2024-04-26T12:20:30,586 Created temporary directory: /tmp/pip-build-tracker-i2xbnau_ 2024-04-26T12:20:30,588 Initialized build tracking at /tmp/pip-build-tracker-i2xbnau_ 2024-04-26T12:20:30,588 Created build tracker: /tmp/pip-build-tracker-i2xbnau_ 2024-04-26T12:20:30,588 Entered build tracker: /tmp/pip-build-tracker-i2xbnau_ 2024-04-26T12:20:30,589 Created temporary directory: /tmp/pip-wheel-z2ft0ko_ 2024-04-26T12:20:30,593 Created temporary directory: /tmp/pip-ephem-wheel-cache-0isdxt5j 2024-04-26T12:20:30,617 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-26T12:20:30,620 2 location(s) to search for versions of pyemma: 2024-04-26T12:20:30,620 * https://pypi.org/simple/pyemma/ 2024-04-26T12:20:30,620 * https://www.piwheels.org/simple/pyemma/ 2024-04-26T12:20:30,621 Fetching project page and analyzing links: https://pypi.org/simple/pyemma/ 2024-04-26T12:20:30,622 Getting page https://pypi.org/simple/pyemma/ 2024-04-26T12:20:30,623 Found index url https://pypi.org/simple/ 2024-04-26T12:20:30,758 Fetched page https://pypi.org/simple/pyemma/ as application/vnd.pypi.simple.v1+json 2024-04-26T12:20:30,767 Found link https://files.pythonhosted.org/packages/8e/31/2c2e23bbc16b404c8808c1043ebaf3aebfdd31dd90b979f213caad01f5bf/pyEMMA-1.0a2.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a2 2024-04-26T12:20:30,767 Found link https://files.pythonhosted.org/packages/1c/e3/453e32e448baa4274c622c82c87862164a34939b5139f4660db1fd470e2c/pyEMMA-1.0a3.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a3 2024-04-26T12:20:30,767 Found link https://files.pythonhosted.org/packages/9d/5a/d614dfaef84835bed7ec482b6fbaf1b94cc6fec0ca1e2f2ada7d3fdb9b7e/pyEMMA-1.0.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0 2024-04-26T12:20:30,768 Found link https://files.pythonhosted.org/packages/a9/99/1cd8cd711306a1b5e1461930de3a5aeea69b20640444db8d5c934b5bf4f5/pyEMMA-1.0.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0.1 2024-04-26T12:20:30,768 Found link https://files.pythonhosted.org/packages/7a/bd/5126cb767a26903e90a4d3679d5cc2a62c4f199aa14f26f1aae5ea4bf4e8/pyEMMA-1.0.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0.2 2024-04-26T12:20:30,768 Found link https://files.pythonhosted.org/packages/c3/28/e677fb5d7f98e1fc80442da7fd5bd56b96738d7c63c5dee64321128d7223/pyEMMA-1.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.1 2024-04-26T12:20:30,768 Found link https://files.pythonhosted.org/packages/67/3c/a2a915fe09e7c9fa2a45b4c7d8d1d95e08210930b7e578d7a3f3b478f652/pyEMMA-1.1.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.1.1 2024-04-26T12:20:30,769 Found link https://files.pythonhosted.org/packages/47/96/218449a170c586187e1de74a06a0c0b09cdd5e1b887b3b79156c8079ca68/pyEMMA-1.1.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.1.2 2024-04-26T12:20:30,769 Found link 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https://pypi.org/simple/pyemma/), version: 2.0.1 2024-04-26T12:20:30,770 Found link https://files.pythonhosted.org/packages/85/dd/02b5a23c7a75bfbfa3654f5455dac18374ba9ab179e092a8e89ed5336091/pyEMMA-2.0.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.0.2 2024-04-26T12:20:30,770 Found link https://files.pythonhosted.org/packages/7f/23/4644bd57de697aeed05a915096b6afc93c17a11ef1e4ecaf0e880e371b30/pyEMMA-2.0.3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.0.3 2024-04-26T12:20:30,771 Found link https://files.pythonhosted.org/packages/c1/04/f0d3459815c08a1740ab4cf48c2ea0044cd11507d6103e45fbc15d7741de/pyEMMA-2.0.4.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.0.4 2024-04-26T12:20:30,771 Found link https://files.pythonhosted.org/packages/92/75/afa9da7a4e730829b583eb1e0851397b9a4775d823721fc9d640cb1812a4/pyemma-2.1rc1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc1 2024-04-26T12:20:30,771 Found link 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https://pypi.org/simple/pyemma/), version: 2.2 2024-04-26T12:20:30,772 Found link https://files.pythonhosted.org/packages/8b/fa/5b40eb124d6c6862b4c51579bb71c0c78f076309869902f3fffb64d257b6/pyEMMA-2.2.1.zip (from https://pypi.org/simple/pyemma/), version: 2.2.1 2024-04-26T12:20:30,773 Found link https://files.pythonhosted.org/packages/fd/9c/91875451360dff2aa4ad4c11f89fa3e79020ce776adef66d80e146d704fc/pyEMMA-2.2.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2.2 2024-04-26T12:20:30,773 Found link https://files.pythonhosted.org/packages/d4/85/6430704c7947a7b01c20f864ffffdbc32c22369c32258051219a6e780596/pyEMMA-2.2.3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2.3 2024-04-26T12:20:30,773 Found link https://files.pythonhosted.org/packages/f5/68/281c3f2eea8a056492e97d89c74848a692f2d5f956d65e29fb315055e663/pyEMMA-2.2.4.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2.4 2024-04-26T12:20:30,774 Found link https://files.pythonhosted.org/packages/21/6d/82871b5b782d6934909144e19d312a319b034e2d9bee366b37a713bcac22/pyEMMA-2.2.6.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2.6 2024-04-26T12:20:30,774 Found link https://files.pythonhosted.org/packages/98/81/3449d189b584c10d0ee52fb46cc0ca2602ff6c444b5be14ef2483eba76e7/pyEMMA-2.2.7.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2.7 2024-04-26T12:20:30,774 Found link https://files.pythonhosted.org/packages/d6/51/799c7406a1b5d6433360be894123ad0e326fd0c2370752d8b386c35cbbb7/pyEMMA-2.3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.3 2024-04-26T12:20:30,774 Found link https://files.pythonhosted.org/packages/94/5f/4553bd29e1acbbfab6693c53e6c8a983094115528a7ef103a905e3bf5bbb/pyEMMA-2.3.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.3.1 2024-04-26T12:20:30,774 Found link https://files.pythonhosted.org/packages/ff/21/6deb0b2673f5d0c6c95838d12006d651e3796b4d497fa908926ba40f2841/pyEMMA-2.3.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.3.2 2024-04-26T12:20:30,775 Found link https://files.pythonhosted.org/packages/45/d1/017a5298d6e67ab777268989c1793eb4d5d0869f366df7f1adf2a36a84e7/pyEMMA-2.4.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.4 2024-04-26T12:20:30,775 Found link https://files.pythonhosted.org/packages/8e/f7/9e5573f5da3d5314dcc79a41e138c5c9a6891bd72b92f9d18b7f59e85ab6/pyEMMA-2.5.zip (from https://pypi.org/simple/pyemma/), version: 2.5 2024-04-26T12:20:30,775 Found link https://files.pythonhosted.org/packages/9c/9c/65d49916d9913a2fd9eb2ae6f54d5fe59ec03c44c47d3706173f71483a6d/pyEMMA-2.5.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.1 2024-04-26T12:20:30,775 Found link https://files.pythonhosted.org/packages/66/f1/b477414811f2eb96e6f4b66a4d2329c4ba32ae5c16333bdfbc51d45ee367/pyEMMA-2.5.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.2 2024-04-26T12:20:30,776 Found link https://files.pythonhosted.org/packages/be/07/b646fa951d631a57d022a79a82a2f28ce268b2b1760d21ffd4df6a4bcc1b/pyEMMA-2.5.3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.3 2024-04-26T12:20:30,776 Found link https://files.pythonhosted.org/packages/b9/06/2ea0e6238158d70462d1d274c48b0e6fecc1296c5a2d31d56a10fbb1ec69/pyEMMA-2.5.4.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.4 2024-04-26T12:20:30,776 Found link https://files.pythonhosted.org/packages/16/67/b086d88f3fdda0263856214dc53484299c0576d749256771b7f15513dcf8/pyEMMA-2.5.5.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.5 2024-04-26T12:20:30,777 Found link https://files.pythonhosted.org/packages/33/9c/bccb53b4377849d7f34a0206e3fe0d70d4062957a634a875ae3754a9c5a8/pyEMMA-2.5.6.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.6 2024-04-26T12:20:30,777 Found link https://files.pythonhosted.org/packages/74/dd/efc917ca0ae55e8ae1930954fa867a4fca868ec9bce43fc4b7db66e40d4b/pyEMMA-2.5.7.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.7 2024-04-26T12:20:30,777 Found link https://files.pythonhosted.org/packages/ef/20/86a0791773019fdd900f3c5cec4bf24fa7f31d23ff8898feed03965bfe08/pyEMMA-2.5.8.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.8 2024-04-26T12:20:30,777 Found link https://files.pythonhosted.org/packages/c4/a5/4dd5a28342db2d7664bfea39afb5945de82ed72ceca7230509b9615e1241/pyEMMA-2.5.9.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.9 2024-04-26T12:20:30,778 Found link https://files.pythonhosted.org/packages/4d/db/a8d56cf87e94b7b1f1b16b68b619b8bcc9cfea9b7527b38f58e6dfc7e227/pyEMMA-2.5.10.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.10 2024-04-26T12:20:30,778 Found link https://files.pythonhosted.org/packages/b8/f0/8453c5a9d5d7f84b3f49f283d200965ae9fd3648e18c450980e0a2faf90b/pyEMMA-2.5.11.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.11 2024-04-26T12:20:30,778 Found link https://files.pythonhosted.org/packages/fb/f2/7bb51bcfad7bd49ab6f86c597fff4ac9a7143dd906e5ed707d9922a7be51/pyEMMA-2.5.12.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.5.12 2024-04-26T12:20:30,778 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyemma/ 2024-04-26T12:20:30,779 Getting page https://www.piwheels.org/simple/pyemma/ 2024-04-26T12:20:30,780 Found index url https://www.piwheels.org/simple/ 2024-04-26T12:20:30,843 Fetched page https://www.piwheels.org/simple/pyemma/ as text/html 2024-04-26T12:20:30,844 Skipping link: not a file: https://www.piwheels.org/simple/pyemma/ 2024-04-26T12:20:30,844 Skipping link: not a file: https://pypi.org/simple/pyemma/ 2024-04-26T12:20:30,866 Given no hashes to check 1 links for project 'pyemma': discarding no candidates 2024-04-26T12:20:30,882 Collecting pyemma==2.1.1 2024-04-26T12:20:30,884 Created temporary directory: /tmp/pip-unpack-_pzex43m 2024-04-26T12:20:31,036 Downloading pyEMMA-2.1.1.tar.gz (669 kB) 2024-04-26T12:20:31,615 Added pyemma==2.1.1 from https://files.pythonhosted.org/packages/79/87/d9d41d3dd1b4048f078935e7a99991680af380ee46798db3635adf99de0a/pyEMMA-2.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-i2xbnau_' 2024-04-26T12:20:31,617 Running setup.py (path:/tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/setup.py) egg_info for package pyemma 2024-04-26T12:20:31,617 Created temporary directory: /tmp/pip-pip-egg-info-sqrt0ljn 2024-04-26T12:20:31,617 Preparing metadata (setup.py): started 2024-04-26T12:20:31,618 Running command python setup.py egg_info 2024-04-26T12:20:32,204 /tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T12:20:32,204 from pkg_resources import VersionConflict 2024-04-26T12:20:32,438 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T12:20:32,439 !! 2024-04-26T12:20:32,439 ******************************************************************************** 2024-04-26T12:20:32,439 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T12:20:32,439 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T12:20:32,439 ******************************************************************************** 2024-04-26T12:20:32,440 !! 2024-04-26T12:20:32,440 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T12:35:49,526 running egg_info 2024-04-26T12:35:49,529 creating /tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info 2024-04-26T12:35:49,573 writing /tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info/PKG-INFO 2024-04-26T12:35:49,579 writing dependency_links to /tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info/dependency_links.txt 2024-04-26T12:35:49,582 writing requirements to /tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info/requires.txt 2024-04-26T12:35:49,606 creating /tmp/hasfunction-b20wz322/tmp 2024-04-26T12:35:49,606 creating /tmp/hasfunction-b20wz322/tmp/hasfunction-b20wz322 2024-04-26T12:35:49,607 cc -c /tmp/hasfunction-b20wz322/funcname.c -o /tmp/hasfunction-b20wz322/tmp/hasfunction-b20wz322/funcname.o 2024-04-26T12:35:49,681 cc /tmp/hasfunction-b20wz322/tmp/hasfunction-b20wz322/funcname.o -o /tmp/hasfunction-b20wz322/a.out 2024-04-26T12:35:49,782 creating /tmp/hasfunction-_3zv8qhy/tmp 2024-04-26T12:35:49,782 creating /tmp/hasfunction-_3zv8qhy/tmp/hasfunction-_3zv8qhy 2024-04-26T12:35:49,783 cc -c /tmp/hasfunction-_3zv8qhy/funcname.c -o /tmp/hasfunction-_3zv8qhy/tmp/hasfunction-_3zv8qhy/funcname.o 2024-04-26T12:35:49,855 cc /tmp/hasfunction-_3zv8qhy/tmp/hasfunction-_3zv8qhy/funcname.o -lgomp -o /tmp/hasfunction-_3zv8qhy/a.out 2024-04-26T12:35:52,827 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T12:35:52,827 tree = Parsing.p_module(s, pxd, full_module_name) 2024-04-26T12:35:53,776 Compiling pyemma/coordinates/estimators/covar/covar_c/covartools.pyx because it changed. 