2026-05-22T09:11:53,198 Created temporary directory: /tmp/pip-ephem-wheel-cache-l36nst6x
2026-05-22T09:11:53,200 Created temporary directory: /tmp/pip-build-tracker-58v6xr8h
2026-05-22T09:11:53,200 Initialized build tracking at /tmp/pip-build-tracker-58v6xr8h
2026-05-22T09:11:53,201 Created build tracker: /tmp/pip-build-tracker-58v6xr8h
2026-05-22T09:11:53,201 Entered build tracker: /tmp/pip-build-tracker-58v6xr8h
2026-05-22T09:11:53,202 Created temporary directory: /tmp/pip-wheel-tke5h2ls
2026-05-22T09:11:53,205 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
2026-05-22T09:11:53,207 Created temporary directory: /tmp/pip-ephem-wheel-cache-24f6gqoj
2026-05-22T09:11:53,228 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-05-22T09:11:53,232 2 location(s) to search for versions of torchref:
2026-05-22T09:11:53,232 * https://pypi.org/simple/torchref/
2026-05-22T09:11:53,232 * https://www.piwheels.org/simple/torchref/
2026-05-22T09:11:53,233 Fetching project page and analyzing links: https://pypi.org/simple/torchref/
2026-05-22T09:11:53,233 Getting page https://pypi.org/simple/torchref/
2026-05-22T09:11:53,235 Found index url https://pypi.org/simple
2026-05-22T09:11:53,462 Fetched page https://pypi.org/simple/torchref/ as application/vnd.pypi.simple.v1+json
2026-05-22T09:11:53,467   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/64/ac/2604e364cc5df69ccdc7f3c9f0cdccaf9c51e96c4d622e64b508ed42d102/torchref-0.3.0-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.9)
2026-05-22T09:11:53,468   Found link https://files.pythonhosted.org/packages/73/7f/9c1e4112b5dd16c6712d7a8542a20f84bfd290f42c79dbcc4124a4df4ec9/torchref-0.3.0.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.9), version: 0.3.0
2026-05-22T09:11:53,468   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/2c/60/fa60e785ed08bc2e5a786869b7143e31881874cf9e87a83b7602322bb6e5/torchref-0.3.1-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.9)
2026-05-22T09:11:53,469   Found link https://files.pythonhosted.org/packages/70/0e/584b23bda864347754d7b0c9fcced9ee05dc5f7d3424d8cfd74717b6bb2f/torchref-0.3.1.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.9), version: 0.3.1
2026-05-22T09:11:53,470   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/e8/b3/f063b38c335c7b0c625fd7306e6b594e5ff453ab41b33317decaa6feadc3/torchref-0.3.2-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.9)
2026-05-22T09:11:53,471   Found link https://files.pythonhosted.org/packages/da/78/277f71170bd394e88380562379e2fe3b292acd3eb6d95ce110671da4ef59/torchref-0.3.2.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.9), version: 0.3.2
2026-05-22T09:11:53,472   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/fb/01/2471acb3667c71a9a0d2a93bdfdb998c35e85eea6487641b27ab99b7d0f0/torchref-0.4.1-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,473   Found link https://files.pythonhosted.org/packages/16/bd/cfbdc266a4fe7c8868b100eda000f82419609e89158bda8524efa51748be/torchref-0.4.1.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.4.1
2026-05-22T09:11:53,474   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/15/37/ed32c8184a2173783ba9429a9a0b2932172539ba3cb7b23f3ca26dfba1fd/torchref-0.4.2-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,475   Found link https://files.pythonhosted.org/packages/ae/0d/52864d8146269e718c1cb7b47a20f899e4035f19e0ccb7e5d59315f65bb4/torchref-0.4.2.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.4.2
2026-05-22T09:11:53,475   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/a7/3a/847415e01c63f1d7d71316d541be7464628096ed37f5fc9020d147463263/torchref-0.4.3-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,477   Found link https://files.pythonhosted.org/packages/cc/11/709f9abb6ad3da0752480f1a77de7d3c311393d6193f89d6ce18cc7d5099/torchref-0.4.3.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.4.3
2026-05-22T09:11:53,477   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/1b/b8/36df377748164e20a46356722963af74331445792bdbf08a0cdf1dbdbbdd/torchref-0.5.0-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,478   Found link https://files.pythonhosted.org/packages/25/f4/c18b875b712da914d708badea4ed1c2312935dc84d561b799c337185cf6e/torchref-0.5.0.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.5.0
2026-05-22T09:11:53,479   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/26/a0/7aceb00564e0dabc8d2cf6412cf7dba08013709a3ec915d33e40eabf72e0/torchref-0.5.1-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,479   Found link https://files.pythonhosted.org/packages/c8/0e/388f73407fc7bfe62c48f8e6983fd0b167b0739c260c2e08953ecaaac1bb/torchref-0.5.1.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.5.1
2026-05-22T09:11:53,480   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/3b/ad/f555bfcd4d9fdf1e3d542b593b2bebadf467e161cf643ff0c263db2cfcc3/torchref-0.5.2-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,481   Found link https://files.pythonhosted.org/packages/4d/d1/961979d80eaa39ceac37b9b8b641c3e2b4076705b775b3bcdcb1054f3642/torchref-0.5.2.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.5.2
2026-05-22T09:11:53,482   Skipping link: No binaries permitted for torchref: https://files.pythonhosted.org/packages/89/f8/40a59b5f087446e5b723954f28d67000cacc83cee4d0c6f22923641ffbbc/torchref-0.5.3-py3-none-any.whl (from https://pypi.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,483   Found link https://files.pythonhosted.org/packages/b2/d6/db2c7811699816ae29d052b1a38f04ac57bb15b612ee962cfa4563e372cb/torchref-0.5.3.tar.gz (from https://pypi.org/simple/torchref/) (requires-python:>=3.10), version: 0.5.3
2026-05-22T09:11:53,484 Fetching project page and analyzing links: https://www.piwheels.org/simple/torchref/
2026-05-22T09:11:53,484 Getting page https://www.piwheels.org/simple/torchref/
2026-05-22T09:11:53,486 Found index url https://www.piwheels.org/simple
2026-05-22T09:11:53,663 Fetched page https://www.piwheels.org/simple/torchref/ as text/html
2026-05-22T09:11:53,667   Skipping link: No binaries permitted for torchref: https://www.piwheels.org/simple/torchref/torchref-0.5.2-py3-none-any.whl#sha256=243d4c01af453def03a1e0667e20d3a8dc738f6af546aa60605b8a99369e41e3 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,668   Skipping link: No binaries permitted for torchref: https://www.piwheels.org/simple/torchref/torchref-0.5.1-py3-none-any.whl#sha256=c9b0bd6e0eba9eb14b81da89125965a0bb458251fd153ba4216811b24c993227 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,668   Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.5.0-py3-none-any.whl#sha256=81412a83cb1884393fe067281c4c70763169b28f13a642e80110fdc7eb65b9d2 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,669   Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.4.3-py3-none-any.whl#sha256=3224a4185d64c6f2b269ee377bc5c0f6dacf3a13898fd11e73a727a462a2d878 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,670   Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.4.2-py3-none-any.whl#sha256=c4c77a7e34aad8245da2d04a76477bdf30f94ca67cd531f721e4bf47ee67114a (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,670   Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.4.1-py3-none-any.whl#sha256=51e933f2f0edf7f44aa74d08f32f7530006300c4b6def2437f9257d02b3e175e (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.10)
2026-05-22T09:11:53,671   Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.3.2-py3-none-any.whl#sha256=30e0c5727c1872459a9dcff4416e224ff7486dea2f43a6c20dab66a307492093 (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.9)
2026-05-22T09:11:53,671   Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.3.1-py3-none-any.whl#sha256=25deb48a634dda8c799c2d7c32d9749bf327e976900dbd2a5fedf435ee5e921f (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.9)
2026-05-22T09:11:53,672   Skipping link: No binaries permitted for torchref: https://archive1.piwheels.org/simple/torchref/torchref-0.3.0-py3-none-any.whl#sha256=3032f506e2c816e7e7638e151ed6e70bf0f6b0213e92f8f790dce96c53c0d65f (from https://www.piwheels.org/simple/torchref/) (requires-python:>=3.9)
2026-05-22T09:11:53,672 Skipping link: not a file: https://www.piwheels.org/simple/torchref/
2026-05-22T09:11:53,673 Skipping link: not a file: https://pypi.org/simple/torchref/
2026-05-22T09:11:53,692 Given no hashes to check 1 links for project 'torchref': discarding no candidates
2026-05-22T09:11:53,710 Collecting torchref==0.5.3
2026-05-22T09:11:53,712   Created temporary directory: /tmp/pip-unpack-rqgupoxo
2026-05-22T09:11:53,861   Downloading torchref-0.5.3.tar.gz (3.0 MB)
2026-05-22T09:11:55,041   Added torchref==0.5.3 from https://files.pythonhosted.org/packages/b2/d6/db2c7811699816ae29d052b1a38f04ac57bb15b612ee962cfa4563e372cb/torchref-0.5.3.tar.gz to build tracker '/tmp/pip-build-tracker-58v6xr8h'
2026-05-22T09:11:55,047   Created temporary directory: /tmp/pip-build-env-3h_cdhiz
2026-05-22T09:11:55,052   Installing build dependencies: started
2026-05-22T09:11:55,053   Running command pip subprocess to install build dependencies
2026-05-22T09:11:56,214   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-05-22T09:11:56,619   DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-05-22T09:11:56,642   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-05-22T09:11:58,484   Collecting setuptools>=42
2026-05-22T09:11:58,485     Obtaining dependency information for setuptools>=42 from https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata
2026-05-22T09:11:58,505     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
2026-05-22T09:11:58,737   Collecting wheel
2026-05-22T09:11:58,738     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-05-22T09:11:58,754     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-05-22T09:11:58,945   Collecting packaging>=24.0
2026-05-22T09:11:58,946     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-05-22T09:11:58,959     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-05-22T09:11:59,154   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-05-22T09:11:59,173   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-05-22T09:11:59,257   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-05-22T09:11:59,297   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-05-22T09:11:59,331   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-05-22T09:11:59,425   Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-05-22T09:12:02,136   Installing collected packages: setuptools, packaging, wheel
2026-05-22T09:12:05,514     Creating /tmp/pip-build-env-3h_cdhiz/overlay/local/bin
2026-05-22T09:12:05,516     changing mode of /tmp/pip-build-env-3h_cdhiz/overlay/local/bin/wheel to 755
2026-05-22T09:12:05,537   Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0
2026-05-22T09:12:05,821   Installing build dependencies: finished with status 'done'
2026-05-22T09:12:05,828   Getting requirements to build wheel: started
2026-05-22T09:12:05,829   Running command Getting requirements to build wheel
2026-05-22T09:12:06,545   running egg_info
2026-05-22T09:12:06,551   writing torchref.egg-info/PKG-INFO
2026-05-22T09:12:06,558   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-05-22T09:12:06,561   writing entry points to torchref.egg-info/entry_points.txt
2026-05-22T09:12:06,565   writing requirements to torchref.egg-info/requires.txt
2026-05-22T09:12:06,566   writing top-level names to torchref.egg-info/top_level.txt
2026-05-22T09:12:06,652   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-22T09:12:06,667   adding license file 'LICENSE'
2026-05-22T09:12:06,681   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-22T09:12:06,779   Getting requirements to build wheel: finished with status 'done'
2026-05-22T09:12:06,782   Created temporary directory: /tmp/pip-modern-metadata-l44fz8c2
2026-05-22T09:12:06,785   Preparing metadata (pyproject.toml): started
2026-05-22T09:12:06,786   Running command Preparing metadata (pyproject.toml)
2026-05-22T09:12:07,445   running dist_info
2026-05-22T09:12:07,456   creating /tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info
2026-05-22T09:12:07,457   writing /tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/PKG-INFO
2026-05-22T09:12:07,465   writing dependency_links to /tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/dependency_links.txt
2026-05-22T09:12:07,467   writing entry points to /tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/entry_points.txt
2026-05-22T09:12:07,471   writing requirements to /tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/requires.txt
2026-05-22T09:12:07,472   writing top-level names to /tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/top_level.txt
2026-05-22T09:12:07,474   writing manifest file '/tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/SOURCES.txt'
