2025-09-08T13:35:01,051 Created temporary directory: /tmp/pip-build-tracker-hjt814d0 2025-09-08T13:35:01,052 Initialized build tracking at /tmp/pip-build-tracker-hjt814d0 2025-09-08T13:35:01,052 Created build tracker: /tmp/pip-build-tracker-hjt814d0 2025-09-08T13:35:01,052 Entered build tracker: /tmp/pip-build-tracker-hjt814d0 2025-09-08T13:35:01,052 Created temporary directory: /tmp/pip-wheel-m4q2vftq 2025-09-08T13:35:01,055 Created temporary directory: /tmp/pip-ephem-wheel-cache-6hl7swic 2025-09-08T13:35:01,112 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T13:35:01,115 2 location(s) to search for versions of adaptivepele: 2025-09-08T13:35:01,115 * https://pypi.org/simple/adaptivepele/ 2025-09-08T13:35:01,115 * https://www.piwheels.org/simple/adaptivepele/ 2025-09-08T13:35:01,115 Fetching project page and analyzing links: https://pypi.org/simple/adaptivepele/ 2025-09-08T13:35:01,115 Getting page https://pypi.org/simple/adaptivepele/ 2025-09-08T13:35:01,117 Found index url https://pypi.org/simple/ 2025-09-08T13:35:01,266 Fetched page https://pypi.org/simple/adaptivepele/ as application/vnd.pypi.simple.v1+json 2025-09-08T13:35:01,269 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 2025-09-08T13:35:01,270 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 2025-09-08T13:35:01,270 Found link https://files.pythonhosted.org/packages/48/3b/f12bfdcfd7f0fdcb2f58d659ff94c26666767eec4ca8454750a3241c395e/AdaptivePELE-1.6.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.6 2025-09-08T13:35:01,271 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 2025-09-08T13:35:01,271 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 2025-09-08T13:35:01,272 Found link https://files.pythonhosted.org/packages/2b/34/d4545814438fa2992d83f5be0389f6465ab3e542ada0c02f90dbc4cc5695/AdaptivePELE-1.7.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.7 2025-09-08T13:35:01,272 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 2025-09-08T13:35:01,273 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 2025-09-08T13:35:01,273 Fetching project page and analyzing links: https://www.piwheels.org/simple/adaptivepele/ 2025-09-08T13:35:01,274 Getting page https://www.piwheels.org/simple/adaptivepele/ 2025-09-08T13:35:01,276 Found index url https://www.piwheels.org/simple/ 2025-09-08T13:35:01,370 Fetched page https://www.piwheels.org/simple/adaptivepele/ as text/html 2025-09-08T13:35:01,379 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/) 2025-09-08T13:35:01,379 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/) 2025-09-08T13:35:01,379 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/) 2025-09-08T13:35:01,379 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/) 2025-09-08T13:35:01,379 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/) 2025-09-08T13:35:01,380 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/) 2025-09-08T13:35:01,380 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/) 2025-09-08T13:35:01,380 Skipping link: No binaries permitted for adaptivepele: 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https://archive1.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp34-cp34m-linux_armv6l.whl#sha256=803d5b49a0992dd6aab76657a4fd7da709ba29ae19ef407b3c263abcfa9cef71 (from https://www.piwheels.org/simple/adaptivepele/) 2025-09-08T13:35:01,384 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/) 2025-09-08T13:35:01,384 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/) 2025-09-08T13:35:01,384 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/) 2025-09-08T13:35:01,384 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/) 2025-09-08T13:35:01,384 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/) 2025-09-08T13:35:01,384 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/) 2025-09-08T13:35:01,385 Skipping link: not a file: https://www.piwheels.org/simple/adaptivepele/ 2025-09-08T13:35:01,385 Skipping link: not a file: https://pypi.org/simple/adaptivepele/ 2025-09-08T13:35:01,410 Given no hashes to check 1 links for project 'adaptivepele': discarding no candidates 2025-09-08T13:35:01,411 Collecting adaptivepele==1.5.1 2025-09-08T13:35:01,412 Created temporary directory: /tmp/pip-unpack-jxspl_t0 2025-09-08T13:35:01,684 Downloading AdaptivePELE-1.5.1.tar.gz (3.0 MB) 2025-09-08T13:35:02,425 Added adaptivepele==1.5.1 from https://files.pythonhosted.org/packages/33/ee/476a691d254663e61362e5c2754180ff0b92980e6db1afc829265f001706/AdaptivePELE-1.5.1.tar.gz to build tracker '/tmp/pip-build-tracker-hjt814d0' 2025-09-08T13:35:02,426 Running setup.py (path:/tmp/pip-wheel-m4q2vftq/adaptivepele_d18f17c3e7a348ed8aeb83e146beef18/setup.py) egg_info for package adaptivepele 2025-09-08T13:35:02,427 Created temporary directory: /tmp/pip-pip-egg-info-rd1y8p3o 2025-09-08T13:35:02,427 Preparing metadata (setup.py): started 2025-09-08T13:35:02,428 Running command python setup.py egg_info 2025-09-08T13:35:03,802 Warning: 'classifiers' should be a list, got type 'tuple' 2025-09-08T13:35:04,010 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T13:35:04,010 !! 