2024-04-26T13:19:46,005 Created temporary directory: /tmp/pip-build-tracker-mh70yfnq 2024-04-26T13:19:46,006 Initialized build tracking at /tmp/pip-build-tracker-mh70yfnq 2024-04-26T13:19:46,007 Created build tracker: /tmp/pip-build-tracker-mh70yfnq 2024-04-26T13:19:46,007 Entered build tracker: /tmp/pip-build-tracker-mh70yfnq 2024-04-26T13:19:46,007 Created temporary directory: /tmp/pip-wheel-4wo8uw3u 2024-04-26T13:19:46,011 Created temporary directory: /tmp/pip-ephem-wheel-cache-1s9byull 2024-04-26T13:19:46,035 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-26T13:19:46,039 2 location(s) to search for versions of pyemma: 2024-04-26T13:19:46,039 * https://pypi.org/simple/pyemma/ 2024-04-26T13:19:46,039 * https://www.piwheels.org/simple/pyemma/ 2024-04-26T13:19:46,039 Fetching project page and analyzing links: https://pypi.org/simple/pyemma/ 2024-04-26T13:19:46,040 Getting page https://pypi.org/simple/pyemma/ 2024-04-26T13:19:46,041 Found index url https://pypi.org/simple/ 2024-04-26T13:19:46,092 Fetched page https://pypi.org/simple/pyemma/ as application/vnd.pypi.simple.v1+json 2024-04-26T13:19:46,100 Found link https://files.pythonhosted.org/packages/8e/31/2c2e23bbc16b404c8808c1043ebaf3aebfdd31dd90b979f213caad01f5bf/pyEMMA-1.0a2.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a2 2024-04-26T13:19:46,101 Found link https://files.pythonhosted.org/packages/1c/e3/453e32e448baa4274c622c82c87862164a34939b5139f4660db1fd470e2c/pyEMMA-1.0a3.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a3 2024-04-26T13:19:46,101 Found link https://files.pythonhosted.org/packages/9d/5a/d614dfaef84835bed7ec482b6fbaf1b94cc6fec0ca1e2f2ada7d3fdb9b7e/pyEMMA-1.0.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0 2024-04-26T13:19:46,101 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 2024-04-26T13:19:46,102 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 2024-04-26T13:19:46,102 Found link https://files.pythonhosted.org/packages/c3/28/e677fb5d7f98e1fc80442da7fd5bd56b96738d7c63c5dee64321128d7223/pyEMMA-1.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.1 2024-04-26T13:19:46,102 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 2024-04-26T13:19:46,102 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 2024-04-26T13:19:46,103 Found link https://files.pythonhosted.org/packages/a9/f4/d6db0d7f70baf531ec67a59f85a31e1f0940fcea4a9389527ddb47c0ac8b/pyEMMA-1.2.zip (from https://pypi.org/simple/pyemma/), version: 1.2 2024-04-26T13:19:46,103 Found link https://files.pythonhosted.org/packages/d1/34/5b0f37c1c3236e03508b304d34ed7b44e312664ad937fa7c6552ddd40e66/pyEMMA-1.2.1.zip (from https://pypi.org/simple/pyemma/), version: 1.2.1 2024-04-26T13:19:46,103 Found link https://files.pythonhosted.org/packages/05/61/da32c04877549e4e9670608bf59e77a2fb0740ad21fcb62c4ee5d8b062bf/pyEMMA-1.2.2.zip (from https://pypi.org/simple/pyemma/), version: 1.2.2 2024-04-26T13:19:46,104 Found link https://files.pythonhosted.org/packages/88/aa/78bbf546f420dc9c54b8d71f23ab0e17a7f6860ac986f36303544d13c747/pyEMMA-2.0.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.0 2024-04-26T13:19:46,104 Found link https://files.pythonhosted.org/packages/d8/06/061aae0063cce0512e6a9fbaaba83c18e3a27e2e941e574fcd5378c2251f/pyEMMA-2.0.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.0.1 2024-04-26T13:19:46,104 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 2024-04-26T13:19:46,104 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 2024-04-26T13:19:46,105 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 2024-04-26T13:19:46,105 Found link https://files.pythonhosted.org/packages/92/75/afa9da7a4e730829b583eb1e0851397b9a4775d823721fc9d640cb1812a4/pyemma-2.1rc1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc1 2024-04-26T13:19:46,105 Found link https://files.pythonhosted.org/packages/3e/99/e330c14650f11a7660b41d209d75b7de8f92173216c2f6b61041006b9429/pyEMMA-2.1rc2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc2 2024-04-26T13:19:46,106 Found link https://files.pythonhosted.org/packages/43/59/2d2adbb91b148051a271b4b5ae7676313622c5427b62e552762bbf829790/pyEMMA-2.1rc3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc3 2024-04-26T13:19:46,106 Found link https://files.pythonhosted.org/packages/52/19/fc61cfeb577540e680beba38ee21fe917e5f2bd74fcd60e9347c24199739/pyEMMA-2.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1 2024-04-26T13:19:46,106 Found link https://files.pythonhosted.org/packages/79/87/d9d41d3dd1b4048f078935e7a99991680af380ee46798db3635adf99de0a/pyEMMA-2.1.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1.1 2024-04-26T13:19:46,106 Found link https://files.pythonhosted.org/packages/ae/1f/61acb5b29f8bd8afd313d07a52ac91f47a4738c508b8a6e08cd2be82bc4b/pyEMMA-2.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2 2024-04-26T13:19:46,107 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 2024-04-26T13:19:46,107 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 2024-04-26T13:19:46,107 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 2024-04-26T13:19:46,107 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 2024-04-26T13:19:46,108 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 2024-04-26T13:19:46,108 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 2024-04-26T13:19:46,108 Found link https://files.pythonhosted.org/packages/d6/51/799c7406a1b5d6433360be894123ad0e326fd0c2370752d8b386c35cbbb7/pyEMMA-2.3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.3 2024-04-26T13:19:46,108 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 2024-04-26T13:19:46,109 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 2024-04-26T13:19:46,109 Found link https://files.pythonhosted.org/packages/45/d1/017a5298d6e67ab777268989c1793eb4d5d0869f366df7f1adf2a36a84e7/pyEMMA-2.4.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.4 2024-04-26T13:19:46,109 Found link https://files.pythonhosted.org/packages/8e/f7/9e5573f5da3d5314dcc79a41e138c5c9a6891bd72b92f9d18b7f59e85ab6/pyEMMA-2.5.zip (from https://pypi.org/simple/pyemma/), version: 2.5 2024-04-26T13:19:46,109 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 2024-04-26T13:19:46,110 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 2024-04-26T13:19:46,110 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 2024-04-26T13:19:46,110 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 2024-04-26T13:19:46,111 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 2024-04-26T13:19:46,111 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 2024-04-26T13:19:46,111 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 2024-04-26T13:19:46,111 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 2024-04-26T13:19:46,112 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 2024-04-26T13:19:46,112 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 2024-04-26T13:19:46,112 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 2024-04-26T13:19:46,112 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 2024-04-26T13:19:46,113 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyemma/ 2024-04-26T13:19:46,113 Getting page https://www.piwheels.org/simple/pyemma/ 2024-04-26T13:19:46,114 Found index url https://www.piwheels.org/simple/ 2024-04-26T13:19:46,188 Fetched page https://www.piwheels.org/simple/pyemma/ as text/html 2024-04-26T13:19:46,190 Skipping link: No binaries permitted for pyemma: https://www.piwheels.org/simple/pyemma/pyEMMA-2.1.1-cp39-cp39-linux_armv6l.whl#sha256=83cc6795c4869158d9287b93439aeb1f8acf18e327510afa0515fdc2e454a996 (from https://www.piwheels.org/simple/pyemma/) 2024-04-26T13:19:46,190 Skipping link: No binaries permitted for pyemma: https://www.piwheels.org/simple/pyemma/pyEMMA-2.1.1-cp39-cp39-linux_armv7l.whl#sha256=83cc6795c4869158d9287b93439aeb1f8acf18e327510afa0515fdc2e454a996 (from https://www.piwheels.org/simple/pyemma/) 2024-04-26T13:19:46,190 Skipping link: not a file: https://www.piwheels.org/simple/pyemma/ 2024-04-26T13:19:46,191 Skipping link: not a file: https://pypi.org/simple/pyemma/ 2024-04-26T13:19:46,214 Given no hashes to check 1 links for project 'pyemma': discarding no candidates 2024-04-26T13:19:46,231 Collecting pyemma==2.2 2024-04-26T13:19:46,234 Created temporary directory: /tmp/pip-unpack-erstwg3k 2024-04-26T13:19:46,471 Downloading pyEMMA-2.2.tar.gz (1.0 MB) 2024-04-26T13:19:47,154 Added pyemma==2.2 from https://files.pythonhosted.org/packages/ae/1f/61acb5b29f8bd8afd313d07a52ac91f47a4738c508b8a6e08cd2be82bc4b/pyEMMA-2.2.tar.gz to build tracker '/tmp/pip-build-tracker-mh70yfnq' 2024-04-26T13:19:47,155 Running setup.py (path:/tmp/pip-wheel-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/setup.py) egg_info for package pyemma 2024-04-26T13:19:47,156 Created temporary directory: /tmp/pip-pip-egg-info-1wki359z 2024-04-26T13:19:47,156 Preparing metadata (setup.py): started 2024-04-26T13:19:47,157 Running command python setup.py egg_info 2024-04-26T13:19:47,735 /tmp/pip-wheel-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T13:19:47,735 from pkg_resources import VersionConflict 2024-04-26T13:19:47,972 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T13:19:47,973 !! 2024-04-26T13:19:47,973 ******************************************************************************** 2024-04-26T13:19:47,973 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T13:19:47,973 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T13:19:47,973 ******************************************************************************** 2024-04-26T13:19:47,973 !! 2024-04-26T13:19:47,974 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T13:28:00,193 running egg_info 2024-04-26T13:28:00,195 creating /tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info 2024-04-26T13:28:00,225 writing /tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info/PKG-INFO 2024-04-26T13:28:00,229 writing dependency_links to /tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info/dependency_links.txt 2024-04-26T13:28:00,232 writing requirements to /tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info/requires.txt 2024-04-26T13:28:00,253 creating /tmp/hasfunction-on_rw991/tmp 2024-04-26T13:28:00,254 creating /tmp/hasfunction-on_rw991/tmp/hasfunction-on_rw991 2024-04-26T13:28:00,255 cc -c /tmp/hasfunction-on_rw991/funcname.c -o /tmp/hasfunction-on_rw991/tmp/hasfunction-on_rw991/funcname.o 2024-04-26T13:28:00,328 cc /tmp/hasfunction-on_rw991/tmp/hasfunction-on_rw991/funcname.o -o /tmp/hasfunction-on_rw991/a.out 2024-04-26T13:28:00,454 creating /tmp/hasfunction-yvazknyv/tmp 2024-04-26T13:28:00,455 creating /tmp/hasfunction-yvazknyv/tmp/hasfunction-yvazknyv 2024-04-26T13:28:00,456 cc -c /tmp/hasfunction-yvazknyv/funcname.c -o /tmp/hasfunction-yvazknyv/tmp/hasfunction-yvazknyv/funcname.o 2024-04-26T13:28:00,527 cc /tmp/hasfunction-yvazknyv/tmp/hasfunction-yvazknyv/funcname.o -lgomp -o /tmp/hasfunction-yvazknyv/a.out 2024-04-26T13:28:03,842 /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-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T13:28:03,843 tree = Parsing.p_module(s, pxd, full_module_name) 2024-04-26T13:28:04,791 Compiling pyemma/coordinates/estimators/covar/covar_c/covartools.pyx because it changed. 