2025-09-08T09:13:43,670 Created temporary directory: /tmp/pip-build-tracker-atx2i5_5 2025-09-08T09:13:43,670 Initialized build tracking at /tmp/pip-build-tracker-atx2i5_5 2025-09-08T09:13:43,670 Created build tracker: /tmp/pip-build-tracker-atx2i5_5 2025-09-08T09:13:43,671 Entered build tracker: /tmp/pip-build-tracker-atx2i5_5 2025-09-08T09:13:43,671 Created temporary directory: /tmp/pip-wheel-klp8iah7 2025-09-08T09:13:43,674 Created temporary directory: /tmp/pip-ephem-wheel-cache-ytuoy_w1 2025-09-08T09:13:43,731 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T09:13:43,734 2 location(s) to search for versions of yaff: 2025-09-08T09:13:43,734 * https://pypi.org/simple/yaff/ 2025-09-08T09:13:43,734 * https://www.piwheels.org/simple/yaff/ 2025-09-08T09:13:43,734 Fetching project page and analyzing links: https://pypi.org/simple/yaff/ 2025-09-08T09:13:43,734 Getting page https://pypi.org/simple/yaff/ 2025-09-08T09:13:43,735 Found index url https://pypi.org/simple/ 2025-09-08T09:13:43,808 Fetched page https://pypi.org/simple/yaff/ as application/vnd.pypi.simple.v1+json 2025-09-08T09:13:43,809 Found link https://files.pythonhosted.org/packages/c9/f2/047512dde0eb54740406d6a712e96dc03731293ea4cd729be862bf81b6e4/yaff-1.2.0.tar.gz (from https://pypi.org/simple/yaff/), version: 1.2.0 2025-09-08T09:13:43,809 Found link https://files.pythonhosted.org/packages/e5/55/ad679d745f316943d494e44073836d7788cc34877c5d9498b3fb9150c418/yaff-1.3.0.tar.gz (from https://pypi.org/simple/yaff/), version: 1.3.0 2025-09-08T09:13:43,809 Found link https://files.pythonhosted.org/packages/18/d1/80fd22fb23b0991a9f09a7efc0f163d764205bac1eaed4fa6b322a6f7482/yaff-1.4.0.tar.gz (from https://pypi.org/simple/yaff/), version: 1.4.0 2025-09-08T09:13:43,810 Found link https://files.pythonhosted.org/packages/10/fd/8c080b0443c8d200c4dd06378adc1a6877c31c2ecf6f4a41c9be8c73d8a0/yaff-1.4.1.tar.gz (from https://pypi.org/simple/yaff/), version: 1.4.1 2025-09-08T09:13:43,810 Found link https://files.pythonhosted.org/packages/3f/21/6269a78287d1b3efce078e0f81566a9e5d2106655a35b83cc2b35eab69e7/yaff-1.4.2.tar.gz (from https://pypi.org/simple/yaff/), version: 1.4.2 2025-09-08T09:13:43,810 Fetching project page and analyzing links: https://www.piwheels.org/simple/yaff/ 2025-09-08T09:13:43,810 Getting page https://www.piwheels.org/simple/yaff/ 2025-09-08T09:13:43,811 Found index url https://www.piwheels.org/simple/ 2025-09-08T09:13:43,904 Fetched page https://www.piwheels.org/simple/yaff/ as text/html 2025-09-08T09:13:43,910 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.2-cp35-cp35m-linux_armv7l.whl#sha256=05eeae8318b3bf4a5161fdecb47dc62633b3977a877445f48901fba4d349fa94 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,910 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.2-cp35-cp35m-linux_armv6l.whl#sha256=05eeae8318b3bf4a5161fdecb47dc62633b3977a877445f48901fba4d349fa94 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,910 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.2-cp37-cp37m-linux_armv6l.whl#sha256=34b102088d7f75b099d713c83f48230bad7356bda4047a4970465151b3d3045d (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,910 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.2-cp37-cp37m-linux_armv7l.whl#sha256=34b102088d7f75b099d713c83f48230bad7356bda4047a4970465151b3d3045d (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.2-cp39-cp39-linux_armv6l.whl#sha256=9b0058e42bbfc37e4e09b5e25437de94436624c799a0915e1c7fac3195c2ad09 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.2-cp39-cp39-linux_armv7l.whl#sha256=9b0058e42bbfc37e4e09b5e25437de94436624c799a0915e1c7fac3195c2ad09 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.1-cp37-cp37m-linux_armv7l.whl#sha256=ee39b976fef8e83eaebb43b270fcc7fe279dcae59a1afe3fb071231c58a3f73d (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.1-cp37-cp37m-linux_armv6l.whl#sha256=ee39b976fef8e83eaebb43b270fcc7fe279dcae59a1afe3fb071231c58a3f73d (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.1-cp35-cp35m-linux_armv7l.whl#sha256=2299cea4af208ca4f7fe708aedf1580770206c4ef50adddf03bc79243770b251 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.1-cp35-cp35m-linux_armv6l.whl#sha256=2299cea4af208ca4f7fe708aedf1580770206c4ef50adddf03bc79243770b251 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.1-cp39-cp39-linux_armv6l.whl#sha256=32dd02a0a69308ed168af1cefa72335d7eec599ada71910d97ea22b17dfd4703 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,911 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.1-cp39-cp39-linux_armv7l.whl#sha256=32dd02a0a69308ed168af1cefa72335d7eec599ada71910d97ea22b17dfd4703 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.0-cp37-cp37m-linux_armv7l.whl#sha256=2ea621f98879ef71738a38a79c95c9f10f4f49cf4e3d791c9f6dfe60ddaf1e02 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.0-cp37-cp37m-linux_armv6l.whl#sha256=2ea621f98879ef71738a38a79c95c9f10f4f49cf4e3d791c9f6dfe60ddaf1e02 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.0-cp39-cp39-linux_armv6l.whl#sha256=791724fa64558c54f8b3181c8b84bc2540c74f788528493ae829a996173c200c (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.4.0-cp39-cp39-linux_armv7l.whl#sha256=791724fa64558c54f8b3181c8b84bc2540c74f788528493ae829a996173c200c (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.3.0-cp37-cp37m-linux_armv6l.whl#sha256=321de664d883048ebdcc2058ac271776c195e16e3ccd52b5c99a3efb06ddfe36 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.3.0-cp37-cp37m-linux_armv7l.whl#sha256=321de664d883048ebdcc2058ac271776c195e16e3ccd52b5c99a3efb06ddfe36 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.3.0-cp35-cp35m-linux_armv7l.whl#sha256=fd1021a4087710d708884595b480e84cabb77750568fc9624d0967670c7c7cce (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,912 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.3.0-cp35-cp35m-linux_armv6l.whl#sha256=fd1021a4087710d708884595b480e84cabb77750568fc9624d0967670c7c7cce (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,913 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.3.0-cp39-cp39-linux_armv6l.whl#sha256=b7d58b67c3e944f93f1d908241a4438f074f69a0aecb3624519814faa0e9132c (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,913 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.3.0-cp39-cp39-linux_armv7l.whl#sha256=b7d58b67c3e944f93f1d908241a4438f074f69a0aecb3624519814faa0e9132c (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,913 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.2.0-cp37-cp37m-linux_armv6l.whl#sha256=7fd5902f3f017a76bce6f931cf1f474dc3220aa18e663b8060e578b7ef94907a (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,913 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.2.0-cp37-cp37m-linux_armv7l.whl#sha256=7fd5902f3f017a76bce6f931cf1f474dc3220aa18e663b8060e578b7ef94907a (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,913 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.2.0-cp35-cp35m-linux_armv6l.whl#sha256=0e866c86ae0c7d8de5f473f7d81042a6f686c00ccb586ff5349ecdd5eb147303 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,913 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.2.0-cp35-cp35m-linux_armv7l.whl#sha256=0e866c86ae0c7d8de5f473f7d81042a6f686c00ccb586ff5349ecdd5eb147303 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,914 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.2.0-cp39-cp39-linux_armv6l.whl#sha256=a0834da5b114cd8972c0201df0b08bd9b2b7c81fe36ccadd1e2427262b85f8c6 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,914 Skipping link: No binaries permitted for yaff: https://archive1.piwheels.org/simple/yaff/yaff-1.2.0-cp39-cp39-linux_armv7l.whl#sha256=a0834da5b114cd8972c0201df0b08bd9b2b7c81fe36ccadd1e2427262b85f8c6 (from https://www.piwheels.org/simple/yaff/) 2025-09-08T09:13:43,914 Skipping link: not a