2026-05-22T09:12:07,552   reading manifest file '/tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/SOURCES.txt'
2026-05-22T09:12:07,554   adding license file 'LICENSE'
2026-05-22T09:12:07,564   writing manifest file '/tmp/pip-modern-metadata-l44fz8c2/torchref.egg-info/SOURCES.txt'
2026-05-22T09:12:07,565   creating '/tmp/pip-modern-metadata-l44fz8c2/torchref-0.5.3.dist-info'
2026-05-22T09:12:07,691   Preparing metadata (pyproject.toml): finished with status 'done'
2026-05-22T09:12:07,696   Source in /tmp/pip-wheel-tke5h2ls/torchref_c3b7e7b0f3aa4588bd0b8a587e78a543 has version 0.5.3, which satisfies requirement torchref==0.5.3 from https://files.pythonhosted.org/packages/b2/d6/db2c7811699816ae29d052b1a38f04ac57bb15b612ee962cfa4563e372cb/torchref-0.5.3.tar.gz
2026-05-22T09:12:07,697   Removed torchref==0.5.3 from https://files.pythonhosted.org/packages/b2/d6/db2c7811699816ae29d052b1a38f04ac57bb15b612ee962cfa4563e372cb/torchref-0.5.3.tar.gz from build tracker '/tmp/pip-build-tracker-58v6xr8h'
2026-05-22T09:12:07,704 Created temporary directory: /tmp/pip-unpack-s99xql2_
2026-05-22T09:12:07,704 Building wheels for collected packages: torchref
2026-05-22T09:12:07,709   Created temporary directory: /tmp/pip-wheel-kgh7dmmp
2026-05-22T09:12:07,709   Destination directory: /tmp/pip-wheel-kgh7dmmp
2026-05-22T09:12:07,711   Building wheel for torchref (pyproject.toml): started
2026-05-22T09:12:07,712   Running command Building wheel for torchref (pyproject.toml)
2026-05-22T09:12:08,349   running bdist_wheel
2026-05-22T09:12:08,367   running build
2026-05-22T09:12:08,367   running build_py
2026-05-22T09:12:08,373   creating build/lib/torchref
2026-05-22T09:12:08,375   copying torchref/config.py -> build/lib/torchref
2026-05-22T09:12:08,378   copying torchref/__init__.py -> build/lib/torchref
2026-05-22T09:12:08,380   copying torchref/_bootstrap.py -> build/lib/torchref
2026-05-22T09:12:08,382   creating build/lib/torchref/utils
2026-05-22T09:12:08,383   copying torchref/utils/gradnorm.py -> build/lib/torchref/utils
2026-05-22T09:12:08,385   copying torchref/utils/serialization.py -> build/lib/torchref/utils
2026-05-22T09:12:08,387   copying torchref/utils/loss_validation.py -> build/lib/torchref/utils
2026-05-22T09:12:08,390   copying torchref/utils/device_resolution.py -> build/lib/torchref/utils
2026-05-22T09:12:08,391   copying torchref/utils/device_mixin.py -> build/lib/torchref/utils
2026-05-22T09:12:08,394   copying torchref/utils/debug_utils.py -> build/lib/torchref/utils
2026-05-22T09:12:08,397   copying torchref/utils/autograd_introspection.py -> build/lib/torchref/utils
2026-05-22T09:12:08,399   copying torchref/utils/autograd_ops.py -> build/lib/torchref/utils
2026-05-22T09:12:08,400   copying torchref/utils/utils.py -> build/lib/torchref/utils
2026-05-22T09:12:08,403   copying torchref/utils/timing.py -> build/lib/torchref/utils
2026-05-22T09:12:08,405   copying torchref/utils/caching.py -> build/lib/torchref/utils
2026-05-22T09:12:08,407   copying torchref/utils/stats.py -> build/lib/torchref/utils
2026-05-22T09:12:08,410   copying torchref/utils/pse.py -> build/lib/torchref/utils
2026-05-22T09:12:08,412   copying torchref/utils/__init__.py -> build/lib/torchref/utils
2026-05-22T09:12:08,414   copying torchref/utils/hyperparameters.py -> build/lib/torchref/utils
2026-05-22T09:12:08,417   creating build/lib/torchref/cli
2026-05-22T09:12:08,418   copying torchref/cli/_common.py -> build/lib/torchref/cli
2026-05-22T09:12:08,421   copying torchref/cli/add_metadata.py -> build/lib/torchref/cli
2026-05-22T09:12:08,424   copying torchref/cli/phased_difference_map.py -> build/lib/torchref/cli
2026-05-22T09:12:08,426   copying torchref/cli/refine.py -> build/lib/torchref/cli
2026-05-22T09:12:08,428   copying torchref/cli/strip_altlocs.py -> build/lib/torchref/cli
2026-05-22T09:12:08,430   copying torchref/cli/mtz2map.py -> build/lib/torchref/cli
2026-05-22T09:12:08,433   copying torchref/cli/__init__.py -> build/lib/torchref/cli
2026-05-22T09:12:08,434   copying torchref/cli/collection_difference_refine.py -> build/lib/torchref/cli
2026-05-22T09:12:08,438   copying torchref/cli/validate_ded.py -> build/lib/torchref/cli
2026-05-22T09:12:08,441   creating build/lib/torchref/base
2026-05-22T09:12:08,442   copying torchref/base/get_scattering_factor_torch.py -> build/lib/torchref/base
2026-05-22T09:12:08,445   copying torchref/base/math_torch.py -> build/lib/torchref/base
2026-05-22T09:12:08,447   copying torchref/base/math_numpy.py -> build/lib/torchref/base
2026-05-22T09:12:08,450   copying torchref/base/CCTBX_related.py -> build/lib/torchref/base
2026-05-22T09:12:08,452   copying torchref/base/french_wilson.py -> build/lib/torchref/base
2026-05-22T09:12:08,454   copying torchref/base/__init__.py -> build/lib/torchref/base
2026-05-22T09:12:08,457   creating build/lib/torchref/symmetry
2026-05-22T09:12:08,458   copying torchref/symmetry/symmetry.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,460   copying torchref/symmetry/map_symmetry_interpolation.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,462   copying torchref/symmetry/grid_utils.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,465   copying torchref/symmetry/reciprocal_symmetry.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,467   copying torchref/symmetry/cell.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,470   copying torchref/symmetry/spacegroup.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,473   copying torchref/symmetry/map_symmetry.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,475   copying torchref/symmetry/__init__.py -> build/lib/torchref/symmetry
2026-05-22T09:12:08,478   creating build/lib/torchref/alignment
2026-05-22T09:12:08,478   copying torchref/alignment/sampling.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,481   copying torchref/alignment/translation.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,483   copying torchref/alignment/rigid_body.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,486   copying torchref/alignment/ball_transform.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,489   copying torchref/alignment/clashscore.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,491   copying torchref/alignment/distributions.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,494   copying torchref/alignment/jax_subpixel_peaks.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,496   copying torchref/alignment/pipeline.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,498   copying torchref/alignment/transform.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,501   copying torchref/alignment/__init__.py -> build/lib/torchref/alignment
2026-05-22T09:12:08,504   creating build/lib/torchref/scaling
2026-05-22T09:12:08,505   copying torchref/scaling/scaler_base.py -> build/lib/torchref/scaling
2026-05-22T09:12:08,508   copying torchref/scaling/solvent.py -> build/lib/torchref/scaling
2026-05-22T09:12:08,511   copying torchref/scaling/scaler.py -> build/lib/torchref/scaling
2026-05-22T09:12:08,514   copying torchref/scaling/__init__.py -> build/lib/torchref/scaling
2026-05-22T09:12:08,516   copying torchref/scaling/collection_scaler.py -> build/lib/torchref/scaling
2026-05-22T09:12:08,519   creating build/lib/torchref/scripts
2026-05-22T09:12:08,520   copying torchref/scripts/generate_scattering_table.py -> build/lib/torchref/scripts
2026-05-22T09:12:08,522   copying torchref/scripts/__init__.py -> build/lib/torchref/scripts
2026-05-22T09:12:08,525   creating build/lib/torchref/maps
2026-05-22T09:12:08,526   copying torchref/maps/difference_map.py -> build/lib/torchref/maps
2026-05-22T09:12:08,528   copying torchref/maps/map.py -> build/lib/torchref/maps
2026-05-22T09:12:08,530   copying torchref/maps/__init__.py -> build/lib/torchref/maps
2026-05-22T09:12:08,533   creating build/lib/torchref/restraints
2026-05-22T09:12:08,534   copying torchref/restraints/hydrogen_topology.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,537   copying torchref/restraints/builders_fast.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,541   copying torchref/restraints/ramachandran.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,543   copying torchref/restraints/neighbor_search.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,546   copying torchref/restraints/restraints_helper.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,549   copying torchref/restraints/builders.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,553   copying torchref/restraints/builders_numba.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,555   copying torchref/restraints/restraints.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,560   copying torchref/restraints/__init__.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,562   copying torchref/restraints/library.py -> build/lib/torchref/restraints
2026-05-22T09:12:08,565   creating build/lib/torchref/model
2026-05-22T09:12:08,566   copying torchref/model/mixed_model.py -> build/lib/torchref/model
2026-05-22T09:12:08,568   copying torchref/model/internal_coordinates.py -> build/lib/torchref/model
2026-05-22T09:12:08,572   copying torchref/model/model_collection.py -> build/lib/torchref/model
2026-05-22T09:12:08,574   copying torchref/model/model.py -> build/lib/torchref/model
2026-05-22T09:12:08,580   copying torchref/model/segmented_internal_coordinates.py -> build/lib/torchref/model
2026-05-22T09:12:08,584   copying torchref/model/parameter_wrappers.py -> build/lib/torchref/model
2026-05-22T09:12:08,587   copying torchref/model/model_ft.py -> build/lib/torchref/model
2026-05-22T09:12:08,590   copying torchref/model/closed_segmented_internal_coordinates.py -> build/lib/torchref/model
2026-05-22T09:12:08,594   copying torchref/model/sf_fft.py -> build/lib/torchref/model
2026-05-22T09:12:08,597   copying torchref/model/__init__.py -> build/lib/torchref/model
2026-05-22T09:12:08,599   copying torchref/model/sf_ds.py -> build/lib/torchref/model
2026-05-22T09:12:08,602   creating build/lib/torchref/kinetic
2026-05-22T09:12:08,604   copying torchref/kinetic/occupancies.py -> build/lib/torchref/kinetic
2026-05-22T09:12:08,607   copying torchref/kinetic/refinement.py -> build/lib/torchref/kinetic
2026-05-22T09:12:08,610   copying torchref/kinetic/targets.py -> build/lib/torchref/kinetic
2026-05-22T09:12:08,612   copying torchref/kinetic/kinetics.py -> build/lib/torchref/kinetic
2026-05-22T09:12:08,616   copying torchref/kinetic/__init__.py -> build/lib/torchref/kinetic
2026-05-22T09:12:08,618   creating build/lib/torchref/io
2026-05-22T09:12:08,620   copying torchref/io/ihm_mapping.py -> build/lib/torchref/io
2026-05-22T09:12:08,623   copying torchref/io/data_router.py -> build/lib/torchref/io
2026-05-22T09:12:08,625   copying torchref/io/cif_readers.py -> build/lib/torchref/io
2026-05-22T09:12:08,630   copying torchref/io/metadata.py -> build/lib/torchref/io
2026-05-22T09:12:08,632   copying torchref/io/cif.py -> build/lib/torchref/io
2026-05-22T09:12:08,635   copying torchref/io/pdb.py -> build/lib/torchref/io
2026-05-22T09:12:08,638   copying torchref/io/mtz.py -> build/lib/torchref/io
2026-05-22T09:12:08,641   copying torchref/io/__init__.py -> build/lib/torchref/io
2026-05-22T09:12:08,643   copying torchref/io/ihm.py -> build/lib/torchref/io
2026-05-22T09:12:08,647   creating build/lib/torchref/refinement
2026-05-22T09:12:08,648   copying torchref/refinement/lbfgs_refinement.py -> build/lib/torchref/refinement
2026-05-22T09:12:08,651   copying torchref/refinement/loss_state.py -> build/lib/torchref/refinement
2026-05-22T09:12:08,655   copying torchref/refinement/base_refinement.py -> build/lib/torchref/refinement
2026-05-22T09:12:08,658   copying torchref/refinement/__init__.py -> build/lib/torchref/refinement
2026-05-22T09:12:08,660   copying torchref/refinement/logger.py -> build/lib/torchref/refinement
2026-05-22T09:12:08,663   creating build/lib/torchref/base/metrics
2026-05-22T09:12:08,665   copying torchref/base/metrics/__init__.py -> build/lib/torchref/base/metrics
2026-05-22T09:12:08,667   copying torchref/base/metrics/rfactor.py -> build/lib/torchref/base/metrics
2026-05-22T09:12:08,670   copying torchref/base/metrics/loss.py -> build/lib/torchref/base/metrics
2026-05-22T09:12:08,673   creating build/lib/torchref/base/fourier
2026-05-22T09:12:08,674   copying torchref/base/fourier/fft.py -> build/lib/torchref/base/fourier
2026-05-22T09:12:08,677   copying torchref/base/fourier/grid.py -> build/lib/torchref/base/fourier
2026-05-22T09:12:08,679   copying torchref/base/fourier/__init__.py -> build/lib/torchref/base/fourier
2026-05-22T09:12:08,682   creating build/lib/torchref/base/electron_density
2026-05-22T09:12:08,683   copying torchref/base/electron_density/solvent_mask.py -> build/lib/torchref/base/electron_density