2025-09-08T13:35:04,010 ******************************************************************************** 2025-09-08T13:35:04,010 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T13:35:04,011 License :: OSI Approved :: MIT License 2025-09-08T13:35:04,011 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T13:35:04,011 ******************************************************************************** 2025-09-08T13:35:04,011 !! 2025-09-08T13:35:04,011 self._finalize_license_expression() 2025-09-08T13:35:04,088 running egg_info 2025-09-08T13:35:04,162 creating /tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info 2025-09-08T13:35:04,162 writing /tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info/PKG-INFO 2025-09-08T13:35:04,163 writing dependency_links to /tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info/dependency_links.txt 2025-09-08T13:35:04,164 writing requirements to /tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info/requires.txt 2025-09-08T13:35:04,164 writing top-level names to /tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info/top_level.txt 2025-09-08T13:35:04,165 writing manifest file '/tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info/SOURCES.txt' 2025-09-08T13:35:04,466 reading manifest file '/tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info/SOURCES.txt' 2025-09-08T13:35:04,467 reading manifest template 'MANIFEST.in' 2025-09-08T13:35:04,477 writing manifest file '/tmp/pip-pip-egg-info-rd1y8p3o/AdaptivePELE.egg-info/SOURCES.txt' 2025-09-08T13:35:04,645 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T13:35:04,649 Source in /tmp/pip-wheel-m4q2vftq/adaptivepele_d18f17c3e7a348ed8aeb83e146beef18 has version 1.5.1, which satisfies requirement adaptivepele==1.5.1 from https://files.pythonhosted.org/packages/33/ee/476a691d254663e61362e5c2754180ff0b92980e6db1afc829265f001706/AdaptivePELE-1.5.1.tar.gz 2025-09-08T13:35:04,650 Removed adaptivepele==1.5.1 from https://files.pythonhosted.org/packages/33/ee/476a691d254663e61362e5c2754180ff0b92980e6db1afc829265f001706/AdaptivePELE-1.5.1.tar.gz from build tracker '/tmp/pip-build-tracker-hjt814d0' 2025-09-08T13:35:04,653 Created temporary directory: /tmp/pip-unpack-c4zkwo48 2025-09-08T13:35:04,654 Created temporary directory: /tmp/pip-unpack-ik979o28 2025-09-08T13:35:04,654 Building wheels for collected packages: adaptivepele 2025-09-08T13:35:04,655 Created temporary directory: /tmp/pip-wheel-k1zv_6eq 2025-09-08T13:35:04,655 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 2025-09-08T13:35:04,656 Building wheel for adaptivepele (setup.py): started 2025-09-08T13:35:04,657 Destination directory: /tmp/pip-wheel-k1zv_6eq 2025-09-08T13:35:04,657 Running command python setup.py bdist_wheel 2025-09-08T13:35:06,062 Warning: 'classifiers' should be a list, got type 'tuple' 2025-09-08T13:35:06,276 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T13:35:06,276 !! 2025-09-08T13:35:06,276 ******************************************************************************** 2025-09-08T13:35:06,276 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T13:35:06,276 License :: OSI Approved :: MIT License 2025-09-08T13:35:06,277 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T13:35:06,277 ******************************************************************************** 2025-09-08T13:35:06,277 !! 2025-09-08T13:35:06,277 self._finalize_license_expression() 2025-09-08T13:35:06,277 running bdist_wheel 2025-09-08T13:35:06,658 running build 2025-09-08T13:35:06,658 running build_py 2025-09-08T13:35:06,735 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE 2025-09-08T13:35:06,736 copying AdaptivePELE/makeRelease.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE 2025-09-08T13:35:06,736 copying AdaptivePELE/adaptiveSampling.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE 2025-09-08T13:35:06,737 copying AdaptivePELE/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE 2025-09-08T13:35:06,738 copying AdaptivePELE/automateRoundsAdaptive.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE 2025-09-08T13:35:06,738 copying AdaptivePELE/runAllTests.