2024-04-26T12:35:53,777 [1/1] Cythonizing pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T12:35:53,777 /tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/setup.py:154: UserWarning: enabled openmp 2024-04-26T12:35:53,777 warnings.warn('enabled openmp') 2024-04-26T12:35:53,777 writing top-level names to /tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info/top_level.txt 2024-04-26T12:35:53,778 writing manifest file '/tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T12:35:53,869 /usr/local/lib/python3.9/dist-packages/setuptools/command/sdist.py:115: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2024-04-26T12:35:53,869 !! 2024-04-26T12:35:53,870 ******************************************************************************** 2024-04-26T12:35:53,870 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2024-04-26T12:35:53,870 Please extend command classes from setuptools instead of distutils. 2024-04-26T12:35:53,870 See https://peps.python.org/pep-0632/ for details. 2024-04-26T12:35:53,870 ******************************************************************************** 2024-04-26T12:35:53,871 !! 2024-04-26T12:35:53,871 self._add_data_files(self._safe_data_files(build_py)) 2024-04-26T12:35:53,907 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:35:53,907 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:35:53,907 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:35:53,907 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:35:53,907 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:35:53,939 reading manifest file '/tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T12:35:53,941 reading manifest template 'MANIFEST.in' 2024-04-26T12:35:54,096 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T12:35:54,098 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T12:35:54,099 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T12:35:54,104 no previously-included directories found matching 'doc/build' 2024-04-26T12:35:54,104 no previously-included directories found matching 'doc/source/generated' 2024-04-26T12:35:54,105 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T12:35:54,106 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T12:35:54,107 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T12:35:54,334 no previously-included directories found matching '.eggs' 2024-04-26T12:35:54,334 adding license file 'LICENSE.txt' 2024-04-26T12:35:54,345 writing manifest file '/tmp/pip-pip-egg-info-sqrt0ljn/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T12:35:54,696 Preparing metadata (setup.py): finished with status 'done' 2024-04-26T12:35:54,701 Source in /tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac has version 2.1.1, which satisfies requirement pyemma==2.1.1 from https://files.pythonhosted.org/packages/79/87/d9d41d3dd1b4048f078935e7a99991680af380ee46798db3635adf99de0a/pyEMMA-2.1.1.tar.gz 2024-04-26T12:35:54,702 Removed pyemma==2.1.1 from https://files.pythonhosted.org/packages/79/87/d9d41d3dd1b4048f078935e7a99991680af380ee46798db3635adf99de0a/pyEMMA-2.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-i2xbnau_' 2024-04-26T12:35:54,707 Created temporary directory: /tmp/pip-unpack-phh9g1ex 2024-04-26T12:35:54,708 Created temporary directory: /tmp/pip-unpack-haso_p9k 2024-04-26T12:35:54,726 Building wheels for collected packages: pyemma 2024-04-26T12:35:54,730 Created temporary directory: /tmp/pip-wheel-twawaqz_ 2024-04-26T12:35:54,730 Building wheel for pyemma (setup.py): started 2024-04-26T12:35:54,731 Destination directory: /tmp/pip-wheel-twawaqz_ 2024-04-26T12:35:54,731 Running command python setup.py bdist_wheel 2024-04-26T12:35:55,298 /tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T12:35:55,299 from pkg_resources import VersionConflict 2024-04-26T12:35:55,523 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T12:35:55,523 !! 2024-04-26T12:35:55,524 ******************************************************************************** 2024-04-26T12:35:55,524 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T12:35:55,524 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T12:35:55,524 ******************************************************************************** 2024-04-26T12:35:55,524 !! 2024-04-26T12:35:55,525 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T12:35:56,526 running bdist_wheel 2024-04-26T12:35:56,602 creating /tmp/hasfunction-t5ego3ys/tmp 2024-04-26T12:35:56,603 creating /tmp/hasfunction-t5ego3ys/tmp/hasfunction-t5ego3ys 2024-04-26T12:35:56,604 cc -c /tmp/hasfunction-t5ego3ys/funcname.c -o /tmp/hasfunction-t5ego3ys/tmp/hasfunction-t5ego3ys/funcname.o 2024-04-26T12:35:56,675 cc /tmp/hasfunction-t5ego3ys/tmp/hasfunction-t5ego3ys/funcname.o -o /tmp/hasfunction-t5ego3ys/a.out 2024-04-26T12:35:56,774 creating /tmp/hasfunction-3ofc4ua7/tmp 2024-04-26T12:35:56,774 creating /tmp/hasfunction-3ofc4ua7/tmp/hasfunction-3ofc4ua7 2024-04-26T12:35:56,775 cc -c /tmp/hasfunction-3ofc4ua7/funcname.c -o /tmp/hasfunction-3ofc4ua7/tmp/hasfunction-3ofc4ua7/funcname.o 2024-04-26T12:35:56,846 cc /tmp/hasfunction-3ofc4ua7/tmp/hasfunction-3ofc4ua7/funcname.o -lgomp -o /tmp/hasfunction-3ofc4ua7/a.out 2024-04-26T12:35:58,354 /tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/setup.py:154: UserWarning: enabled openmp 2024-04-26T12:35:58,354 warnings.warn('enabled openmp') 2024-04-26T12:35:58,416 running build 2024-04-26T12:35:58,417 running build_py 2024-04-26T12:35:58,425 creating build 2024-04-26T12:35:58,425 creating build/lib.linux-armv7l-cpython-39 2024-04-26T12:35:58,426 creating build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T12:35:58,427 copying pyemma/_version.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T12:35:58,429 copying pyemma/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T12:35:58,431 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T12:35:58,432 copying pyemma/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T12:35:58,434 copying pyemma/coordinates/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T12:35:58,437 copying pyemma/coordinates/acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T12:35:58,439 copying pyemma/coordinates/pipelines.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T12:35:58,442 creating build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T12:35:58,442 copying pyemma/datasets/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T12:35:58,444 copying pyemma/datasets/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T12:35:58,446 copying pyemma/datasets/double_well_discrete.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T12:35:58,449 creating build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,450 copying pyemma/util/units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,452 copying pyemma/util/numeric.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,454 copying pyemma/util/annotators.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,456 copying pyemma/util/linalg.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,458 copying pyemma/util/exceptions.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,460 copying pyemma/util/reflection.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,463 copying pyemma/util/discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,465 copying pyemma/util/debug.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,467 copying pyemma/util/contexts.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,469 copying pyemma/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,470 copying pyemma/util/config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,473 copying pyemma/util/types.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,475 copying pyemma/util/statistics.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,477 copying pyemma/util/indices.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,479 copying pyemma/util/files.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,480 copying pyemma/util/log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,482 copying pyemma/util/testing_tools.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T12:35:58,484 creating build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T12:35:58,485 copying pyemma/_base/estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T12:35:58,488 copying pyemma/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T12:35:58,490 copying pyemma/_base/model.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T12:35:58,492 copying pyemma/_base/logging.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T12:35:58,494 creating build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T12:35:58,495 copying pyemma/msm/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T12:35:58,497 copying pyemma/msm/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T12:35:58,501 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T12:35:58,502 copying pyemma/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T12:35:58,504 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T12:35:58,505 copying pyemma/thermo/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T12:35:58,507 copying pyemma/thermo/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T12:35:58,510 creating build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T12:35:58,511 copying pyemma/plots/plots2d.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T12:35:58,513 copying pyemma/plots/markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T12:35:58,515 copying pyemma/plots/timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T12:35:58,518 copying pyemma/plots/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T12:35:58,520 copying pyemma/plots/networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T12:35:58,523 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T12:35:58,524 copying pyemma/coordinates/util/patches.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T12:35:58,526 copying pyemma/coordinates/util/stat.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T12:35:58,528 copying pyemma/coordinates/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T12:35:58,529 copying pyemma/coordinates/util/change_notification.