2026-05-22T09:12:08,686   copying torchref/base/electron_density/main.py -> build/lib/torchref/base/electron_density
2026-05-22T09:12:08,689   copying torchref/base/electron_density/voxel_utils.py -> build/lib/torchref/base/electron_density
2026-05-22T09:12:08,692   copying torchref/base/electron_density/map_building.py -> build/lib/torchref/base/electron_density
2026-05-22T09:12:08,694   copying torchref/base/electron_density/__init__.py -> build/lib/torchref/base/electron_density
2026-05-22T09:12:08,697   creating build/lib/torchref/base/scattering
2026-05-22T09:12:08,698   copying torchref/base/scattering/itc92.py -> build/lib/torchref/base/scattering
2026-05-22T09:12:08,701   copying torchref/base/scattering/scattering_table.py -> build/lib/torchref/base/scattering
2026-05-22T09:12:08,704   copying torchref/base/scattering/anomalous_table.py -> build/lib/torchref/base/scattering
2026-05-22T09:12:08,706   copying torchref/base/scattering/__init__.py -> build/lib/torchref/base/scattering
2026-05-22T09:12:08,709   creating build/lib/torchref/base/reciprocal
2026-05-22T09:12:08,710   copying torchref/base/reciprocal/symmetry.py -> build/lib/torchref/base/reciprocal
2026-05-22T09:12:08,713   copying torchref/base/reciprocal/hkl.py -> build/lib/torchref/base/reciprocal
2026-05-22T09:12:08,715   copying torchref/base/reciprocal/interpolation.py -> build/lib/torchref/base/reciprocal
2026-05-22T09:12:08,718   copying torchref/base/reciprocal/basis.py -> build/lib/torchref/base/reciprocal
2026-05-22T09:12:08,720   copying torchref/base/reciprocal/grid_operations.py -> build/lib/torchref/base/reciprocal
2026-05-22T09:12:08,723   copying torchref/base/reciprocal/__init__.py -> build/lib/torchref/base/reciprocal
2026-05-22T09:12:08,725   creating build/lib/torchref/base/coordinates
2026-05-22T09:12:08,727   copying torchref/base/coordinates/periodic_boundary.py -> build/lib/torchref/base/coordinates
2026-05-22T09:12:08,729   copying torchref/base/coordinates/transforms_numpy.py -> build/lib/torchref/base/coordinates
2026-05-22T09:12:08,731   copying torchref/base/coordinates/transforms_torch.py -> build/lib/torchref/base/coordinates
2026-05-22T09:12:08,734   copying torchref/base/coordinates/__init__.py -> build/lib/torchref/base/coordinates
2026-05-22T09:12:08,736   creating build/lib/torchref/base/alignment
2026-05-22T09:12:08,738   copying torchref/base/alignment/normalization.py -> build/lib/torchref/base/alignment
2026-05-22T09:12:08,740   copying torchref/base/alignment/scoring.py -> build/lib/torchref/base/alignment
2026-05-22T09:12:08,743   copying torchref/base/alignment/superposition.py -> build/lib/torchref/base/alignment
2026-05-22T09:12:08,746   copying torchref/base/alignment/__init__.py -> build/lib/torchref/base/alignment
2026-05-22T09:12:08,748   copying torchref/base/alignment/rotation.py -> build/lib/torchref/base/alignment
2026-05-22T09:12:08,751   creating build/lib/torchref/base/targets
2026-05-22T09:12:08,752   copying torchref/base/targets/angle.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,754   copying torchref/base/targets/_common.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,756   copying torchref/base/targets/xray_ml.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,758   copying torchref/base/targets/bond.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,760   copying torchref/base/targets/ramachandran.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,761   copying torchref/base/targets/torsion.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,763   copying torchref/base/targets/_dispatch.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,765   copying torchref/base/targets/adp.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,767   copying torchref/base/targets/xray_bhattacharyya.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,769   copying torchref/base/targets/xray_ls.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,771   copying torchref/base/targets/nonbonded.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,773   copying torchref/base/targets/planarity.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,775   copying torchref/base/targets/xray_gaussian.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,777   copying torchref/base/targets/__init__.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,779   copying torchref/base/targets/chiral.py -> build/lib/torchref/base/targets
2026-05-22T09:12:08,781   creating build/lib/torchref/base/chain_closure
2026-05-22T09:12:08,782   copying torchref/base/chain_closure/closure.py -> build/lib/torchref/base/chain_closure
2026-05-22T09:12:08,784   copying torchref/base/chain_closure/backbone_utils.py -> build/lib/torchref/base/chain_closure
2026-05-22T09:12:08,787   copying torchref/base/chain_closure/__init__.py -> build/lib/torchref/base/chain_closure
2026-05-22T09:12:08,789   creating build/lib/torchref/base/direct_summation
2026-05-22T09:12:08,790   copying torchref/base/direct_summation/anisotropic.py -> build/lib/torchref/base/direct_summation
2026-05-22T09:12:08,792   copying torchref/base/direct_summation/isotropic.py -> build/lib/torchref/base/direct_summation
2026-05-22T09:12:08,794   copying torchref/base/direct_summation/__init__.py -> build/lib/torchref/base/direct_summation
2026-05-22T09:12:08,796   copying torchref/base/direct_summation/corrections.py -> build/lib/torchref/base/direct_summation
2026-05-22T09:12:08,798   creating build/lib/torchref/base/kernels
2026-05-22T09:12:08,799   copying torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/lib/torchref/base/kernels
2026-05-22T09:12:08,802   copying torchref/base/kernels/triton_kernel.py -> build/lib/torchref/base/kernels
2026-05-22T09:12:08,805   copying torchref/base/kernels/cpu_scatter.py -> build/lib/torchref/base/kernels
2026-05-22T09:12:08,807   copying torchref/base/kernels/separable_triton_kernel.py -> build/lib/torchref/base/kernels
2026-05-22T09:12:08,810   copying torchref/base/kernels/optimized_ops.py -> build/lib/torchref/base/kernels
2026-05-22T09:12:08,813   copying torchref/base/kernels/__init__.py -> build/lib/torchref/base/kernels
2026-05-22T09:12:08,815   creating build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,816   copying torchref/base/targets/triton/angle.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,819   copying torchref/base/targets/triton/adp_simu.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,821   copying torchref/base/targets/triton/xray_ml.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,823   copying torchref/base/targets/triton/bond.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,825   copying torchref/base/targets/triton/ramachandran.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,828   copying torchref/base/targets/triton/torsion.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,830   copying torchref/base/targets/triton/_dihedral.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,832   copying torchref/base/targets/triton/xray_bhattacharyya.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,835   copying torchref/base/targets/triton/xray_ls.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,837   copying torchref/base/targets/triton/nonbonded.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,840   copying torchref/base/targets/triton/planarity.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,843   copying torchref/base/targets/triton/xray_gaussian.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,844   copying torchref/base/targets/triton/__init__.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,846   copying torchref/base/targets/triton/place_hydrogens.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,849   copying torchref/base/targets/triton/chiral.py -> build/lib/torchref/base/targets/triton
2026-05-22T09:12:08,852   creating build/lib/torchref/io/datasets
2026-05-22T09:12:08,853   copying torchref/io/datasets/base.py -> build/lib/torchref/io/datasets
2026-05-22T09:12:08,855   copying torchref/io/datasets/reflection_data.py -> build/lib/torchref/io/datasets
2026-05-22T09:12:08,860   copying torchref/io/datasets/fcalc_data.py -> build/lib/torchref/io/datasets
2026-05-22T09:12:08,862   copying torchref/io/datasets/collection.py -> build/lib/torchref/io/datasets
2026-05-22T09:12:08,864   copying torchref/io/datasets/__init__.py -> build/lib/torchref/io/datasets
2026-05-22T09:12:08,867   creating build/lib/torchref/refinement/weighting
2026-05-22T09:12:08,868   copying torchref/refinement/weighting/random_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-22T09:12:08,871   copying torchref/refinement/weighting/policy_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-22T09:12:08,873   copying torchref/refinement/weighting/component_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-22T09:12:08,875   copying torchref/refinement/weighting/__init__.py -> build/lib/torchref/refinement/weighting
2026-05-22T09:12:08,877   copying torchref/refinement/weighting/es_policy_training.py -> build/lib/torchref/refinement/weighting
2026-05-22T09:12:08,879   copying torchref/refinement/weighting/base_weighting.py -> build/lib/torchref/refinement/weighting
2026-05-22T09:12:08,882   creating build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,883   copying torchref/refinement/optimizers/simulated_annealing.py -> build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,885   copying torchref/refinement/optimizers/momentum_sa.py -> build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,887   copying torchref/refinement/optimizers/internal_coord_sa.py -> build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,889   copying torchref/refinement/optimizers/exploratory_lbfgs.py -> build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,892   copying torchref/refinement/optimizers/langevin_sa.py -> build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,895   copying torchref/refinement/optimizers/adam_noise.py -> build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,897   copying torchref/refinement/optimizers/__init__.py -> build/lib/torchref/refinement/optimizers
2026-05-22T09:12:08,900   creating build/lib/torchref/refinement/targets
2026-05-22T09:12:08,901   copying torchref/refinement/targets/difference.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,906   copying torchref/refinement/targets/forcefield_target.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,909   copying torchref/refinement/targets/similarity.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,911   copying torchref/refinement/targets/combined.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,914   copying torchref/refinement/targets/base.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,917   copying torchref/refinement/targets/amber_target.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,921   copying torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,923   copying torchref/refinement/targets/realspace.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,926   copying torchref/refinement/targets/sampled_ml_phase_target.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,930   copying torchref/refinement/targets/__init__.py -> build/lib/torchref/refinement/targets
2026-05-22T09:12:08,932   creating build/lib/torchref/refinement/targets/xray
2026-05-22T09:12:08,933   copying torchref/refinement/targets/xray/maximum_likelihood.py -> build/lib/torchref/refinement/targets/xray
2026-05-22T09:12:08,935   copying torchref/refinement/targets/xray/bhattacharyya.py -> build/lib/torchref/refinement/targets/xray
2026-05-22T09:12:08,938   copying torchref/refinement/targets/xray/base.py -> build/lib/torchref/refinement/targets/xray
2026-05-22T09:12:08,941   copying torchref/refinement/targets/xray/gaussian.py -> build/lib/torchref/refinement/targets/xray
2026-05-22T09:12:08,943   copying torchref/refinement/targets/xray/least_squares.py -> build/lib/torchref/refinement/targets/xray
2026-05-22T09:12:08,945   copying torchref/refinement/targets/xray/__init__.py -> build/lib/torchref/refinement/targets/xray
2026-05-22T09:12:08,947   creating build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,948   copying torchref/refinement/targets/geometry/bonds.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,950   copying torchref/refinement/targets/geometry/angles.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,952   copying torchref/refinement/targets/geometry/ramachandran.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,953   copying torchref/refinement/targets/geometry/base.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,955   copying torchref/refinement/targets/geometry/torsions.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,957   copying torchref/refinement/targets/geometry/non_bonded.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,960   copying torchref/refinement/targets/geometry/planarity.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,962   copying torchref/refinement/targets/geometry/__init__.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,964   copying torchref/refinement/targets/geometry/chiral.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,966   copying torchref/refinement/targets/geometry/non_bonded_h.py -> build/lib/torchref/refinement/targets/geometry
