2025-10-17T21:15:23,118 Created temporary directory: /tmp/pip-build-tracker-a3pjz482
2025-10-17T21:15:23,118 Initialized build tracking at /tmp/pip-build-tracker-a3pjz482
2025-10-17T21:15:23,119 Created build tracker: /tmp/pip-build-tracker-a3pjz482
2025-10-17T21:15:23,119 Entered build tracker: /tmp/pip-build-tracker-a3pjz482
2025-10-17T21:15:23,119 Created temporary directory: /tmp/pip-wheel-tdj1m93a
2025-10-17T21:15:23,122 Created temporary directory: /tmp/pip-ephem-wheel-cache-tq3sxgxz
2025-10-17T21:15:23,180 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-17T21:15:23,182 2 location(s) to search for versions of adaptivepele:
2025-10-17T21:15:23,182 * https://pypi.org/simple/adaptivepele/
2025-10-17T21:15:23,182 * https://www.piwheels.org/simple/adaptivepele/
2025-10-17T21:15:23,182 Fetching project page and analyzing links: https://pypi.org/simple/adaptivepele/
2025-10-17T21:15:23,182 Getting page https://pypi.org/simple/adaptivepele/
2025-10-17T21:15:23,184 Found index url https://pypi.org/simple/
2025-10-17T21:15:23,330 Fetched page https://pypi.org/simple/adaptivepele/ as application/vnd.pypi.simple.v1+json
2025-10-17T21:15:23,332   Found link https://files.pythonhosted.org/packages/33/ee/476a691d254663e61362e5c2754180ff0b92980e6db1afc829265f001706/AdaptivePELE-1.5.1.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.5.1
2025-10-17T21:15:23,332   Found link https://files.pythonhosted.org/packages/d9/82/be65cbae39642401f6e6923e5511fd466d107920ee9673bb84581a243a4e/AdaptivePELE-1.5.2.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.5.2
2025-10-17T21:15:23,333   Found link https://files.pythonhosted.org/packages/48/3b/f12bfdcfd7f0fdcb2f58d659ff94c26666767eec4ca8454750a3241c395e/AdaptivePELE-1.6.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.6
2025-10-17T21:15:23,333   Found link https://files.pythonhosted.org/packages/d0/1b/f731952d133f4a684ae4376f67513af80d1f759b9ef4d6137767e0fc8ed9/AdaptivePELE-1.6.2.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.6.2
2025-10-17T21:15:23,333   Found link https://files.pythonhosted.org/packages/25/2c/65b787dc210294855b8f27abeb4a7761f25fce34e0b8bfd56779c679440d/AdaptivePELE-1.6.3.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.6.3
2025-10-17T21:15:23,334   Found link https://files.pythonhosted.org/packages/2b/34/d4545814438fa2992d83f5be0389f6465ab3e542ada0c02f90dbc4cc5695/AdaptivePELE-1.7.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.7
2025-10-17T21:15:23,334   Found link https://files.pythonhosted.org/packages/21/7d/8c8eb27cbe21dfcfbf80d5f16c889ee2d5bf0eec8dd8bcd03567d06bef98/AdaptivePELE-1.7.1.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.7.1
2025-10-17T21:15:23,334   Found link https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.7.4
2025-10-17T21:15:23,335 Fetching project page and analyzing links: https://www.piwheels.org/simple/adaptivepele/
2025-10-17T21:15:23,335 Getting page https://www.piwheels.org/simple/adaptivepele/
2025-10-17T21:15:23,336 Found index url https://www.piwheels.org/simple/
2025-10-17T21:15:23,487 Fetched page https://www.piwheels.org/simple/adaptivepele/ as text/html
2025-10-17T21:15:23,495   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.4-cp311-cp311-linux_armv6l.whl#sha256=8322937309a7efabf90fbc15d3d59ca9db71870cd9bb872bc4fefc2548447801 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,496   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.4-cp311-cp311-linux_armv7l.whl#sha256=8322937309a7efabf90fbc15d3d59ca9db71870cd9bb872bc4fefc2548447801 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,496   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.4-cp37-cp37m-linux_armv6l.whl#sha256=92d2fd2578aa02d8403fcd8ad2120883c524e2bce2be63df388ea24ad74eefd4 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,496   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.4-cp37-cp37m-linux_armv7l.whl#sha256=92d2fd2578aa02d8403fcd8ad2120883c524e2bce2be63df388ea24ad74eefd4 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,496   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.4-cp39-cp39-linux_armv6l.whl#sha256=6b765ee382a855a7704db9039fae9a5d842fcce59a92087f71b40dc636ca1fe8 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,496   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.4-cp39-cp39-linux_armv7l.whl#sha256=6b765ee382a855a7704db9039fae9a5d842fcce59a92087f71b40dc636ca1fe8 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,497   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp37-cp37m-linux_armv6l.whl#sha256=3292b60b31353aeff2e1832f504c186c202729cba0948d5ed44a194fab7eb63d (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,497   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp37-cp37m-linux_armv7l.whl#sha256=3292b60b31353aeff2e1832f504c186c202729cba0948d5ed44a194fab7eb63d (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,497   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp35-cp35m-linux_armv6l.whl#sha256=0208e16fec704fe2c144f233c3bcad9bd699844776c4d69a84cbeea650e527cf (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,497   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp35-cp35m-linux_armv7l.whl#sha256=0208e16fec704fe2c144f233c3bcad9bd699844776c4d69a84cbeea650e527cf (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,497   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp39-cp39-linux_armv6l.whl#sha256=8ba47dab67ab6fbd1e1bd022bdee1d4de408ec335fecc88108e7a3d295f378e9 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,497   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp39-cp39-linux_armv7l.whl#sha256=8ba47dab67ab6fbd1e1bd022bdee1d4de408ec335fecc88108e7a3d295f378e9 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,497   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp35-cp35m-linux_armv6l.whl#sha256=68bfb28f19f03bbd0d90143f2e191708ad9d2541088ece0035c08b89001d3f02 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,498   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp35-cp35m-linux_armv7l.whl#sha256=68bfb28f19f03bbd0d90143f2e191708ad9d2541088ece0035c08b89001d3f02 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,498   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp37-cp37m-linux_armv6l.whl#sha256=9ceafd1bdad9148abd951ec26b53c062af8565c6ed7df8a4833b0a5b1af150b6 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,498   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp37-cp37m-linux_armv7l.whl#sha256=9ceafd1bdad9148abd951ec26b53c062af8565c6ed7df8a4833b0a5b1af150b6 