file: https://www.piwheels.org/simple/yaff/ 2025-09-08T09:13:43,914 Skipping link: not a file: https://pypi.org/simple/yaff/ 2025-09-08T09:13:43,938 Given no hashes to check 1 links for project 'yaff': discarding no candidates 2025-09-08T09:13:43,939 Collecting yaff==1.4.0 2025-09-08T09:13:43,941 Created temporary directory: /tmp/pip-unpack-x7qbxgib 2025-09-08T09:13:44,093 Downloading yaff-1.4.0.tar.gz (666 kB) 2025-09-08T09:13:44,358 Added yaff==1.4.0 from https://files.pythonhosted.org/packages/18/d1/80fd22fb23b0991a9f09a7efc0f163d764205bac1eaed4fa6b322a6f7482/yaff-1.4.0.tar.gz to build tracker '/tmp/pip-build-tracker-atx2i5_5' 2025-09-08T09:13:44,359 Running setup.py (path:/tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/setup.py) egg_info for package yaff 2025-09-08T09:13:44,359 Created temporary directory: /tmp/pip-pip-egg-info-9l0y1vot 2025-09-08T09:13:44,360 Preparing metadata (setup.py): started 2025-09-08T09:13:44,361 Running command python setup.py egg_info 2025-09-08T09:13:45,305 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:13:45,306 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:13:45,427 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T09:13:45,427 !! 2025-09-08T09:13:45,427 ******************************************************************************** 2025-09-08T09:13:45,427 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T09:13:45,427 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T09:13:45,428 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T09:13:45,428 or your builds will no longer be supported. 2025-09-08T09:13:45,428 ******************************************************************************** 2025-09-08T09:13:45,428 !! 2025-09-08T09:13:45,428 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T09:13:45,845 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:13:45,845 !! 2025-09-08T09:13:45,846 ******************************************************************************** 2025-09-08T09:13:45,846 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:13:45,846 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:13:45,846 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:13:45,846 ******************************************************************************** 2025-09-08T09:13:45,846 !! 2025-09-08T09:13:45,846 self._finalize_license_expression() 2025-09-08T09:13:45,920 Trying to get the version from git describe 2025-09-08T09:13:45,921 Trying to get the version from {} /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/yaff/version.py 2025-09-08T09:13:45,921 Version according to /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/yaff/version.py: 1.4.0 2025-09-08T09:13:45,921 running egg_info 2025-09-08T09:13:45,996 creating /tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info 2025-09-08T09:13:45,996 writing /tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info/PKG-INFO 2025-09-08T09:13:45,997 writing dependency_links to /tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info/dependency_links.txt 2025-09-08T09:13:45,998 writing requirements to /tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info/requires.txt 2025-09-08T09:13:45,998 writing top-level names to /tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info/top_level.txt 2025-09-08T09:13:45,999 writing manifest file '/tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info/SOURCES.txt' 2025-09-08T09:13:46,310 reading manifest file '/tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info/SOURCES.txt' 2025-09-08T09:13:46,311 reading manifest template 'MANIFEST.in' 2025-09-08T09:13:46,312 warning: no files found matching 'README' 2025-09-08T09:13:46,360 warning: no previously-included files matching 'ext.c' found under directory 'yaff' 2025-09-08T09:13:46,368 adding license file 'LICENSE.txt' 2025-09-08T09:13:46,378 writing manifest file '/tmp/pip-pip-egg-info-9l0y1vot/yaff.egg-info/SOURCES.txt' 2025-09-08T09:13:46,521 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T09:13:46,526 Source in /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71 has version 1.4.0, which satisfies requirement yaff==1.4.0 from https://files.pythonhosted.org/packages/18/d1/80fd22fb23b0991a9f09a7efc0f163d764205bac1eaed4fa6b322a6f7482/yaff-1.4.0.tar.gz 2025-09-08T09:13:46,526 Removed yaff==1.4.0 from https://files.pythonhosted.org/packages/18/d1/80fd22fb23b0991a9f09a7efc0f163d764205bac1eaed4fa6b322a6f7482/yaff-1.4.0.tar.gz from build tracker '/tmp/pip-build-tracker-atx2i5_5' 2025-09-08T09:13:46,531 Created temporary directory: /tmp/pip-unpack-34upd3vu 2025-09-08T09:13:46,531 Created temporary directory: /tmp/pip-unpack-nz8si3vr 2025-09-08T09:13:46,532 Building wheels for collected packages: yaff 2025-09-08T09:13:46,533 Created temporary directory: /tmp/pip-wheel-p_aazsgh 2025-09-08T09:13:46,533 DEPRECATION: Building 'yaff' 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 'yaff'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T09:13:46,534 Building wheel for yaff (setup.py): started 2025-09-08T09:13:46,535 Destination directory: /tmp/pip-wheel-p_aazsgh 2025-09-08T09:13:46,535 Running command python setup.py bdist_wheel 2025-09-08T09:13:47,441 Trying to get the version from git describe 2025-09-08T09:13:47,447 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:13:47,447 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:13:47,448 Trying to get the version from {} /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/yaff/version.py 2025-09-08T09:13:47,448 Version according to /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/yaff/version.py: 1.4.0 2025-09-08T09:13:47,568 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T09:13:47,568 !! 2025-09-08T09:13:47,569 ******************************************************************************** 2025-09-08T09:13:47,569 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T09:13:47,569 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T09:13:47,569 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T09:13:47,569 or your builds will no longer be supported. 2025-09-08T09:13:47,569 ******************************************************************************** 2025-09-08T09:13:47,569 !! 2025-09-08T09:13:47,569 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T09:13:48,011 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:13:48,012 !! 2025-09-08T09:13:48,012 ******************************************************************************** 2025-09-08T09:13:48,012 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:13:48,012 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:13:48,012 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:13:48,012 ******************************************************************************** 2025-09-08T09:13:48,012 !! 2025-09-08T09:13:48,012 self._finalize_license_expression() 2025-09-08T09:13:48,014 running bdist_wheel 2025-09-08T09:13:48,305 running build 2025-09-08T09:13:48,305 running build_py 2025-09-08T09:13:48,408 creating build/lib.linux-armv7l-cpython-313/yaff 2025-09-08T09:13:48,409 copying yaff/version.py -> build/lib.linux-armv7l-cpython-313/yaff 2025-09-08T09:13:48,410 copying yaff/system.py -> build/lib.linux-armv7l-cpython-313/yaff 2025-09-08T09:13:48,411 copying yaff/log.py -> build/lib.linux-armv7l-cpython-313/yaff 2025-09-08T09:13:48,412 copying yaff/atselect.py -> build/lib.linux-armv7l-cpython-313/yaff 2025-09-08T09:13:48,413 copying yaff/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff 2025-09-08T09:13:48,414 creating build/lib.linux-armv7l-cpython-313/yaff/test 2025-09-08T09:13:48,414 copying yaff/test/test_system.py -> build/lib.linux-armv7l-cpython-313/yaff/test 2025-09-08T09:13:48,415 copying yaff/test/test_examples.py -> build/lib.linux-armv7l-cpython-313/yaff/test 2025-09-08T09:13:48,416 copying yaff/test/test_atselect.py -> build/lib.linux-armv7l-cpython-313/yaff/test 2025-09-08T09:13:48,417 copying yaff/test/common.py -> build/lib.linux-armv7l-cpython-313/yaff/test 2025-09-08T09:13:48,417 copying yaff/test/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/test 2025-09-08T09:13:48,419 creating build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,419 copying yaff/pes/vlist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,420 copying yaff/pes/scaling.