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE 2025-09-08T13:35:06,739 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,740 copying AdaptivePELE/analysis/writeNetworkFiles.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,740 copying AdaptivePELE/analysis/analyseClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,741 copying AdaptivePELE/analysis/convertTrajectory.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,741 copying AdaptivePELE/analysis/correctRMSD.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,742 copying AdaptivePELE/analysis/writeClusteringStructures.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,742 copying AdaptivePELE/analysis/addRejectedSteps.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,743 copying AdaptivePELE/analysis/analyse.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,743 copying AdaptivePELE/analysis/findfirstbindingevent.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,744 copying AdaptivePELE/analysis/plotSpawningClusters.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,744 copying AdaptivePELE/analysis/plot3DNetwork.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,745 copying AdaptivePELE/analysis/splitTrajectory.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,745 copying AdaptivePELE/analysis/pathwayRMSD.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,746 copying AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,746 copying AdaptivePELE/analysis/numberOfClusters.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,747 copying AdaptivePELE/analysis/plotRMSF.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,747 copying AdaptivePELE/analysis/writeTrajToSnapshot.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,748 copying AdaptivePELE/analysis/compareClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,749 copying AdaptivePELE/analysis/histCM.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,749 copying AdaptivePELE/analysis/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,750 copying AdaptivePELE/analysis/makePNGs.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,750 copying AdaptivePELE/analysis/foldersFirstBindingEvent.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,751 copying AdaptivePELE/analysis/networkCM.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,751 copying AdaptivePELE/analysis/plotAdaptive.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/analysis 2025-09-08T13:35:06,752 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,752 copying AdaptivePELE/freeEnergies/estimate.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,753 copying AdaptivePELE/freeEnergies/getRepresentativeStructures.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,753 copying AdaptivePELE/freeEnergies/extendTrajectories.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,754 copying AdaptivePELE/freeEnergies/extractCoords.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,755 copying AdaptivePELE/freeEnergies/computeDeltaG.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,755 copying AdaptivePELE/freeEnergies/checkDetailedBalance.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,756 copying AdaptivePELE/freeEnergies/calculateDGiterations.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,756 copying AdaptivePELE/freeEnergies/runMarkovChainModel.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,757 copying AdaptivePELE/freeEnergies/estimateDGAdaptive.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,757 copying AdaptivePELE/freeEnergies/prepareMSMFolders.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,758 copying AdaptivePELE/freeEnergies/estimateDG.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,758 copying AdaptivePELE/freeEnergies/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,759 copying AdaptivePELE/freeEnergies/ownBuildMSM.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,759 copying AdaptivePELE/freeEnergies/computeDGGrid.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,760 copying AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,760 copying AdaptivePELE/freeEnergies/cluster.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,761 copying AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/freeEnergies 2025-09-08T13:35:06,762 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator 2025-09-08T13:35:06,762 copying AdaptivePELE/validator/controlFileValidator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator 2025-09-08T13:35:06,762 copying AdaptivePELE/validator/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator 2025-09-08T13:35:06,763 copying AdaptivePELE/validator/validatorBlockNames.