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,498   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp37-cp37m-linux_armv6l.whl#sha256=fc72f5016a0826fbe3b3a251f574c128cfffc1e1080f6ef21d32ae9134214087 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,498   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp37-cp37m-linux_armv7l.whl#sha256=fc72f5016a0826fbe3b3a251f574c128cfffc1e1080f6ef21d32ae9134214087 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,498   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp35-cp35m-linux_armv6l.whl#sha256=843a4ba6b03c34f08d3926f9c672ffecbe27f2d3a031f4e04cfba5ab92bf081b (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,499   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp35-cp35m-linux_armv7l.whl#sha256=843a4ba6b03c34f08d3926f9c672ffecbe27f2d3a031f4e04cfba5ab92bf081b (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,499   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp34-cp34m-linux_armv7l.whl#sha256=4f4aaf9237f2698965935feac86131663c03ebcf1f93aec451b35f8ce80d4c09 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,499   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp34-cp34m-linux_armv6l.whl#sha256=4f4aaf9237f2698965935feac86131663c03ebcf1f93aec451b35f8ce80d4c09 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,499   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp35-cp35m-linux_armv7l.whl#sha256=36de6189a08732016ffd1c173924fa40f32b8ff581b3fe9ef9593c21a09c2a1e (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,499   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp35-cp35m-linux_armv6l.whl#sha256=36de6189a08732016ffd1c173924fa40f32b8ff581b3fe9ef9593c21a09c2a1e (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,499   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp37-cp37m-linux_armv7l.whl#sha256=a444a2d3065cfad76489b3dff07638244e394ee86317ad4f9f738963ae9412e1 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,499   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp37-cp37m-linux_armv6l.whl#sha256=a444a2d3065cfad76489b3dff07638244e394ee86317ad4f9f738963ae9412e1 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,500   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp34-cp34m-linux_armv7l.whl#sha256=bb8b9f8f462d1c73c4a799c01c4e9913f7f3047d5b536180b305caaaa283e0d8 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,500   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp34-cp34m-linux_armv6l.whl#sha256=bb8b9f8f462d1c73c4a799c01c4e9913f7f3047d5b536180b305caaaa283e0d8 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,500   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp35-cp35m-linux_armv7l.whl#sha256=be4d1c98b4b7053819231567db9e10f930245d5dbcd03c764cfedc72479568ae (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,500   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp35-cp35m-linux_armv6l.whl#sha256=be4d1c98b4b7053819231567db9e10f930245d5dbcd03c764cfedc72479568ae (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,500   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp34-cp34m-linux_armv7l.whl#sha256=803d5b49a0992dd6aab76657a4fd7da709ba29ae19ef407b3c263abcfa9cef71 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,500   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp34-cp34m-linux_armv6l.whl#sha256=803d5b49a0992dd6aab76657a4fd7da709ba29ae19ef407b3c263abcfa9cef71 (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,500   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp35-cp35m-linux_armv6l.whl#sha256=7bee2048d0a5a4bf74907584a5db700ec2fe7aa35a7682a87c05ad5e92d00c5f (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,501   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp35-cp35m-linux_armv7l.whl#sha256=7bee2048d0a5a4bf74907584a5db700ec2fe7aa35a7682a87c05ad5e92d00c5f (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,501   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp35-cp35m-linux_armv7l.whl#sha256=11454cd28dbb1fac72eedb48155487d4e6a36fe5bf4ba70d1df2f81984690f5f (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,501   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp35-cp35m-linux_armv6l.whl#sha256=11454cd28dbb1fac72eedb48155487d4e6a36fe5bf4ba70d1df2f81984690f5f (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,501   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp34-cp34m-linux_armv6l.whl#sha256=ae482fbe798dddf382cbba7468496c022b12752804d218c198b78c1183e5342a (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,501   Skipping link: No binaries permitted for adaptivepele: https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp34-cp34m-linux_armv7l.whl#sha256=ae482fbe798dddf382cbba7468496c022b12752804d218c198b78c1183e5342a (from https://www.piwheels.org/simple/adaptivepele/)
2025-10-17T21:15:23,501 Skipping link: not a file: https://www.piwheels.org/simple/adaptivepele/
2025-10-17T21:15:23,502 Skipping link: not a file: https://pypi.org/simple/adaptivepele/
2025-10-17T21:15:23,526 Given no hashes to check 1 links for project 'adaptivepele': discarding no candidates
2025-10-17T21:15:23,527 Collecting adaptivepele==1.7.4
2025-10-17T21:15:23,528   Created temporary directory: /tmp/pip-unpack-_lrdefms
2025-10-17T21:15:23,591   Downloading AdaptivePELE-1.7.4.tar.gz (219 kB)
2025-10-17T21:15:23,739   Added adaptivepele==1.7.4 from https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz to build tracker '/tmp/pip-build-tracker-a3pjz482'
2025-10-17T21:15:23,741   Running setup.py (path:/tmp/pip-wheel-tdj1m93a/adaptivepele_9b61e46798374b7bacdd1e4fed81d59e/setup.py) egg_info for package adaptivepele
2025-10-17T21:15:23,741   Created temporary directory: /tmp/pip-pip-egg-info-v4q9pngr
2025-10-17T21:15:23,741   Preparing metadata (setup.py): started
2025-10-17T21:15:23,742   Running command python setup.py egg_info
2025-10-17T21:15:24,914   Warning: 'classifiers' should be a list, got type 'tuple'
2025-10-17T21:15:25,134   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-17T21:15:25,134   !!

2025-10-17T21:15:25,134           ********************************************************************************
2025-10-17T21:15:25,134           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-17T21:15:25,135           License :: OSI Approved :: MIT License

2025-10-17T21:15:25,135           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-17T21:15:25,135           ********************************************************************************

2025-10-17T21:15:25,135   !!