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T12:35:58,532 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T12:35:58,533 copying pyemma/coordinates/data/data_in_memory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T12:35:58,535 copying pyemma/coordinates/data/numpy_filereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T12:35:58,538 copying pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T12:35:58,540 copying pyemma/coordinates/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T12:35:58,542 copying pyemma/coordinates/data/feature_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T12:35:58,545 copying pyemma/coordinates/data/py_csv_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T12:35:58,549 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,550 copying pyemma/coordinates/tests/test_regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,552 copying pyemma/coordinates/tests/test_api_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,555 copying pyemma/coordinates/tests/test_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,557 copying pyemma/coordinates/tests/test_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,560 copying pyemma/coordinates/tests/test_traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,562 copying pyemma/coordinates/tests/test_save_trajs.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,564 copying pyemma/coordinates/tests/test_featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,568 copying pyemma/coordinates/tests/test_api_load.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,569 copying pyemma/coordinates/tests/test_datainmemory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,571 copying pyemma/coordinates/tests/test_coordinates_iterator.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,574 copying pyemma/coordinates/tests/test_frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,576 copying pyemma/coordinates/tests/test_assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,578 copying pyemma/coordinates/tests/test_random_access_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,581 copying pyemma/coordinates/tests/test_pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,583 copying pyemma/coordinates/tests/test_csvreader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,585 copying pyemma/coordinates/tests/test_numpyfilereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,588 copying pyemma/coordinates/tests/test_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,590 copying pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,592 copying pyemma/coordinates/tests/test_featurereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,594 copying pyemma/coordinates/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,596 copying pyemma/coordinates/tests/test_acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,598 copying pyemma/coordinates/tests/test_discretizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,600 copying pyemma/coordinates/tests/test_cluster_samples.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,602 copying pyemma/coordinates/tests/test_save_traj.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,604 copying pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,606 copying pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,607 copying pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,610 copying pyemma/coordinates/tests/test_pipeline.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,612 copying pyemma/coordinates/tests/test_cluster.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,614 copying pyemma/coordinates/tests/test_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,616 copying pyemma/coordinates/tests/test_uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T12:35:58,618 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T12:35:58,619 copying pyemma/coordinates/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T12:35:58,621 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,621 copying pyemma/coordinates/clustering/assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,623 copying pyemma/coordinates/clustering/interface.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,625 copying pyemma/coordinates/clustering/uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,627 copying pyemma/coordinates/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,629 copying pyemma/coordinates/clustering/regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,630 copying pyemma/coordinates/clustering/kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,633 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T12:35:58,634 copying pyemma/coordinates/transform/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T12:35:58,636 copying pyemma/coordinates/transform/transformer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T12:35:58,638 copying pyemma/coordinates/transform/tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T12:35:58,640 copying pyemma/coordinates/transform/pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T12:35:58,643 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T12:35:58,644 copying pyemma/coordinates/data/util/traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T12:35:58,647 copying pyemma/coordinates/data/util/frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T12:35:58,649 copying pyemma/coordinates/data/util/reader_utils.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T12:35:58,651 copying pyemma/coordinates/data/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T12:35:58,653 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T12:35:58,654 copying pyemma/coordinates/data/_base/datasource.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T12:35:58,657 copying pyemma/coordinates/data/_base/iterable.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T12:35:58,659 copying pyemma/coordinates/data/_base/random_accessible.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T12:35:58,662 copying pyemma/coordinates/data/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T12:35:58,665 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,666 copying pyemma/coordinates/data/featurization/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,668 copying pyemma/coordinates/data/featurization/featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,671 copying pyemma/coordinates/data/featurization/_base.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,673 copying pyemma/coordinates/data/featurization/angles.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,675 copying pyemma/coordinates/data/featurization/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,678 copying pyemma/coordinates/data/featurization/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,679 copying pyemma/coordinates/data/featurization/distances.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T12:35:58,682 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T12:35:58,683 copying pyemma/coordinates/estimators/covar/moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T12:35:58,686 copying pyemma/coordinates/estimators/covar/running_moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T12:35:58,688 copying pyemma/coordinates/estimators/covar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T12:35:58,690 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T12:35:58,692 copying pyemma/coordinates/estimators/covar/covar_c/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T12:35:58,694 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,695 copying pyemma/util/tests/test_log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,697 copying pyemma/util/tests/test_units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,698 copying pyemma/util/tests/test_config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,700 copying pyemma/util/tests/statistics_test.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,702 copying pyemma/util/tests/test_estimation_required_decorator.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,704 copying pyemma/util/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,706 copying pyemma/util/tests/test_discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,708 copying pyemma/util/tests/test_shortcut.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T12:35:58,710 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T12:35:58,711 copying pyemma/_base/tests/test_progress.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T12:35:58,713 copying pyemma/_base/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T12:35:58,715 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T12:35:58,716 copying pyemma/_base/progress/reporter.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T12:35:58,719 copying pyemma/_base/progress/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T12:35:58,721 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T12:35:58,722 copying pyemma/_base/progress/bar/gui.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T12:35:58,724 copying pyemma/_base/progress/bar/_impl.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T12:35:58,726 copying pyemma/_base/progress/bar/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T12:35:58,728 copying pyemma/_base/progress/bar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T12:35:58,731 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,732 copying pyemma/msm/tests/test_bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,734 copying pyemma/msm/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,736 copying pyemma/msm/tests/test_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,739 copying pyemma/msm/tests/test_cktest.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,742 copying pyemma/msm/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,743 copying pyemma/msm/tests/test_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,746 copying pyemma/msm/tests/test_tpt.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,748 copying pyemma/msm/tests/test_bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,750 copying pyemma/msm/tests/birth_death_chain.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T12:35:58,753 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T12:35:58,754 copying pyemma/msm/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T12:35:58,755 copying pyemma/msm/models/msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T12:35:58,759 copying pyemma/msm/models/hmsm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T12:35:58,761 copying pyemma/msm/models/msm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T12:35:58,764 copying pyemma/msm/models/hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T12:35:58,767 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,768 copying pyemma/msm/estimators/bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,771 copying pyemma/msm/estimators/bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,773 copying pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,776 copying pyemma/msm/estimators/maximum_likelihood_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,780 copying pyemma/msm/estimators/implied_timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,782 copying pyemma/msm/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,784 copying pyemma/msm/estimators/_dtraj_stats.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,787 copying pyemma/msm/estimators/lagged_model_validators.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T12:35:58,790 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T12:35:58,791 copying pyemma/_ext/sklearn/base.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T12:35:58,795 copying pyemma/_ext/sklearn/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T12:35:58,796 copying pyemma/_ext/sklearn/parameter_search.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T12:35:58,799 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T12:35:58,800 copying pyemma/thermo/util/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T12:35:58,803 copying pyemma/thermo/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T12:35:58,805 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T12:35:58,806 copying pyemma/thermo/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T12:35:58,808 copying pyemma/thermo/models/stationary.