2024-04-26T13:28:04,792 [1/1] Cythonizing pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T13:28:04,792 /tmp/pip-wheel-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/setup.py:154: UserWarning: enabled openmp 2024-04-26T13:28:04,792 warnings.warn('enabled openmp') 2024-04-26T13:28:04,793 writing top-level names to /tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info/top_level.txt 2024-04-26T13:28:04,794 writing manifest file '/tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T13:28:04,932 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 2024-04-26T13:28:04,933 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 2024-04-26T13:28:04,933 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 2024-04-26T13:28:04,934 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 2024-04-26T13:28:04,934 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 2024-04-26T13:28:04,965 reading manifest file '/tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T13:28:04,967 reading manifest template 'MANIFEST.in' 2024-04-26T13:28:05,120 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T13:28:05,122 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T13:28:05,123 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T13:28:05,128 no previously-included directories found matching 'doc/build' 2024-04-26T13:28:05,129 no previously-included directories found matching 'doc/source/generated' 2024-04-26T13:28:05,131 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T13:28:05,132 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T13:28:05,133 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T13:28:05,365 no previously-included directories found matching '.eggs' 2024-04-26T13:28:05,365 adding license file 'LICENSE.txt' 2024-04-26T13:28:05,376 writing manifest file '/tmp/pip-pip-egg-info-1wki359z/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T13:28:05,728 Preparing metadata (setup.py): finished with status 'done' 2024-04-26T13:28:05,733 Source in /tmp/pip-wheel-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f has version 2.2, which satisfies requirement pyemma==2.2 from https://files.pythonhosted.org/packages/ae/1f/61acb5b29f8bd8afd313d07a52ac91f47a4738c508b8a6e08cd2be82bc4b/pyEMMA-2.2.tar.gz 2024-04-26T13:28:05,734 Removed pyemma==2.2 from https://files.pythonhosted.org/packages/ae/1f/61acb5b29f8bd8afd313d07a52ac91f47a4738c508b8a6e08cd2be82bc4b/pyEMMA-2.2.tar.gz from build tracker '/tmp/pip-build-tracker-mh70yfnq' 2024-04-26T13:28:05,739 Created temporary directory: /tmp/pip-unpack-esndsvwt 2024-04-26T13:28:05,740 Created temporary directory: /tmp/pip-unpack-782z011o 2024-04-26T13:28:05,758 Building wheels for collected packages: pyemma 2024-04-26T13:28:05,762 Created temporary directory: /tmp/pip-wheel-zq48qpin 2024-04-26T13:28:05,763 Building wheel for pyemma (setup.py): started 2024-04-26T13:28:05,763 Destination directory: /tmp/pip-wheel-zq48qpin 2024-04-26T13:28:05,764 Running command python setup.py bdist_wheel 2024-04-26T13:28:06,310 /tmp/pip-wheel-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T13:28:06,310 from pkg_resources import VersionConflict 2024-04-26T13:28:06,536 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T13:28:06,537 !! 2024-04-26T13:28:06,537 ******************************************************************************** 2024-04-26T13:28:06,537 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T13:28:06,537 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T13:28:06,537 ******************************************************************************** 2024-04-26T13:28:06,537 !! 2024-04-26T13:28:06,538 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T13:28:07,516 running bdist_wheel 2024-04-26T13:28:07,592 creating /tmp/hasfunction-cbgz4_b4/tmp 2024-04-26T13:28:07,592 creating /tmp/hasfunction-cbgz4_b4/tmp/hasfunction-cbgz4_b4 2024-04-26T13:28:07,593 cc -c /tmp/hasfunction-cbgz4_b4/funcname.c -o /tmp/hasfunction-cbgz4_b4/tmp/hasfunction-cbgz4_b4/funcname.o 2024-04-26T13:28:07,665 cc /tmp/hasfunction-cbgz4_b4/tmp/hasfunction-cbgz4_b4/funcname.o -o /tmp/hasfunction-cbgz4_b4/a.out 2024-04-26T13:28:07,763 creating /tmp/hasfunction-9epetlsa/tmp 2024-04-26T13:28:07,763 creating /tmp/hasfunction-9epetlsa/tmp/hasfunction-9epetlsa 2024-04-26T13:28:07,764 cc -c /tmp/hasfunction-9epetlsa/funcname.c -o /tmp/hasfunction-9epetlsa/tmp/hasfunction-9epetlsa/funcname.o 2024-04-26T13:28:07,837 cc /tmp/hasfunction-9epetlsa/tmp/hasfunction-9epetlsa/funcname.o -lgomp -o /tmp/hasfunction-9epetlsa/a.out 2024-04-26T13:28:09,370 /tmp/pip-wheel-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/setup.py:154: UserWarning: enabled openmp 2024-04-26T13:28:09,370 warnings.warn('enabled openmp') 2024-04-26T13:28:09,431 running build 2024-04-26T13:28:09,432 running build_py 2024-04-26T13:28:09,437 creating build 2024-04-26T13:28:09,438 creating build/lib.linux-armv7l-cpython-39 2024-04-26T13:28:09,438 creating build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T13:28:09,439 copying pyemma/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T13:28:09,441 copying pyemma/_version.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T13:28:09,443 creating build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T13:28:09,444 copying pyemma/plots/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T13:28:09,446 copying pyemma/plots/networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T13:28:09,448 copying pyemma/plots/thermoplots.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T13:28:09,450 copying pyemma/plots/plots2d.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T13:28:09,452 copying pyemma/plots/timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T13:28:09,454 copying pyemma/plots/markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T13:28:09,457 creating build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T13:28:09,458 copying pyemma/_base/model.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T13:28:09,460 copying pyemma/_base/estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T13:28:09,462 copying pyemma/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T13:28:09,464 copying pyemma/_base/logging.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T13:28:09,466 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T13:28:09,467 copying pyemma/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T13:28:09,469 creating build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T13:28:09,470 copying pyemma/msm/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T13:28:09,473 copying pyemma/msm/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T13:28:09,476 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T13:28:09,476 copying pyemma/coordinates/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T13:28:09,480 copying pyemma/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T13:28:09,481 copying pyemma/coordinates/acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T13:28:09,483 copying pyemma/coordinates/pipelines.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T13:28:09,487 creating build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,488 copying pyemma/util/testing_tools.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,489 copying pyemma/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,491 copying pyemma/util/indices.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,492 copying pyemma/util/log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,494 copying pyemma/util/units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,496 copying pyemma/util/types.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,499 copying pyemma/util/exceptions.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,500 copying pyemma/util/numeric.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,502 copying pyemma/util/statistics.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,504 copying pyemma/util/contexts.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,505 copying pyemma/util/config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,508 copying pyemma/util/linalg.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,510 copying pyemma/util/files.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,511 copying pyemma/util/annotators.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,513 copying pyemma/util/reflection.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,515 copying pyemma/util/debug.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,517 copying pyemma/util/discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T13:28:09,520 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T13:28:09,520 copying pyemma/thermo/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T13:28:09,523 copying pyemma/thermo/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T13:28:09,525 creating build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T13:28:09,526 copying pyemma/datasets/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T13:28:09,528 copying pyemma/datasets/double_well_discrete.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T13:28:09,530 copying pyemma/datasets/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T13:28:09,532 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T13:28:09,532 copying pyemma/plots/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T13:28:09,534 copying pyemma/plots/_ext/fruchterman_reingold.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T13:28:09,536 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T13:28:09,537 copying pyemma/plots/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T13:28:09,538 copying pyemma/plots/tests/test_networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T13:28:09,540 copying pyemma/plots/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T13:28:09,542 copying pyemma/plots/tests/test_markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T13:28:09,544 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T13:28:09,544 copying pyemma/_base/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T13:28:09,546 copying pyemma/_base/tests/test_progress.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T13:28:09,548 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T13:28:09,549 copying pyemma/_base/progress/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T13:28:09,551 copying pyemma/_base/progress/reporter.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T13:28:09,553 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T13:28:09,554 copying pyemma/_base/progress/bar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T13:28:09,556 copying pyemma/_base/progress/bar/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T13:28:09,558 copying pyemma/_base/progress/bar/gui.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T13:28:09,560 copying pyemma/_base/progress/bar/_impl.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T13:28:09,562 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T13:28:09,563 copying pyemma/_ext/sklearn/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T13:28:09,565 copying pyemma/_ext/sklearn/parameter_search.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T13:28:09,567 copying pyemma/_ext/sklearn/base.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T13:28:09,570 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,571 copying pyemma/msm/tests/test_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,574 copying pyemma/msm/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,575 copying pyemma/msm/tests/test_reactive_flux.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,577 copying pyemma/msm/tests/test_bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,579 copying pyemma/msm/tests/test_tpt.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,581 copying pyemma/msm/tests/test_bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,584 copying pyemma/msm/tests/test_msm_lowlevel_deprecation.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,586 copying pyemma/msm/tests/test_cktest.