2025-10-17T21:15:25,135     self._finalize_license_expression()
2025-10-17T21:15:25,208   running egg_info
2025-10-17T21:15:25,282   creating /tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info
2025-10-17T21:15:25,282   writing /tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info/PKG-INFO
2025-10-17T21:15:25,283   writing dependency_links to /tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info/dependency_links.txt
2025-10-17T21:15:25,284   writing requirements to /tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info/requires.txt
2025-10-17T21:15:25,284   writing top-level names to /tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info/top_level.txt
2025-10-17T21:15:25,285   writing manifest file '/tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info/SOURCES.txt'
2025-10-17T21:15:25,518   reading manifest file '/tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info/SOURCES.txt'
2025-10-17T21:15:25,519   reading manifest template 'MANIFEST.in'
2025-10-17T21:15:25,522   warning: no files found matching 'utils.c' under directory 'AdaptivePELE/freeEnergies'
2025-10-17T21:15:25,523   warning: no files found matching 'utils*.so' under directory 'AdaptivePELE/freeEnergies'
2025-10-17T21:15:25,523   adding license file 'LICENSE'
2025-10-17T21:15:25,528   writing manifest file '/tmp/pip-pip-egg-info-v4q9pngr/AdaptivePELE.egg-info/SOURCES.txt'
2025-10-17T21:15:25,664   Preparing metadata (setup.py): finished with status 'done'
2025-10-17T21:15:25,669   Source in /tmp/pip-wheel-tdj1m93a/adaptivepele_9b61e46798374b7bacdd1e4fed81d59e has version 1.7.4, which satisfies requirement adaptivepele==1.7.4 from https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz
2025-10-17T21:15:25,670   Removed adaptivepele==1.7.4 from https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz from build tracker '/tmp/pip-build-tracker-a3pjz482'
2025-10-17T21:15:25,674 Created temporary directory: /tmp/pip-unpack-dj4bfugv
2025-10-17T21:15:25,674 Created temporary directory: /tmp/pip-unpack-287x4a9u
2025-10-17T21:15:25,674 Building wheels for collected packages: adaptivepele
2025-10-17T21:15:25,676   Created temporary directory: /tmp/pip-wheel-_k6gnjxx
2025-10-17T21:15:25,676   DEPRECATION: Building 'adaptivepele' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'adaptivepele'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-10-17T21:15:25,677   Building wheel for adaptivepele (setup.py): started
2025-10-17T21:15:25,678   Destination directory: /tmp/pip-wheel-_k6gnjxx
2025-10-17T21:15:25,678   Running command python setup.py bdist_wheel
2025-10-17T21:15:26,766   Warning: 'classifiers' should be a list, got type 'tuple'
2025-10-17T21:15:26,980   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-17T21:15:26,980   !!

2025-10-17T21:15:26,980           ********************************************************************************
2025-10-17T21:15:26,980           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-17T21:15:26,980           License :: OSI Approved :: MIT License

2025-10-17T21:15:26,981           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-17T21:15:26,981           ********************************************************************************

2025-10-17T21:15:26,981   !!
2025-10-17T21:15:26,981     self._finalize_license_expression()
2025-10-17T21:15:26,981   running bdist_wheel
2025-10-17T21:15:27,277   running build
2025-10-17T21:15:27,277   running build_py
2025-10-17T21:15:27,354   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE
2025-10-17T21:15:27,355   copying AdaptivePELE/runAllTests.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE
2025-10-17T21:15:27,355   copying AdaptivePELE/makeRelease.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE
2025-10-17T21:15:27,356   copying AdaptivePELE/automateRoundsAdaptive.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE
2025-10-17T21:15:27,356   copying AdaptivePELE/adaptiveSampling.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE
2025-10-17T21:15:27,357   copying AdaptivePELE/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE
2025-10-17T21:15:27,358   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator
2025-10-17T21:15:27,358   copying AdaptivePELE/validator/validatorBlockNames.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator
2025-10-17T21:15:27,359   copying AdaptivePELE/validator/controlFileValidator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator
2025-10-17T21:15:27,359   copying AdaptivePELE/validator/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator
2025-10-17T21:15:27,360   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,360   copying AdaptivePELE/utilities/utilities.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,361   copying AdaptivePELE/utilities/synchronization.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,362   copying AdaptivePELE/utilities/generate_topology_object.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,362   copying AdaptivePELE/utilities/conda_deployment.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,363   copying AdaptivePELE/utilities/clusteringUtilities.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,363   copying AdaptivePELE/utilities/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,364   copying AdaptivePELE/utilities/PDBLoader.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities
2025-10-17T21:15:27,365   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,365   copying AdaptivePELE/tests/testThresholdcalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,366   copying AdaptivePELE/tests/testSpawning.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,366   copying AdaptivePELE/tests/testSimulationRunner.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,367   copying AdaptivePELE/tests/testReporter.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,367   copying AdaptivePELE/tests/testMD_CUDA.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,368   copying AdaptivePELE/tests/testMD.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,368   copying AdaptivePELE/tests/testDensityCalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,369   copying AdaptivePELE/tests/testClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,369   copying AdaptivePELE/tests/testAtomset.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,370   copying AdaptivePELE/tests/testAdaptiveSampling.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,370   copying AdaptivePELE/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests
2025-10-17T21:15:27,371   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning
2025-10-17T21:15:27,371   copying AdaptivePELE/spawning/spawningTypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning
2025-10-17T21:15:27,372   copying AdaptivePELE/spawning/spawning.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning
2025-10-17T21:15:27,373   copying AdaptivePELE/spawning/densitycalculatortypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning
2025-10-17T21:15:27,373   copying AdaptivePELE/spawning/densitycalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning
2025-10-17T21:15:27,374   copying AdaptivePELE/spawning/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning
2025-10-17T21:15:27,374   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation
2025-10-17T21:15:27,375   copying AdaptivePELE/simulation/simulationrunner.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation
2025-10-17T21:15:27,376   copying AdaptivePELE/simulation/simulationTypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation
2025-10-17T21:15:27,376   copying AdaptivePELE/simulation/openmm_simulations.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation
2025-10-17T21:15:27,377   copying AdaptivePELE/simulation/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation
2025-10-17T21:15:27,378   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,378   copying AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,379   copying AdaptivePELE/freeEnergies/utilitiesFreeEnergies.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,379   copying AdaptivePELE/freeEnergies/runMarkovChainModel.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,380   copying AdaptivePELE/freeEnergies/prepareMSMFolders.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,380   copying AdaptivePELE/freeEnergies/ownBuildMSM.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,381   copying AdaptivePELE/freeEnergies/getRepresentativeStructures.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,381   copying AdaptivePELE/freeEnergies/extractCoords.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,382   copying AdaptivePELE/freeEnergies/extendTrajectories.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,382   copying AdaptivePELE/freeEnergies/estimateDGAdaptive.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,383   copying AdaptivePELE/freeEnergies/estimateDG.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,383   copying AdaptivePELE/freeEnergies/estimate.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,384   copying AdaptivePELE/freeEnergies/computeDeltaG.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,384   copying AdaptivePELE/freeEnergies/computeDGGrid.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,385   copying AdaptivePELE/freeEnergies/cluster.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,385   copying AdaptivePELE/freeEnergies/checkDetailedBalance.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,386   copying AdaptivePELE/freeEnergies/calculateDGiterations.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,386   copying AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,387   copying AdaptivePELE/freeEnergies/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:15:27,388   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants
2025-10-17T21:15:27,388   copying AdaptivePELE/constants/symmetries.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants
2025-10-17T21:15:27,389   copying AdaptivePELE/constants/constants.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants
2025-10-17T21:15:27,389   copying AdaptivePELE/constants/buildEnvironments.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants
2025-10-17T21:15:27,390   copying AdaptivePELE/constants/blockNames.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants
2025-10-17T21:15:27,390   copying AdaptivePELE/constants/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants
2025-10-17T21:15:27,391   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering
2025-10-17T21:15:27,391   copying AdaptivePELE/clustering/thresholdcalculatortypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering
2025-10-17T21:15:27,392   copying AdaptivePELE/clustering/thresholdcalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering
2025-10-17T21:15:27,392   copying AdaptivePELE/clustering/clusteringTypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering
2025-10-17T21:15:27,393   copying AdaptivePELE/clustering/clustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering
2025-10-17T21:15:27,394   copying AdaptivePELE/clustering/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering
2025-10-17T21:15:27,394   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset
2025-10-17T21:15:27,395   copying AdaptivePELE/atomset/setup.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset
2025-10-17T21:15:27,395   copying AdaptivePELE/atomset/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset
2025-10-17T21:15:27,397   creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,397   copying AdaptivePELE/analysis/writeTrajToSnapshot.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,397   copying AdaptivePELE/analysis/writeNetworkFiles.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,398   copying AdaptivePELE/analysis/writeClusteringStructures.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,398   copying AdaptivePELE/analysis/unbinding.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,399   copying AdaptivePELE/analysis/trajectory_processing.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,400   copying AdaptivePELE/analysis/standarize_MD_energies.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,400   copying AdaptivePELE/analysis/splitTrajectory.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,401   copying AdaptivePELE/analysis/simulationToCsv.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,401   copying AdaptivePELE/analysis/simple_postprocessing.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,402   copying AdaptivePELE/analysis/selectOnPlot.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,402   copying AdaptivePELE/analysis/reportSimulation.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,403   copying AdaptivePELE/analysis/plotSpawningClusters.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,403   copying AdaptivePELE/analysis/plotRMSF.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,404   copying AdaptivePELE/analysis/plotAdaptive.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,404   copying AdaptivePELE/analysis/plot3DNetwork.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,405   copying AdaptivePELE/analysis/pathwayRMSD.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,405   copying AdaptivePELE/analysis/numberOfClusters.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,406   copying AdaptivePELE/analysis/networkCM.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,406   copying AdaptivePELE/analysis/makeRMSDClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,407   copying AdaptivePELE/analysis/makePNGs.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,407   copying AdaptivePELE/analysis/interactivePlot.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,408   copying AdaptivePELE/analysis/identifyClusterSnapshot.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,408   copying AdaptivePELE/analysis/histCM.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,409   copying AdaptivePELE/analysis/generateBox.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,409   copying AdaptivePELE/analysis/foldersFirstBindingEvent.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,410   copying AdaptivePELE/analysis/findfirstbindingevent.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,410   copying AdaptivePELE/analysis/filter_by_radius.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,411   copying AdaptivePELE/analysis/extract_ligand_traj.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,411   copying AdaptivePELE/analysis/dehidratate_and_align.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,412   copying AdaptivePELE/analysis/crossValidationClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,412   copying AdaptivePELE/analysis/count_clusters.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,413   copying AdaptivePELE/analysis/correctRMSD.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,413   copying AdaptivePELE/analysis/convertTrajectory.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,414   copying AdaptivePELE/analysis/compareClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,414   copying AdaptivePELE/analysis/clusters_lagtime_grid.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,415   copying AdaptivePELE/analysis/clusterAdaptiveRun.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,415   copying AdaptivePELE/analysis/cluster.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,416   copying AdaptivePELE/analysis/calculateSASAvalues.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,416   copying AdaptivePELE/analysis/calculateDistances.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,417   copying AdaptivePELE/analysis/bestStructs.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,417   copying AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,418   copying AdaptivePELE/analysis/autoCorrelation.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,419   copying AdaptivePELE/analysis/analysis_utils.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,419   copying AdaptivePELE/analysis/analyseClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,420   copying AdaptivePELE/analysis/analyse.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,420   copying AdaptivePELE/analysis/addRejectedSteps.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,421   copying AdaptivePELE/analysis/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis
2025-10-17T21:15:27,428   running build_ext
2025-10-17T21:15:28,044   Compiling AdaptivePELE/atomset/atomset.pyx because it changed.
2025-10-17T21:15:28,044   [1/1] Cythonizing AdaptivePELE/atomset/atomset.pyx
2025-10-17T21:15:31,585   warning: AdaptivePELE/atomset/atomset.pyx:265:46: Item lookup of unicode character codes now always converts to a Unicode string. Use an explicit C integer cast to get back the previous integer lookup behaviour.
2025-10-17T21:15:31,596   warning: AdaptivePELE/atomset/atomset.pyx:317:42: Item lookup of unicode character codes now always converts to a Unicode string. Use an explicit C integer cast to get back the previous integer lookup behaviour.