2026-05-22T09:12:08,968   creating build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,969   copying torchref/refinement/targets/adp/scaler_u.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,971   copying torchref/refinement/targets/adp/similarity.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,973   copying torchref/refinement/targets/adp/base.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,975   copying torchref/refinement/targets/adp/scaler_log_scale.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,977   copying torchref/refinement/targets/adp/__init__.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,979   copying torchref/refinement/targets/adp/locality.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,981   copying torchref/refinement/targets/adp/entropy.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,983   copying torchref/refinement/targets/adp/rigid_bond.py -> build/lib/torchref/refinement/targets/adp
2026-05-22T09:12:08,991   running egg_info
2026-05-22T09:12:09,000   writing torchref.egg-info/PKG-INFO
2026-05-22T09:12:09,007   writing dependency_links to torchref.egg-info/dependency_links.txt
2026-05-22T09:12:09,009   writing entry points to torchref.egg-info/entry_points.txt
2026-05-22T09:12:09,013   writing requirements to torchref.egg-info/requires.txt
2026-05-22T09:12:09,014   writing top-level names to torchref.egg-info/top_level.txt
2026-05-22T09:12:09,074   reading manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-22T09:12:09,089   adding license file 'LICENSE'
2026-05-22T09:12:09,102   writing manifest file 'torchref.egg-info/SOURCES.txt'
2026-05-22T09:12:09,137   creating build/lib/torchref/data
2026-05-22T09:12:09,138   copying torchref/data/atomic_vdw_radii.csv -> build/lib/torchref/data
2026-05-22T09:12:09,141   copying torchref/data/itc92_scattering_factors.pt -> build/lib/torchref/data
2026-05-22T09:12:09,143   copying torchref/data/rama_nll_surfaces.pt -> build/lib/torchref/data
2026-05-22T09:12:09,188   creating build/lib/torchref/data/monomer_library/g
2026-05-22T09:12:09,190   copying torchref/data/monomer_library/g/G.cif -> build/lib/torchref/data/monomer_library/g
2026-05-22T09:12:09,193   copying torchref/data/monomer_library/g/GLY.cif -> build/lib/torchref/data/monomer_library/g
2026-05-22T09:12:09,195   copying torchref/data/monomer_library/g/GLN.cif -> build/lib/torchref/data/monomer_library/g
2026-05-22T09:12:09,198   copying torchref/data/monomer_library/g/GLU.cif -> build/lib/torchref/data/monomer_library/g
2026-05-22T09:12:09,201   creating build/lib/torchref/data/monomer_library/m
2026-05-22T09:12:09,202   copying torchref/data/monomer_library/m/MET.cif -> build/lib/torchref/data/monomer_library/m
2026-05-22T09:12:09,204   copying torchref/data/monomer_library/m/MSE.cif -> build/lib/torchref/data/monomer_library/m
2026-05-22T09:12:09,206   creating build/lib/torchref/data/monomer_library/a
2026-05-22T09:12:09,207   copying torchref/data/monomer_library/a/ARG.cif -> build/lib/torchref/data/monomer_library/a
2026-05-22T09:12:09,210   copying torchref/data/monomer_library/a/A.cif -> build/lib/torchref/data/monomer_library/a
2026-05-22T09:12:09,213   copying torchref/data/monomer_library/a/ASP.cif -> build/lib/torchref/data/monomer_library/a
2026-05-22T09:12:09,215   copying torchref/data/monomer_library/a/ASN.cif -> build/lib/torchref/data/monomer_library/a
2026-05-22T09:12:09,218   copying torchref/data/monomer_library/a/ALA.cif -> build/lib/torchref/data/monomer_library/a
2026-05-22T09:12:09,221   creating build/lib/torchref/data/monomer_library/v
2026-05-22T09:12:09,222   copying torchref/data/monomer_library/v/VAL.cif -> build/lib/torchref/data/monomer_library/v
2026-05-22T09:12:09,224   creating build/lib/torchref/data/monomer_library/d
2026-05-22T09:12:09,225   copying torchref/data/monomer_library/d/DC.cif -> build/lib/torchref/data/monomer_library/d
2026-05-22T09:12:09,228   copying torchref/data/monomer_library/d/DT.cif -> build/lib/torchref/data/monomer_library/d
2026-05-22T09:12:09,231   copying torchref/data/monomer_library/d/DG.cif -> build/lib/torchref/data/monomer_library/d
2026-05-22T09:12:09,234   copying torchref/data/monomer_library/d/DA.cif -> build/lib/torchref/data/monomer_library/d
2026-05-22T09:12:09,236   creating build/lib/torchref/data/monomer_library/h
2026-05-22T09:12:09,237   copying torchref/data/monomer_library/h/HYP.cif -> build/lib/torchref/data/monomer_library/h
2026-05-22T09:12:09,240   copying torchref/data/monomer_library/h/HOH.cif -> build/lib/torchref/data/monomer_library/h
2026-05-22T09:12:09,242   copying torchref/data/monomer_library/h/HIS.cif -> build/lib/torchref/data/monomer_library/h
2026-05-22T09:12:09,245   creating build/lib/torchref/data/monomer_library/p
2026-05-22T09:12:09,246   copying torchref/data/monomer_library/p/PRO.cif -> build/lib/torchref/data/monomer_library/p
2026-05-22T09:12:09,248   copying torchref/data/monomer_library/p/PHE.cif -> build/lib/torchref/data/monomer_library/p
2026-05-22T09:12:09,251   copying torchref/data/monomer_library/p/PTR.cif -> build/lib/torchref/data/monomer_library/p
2026-05-22T09:12:09,253   creating build/lib/torchref/data/monomer_library/l
2026-05-22T09:12:09,255   copying torchref/data/monomer_library/l/LYS.cif -> build/lib/torchref/data/monomer_library/l
2026-05-22T09:12:09,257   copying torchref/data/monomer_library/l/LEU.cif -> build/lib/torchref/data/monomer_library/l
2026-05-22T09:12:09,260   creating build/lib/torchref/data/monomer_library/s
2026-05-22T09:12:09,261   copying torchref/data/monomer_library/s/SER.cif -> build/lib/torchref/data/monomer_library/s
2026-05-22T09:12:09,263   copying torchref/data/monomer_library/s/SEP.cif -> build/lib/torchref/data/monomer_library/s
2026-05-22T09:12:09,266   creating build/lib/torchref/data/monomer_library/list
2026-05-22T09:12:09,267   copying torchref/data/monomer_library/list/mon_lib_list.cif -> build/lib/torchref/data/monomer_library/list
2026-05-22T09:12:09,352   creating build/lib/torchref/data/monomer_library/u
2026-05-22T09:12:09,353   copying torchref/data/monomer_library/u/U.cif -> build/lib/torchref/data/monomer_library/u
2026-05-22T09:12:09,356   creating build/lib/torchref/data/monomer_library/i
2026-05-22T09:12:09,357   copying torchref/data/monomer_library/i/ILE.cif -> build/lib/torchref/data/monomer_library/i
2026-05-22T09:12:09,360   creating build/lib/torchref/data/monomer_library/t
2026-05-22T09:12:09,361   copying torchref/data/monomer_library/t/TYR.cif -> build/lib/torchref/data/monomer_library/t
2026-05-22T09:12:09,364   copying torchref/data/monomer_library/t/TRP.cif -> build/lib/torchref/data/monomer_library/t
2026-05-22T09:12:09,367   copying torchref/data/monomer_library/t/TPO.cif -> build/lib/torchref/data/monomer_library/t
2026-05-22T09:12:09,370   copying torchref/data/monomer_library/t/THR.cif -> build/lib/torchref/data/monomer_library/t
2026-05-22T09:12:09,372   creating build/lib/torchref/data/monomer_library/c
2026-05-22T09:12:09,373   copying torchref/data/monomer_library/c/C.cif -> build/lib/torchref/data/monomer_library/c
2026-05-22T09:12:09,376   copying torchref/data/monomer_library/c/CYS.cif -> build/lib/torchref/data/monomer_library/c
2026-05-22T09:12:09,423   installing to build/bdist.linux-armv7l/wheel
2026-05-22T09:12:09,423   running install
2026-05-22T09:12:09,446   running install_lib
2026-05-22T09:12:09,451   creating build/bdist.linux-armv7l/wheel
2026-05-22T09:12:09,454   creating build/bdist.linux-armv7l/wheel/torchref
2026-05-22T09:12:09,456   creating build/bdist.linux-armv7l/wheel/torchref/utils
2026-05-22T09:12:09,457   copying build/lib/torchref/utils/gradnorm.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,459   copying build/lib/torchref/utils/serialization.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,460   copying build/lib/torchref/utils/loss_validation.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,463   copying build/lib/torchref/utils/device_resolution.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,464   copying build/lib/torchref/utils/device_mixin.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,467   copying build/lib/torchref/utils/debug_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,469   copying build/lib/torchref/utils/autograd_introspection.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,471   copying build/lib/torchref/utils/autograd_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,473   copying build/lib/torchref/utils/utils.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,476   copying build/lib/torchref/utils/timing.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,478   copying build/lib/torchref/utils/caching.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,480   copying build/lib/torchref/utils/stats.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,482   copying build/lib/torchref/utils/pse.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,485   copying build/lib/torchref/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,486   copying build/lib/torchref/utils/hyperparameters.py -> build/bdist.linux-armv7l/wheel/./torchref/utils
2026-05-22T09:12:09,489   creating build/bdist.linux-armv7l/wheel/torchref/cli
2026-05-22T09:12:09,490   copying build/lib/torchref/cli/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,493   copying build/lib/torchref/cli/add_metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,495   copying build/lib/torchref/cli/phased_difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,498   copying build/lib/torchref/cli/refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,500   copying build/lib/torchref/cli/strip_altlocs.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,502   copying build/lib/torchref/cli/mtz2map.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,504   copying build/lib/torchref/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,506   copying build/lib/torchref/cli/collection_difference_refine.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,509   copying build/lib/torchref/cli/validate_ded.py -> build/bdist.linux-armv7l/wheel/./torchref/cli
2026-05-22T09:12:09,512   creating build/bdist.linux-armv7l/wheel/torchref/base
2026-05-22T09:12:09,514   creating build/bdist.linux-armv7l/wheel/torchref/base/metrics
2026-05-22T09:12:09,515   copying build/lib/torchref/base/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-05-22T09:12:09,517   copying build/lib/torchref/base/metrics/rfactor.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-05-22T09:12:09,519   copying build/lib/torchref/base/metrics/loss.py -> build/bdist.linux-armv7l/wheel/./torchref/base/metrics
2026-05-22T09:12:09,522   creating build/bdist.linux-armv7l/wheel/torchref/base/fourier
2026-05-22T09:12:09,523   copying build/lib/torchref/base/fourier/fft.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-05-22T09:12:09,525   copying build/lib/torchref/base/fourier/grid.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-05-22T09:12:09,527   copying build/lib/torchref/base/fourier/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/fourier
2026-05-22T09:12:09,529   copying build/lib/torchref/base/get_scattering_factor_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-22T09:12:09,531   copying build/lib/torchref/base/math_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-22T09:12:09,534   creating build/bdist.linux-armv7l/wheel/torchref/base/electron_density
2026-05-22T09:12:09,535   copying build/lib/torchref/base/electron_density/solvent_mask.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-22T09:12:09,537   copying build/lib/torchref/base/electron_density/main.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-22T09:12:09,540   copying build/lib/torchref/base/electron_density/voxel_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-22T09:12:09,542   copying build/lib/torchref/base/electron_density/map_building.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-22T09:12:09,545   copying build/lib/torchref/base/electron_density/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/electron_density
2026-05-22T09:12:09,547   creating build/bdist.linux-armv7l/wheel/torchref/base/scattering