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T12:35:58,810 copying pyemma/thermo/models/multi_therm.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T12:35:58,812 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T12:35:58,813 copying pyemma/thermo/estimators/DTRAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T12:35:58,815 copying pyemma/thermo/estimators/WHAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T12:35:58,817 copying pyemma/thermo/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T12:35:58,820 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T12:35:58,820 copying pyemma/plots/tests/test_markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T12:35:58,823 copying pyemma/plots/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T12:35:58,825 copying pyemma/plots/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T12:35:58,827 copying pyemma/plots/tests/test_networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T12:35:58,829 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T12:35:58,830 copying pyemma/plots/_ext/fruchterman_reingold.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T12:35:58,832 copying pyemma/plots/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T12:35:58,834 copying pyemma/pyemma.cfg -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T12:35:58,836 copying pyemma/logging.yml -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T12:35:58,838 copying pyemma/datasets/double_well_discrete.npz -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T12:35:58,841 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,842 copying pyemma/coordinates/tests/data/test.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,844 copying pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,847 copying pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,851 copying pyemma/coordinates/tests/data/bpti_ca.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,853 copying pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,855 copying pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,858 copying pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,861 copying pyemma/coordinates/tests/data/bpti_mini.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T12:35:58,863 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T12:35:58,864 copying pyemma/util/tests/data/dtraj.dat -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T12:35:58,866 copying pyemma/util/tests/data/dtraj.npy -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T12:35:58,890 UPDATING build/lib.linux-armv7l-cpython-39/pyemma/_version.py 2024-04-26T12:35:58,891 set build/lib.linux-armv7l-cpython-39/pyemma/_version.py to '2.1.1' 2024-04-26T12:35:58,891 running build_ext 2024-04-26T12:35:58,895 building 'pyemma.coordinates.clustering.regspatial' extension 2024-04-26T12:35:58,896 creating build/temp.linux-armv7l-cpython-39 2024-04-26T12:35:58,896 creating build/temp.linux-armv7l-cpython-39/pyemma 2024-04-26T12:35:58,897 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T12:35:58,898 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T12:35:58,898 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src 2024-04-26T12:35:58,900 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_OPENMP -I/tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/.eggs/mdtraj-1.9.9-py3.9-linux-armv7l.egg/mdtraj/core/lib -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -Ipyemma/coordinates/clustering/include -I/usr/include/python3.9 -c pyemma/coordinates/clustering/src/clustering.c -o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/clustering.o -std=c99 -g -O3 -pg -fopenmp 2024-04-26T12:35:59,220 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T12:35:59,221 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T12:35:59,221 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T12:35:59,221 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T12:35:59,221 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T12:35:59,221 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-26T12:35:59,221 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T12:35:59,221 | ^~~~~~~ 2024-04-26T12:35:59,251 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T12:35:59,252 pyemma/coordinates/clustering/src/clustering.c:77:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T12:35:59,252 77 | float d, mindist, trace_centers; 2024-04-26T12:35:59,252 | ^ 2024-04-26T12:35:59,260 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T12:35:59,261 At top level: 2024-04-26T12:35:59,261 pyemma/coordinates/clustering/include/clustering.h:53:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T12:35:59,261 53 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T12:35:59,261 | ^~~~~~~~~~~~ 2024-04-26T12:35:59,383 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T12:35:59,383 pyemma/coordinates/clustering/src/clustering.c:150:5: warning: ‘dists’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T12:35:59,383 150 | free(dists); 2024-04-26T12:35:59,384 | ^~~~~~~~~~~ 2024-04-26T12:35:59,517 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_OPENMP -I/tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/.eggs/mdtraj-1.9.9-py3.9-linux-armv7l.egg/mdtraj/core/lib -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -Ipyemma/coordinates/clustering/include -I/usr/include/python3.9 -c pyemma/coordinates/clustering/src/regspatial.c -o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/regspatial.o -std=c99 -g -O3 -pg -fopenmp 2024-04-26T12:35:59,821 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T12:35:59,822 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T12:35:59,822 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T12:35:59,822 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T12:35:59,822 from pyemma/coordinates/clustering/src/regspatial.c:19: 2024-04-26T12:35:59,822 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-26T12:35:59,822 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T12:35:59,822 | ^~~~~~~ 2024-04-26T12:35:59,859 pyemma/coordinates/clustering/src/regspatial.c:177:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T12:35:59,860 177 | error_out(PyObject *m) { 2024-04-26T12:35:59,860 | ^~~~~~~~~ 2024-04-26T12:35:59,860 pyemma/coordinates/clustering/src/regspatial.c:127:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T12:35:59,860 127 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T12:35:59,860 | ^~~~~~~~~ 2024-04-26T12:36:00,133 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/clustering.o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/regspatial.o -L/tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/.eggs/mdtraj-1.9.9-py3.9-linux-armv7l.egg/mdtraj/core/lib -L/usr/lib -ltheobald -o build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/regspatial.cpython-39-arm-linux-gnueabihf.so -lgomp 2024-04-26T12:36:00,259 building 'pyemma.coordinates.clustering.kmeans_clustering' extension 2024-04-26T12:36:00,259 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_OPENMP -I/tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/.eggs/mdtraj-1.9.9-py3.9-linux-armv7l.egg/mdtraj/core/lib -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -Ipyemma/coordinates/clustering/include -I/usr/include/python3.9 -c pyemma/coordinates/clustering/src/clustering.c -o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/clustering.o -std=c99 -fopenmp 2024-04-26T12:36:00,563 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T12:36:00,563 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T12:36:00,564 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T12:36:00,564 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T12:36:00,564 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T12:36:00,564 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-26T12:36:00,564 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T12:36:00,564 | ^~~~~~~ 2024-04-26T12:36:00,590 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T12:36:00,590 pyemma/coordinates/clustering/src/clustering.c:77:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T12:36:00,591 77 | float d, mindist, trace_centers; 2024-04-26T12:36:00,591 | ^ 2024-04-26T12:36:00,600 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T12:36:00,600 At top level: 2024-04-26T12:36:00,601 pyemma/coordinates/clustering/include/clustering.h:53:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T12:36:00,601 53 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T12:36:00,601 | ^~~~~~~~~~~~ 2024-04-26T12:36:00,718 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T12:36:00,718 pyemma/coordinates/clustering/src/clustering.c:150:5: warning: ‘dists’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T12:36:00,719 150 | free(dists); 2024-04-26T12:36:00,719 | ^~~~~~~~~~~ 2024-04-26T12:36:00,853 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_OPENMP -I/tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/.eggs/mdtraj-1.9.9-py3.9-linux-armv7l.egg/mdtraj/core/lib -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -Ipyemma/coordinates/clustering/include -I/usr/include/python3.9 -c pyemma/coordinates/clustering/src/kmeans.c -o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/kmeans.o -std=c99 -fopenmp 2024-04-26T12:36:01,105 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T12:36:01,106 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T12:36:01,106 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T12:36:01,106 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T12:36:01,106 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T12:36:01,106 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-26T12:36:01,106 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T12:36:01,106 | ^~~~~~~ 2024-04-26T12:36:01,126 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T12:36:01,127 pyemma/coordinates/clustering/src/kmeans.c:106:18: warning: assignment to ‘float (*)(float *, float *, size_t, float *, float *)’ {aka ‘float (*)(float *, float *, unsigned int, float *, float *)’} from incompatible pointer type ‘float (*)(float * restrict, float * restrict, size_t, float *, float *, float *)’ {aka ‘float (*)(float * restrict, float * restrict, unsigned int, float *, float *, float *)’} [-Wincompatible-pointer-types] 2024-04-26T12:36:01,127 106 | distance = euclidean_distance; 2024-04-26T12:36:01,127 | ^ 2024-04-26T12:36:01,127 pyemma/coordinates/clustering/src/kmeans.c:108:18: warning: assignment to ‘float (*)(float *, float *, size_t, float *, float *)’ {aka ‘float (*)(float *, float *, unsigned int, float *, float *)’} from incompatible pointer type ‘float (*)(float * restrict, float * restrict, size_t, float * restrict, float * restrict, float *)’ {aka ‘float (*)(float * restrict, float * restrict, unsigned int, float * restrict, float * restrict, float *)’} [-Wincompatible-pointer-types] 2024-04-26T12:36:01,127 108 | distance = minRMSD_distance; 2024-04-26T12:36:01,128 | ^ 2024-04-26T12:36:01,132 pyemma/coordinates/clustering/src/kmeans.c:51:38: warning: variable ‘py_res’ set but not used [-Wunused-but-set-variable] 2024-04-26T12:36:01,132 51 | PyObject *py_centers, *py_item, *py_res; 2024-04-26T12:36:01,132 | ^~~~~~ 2024-04-26T12:36:01,133 pyemma/coordinates/clustering/src/kmeans.c: In function ‘costFunction’: 2024-04-26T12:36:01,133 pyemma/coordinates/clustering/src/kmeans.c:239:18: warning: assignment to ‘float (*)(float *, float *, size_t, float *, float *)’ {aka ‘float (*)(float *, float *, unsigned int, float *, float *)’} from incompatible pointer type ‘float (*)(float * restrict, float * restrict, size_t, float *, float *, float *)’ {aka ‘float (*)(float * restrict, float * restrict, unsigned int, float *, float *, float *)’} [-Wincompatible-pointer-types] 2024-04-26T12:36:01,133 239 | distance = euclidean_distance; 2024-04-26T12:36:01,134 | ^ 2024-04-26T12:36:01,134 pyemma/coordinates/clustering/src/kmeans.c:241:18: warning: assignment to ‘float (*)(float *, float *, size_t, float *, float *)’ {aka ‘float (*)(float *, float *, unsigned int, float *, float *)’} from incompatible pointer type ‘float (*)(float * restrict, float * restrict, size_t, float * restrict, float * restrict, float *)’ {aka ‘float (*)(float * restrict, float * restrict, unsigned int, float * restrict, float * restrict, float *)’} [-Wincompatible-pointer-types] 2024-04-26T12:36:01,134 241 | distance = minRMSD_distance; 2024-04-26T12:36:01,134 | ^ 2024-04-26T12:36:01,136 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T12:36:01,136 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T12:36:01,136 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T12:36:01,136 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T12:36:01,137 pyemma/coordinates/clustering/src/kmeans.c:251:47: warning: passing argument 1 of ‘PyList_GetItem’ from incompatible pointer type [-Wincompatible-pointer-types] 2024-04-26T12:36:01,137 251 | centers = PyArray_DATA(PyList_GetItem(np_centers,r)); 2024-04-26T12:36:01,137 | ^~~~~~~~~~ 2024-04-26T12:36:01,137 | | 2024-04-26T12:36:01,137 | PyArrayObject * {aka struct tagPyArrayObject_fields *} 2024-04-26T12:36:01,137 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1605:62: note: in definition of macro ‘PyArray_DATA’ 2024-04-26T12:36:01,137 1605 | #define PyArray_DATA(obj) ((void *)((PyArrayObject_fields *)(obj))->data) 2024-04-26T12:36:01,137 | ^~~ 2024-04-26T12:36:01,138 In file included from /usr/include/python3.9/Python.h:106, 2024-04-26T12:36:01,138 from pyemma/coordinates/clustering/include/clustering.h:25, 2024-04-26T12:36:01,138 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T12:36:01,138 /usr/include/python3.9/listobject.h:31:39: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PyArrayObject *’ {aka ‘struct tagPyArrayObject_fields *’} 2024-04-26T12:36:01,139 31 | PyAPI_FUNC(PyObject *) PyList_GetItem(PyObject *, Py_ssize_t); 2024-04-26T12:36:01,139 | ^~~~~~~~~~ 2024-04-26T12:36:01,139 pyemma/coordinates/clustering/src/kmeans.c:217:18: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] 2024-04-26T12:36:01,140 217 | float value, d; 2024-04-26T12:36:01,140 | ^ 2024-04-26T12:36:01,140 pyemma/coordinates/clustering/src/kmeans.c:216:15: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 2024-04-26T12:36:01,140 216 | int k, i, j, r; 2024-04-26T12:36:01,140 | ^ 2024-04-26T12:36:01,142 pyemma/coordinates/clustering/src/kmeans.c: In function ‘initCentersKMpp’: 2024-04-26T12:36:01,142 pyemma/coordinates/clustering/src/kmeans.c:337:18: warning: assignment to ‘float (*)(float *, float *, size_t, float *, float *)’ {aka ‘float (*)(float *, float *, unsigned int, float *, float *)’} from incompatible pointer type ‘float (*)(float * restrict, float * restrict, size_t, float *, float *, float *)’ {aka ‘float (*)(float * restrict, float * restrict, unsigned int, float *, float *, float *)’} [-Wincompatible-pointer-types] 2024-04-26T12:36:01,142 337 | distance = euclidean_distance; 2024-04-26T12:36:01,142 | ^ 2024-04-26T12:36:01,143 pyemma/coordinates/clustering/src/kmeans.c:339:18: warning: assignment to ‘float (*)(float *, float *, size_t, float *, float *)’ {aka ‘float (*)(float *, float *, unsigned int, float *, float *)’} from incompatible pointer type ‘float (*)(float * restrict, float * restrict, size_t, float * restrict, float * restrict, float *)’ {aka ‘float (*)(float * restrict, float * restrict, unsigned int, float * restrict, float * restrict, float *)’} [-Wincompatible-pointer-types] 2024-04-26T12:36:01,143 339 | distance = minRMSD_distance; 2024-04-26T12:36:01,143 | ^ 2024-04-26T12:36:01,160 At top level: 2024-04-26T12:36:01,160 pyemma/coordinates/clustering/src/kmeans.c:581:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T12:36:01,160 581 | error_out(PyObject *m) { 2024-04-26T12:36:01,161 | ^~~~~~~~~ 2024-04-26T12:36:01,161 pyemma/coordinates/clustering/src/kmeans.c:509:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T12:36:01,161 509 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T12:36:01,161 | ^~~~~~~~~ 2024-04-26T12:36:01,322 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T12:36:01,322 pyemma/coordinates/clustering/src/kmeans.c:171:50: warning: ‘closest_center_index’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T12:36:01,322 171 | new_centers[closest_center_index*dim+j] += chunk[i*dim+j]; 2024-04-26T12:36:01,322 | ^~ 2024-04-26T12:36:01,844 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/clustering.o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src/kmeans.o -L/tmp/pip-wheel-z2ft0ko_/pyemma_e595236e06e641e293ee549ea3dcfdac/.eggs/mdtraj-1.9.9-py3.9-linux-armv7l.egg/mdtraj/core/lib -L/usr/lib -ltheobald -o build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/kmeans_clustering.cpython-39-arm-linux-gnueabihf.so -lgomp 2024-04-26T12:36:01,969 building 'pyemma.coordinates.estimators.covar.covar_c.covartools' extension 2024-04-26T12:36:01,970 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T12:36:01,970 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T12:36:01,971 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T12:36:01,972 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_OPENMP -Ipyemma/coordinates/estimators/covar/covar_c -Ipyemma/coordinates/estimators/covar/covar_c/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c pyemma/coordinates/estimators/covar/covar_c/_covartools.c -o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c/_covartools.o -std=c99 -O3 -fopenmp 2024-04-26T12:36:02,400 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_OPENMP -Ipyemma/coordinates/estimators/covar/covar_c -Ipyemma/coordinates/estimators/covar/covar_c/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c pyemma/coordinates/estimators/covar/covar_c/covartools.c -o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c/covartools.o -std=c99 -O3 -fopenmp 2024-04-26T12:36:02,715 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T12:36:02,715 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T12:36:02,715 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T12:36:02,715 from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1257: 2024-04-26T12:36:02,715 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-26T12:36:02,715 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T12:36:02,716 | ^~~~~~~ 2024-04-26T12:36:02,824 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_12subtract_row_float’: 2024-04-26T12:36:02,827 pyemma/coordinates/estimators/covar/covar_c/covartools.c:6712:23: warning: passing argument 1 of ‘_subtract_row_float’ from incompatible pointer type [-Wincompatible-pointer-types] 2024-04-26T12:36:02,828 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T12:36:02,828 | ^~~~~~~~~~ 2024-04-26T12:36:02,828 | | 2024-04-26T12:36:02,828 | float * 2024-04-26T12:36:02,828 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T12:36:02,828 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:34: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T12:36:02,828 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T12:36:02,828 | ~~~~~~~~^ 2024-04-26T12:36:02,831 pyemma/coordinates/estimators/covar/covar_c/covartools.c:6712:35: warning: passing argument 2 of ‘_subtract_row_float’ from incompatible pointer type [-Wincompatible-pointer-types] 2024-04-26T12:36:02,832 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T12:36:02,832 | ^~~~~~~~~~~~ 2024-04-26T12:36:02,832 | | 2024-04-26T12:36:02,832 | float * 2024-04-26T12:36:02,832 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T12:36:02,832 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:45: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T12:36:02,832 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T12:36:02,833 | ~~~~~~~~^~~ 2024-04-26T12:36:02,871 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_18subtract_row_float_copy’: 2024-04-26T12:36:02,877 pyemma/coordinates/estimators/covar/covar_c/covartools.c:7472:3: warning: implicit declaration of function ‘_subtract_row_float_copy’; did you mean ‘_subtract_row_float’? [-Wimplicit-function-declaration] 2024-04-26T12:36:02,878 7472 | _subtract_row_float_copy(__pyx_v_pX0, __pyx_v_pX, __pyx_v_prow, __pyx_t_6, __pyx_t_7); 2024-04-26T12:36:02,878 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2024-04-26T12:36:02,878 | _subtract_row_float 2024-04-26T12:36:13,906 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c/_covartools.o build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c/covartools.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c/covartools.cpython-39-arm-linux-gnueabihf.so -lgomp 2024-04-26T12:36:14,067 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-04-26T12:36:14,067 !! 2024-04-26T12:36:14,067 ******************************************************************************** 2024-04-26T12:36:14,068 Please avoid running ``setup.py`` directly. 2024-04-26T12:36:14,068 Instead, use pypa/build, pypa/installer or other 2024-04-26T12:36:14,068 standards-based tools. 2024-04-26T12:36:14,068 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-04-26T12:36:14,068 ******************************************************************************** 2024-04-26T12:36:14,068 !! 2024-04-26T12:36:14,069 self.initialize_options() 2024-04-26T12:36:14,096 installing to build/bdist.linux-armv7l/wheel 2024-04-26T12:36:14,096 running install 2024-04-26T12:36:14,122 running install_lib 2024-04-26T12:36:14,152 creating build/bdist.linux-armv7l 2024-04-26T12:36:14,152 creating build/bdist.linux-armv7l/wheel 2024-04-26T12:36:14,154 creating build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T12:36:14,155 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T12:36:14,157 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T12:36:14,158 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/patches.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T12:36:14,160 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/stat.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T12:36:14,162 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T12:36:14,163 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/change_notification.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T12:36:14,166 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T12:36:14,166 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/data_in_memory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T12:36:14,169 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/numpy_filereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T12:36:14,171 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T12:36:14,172 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T12:36:14,174 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T12:36:14,176 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/reader_utils.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T12:36:14,178 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T12:36:14,181 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T12:36:14,181 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/datasource.