2025-10-17T21:15:32,736   building 'AdaptivePELE.atomset.atomset' extension
2025-10-17T21:15:32,737   creating build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset
2025-10-17T21:15:32,738   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -IAdaptivePELE -IAdaptivePELE/atomset -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c AdaptivePELE/atomset/atomset.c -o build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset/atomset.o
2025-10-17T21:16:16,799   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset/atomset.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/atomset.cpython-313-arm-linux-gnueabihf.so
2025-10-17T21:16:17,230   Compiling AdaptivePELE/atomset/SymmetryContactMapEvaluator.pyx because it changed.
2025-10-17T21:16:17,231   [1/1] Cythonizing AdaptivePELE/atomset/SymmetryContactMapEvaluator.pyx
2025-10-17T21:16:18,977   building 'AdaptivePELE.atomset.SymmetryContactMapEvaluator' extension
2025-10-17T21:16:18,978   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -IAdaptivePELE -IAdaptivePELE/atomset -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c AdaptivePELE/atomset/SymmetryContactMapEvaluator.c -o build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset/SymmetryContactMapEvaluator.o
2025-10-17T21:16:37,938   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset/SymmetryContactMapEvaluator.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-313-arm-linux-gnueabihf.so
2025-10-17T21:16:38,077   Compiling AdaptivePELE/atomset/RMSDCalculator.pyx because it changed.
2025-10-17T21:16:38,078   [1/1] Cythonizing AdaptivePELE/atomset/RMSDCalculator.pyx
2025-10-17T21:16:39,362   building 'AdaptivePELE.atomset.RMSDCalculator' extension
2025-10-17T21:16:39,362   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -IAdaptivePELE -IAdaptivePELE/atomset -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c AdaptivePELE/atomset/RMSDCalculator.c -o build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset/RMSDCalculator.o
2025-10-17T21:16:49,216   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset/RMSDCalculator.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/RMSDCalculator.cpython-313-arm-linux-gnueabihf.so
2025-10-17T21:16:49,446   Compiling AdaptivePELE/freeEnergies/utils.pyx because it changed.
2025-10-17T21:16:49,446   [1/1] Cythonizing AdaptivePELE/freeEnergies/utils.pyx
2025-10-17T21:16:53,896   building 'AdaptivePELE.freeEnergies.utils' extension
2025-10-17T21:16:53,897   creating build/temp.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies
2025-10-17T21:16:53,897   arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -IAdaptivePELE -IAdaptivePELE/freeEnergies -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c AdaptivePELE/freeEnergies/utils.c -o build/temp.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/utils.o
2025-10-17T21:17:18,915   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/utils.cpython-313-arm-linux-gnueabihf.so
2025-10-17T21:17:19,207   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-10-17T21:17:19,207   !!

2025-10-17T21:17:19,207           ********************************************************************************
2025-10-17T21:17:19,207           Please avoid running ``setup.py`` directly.
2025-10-17T21:17:19,208           Instead, use pypa/build, pypa/installer or other
2025-10-17T21:17:19,208           standards-based tools.

2025-10-17T21:17:19,208           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-10-17T21:17:19,208           or your builds will no longer be supported.

2025-10-17T21:17:19,208           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-10-17T21:17:19,208           ********************************************************************************

2025-10-17T21:17:19,209   !!
2025-10-17T21:17:19,209     self.initialize_options()
2025-10-17T21:17:19,284   installing to build/bdist.linux-armv7l/wheel
2025-10-17T21:17:19,284   running install
2025-10-17T21:17:19,307   running install_lib
2025-10-17T21:17:19,383   creating build/bdist.linux-armv7l/wheel
2025-10-17T21:17:19,384   creating build/bdist.linux-armv7l/wheel/AdaptivePELE
2025-10-17T21:17:19,384   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2025-10-17T21:17:19,385   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,385   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/addRejectedSteps.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,385   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/analyse.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,386   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/analyseClustering.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,386   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/analysis_utils.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,386   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/autoCorrelation.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,387   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,387   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/bestStructs.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,388   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/calculateDistances.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,388   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/calculateSASAvalues.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,388   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/cluster.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,389   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/clusterAdaptiveRun.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,389   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/clusters_lagtime_grid.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,390   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/compareClustering.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,390   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/convertTrajectory.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,390   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/correctRMSD.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,391   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/count_clusters.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,391   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/crossValidationClustering.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,392   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/dehidratate_and_align.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,392   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/extract_ligand_traj.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,392   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/filter_by_radius.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,393   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/findfirstbindingevent.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,393   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/foldersFirstBindingEvent.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,393   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/generateBox.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,394   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/histCM.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,394   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/identifyClusterSnapshot.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,395   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/interactivePlot.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,395   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/makePNGs.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,395   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/makeRMSDClustering.