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,421 copying yaff/pes/parameters.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,421 copying yaff/pes/nlist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,422 copying yaff/pes/iclist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,423 copying yaff/pes/generator.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,424 copying yaff/pes/ff.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,425 copying yaff/pes/dlist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,425 copying yaff/pes/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,427 creating build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,427 copying yaff/pes/test/test_vlist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,428 copying yaff/pes/test/test_truncation.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,429 copying yaff/pes/test/test_topology.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,429 copying yaff/pes/test/test_scaling.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,430 copying yaff/pes/test/test_pext.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,431 copying yaff/pes/test/test_parameters.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,432 copying yaff/pes/test/test_pair_pot.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,432 copying yaff/pes/test/test_nlist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,433 copying yaff/pes/test/test_md.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,434 copying yaff/pes/test/test_iclist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,435 copying yaff/pes/test/test_grid.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,435 copying yaff/pes/test/test_generator.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,436 copying yaff/pes/test/test_ewald.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,437 copying yaff/pes/test/test_dlist.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,438 copying yaff/pes/test/test_cell.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,438 copying yaff/pes/test/common.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,439 copying yaff/pes/test/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/pes/test 2025-09-08T09:13:48,440 creating build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,441 copying yaff/sampling/verlet.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,442 copying yaff/sampling/utils.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,442 copying yaff/sampling/trajectory.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,443 copying yaff/sampling/opt.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,444 copying yaff/sampling/nvt.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,445 copying yaff/sampling/npt.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,446 copying yaff/sampling/iterative.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,446 copying yaff/sampling/io.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,447 copying yaff/sampling/harmonic.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,448 copying yaff/sampling/dof.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,449 copying yaff/sampling/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling 2025-09-08T09:13:48,450 creating build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,450 copying yaff/sampling/test/test_verlet.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,451 copying yaff/sampling/test/test_utils.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,452 copying yaff/sampling/test/test_opt.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,452 copying yaff/sampling/test/test_nvt.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,453 copying yaff/sampling/test/test_npt.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,454 copying yaff/sampling/test/test_harmonic.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,454 copying yaff/sampling/test/test_dof.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,455 copying yaff/sampling/test/common.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,456 copying yaff/sampling/test/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/sampling/test 2025-09-08T09:13:48,457 creating build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,457 copying yaff/analysis/utils.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,458 copying yaff/analysis/spectrum.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,459 copying yaff/analysis/rdf.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,460 copying yaff/analysis/pca.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,460 copying yaff/analysis/hook.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,461 copying yaff/analysis/diffusion.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,462 copying yaff/analysis/blav.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,463 copying yaff/analysis/basic.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,463 copying yaff/analysis/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis 2025-09-08T09:13:48,464 creating build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,465 copying yaff/analysis/test/test_spectrum.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,466 copying yaff/analysis/test/test_rdf.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,466 copying yaff/analysis/test/test_diffusion.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,467 copying yaff/analysis/test/test_blav.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,468 copying yaff/analysis/test/test_basic.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,468 copying yaff/analysis/test/common.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,469 copying yaff/analysis/test/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/analysis/test 2025-09-08T09:13:48,470 creating build/lib.linux-armv7l-cpython-313/yaff/tune 2025-09-08T09:13:48,471 copying yaff/tune/transform.py -> build/lib.linux-armv7l-cpython-313/yaff/tune 2025-09-08T09:13:48,471 copying yaff/tune/cost.py -> build/lib.linux-armv7l-cpython-313/yaff/tune 2025-09-08T09:13:48,472 copying yaff/tune/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/tune 2025-09-08T09:13:48,473 creating build/lib.linux-armv7l-cpython-313/yaff/tune/test 2025-09-08T09:13:48,474 copying yaff/tune/test/test_transform.py -> build/lib.linux-armv7l-cpython-313/yaff/tune/test 2025-09-08T09:13:48,474 copying yaff/tune/test/test_cost.py -> build/lib.linux-armv7l-cpython-313/yaff/tune/test 2025-09-08T09:13:48,475 copying yaff/tune/test/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/tune/test 2025-09-08T09:13:48,476 creating build/lib.linux-armv7l-cpython-313/yaff/conversion 2025-09-08T09:13:48,476 copying yaff/conversion/xyz.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion 2025-09-08T09:13:48,477 copying yaff/conversion/gaussian.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion 2025-09-08T09:13:48,478 copying yaff/conversion/dlpoly.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion 2025-09-08T09:13:48,479 copying yaff/conversion/cp2k.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion 2025-09-08T09:13:48,479 copying yaff/conversion/common.