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T12:36:14,184 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/iterable.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T12:36:14,186 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/random_accessible.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T12:36:14,188 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T12:36:14,190 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T12:36:14,192 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T12:36:14,194 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,195 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/util.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,197 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,200 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/_base.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,201 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/angles.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,203 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,205 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,207 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/distances.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T12:36:14,209 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/feature_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T12:36:14,211 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/py_csv_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T12:36:14,214 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,215 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,217 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,219 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,221 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,223 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,226 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_trajs.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,228 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,230 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_load.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,232 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_datainmemory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,234 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_coordinates_iterator.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,236 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,238 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,240 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_random_access_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,243 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,244 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/test.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,246 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,248 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,251 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_ca.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,253 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,256 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,258 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,260 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T12:36:14,262 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,264 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_csvreader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,266 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_numpyfilereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,269 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,271 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,273 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,275 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,277 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,278 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_discretizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,280 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster_samples.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,282 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_traj.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,284 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,286 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,288 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,290 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pipeline.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,292 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,294 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,296 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T12:36:14,298 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T12:36:14,299 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/api.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T12:36:14,303 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T12:36:14,305 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T12:36:14,306 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T12:36:14,308 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T12:36:14,309 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T12:36:14,310 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c/covartools.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T12:36:14,321 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T12:36:14,322 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T12:36:14,325 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/running_moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T12:36:14,327 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T12:36:14,329 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,329 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/regspatial.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,333 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,335 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/interface.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,337 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,339 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,341 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,343 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/kmeans_clustering.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,347 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T12:36:14,349 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T12:36:14,350 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T12:36:14,352 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/transformer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T12:36:14,354 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T12:36:14,357 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T12:36:14,359 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/pipelines.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T12:36:14,361 creating build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T12:36:14,362 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.npz -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T12:36:14,366 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T12:36:14,367 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/api.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T12:36:14,369 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T12:36:14,372 creating build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,372 copying build/lib.linux-armv7l-cpython-39/pyemma/util/units.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,375 copying build/lib.linux-armv7l-cpython-39/pyemma/util/numeric.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,376 copying build/lib.linux-armv7l-cpython-39/pyemma/util/annotators.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,378 copying build/lib.linux-armv7l-cpython-39/pyemma/util/linalg.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,380 copying build/lib.linux-armv7l-cpython-39/pyemma/util/exceptions.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,382 copying build/lib.linux-armv7l-cpython-39/pyemma/util/reflection.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,384 copying build/lib.linux-armv7l-cpython-39/pyemma/util/discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,387 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,388 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_log.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,390 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_units.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,392 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_config.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,394 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/statistics_test.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,396 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_estimation_required_decorator.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,398 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T12:36:14,399 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.dat -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T12:36:14,403 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.npy -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T12:36:14,408 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,411 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,414 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_shortcut.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T12:36:14,417 copying build/lib.linux-armv7l-cpython-39/pyemma/util/debug.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,419 copying build/lib.linux-armv7l-cpython-39/pyemma/util/contexts.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,422 copying build/lib.linux-armv7l-cpython-39/pyemma/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,425 copying build/lib.linux-armv7l-cpython-39/pyemma/util/config.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,428 copying build/lib.linux-armv7l-cpython-39/pyemma/util/types.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,431 copying build/lib.linux-armv7l-cpython-39/pyemma/util/statistics.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,434 copying build/lib.linux-armv7l-cpython-39/pyemma/util/indices.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,437 copying build/lib.linux-armv7l-cpython-39/pyemma/util/files.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,439 copying build/lib.linux-armv7l-cpython-39/pyemma/util/log.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,442 copying build/lib.linux-armv7l-cpython-39/pyemma/util/testing_tools.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T12:36:14,444 copying build/lib.linux-armv7l-cpython-39/pyemma/pyemma.cfg -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T12:36:14,447 creating build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T12:36:14,448 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T12:36:14,452 creating build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T12:36:14,453 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/test_progress.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T12:36:14,455 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T12:36:14,458 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T12:36:14,461 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T12:36:14,462 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/reporter.