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,396   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/networkCM.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,396   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/numberOfClusters.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,396   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/pathwayRMSD.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,397   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/plot3DNetwork.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,397   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/plotAdaptive.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,398   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/plotRMSF.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,398   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/plotSpawningClusters.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,398   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/reportSimulation.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,399   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/selectOnPlot.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,399   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/simple_postprocessing.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,400   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/simulationToCsv.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,400   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/splitTrajectory.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,400   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/standarize_MD_energies.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,401   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/trajectory_processing.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,401   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/unbinding.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,401   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/writeClusteringStructures.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,402   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/writeNetworkFiles.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,402   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis/writeTrajToSnapshot.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/analysis
2025-10-17T21:17:19,403   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/atomset
2025-10-17T21:17:19,403   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/RMSDCalculator.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/atomset
2025-10-17T21:17:19,405   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/atomset
2025-10-17T21:17:19,409   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/atomset.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/atomset
2025-10-17T21:17:19,417   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/atomset
2025-10-17T21:17:19,417   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset/setup.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/atomset
2025-10-17T21:17:19,418   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/clustering
2025-10-17T21:17:19,418   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/clustering
2025-10-17T21:17:19,418   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering/clustering.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/clustering
2025-10-17T21:17:19,419   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering/clusteringTypes.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/clustering
2025-10-17T21:17:19,420   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering/thresholdcalculator.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/clustering
2025-10-17T21:17:19,420   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering/thresholdcalculatortypes.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/clustering
2025-10-17T21:17:19,421   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/constants
2025-10-17T21:17:19,421   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/constants
2025-10-17T21:17:19,421   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants/blockNames.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/constants
2025-10-17T21:17:19,422   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants/buildEnvironments.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/constants
2025-10-17T21:17:19,422   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants/constants.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/constants
2025-10-17T21:17:19,422   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants/symmetries.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/constants
2025-10-17T21:17:19,423   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2025-10-17T21:17:19,423   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/utils.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,428   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,428   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,429   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/calculateDGiterations.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,429   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/checkDetailedBalance.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,429   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/cluster.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,430   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/computeDGGrid.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,430   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/computeDeltaG.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,431   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/estimate.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,431   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/estimateDG.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,431   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/estimateDGAdaptive.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,432   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/extendTrajectories.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,432   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/extractCoords.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,433   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/getRepresentativeStructures.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,433   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/ownBuildMSM.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,433   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/prepareMSMFolders.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,434   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/runMarkovChainModel.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,434   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/utilitiesFreeEnergies.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,434   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/freeEnergies
2025-10-17T21:17:19,435   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/simulation
2025-10-17T21:17:19,435   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/simulation
2025-10-17T21:17:19,436   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation/openmm_simulations.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/simulation
2025-10-17T21:17:19,436   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation/simulationTypes.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/simulation
2025-10-17T21:17:19,437   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation/simulationrunner.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/simulation
2025-10-17T21:17:19,437   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/spawning