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion 2025-09-08T09:13:48,480 copying yaff/conversion/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion 2025-09-08T09:13:48,481 creating build/lib.linux-armv7l-cpython-313/yaff/conversion/test 2025-09-08T09:13:48,481 copying yaff/conversion/test/test_xyz.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion/test 2025-09-08T09:13:48,482 copying yaff/conversion/test/test_gaussian.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion/test 2025-09-08T09:13:48,483 copying yaff/conversion/test/test_dlpoly.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion/test 2025-09-08T09:13:48,484 copying yaff/conversion/test/test_cp2k.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion/test 2025-09-08T09:13:48,484 copying yaff/conversion/test/__init__.py -> build/lib.linux-armv7l-cpython-313/yaff/conversion/test 2025-09-08T09:13:48,485 running egg_info 2025-09-08T09:13:48,558 writing yaff.egg-info/PKG-INFO 2025-09-08T09:13:48,560 writing dependency_links to yaff.egg-info/dependency_links.txt 2025-09-08T09:13:48,561 writing requirements to yaff.egg-info/requires.txt 2025-09-08T09:13:48,561 writing top-level names to yaff.egg-info/top_level.txt 2025-09-08T09:13:48,643 reading manifest file 'yaff.egg-info/SOURCES.txt' 2025-09-08T09:13:48,657 reading manifest template 'MANIFEST.in' 2025-09-08T09:13:48,658 warning: no files found matching 'README' 2025-09-08T09:13:48,705 warning: no previously-included files matching 'ext.c' found under directory 'yaff' 2025-09-08T09:13:48,712 adding license file 'LICENSE.txt' 2025-09-08T09:13:48,724 writing manifest file 'yaff.egg-info/SOURCES.txt' 2025-09-08T09:13:48,727 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'yaff.data.opttest' is absent from the `packages` configuration. 2025-09-08T09:13:48,727 !! 2025-09-08T09:13:48,727 ******************************************************************************** 2025-09-08T09:13:48,727 ############################ 2025-09-08T09:13:48,727 # Package would be ignored # 2025-09-08T09:13:48,727 ############################ 2025-09-08T09:13:48,728 Python recognizes 'yaff.data.opttest' as an importable package[^1], 2025-09-08T09:13:48,728 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:13:48,728 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:13:48,728 package, please make sure that 'yaff.data.opttest' is explicitly added 2025-09-08T09:13:48,728 to the `packages` configuration field. 2025-09-08T09:13:48,728 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:13:48,728 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:13:48,728 instead of `find_packages(...)`/`find:`). 2025-09-08T09:13:48,729 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:13:48,729 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:13:48,729 If you don't want 'yaff.data.opttest' to be distributed and are 2025-09-08T09:13:48,729 already explicitly excluding 'yaff.data.opttest' via 2025-09-08T09:13:48,729 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:13:48,729 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:13:48,729 combination with a more fine grained `package-data` configuration. 2025-09-08T09:13:48,729 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:13:48,730 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:13:48,730 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:13:48,730 even if it does not contain any `.py` files. 2025-09-08T09:13:48,731 On the other hand, currently there is no concept of package data 2025-09-08T09:13:48,731 directory, all directories are treated like packages. 2025-09-08T09:13:48,731 ******************************************************************************** 2025-09-08T09:13:48,732 !! 2025-09-08T09:13:48,732 check.warn(importable) 2025-09-08T09:13:48,732 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'yaff.data.test' is absent from the `packages` configuration. 2025-09-08T09:13:48,732 !! 2025-09-08T09:13:48,732 ******************************************************************************** 2025-09-08T09:13:48,732 ############################ 2025-09-08T09:13:48,732 # Package would be ignored # 2025-09-08T09:13:48,732 ############################ 2025-09-08T09:13:48,732 Python recognizes 'yaff.data.test' as an importable package[^1], 2025-09-08T09:13:48,732 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:13:48,733 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:13:48,733 package, please make sure that 'yaff.data.test' is explicitly added 2025-09-08T09:13:48,733 to the `packages` configuration field. 2025-09-08T09:13:48,733 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:13:48,733 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:13:48,733 instead of `find_packages(...)`/`find:`). 2025-09-08T09:13:48,733 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:13:48,734 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:13:48,734 If you don't want 'yaff.data.test' to be distributed and are 2025-09-08T09:13:48,734 already explicitly excluding 'yaff.data.test' via 2025-09-08T09:13:48,734 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:13:48,734 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:13:48,734 combination with a more fine grained `package-data` configuration. 2025-09-08T09:13:48,734 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:13:48,734 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:13:48,735 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:13:48,735 even if it does not contain any `.py` files. 2025-09-08T09:13:48,735 On the other hand, currently there is no concept of package data 2025-09-08T09:13:48,735 directory, all directories are treated like packages. 2025-09-08T09:13:48,735 ******************************************************************************** 2025-09-08T09:13:48,735 !! 2025-09-08T09:13:48,735 check.warn(importable) 2025-09-08T09:13:48,735 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'yaff.examples' is absent from the `packages` configuration. 2025-09-08T09:13:48,735 !! 2025-09-08T09:13:48,736 ******************************************************************************** 2025-09-08T09:13:48,736 ############################ 2025-09-08T09:13:48,736 # Package would be ignored # 2025-09-08T09:13:48,736 ############################ 2025-09-08T09:13:48,736 Python recognizes 'yaff.examples' as an importable package[^1], 2025-09-08T09:13:48,736 but it is absent from setuptools' `packages` configuration. 2025-09-08T09:13:48,736 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T09:13:48,736 package, please make sure that 'yaff.examples' is explicitly added 2025-09-08T09:13:48,736 to the `packages` configuration field. 2025-09-08T09:13:48,737 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T09:13:48,737 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T09:13:48,737 instead of `find_packages(...)`/`find:`). 2025-09-08T09:13:48,737 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T09:13:48,737 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T09:13:48,737 If you don't want 'yaff.examples' to be distributed and are 2025-09-08T09:13:48,737 already explicitly excluding 'yaff.examples' via 2025-09-08T09:13:48,737 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T09:13:48,737 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T09:13:48,738 combination with a more fine grained `package-data` configuration. 2025-09-08T09:13:48,738 You can read more about "package data files" on setuptools documentation page: 2025-09-08T09:13:48,738 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T09:13:48,738 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T09:13:48,738 even if it does not contain any `.py` files. 