7l/wheel/cryodrgn
2023-11-03T15:30:49,397   running install_egg_info
2023-11-03T15:30:49,408   Copying cryodrgn.egg-info to build/bdist.linux-armv7l/wheel/cryodrgn-3.0.1b0-py3.11.egg-info
2023-11-03T15:30:49,432   running install_scripts
2023-11-03T15:30:49,465   creating build/bdist.linux-armv7l/wheel/cryodrgn-3.0.1b0.dist-info/WHEEL
2023-11-03T15:30:49,469   creating '/tmp/pip-wheel-jm1xx92e/.tmp-yh4l6k99/cryodrgn-3.0.1b0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-11-03T15:30:49,473   adding 'cryodrgn/__init__.py'
2023-11-03T15:30:49,475   adding 'cryodrgn/__main__.py'
2023-11-03T15:30:49,477   adding 'cryodrgn/_version.py'
2023-11-03T15:30:49,482   adding 'cryodrgn/analysis.py'
2023-11-03T15:30:49,484   adding 'cryodrgn/beta_schedule.py'
2023-11-03T15:30:49,487   adding 'cryodrgn/config.py'
2023-11-03T15:30:49,489   adding 'cryodrgn/ctf.py'
2023-11-03T15:30:49,494   adding 'cryodrgn/dataset.py'
2023-11-03T15:30:49,496   adding 'cryodrgn/fft.py'
2023-11-03T15:30:50,270   adding 'cryodrgn/healpy_grid.json'
2023-11-03T15:30:50,473   adding 'cryodrgn/lattice.py'
2023-11-03T15:30:50,736   adding 'cryodrgn/lie_tools.py'
2023-11-03T15:30:50,835   adding 'cryodrgn/losses.py'
2023-11-03T15:30:50,930   adding 'cryodrgn/make_healpy.py'
2023-11-03T15:30:51,044   adding 'cryodrgn/models.py'
2023-11-03T15:30:51,050   adding 'cryodrgn/mrc.py'
2023-11-03T15:30:51,055   adding 'cryodrgn/pose.py'
2023-11-03T15:30:51,061   adding 'cryodrgn/pose_search.py'
2023-11-03T15:30:51,065   adding 'cryodrgn/shift_grid.py'
2023-11-03T15:30:51,068   adding 'cryodrgn/shift_grid3.py'
2023-11-03T15:30:51,071   adding 'cryodrgn/so3_grid.py'
2023-11-03T15:30:51,077   adding 'cryodrgn/source.py'
2023-11-03T15:30:51,081   adding 'cryodrgn/starfile.py'
2023-11-03T15:30:51,085   adding 'cryodrgn/utils.py'
2023-11-03T15:30:51,088   adding 'cryodrgn/utils_exec.py'
2023-11-03T15:30:51,091   adding 'cryodrgn/commands/__init__.py'
2023-11-03T15:30:51,100   adding 'cryodrgn/commands/abinit_het.py'
2023-11-03T15:30:51,108   adding 'cryodrgn/commands/abinit_homo.py'
2023-11-03T15:30:51,113   adding 'cryodrgn/commands/analyze.py'
2023-11-03T15:30:51,120   adding 'cryodrgn/commands/analyze_landscape.py'
2023-11-03T15:30:51,124   adding 'cryodrgn/commands/analyze_landscape_full.py'
2023-11-03T15:30:51,128   adding 'cryodrgn/commands/backproject_voxel.py'
2023-11-03T15:30:51,131   adding 'cryodrgn/commands/direct_traversal.py'
2023-11-03T15:30:51,134   adding 'cryodrgn/commands/downsample.py'
2023-11-03T15:30:51,139   adding 'cryodrgn/commands/eval_images.py'
2023-11-03T15:30:51,142   adding 'cryodrgn/commands/eval_vol.py'
2023-11-03T15:30:51,144   adding 'cryodrgn/commands/graph_traversal.py'
2023-11-03T15:30:51,145   adding 'cryodrgn/commands/parse_ctf_csparc.py'
2023-11-03T15:30:51,147   adding 'cryodrgn/commands/parse_ctf_star.py'
2023-11-03T15:30:51,148   adding 'cryodrgn/commands/parse_pose_csparc.py'
2023-11-03T15:30:51,149   adding 'cryodrgn/commands/parse_pose_star.py'
2023-11-03T15:30:51,151   adding 'cryodrgn/commands/pc_traversal.py'