2025-10-17T21:17:19,438   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/spawning
2025-10-17T21:17:19,438   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning/densitycalculator.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/spawning
2025-10-17T21:17:19,439   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning/densitycalculatortypes.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/spawning
2025-10-17T21:17:19,439   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning/spawning.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/spawning
2025-10-17T21:17:19,440   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning/spawningTypes.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/spawning
2025-10-17T21:17:19,440   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2025-10-17T21:17:19,441   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,441   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testAdaptiveSampling.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,441   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testAtomset.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,442   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testClustering.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,442   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testDensityCalculator.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,443   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testMD.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,443   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testMD_CUDA.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,443   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testReporter.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,444   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testSimulationRunner.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,444   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testSpawning.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,444   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests/testThresholdcalculator.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/tests
2025-10-17T21:17:19,445   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2025-10-17T21:17:19,445   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities/PDBLoader.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/utilities
2025-10-17T21:17:19,446   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/utilities
2025-10-17T21:17:19,446   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities/clusteringUtilities.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/utilities
2025-10-17T21:17:19,447   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities/conda_deployment.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/utilities
2025-10-17T21:17:19,447   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities/generate_topology_object.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/utilities
2025-10-17T21:17:19,447   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities/synchronization.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/utilities
2025-10-17T21:17:19,448   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities/utilities.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/utilities
2025-10-17T21:17:19,448   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/validator
2025-10-17T21:17:19,449   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/validator
2025-10-17T21:17:19,449   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator/controlFileValidator.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/validator
2025-10-17T21:17:19,449   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator/validatorBlockNames.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE/validator
2025-10-17T21:17:19,450   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/__init__.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE
2025-10-17T21:17:19,450   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/adaptiveSampling.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE
2025-10-17T21:17:19,451   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/automateRoundsAdaptive.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE
2025-10-17T21:17:19,451   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/makeRelease.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE
2025-10-17T21:17:19,452   copying build/lib.linux-armv7l-cpython-313/AdaptivePELE/runAllTests.py -> build/bdist.linux-armv7l/wheel/./AdaptivePELE
2025-10-17T21:17:19,452   running install_egg_info
2025-10-17T21:17:19,530   running egg_info
2025-10-17T21:17:19,606   writing AdaptivePELE.egg-info/PKG-INFO
2025-10-17T21:17:19,607   writing dependency_links to AdaptivePELE.egg-info/dependency_links.txt
2025-10-17T21:17:19,608   writing requirements to AdaptivePELE.egg-info/requires.txt
2025-10-17T21:17:19,608   writing top-level names to AdaptivePELE.egg-info/top_level.txt
2025-10-17T21:17:19,691   reading manifest file 'AdaptivePELE.egg-info/SOURCES.txt'
2025-10-17T21:17:19,698   reading manifest template 'MANIFEST.in'
2025-10-17T21:17:19,702   warning: no files found matching 'utils*.so' under directory 'AdaptivePELE/freeEnergies'
2025-10-17T21:17:19,702   adding license file 'LICENSE'
2025-10-17T21:17:19,709   writing manifest file 'AdaptivePELE.egg-info/SOURCES.txt'
2025-10-17T21:17:19,710   Copying AdaptivePELE.egg-info to build/bdist.linux-armv7l/wheel/./AdaptivePELE-1.7.4-py3.13.egg-info
2025-10-17T21:17:19,712   running install_scripts
2025-10-17T21:17:19,787   creating build/bdist.linux-armv7l/wheel/adaptivepele-1.7.4.dist-info/WHEEL
2025-10-17T21:17:19,788   creating '/tmp/pip-wheel-_k6gnjxx/adaptivepele-1.7.4-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-17T21:17:19,789   adding 'AdaptivePELE/__init__.py'
2025-10-17T21:17:19,793   adding 'AdaptivePELE/adaptiveSampling.py'
2025-10-17T21:17:19,794   adding 'AdaptivePELE/automateRoundsAdaptive.py'
2025-10-17T21:17:19,795   adding 'AdaptivePELE/makeRelease.py'
2025-10-17T21:17:19,796   adding 'AdaptivePELE/runAllTests.py'
2025-10-17T21:17:19,796   adding 'AdaptivePELE/analysis/__init__.py'
2025-10-17T21:17:19,797   adding 'AdaptivePELE/analysis/addRejectedSteps.py'
2025-10-17T21:17:19,798   adding 'AdaptivePELE/analysis/analyse.py'
2025-10-17T21:17:19,799   adding 'AdaptivePELE/analysis/analyseClustering.py'
2025-10-17T21:17:19,800   adding 'AdaptivePELE/analysis/analysis_utils.py'
2025-10-17T21:17:19,801   adding 'AdaptivePELE/analysis/autoCorrelation.py'
2025-10-17T21:17:19,802   adding 'AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py'
2025-10-17T21:17:19,803   adding 'AdaptivePELE/analysis/bestStructs.py'
2025-10-17T21:17:19,804   adding 'AdaptivePELE/analysis/calculateDistances.py'
2025-10-17T21:17:19,805   adding 'AdaptivePELE/analysis/calculateSASAvalues.py'
2025-10-17T21:17:19,807   adding 'AdaptivePELE/analysis/cluster.py'
2025-10-17T21:17:19,809   adding 'AdaptivePELE/analysis/clusterAdaptiveRun.py'
2025-10-17T21:17:19,810   adding 'AdaptivePELE/analysis/clusters_lagtime_grid.py'
2025-10-17T21:17:19,811   adding 'AdaptivePELE/analysis/compareClustering.py'
2025-10-17T21:17:19,812   adding 'AdaptivePELE/analysis/convertTrajectory.py'
2025-10-17T21:17:19,813   adding 'AdaptivePELE/analysis/correctRMSD.py'
2025-10-17T21:17:19,814   adding 'AdaptivePELE/analysis/count_clusters.py'
2025-10-17T21:17:19,815   adding 'AdaptivePELE/analysis/crossValidationClustering.py'
2025-10-17T21:17:19,815   adding 'AdaptivePELE/analysis/dehidratate_and_align.py'
2025-10-17T21:17:19,816   adding 'AdaptivePELE/analysis/extract_ligand_traj.py'
2025-10-17T21:17:19,817   adding 'AdaptivePELE/analysis/filter_by_radius.py'
2025-10-17T21:17:19,818   adding 'AdaptivePELE/analysis/findfirstbindingevent.py'