2025-09-08T09:13:48,738 On the other hand, currently there is no concept of package data 2025-09-08T09:13:48,738 directory, all directories are treated like packages. 2025-09-08T09:13:48,738 ******************************************************************************** 2025-09-08T09:13:48,739 !! 2025-09-08T09:13:48,739 check.warn(importable) 2025-09-08T09:13:48,742 creating build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,742 copying yaff/data/opttest/DUBXXKHIPWMCDR-UHFFFAOYSA-N-pars-quickff.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,743 copying yaff/data/opttest/DUBXXKHIPWMCDR-UHFFFAOYSA-N.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,744 copying yaff/data/opttest/GZLNXARBGMAZKZ-KVFPUHGPSA-N-pars-quickff.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,745 copying yaff/data/opttest/GZLNXARBGMAZKZ-KVFPUHGPSA-N.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,745 copying yaff/data/opttest/JQWBTFGGAKGQPA-UHFFFAOYSA-N-pars-quickff.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,746 copying yaff/data/opttest/JQWBTFGGAKGQPA-UHFFFAOYSA-N.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,747 copying yaff/data/opttest/QRMPKOFEUHIBNM-ZKCHVHJHSA-N-pars-quickff.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,747 copying yaff/data/opttest/QRMPKOFEUHIBNM-ZKCHVHJHSA-N.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,748 copying yaff/data/opttest/WFZUBZAEFXETBF-UHFFFAOYSA-N-pars-quickff.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,748 copying yaff/data/opttest/WFZUBZAEFXETBF-UHFFFAOYSA-N.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,749 copying yaff/data/opttest/ZPJJOVNASWLIRQ-UHFFFAOYSA-N-pars-quickff.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,750 copying yaff/data/opttest/ZPJJOVNASWLIRQ-UHFFFAOYSA-N.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,750 copying yaff/data/opttest/alpha_quartz.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,751 copying yaff/data/opttest/alpha_quartz_distorted.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,751 copying yaff/data/opttest/cases.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,752 copying yaff/data/opttest/merlonite_debug.pot -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,752 copying yaff/data/opttest/merlonite_fragment.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,753 copying yaff/data/opttest/merlonite_fragment_overbonded.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,754 copying yaff/data/opttest/water_dimer.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/opttest 2025-09-08T09:13:48,754 creating build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,755 copying yaff/data/test/chloro_pos.xyz -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,756 copying yaff/data/test/chloro_vol.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,757 copying yaff/data/test/cp2k-1.ener -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,758 copying yaff/data/test/dlpoly_HISTORY_an1 -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,759 copying yaff/data/test/dlpoly_HISTORY_an2 -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,759 copying yaff/data/test/dlpoly_HISTORY_sam -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,760 copying yaff/data/test/dlpoly_HISTORY_uo -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,761 copying yaff/data/test/gaussian_sioh4_md.log -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,762 copying yaff/data/test/gaussian_sioh4_md.xyz -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,762 copying yaff/data/test/guaianolide.xyz -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,763 copying yaff/data/test/guaianolide_framework_ordered.xyz -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,764 copying yaff/data/test/nobornane.xyz -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,764 copying yaff/data/test/parameters_alkane.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,765 copying yaff/data/test/parameters_bks.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,765 copying yaff/data/test/parameters_fake_d3bj.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,766 copying yaff/data/test/parameters_fake_dampdisp1.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,767 copying yaff/data/test/parameters_fake_exprep1.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,767 copying yaff/data/test/parameters_fake_lj.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,768 copying yaff/data/test/parameters_fake_mm3.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,768 copying yaff/data/test/parameters_fake_qmdffrep.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,769 copying yaff/data/test/parameters_fake_torsion1.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,769 copying yaff/data/test/parameters_fake_torsion2.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,770 copying yaff/data/test/parameters_formaldehyde_cross.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,770 copying yaff/data/test/parameters_formaldehyde_cross_alt.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,771 copying yaff/data/test/parameters_formaldehyde_inversion.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,771 copying yaff/data/test/parameters_formaldehyde_wrong_cross.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,772 copying yaff/data/test/parameters_glycine_fixq.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,772 copying yaff/data/test/parameters_glycine_torsion.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,773 copying yaff/data/test/parameters_nacl.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,773 copying yaff/data/test/parameters_polyene.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,774 copying yaff/data/test/parameters_water.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,774 copying yaff/data/test/parameters_water_bendaharm.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,775 copying yaff/data/test/parameters_water_bendcharm.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,775 copying yaff/data/test/parameters_water_bondcross.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,776 copying yaff/data/test/parameters_water_bondfues.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,776 copying yaff/data/test/parameters_water_bondharm.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,777 copying yaff/data/test/parameters_water_cross.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,777 copying yaff/data/test/parameters_water_dampdisp1.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,778 copying yaff/data/test/parameters_water_dampdisp2.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,778 copying yaff/data/test/parameters_water_exprep1.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,779 copying yaff/data/test/parameters_water_exprep2.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,779 copying yaff/data/test/parameters_water_exprep3.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,780 copying yaff/data/test/parameters_water_fixq.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,780 copying yaff/data/test/parameters_water_fixq_dielectric.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,781 copying yaff/data/test/parameters_water_lj.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,781 copying yaff/data/test/parameters_water_mm3.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,782 copying yaff/data/test/parameters_water_ubharm.