2023-11-03T15:30:51,152   adding 'cryodrgn/commands/preprocess.py'
2023-11-03T15:30:51,155   adding 'cryodrgn/commands/train_nn.py'
2023-11-03T15:30:51,159   adding 'cryodrgn/commands/train_vae.py'
2023-11-03T15:30:51,161   adding 'cryodrgn/commands/view_config.py'
2023-11-03T15:30:51,163   adding 'cryodrgn/commands_utils/__init__.py'
2023-11-03T15:30:51,164   adding 'cryodrgn/commands_utils/add_psize.py'
2023-11-03T15:30:51,165   adding 'cryodrgn/commands_utils/concat_pkls.py'
2023-11-03T15:30:51,167   adding 'cryodrgn/commands_utils/filter_mrcs.py'
2023-11-03T15:30:51,168   adding 'cryodrgn/commands_utils/filter_pkl.py'
2023-11-03T15:30:51,170   adding 'cryodrgn/commands_utils/filter_star.py'
2023-11-03T15:30:51,171   adding 'cryodrgn/commands_utils/flip_hand.py'
2023-11-03T15:30:51,173   adding 'cryodrgn/commands_utils/invert_contrast.py'
2023-11-03T15:30:51,174   adding 'cryodrgn/commands_utils/phase_flip.py'
2023-11-03T15:30:51,176   adding 'cryodrgn/commands_utils/select_clusters.py'
2023-11-03T15:30:51,177   adding 'cryodrgn/commands_utils/select_random.py'
2023-11-03T15:30:51,178   adding 'cryodrgn/commands_utils/translate_mrcs.py'
2023-11-03T15:30:51,180   adding 'cryodrgn/commands_utils/view_cs_header.py'
2023-11-03T15:30:51,181   adding 'cryodrgn/commands_utils/view_header.py'
2023-11-03T15:30:51,183   adding 'cryodrgn/commands_utils/view_mrcs.py'
2023-11-03T15:30:51,184   adding 'cryodrgn/commands_utils/write_cs.py'
2023-11-03T15:30:51,186   adding 'cryodrgn/commands_utils/write_star.py'
2023-11-03T15:30:51,189   adding 'cryodrgn/templates/cryoDRGN_ET_viz_template.ipynb'
2023-11-03T15:30:51,191   adding 'cryodrgn/templates/cryoDRGN_analyze_landscape_template.ipynb'
2023-11-03T15:30:51,193   adding 'cryodrgn/templates/cryoDRGN_figures_template.ipynb'
2023-11-03T15:30:51,196   adding 'cryodrgn/templates/cryoDRGN_filtering_template.ipynb'
2023-11-03T15:30:51,199   adding 'cryodrgn/templates/cryoDRGN_viz_template.ipynb'
2023-11-03T15:30:51,206   adding 'cryodrgn-3.0.1b0.dist-info/LICENSE.txt'
2023-11-03T15:30:51,211   adding 'cryodrgn-3.0.1b0.dist-info/METADATA'
2023-11-03T15:30:51,213   adding 'cryodrgn-3.0.1b0.dist-info/WHEEL'
2023-11-03T15:30:51,214   adding 'cryodrgn-3.0.1b0.dist-info/entry_points.txt'
2023-11-03T15:30:51,215   adding 'cryodrgn-3.0.1b0.dist-info/top_level.txt'
2023-11-03T15:30:51,217   adding 'cryodrgn-3.0.1b0.dist-info/RECORD'
2023-11-03T15:30:51,232   removing build/bdist.linux-armv7l/wheel
2023-11-03T15:30:51,389   Building wheel for cryodrgn (pyproject.toml): finished with status 'done'
2023-11-03T15:30:51,420   Created wheel for cryodrgn: filename=cryodrgn-3.0.1b0-py3-none-any.whl size=1143528 sha256=c5aa67408ca576f776a9b8a331b966eb87343cb2d3713e29768705555e85f930
2023-11-03T15:30:51,421   Stored in directory: /tmp/pip-ephem-wheel-cache-bvf3t_di/wheels/f2/9e/19/3013eb54c69370fabd990b2fed70510c7f7d11908de095567c
2023-11-03T15:30:51,440 Successfully built cryodrgn
2023-11-03T15:30:51,472 Removed build tracker: '/tmp/pip-build-tracker-ux95_o8t'