2025-10-17T21:17:19,819   adding 'AdaptivePELE/analysis/foldersFirstBindingEvent.py'
2025-10-17T21:17:19,820   adding 'AdaptivePELE/analysis/generateBox.py'
2025-10-17T21:17:19,820   adding 'AdaptivePELE/analysis/histCM.py'
2025-10-17T21:17:19,821   adding 'AdaptivePELE/analysis/identifyClusterSnapshot.py'
2025-10-17T21:17:19,823   adding 'AdaptivePELE/analysis/interactivePlot.py'
2025-10-17T21:17:19,824   adding 'AdaptivePELE/analysis/makePNGs.py'
2025-10-17T21:17:19,825   adding 'AdaptivePELE/analysis/makeRMSDClustering.py'
2025-10-17T21:17:19,826   adding 'AdaptivePELE/analysis/networkCM.py'
2025-10-17T21:17:19,827   adding 'AdaptivePELE/analysis/numberOfClusters.py'
2025-10-17T21:17:19,828   adding 'AdaptivePELE/analysis/pathwayRMSD.py'
2025-10-17T21:17:19,829   adding 'AdaptivePELE/analysis/plot3DNetwork.py'
2025-10-17T21:17:19,830   adding 'AdaptivePELE/analysis/plotAdaptive.py'
2025-10-17T21:17:19,831   adding 'AdaptivePELE/analysis/plotRMSF.py'
2025-10-17T21:17:19,832   adding 'AdaptivePELE/analysis/plotSpawningClusters.py'
2025-10-17T21:17:19,833   adding 'AdaptivePELE/analysis/reportSimulation.py'
2025-10-17T21:17:19,835   adding 'AdaptivePELE/analysis/selectOnPlot.py'
2025-10-17T21:17:19,836   adding 'AdaptivePELE/analysis/simple_postprocessing.py'
2025-10-17T21:17:19,837   adding 'AdaptivePELE/analysis/simulationToCsv.py'
2025-10-17T21:17:19,837   adding 'AdaptivePELE/analysis/splitTrajectory.py'
2025-10-17T21:17:19,838   adding 'AdaptivePELE/analysis/standarize_MD_energies.py'
2025-10-17T21:17:19,839   adding 'AdaptivePELE/analysis/trajectory_processing.py'
2025-10-17T21:17:19,840   adding 'AdaptivePELE/analysis/unbinding.py'
2025-10-17T21:17:19,841   adding 'AdaptivePELE/analysis/writeClusteringStructures.py'
2025-10-17T21:17:19,841   adding 'AdaptivePELE/analysis/writeNetworkFiles.py'
2025-10-17T21:17:19,842   adding 'AdaptivePELE/analysis/writeTrajToSnapshot.py'
2025-10-17T21:17:19,946   adding 'AdaptivePELE/atomset/RMSDCalculator.cpython-313-arm-linux-gnueabihf.so'
2025-10-17T21:17:20,130   adding 'AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-313-arm-linux-gnueabihf.so'
2025-10-17T21:17:20,136   adding 'AdaptivePELE/atomset/__init__.py'
2025-10-17T21:17:20,515   adding 'AdaptivePELE/atomset/atomset.cpython-313-arm-linux-gnueabihf.so'
2025-10-17T21:17:20,529   adding 'AdaptivePELE/atomset/setup.py'
2025-10-17T21:17:20,529   adding 'AdaptivePELE/clustering/__init__.py'
2025-10-17T21:17:20,538   adding 'AdaptivePELE/clustering/clustering.py'
2025-10-17T21:17:20,539   adding 'AdaptivePELE/clustering/clusteringTypes.py'
2025-10-17T21:17:20,540   adding 'AdaptivePELE/clustering/thresholdcalculator.py'
2025-10-17T21:17:20,541   adding 'AdaptivePELE/clustering/thresholdcalculatortypes.py'
2025-10-17T21:17:20,541   adding 'AdaptivePELE/constants/__init__.py'
2025-10-17T21:17:20,542   adding 'AdaptivePELE/constants/blockNames.py'
2025-10-17T21:17:20,543   adding 'AdaptivePELE/constants/buildEnvironments.py'
2025-10-17T21:17:20,544   adding 'AdaptivePELE/constants/constants.py'
2025-10-17T21:17:20,545   adding 'AdaptivePELE/constants/symmetries.py'
2025-10-17T21:17:20,545   adding 'AdaptivePELE/freeEnergies/__init__.py'
2025-10-17T21:17:20,546   adding 'AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py'
2025-10-17T21:17:20,547   adding 'AdaptivePELE/freeEnergies/calculateDGiterations.py'
2025-10-17T21:17:20,548   adding 'AdaptivePELE/freeEnergies/checkDetailedBalance.py'
2025-10-17T21:17:20,549   adding 'AdaptivePELE/freeEnergies/cluster.py'
2025-10-17T21:17:20,550   adding 'AdaptivePELE/freeEnergies/computeDGGrid.py'
2025-10-17T21:17:20,552   adding 'AdaptivePELE/freeEnergies/computeDeltaG.py'
2025-10-17T21:17:20,553   adding 'AdaptivePELE/freeEnergies/estimate.py'
2025-10-17T21:17:20,554   adding 'AdaptivePELE/freeEnergies/estimateDG.py'
2025-10-17T21:17:20,555   adding 'AdaptivePELE/freeEnergies/estimateDGAdaptive.py'
2025-10-17T21:17:20,556   adding 'AdaptivePELE/freeEnergies/extendTrajectories.py'
2025-10-17T21:17:20,560   adding 'AdaptivePELE/freeEnergies/extractCoords.py'
2025-10-17T21:17:20,561   adding 'AdaptivePELE/freeEnergies/getRepresentativeStructures.py'
2025-10-17T21:17:20,561   adding 'AdaptivePELE/freeEnergies/ownBuildMSM.py'
2025-10-17T21:17:20,562   adding 'AdaptivePELE/freeEnergies/prepareMSMFolders.py'
2025-10-17T21:17:20,564   adding 'AdaptivePELE/freeEnergies/runMarkovChainModel.py'
2025-10-17T21:17:20,564   adding 'AdaptivePELE/freeEnergies/utilitiesFreeEnergies.py'
2025-10-17T21:17:20,808   adding 'AdaptivePELE/freeEnergies/utils.cpython-313-arm-linux-gnueabihf.so'
2025-10-17T21:17:20,816   adding 'AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py'
2025-10-17T21:17:20,817   adding 'AdaptivePELE/simulation/__init__.py'
2025-10-17T21:17:20,821   adding 'AdaptivePELE/simulation/openmm_simulations.py'
2025-10-17T21:17:20,822   adding 'AdaptivePELE/simulation/simulationTypes.py'
2025-10-17T21:17:20,830   adding 'AdaptivePELE/simulation/simulationrunner.py'
2025-10-17T21:17:20,831   adding 'AdaptivePELE/spawning/__init__.py'
2025-10-17T21:17:20,832   adding 'AdaptivePELE/spawning/densitycalculator.py'
2025-10-17T21:17:20,833   adding 'AdaptivePELE/spawning/densitycalculatortypes.py'
2025-10-17T21:17:20,838   adding 'AdaptivePELE/spawning/spawning.py'
2025-10-17T21:17:20,839   adding 'AdaptivePELE/spawning/spawningTypes.py'
2025-10-17T21:17:20,840   adding 'AdaptivePELE/tests/__init__.py'
2025-10-17T21:17:20,841   adding 'AdaptivePELE/tests/testAdaptiveSampling.py'
2025-10-17T21:17:20,843   adding 'AdaptivePELE/tests/testAtomset.py'
2025-10-17T21:17:20,844   adding 'AdaptivePELE/tests/testClustering.py'
2025-10-17T21:17:20,845   adding 'AdaptivePELE/tests/testDensityCalculator.py'
2025-10-17T21:17:20,846   adding 'AdaptivePELE/tests/testMD.py'
2025-10-17T21:17:20,846   adding 'AdaptivePELE/tests/testMD_CUDA.py'
2025-10-17T21:17:20,847   adding 'AdaptivePELE/tests/testReporter.py'
2025-10-17T21:17:20,848   adding 'AdaptivePELE/tests/testSimulationRunner.py'
2025-10-17T21:17:20,849   adding 'AdaptivePELE/tests/testSpawning.py'
2025-10-17T21:17:20,850   adding 'AdaptivePELE/tests/testThresholdcalculator.py'
2025-10-17T21:17:20,853   adding 'AdaptivePELE/utilities/PDBLoader.py'
2025-10-17T21:17:20,854   adding 'AdaptivePELE/utilities/__init__.py'
2025-10-17T21:17:20,854   adding 'AdaptivePELE/utilities/clusteringUtilities.py'
2025-10-17T21:17:20,855   adding 'AdaptivePELE/utilities/conda_deployment.py'
2025-10-17T21:17:20,855   adding 'AdaptivePELE/utilities/generate_topology_object.py'
2025-10-17T21:17:20,857   adding 'AdaptivePELE/utilities/synchronization.py'
2025-10-17T21:17:20,860   adding 'AdaptivePELE/utilities/utilities.py'
2025-10-17T21:17:20,861   adding 'AdaptivePELE/validator/__init__.py'
2025-10-17T21:17:20,862   adding 'AdaptivePELE/validator/controlFileValidator.py'
2025-10-17T21:17:20,863   adding 'AdaptivePELE/validator/validatorBlockNames.py'
2025-10-17T21:17:20,864   adding 'adaptivepele-1.7.4.dist-info/licenses/LICENSE'
2025-10-17T21:17:20,865   adding 'adaptivepele-1.7.4.dist-info/METADATA'
2025-10-17T21:17:20,866   adding 'adaptivepele-1.7.4.dist-info/WHEEL'
2025-10-17T21:17:20,866   adding 'adaptivepele-1.7.4.dist-info/top_level.txt'
2025-10-17T21:17:20,868   adding 'adaptivepele-1.7.4.dist-info/RECORD'
2025-10-17T21:17:20,870   removing build/bdist.linux-armv7l/wheel
2025-10-17T21:17:21,625   Building wheel for adaptivepele (setup.py): finished with status 'done'
2025-10-17T21:17:21,647   Created wheel for adaptivepele: filename=adaptivepele-1.7.4-cp313-cp313-linux_armv7l.whl size=2062020 sha256=dcb6b65156c98bf8956db4c30b1c8138952d9d0b32e5f9565d71497106814eeb
2025-10-17T21:17:21,648   Stored in directory: /tmp/pip-ephem-wheel-cache-tq3sxgxz/wheels/1d/f5/c1/8b6d4823582c1061f3ba7309e217e706b729a155aeb632ee90
2025-10-17T21:17:21,661 Successfully built adaptivepele
2025-10-17T21:17:21,667 Removed build tracker: '/tmp/pip-build-tracker-a3pjz482'