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,782 copying yaff/data/test/parameters_water_wrong_cross.txt -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,783 copying yaff/data/test/rhodium_complex_nobornane.xyz -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,783 copying yaff/data/test/water_hessian.chk -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,784 copying yaff/data/test/water_trajectory.xyz -> build/lib.linux-armv7l-cpython-313/yaff/data/test 2025-09-08T09:13:48,784 creating build/lib.linux-armv7l-cpython-313/yaff/examples 2025-09-08T09:13:48,784 copying yaff/examples/.gitignore -> build/lib.linux-armv7l-cpython-313/yaff/examples 2025-09-08T09:13:48,785 creating build/lib.linux-armv7l-cpython-313/yaff/examples/000_overview 2025-09-08T09:13:48,785 copying yaff/examples/000_overview/parameters.txt -> build/lib.linux-armv7l-cpython-313/yaff/examples/000_overview 2025-09-08T09:13:48,786 copying yaff/examples/000_overview/simulation.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/000_overview 2025-09-08T09:13:48,786 copying yaff/examples/000_overview/system.chk -> build/lib.linux-armv7l-cpython-313/yaff/examples/000_overview 2025-09-08T09:13:48,787 creating build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks 2025-09-08T09:13:48,787 copying yaff/examples/001_tutorial_bks/bks.pot -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks 2025-09-08T09:13:48,788 copying yaff/examples/001_tutorial_bks/runall.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks 2025-09-08T09:13:48,788 creating build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/init 2025-09-08T09:13:48,788 copying yaff/examples/001_tutorial_bks/init/mksystem.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/init 2025-09-08T09:13:48,789 copying yaff/examples/001_tutorial_bks/init/rvecs.txt -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/init 2025-09-08T09:13:48,789 copying yaff/examples/001_tutorial_bks/init/struct.xyz -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/init 2025-09-08T09:13:48,790 creating build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/nvt 2025-09-08T09:13:48,790 copying yaff/examples/001_tutorial_bks/nvt/analysis.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/nvt 2025-09-08T09:13:48,791 copying yaff/examples/001_tutorial_bks/nvt/simulation.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/nvt 2025-09-08T09:13:48,791 creating build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/opt 2025-09-08T09:13:48,791 copying yaff/examples/001_tutorial_bks/opt/analysis.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/opt 2025-09-08T09:13:48,792 copying yaff/examples/001_tutorial_bks/opt/simulation.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/001_tutorial_bks/opt 2025-09-08T09:13:48,792 creating build/lib.linux-armv7l-cpython-313/yaff/examples/002_external_trajectory 2025-09-08T09:13:48,793 copying yaff/examples/002_external_trajectory/rdf.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/002_external_trajectory 2025-09-08T09:13:48,793 copying yaff/examples/002_external_trajectory/trajectory.xyz -> build/lib.linux-armv7l-cpython-313/yaff/examples/002_external_trajectory 2025-09-08T09:13:48,794 creating build/lib.linux-armv7l-cpython-313/yaff/examples/003_water_thermostat 2025-09-08T09:13:48,794 copying yaff/examples/003_water_thermostat/md.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/003_water_thermostat 2025-09-08T09:13:48,794 copying yaff/examples/003_water_thermostat/parameters.txt -> build/lib.linux-armv7l-cpython-313/yaff/examples/003_water_thermostat 2025-09-08T09:13:48,795 copying yaff/examples/003_water_thermostat/system.chk -> build/lib.linux-armv7l-cpython-313/yaff/examples/003_water_thermostat 2025-09-08T09:13:48,795 creating build/lib.linux-armv7l-cpython-313/yaff/examples/999_back_propagation 2025-09-08T09:13:48,796 copying yaff/examples/999_back_propagation/bp.py -> build/lib.linux-armv7l-cpython-313/yaff/examples/999_back_propagation 2025-09-08T09:13:48,796 copying yaff/pes/cell.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,797 copying yaff/pes/cell.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,797 copying yaff/pes/cell.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,798 copying yaff/pes/constants.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,799 copying yaff/pes/dlist.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,799 copying yaff/pes/dlist.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,800 copying yaff/pes/dlist.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,800 copying yaff/pes/ewald.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,801 copying yaff/pes/ewald.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,802 copying yaff/pes/ewald.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,802 copying yaff/pes/ext.pyx -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,803 copying yaff/pes/grid.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,804 copying yaff/pes/grid.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,804 copying yaff/pes/grid.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,805 copying yaff/pes/iclist.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,806 copying yaff/pes/iclist.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,806 copying yaff/pes/iclist.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,807 copying yaff/pes/nlist.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,807 copying yaff/pes/nlist.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,808 copying yaff/pes/nlist.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,809 copying yaff/pes/pair_pot.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,810 copying yaff/pes/pair_pot.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,810 copying yaff/pes/pair_pot.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,811 copying yaff/pes/slater.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,812 copying yaff/pes/slater.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,812 copying yaff/pes/slater.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,813 copying yaff/pes/truncation.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,813 copying yaff/pes/truncation.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,814 copying yaff/pes/truncation.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,814 copying yaff/pes/vlist.c -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,815 copying yaff/pes/vlist.h -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,815 copying yaff/pes/vlist.pxd -> build/lib.linux-armv7l-cpython-313/yaff/pes 2025-09-08T09:13:48,819 running build_ext 2025-09-08T09:13:49,316 Compiling yaff/pes/ext.pyx because it changed. 2025-09-08T09:13:49,316 [1/1] Cythonizing yaff/pes/ext.pyx 2025-09-08T09:13:51,182 Error compiling Cython file: 2025-09-08T09:13:51,183 ------------------------------------------------------------ 2025-09-08T09:13:51,183 ... 2025-09-08T09:13:51,183 from __future__ import division 2025-09-08T09:13:51,183 import numpy as np 2025-09-08T09:13:51,184 cimport numpy as np 2025-09-08T09:13:51,184 cimport cell 2025-09-08T09:13:51,184 ^ 2025-09-08T09:13:51,184 ------------------------------------------------------------ 2025-09-08T09:13:51,184 yaff/pes/ext.pyx:37:8: 'cell.pxd' not found 2025-09-08T09:13:51,218 Error compiling Cython file: 2025-09-08T09:13:51,218 ------------------------------------------------------------ 2025-09-08T09:13:51,218 ... 2025-09-08T09:13:51,219 import numpy as np 2025-09-08T09:13:51,219 cimport numpy as np 2025-09-08T09:13:51,219 cimport cell 2025-09-08T09:13:51,219 cimport nlist 2025-09-08T09:13:51,219 ^ 2025-09-08T09:13:51,219 ------------------------------------------------------------ 2025-09-08T09:13:51,220 yaff/pes/ext.pyx:38:8: 'nlist.pxd' not found 2025-09-08T09:13:51,250 Error compiling Cython file: 2025-09-08T09:13:51,250 ------------------------------------------------------------ 2025-09-08T09:13:51,250 ... 