2026-05-22T09:12:09,548   copying build/lib/torchref/base/scattering/itc92.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-22T09:12:09,551   copying build/lib/torchref/base/scattering/scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-22T09:12:09,553   copying build/lib/torchref/base/scattering/anomalous_table.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-22T09:12:09,555   copying build/lib/torchref/base/scattering/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/scattering
2026-05-22T09:12:09,557   creating build/bdist.linux-armv7l/wheel/torchref/base/reciprocal
2026-05-22T09:12:09,558   copying build/lib/torchref/base/reciprocal/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-22T09:12:09,561   copying build/lib/torchref/base/reciprocal/hkl.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-22T09:12:09,562   copying build/lib/torchref/base/reciprocal/interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-22T09:12:09,565   copying build/lib/torchref/base/reciprocal/basis.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-22T09:12:09,567   copying build/lib/torchref/base/reciprocal/grid_operations.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-22T09:12:09,569   copying build/lib/torchref/base/reciprocal/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/reciprocal
2026-05-22T09:12:09,572   creating build/bdist.linux-armv7l/wheel/torchref/base/coordinates
2026-05-22T09:12:09,573   copying build/lib/torchref/base/coordinates/periodic_boundary.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-22T09:12:09,575   copying build/lib/torchref/base/coordinates/transforms_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-22T09:12:09,577   copying build/lib/torchref/base/coordinates/transforms_torch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-22T09:12:09,579   copying build/lib/torchref/base/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/coordinates
2026-05-22T09:12:09,581   creating build/bdist.linux-armv7l/wheel/torchref/base/alignment
2026-05-22T09:12:09,582   copying build/lib/torchref/base/alignment/normalization.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-22T09:12:09,584   copying build/lib/torchref/base/alignment/scoring.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-22T09:12:09,586   copying build/lib/torchref/base/alignment/superposition.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-22T09:12:09,589   copying build/lib/torchref/base/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-22T09:12:09,591   copying build/lib/torchref/base/alignment/rotation.py -> build/bdist.linux-armv7l/wheel/./torchref/base/alignment
2026-05-22T09:12:09,593   copying build/lib/torchref/base/math_numpy.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-22T09:12:09,596   creating build/bdist.linux-armv7l/wheel/torchref/base/targets
2026-05-22T09:12:09,597   copying build/lib/torchref/base/targets/angle.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,599   copying build/lib/torchref/base/targets/_common.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,601   copying build/lib/torchref/base/targets/xray_ml.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,603   copying build/lib/torchref/base/targets/bond.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,604   copying build/lib/torchref/base/targets/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,606   copying build/lib/torchref/base/targets/torsion.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,608   copying build/lib/torchref/base/targets/_dispatch.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,610   copying build/lib/torchref/base/targets/adp.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,612   copying build/lib/torchref/base/targets/xray_bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,614   copying build/lib/torchref/base/targets/xray_ls.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,615   copying build/lib/torchref/base/targets/nonbonded.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,617   copying build/lib/torchref/base/targets/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,619   copying build/lib/torchref/base/targets/xray_gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,621   copying build/lib/torchref/base/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,624   creating build/bdist.linux-armv7l/wheel/torchref/base/targets/triton
2026-05-22T09:12:09,625   copying build/lib/torchref/base/targets/triton/angle.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,627   copying build/lib/torchref/base/targets/triton/adp_simu.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,629   copying build/lib/torchref/base/targets/triton/xray_ml.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,632   copying build/lib/torchref/base/targets/triton/bond.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,634   copying build/lib/torchref/base/targets/triton/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,637   copying build/lib/torchref/base/targets/triton/torsion.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,639   copying build/lib/torchref/base/targets/triton/_dihedral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,641   copying build/lib/torchref/base/targets/triton/xray_bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,643   copying build/lib/torchref/base/targets/triton/xray_ls.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,645   copying build/lib/torchref/base/targets/triton/nonbonded.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,647   copying build/lib/torchref/base/targets/triton/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,650   copying build/lib/torchref/base/targets/triton/xray_gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,652   copying build/lib/torchref/base/targets/triton/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,653   copying build/lib/torchref/base/targets/triton/place_hydrogens.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,656   copying build/lib/torchref/base/targets/triton/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets/triton
2026-05-22T09:12:09,658   copying build/lib/torchref/base/targets/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/base/targets
2026-05-22T09:12:09,660   creating build/bdist.linux-armv7l/wheel/torchref/base/chain_closure
2026-05-22T09:12:09,661   copying build/lib/torchref/base/chain_closure/closure.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-05-22T09:12:09,664   copying build/lib/torchref/base/chain_closure/backbone_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-05-22T09:12:09,667   copying build/lib/torchref/base/chain_closure/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/chain_closure
2026-05-22T09:12:09,669   creating build/bdist.linux-armv7l/wheel/torchref/base/direct_summation
2026-05-22T09:12:09,670   copying build/lib/torchref/base/direct_summation/anisotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-22T09:12:09,673   copying build/lib/torchref/base/direct_summation/isotropic.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-22T09:12:09,675   copying build/lib/torchref/base/direct_summation/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-22T09:12:09,677   copying build/lib/torchref/base/direct_summation/corrections.py -> build/bdist.linux-armv7l/wheel/./torchref/base/direct_summation
2026-05-22T09:12:09,679   creating build/bdist.linux-armv7l/wheel/torchref/base/kernels
2026-05-22T09:12:09,681   copying build/lib/torchref/base/kernels/jit_kernel_vectorized_add_to_map.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-22T09:12:09,683   copying build/lib/torchref/base/kernels/triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-22T09:12:09,687   copying build/lib/torchref/base/kernels/cpu_scatter.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-22T09:12:09,689   copying build/lib/torchref/base/kernels/separable_triton_kernel.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-22T09:12:09,693   copying build/lib/torchref/base/kernels/optimized_ops.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-22T09:12:09,695   copying build/lib/torchref/base/kernels/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base/kernels
2026-05-22T09:12:09,697   copying build/lib/torchref/base/CCTBX_related.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-22T09:12:09,699   copying build/lib/torchref/base/french_wilson.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-22T09:12:09,702   copying build/lib/torchref/base/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/base
2026-05-22T09:12:09,705   creating build/bdist.linux-armv7l/wheel/torchref/symmetry
2026-05-22T09:12:09,706   copying build/lib/torchref/symmetry/symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,708   copying build/lib/torchref/symmetry/map_symmetry_interpolation.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,710   copying build/lib/torchref/symmetry/grid_utils.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,712   copying build/lib/torchref/symmetry/reciprocal_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,716   copying build/lib/torchref/symmetry/cell.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,718   copying build/lib/torchref/symmetry/spacegroup.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,721   copying build/lib/torchref/symmetry/map_symmetry.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,723   copying build/lib/torchref/symmetry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/symmetry
2026-05-22T09:12:09,725   copying build/lib/torchref/config.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-05-22T09:12:09,728   creating build/bdist.linux-armv7l/wheel/torchref/alignment
2026-05-22T09:12:09,729   copying build/lib/torchref/alignment/sampling.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,731   copying build/lib/torchref/alignment/translation.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,734   copying build/lib/torchref/alignment/rigid_body.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,736   copying build/lib/torchref/alignment/ball_transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,740   copying build/lib/torchref/alignment/clashscore.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,742   copying build/lib/torchref/alignment/distributions.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,744   copying build/lib/torchref/alignment/jax_subpixel_peaks.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,746   copying build/lib/torchref/alignment/pipeline.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,749   copying build/lib/torchref/alignment/transform.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,751   copying build/lib/torchref/alignment/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/alignment
2026-05-22T09:12:09,755   creating build/bdist.linux-armv7l/wheel/torchref/scaling
2026-05-22T09:12:09,756   copying build/lib/torchref/scaling/scaler_base.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-22T09:12:09,759   copying build/lib/torchref/scaling/solvent.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-22T09:12:09,762   copying build/lib/torchref/scaling/scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-22T09:12:09,764   copying build/lib/torchref/scaling/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-22T09:12:09,766   copying build/lib/torchref/scaling/collection_scaler.py -> build/bdist.linux-armv7l/wheel/./torchref/scaling
2026-05-22T09:12:09,769   creating build/bdist.linux-armv7l/wheel/torchref/scripts
2026-05-22T09:12:09,770   copying build/lib/torchref/scripts/generate_scattering_table.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-05-22T09:12:09,773   copying build/lib/torchref/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/scripts
2026-05-22T09:12:09,775   creating build/bdist.linux-armv7l/wheel/torchref/maps
2026-05-22T09:12:09,776   copying build/lib/torchref/maps/difference_map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-05-22T09:12:09,778   copying build/lib/torchref/maps/map.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-05-22T09:12:09,781   copying build/lib/torchref/maps/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/maps
2026-05-22T09:12:09,783   creating build/bdist.linux-armv7l/wheel/torchref/restraints