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/validator 2025-09-08T13:35:06,764 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants 2025-09-08T13:35:06,764 copying AdaptivePELE/constants/symmetries.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants 2025-09-08T13:35:06,764 copying AdaptivePELE/constants/blockNames.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants 2025-09-08T13:35:06,765 copying AdaptivePELE/constants/constants.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants 2025-09-08T13:35:06,765 copying AdaptivePELE/constants/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/constants 2025-09-08T13:35:06,766 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation 2025-09-08T13:35:06,766 copying AdaptivePELE/simulation/simulationTypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation 2025-09-08T13:35:06,767 copying AdaptivePELE/simulation/simulationrunner.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation 2025-09-08T13:35:06,768 copying AdaptivePELE/simulation/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/simulation 2025-09-08T13:35:06,769 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering 2025-09-08T13:35:06,769 copying AdaptivePELE/clustering/thresholdcalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering 2025-09-08T13:35:06,769 copying AdaptivePELE/clustering/thresholdcalculatortypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering 2025-09-08T13:35:06,770 copying AdaptivePELE/clustering/clusteringTypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering 2025-09-08T13:35:06,770 copying AdaptivePELE/clustering/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering 2025-09-08T13:35:06,771 copying AdaptivePELE/clustering/clustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/clustering 2025-09-08T13:35:06,772 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset 2025-09-08T13:35:06,772 copying AdaptivePELE/atomset/setup.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset 2025-09-08T13:35:06,773 copying AdaptivePELE/atomset/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/atomset 2025-09-08T13:35:06,773 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,774 copying AdaptivePELE/tests/testClustering.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,774 copying AdaptivePELE/tests/testThresholdcalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,775 copying AdaptivePELE/tests/testSpawning.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,775 copying AdaptivePELE/tests/testDensityCalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,776 copying AdaptivePELE/tests/testAdaptiveSampling.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,776 copying AdaptivePELE/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,777 copying AdaptivePELE/tests/testAtomset.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/tests 2025-09-08T13:35:06,778 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities 2025-09-08T13:35:06,778 copying AdaptivePELE/utilities/utilities.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities 2025-09-08T13:35:06,779 copying AdaptivePELE/utilities/clusteringUtilities.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities 2025-09-08T13:35:06,779 copying AdaptivePELE/utilities/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/utilities 2025-09-08T13:35:06,780 creating build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning 2025-09-08T13:35:06,780 copying AdaptivePELE/spawning/spawningTypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning 2025-09-08T13:35:06,781 copying AdaptivePELE/spawning/densitycalculator.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning 2025-09-08T13:35:06,781 copying AdaptivePELE/spawning/spawning.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning 2025-09-08T13:35:06,782 copying AdaptivePELE/spawning/densitycalculatortypes.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning 2025-09-08T13:35:06,782 copying AdaptivePELE/spawning/__init__.py -> build/lib.linux-armv7l-cpython-313/AdaptivePELE/spawning 2025-09-08T13:35:06,789 running build_ext 2025-09-08T13:35:06,797 building 'AdaptivePELE.atomset.atomset' extension 2025-09-08T13:35:06,798 creating build/temp.linux-armv7l-cpython-313/AdaptivePELE/atomset 2025-09-08T13:35:06,798 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 2025-09-08T13:35:07,168 AdaptivePELE/atomset/atomset.c:179:12: fatal error: longintrepr.h: No such file or directory 2025-09-08T13:35:07,169 179 | #include "longintrepr.h" 2025-09-08T13:35:07,169 | ^~~~~~~~~~~~~~~ 2025-09-08T13:35:07,169 compilation terminated. 