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T12:36:14,465 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T12:36:14,466 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/gui.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T12:36:14,469 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/_impl.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T12:36:14,472 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T12:36:14,475 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T12:36:14,477 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T12:36:14,480 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/model.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T12:36:14,483 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/logging.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T12:36:14,485 creating build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T12:36:14,487 creating build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,488 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,492 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,494 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,499 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_cktest.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,501 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,503 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,505 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_tpt.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,507 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,510 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/birth_death_chain.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T12:36:14,512 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T12:36:14,514 creating build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T12:36:14,515 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T12:36:14,517 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T12:36:14,520 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T12:36:14,522 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T12:36:14,524 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T12:36:14,527 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/api.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T12:36:14,530 creating build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,531 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,534 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,536 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,538 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,541 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/implied_timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,544 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,545 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/_dtraj_stats.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,548 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/lagged_model_validators.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T12:36:14,550 creating build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T12:36:14,551 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T12:36:14,554 creating build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T12:36:14,554 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/base.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T12:36:14,557 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T12:36:14,559 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/parameter_search.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T12:36:14,561 copying build/lib.linux-armv7l-cpython-39/pyemma/_version.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T12:36:14,562 copying build/lib.linux-armv7l-cpython-39/pyemma/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T12:36:14,564 copying build/lib.linux-armv7l-cpython-39/pyemma/logging.yml -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T12:36:14,566 creating build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T12:36:14,567 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T12:36:14,568 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/util.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T12:36:14,570 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T12:36:14,572 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T12:36:14,574 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T12:36:14,575 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T12:36:14,577 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/stationary.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T12:36:14,579 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/multi_therm.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T12:36:14,581 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/api.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T12:36:14,583 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T12:36:14,584 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/DTRAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T12:36:14,586 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/WHAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T12:36:14,588 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T12:36:14,590 creating build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T12:36:14,591 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/plots2d.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T12:36:14,594 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T12:36:14,596 creating build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T12:36:14,597 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T12:36:14,599 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T12:36:14,600 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T12:36:14,602 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T12:36:14,604 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T12:36:14,606 creating build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T12:36:14,607 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/fruchterman_reingold.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T12:36:14,609 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T12:36:14,610 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T12:36:14,612 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T12:36:14,614 running install_egg_info 2024-04-26T12:36:14,678 running egg_info 2024-04-26T12:36:14,707 writing pyEMMA.egg-info/PKG-INFO 2024-04-26T12:36:14,710 writing dependency_links to pyEMMA.egg-info/dependency_links.txt 2024-04-26T12:36:14,712 writing requirements to pyEMMA.egg-info/requires.txt 2024-04-26T12:36:14,714 writing top-level names to pyEMMA.egg-info/top_level.txt 2024-04-26T12:36:14,758 /usr/local/lib/python3.9/dist-packages/setuptools/command/sdist.py:115: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2024-04-26T12:36:14,758 !! 2024-04-26T12:36:14,759 ******************************************************************************** 2024-04-26T12:36:14,759 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2024-04-26T12:36:14,759 Please extend command classes from setuptools instead of distutils. 2024-04-26T12:36:14,759 See https://peps.python.org/pep-0632/ for details. 2024-04-26T12:36:14,759 ******************************************************************************** 2024-04-26T12:36:14,760 !! 2024-04-26T12:36:14,760 self._add_data_files(self._safe_data_files(build_py)) 2024-04-26T12:36:14,763 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:36:14,763 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:36:14,763 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:36:14,763 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:36:14,764 dependency /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-26T12:36:14,793 reading manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T12:36:14,804 reading manifest template 'MANIFEST.in' 2024-04-26T12:36:14,933 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T12:36:14,935 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T12:36:14,937 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T12:36:14,941 no previously-included directories found matching 'doc/build' 2024-04-26T12:36:14,942 no previously-included directories found matching 'doc/source/generated' 2024-04-26T12:36:14,943 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T12:36:14,944 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T12:36:14,946 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T12:36:15,158 no previously-included directories found matching '.eggs' 2024-04-26T12:36:15,158 adding license file 'LICENSE.txt' 2024-04-26T12:36:15,172 writing manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T12:36:15,174 Copying pyEMMA.egg-info to build/bdist.linux-armv7l/wheel/pyEMMA-2.1.1-py3.9.egg-info 2024-04-26T12:36:15,187 running install_scripts 2024-04-26T12:36:15,211 adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") 2024-04-26T12:36:15,216 creating build/bdist.linux-armv7l/wheel/pyEMMA-2.1.1.dist-info/WHEEL 2024-04-26T12:36:15,218 creating '/tmp/pip-wheel-twawaqz_/pyEMMA-2.1.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-04-26T12:36:15,222 adding 'pyemma/__init__.py' 2024-04-26T12:36:15,223 adding 'pyemma/_version.py' 2024-04-26T12:36:15,224 adding 'pyemma/logging.yml' 2024-04-26T12:36:15,225 adding 'pyemma/pyemma.cfg' 2024-04-26T12:36:15,227 adding 'pyemma/_base/__init__.py' 2024-04-26T12:36:15,229 adding 'pyemma/_base/estimator.py' 2024-04-26T12:36:15,231 adding 'pyemma/_base/logging.py' 2024-04-26T12:36:15,233 adding 'pyemma/_base/model.py' 2024-04-26T12:36:15,235 adding 'pyemma/_base/progress/__init__.py' 2024-04-26T12:36:15,457 adding 'pyemma/_base/progress/reporter.py' 2024-04-26T12:36:15,459 adding 'pyemma/_base/progress/bar/__init__.py' 2024-04-26T12:36:15,461 adding 'pyemma/_base/progress/bar/_impl.py' 2024-04-26T12:36:15,463 adding 'pyemma/_base/progress/bar/gui.py' 2024-04-26T12:36:15,465 adding 'pyemma/_base/progress/bar/misc.py' 2024-04-26T12:36:15,466 adding 'pyemma/_base/tests/__init__.py' 2024-04-26T12:36:15,468 adding 'pyemma/_base/tests/test_progress.py' 2024-04-26T12:36:15,470 adding 'pyemma/_ext/__init__.py' 2024-04-26T12:36:15,471 adding 'pyemma/_ext/sklearn/__init__.py' 2024-04-26T12:36:15,474 adding 'pyemma/_ext/sklearn/base.py' 2024-04-26T12:36:15,475 adding 'pyemma/_ext/sklearn/parameter_search.py' 2024-04-26T12:36:15,477 adding 'pyemma/coordinates/__init__.py' 2024-04-26T12:36:15,479 adding 'pyemma/coordinates/acf.py' 2024-04-26T12:36:15,487 adding 'pyemma/coordinates/api.py' 2024-04-26T12:36:15,490 adding 'pyemma/coordinates/pipelines.py' 2024-04-26T12:36:15,492 adding 'pyemma/coordinates/clustering/__init__.py' 2024-04-26T12:36:15,493 adding 'pyemma/coordinates/clustering/assign.py' 2024-04-26T12:36:15,495 adding 'pyemma/coordinates/clustering/interface.py' 2024-04-26T12:36:15,498 adding 'pyemma/coordinates/clustering/kmeans.py' 2024-04-26T12:36:15,520 adding 'pyemma/coordinates/clustering/kmeans_clustering.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T12:36:15,522 adding 'pyemma/coordinates/clustering/regspace.py' 2024-04-26T12:36:15,541 adding 'pyemma/coordinates/clustering/regspatial.