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,588 copying pyemma/msm/tests/test_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,590 copying pyemma/msm/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,592 copying pyemma/msm/tests/test_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,594 copying pyemma/msm/tests/birth_death_chain.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T13:28:09,597 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/dtraj 2024-04-26T13:28:09,597 copying pyemma/msm/dtraj/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/dtraj 2024-04-26T13:28:09,600 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,601 copying pyemma/msm/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,603 copying pyemma/msm/estimators/_dtraj_stats.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,605 copying pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,607 copying pyemma/msm/estimators/implied_timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,610 copying pyemma/msm/estimators/lagged_model_validators.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,612 copying pyemma/msm/estimators/maximum_likelihood_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,614 copying pyemma/msm/estimators/bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,617 copying pyemma/msm/estimators/bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T13:28:09,619 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/flux 2024-04-26T13:28:09,620 copying pyemma/msm/flux/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/flux 2024-04-26T13:28:09,622 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T13:28:09,623 copying pyemma/msm/models/hmsm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T13:28:09,625 copying pyemma/msm/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T13:28:09,626 copying pyemma/msm/models/msm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T13:28:09,629 copying pyemma/msm/models/hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T13:28:09,631 copying pyemma/msm/models/reactive_flux.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T13:28:09,633 copying pyemma/msm/models/msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T13:28:09,636 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/estimation 2024-04-26T13:28:09,637 copying pyemma/msm/estimation/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimation 2024-04-26T13:28:09,639 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/analysis 2024-04-26T13:28:09,640 copying pyemma/msm/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/analysis 2024-04-26T13:28:09,642 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/generation 2024-04-26T13:28:09,643 copying pyemma/msm/generation/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/generation 2024-04-26T13:28:09,647 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,647 copying pyemma/coordinates/tests/test_pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,650 copying pyemma/coordinates/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,651 copying pyemma/coordinates/tests/test_frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,653 copying pyemma/coordinates/tests/test_acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,655 copying pyemma/coordinates/tests/test_featurereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,657 copying pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,659 copying pyemma/coordinates/tests/test_uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,661 copying pyemma/coordinates/tests/test_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,663 copying pyemma/coordinates/tests/test_api_load.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,664 copying pyemma/coordinates/tests/test_random_access_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,667 copying pyemma/coordinates/tests/test_api_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,669 copying pyemma/coordinates/tests/test_cluster_samples.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,671 copying pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,673 copying pyemma/coordinates/tests/test_datainmemory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,675 copying pyemma/coordinates/tests/test_regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,677 copying pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,679 copying pyemma/coordinates/tests/test_featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,681 copying pyemma/coordinates/tests/test_csvreader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,684 copying pyemma/coordinates/tests/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,685 copying pyemma/coordinates/tests/test_traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,687 copying pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,689 copying pyemma/coordinates/tests/test_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,691 copying pyemma/coordinates/tests/test_discretizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,693 copying pyemma/coordinates/tests/test_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,695 copying pyemma/coordinates/tests/test_cluster.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,697 copying pyemma/coordinates/tests/test_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,699 copying pyemma/coordinates/tests/test_save_traj.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,701 copying pyemma/coordinates/tests/test_pipeline.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,703 copying pyemma/coordinates/tests/test_coordinates_iterator.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,705 copying pyemma/coordinates/tests/test_save_trajs.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,707 copying pyemma/coordinates/tests/test_numpyfilereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,709 copying pyemma/coordinates/tests/test_assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T13:28:09,711 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T13:28:09,712 copying pyemma/coordinates/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T13:28:09,714 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T13:28:09,715 copying pyemma/coordinates/transform/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T13:28:09,717 copying pyemma/coordinates/transform/pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T13:28:09,719 copying pyemma/coordinates/transform/tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T13:28:09,721 copying pyemma/coordinates/transform/transformer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T13:28:09,724 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,725 copying pyemma/coordinates/clustering/assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,726 copying pyemma/coordinates/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,729 copying pyemma/coordinates/clustering/uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,730 copying pyemma/coordinates/clustering/kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,732 copying pyemma/coordinates/clustering/regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,734 copying pyemma/coordinates/clustering/interface.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,737 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T13:28:09,738 copying pyemma/coordinates/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T13:28:09,740 copying pyemma/coordinates/util/patches.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T13:28:09,742 copying pyemma/coordinates/util/stat.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T13:28:09,743 copying pyemma/coordinates/util/change_notification.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T13:28:09,746 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T13:28:09,747 copying pyemma/coordinates/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T13:28:09,748 copying pyemma/coordinates/data/numpy_filereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T13:28:09,750 copying pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T13:28:09,753 copying pyemma/coordinates/data/data_in_memory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T13:28:09,755 copying pyemma/coordinates/data/feature_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T13:28:09,757 copying pyemma/coordinates/data/py_csv_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T13:28:09,760 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T13:28:09,763 copying pyemma/coordinates/estimators/covar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T13:28:09,764 copying pyemma/coordinates/estimators/covar/moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T13:28:09,767 copying pyemma/coordinates/estimators/covar/running_moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T13:28:09,769 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T13:28:09,770 copying pyemma/coordinates/estimators/covar/covar_c/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T13:28:09,772 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T13:28:09,773 copying pyemma/coordinates/data/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T13:28:09,775 copying pyemma/coordinates/data/_base/random_accessible.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T13:28:09,777 copying pyemma/coordinates/data/_base/iterable.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T13:28:09,779 copying pyemma/coordinates/data/_base/datasource.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T13:28:09,782 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,783 copying pyemma/coordinates/data/featurization/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,784 copying pyemma/coordinates/data/featurization/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,786 copying pyemma/coordinates/data/featurization/angles.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,788 copying pyemma/coordinates/data/featurization/_base.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,790 copying pyemma/coordinates/data/featurization/distances.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,792 copying pyemma/coordinates/data/featurization/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,794 copying pyemma/coordinates/data/featurization/featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T13:28:09,797 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T13:28:09,798 copying pyemma/coordinates/data/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T13:28:09,800 copying pyemma/coordinates/data/util/frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T13:28:09,802 copying pyemma/coordinates/data/util/traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T13:28:09,804 copying pyemma/coordinates/data/util/reader_utils.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T13:28:09,806 creating build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T13:28:09,807 copying pyemma/util/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T13:28:09,809 copying pyemma/util/_ext/shimmodule.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T13:28:09,811 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,812 copying pyemma/util/tests/test_discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,814 copying pyemma/util/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,816 copying pyemma/util/tests/test_units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,817 copying pyemma/util/tests/statistics_test.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,819 copying pyemma/util/tests/test_log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,820 copying pyemma/util/tests/test_config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,822 copying pyemma/util/tests/test_estimation_required_decorator.