2026-05-22T09:12:09,784   copying build/lib/torchref/restraints/hydrogen_topology.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,787   copying build/lib/torchref/restraints/builders_fast.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,792   copying build/lib/torchref/restraints/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,794   copying build/lib/torchref/restraints/neighbor_search.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,797   copying build/lib/torchref/restraints/restraints_helper.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,800   copying build/lib/torchref/restraints/builders.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,803   copying build/lib/torchref/restraints/builders_numba.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,808   copying build/lib/torchref/restraints/restraints.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,811   copying build/lib/torchref/restraints/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,813   copying build/lib/torchref/restraints/library.py -> build/bdist.linux-armv7l/wheel/./torchref/restraints
2026-05-22T09:12:09,816   creating build/bdist.linux-armv7l/wheel/torchref/model
2026-05-22T09:12:09,817   copying build/lib/torchref/model/mixed_model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,820   copying build/lib/torchref/model/internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,823   copying build/lib/torchref/model/model_collection.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,826   copying build/lib/torchref/model/model.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,830   copying build/lib/torchref/model/segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,834   copying build/lib/torchref/model/parameter_wrappers.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,838   copying build/lib/torchref/model/model_ft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,840   copying build/lib/torchref/model/closed_segmented_internal_coordinates.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,844   copying build/lib/torchref/model/sf_fft.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,846   copying build/lib/torchref/model/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,848   copying build/lib/torchref/model/sf_ds.py -> build/bdist.linux-armv7l/wheel/./torchref/model
2026-05-22T09:12:09,852   creating build/bdist.linux-armv7l/wheel/torchref/kinetic
2026-05-22T09:12:09,853   copying build/lib/torchref/kinetic/occupancies.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-22T09:12:09,856   copying build/lib/torchref/kinetic/refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-22T09:12:09,858   copying build/lib/torchref/kinetic/targets.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-22T09:12:09,861   copying build/lib/torchref/kinetic/kinetics.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-22T09:12:09,864   copying build/lib/torchref/kinetic/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/kinetic
2026-05-22T09:12:09,867   creating build/bdist.linux-armv7l/wheel/torchref/io
2026-05-22T09:12:09,868   copying build/lib/torchref/io/ihm_mapping.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,870   copying build/lib/torchref/io/data_router.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,872   creating build/bdist.linux-armv7l/wheel/torchref/io/datasets
2026-05-22T09:12:09,873   copying build/lib/torchref/io/datasets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-22T09:12:09,876   copying build/lib/torchref/io/datasets/reflection_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-22T09:12:09,879   copying build/lib/torchref/io/datasets/fcalc_data.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-22T09:12:09,882   copying build/lib/torchref/io/datasets/collection.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-22T09:12:09,884   copying build/lib/torchref/io/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io/datasets
2026-05-22T09:12:09,886   copying build/lib/torchref/io/cif_readers.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,889   copying build/lib/torchref/io/metadata.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,892   copying build/lib/torchref/io/cif.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,894   copying build/lib/torchref/io/pdb.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,897   copying build/lib/torchref/io/mtz.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,900   copying build/lib/torchref/io/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,902   copying build/lib/torchref/io/ihm.py -> build/bdist.linux-armv7l/wheel/./torchref/io
2026-05-22T09:12:09,906   creating build/bdist.linux-armv7l/wheel/torchref/refinement
2026-05-22T09:12:09,907   creating build/bdist.linux-armv7l/wheel/torchref/refinement/weighting
2026-05-22T09:12:09,909   copying build/lib/torchref/refinement/weighting/random_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-22T09:12:09,911   copying build/lib/torchref/refinement/weighting/policy_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-22T09:12:09,914   copying build/lib/torchref/refinement/weighting/component_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-22T09:12:09,917   copying build/lib/torchref/refinement/weighting/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-22T09:12:09,919   copying build/lib/torchref/refinement/weighting/es_policy_training.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-22T09:12:09,921   copying build/lib/torchref/refinement/weighting/base_weighting.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/weighting
2026-05-22T09:12:09,924   creating build/bdist.linux-armv7l/wheel/torchref/refinement/optimizers
2026-05-22T09:12:09,925   copying build/lib/torchref/refinement/optimizers/simulated_annealing.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-22T09:12:09,928   copying build/lib/torchref/refinement/optimizers/momentum_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-22T09:12:09,930   copying build/lib/torchref/refinement/optimizers/internal_coord_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-22T09:12:09,934   copying build/lib/torchref/refinement/optimizers/exploratory_lbfgs.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-22T09:12:09,937   copying build/lib/torchref/refinement/optimizers/langevin_sa.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-22T09:12:09,939   copying build/lib/torchref/refinement/optimizers/adam_noise.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-22T09:12:09,942   copying build/lib/torchref/refinement/optimizers/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/optimizers
2026-05-22T09:12:09,944   copying build/lib/torchref/refinement/lbfgs_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-22T09:12:09,947   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets
2026-05-22T09:12:09,949   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/xray
2026-05-22T09:12:09,950   copying build/lib/torchref/refinement/targets/xray/maximum_likelihood.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-22T09:12:09,952   copying build/lib/torchref/refinement/targets/xray/bhattacharyya.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-22T09:12:09,954   copying build/lib/torchref/refinement/targets/xray/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-22T09:12:09,956   copying build/lib/torchref/refinement/targets/xray/gaussian.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-22T09:12:09,958   copying build/lib/torchref/refinement/targets/xray/least_squares.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-22T09:12:09,960   copying build/lib/torchref/refinement/targets/xray/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/xray
2026-05-22T09:12:09,961   copying build/lib/torchref/refinement/targets/difference.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:09,964   copying build/lib/torchref/refinement/targets/forcefield_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:09,967   copying build/lib/torchref/refinement/targets/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:09,970   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/geometry
2026-05-22T09:12:09,971   copying build/lib/torchref/refinement/targets/geometry/bonds.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,973   copying build/lib/torchref/refinement/targets/geometry/angles.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,974   copying build/lib/torchref/refinement/targets/geometry/ramachandran.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,976   copying build/lib/torchref/refinement/targets/geometry/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,978   copying build/lib/torchref/refinement/targets/geometry/torsions.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,980   copying build/lib/torchref/refinement/targets/geometry/non_bonded.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,983   copying build/lib/torchref/refinement/targets/geometry/planarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,985   copying build/lib/torchref/refinement/targets/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,987   copying build/lib/torchref/refinement/targets/geometry/chiral.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,989   copying build/lib/torchref/refinement/targets/geometry/non_bonded_h.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/geometry
2026-05-22T09:12:09,991   copying build/lib/torchref/refinement/targets/combined.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:09,994   copying build/lib/torchref/refinement/targets/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:09,996   copying build/lib/torchref/refinement/targets/amber_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:09,999   copying build/lib/torchref/refinement/targets/occupancy_floor_diagnostic.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:10,002   copying build/lib/torchref/refinement/targets/realspace.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:10,005   copying build/lib/torchref/refinement/targets/sampled_ml_phase_target.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:10,007   copying build/lib/torchref/refinement/targets/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets
2026-05-22T09:12:10,010   creating build/bdist.linux-armv7l/wheel/torchref/refinement/targets/adp
2026-05-22T09:12:10,011   copying build/lib/torchref/refinement/targets/adp/scaler_u.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,013   copying build/lib/torchref/refinement/targets/adp/similarity.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,014   copying build/lib/torchref/refinement/targets/adp/base.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,016   copying build/lib/torchref/refinement/targets/adp/scaler_log_scale.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,018   copying build/lib/torchref/refinement/targets/adp/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,020   copying build/lib/torchref/refinement/targets/adp/locality.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,022   copying build/lib/torchref/refinement/targets/adp/entropy.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,024   copying build/lib/torchref/refinement/targets/adp/rigid_bond.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement/targets/adp
2026-05-22T09:12:10,026   copying build/lib/torchref/refinement/loss_state.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-22T09:12:10,029   copying build/lib/torchref/refinement/base_refinement.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-22T09:12:10,032   copying build/lib/torchref/refinement/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-22T09:12:10,034   copying build/lib/torchref/refinement/logger.py -> build/bdist.linux-armv7l/wheel/./torchref/refinement
2026-05-22T09:12:10,036   copying build/lib/torchref/__init__.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-05-22T09:12:10,038   copying build/lib/torchref/_bootstrap.py -> build/bdist.linux-armv7l/wheel/./torchref
2026-05-22T09:12:10,040   creating build/bdist.linux-armv7l/wheel/torchref/data
2026-05-22T09:12:10,041   copying build/lib/torchref/data/itc92_scattering_factors.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-05-22T09:12:10,044   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library
2026-05-22T09:12:10,046   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/g
2026-05-22T09:12:10,047   copying build/lib/torchref/data/monomer_library/g/G.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-22T09:12:10,050   copying build/lib/torchref/data/monomer_library/g/GLY.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-22T09:12:10,052   copying build/lib/torchref/data/monomer_library/g/GLN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-22T09:12:10,054   copying build/lib/torchref/data/monomer_library/g/GLU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/g
2026-05-22T09:12:10,056   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/m
2026-05-22T09:12:10,057   copying build/lib/torchref/data/monomer_library/m/MET.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-05-22T09:12:10,060   copying build/lib/torchref/data/monomer_library/m/MSE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/m