2025-09-08T13:35:07,172 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T13:35:07,346 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T13:35:07,358 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T13:35:07,358 exec(compile('"'"''"'"''"'"' 2025-09-08T13:35:07,358 # This is -- a caller that pip uses to run setup.py 2025-09-08T13:35:07,358 # 2025-09-08T13:35:07,358 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T13:35:07,358 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T13:35:07,358 # - It provides a clear error message when setuptools is not installed. 2025-09-08T13:35:07,358 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T13:35:07,358 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T13:35:07,358 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T13:35:07,358 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T13:35:07,358 import os, sys, tokenize, traceback 2025-09-08T13:35:07,358 2025-09-08T13:35:07,358 try: 2025-09-08T13:35:07,358 import setuptools 2025-09-08T13:35:07,358 except ImportError: 2025-09-08T13:35:07,358 print( 2025-09-08T13:35:07,358 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T13:35:07,358 "the build environment with exception:", 2025-09-08T13:35:07,358 file=sys.stderr, 2025-09-08T13:35:07,358 ) 2025-09-08T13:35:07,358 traceback.print_exc() 2025-09-08T13:35:07,358 sys.exit(1) 2025-09-08T13:35:07,358 2025-09-08T13:35:07,358 __file__ = %r 2025-09-08T13:35:07,358 sys.argv[0] = __file__ 2025-09-08T13:35:07,358 2025-09-08T13:35:07,358 if os.path.exists(__file__): 2025-09-08T13:35:07,358 filename = __file__ 2025-09-08T13:35:07,358 with tokenize.open(__file__) as f: 2025-09-08T13:35:07,358 setup_py_code = f.read() 2025-09-08T13:35:07,358 else: 2025-09-08T13:35:07,358 filename = "" 2025-09-08T13:35:07,358 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T13:35:07,358 2025-09-08T13:35:07,358 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T13:35:07,358 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-m4q2vftq/adaptivepele_d18f17c3e7a348ed8aeb83e146beef18/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-k1zv_6eq[/] 2025-09-08T13:35:07,358 [bold magenta]cwd[/]: /tmp/pip-wheel-m4q2vftq/adaptivepele_d18f17c3e7a348ed8aeb83e146beef18/ 2025-09-08T13:35:07,358 Building wheel for adaptivepele (setup.py): finished with status 'error' 2025-09-08T13:35:07,359 ERROR: Failed building wheel for adaptivepele 2025-09-08T13:35:07,359 Running setup.py clean for adaptivepele 2025-09-08T13:35:07,360 Running command python setup.py clean 2025-09-08T13:35:08,763 Warning: 'classifiers' should be a list, got type 'tuple' 2025-09-08T13:35:08,978 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T13:35:08,978 !! 2025-09-08T13:35:08,979 ******************************************************************************** 2025-09-08T13:35:08,979 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T13:35:08,979 License :: OSI Approved :: MIT License 2025-09-08T13:35:08,979 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T13:35:08,979 ******************************************************************************** 2025-09-08T13:35:08,979 !! 2025-09-08T13:35:08,979 self._finalize_license_expression() 2025-09-08T13:35:09,056 running clean 2025-09-08T13:35:09,205 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T13:35:09,206 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T13:35:09,209 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T13:35:09,209 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T13:35:09,209 removing 'build' 2025-09-08T13:35:09,376 Failed to build adaptivepele 2025-09-08T13:35:09,377 ERROR: Failed to build one or more wheels 2025-09-08T13:35:09,378 Exception information: 2025-09-08T13:35:09,378 Traceback (most recent call last): 2025-09-08T13:35:09,378 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T13:35:09,378 status = _inner_run() 2025-09-08T13:35:09,378 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T13:35:09,378 return self.run(options, args) 2025-09-08T13:35:09,378 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T13:35:09,378 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T13:35:09,378 return func(self, options, args) 2025-09-08T13:35:09,378 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T13:35:09,378 raise CommandError("Failed to build one or more wheels") 2025-09-08T13:35:09,378 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T13:35:09,383 Removed build tracker: '/tmp/pip-build-tracker-hjt814d0'