2025-09-08T09:13:51,250 import numpy as np 2025-09-08T09:13:51,251 cimport numpy as np 2025-09-08T09:13:51,251 cimport cell 2025-09-08T09:13:51,251 cimport nlist 2025-09-08T09:13:51,251 cimport pair_pot 2025-09-08T09:13:51,251 ^ 2025-09-08T09:13:51,251 ------------------------------------------------------------ 2025-09-08T09:13:51,252 yaff/pes/ext.pyx:39:8: 'pair_pot.pxd' not found 2025-09-08T09:13:51,280 Error compiling Cython file: 2025-09-08T09:13:51,280 ------------------------------------------------------------ 2025-09-08T09:13:51,281 ... 2025-09-08T09:13:51,281 import numpy as np 2025-09-08T09:13:51,281 cimport numpy as np 2025-09-08T09:13:51,281 cimport cell 2025-09-08T09:13:51,281 cimport nlist 2025-09-08T09:13:51,281 cimport pair_pot 2025-09-08T09:13:51,282 cimport ewald 2025-09-08T09:13:51,282 ^ 2025-09-08T09:13:51,282 ------------------------------------------------------------ 2025-09-08T09:13:51,282 yaff/pes/ext.pyx:40:8: 'ewald.pxd' not found 2025-09-08T09:13:51,312 Error compiling Cython file: 2025-09-08T09:13:51,312 ------------------------------------------------------------ 2025-09-08T09:13:51,312 ... 2025-09-08T09:13:51,312 cimport numpy as np 2025-09-08T09:13:51,312 cimport cell 2025-09-08T09:13:51,312 cimport nlist 2025-09-08T09:13:51,313 cimport pair_pot 2025-09-08T09:13:51,313 cimport ewald 2025-09-08T09:13:51,313 cimport dlist 2025-09-08T09:13:51,313 ^ 2025-09-08T09:13:51,313 ------------------------------------------------------------ 2025-09-08T09:13:51,313 yaff/pes/ext.pyx:41:8: 'dlist.pxd' not found 2025-09-08T09:13:51,343 Error compiling Cython file: 2025-09-08T09:13:51,343 ------------------------------------------------------------ 2025-09-08T09:13:51,343 ... 2025-09-08T09:13:51,343 cimport cell 2025-09-08T09:13:51,344 cimport nlist 2025-09-08T09:13:51,344 cimport pair_pot 2025-09-08T09:13:51,344 cimport ewald 2025-09-08T09:13:51,344 cimport dlist 2025-09-08T09:13:51,344 cimport iclist 2025-09-08T09:13:51,344 ^ 2025-09-08T09:13:51,345 ------------------------------------------------------------ 2025-09-08T09:13:51,345 yaff/pes/ext.pyx:42:8: 'iclist.pxd' not found 2025-09-08T09:13:51,374 Error compiling Cython file: 2025-09-08T09:13:51,374 ------------------------------------------------------------ 2025-09-08T09:13:51,375 ... 2025-09-08T09:13:51,375 cimport nlist 2025-09-08T09:13:51,375 cimport pair_pot 2025-09-08T09:13:51,375 cimport ewald 2025-09-08T09:13:51,375 cimport dlist 2025-09-08T09:13:51,375 cimport iclist 2025-09-08T09:13:51,376 cimport vlist 2025-09-08T09:13:51,376 ^ 2025-09-08T09:13:51,376 ------------------------------------------------------------ 2025-09-08T09:13:51,376 yaff/pes/ext.pyx:43:8: 'vlist.pxd' not found 2025-09-08T09:13:51,406 Error compiling Cython file: 2025-09-08T09:13:51,406 ------------------------------------------------------------ 2025-09-08T09:13:51,406 ... 2025-09-08T09:13:51,407 cimport pair_pot 2025-09-08T09:13:51,407 cimport ewald 2025-09-08T09:13:51,407 cimport dlist 2025-09-08T09:13:51,407 cimport iclist 2025-09-08T09:13:51,407 cimport vlist 2025-09-08T09:13:51,407 cimport truncation 2025-09-08T09:13:51,408 ^ 2025-09-08T09:13:51,408 ------------------------------------------------------------ 2025-09-08T09:13:51,408 yaff/pes/ext.pyx:44:8: 'truncation.pxd' not found 2025-09-08T09:13:51,437 Error compiling Cython file: 2025-09-08T09:13:51,438 ------------------------------------------------------------ 2025-09-08T09:13:51,438 ... 2025-09-08T09:13:51,438 cimport ewald 2025-09-08T09:13:51,438 cimport dlist 2025-09-08T09:13:51,438 cimport iclist 2025-09-08T09:13:51,438 cimport vlist 2025-09-08T09:13:51,438 cimport truncation 2025-09-08T09:13:51,438 cimport grid 2025-09-08T09:13:51,438 ^ 2025-09-08T09:13:51,439 ------------------------------------------------------------ 2025-09-08T09:13:51,439 yaff/pes/ext.pyx:45:8: 'grid.pxd' not found 2025-09-08T09:13:51,439 Error compiling Cython file: 2025-09-08T09:13:51,439 ------------------------------------------------------------ 2025-09-08T09:13:51,439 ... 2025-09-08T09:13:51,439 '''Representation of periodic boundary conditions. 2025-09-08T09:13:51,439 0, 1, 2 and 3 dimensional systems are supported. The cell vectors need 2025-09-08T09:13:51,440 not to be orthogonal. 2025-09-08T09:13:51,440 ''' 2025-09-08T09:13:51,440 cdef cell.cell_type* _c_cell 2025-09-08T09:13:51,440 ^ 2025-09-08T09:13:51,440 ------------------------------------------------------------ 2025-09-08T09:13:51,440 yaff/pes/ext.pyx:78:9: 'cell_type' is not a type identifier 2025-09-08T09:13:51,444 Error compiling Cython file: 2025-09-08T09:13:51,444 ------------------------------------------------------------ 2025-09-08T09:13:51,444 ... 2025-09-08T09:13:51,444 # 2025-09-08T09:13:51,444 # Neighbor lists 2025-09-08T09:13:51,444 # 2025-09-08T09:13:51,444 cdef nlist.neigh_row_type _neigh_row_tmp 2025-09-08T09:13:51,445 ^ 2025-09-08T09:13:51,445 ------------------------------------------------------------ 2025-09-08T09:13:51,445 yaff/pes/ext.pyx:352:5: 'neigh_row_type' is not a type identifier 2025-09-08T09:13:51,445 Error compiling Cython file: 2025-09-08T09:13:51,445 ------------------------------------------------------------ 2025-09-08T09:13:51,445 ... 2025-09-08T09:13:51,446 def nlist_build(np.ndarray[double, ndim=2] pos, double rcut, 2025-09-08T09:13:51,446 np.ndarray[long, ndim=1] rmax, 2025-09-08T09:13:51,446 Cell unitcell, np.ndarray[long, ndim=1] status, 2025-09-08T09:13:51,446 np.ndarray[nlist.neigh_row_type, ndim=1] neighs): 2025-09-08T09:13:51,446 ^ 2025-09-08T09:13:51,446 ------------------------------------------------------------ 2025-09-08T09:13:51,446 yaff/pes/ext.pyx:378:33: Invalid type. 2025-09-08T09:13:51,458 Traceback (most recent call last): 2025-09-08T09:13:51,468 File "", line 2, in 2025-09-08T09:13:51,468 exec(compile(''' 2025-09-08T09:13:51,468 ~~~~^^^^^^^^^^^^ 2025-09-08T09:13:51,468 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:13:51,468 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:13:51,468 ...<32 lines>... 2025-09-08T09:13:51,468 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:13:51,468 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:13:51,468 ''' % ('/tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/setup.py',), "", "exec")) 2025-09-08T09:13:51,469 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:13:51,469 File "", line 35, in 2025-09-08T09:13:51,469 File "/tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/setup.py", line 76, in 2025-09-08T09:13:51,469 setup( 2025-09-08T09:13:51,469 ~~~~~^ 2025-09-08T09:13:51,469 name='yaff', 2025-09-08T09:13:51,469 ^^^^^^^^^^^^ 2025-09-08T09:13:51,470 ...<47 lines>... 2025-09-08T09:13:51,470 ], 2025-09-08T09:13:51,470 ^^ 2025-09-08T09:13:51,470 ) 2025-09-08T09:13:51,470 ^ 2025-09-08T09:13:51,470 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T09:13:51,470 return distutils.core.setup(**attrs) 2025-09-08T09:13:51,470 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:13:51,471 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T09:13:51,471 return run_commands(dist) 2025-09-08T09:13:51,471 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T09:13:51,471 dist.run_commands() 2025-09-08T09:13:51,471 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:13:51,471 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T09:13:51,471 self.run_command(cmd) 2025-09-08T09:13:51,471 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T09:13:51,471 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:13:51,472 super().run_command(command) 2025-09-08T09:13:51,472 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:13:51,472 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:13:51,472 cmd_obj.run() 2025-09-08T09:13:51,472 ~~~~~~~~~~~^^ 2025-09-08T09:13:51,472 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T09:13:51,472 self.run_command("build") 2025-09-08T09:13:51,472 