2026-05-22T09:12:10,062   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/a
2026-05-22T09:12:10,064   copying build/lib/torchref/data/monomer_library/a/ARG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-22T09:12:10,066   copying build/lib/torchref/data/monomer_library/a/A.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-22T09:12:10,068   copying build/lib/torchref/data/monomer_library/a/ASP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-22T09:12:10,070   copying build/lib/torchref/data/monomer_library/a/ASN.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-22T09:12:10,072   copying build/lib/torchref/data/monomer_library/a/ALA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/a
2026-05-22T09:12:10,075   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/v
2026-05-22T09:12:10,076   copying build/lib/torchref/data/monomer_library/v/VAL.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/v
2026-05-22T09:12:10,078   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/d
2026-05-22T09:12:10,079   copying build/lib/torchref/data/monomer_library/d/DC.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-22T09:12:10,082   copying build/lib/torchref/data/monomer_library/d/DT.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-22T09:12:10,084   copying build/lib/torchref/data/monomer_library/d/DG.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-22T09:12:10,087   copying build/lib/torchref/data/monomer_library/d/DA.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/d
2026-05-22T09:12:10,090   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/h
2026-05-22T09:12:10,091   copying build/lib/torchref/data/monomer_library/h/HYP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-05-22T09:12:10,093   copying build/lib/torchref/data/monomer_library/h/HOH.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-05-22T09:12:10,095   copying build/lib/torchref/data/monomer_library/h/HIS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/h
2026-05-22T09:12:10,098   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/p
2026-05-22T09:12:10,099   copying build/lib/torchref/data/monomer_library/p/PRO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-05-22T09:12:10,101   copying build/lib/torchref/data/monomer_library/p/PHE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-05-22T09:12:10,103   copying build/lib/torchref/data/monomer_library/p/PTR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/p
2026-05-22T09:12:10,106   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/l
2026-05-22T09:12:10,107   copying build/lib/torchref/data/monomer_library/l/LYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-05-22T09:12:10,109   copying build/lib/torchref/data/monomer_library/l/LEU.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/l
2026-05-22T09:12:10,112   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/s
2026-05-22T09:12:10,113   copying build/lib/torchref/data/monomer_library/s/SER.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-05-22T09:12:10,115   copying build/lib/torchref/data/monomer_library/s/SEP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/s
2026-05-22T09:12:10,118   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/list
2026-05-22T09:12:10,119   copying build/lib/torchref/data/monomer_library/list/mon_lib_list.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/list
2026-05-22T09:12:10,223   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/u
2026-05-22T09:12:10,224   copying build/lib/torchref/data/monomer_library/u/U.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/u
2026-05-22T09:12:10,227   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/i
2026-05-22T09:12:10,229   copying build/lib/torchref/data/monomer_library/i/ILE.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/i
2026-05-22T09:12:10,232   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/t
2026-05-22T09:12:10,233   copying build/lib/torchref/data/monomer_library/t/TYR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-22T09:12:10,236   copying build/lib/torchref/data/monomer_library/t/TRP.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-22T09:12:10,238   copying build/lib/torchref/data/monomer_library/t/TPO.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-22T09:12:10,241   copying build/lib/torchref/data/monomer_library/t/THR.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/t
2026-05-22T09:12:10,244   creating build/bdist.linux-armv7l/wheel/torchref/data/monomer_library/c
2026-05-22T09:12:10,245   copying build/lib/torchref/data/monomer_library/c/C.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-05-22T09:12:10,248   copying build/lib/torchref/data/monomer_library/c/CYS.cif -> build/bdist.linux-armv7l/wheel/./torchref/data/monomer_library/c
2026-05-22T09:12:10,251   copying build/lib/torchref/data/rama_nll_surfaces.pt -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-05-22T09:12:10,317   copying build/lib/torchref/data/atomic_vdw_radii.csv -> build/bdist.linux-armv7l/wheel/./torchref/data
2026-05-22T09:12:10,319   running install_egg_info
2026-05-22T09:12:10,326   Copying torchref.egg-info to build/bdist.linux-armv7l/wheel/./torchref-0.5.3-py3.11.egg-info
2026-05-22T09:12:10,340   running install_scripts
2026-05-22T09:12:10,353   creating build/bdist.linux-armv7l/wheel/torchref-0.5.3.dist-info/WHEEL
2026-05-22T09:12:10,356   creating '/tmp/pip-wheel-kgh7dmmp/.tmp-b2l09l4h/torchref-0.5.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-05-22T09:12:10,358   adding 'torchref/__init__.py'
2026-05-22T09:12:10,360   adding 'torchref/_bootstrap.py'
2026-05-22T09:12:10,362   adding 'torchref/config.py'
2026-05-22T09:12:10,364   adding 'torchref/alignment/__init__.py'
2026-05-22T09:12:10,371   adding 'torchref/alignment/ball_transform.py'
2026-05-22T09:12:10,374   adding 'torchref/alignment/clashscore.py'
2026-05-22T09:12:10,375   adding 'torchref/alignment/distributions.py'
2026-05-22T09:12:10,377   adding 'torchref/alignment/jax_subpixel_peaks.py'
2026-05-22T09:12:10,380   adding 'torchref/alignment/pipeline.py'
2026-05-22T09:12:10,382   adding 'torchref/alignment/rigid_body.py'
2026-05-22T09:12:10,384   adding 'torchref/alignment/sampling.py'
2026-05-22T09:12:10,387   adding 'torchref/alignment/transform.py'
2026-05-22T09:12:10,389   adding 'torchref/alignment/translation.py'
2026-05-22T09:12:10,391   adding 'torchref/base/CCTBX_related.py'
2026-05-22T09:12:10,393   adding 'torchref/base/__init__.py'
2026-05-22T09:12:10,396   adding 'torchref/base/french_wilson.py'
2026-05-22T09:12:10,398   adding 'torchref/base/get_scattering_factor_torch.py'
2026-05-22T09:12:10,401   adding 'torchref/base/math_numpy.py'
2026-05-22T09:12:10,403   adding 'torchref/base/math_torch.py'
2026-05-22T09:12:10,405   adding 'torchref/base/alignment/__init__.py'
2026-05-22T09:12:10,407   adding 'torchref/base/alignment/normalization.py'
2026-05-22T09:12:10,409   adding 'torchref/base/alignment/rotation.py'
2026-05-22T09:12:10,410   adding 'torchref/base/alignment/scoring.py'
2026-05-22T09:12:10,412   adding 'torchref/base/alignment/superposition.py'
2026-05-22T09:12:10,414   adding 'torchref/base/chain_closure/__init__.py'
2026-05-22T09:12:10,416   adding 'torchref/base/chain_closure/backbone_utils.py'
2026-05-22T09:12:10,419   adding 'torchref/base/chain_closure/closure.py'
2026-05-22T09:12:10,421   adding 'torchref/base/coordinates/__init__.py'
2026-05-22T09:12:10,422   adding 'torchref/base/coordinates/periodic_boundary.py'
2026-05-22T09:12:10,424   adding 'torchref/base/coordinates/transforms_numpy.py'
2026-05-22T09:12:10,425   adding 'torchref/base/coordinates/transforms_torch.py'
2026-05-22T09:12:10,426   adding 'torchref/base/direct_summation/__init__.py'
2026-05-22T09:12:10,428   adding 'torchref/base/direct_summation/anisotropic.py'
2026-05-22T09:12:10,429   adding 'torchref/base/direct_summation/corrections.py'
2026-05-22T09:12:10,431   adding 'torchref/base/direct_summation/isotropic.py'
2026-05-22T09:12:10,433   adding 'torchref/base/electron_density/__init__.py'
2026-05-22T09:12:10,437   adding 'torchref/base/electron_density/main.py'
2026-05-22T09:12:10,438   adding 'torchref/base/electron_density/map_building.py'
2026-05-22T09:12:10,441   adding 'torchref/base/electron_density/solvent_mask.py'
2026-05-22T09:12:10,442   adding 'torchref/base/electron_density/voxel_utils.py'
2026-05-22T09:12:10,444   adding 'torchref/base/fourier/__init__.py'
2026-05-22T09:12:10,445   adding 'torchref/base/fourier/fft.py'
2026-05-22T09:12:10,446   adding 'torchref/base/fourier/grid.py'
2026-05-22T09:12:10,448   adding 'torchref/base/kernels/__init__.py'
2026-05-22T09:12:10,451   adding 'torchref/base/kernels/cpu_scatter.py'
2026-05-22T09:12:10,453   adding 'torchref/base/kernels/jit_kernel_vectorized_add_to_map.py'
2026-05-22T09:12:10,455   adding 'torchref/base/kernels/optimized_ops.py'
2026-05-22T09:12:10,459   adding 'torchref/base/kernels/separable_triton_kernel.py'
2026-05-22T09:12:10,463   adding 'torchref/base/kernels/triton_kernel.py'
2026-05-22T09:12:10,465   adding 'torchref/base/metrics/__init__.py'
2026-05-22T09:12:10,466   adding 'torchref/base/metrics/loss.py'
2026-05-22T09:12:10,468   adding 'torchref/base/metrics/rfactor.py'
2026-05-22T09:12:10,470   adding 'torchref/base/reciprocal/__init__.py'
2026-05-22T09:12:10,471   adding 'torchref/base/reciprocal/basis.py'
2026-05-22T09:12:10,473   adding 'torchref/base/reciprocal/grid_operations.py'
2026-05-22T09:12:10,474   adding 'torchref/base/reciprocal/hkl.py'
2026-05-22T09:12:10,476   adding 'torchref/base/reciprocal/interpolation.py'
2026-05-22T09:12:10,478   adding 'torchref/base/reciprocal/symmetry.py'
2026-05-22T09:12:10,480   adding 'torchref/base/scattering/__init__.py'
2026-05-22T09:12:10,482   adding 'torchref/base/scattering/anomalous_table.py'
2026-05-22T09:12:10,483   adding 'torchref/base/scattering/itc92.py'
2026-05-22T09:12:10,485   adding 'torchref/base/scattering/scattering_table.py'
2026-05-22T09:12:10,487   adding 'torchref/base/targets/__init__.py'
2026-05-22T09:12:10,488   adding 'torchref/base/targets/_common.py'
2026-05-22T09:12:10,490   adding 'torchref/base/targets/_dispatch.py'
2026-05-22T09:12:10,491   adding 'torchref/base/targets/adp.py'
2026-05-22T09:12:10,492   adding 'torchref/base/targets/angle.py'
2026-05-22T09:12:10,494   adding 'torchref/base/targets/bond.py'
2026-05-22T09:12:10,495   adding 'torchref/base/targets/chiral.py'
2026-05-22T09:12:10,496   adding 'torchref/base/targets/nonbonded.py'
2026-05-22T09:12:10,498   adding 'torchref/base/targets/planarity.py'
2026-05-22T09:12:10,499   adding 'torchref/base/targets/ramachandran.py'
2026-05-22T09:12:10,500   adding 'torchref/base/targets/torsion.py'
2026-05-22T09:12:10,502   adding 'torchref/base/targets/xray_bhattacharyya.py'
2026-05-22T09:12:10,503   adding 'torchref/base/targets/xray_gaussian.py'
2026-05-22T09:12:10,504   adding 'torchref/base/targets/xray_ls.py'
2026-05-22T09:12:10,506   adding 'torchref/base/targets/xray_ml.py'
2026-05-22T09:12:10,508   adding 'torchref/base/targets/triton/__init__.py'
2026-05-22T09:12:10,509   adding 'torchref/base/targets/triton/_dihedral.py'
2026-05-22T09:12:10,510   adding 'torchref/base/targets/triton/adp_simu.py'
2026-05-22T09:12:10,512   adding 'torchref/base/targets/triton/angle.py'
2026-05-22T09:12:10,514   adding 'torchref/base/targets/triton/bond.py'
2026-05-22T09:12:10,515   adding 'torchref/base/targets/triton/chiral.py'
2026-05-22T09:12:10,517   adding 'torchref/base/targets/triton/nonbonded.py'
2026-05-22T09:12:10,520   adding 'torchref/base/targets/triton/place_hydrogens.py'
2026-05-22T09:12:10,522   adding 'torchref/base/targets/triton/planarity.py'
2026-05-22T09:12:10,523   adding 'torchref/base/targets/triton/ramachandran.py'
2026-05-22T09:12:10,525   adding 'torchref/base/targets/triton/torsion.py'
2026-05-22T09:12:10,527   adding 'torchref/base/targets/triton/xray_bhattacharyya.py'
2026-05-22T09:12:10,528   adding 'torchref/base/targets/triton/xray_gaussian.py'
2026-05-22T09:12:10,529   adding 'torchref/base/targets/triton/xray_ls.py'
2026-05-22T09:12:10,531   adding 'torchref/base/targets/triton/xray_ml.py'
2026-05-22T09:12:10,533   adding 'torchref/cli/__init__.py'
2026-05-22T09:12:10,536   adding 'torchref/cli/_common.py'
2026-05-22T09:12:10,537   adding 'torchref/cli/add_metadata.py'
2026-05-22T09:12:10,542   adding 'torchref/cli/collection_difference_refine.py'
2026-05-22T09:12:10,544   adding 'torchref/cli/mtz2map.py'
2026-05-22T09:12:10,546   adding 'torchref/cli/phased_difference_map.py'
2026-05-22T09:12:10,548   adding 'torchref/cli/refine.py'
2026-05-22T09:12:10,549   adding 'torchref/cli/strip_altlocs.py'
2026-05-22T09:12:10,553   adding 'torchref/cli/validate_ded.py'
2026-05-22T09:12:10,555   adding 'torchref/data/atomic_vdw_radii.csv'