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,824 copying pyemma/util/tests/test_shortcut.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T13:28:09,826 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T13:28:09,827 copying pyemma/thermo/estimators/_callback.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T13:28:09,829 copying pyemma/thermo/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T13:28:09,831 copying pyemma/thermo/estimators/DTRAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T13:28:09,833 copying pyemma/thermo/estimators/WHAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T13:28:09,835 copying pyemma/thermo/estimators/TRAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T13:28:09,838 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T13:28:09,839 copying pyemma/thermo/models/multi_therm.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T13:28:09,841 copying pyemma/thermo/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T13:28:09,842 copying pyemma/thermo/models/stationary.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T13:28:09,845 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T13:28:09,845 copying pyemma/thermo/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T13:28:09,847 copying pyemma/thermo/util/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T13:28:09,867 copying pyemma/pyemma.cfg -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T13:28:09,869 copying pyemma/logging.yml -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T13:28:09,870 copying pyemma/datasets/double_well_discrete.npz -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T13:28:09,874 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,875 copying pyemma/coordinates/tests/data/bpti_mini.binpos -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,879 copying pyemma/coordinates/tests/data/bpti_ca.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,881 copying pyemma/coordinates/tests/data/bpti_mini.h5 -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,885 copying pyemma/coordinates/tests/data/bpti_mini.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,888 copying pyemma/coordinates/tests/data/bpti_mini.lh5 -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,892 copying pyemma/coordinates/tests/data/test.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,894 copying pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,896 copying pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,900 copying pyemma/coordinates/tests/data/bpti_mini.nc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,904 copying pyemma/coordinates/tests/data/bpti_mini.netcdf -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,908 copying pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,910 copying pyemma/coordinates/tests/data/bpti_mini.trr -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,914 copying pyemma/coordinates/tests/data/bpti_mini.dcd -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,918 copying pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,920 copying pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T13:28:09,923 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T13:28:09,923 copying pyemma/util/tests/data/dtraj.dat -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T13:28:09,926 copying pyemma/util/tests/data/dtraj.npy -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T13:28:09,950 UPDATING build/lib.linux-armv7l-cpython-39/pyemma/_version.py 2024-04-26T13:28:09,951 set build/lib.linux-armv7l-cpython-39/pyemma/_version.py to '2.2' 2024-04-26T13:28:09,951 running build_ext 2024-04-26T13:28:09,955 building 'pyemma.coordinates.clustering.regspatial' extension 2024-04-26T13:28:09,956 creating build/temp.linux-armv7l-cpython-39 2024-04-26T13:28:09,957 creating build/temp.linux-armv7l-cpython-39/pyemma 2024-04-26T13:28:09,957 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T13:28:09,958 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T13:28:09,959 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src 2024-04-26T13:28:09,960 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-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/.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 2024-04-26T13:28:10,276 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T13:28:10,276 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T13:28:10,276 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T13:28:10,277 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T13:28:10,277 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T13:28:10,277 /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] 2024-04-26T13:28:10,277 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T13:28:10,277 | ^~~~~~~ 2024-04-26T13:28:10,306 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T13:28:10,306 pyemma/coordinates/clustering/src/clustering.c:77:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T13:28:10,306 77 | float d, mindist, trace_centers; 2024-04-26T13:28:10,307 | ^ 2024-04-26T13:28:10,315 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T13:28:10,315 At top level: 2024-04-26T13:28:10,316 pyemma/coordinates/clustering/include/clustering.h:53:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T13:28:10,316 53 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T13:28:10,316 | ^~~~~~~~~~~~ 2024-04-26T13:28:10,318 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T13:28:10,318 pyemma/coordinates/clustering/src/clustering.c:89:7: warning: ‘debug’ is used uninitialized in this function [-Wuninitialized] 2024-04-26T13:28:10,319 89 | if(debug) printf("using openmp; n_threads=%i\n", n_threads); 2024-04-26T13:28:10,319 | ^ 2024-04-26T13:28:10,448 pyemma/coordinates/clustering/src/clustering.c:127:13: warning: ‘distance’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T13:28:10,449 127 | #pragma omp parallel private(buffer_a, buffer_b, i, j, chunk_p, mindist, argmin) 2024-04-26T13:28:10,449 | ^~~ 2024-04-26T13:28:10,581 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-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/.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 2024-04-26T13:28:10,884 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T13:28:10,884 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T13:28:10,884 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T13:28:10,885 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T13:28:10,885 from pyemma/coordinates/clustering/src/regspatial.c:19: 2024-04-26T13:28:10,885 /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] 2024-04-26T13:28:10,885 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T13:28:10,885 | ^~~~~~~ 2024-04-26T13:28:10,921 pyemma/coordinates/clustering/src/regspatial.c:177:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T13:28:10,921 177 | error_out(PyObject *m) { 2024-04-26T13:28:10,922 | ^~~~~~~~~ 2024-04-26T13:28:10,922 pyemma/coordinates/clustering/src/regspatial.c:127:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T13:28:10,922 127 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T13:28:10,922 | ^~~~~~~~~ 2024-04-26T13:28:11,220 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-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/.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 2024-04-26T13:28:11,375 building 'pyemma.coordinates.clustering.kmeans_clustering' extension 2024-04-26T13:28:11,376 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-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/.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 2024-04-26T13:28:11,690 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T13:28:11,690 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T13:28:11,691 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T13:28:11,691 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T13:28:11,691 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T13:28:11,691 /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] 2024-04-26T13:28:11,691 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T13:28:11,691 | ^~~~~~~ 2024-04-26T13:28:11,717 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T13:28:11,717 pyemma/coordinates/clustering/src/clustering.c:77:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T13:28:11,718 77 | float d, mindist, trace_centers; 2024-04-26T13:28:11,718 | ^ 2024-04-26T13:28:11,726 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T13:28:11,727 At top level: 2024-04-26T13:28:11,727 pyemma/coordinates/clustering/include/clustering.h:53:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T13:28:11,727 53 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T13:28:11,727 | ^~~~~~~~~~~~ 2024-04-26T13:28:11,729 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T13:28:11,729 pyemma/coordinates/clustering/src/clustering.c:89:7: warning: ‘debug’ is used uninitialized in this function [-Wuninitialized] 2024-04-26T13:28:11,730 89 | if(debug) printf("using openmp; n_threads=%i\n", n_threads); 2024-04-26T13:28:11,730 | ^ 2024-04-26T13:28:11,855 pyemma/coordinates/clustering/src/clustering.c:127:13: warning: ‘distance’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T13:28:11,855 127 | #pragma omp parallel private(buffer_a, buffer_b, i, j, chunk_p, mindist, argmin) 2024-04-26T13:28:11,856 | ^~~ 2024-04-26T13:28:11,986 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-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/.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 2024-04-26T13:28:12,236 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T13:28:12,236 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T13:28:12,236 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T13:28:12,236 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T13:28:12,237 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T13:28:12,237 /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] 2024-04-26T13:28:12,237 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T13:28:12,237 | ^~~~~~~ 2024-04-26T13:28:12,255 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T13:28:12,256 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] 2024-04-26T13:28:12,256 106 | distance = euclidean_distance; 2024-04-26T13:28:12,256 | ^ 2024-04-26T13:28:12,256 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] 2024-04-26T13:28:12,256 108 | distance = minRMSD_distance; 2024-04-26T13:28:12,257 | ^ 2024-04-26T13:28:12,259 pyemma/coordinates/clustering/src/kmeans.c:51:38: warning: variable ‘py_res’ set but not used [-Wunused-but-set-variable] 2024-04-26T13:28:12,260 51 | PyObject *py_centers, *py_item, *py_res; 2024-04-26T13:28:12,260 | ^~~~~~ 2024-04-26T13:28:12,260 pyemma/coordinates/clustering/src/kmeans.c: In function ‘costFunction’: 2024-04-26T13:28:12,260 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] 2024-04-26T13:28:12,260 239 | distance = euclidean_distance; 2024-04-26T13:28:12,261 | ^ 2024-04-26T13:28:12,261 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] 2024-04-26T13:28:12,261 241 | distance = minRMSD_distance; 2024-04-26T13:28:12,261 | ^ 2024-04-26T13:28:12,262 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T13:28:12,262 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T13:28:12,262 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T13:28:12,262 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T13:28:12,263 pyemma/coordinates/clustering/src/kmeans.c:251:47: warning: passing argument 1 of ‘PyList_GetItem’ from incompatible pointer type [-Wincompatible-pointer-types] 2024-04-26T13:28:12,263 251 | centers = PyArray_DATA(PyList_GetItem(np_centers,r)); 2024-04-26T13:28:12,263 | ^~~~~~~~~~ 2024-04-26T13:28:12,263 | | 2024-04-26T13:28:12,263 | PyArrayObject * {aka struct tagPyArrayObject_fields *} 2024-04-26T13:28:12,263 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1605:62: note: in definition of macro ‘PyArray_DATA’ 2024-04-26T13:28:12,263 1605 | #define PyArray_DATA(obj) ((void *)((PyArrayObject_fields *)(obj))->data) 2024-04-26T13:28:12,264 | ^~~ 2024-04-26T13:28:12,264 In file included from /usr/include/python3.9/Python.h:106, 2024-04-26T13:28:12,264 from pyemma/coordinates/clustering/include/clustering.h:25, 2024-04-26T13:28:12,264 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T13:28:12,264 /usr/include/python3.9/listobject.h:31:39: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PyArrayObject *’ {aka ‘struct tagPyArrayObject_fields *’} 2024-04-26T13:28:12,264 31 | PyAPI_FUNC(PyObject *) PyList_GetItem(PyObject *, Py_ssize_t); 2024-04-26T13:28:12,264 | ^~~~~~~~~~ 2024-04-26T13:28:12,265 pyemma/coordinates/clustering/src/kmeans.c:217:18: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] 2024-04-26T13:28:12,265 217 | float value, d; 2024-04-26T13:28:12,265 | ^ 2024-04-26T13:28:12,265 pyemma/coordinates/clustering/src/kmeans.c:216:15: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 2024-04-26T13:28:12,265 216 | int k, i, j, r; 2024-04-26T13:28:12,265 | ^ 2024-04-26T13:28:12,265 pyemma/coordinates/clustering/src/kmeans.c: In function ‘initCentersKMpp’: 2024-04-26T13:28:12,266 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] 2024-04-26T13:28:12,266 337 | distance = euclidean_distance; 2024-04-26T13:28:12,266 | ^ 2024-04-26T13:28:12,266 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] 2024-04-26T13:28:12,266 339 | distance = minRMSD_distance; 2024-04-26T13:28:12,266 | ^ 2024-04-26T13:28:12,281 At top level: 2024-04-26T13:28:12,281 pyemma/coordinates/clustering/src/kmeans.c:581:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T13:28:12,281 581 | error_out(PyObject *m) { 2024-04-26T13:28:12,281 | ^~~~~~~~~ 2024-04-26T13:28:12,281 pyemma/coordinates/clustering/src/kmeans.c:509:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T13:28:12,281 509 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T13:28:12,282 | ^~~~~~~~~ 2024-04-26T13:28:12,442 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T13:28:12,442 pyemma/coordinates/clustering/src/kmeans.c:171:50: warning: ‘closest_center_index’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T13:28:12,442 171 | new_centers[closest_center_index*dim+j] += chunk[i*dim+j]; 2024-04-26T13:28:12,442 | ^~ 2024-04-26T13:28:12,965 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-4wo8uw3u/pyemma_d03290b547df4a6ba8e7cd2050b3c02f/.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 2024-04-26T13:28:13,088 building 'pyemma.coordinates.estimators.covar.covar_c.covartools' extension 2024-04-26T13:28:13,089 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T13:28:13,090 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T13:28:13,090 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T13:28:13,091 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 2024-04-26T13:28:13,520 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 2024-04-26T13:28:13,840 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T13:28:13,840 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T13:28:13,840 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T13:28:13,840 from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1257: 2024-04-26T13:28:13,840 /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] 2024-04-26T13:28:13,841 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T13:28:13,841 | ^~~~~~~ 2024-04-26T13:28:13,952 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_12subtract_row_float’: 2024-04-26T13:28:13,955 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] 2024-04-26T13:28:13,955 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T13:28:13,955 | ^~~~~~~~~~ 2024-04-26T13:28:13,955 | | 2024-04-26T13:28:13,955 | float * 2024-04-26T13:28:13,956 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T13:28:13,956 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:34: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T13:28:13,956 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T13:28:13,956 | ~~~~~~~~^ 2024-04-26T13:28:13,959 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] 2024-04-26T13:28:13,959 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T13:28:13,959 | ^~~~~~~~~~~~ 2024-04-26T13:28:13,959 | | 2024-04-26T13:28:13,960 | float * 2024-04-26T13:28:13,960 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T13:28:13,960 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:45: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T13:28:13,960 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T13:28:13,960 | ~~~~~~~~^~~ 2024-04-26T13:28:13,998 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_18subtract_row_float_copy’: 2024-04-26T13:28:14,005 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] 2024-04-26T13:28:14,005 7472 | _subtract_row_float_copy(__pyx_v_pX0, __pyx_v_pX, __pyx_v_prow, __pyx_t_6, __pyx_t_7); 2024-04-26T13:28:14,005 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2024-04-26T13:28:14,005 | _subtract_row_float 2024-04-26T13:28:25,042 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 2024-04-26T13:28:25,206 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-04-26T13:28:25,207 !! 2024-04-26T13:28:25,207 ******************************************************************************** 2024-04-26T13:28:25,207 Please avoid running ``setup.py`` directly. 2024-04-26T13:28:25,207 Instead, use pypa/build, pypa/installer or other 2024-04-26T13:28:25,207 standards-based tools. 2024-04-26T13:28:25,208 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-04-26T13:28:25,208 ******************************************************************************** 2024-04-26T13:28:25,208 !! 2024-04-26T13:28:25,208 self.initialize_options() 2024-04-26T13:28:25,235 installing to build/bdist.linux-armv7l/wheel 2024-04-26T13:28:25,236 running install 2024-04-26T13:28:25,261 running install_lib 2024-04-26T13:28:25,291 creating build/bdist.linux-armv7l 2024-04-26T13:28:25,291 creating build/bdist.linux-armv7l/wheel 2024-04-26T13:28:25,293 creating build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T13:28:25,294 creating build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T13:28:25,295 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T13:28:25,297 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T13:28:25,300 creating build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T13:28:25,301 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T13:28:25,302 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/fruchterman_reingold.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T13:28:25,305 creating build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T13:28:25,305 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T13:28:25,307 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T13:28:25,309 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T13:28:25,310 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T13:28:25,312 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/thermoplots.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T13:28:25,314 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/plots2d.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T13:28:25,316 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T13:28:25,318 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T13:28:25,320 copying build/lib.linux-armv7l-cpython-39/pyemma/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T13:28:25,322 creating build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T13:28:25,323 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/model.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T13:28:25,325 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T13:28:25,327 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T13:28:25,329 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/logging.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T13:28:25,331 creating build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T13:28:25,332 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T13:28:25,333 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/test_progress.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T13:28:25,336 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T13:28:25,336 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T13:28:25,338 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/reporter.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T13:28:25,341 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T13:28:25,341 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T13:28:25,343 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T13:28:25,345 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/gui.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T13:28:25,347 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/_impl.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T13:28:25,350 creating build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T13:28:25,351 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T13:28:25,353 creating build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T13:28:25,354 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T13:28:25,355 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/parameter_search.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T13:28:25,357 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/base.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T13:28:25,360 copying build/lib.linux-armv7l-cpython-39/pyemma/pyemma.cfg -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T13:28:25,361 copying build/lib.linux-armv7l-cpython-39/pyemma/logging.yml -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T13:28:25,363 creating build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T13:28:25,364 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/api.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T13:28:25,367 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T13:28:25,370 creating build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,370 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,373 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,375 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_reactive_flux.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,377 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,379 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_tpt.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,381 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,384 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_msm_lowlevel_deprecation.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,386 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_cktest.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,388 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,390 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,392 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,394 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/birth_death_chain.