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:13:51,473 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T09:13:51,473 self.distribution.run_command(command) 2025-09-08T09:13:51,473 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:13:51,473 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:13:51,473 super().run_command(command) 2025-09-08T09:13:51,473 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:13:51,473 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:13:51,473 cmd_obj.run() 2025-09-08T09:13:51,474 ~~~~~~~~~~~^^ 2025-09-08T09:13:51,474 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T09:13:51,474 self.run_command(cmd_name) 2025-09-08T09:13:51,474 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T09:13:51,474 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T09:13:51,474 self.distribution.run_command(command) 2025-09-08T09:13:51,474 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:13:51,474 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T09:13:51,475 super().run_command(command) 2025-09-08T09:13:51,475 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T09:13:51,475 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T09:13:51,475 cmd_obj.run() 2025-09-08T09:13:51,475 ~~~~~~~~~~~^^ 2025-09-08T09:13:51,475 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-08T09:13:51,475 self.build_extensions() 2025-09-08T09:13:51,475 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:13:51,476 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-08T09:13:51,476 self._build_extensions_serial() 2025-09-08T09:13:51,476 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:13:51,476 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-08T09:13:51,476 self.build_extension(ext) 2025-09-08T09:13:51,476 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T09:13:51,476 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-08T09:13:51,476 new_ext = cythonize( 2025-09-08T09:13:51,476 ~~~~~~~~~^ 2025-09-08T09:13:51,477 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-08T09:13:51,477 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:13:51,477 )[0] 2025-09-08T09:13:51,477 ^ 2025-09-08T09:13:51,477 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-08T09:13:51,477 cythonize_one(*args) 2025-09-08T09:13:51,477 ~~~~~~~~~~~~~^^^^^^^ 2025-09-08T09:13:51,477 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-08T09:13:51,478 raise CompileError(None, pyx_file) 2025-09-08T09:13:51,478 Cython.Compiler.Errors.CompileError: yaff/pes/ext.pyx 2025-09-08T09:13:51,845 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T09:13:51,858 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T09:13:51,858 exec(compile('"'"''"'"''"'"' 2025-09-08T09:13:51,858 # This is -- a caller that pip uses to run setup.py 2025-09-08T09:13:51,858 # 2025-09-08T09:13:51,858 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T09:13:51,858 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T09:13:51,858 # - It provides a clear error message when setuptools is not installed. 2025-09-08T09:13:51,858 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T09:13:51,858 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T09:13:51,858 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T09:13:51,858 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T09:13:51,858 import os, sys, tokenize, traceback 2025-09-08T09:13:51,858 2025-09-08T09:13:51,858 try: 2025-09-08T09:13:51,858 import setuptools 2025-09-08T09:13:51,858 except ImportError: 2025-09-08T09:13:51,858 print( 2025-09-08T09:13:51,858 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T09:13:51,858 "the build environment with exception:", 2025-09-08T09:13:51,858 file=sys.stderr, 2025-09-08T09:13:51,858 ) 2025-09-08T09:13:51,858 traceback.print_exc() 2025-09-08T09:13:51,858 sys.exit(1) 2025-09-08T09:13:51,858 2025-09-08T09:13:51,858 __file__ = %r 2025-09-08T09:13:51,858 sys.argv[0] = __file__ 2025-09-08T09:13:51,858 2025-09-08T09:13:51,858 if os.path.exists(__file__): 2025-09-08T09:13:51,858 filename = __file__ 2025-09-08T09:13:51,858 with tokenize.open(__file__) as f: 2025-09-08T09:13:51,858 setup_py_code = f.read() 2025-09-08T09:13:51,858 else: 2025-09-08T09:13:51,858 filename = "" 2025-09-08T09:13:51,858 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T09:13:51,858 2025-09-08T09:13:51,858 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T09:13:51,858 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-p_aazsgh[/] 2025-09-08T09:13:51,858 [bold magenta]cwd[/]: /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/ 2025-09-08T09:13:51,858 Building wheel for yaff (setup.py): finished with status 'error' 2025-09-08T09:13:51,859 ERROR: Failed building wheel for yaff 2025-09-08T09:13:51,860 Running setup.py clean for yaff 2025-09-08T09:13:51,861 Running command python setup.py clean 2025-09-08T09:13:52,807 Trying to get the version from git describe 2025-09-08T09:13:52,813 fatal: not a git repository (or any parent up to mount point /) 2025-09-08T09:13:52,813 Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). 2025-09-08T09:13:52,814 Trying to get the version from {} /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/yaff/version.py 2025-09-08T09:13:52,814 Version according to /tmp/pip-wheel-klp8iah7/yaff_9b96efe0d1cf434bbc42a42018374e71/yaff/version.py: 1.4.0 2025-09-08T09:13:52,933 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T09:13:52,933 !! 2025-09-08T09:13:52,933 ******************************************************************************** 2025-09-08T09:13:52,933 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T09:13:52,933 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T09:13:52,934 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T09:13:52,934 or your builds will no longer be supported. 2025-09-08T09:13:52,934 ******************************************************************************** 2025-09-08T09:13:52,934 !! 2025-09-08T09:13:52,934 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T09:13:53,363 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T09:13:53,364 !! 2025-09-08T09:13:53,364 ******************************************************************************** 2025-09-08T09:13:53,364 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T09:13:53,364 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-08T09:13:53,364 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T09:13:53,364 ******************************************************************************** 2025-09-08T09:13:53,365 !! 2025-09-08T09:13:53,365 self._finalize_license_expression() 2025-09-08T09:13:53,438 running clean 2025-09-08T09:13:53,588 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T09:13:53,596 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T09:13:53,597 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T09:13:53,597 removing 'build' 2025-09-08T09:13:53,739 Failed to build yaff 2025-09-08T09:13:53,739 ERROR: Failed to build one or more wheels 2025-09-08T09:13:53,740 Exception information: 2025-09-08T09:13:53,740 Traceback (most recent call last): 2025-09-08T09:13:53,740 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T09:13:53,740 status = _inner_run() 2025-09-08T09:13:53,740 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T09:13:53,740 return self.run(options, args) 2025-09-08T09:13:53,740 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T09:13:53,740 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T09:13:53,740 return func(self, options, args) 2025-09-08T09:13:53,740 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T09:13:53,740 raise CommandError("Failed to build one or more wheels") 2025-09-08T09:13:53,740 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T09:13:53,745 Removed build tracker: '/tmp/pip-build-tracker-atx2i5_5'