2026-05-22T09:12:10,557   adding 'torchref/data/itc92_scattering_factors.pt'
2026-05-22T09:12:10,791   adding 'torchref/data/rama_nll_surfaces.pt'
2026-05-22T09:12:10,814   adding 'torchref/data/monomer_library/a/A.cif'
2026-05-22T09:12:10,815   adding 'torchref/data/monomer_library/a/ALA.cif'
2026-05-22T09:12:10,817   adding 'torchref/data/monomer_library/a/ARG.cif'
2026-05-22T09:12:10,819   adding 'torchref/data/monomer_library/a/ASN.cif'
2026-05-22T09:12:10,820   adding 'torchref/data/monomer_library/a/ASP.cif'
2026-05-22T09:12:10,823   adding 'torchref/data/monomer_library/c/C.cif'
2026-05-22T09:12:10,824   adding 'torchref/data/monomer_library/c/CYS.cif'
2026-05-22T09:12:10,827   adding 'torchref/data/monomer_library/d/DA.cif'
2026-05-22T09:12:10,829   adding 'torchref/data/monomer_library/d/DC.cif'
2026-05-22T09:12:10,832   adding 'torchref/data/monomer_library/d/DG.cif'
2026-05-22T09:12:10,834   adding 'torchref/data/monomer_library/d/DT.cif'
2026-05-22T09:12:10,837   adding 'torchref/data/monomer_library/g/G.cif'
2026-05-22T09:12:10,838   adding 'torchref/data/monomer_library/g/GLN.cif'
2026-05-22T09:12:10,840   adding 'torchref/data/monomer_library/g/GLU.cif'
2026-05-22T09:12:10,842   adding 'torchref/data/monomer_library/g/GLY.cif'
2026-05-22T09:12:10,844   adding 'torchref/data/monomer_library/h/HIS.cif'
2026-05-22T09:12:10,845   adding 'torchref/data/monomer_library/h/HOH.cif'
2026-05-22T09:12:10,847   adding 'torchref/data/monomer_library/h/HYP.cif'
2026-05-22T09:12:10,849   adding 'torchref/data/monomer_library/i/ILE.cif'
2026-05-22T09:12:10,851   adding 'torchref/data/monomer_library/l/LEU.cif'
2026-05-22T09:12:10,853   adding 'torchref/data/monomer_library/l/LYS.cif'
2026-05-22T09:12:11,408   adding 'torchref/data/monomer_library/list/mon_lib_list.cif'
2026-05-22T09:12:11,435   adding 'torchref/data/monomer_library/m/MET.cif'
2026-05-22T09:12:11,436   adding 'torchref/data/monomer_library/m/MSE.cif'
2026-05-22T09:12:11,439   adding 'torchref/data/monomer_library/p/PHE.cif'
2026-05-22T09:12:11,440   adding 'torchref/data/monomer_library/p/PRO.cif'
2026-05-22T09:12:11,442   adding 'torchref/data/monomer_library/p/PTR.cif'
2026-05-22T09:12:11,444   adding 'torchref/data/monomer_library/s/SEP.cif'
2026-05-22T09:12:11,446   adding 'torchref/data/monomer_library/s/SER.cif'
2026-05-22T09:12:11,448   adding 'torchref/data/monomer_library/t/THR.cif'
2026-05-22T09:12:11,449   adding 'torchref/data/monomer_library/t/TPO.cif'
2026-05-22T09:12:11,451   adding 'torchref/data/monomer_library/t/TRP.cif'
2026-05-22T09:12:11,453   adding 'torchref/data/monomer_library/t/TYR.cif'
2026-05-22T09:12:11,456   adding 'torchref/data/monomer_library/u/U.cif'
2026-05-22T09:12:11,458   adding 'torchref/data/monomer_library/v/VAL.cif'
2026-05-22T09:12:11,460   adding 'torchref/io/__init__.py'
2026-05-22T09:12:11,462   adding 'torchref/io/cif.py'
2026-05-22T09:12:11,469   adding 'torchref/io/cif_readers.py'
2026-05-22T09:12:11,471   adding 'torchref/io/data_router.py'
2026-05-22T09:12:11,476   adding 'torchref/io/ihm.py'
2026-05-22T09:12:11,478   adding 'torchref/io/ihm_mapping.py'
2026-05-22T09:12:11,480   adding 'torchref/io/metadata.py'
2026-05-22T09:12:11,483   adding 'torchref/io/mtz.py'
2026-05-22T09:12:11,485   adding 'torchref/io/pdb.py'
2026-05-22T09:12:11,487   adding 'torchref/io/datasets/__init__.py'
2026-05-22T09:12:11,489   adding 'torchref/io/datasets/base.py'
2026-05-22T09:12:11,491   adding 'torchref/io/datasets/collection.py'
2026-05-22T09:12:11,493   adding 'torchref/io/datasets/fcalc_data.py'
2026-05-22T09:12:11,506   adding 'torchref/io/datasets/reflection_data.py'
2026-05-22T09:12:11,508   adding 'torchref/kinetic/__init__.py'
2026-05-22T09:12:11,513   adding 'torchref/kinetic/kinetics.py'
2026-05-22T09:12:11,516   adding 'torchref/kinetic/occupancies.py'
2026-05-22T09:12:11,518   adding 'torchref/kinetic/refinement.py'
2026-05-22T09:12:11,521   adding 'torchref/kinetic/targets.py'
2026-05-22T09:12:11,523   adding 'torchref/maps/__init__.py'
2026-05-22T09:12:11,524   adding 'torchref/maps/difference_map.py'
2026-05-22T09:12:11,526   adding 'torchref/maps/map.py'
2026-05-22T09:12:11,528   adding 'torchref/model/__init__.py'
2026-05-22T09:12:11,536   adding 'torchref/model/closed_segmented_internal_coordinates.py'
2026-05-22T09:12:11,545   adding 'torchref/model/internal_coordinates.py'
2026-05-22T09:12:11,548   adding 'torchref/model/mixed_model.py'
2026-05-22T09:12:11,563   adding 'torchref/model/model.py'
2026-05-22T09:12:11,566   adding 'torchref/model/model_collection.py'
2026-05-22T09:12:11,571   adding 'torchref/model/model_ft.py'
2026-05-22T09:12:11,580   adding 'torchref/model/parameter_wrappers.py'
2026-05-22T09:12:11,588   adding 'torchref/model/segmented_internal_coordinates.py'
2026-05-22T09:12:11,591   adding 'torchref/model/sf_ds.py'
2026-05-22T09:12:11,594   adding 'torchref/model/sf_fft.py'
2026-05-22T09:12:11,596   adding 'torchref/refinement/__init__.py'
2026-05-22T09:12:11,600   adding 'torchref/refinement/base_refinement.py'
2026-05-22T09:12:11,603   adding 'torchref/refinement/lbfgs_refinement.py'
2026-05-22T09:12:11,606   adding 'torchref/refinement/logger.py'
2026-05-22T09:12:11,610   adding 'torchref/refinement/loss_state.py'
2026-05-22T09:12:11,612   adding 'torchref/refinement/optimizers/__init__.py'
2026-05-22T09:12:11,614   adding 'torchref/refinement/optimizers/adam_noise.py'
2026-05-22T09:12:11,617   adding 'torchref/refinement/optimizers/exploratory_lbfgs.py'
2026-05-22T09:12:11,621   adding 'torchref/refinement/optimizers/internal_coord_sa.py'
2026-05-22T09:12:11,623   adding 'torchref/refinement/optimizers/langevin_sa.py'
2026-05-22T09:12:11,624   adding 'torchref/refinement/optimizers/momentum_sa.py'
2026-05-22T09:12:11,626   adding 'torchref/refinement/optimizers/simulated_annealing.py'
2026-05-22T09:12:11,628   adding 'torchref/refinement/targets/__init__.py'
2026-05-22T09:12:11,634   adding 'torchref/refinement/targets/amber_target.py'
2026-05-22T09:12:11,636   adding 'torchref/refinement/targets/base.py'
2026-05-22T09:12:11,638   adding 'torchref/refinement/targets/combined.py'
2026-05-22T09:12:11,644   adding 'torchref/refinement/targets/difference.py'
2026-05-22T09:12:11,645   adding 'torchref/refinement/targets/forcefield_target.py'
2026-05-22T09:12:11,648   adding 'torchref/refinement/targets/occupancy_floor_diagnostic.py'
2026-05-22T09:12:11,651   adding 'torchref/refinement/targets/realspace.py'
2026-05-22T09:12:11,655   adding 'torchref/refinement/targets/sampled_ml_phase_target.py'
2026-05-22T09:12:11,656   adding 'torchref/refinement/targets/similarity.py'
2026-05-22T09:12:11,658   adding 'torchref/refinement/targets/adp/__init__.py'
2026-05-22T09:12:11,660   adding 'torchref/refinement/targets/adp/base.py'
2026-05-22T09:12:11,661   adding 'torchref/refinement/targets/adp/entropy.py'
2026-05-22T09:12:11,663   adding 'torchref/refinement/targets/adp/locality.py'
2026-05-22T09:12:11,665   adding 'torchref/refinement/targets/adp/rigid_bond.py'
2026-05-22T09:12:11,666   adding 'torchref/refinement/targets/adp/scaler_log_scale.py'
2026-05-22T09:12:11,667   adding 'torchref/refinement/targets/adp/scaler_u.py'
2026-05-22T09:12:11,669   adding 'torchref/refinement/targets/adp/similarity.py'
2026-05-22T09:12:11,670   adding 'torchref/refinement/targets/geometry/__init__.py'
2026-05-22T09:12:11,672   adding 'torchref/refinement/targets/geometry/angles.py'
2026-05-22T09:12:11,673   adding 'torchref/refinement/targets/geometry/base.py'
2026-05-22T09:12:11,674   adding 'torchref/refinement/targets/geometry/bonds.py'
2026-05-22T09:12:11,676   adding 'torchref/refinement/targets/geometry/chiral.py'
2026-05-22T09:12:11,678   adding 'torchref/refinement/targets/geometry/non_bonded.py'
2026-05-22T09:12:11,681   adding 'torchref/refinement/targets/geometry/non_bonded_h.py'
2026-05-22T09:12:11,682   adding 'torchref/refinement/targets/geometry/planarity.py'
2026-05-22T09:12:11,684   adding 'torchref/refinement/targets/geometry/ramachandran.py'
2026-05-22T09:12:11,686   adding 'torchref/refinement/targets/geometry/torsions.py'
2026-05-22T09:12:11,688   adding 'torchref/refinement/targets/xray/__init__.py'
2026-05-22T09:12:11,690   adding 'torchref/refinement/targets/xray/base.py'
2026-05-22T09:12:11,692   adding 'torchref/refinement/targets/xray/bhattacharyya.py'
2026-05-22T09:12:11,693   adding 'torchref/refinement/targets/xray/gaussian.py'
2026-05-22T09:12:11,694   adding 'torchref/refinement/targets/xray/least_squares.py'
2026-05-22T09:12:11,696   adding 'torchref/refinement/targets/xray/maximum_likelihood.py'
2026-05-22T09:12:11,698   adding 'torchref/refinement/weighting/__init__.py'
2026-05-22T09:12:11,699   adding 'torchref/refinement/weighting/base_weighting.py'
2026-05-22T09:12:11,701   adding 'torchref/refinement/weighting/component_weighting.py'
2026-05-22T09:12:11,703   adding 'torchref/refinement/weighting/es_policy_training.py'
2026-05-22T09:12:11,707   adding 'torchref/refinement/weighting/policy_weighting.py'
2026-05-22T09:12:11,709   adding 'torchref/refinement/weighting/random_weighting.py'
2026-05-22T09:12:11,712   adding 'torchref/restraints/__init__.py'
2026-05-22T09:12:11,716   adding 'torchref/restraints/builders.py'
2026-05-22T09:12:11,724   adding 'torchref/restraints/builders_fast.py'
2026-05-22T09:12:11,728   adding 'torchref/restraints/builders_numba.py'
2026-05-22T09:12:11,732   adding 'torchref/restraints/hydrogen_topology.py'
2026-05-22T09:12:11,734   adding 'torchref/restraints/library.py'
2026-05-22T09:12:11,740   adding 'torchref/restraints/neighbor_search.py'
2026-05-22T09:12:11,741   adding 'torchref/restraints/ramachandran.py'
2026-05-22T09:12:11,751   adding 'torchref/restraints/restraints.py'
2026-05-22T09:12:11,755   adding 'torchref/restraints/restraints_helper.py'
2026-05-22T09:12:11,757   adding 'torchref/scaling/__init__.py'
2026-05-22T09:12:11,759   adding 'torchref/scaling/collection_scaler.py'
2026-05-22T09:12:11,762   adding 'torchref/scaling/scaler.py'
2026-05-22T09:12:11,767   adding 'torchref/scaling/scaler_base.py'
2026-05-22T09:12:11,770   adding 'torchref/scaling/solvent.py'
2026-05-22T09:12:11,772   adding 'torchref/scripts/__init__.py'
2026-05-22T09:12:11,774   adding 'torchref/scripts/generate_scattering_table.py'
2026-05-22T09:12:11,776   adding 'torchref/symmetry/__init__.py'
2026-05-22T09:12:11,778   adding 'torchref/symmetry/cell.py'
2026-05-22T09:12:11,780   adding 'torchref/symmetry/grid_utils.py'
2026-05-22T09:12:11,782   adding 'torchref/symmetry/map_symmetry.py'
2026-05-22T09:12:11,784   adding 'torchref/symmetry/map_symmetry_interpolation.py'
2026-05-22T09:12:11,791   adding 'torchref/symmetry/reciprocal_symmetry.py'
2026-05-22T09:12:11,794   adding 'torchref/symmetry/spacegroup.py'
2026-05-22T09:12:11,796   adding 'torchref/symmetry/symmetry.py'
2026-05-22T09:12:11,798   adding 'torchref/utils/__init__.py'
2026-05-22T09:12:11,800   adding 'torchref/utils/autograd_introspection.py'
2026-05-22T09:12:11,801   adding 'torchref/utils/autograd_ops.py'
2026-05-22T09:12:11,803   adding 'torchref/utils/caching.py'
2026-05-22T09:12:11,804   adding 'torchref/utils/debug_utils.py'
2026-05-22T09:12:11,807   adding 'torchref/utils/device_mixin.py'
2026-05-22T09:12:11,808   adding 'torchref/utils/device_resolution.py'
2026-05-22T09:12:11,809   adding 'torchref/utils/gradnorm.py'
2026-05-22T09:12:11,811   adding 'torchref/utils/hyperparameters.py'
2026-05-22T09:12:11,813   adding 'torchref/utils/loss_validation.py'
2026-05-22T09:12:11,815   adding 'torchref/utils/pse.py'
2026-05-22T09:12:11,816   adding 'torchref/utils/serialization.py'
2026-05-22T09:12:11,817   adding 'torchref/utils/stats.py'
2026-05-22T09:12:11,819   adding 'torchref/utils/timing.py'
2026-05-22T09:12:11,823   adding 'torchref/utils/utils.py'
2026-05-22T09:12:11,826   adding 'torchref-0.5.3.dist-info/licenses/LICENSE'
2026-05-22T09:12:11,827   adding 'torchref-0.5.3.dist-info/METADATA'
2026-05-22T09:12:11,828   adding 'torchref-0.5.3.dist-info/WHEEL'
2026-05-22T09:12:11,829   adding 'torchref-0.5.3.dist-info/entry_points.txt'
2026-05-22T09:12:11,830   adding 'torchref-0.5.3.dist-info/top_level.txt'
2026-05-22T09:12:11,834   adding 'torchref-0.5.3.dist-info/RECORD'
2026-05-22T09:12:11,892   removing build/bdist.linux-armv7l/wheel
2026-05-22T09:12:12,073   Building wheel for torchref (pyproject.toml): finished with status 'done'
2026-05-22T09:12:12,147   Created wheel for torchref: filename=torchref-0.5.3-py3-none-any.whl size=3130504 sha256=46e6766130f0e3c77ae9734e25a717a2ca237cf1f3e3bb23a12a528ddd0b0848
2026-05-22T09:12:12,148   Stored in directory: /tmp/pip-ephem-wheel-cache-24f6gqoj/wheels/ed/24/b7/8c39354c4d25e7cc0f0dc57673091051752eab12ae928080a3
2026-05-22T09:12:12,168 Successfully built torchref
2026-05-22T09:12:12,243 Removed build tracker: '/tmp/pip-build-tracker-58v6xr8h'