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T13:28:25,397 creating build/bdist.linux-armv7l/wheel/pyemma/msm/dtraj 2024-04-26T13:28:25,397 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/dtraj/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/dtraj 2024-04-26T13:28:25,399 creating build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,400 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,402 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/_dtraj_stats.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,404 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,407 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/implied_timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,409 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/lagged_model_validators.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,411 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,414 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,416 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T13:28:25,419 creating build/bdist.linux-armv7l/wheel/pyemma/msm/flux 2024-04-26T13:28:25,419 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/flux/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/flux 2024-04-26T13:28:25,422 creating build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T13:28:25,423 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T13:28:25,425 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T13:28:25,426 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T13:28:25,429 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T13:28:25,431 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/reactive_flux.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T13:28:25,433 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T13:28:25,437 creating build/bdist.linux-armv7l/wheel/pyemma/msm/estimation 2024-04-26T13:28:25,438 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimation/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimation 2024-04-26T13:28:25,440 creating build/bdist.linux-armv7l/wheel/pyemma/msm/analysis 2024-04-26T13:28:25,440 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/analysis 2024-04-26T13:28:25,443 creating build/bdist.linux-armv7l/wheel/pyemma/msm/generation 2024-04-26T13:28:25,443 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/generation/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/generation 2024-04-26T13:28:25,446 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T13:28:25,446 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/api.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T13:28:25,449 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T13:28:25,452 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,453 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,455 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,457 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,459 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,461 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,463 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,465 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,467 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,469 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_load.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,471 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_random_access_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,473 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,475 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster_samples.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,477 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,479 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_datainmemory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,481 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,483 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,485 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,488 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_csvreader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,490 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/util.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,492 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,494 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,495 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,498 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_discretizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,500 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,502 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,503 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.binpos -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,506 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_ca.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,508 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.h5 -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,512 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,515 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.lh5 -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,518 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/test.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,520 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,522 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 2024-04-26T13:28:25,525 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.nc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,529 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.netcdf -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,532 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 2024-04-26T13:28:25,535 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.trr -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,538 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.dcd -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,542 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,545 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T13:28:25,548 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,550 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,552 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_traj.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,555 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pipeline.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,557 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_coordinates_iterator.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,559 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_trajs.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,562 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_numpyfilereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,564 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T13:28:25,567 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T13:28:25,569 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T13:28:25,570 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T13:28:25,573 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T13:28:25,574 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T13:28:25,575 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T13:28:25,579 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T13:28:25,580 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 2024-04-26T13:28:25,582 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 2024-04-26T13:28:25,598 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/running_moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T13:28:25,601 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T13:28:25,602 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T13:28:25,604 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T13:28:25,607 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T13:28:25,610 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/transformer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T13:28:25,613 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T13:28:25,614 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T13:28:25,616 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T13:28:25,618 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T13:28:25,620 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T13:28:25,623 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 2024-04-26T13:28:25,628 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T13:28:25,630 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 2024-04-26T13:28:25,635 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/interface.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T13:28:25,637 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T13:28:25,639 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T13:28:25,641 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/patches.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T13:28:25,643 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/stat.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T13:28:25,645 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/change_notification.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T13:28:25,647 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T13:28:25,649 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T13:28:25,651 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T13:28:25,652 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T13:28:25,654 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/random_accessible.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T13:28:25,656 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/iterable.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T13:28:25,659 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/datasource.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T13:28:25,661 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/numpy_filereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T13:28:25,664 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T13:28:25,666 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/data_in_memory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T13:28:25,669 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,671 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,673 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,675 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/angles.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,677 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/_base.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,679 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/distances.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,681 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/util.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,684 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T13:28:25,687 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/feature_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T13:28:25,690 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T13:28:25,691 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T13:28:25,693 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T13:28:25,695 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T13:28:25,698 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/reader_utils.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T13:28:25,700 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/py_csv_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T13:28:25,703 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/pipelines.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T13:28:25,706 creating build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,707 copying build/lib.linux-armv7l-cpython-39/pyemma/util/testing_tools.