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T12:36:15,543 adding 'pyemma/coordinates/clustering/uniform_time.py' 2024-04-26T12:36:15,545 adding 'pyemma/coordinates/data/__init__.py' 2024-04-26T12:36:15,547 adding 'pyemma/coordinates/data/data_in_memory.py' 2024-04-26T12:36:15,550 adding 'pyemma/coordinates/data/feature_reader.py' 2024-04-26T12:36:15,552 adding 'pyemma/coordinates/data/fragmented_trajectory_reader.py' 2024-04-26T12:36:15,554 adding 'pyemma/coordinates/data/numpy_filereader.py' 2024-04-26T12:36:15,556 adding 'pyemma/coordinates/data/py_csv_reader.py' 2024-04-26T12:36:15,558 adding 'pyemma/coordinates/data/_base/__init__.py' 2024-04-26T12:36:15,561 adding 'pyemma/coordinates/data/_base/datasource.py' 2024-04-26T12:36:15,563 adding 'pyemma/coordinates/data/_base/iterable.py' 2024-04-26T12:36:15,564 adding 'pyemma/coordinates/data/_base/random_accessible.py' 2024-04-26T12:36:15,566 adding 'pyemma/coordinates/data/featurization/__init__.py' 2024-04-26T12:36:15,568 adding 'pyemma/coordinates/data/featurization/_base.py' 2024-04-26T12:36:15,569 adding 'pyemma/coordinates/data/featurization/angles.py' 2024-04-26T12:36:15,571 adding 'pyemma/coordinates/data/featurization/distances.py' 2024-04-26T12:36:15,574 adding 'pyemma/coordinates/data/featurization/featurizer.py' 2024-04-26T12:36:15,576 adding 'pyemma/coordinates/data/featurization/misc.py' 2024-04-26T12:36:15,578 adding 'pyemma/coordinates/data/featurization/util.py' 2024-04-26T12:36:15,580 adding 'pyemma/coordinates/data/util/__init__.py' 2024-04-26T12:36:15,582 adding 'pyemma/coordinates/data/util/frames_from_file.py' 2024-04-26T12:36:15,583 adding 'pyemma/coordinates/data/util/reader_utils.py' 2024-04-26T12:36:15,585 adding 'pyemma/coordinates/data/util/traj_info_cache.py' 2024-04-26T12:36:15,587 adding 'pyemma/coordinates/estimators/__init__.py' 2024-04-26T12:36:15,589 adding 'pyemma/coordinates/estimators/covar/__init__.py' 2024-04-26T12:36:15,592 adding 'pyemma/coordinates/estimators/covar/moments.py' 2024-04-26T12:36:15,595 adding 'pyemma/coordinates/estimators/covar/running_moments.py' 2024-04-26T12:36:15,596 adding 'pyemma/coordinates/estimators/covar/covar_c/__init__.py' 2024-04-26T12:36:15,713 adding 'pyemma/coordinates/estimators/covar/covar_c/covartools.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T12:36:15,720 adding 'pyemma/coordinates/tests/__init__.py' 2024-04-26T12:36:15,721 adding 'pyemma/coordinates/tests/test_acf.py' 2024-04-26T12:36:15,722 adding 'pyemma/coordinates/tests/test_api_load.py' 2024-04-26T12:36:15,724 adding 'pyemma/coordinates/tests/test_api_source.py' 2024-04-26T12:36:15,726 adding 'pyemma/coordinates/tests/test_assign.py' 2024-04-26T12:36:15,727 adding 'pyemma/coordinates/tests/test_cluster.py' 2024-04-26T12:36:15,729 adding 'pyemma/coordinates/tests/test_cluster_samples.py' 2024-04-26T12:36:15,730 adding 'pyemma/coordinates/tests/test_coordinates_iterator.py' 2024-04-26T12:36:15,732 adding 'pyemma/coordinates/tests/test_csvreader.py' 2024-04-26T12:36:15,734 adding 'pyemma/coordinates/tests/test_datainmemory.py' 2024-04-26T12:36:15,735 adding 'pyemma/coordinates/tests/test_discretizer.py' 2024-04-26T12:36:15,737 adding 'pyemma/coordinates/tests/test_featurereader.py' 2024-04-26T12:36:15,739 adding 'pyemma/coordinates/tests/test_featurereader_and_tica.py' 2024-04-26T12:36:15,741 adding 'pyemma/coordinates/tests/test_featurereader_and_tica_projection.py' 2024-04-26T12:36:15,744 adding 'pyemma/coordinates/tests/test_featurizer.py' 2024-04-26T12:36:15,746 adding 'pyemma/coordinates/tests/test_fragmented_trajectory.py' 2024-04-26T12:36:15,747 adding 'pyemma/coordinates/tests/test_frames_from_file.py' 2024-04-26T12:36:15,749 adding 'pyemma/coordinates/tests/test_kmeans.py' 2024-04-26T12:36:15,750 adding 'pyemma/coordinates/tests/test_mini_batch_kmeans.py' 2024-04-26T12:36:15,752 adding 'pyemma/coordinates/tests/test_numpyfilereader.py' 2024-04-26T12:36:15,754 adding 'pyemma/coordinates/tests/test_pca.py' 2024-04-26T12:36:15,755 adding 'pyemma/coordinates/tests/test_pipeline.py' 2024-04-26T12:36:15,757 adding 'pyemma/coordinates/tests/test_random_access_stride.py' 2024-04-26T12:36:15,759 adding 'pyemma/coordinates/tests/test_regspace.py' 2024-04-26T12:36:15,761 adding 'pyemma/coordinates/tests/test_save_traj.py' 2024-04-26T12:36:15,762 adding 'pyemma/coordinates/tests/test_save_trajs.py' 2024-04-26T12:36:15,764 adding 'pyemma/coordinates/tests/test_source.py' 2024-04-26T12:36:15,765 adding 'pyemma/coordinates/tests/test_stride.py' 2024-04-26T12:36:15,767 adding 'pyemma/coordinates/tests/test_tica.py' 2024-04-26T12:36:15,769 adding 'pyemma/coordinates/tests/test_traj_info_cache.py' 2024-04-26T12:36:15,771 adding 'pyemma/coordinates/tests/test_uniform_time.py' 2024-04-26T12:36:15,773 adding 'pyemma/coordinates/tests/data/bpti_001-033.xtc' 2024-04-26T12:36:15,775 adding 'pyemma/coordinates/tests/data/bpti_034-066.xtc' 2024-04-26T12:36:15,777 adding 'pyemma/coordinates/tests/data/bpti_067-100.xtc' 2024-04-26T12:36:15,779 adding 'pyemma/coordinates/tests/data/bpti_ca.pdb' 2024-04-26T12:36:15,784 adding 'pyemma/coordinates/tests/data/bpti_mini.xtc' 2024-04-26T12:36:15,785 adding 'pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz' 2024-04-26T12:36:15,795 adding 'pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz' 2024-04-26T12:36:15,797 adding 'pyemma/coordinates/tests/data/test.pdb' 2024-04-26T12:36:15,799 adding 'pyemma/coordinates/transform/__init__.py' 2024-04-26T12:36:15,800 adding 'pyemma/coordinates/transform/pca.py' 2024-04-26T12:36:15,803 adding 'pyemma/coordinates/transform/tica.py' 2024-04-26T12:36:15,809 adding 'pyemma/coordinates/transform/transformer.py' 2024-04-26T12:36:15,811 adding 'pyemma/coordinates/util/__init__.py' 2024-04-26T12:36:15,812 adding 'pyemma/coordinates/util/change_notification.py' 2024-04-26T12:36:15,814 adding 'pyemma/coordinates/util/patches.py' 2024-04-26T12:36:15,816 adding 'pyemma/coordinates/util/stat.py' 2024-04-26T12:36:15,817 adding 'pyemma/datasets/__init__.py' 2024-04-26T12:36:15,819 adding 'pyemma/datasets/api.py' 2024-04-26T12:36:15,826 adding 'pyemma/datasets/double_well_discrete.npz' 2024-04-26T12:36:15,828 adding 'pyemma/datasets/double_well_discrete.py' 2024-04-26T12:36:15,830 adding 'pyemma/msm/__init__.py' 2024-04-26T12:36:15,836 adding 'pyemma/msm/api.py' 2024-04-26T12:36:15,838 adding 'pyemma/msm/estimators/__init__.py' 2024-04-26T12:36:15,840 adding 'pyemma/msm/estimators/_dtraj_stats.py' 2024-04-26T12:36:15,842 adding 'pyemma/msm/estimators/bayesian_hmsm.py' 2024-04-26T12:36:15,844 adding 'pyemma/msm/estimators/bayesian_msm.py' 2024-04-26T12:36:15,846 adding 'pyemma/msm/estimators/implied_timescales.py' 2024-04-26T12:36:15,849 adding 'pyemma/msm/estimators/lagged_model_validators.py' 2024-04-26T12:36:15,853 adding 'pyemma/msm/estimators/maximum_likelihood_hmsm.py' 2024-04-26T12:36:15,857 adding 'pyemma/msm/estimators/maximum_likelihood_msm.py' 2024-04-26T12:36:15,859 adding 'pyemma/msm/models/__init__.py' 2024-04-26T12:36:15,861 adding 'pyemma/msm/models/hmsm.py' 2024-04-26T12:36:15,863 adding 'pyemma/msm/models/hmsm_sampled.py' 2024-04-26T12:36:15,867 adding 'pyemma/msm/models/msm.py' 2024-04-26T12:36:15,870 adding 'pyemma/msm/models/msm_sampled.py' 2024-04-26T12:36:15,872 adding 'pyemma/msm/tests/__init__.py' 2024-04-26T12:36:15,873 adding 'pyemma/msm/tests/birth_death_chain.py' 2024-04-26T12:36:15,875 adding 'pyemma/msm/tests/test_bayesian_hmsm.py' 2024-04-26T12:36:15,877 adding 'pyemma/msm/tests/test_bayesian_msm.py' 2024-04-26T12:36:15,879 adding 'pyemma/msm/tests/test_cktest.py' 2024-04-26T12:36:15,881 adding 'pyemma/msm/tests/test_hmsm.py' 2024-04-26T12:36:15,883 adding 'pyemma/msm/tests/test_its.py' 2024-04-26T12:36:15,887 adding 'pyemma/msm/tests/test_msm.py' 2024-04-26T12:36:15,889 adding 'pyemma/msm/tests/test_tpt.py' 2024-04-26T12:36:15,891 adding 'pyemma/plots/__init__.py' 2024-04-26T12:36:15,892 adding 'pyemma/plots/markovtests.py' 2024-04-26T12:36:15,895 adding 'pyemma/plots/networks.py' 2024-04-26T12:36:15,897 adding 'pyemma/plots/plots2d.py' 2024-04-26T12:36:15,899 adding 'pyemma/plots/timescales.py' 2024-04-26T12:36:15,901 adding 'pyemma/plots/_ext/__init__.py' 2024-04-26T12:36:15,902 adding 'pyemma/plots/_ext/fruchterman_reingold.py' 2024-04-26T12:36:15,904 adding 'pyemma/plots/tests/__init__.py' 2024-04-26T12:36:15,905 adding 'pyemma/plots/tests/test_its.py' 2024-04-26T12:36:15,906 adding 'pyemma/plots/tests/test_markovtests.py' 2024-04-26T12:36:15,908 adding 'pyemma/plots/tests/test_networks.py' 2024-04-26T12:36:15,909 adding 'pyemma/thermo/__init__.py' 2024-04-26T12:36:15,911 adding 'pyemma/thermo/api.py' 2024-04-26T12:36:15,914 adding 'pyemma/thermo/estimators/DTRAM_estimator.py' 2024-04-26T12:36:15,916 adding 'pyemma/thermo/estimators/WHAM_estimator.py' 2024-04-26T12:36:15,917 adding 'pyemma/thermo/estimators/__init__.py' 2024-04-26T12:36:15,919 adding 'pyemma/thermo/models/__init__.py' 2024-04-26T12:36:15,920 adding 'pyemma/thermo/models/multi_therm.py' 2024-04-26T12:36:15,922 adding 'pyemma/thermo/models/stationary.py' 2024-04-26T12:36:15,923 adding 'pyemma/thermo/util/__init__.py' 2024-04-26T12:36:15,925 adding 'pyemma/thermo/util/util.py' 2024-04-26T12:36:15,927 adding 'pyemma/util/__init__.py' 2024-04-26T12:36:15,929 adding 'pyemma/util/annotators.py' 2024-04-26T12:36:15,932 adding 'pyemma/util/config.py' 2024-04-26T12:36:15,933 adding 'pyemma/util/contexts.py' 2024-04-26T12:36:15,934 adding 'pyemma/util/debug.py' 2024-04-26T12:36:15,937 adding 'pyemma/util/discrete_trajectories.py' 2024-04-26T12:36:15,938 adding 'pyemma/util/exceptions.py' 2024-04-26T12:36:15,939 adding 'pyemma/util/files.py' 2024-04-26T12:36:15,941 adding 'pyemma/util/indices.py' 2024-04-26T12:36:15,942 adding 'pyemma/util/linalg.py' 2024-04-26T12:36:15,944 adding 'pyemma/util/log.py' 2024-04-26T12:36:15,945 adding 'pyemma/util/numeric.py' 2024-04-26T12:36:15,947 adding 'pyemma/util/reflection.py' 2024-04-26T12:36:15,949 adding 'pyemma/util/statistics.py' 2024-04-26T12:36:15,950 adding 'pyemma/util/testing_tools.py' 2024-04-26T12:36:15,952 adding 'pyemma/util/types.py' 2024-04-26T12:36:15,954 adding 'pyemma/util/units.py' 2024-04-26T12:36:15,956 adding 'pyemma/util/tests/__init__.py' 2024-04-26T12:36:15,957 adding 'pyemma/util/tests/statistics_test.py' 2024-04-26T12:36:15,959 adding 'pyemma/util/tests/test_config.py' 2024-04-26T12:36:15,961 adding 'pyemma/util/tests/test_discrete_trajectories.py' 2024-04-26T12:36:15,962 adding 'pyemma/util/tests/test_estimation_required_decorator.py' 2024-04-26T12:36:15,963 adding 'pyemma/util/tests/test_log.py' 2024-04-26T12:36:15,965 adding 'pyemma/util/tests/test_shortcut.py' 2024-04-26T12:36:15,966 adding 'pyemma/util/tests/test_units.py' 2024-04-26T12:36:15,973 adding 'pyemma/util/tests/data/dtraj.dat' 2024-04-26T12:36:15,982 adding 'pyemma/util/tests/data/dtraj.npy' 2024-04-26T12:36:15,984 adding 'pyEMMA-2.1.1.dist-info/LICENSE.txt' 2024-04-26T12:36:15,985 adding 'pyEMMA-2.1.1.dist-info/METADATA' 2024-04-26T12:36:15,986 adding 'pyEMMA-2.1.1.dist-info/WHEEL' 2024-04-26T12:36:15,987 adding 'pyEMMA-2.1.1.dist-info/pbr.json' 2024-04-26T12:36:15,988 adding 'pyEMMA-2.1.1.dist-info/top_level.txt' 2024-04-26T12:36:15,991 adding 'pyEMMA-2.1.1.dist-info/RECORD' 2024-04-26T12:36:16,011 removing build/bdist.linux-armv7l/wheel 2024-04-26T12:36:16,308 Building wheel for pyemma (setup.py): finished with status 'done' 2024-04-26T12:36:16,321 Created wheel for pyemma: filename=pyEMMA-2.1.1-cp39-cp39-linux_armv7l.whl size=975282 sha256=83cc6795c4869158d9287b93439aeb1f8acf18e327510afa0515fdc2e454a996 2024-04-26T12:36:16,322 Stored in directory: /tmp/pip-ephem-wheel-cache-0isdxt5j/wheels/3e/d5/4a/92b62b295707f968506e2de3eb95807fa53a83ab5b8bfec84e 2024-04-26T12:36:16,339 Successfully built pyemma 2024-04-26T12:36:16,366 Removed build tracker: '/tmp/pip-build-tracker-i2xbnau_'