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,709 copying build/lib.linux-armv7l-cpython-39/pyemma/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,711 copying build/lib.linux-armv7l-cpython-39/pyemma/util/indices.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,713 copying build/lib.linux-armv7l-cpython-39/pyemma/util/log.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,715 copying build/lib.linux-armv7l-cpython-39/pyemma/util/units.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,717 creating build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T13:28:25,718 copying build/lib.linux-armv7l-cpython-39/pyemma/util/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T13:28:25,720 copying build/lib.linux-armv7l-cpython-39/pyemma/util/_ext/shimmodule.py -> build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T13:28:25,723 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,724 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,726 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,728 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_units.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,730 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/statistics_test.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,732 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_log.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,734 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_config.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,737 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T13:28:25,738 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.dat -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T13:28:25,741 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.npy -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T13:28:25,744 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_estimation_required_decorator.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,746 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_shortcut.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T13:28:25,748 copying build/lib.linux-armv7l-cpython-39/pyemma/util/types.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,750 copying build/lib.linux-armv7l-cpython-39/pyemma/util/exceptions.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,752 copying build/lib.linux-armv7l-cpython-39/pyemma/util/numeric.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,754 copying build/lib.linux-armv7l-cpython-39/pyemma/util/statistics.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,757 copying build/lib.linux-armv7l-cpython-39/pyemma/util/contexts.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,759 copying build/lib.linux-armv7l-cpython-39/pyemma/util/config.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,761 copying build/lib.linux-armv7l-cpython-39/pyemma/util/linalg.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,764 copying build/lib.linux-armv7l-cpython-39/pyemma/util/files.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,766 copying build/lib.linux-armv7l-cpython-39/pyemma/util/annotators.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,768 copying build/lib.linux-armv7l-cpython-39/pyemma/util/reflection.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,771 copying build/lib.linux-armv7l-cpython-39/pyemma/util/debug.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,773 copying build/lib.linux-armv7l-cpython-39/pyemma/util/discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T13:28:25,776 creating build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T13:28:25,777 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/api.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T13:28:25,780 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T13:28:25,782 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T13:28:25,783 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/_callback.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T13:28:25,786 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T13:28:25,788 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/DTRAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T13:28:25,790 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/WHAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T13:28:25,793 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/TRAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T13:28:25,796 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T13:28:25,797 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/multi_therm.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T13:28:25,799 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T13:28:25,801 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/stationary.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T13:28:25,804 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T13:28:25,805 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T13:28:25,808 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/util.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T13:28:25,811 creating build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T13:28:25,812 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/api.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T13:28:25,814 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T13:28:25,816 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T13:28:25,818 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.npz -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T13:28:25,822 copying build/lib.linux-armv7l-cpython-39/pyemma/_version.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T13:28:25,824 running install_egg_info 2024-04-26T13:28:25,888 running egg_info 2024-04-26T13:28:25,917 writing pyEMMA.egg-info/PKG-INFO 2024-04-26T13:28:25,921 writing dependency_links to pyEMMA.egg-info/dependency_links.txt 2024-04-26T13:28:25,924 writing requirements to pyEMMA.egg-info/requires.txt 2024-04-26T13:28:25,925 writing top-level names to pyEMMA.egg-info/top_level.txt 2024-04-26T13:28:25,988 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 2024-04-26T13:28:25,988 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 2024-04-26T13:28:25,989 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 2024-04-26T13:28:25,989 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 2024-04-26T13:28:25,989 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 2024-04-26T13:28:26,020 reading manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T13:28:26,031 reading manifest template 'MANIFEST.in' 2024-04-26T13:28:26,168 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T13:28:26,170 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T13:28:26,172 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T13:28:26,176 no previously-included directories found matching 'doc/build' 2024-04-26T13:28:26,177 no previously-included directories found matching 'doc/source/generated' 2024-04-26T13:28:26,179 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T13:28:26,181 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T13:28:26,183 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T13:28:26,405 no previously-included directories found matching '.eggs' 2024-04-26T13:28:26,405 adding license file 'LICENSE.txt' 2024-04-26T13:28:26,420 writing manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T13:28:26,423 Copying pyEMMA.egg-info to build/bdist.linux-armv7l/wheel/pyEMMA-2.2-py3.9.egg-info 2024-04-26T13:28:26,436 running install_scripts 2024-04-26T13:28:26,459 adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") 2024-04-26T13:28:26,465 creating build/bdist.linux-armv7l/wheel/pyEMMA-2.2.dist-info/WHEEL 2024-04-26T13:28:26,467 creating '/tmp/pip-wheel-zq48qpin/pyEMMA-2.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-04-26T13:28:26,471 adding 'pyemma/__init__.py' 2024-04-26T13:28:26,473 adding 'pyemma/_version.py' 2024-04-26T13:28:26,474 adding 'pyemma/logging.yml' 2024-04-26T13:28:26,476 adding 'pyemma/pyemma.cfg' 2024-04-26T13:28:26,478 adding 'pyemma/_base/__init__.py' 2024-04-26T13:28:26,481 adding 'pyemma/_base/estimator.py' 2024-04-26T13:28:26,483 adding 'pyemma/_base/logging.py' 2024-04-26T13:28:26,485 adding 'pyemma/_base/model.py' 2024-04-26T13:28:26,487 adding 'pyemma/_base/progress/__init__.py' 2024-04-26T13:28:26,489 adding 'pyemma/_base/progress/reporter.py' 2024-04-26T13:28:26,491 adding 'pyemma/_base/progress/bar/__init__.py' 2024-04-26T13:28:26,494 adding 'pyemma/_base/progress/bar/_impl.py' 2024-04-26T13:28:26,496 adding 'pyemma/_base/progress/bar/gui.py' 2024-04-26T13:28:26,498 adding 'pyemma/_base/progress/bar/misc.py' 2024-04-26T13:28:26,500 adding 'pyemma/_base/tests/__init__.py' 2024-04-26T13:28:26,502 adding 'pyemma/_base/tests/test_progress.py' 2024-04-26T13:28:26,504 adding 'pyemma/_ext/__init__.py' 2024-04-26T13:28:26,506 adding 'pyemma/_ext/sklearn/__init__.py' 2024-04-26T13:28:26,509 adding 'pyemma/_ext/sklearn/base.py' 2024-04-26T13:28:26,511 adding 'pyemma/_ext/sklearn/parameter_search.py' 2024-04-26T13:28:26,513 adding 'pyemma/coordinates/__init__.py' 2024-04-26T13:28:26,515 adding 'pyemma/coordinates/acf.py' 2024-04-26T13:28:26,523 adding 'pyemma/coordinates/api.py' 2024-04-26T13:28:26,526 adding 'pyemma/coordinates/pipelines.py' 2024-04-26T13:28:26,528 adding 'pyemma/coordinates/clustering/__init__.py' 2024-04-26T13:28:26,530 adding 'pyemma/coordinates/clustering/assign.py' 2024-04-26T13:28:26,532 adding 'pyemma/coordinates/clustering/interface.py' 2024-04-26T13:28:26,535 adding 'pyemma/coordinates/clustering/kmeans.py' 2024-04-26T13:28:26,558 adding 'pyemma/coordinates/clustering/kmeans_clustering.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T13:28:26,560 adding 'pyemma/coordinates/clustering/regspace.py' 2024-04-26T13:28:26,579 adding 'pyemma/coordinates/clustering/regspatial.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T13:28:26,582 adding 'pyemma/coordinates/clustering/uniform_time.py' 2024-04-26T13:28:26,584 adding 'pyemma/coordinates/data/__init__.py' 2024-04-26T13:28:26,586 adding 'pyemma/coordinates/data/data_in_memory.py' 2024-04-26T13:28:26,589 adding 'pyemma/coordinates/data/feature_reader.py' 2024-04-26T13:28:26,592 adding 'pyemma/coordinates/data/fragmented_trajectory_reader.py' 2024-04-26T13:28:26,594 adding 'pyemma/coordinates/data/numpy_filereader.py' 2024-04-26T13:28:26,597 adding 'pyemma/coordinates/data/py_csv_reader.py' 2024-04-26T13:28:26,599 adding 'pyemma/coordinates/data/_base/__init__.py' 2024-04-26T13:28:26,602 adding 'pyemma/coordinates/data/_base/datasource.py' 2024-04-26T13:28:26,604 adding 'pyemma/coordinates/data/_base/iterable.py' 2024-04-26T13:28:26,606 adding 'pyemma/coordinates/data/_base/random_accessible.py' 2024-04-26T13:28:26,608 adding 'pyemma/coordinates/data/featurization/__init__.py' 2024-04-26T13:28:26,610 adding 'pyemma/coordinates/data/featurization/_base.py' 2024-04-26T13:28:26,612 adding 'pyemma/coordinates/data/featurization/angles.py' 2024-04-26T13:28:26,614 adding 'pyemma/coordinates/data/featurization/distances.py' 2024-04-26T13:28:26,617 adding 'pyemma/coordinates/data/featurization/featurizer.py' 2024-04-26T13:28:26,621 adding 'pyemma/coordinates/data/featurization/misc.py' 2024-04-26T13:28:26,623 adding 'pyemma/coordinates/data/featurization/util.py' 2024-04-26T13:28:26,625 adding 'pyemma/coordinates/data/util/__init__.py' 2024-04-26T13:28:26,628 adding 'pyemma/coordinates/data/util/frames_from_file.py' 2024-04-26T13:28:26,630 adding 'pyemma/coordinates/data/util/reader_utils.py' 2024-04-26T13:28:26,632 adding 'pyemma/coordinates/data/util/traj_info_cache.py' 2024-04-26T13:28:26,634 adding 'pyemma/coordinates/estimators/__init__.py' 2024-04-26T13:28:26,636 adding 'pyemma/coordinates/estimators/covar/__init__.py' 2024-04-26T13:28:26,640 adding 'pyemma/coordinates/estimators/covar/moments.py' 2024-04-26T13:28:26,642 adding 'pyemma/coordinates/estimators/covar/running_moments.py' 2024-04-26T13:28:26,644 adding 'pyemma/coordinates/estimators/covar/covar_c/__init__.py' 2024-04-26T13:28:26,763 adding 'pyemma/coordinates/estimators/covar/covar_c/covartools.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T13:28:26,770 adding 'pyemma/coordinates/tests/__init__.py' 2024-04-26T13:28:26,771 adding 'pyemma/coordinates/tests/test_acf.py' 2024-04-26T13:28:26,773 adding 'pyemma/coordinates/tests/test_api_load.py' 2024-04-26T13:28:26,775 adding 'pyemma/coordinates/tests/test_api_source.py' 2024-04-26T13:28:26,777 adding 'pyemma/coordinates/tests/test_assign.py' 2024-04-26T13:28:26,779 adding 'pyemma/coordinates/tests/test_cluster.py' 2024-04-26T13:28:26,785 adding 'pyemma/coordinates/tests/test_cluster_samples.py' 2024-04-26T13:28:26,787 adding 'pyemma/coordinates/tests/test_coordinates_iterator.py' 2024-04-26T13:28:26,789 adding 'pyemma/coordinates/tests/test_csvreader.py' 2024-04-26T13:28:26,791 adding 'pyemma/coordinates/tests/test_datainmemory.py' 2024-04-26T13:28:26,793 adding 'pyemma/coordinates/tests/test_discretizer.py' 2024-04-26T13:28:26,795 adding 'pyemma/coordinates/tests/test_featurereader.py' 2024-04-26T13:28:26,797 adding 'pyemma/coordinates/tests/test_featurereader_and_tica.py' 2024-04-26T13:28:26,799 adding 'pyemma/coordinates/tests/test_featurereader_and_tica_projection.py' 2024-04-26T13:28:26,803 adding 'pyemma/coordinates/tests/test_featurizer.py' 2024-04-26T13:28:26,805 adding 'pyemma/coordinates/tests/test_fragmented_trajectory.py' 2024-04-26T13:28:26,807 adding 'pyemma/coordinates/tests/test_frames_from_file.py' 2024-04-26T13:28:26,809 adding 'pyemma/coordinates/tests/test_kmeans.py' 2024-04-26T13:28:26,811 adding 'pyemma/coordinates/tests/test_mini_batch_kmeans.py' 2024-04-26T13:28:26,813 adding 'pyemma/coordinates/tests/test_numpyfilereader.py' 2024-04-26T13:28:26,815 adding 'pyemma/coordinates/tests/test_pca.py' 2024-04-26T13:28:26,817 adding 'pyemma/coordinates/tests/test_pipeline.py' 2024-04-26T13:28:26,820 adding 'pyemma/coordinates/tests/test_random_access_stride.py' 2024-04-26T13:28:26,822 adding 'pyemma/coordinates/tests/test_regspace.py' 2024-04-26T13:28:26,824 adding 'pyemma/coordinates/tests/test_save_traj.py' 2024-04-26T13:28:26,826 adding 'pyemma/coordinates/tests/test_save_trajs.py' 2024-04-26T13:28:26,828 adding 'pyemma/coordinates/tests/test_source.py' 2024-04-26T13:28:26,830 adding 'pyemma/coordinates/tests/test_stride.py' 2024-04-26T13:28:26,832 adding 'pyemma/coordinates/tests/test_tica.py' 2024-04-26T13:28:26,834 adding 'pyemma/coordinates/tests/test_traj_info_cache.py' 2024-04-26T13:28:26,836 adding 'pyemma/coordinates/tests/test_uniform_time.py' 2024-04-26T13:28:26,837 adding 'pyemma/coordinates/tests/util.py' 2024-04-26T13:28:26,840 adding 'pyemma/coordinates/tests/data/bpti_001-033.xtc' 2024-04-26T13:28:26,843 adding 'pyemma/coordinates/tests/data/bpti_034-066.xtc' 2024-04-26T13:28:26,845 adding 'pyemma/coordinates/tests/data/bpti_067-100.xtc' 2024-04-26T13:28:26,847 adding 'pyemma/coordinates/tests/data/bpti_ca.pdb' 2024-04-26T13:28:26,865 adding 'pyemma/coordinates/tests/data/bpti_mini.binpos' 2024-04-26T13:28:26,882 adding 'pyemma/coordinates/tests/data/bpti_mini.dcd' 2024-04-26T13:28:26,890 adding 'pyemma/coordinates/tests/data/bpti_mini.h5' 2024-04-26T13:28:26,897 adding 'pyemma/coordinates/tests/data/bpti_mini.lh5' 2024-04-26T13:28:26,919 adding 'pyemma/coordinates/tests/data/bpti_mini.nc' 2024-04-26T13:28:26,940 adding 'pyemma/coordinates/tests/data/bpti_mini.netcdf' 2024-04-26T13:28:26,957 adding 'pyemma/coordinates/tests/data/bpti_mini.trr' 2024-04-26T13:28:26,962 adding 'pyemma/coordinates/tests/data/bpti_mini.xtc' 2024-04-26T13:28:26,964 adding 'pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz' 2024-04-26T13:28:26,974 adding 'pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz' 2024-04-26T13:28:26,976 adding 'pyemma/coordinates/tests/data/test.pdb' 2024-04-26T13:28:26,978 adding 'pyemma/coordinates/transform/__init__.py' 2024-04-26T13:28:26,980 adding 'pyemma/coordinates/transform/pca.py' 2024-04-26T13:28:26,983 adding 'pyemma/coordinates/transform/tica.py' 2024-04-26T13:28:26,985 adding 'pyemma/coordinates/transform/transformer.py' 2024-04-26T13:28:26,987 adding 'pyemma/coordinates/util/__init__.py' 2024-04-26T13:28:26,989 adding 'pyemma/coordinates/util/change_notification.py' 2024-04-26T13:28:26,991 adding 'pyemma/coordinates/util/patches.py' 2024-04-26T13:28:26,993 adding 'pyemma/coordinates/util/stat.py' 2024-04-26T13:28:26,995 adding 'pyemma/datasets/__init__.py' 2024-04-26T13:28:26,997 adding 'pyemma/datasets/api.py' 2024-04-26T13:28:27,005 adding 'pyemma/datasets/double_well_discrete.npz' 2024-04-26T13:28:27,007 adding 'pyemma/datasets/double_well_discrete.py' 2024-04-26T13:28:27,009 adding 'pyemma/msm/__init__.py' 2024-04-26T13:28:27,016 adding 'pyemma/msm/api.py' 2024-04-26T13:28:27,018 adding 'pyemma/msm/analysis/__init__.py' 2024-04-26T13:28:27,020 adding 'pyemma/msm/dtraj/__init__.py' 2024-04-26T13:28:27,022 adding 'pyemma/msm/estimation/__init__.py' 2024-04-26T13:28:27,024 adding 'pyemma/msm/estimators/__init__.py' 2024-04-26T13:28:27,026 adding 'pyemma/msm/estimators/_dtraj_stats.py' 2024-04-26T13:28:27,029 adding 'pyemma/msm/estimators/bayesian_hmsm.py' 2024-04-26T13:28:27,031 adding 'pyemma/msm/estimators/bayesian_msm.py' 2024-04-26T13:28:27,034 adding 'pyemma/msm/estimators/implied_timescales.py' 2024-04-26T13:28:27,036 adding 'pyemma/msm/estimators/lagged_model_validators.py' 2024-04-26T13:28:27,041 adding 'pyemma/msm/estimators/maximum_likelihood_hmsm.py' 2024-04-26T13:28:27,046 adding 'pyemma/msm/estimators/maximum_likelihood_msm.py' 2024-04-26T13:28:27,048 adding 'pyemma/msm/flux/__init__.py' 2024-04-26T13:28:27,050 adding 'pyemma/msm/generation/__init__.py' 2024-04-26T13:28:27,052 adding 'pyemma/msm/models/__init__.py' 2024-04-26T13:28:27,054 adding 'pyemma/msm/models/hmsm.py' 2024-04-26T13:28:27,056 adding 'pyemma/msm/models/hmsm_sampled.py' 2024-04-26T13:28:27,061 adding 'pyemma/msm/models/msm.py' 2024-04-26T13:28:27,064 adding 'pyemma/msm/models/msm_sampled.py' 2024-04-26T13:28:27,066 adding 'pyemma/msm/models/reactive_flux.py' 2024-04-26T13:28:27,069 adding 'pyemma/msm/tests/__init__.py' 2024-04-26T13:28:27,071 adding 'pyemma/msm/tests/birth_death_chain.py' 2024-04-26T13:28:27,073 adding 'pyemma/msm/tests/test_bayesian_hmsm.py' 2024-04-26T13:28:27,075 adding 'pyemma/msm/tests/test_bayesian_msm.py' 2024-04-26T13:28:27,077 adding 'pyemma/msm/tests/test_cktest.py' 2024-04-26T13:28:27,079 adding 'pyemma/msm/tests/test_estimator.py' 2024-04-26T13:28:27,082 adding 'pyemma/msm/tests/test_hmsm.py' 2024-04-26T13:28:27,084 adding 'pyemma/msm/tests/test_its.py' 2024-04-26T13:28:27,088 adding 'pyemma/msm/tests/test_msm.py' 2024-04-26T13:28:27,090 adding 'pyemma/msm/tests/test_msm_lowlevel_deprecation.py' 2024-04-26T13:28:27,092 adding 'pyemma/msm/tests/test_reactive_flux.py' 2024-04-26T13:28:27,094 adding 'pyemma/msm/tests/test_tpt.py' 2024-04-26T13:28:27,096 adding 'pyemma/plots/__init__.py' 2024-04-26T13:28:27,098 adding 'pyemma/plots/markovtests.py' 2024-04-26T13:28:27,101 adding 'pyemma/plots/networks.py' 2024-04-26T13:28:27,104 adding 'pyemma/plots/plots2d.py' 2024-04-26T13:28:27,105 adding 'pyemma/plots/thermoplots.py' 2024-04-26T13:28:27,108 adding 'pyemma/plots/timescales.py' 2024-04-26T13:28:27,109 adding 'pyemma/plots/_ext/__init__.py' 2024-04-26T13:28:27,111 adding 'pyemma/plots/_ext/fruchterman_reingold.py' 2024-04-26T13:28:27,113 adding 'pyemma/plots/tests/__init__.py' 2024-04-26T13:28:27,115 adding 'pyemma/plots/tests/test_its.py' 2024-04-26T13:28:27,117 adding 'pyemma/plots/tests/test_markovtests.py' 2024-04-26T13:28:27,118 adding 'pyemma/plots/tests/test_networks.py' 2024-04-26T13:28:27,120 adding 'pyemma/thermo/__init__.py' 2024-04-26T13:28:27,124 adding 'pyemma/thermo/api.py' 2024-04-26T13:28:27,127 adding 'pyemma/thermo/estimators/DTRAM_estimator.py' 2024-04-26T13:28:27,130 adding 'pyemma/thermo/estimators/TRAM_estimator.py' 2024-04-26T13:28:27,132 adding 'pyemma/thermo/estimators/WHAM_estimator.py' 2024-04-26T13:28:27,134 adding 'pyemma/thermo/estimators/__init__.py' 2024-04-26T13:28:27,136 adding 'pyemma/thermo/estimators/_callback.py' 2024-04-26T13:28:27,138 adding 'pyemma/thermo/models/__init__.py' 2024-04-26T13:28:27,140 adding 'pyemma/thermo/models/multi_therm.py' 2024-04-26T13:28:27,142 adding 'pyemma/thermo/models/stationary.py' 2024-04-26T13:28:27,144 adding 'pyemma/thermo/util/__init__.py' 2024-04-26T13:28:27,146 adding 'pyemma/thermo/util/util.py' 2024-04-26T13:28:27,149 adding 'pyemma/util/__init__.py' 2024-04-26T13:28:27,151 adding 'pyemma/util/annotators.py' 2024-04-26T13:28:27,154 adding 'pyemma/util/config.py' 2024-04-26T13:28:27,155 adding 'pyemma/util/contexts.py' 2024-04-26T13:28:27,157 adding 'pyemma/util/debug.py' 2024-04-26T13:28:27,159 adding 'pyemma/util/discrete_trajectories.py' 2024-04-26T13:28:27,161 adding 'pyemma/util/exceptions.py' 2024-04-26T13:28:27,163 adding 'pyemma/util/files.py' 2024-04-26T13:28:27,164 adding 'pyemma/util/indices.py' 2024-04-26T13:28:27,166 adding 'pyemma/util/linalg.py' 2024-04-26T13:28:27,168 adding 'pyemma/util/log.py' 2024-04-26T13:28:27,170 adding 'pyemma/util/numeric.py' 2024-04-26T13:28:27,172 adding 'pyemma/util/reflection.py' 2024-04-26T13:28:27,174 adding 'pyemma/util/statistics.py' 2024-04-26T13:28:27,175 adding 'pyemma/util/testing_tools.py' 2024-04-26T13:28:27,178 adding 'pyemma/util/types.py' 2024-04-26T13:28:27,180 adding 'pyemma/util/units.py' 2024-04-26T13:28:27,182 adding 'pyemma/util/_ext/__init__.py' 2024-04-26T13:28:27,183 adding 'pyemma/util/_ext/shimmodule.py' 2024-04-26T13:28:27,186 adding 'pyemma/util/tests/__init__.py' 2024-04-26T13:28:27,187 adding 'pyemma/util/tests/statistics_test.py' 2024-04-26T13:28:27,189 adding 'pyemma/util/tests/test_config.py' 2024-04-26T13:28:27,191 adding 'pyemma/util/tests/test_discrete_trajectories.py' 2024-04-26T13:28:27,193 adding 'pyemma/util/tests/test_estimation_required_decorator.py' 2024-04-26T13:28:27,195 adding 'pyemma/util/tests/test_log.py' 2024-04-26T13:28:27,196 adding 'pyemma/util/tests/test_shortcut.py' 2024-04-26T13:28:27,198 adding 'pyemma/util/tests/test_units.py' 2024-04-26T13:28:27,205 adding 'pyemma/util/tests/data/dtraj.dat' 2024-04-26T13:28:27,214 adding 'pyemma/util/tests/data/dtraj.npy' 2024-04-26T13:28:27,216 adding 'pyEMMA-2.2.dist-info/LICENSE.txt' 2024-04-26T13:28:27,218 adding 'pyEMMA-2.2.dist-info/METADATA' 2024-04-26T13:28:27,219 adding 'pyEMMA-2.2.dist-info/WHEEL' 2024-04-26T13:28:27,221 adding 'pyEMMA-2.2.dist-info/pbr.json' 2024-04-26T13:28:27,222 adding 'pyEMMA-2.2.dist-info/top_level.txt' 2024-04-26T13:28:27,226 adding 'pyEMMA-2.2.dist-info/RECORD' 2024-04-26T13:28:27,244 removing build/bdist.linux-armv7l/wheel 2024-04-26T13:28:27,534 Building wheel for pyemma (setup.py): finished with status 'done' 2024-04-26T13:28:27,550 Created wheel for pyemma: filename=pyEMMA-2.2-cp39-cp39-linux_armv7l.whl size=1326118 sha256=99ea8563b6c5c5af380aebafdecf899b0573195e2fd0f2f271c4483f4534f5e0 2024-04-26T13:28:27,551 Stored in directory: /tmp/pip-ephem-wheel-cache-1s9byull/wheels/8a/1f/da/6c8ddf65fda4b30609e3cc114e654b2ea3eb6c3ebc8726cff5 2024-04-26T13:28:27,570 Successfully built pyemma 2024-04-26T13:28:27,606 Removed build tracker: '/tmp/pip-build-tracker-mh70yfnq'