2024-04-26T15:45:49,822 Created temporary directory: /tmp/pip-build-tracker-b0g6v2j2 2024-04-26T15:45:49,824 Initialized build tracking at /tmp/pip-build-tracker-b0g6v2j2 2024-04-26T15:45:49,824 Created build tracker: /tmp/pip-build-tracker-b0g6v2j2 2024-04-26T15:45:49,824 Entered build tracker: /tmp/pip-build-tracker-b0g6v2j2 2024-04-26T15:45:49,825 Created temporary directory: /tmp/pip-wheel-jk9pfoya 2024-04-26T15:45:49,831 Created temporary directory: /tmp/pip-ephem-wheel-cache-du3ufbmq 2024-04-26T15:45:49,867 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-26T15:45:49,872 2 location(s) to search for versions of pyemma: 2024-04-26T15:45:49,872 * https://pypi.org/simple/pyemma/ 2024-04-26T15:45:49,872 * https://www.piwheels.org/simple/pyemma/ 2024-04-26T15:45:49,873 Fetching project page and analyzing links: https://pypi.org/simple/pyemma/ 2024-04-26T15:45:49,873 Getting page https://pypi.org/simple/pyemma/ 2024-04-26T15:45:49,875 Found index url https://pypi.org/simple/ 2024-04-26T15:45:49,943 Fetched page https://pypi.org/simple/pyemma/ as application/vnd.pypi.simple.v1+json 2024-04-26T15:45:49,951 Found link https://files.pythonhosted.org/packages/8e/31/2c2e23bbc16b404c8808c1043ebaf3aebfdd31dd90b979f213caad01f5bf/pyEMMA-1.0a2.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a2 2024-04-26T15:45:49,952 Found link https://files.pythonhosted.org/packages/1c/e3/453e32e448baa4274c622c82c87862164a34939b5139f4660db1fd470e2c/pyEMMA-1.0a3.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a3 2024-04-26T15:45:49,952 Found link https://files.pythonhosted.org/packages/9d/5a/d614dfaef84835bed7ec482b6fbaf1b94cc6fec0ca1e2f2ada7d3fdb9b7e/pyEMMA-1.0.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0 2024-04-26T15:45:49,952 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 2024-04-26T15:45:49,952 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 2024-04-26T15:45:49,953 Found link https://files.pythonhosted.org/packages/c3/28/e677fb5d7f98e1fc80442da7fd5bd56b96738d7c63c5dee64321128d7223/pyEMMA-1.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.1 2024-04-26T15:45:49,953 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 2024-04-26T15:45:49,953 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 2024-04-26T15:45:49,953 Found link https://files.pythonhosted.org/packages/a9/f4/d6db0d7f70baf531ec67a59f85a31e1f0940fcea4a9389527ddb47c0ac8b/pyEMMA-1.2.zip (from https://pypi.org/simple/pyemma/), version: 1.2 2024-04-26T15:45:49,954 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 2024-04-26T15:45:49,954 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 2024-04-26T15:45:49,954 Found link https://files.pythonhosted.org/packages/88/aa/78bbf546f420dc9c54b8d71f23ab0e17a7f6860ac986f36303544d13c747/pyEMMA-2.0.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.0 2024-04-26T15:45:49,954 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 2024-04-26T15:45:49,955 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 2024-04-26T15:45:49,955 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 2024-04-26T15:45:49,955 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 2024-04-26T15:45:49,956 Found link https://files.pythonhosted.org/packages/92/75/afa9da7a4e730829b583eb1e0851397b9a4775d823721fc9d640cb1812a4/pyemma-2.1rc1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc1 2024-04-26T15:45:49,956 Found link https://files.pythonhosted.org/packages/3e/99/e330c14650f11a7660b41d209d75b7de8f92173216c2f6b61041006b9429/pyEMMA-2.1rc2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc2 2024-04-26T15:45:49,956 Found link https://files.pythonhosted.org/packages/43/59/2d2adbb91b148051a271b4b5ae7676313622c5427b62e552762bbf829790/pyEMMA-2.1rc3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc3 2024-04-26T15:45:49,956 Found link https://files.pythonhosted.org/packages/52/19/fc61cfeb577540e680beba38ee21fe917e5f2bd74fcd60e9347c24199739/pyEMMA-2.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1 2024-04-26T15:45:49,957 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 2024-04-26T15:45:49,957 Found link https://files.pythonhosted.org/packages/ae/1f/61acb5b29f8bd8afd313d07a52ac91f47a4738c508b8a6e08cd2be82bc4b/pyEMMA-2.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2 2024-04-26T15:45:49,957 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 2024-04-26T15:45:49,957 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 2024-04-26T15:45:49,958 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 2024-04-26T15:45:49,958 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 2024-04-26T15:45:49,958 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 2024-04-26T15:45:49,958 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 2024-04-26T15:45:49,959 Found link https://files.pythonhosted.org/packages/d6/51/799c7406a1b5d6433360be894123ad0e326fd0c2370752d8b386c35cbbb7/pyEMMA-2.3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.3 2024-04-26T15:45:49,959 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 2024-04-26T15:45:49,959 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 2024-04-26T15:45:49,960 Found link https://files.pythonhosted.org/packages/45/d1/017a5298d6e67ab777268989c1793eb4d5d0869f366df7f1adf2a36a84e7/pyEMMA-2.4.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.4 2024-04-26T15:45:49,960 Found link https://files.pythonhosted.org/packages/8e/f7/9e5573f5da3d5314dcc79a41e138c5c9a6891bd72b92f9d18b7f59e85ab6/pyEMMA-2.5.zip (from https://pypi.org/simple/pyemma/), version: 2.5 2024-04-26T15:45:49,960 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 2024-04-26T15:45:49,960 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 2024-04-26T15:45:49,961 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 2024-04-26T15:45:49,961 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 2024-04-26T15:45:49,961 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 2024-04-26T15:45:49,962 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 2024-04-26T15:45:49,962 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 2024-04-26T15:45:49,962 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 2024-04-26T15:45:49,962 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 2024-04-26T15:45:49,963 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 2024-04-26T15:45:49,963 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 2024-04-26T15:45:49,963 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 2024-04-26T15:45:49,963 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyemma/ 2024-04-26T15:45:49,964 Getting page https://www.piwheels.org/simple/pyemma/ 2024-04-26T15:45:49,965 Found index url https://www.piwheels.org/simple/ 2024-04-26T15:45:50,032 Fetched page https://www.piwheels.org/simple/pyemma/ as text/html 2024-04-26T15:45:50,034 Skipping link: No binaries permitted for pyemma: https://www.piwheels.org/simple/pyemma/pyEMMA-2.2.1-cp39-cp39-linux_armv6l.whl#sha256=32d2163e9bc45f473bb9cd7022b5f7d459caa2ec784fcd56e25c186a47cb97ee (from https://www.piwheels.org/simple/pyemma/) 2024-04-26T15:45:50,035 Skipping link: No binaries permitted for pyemma: https://www.piwheels.org/simple/pyemma/pyEMMA-2.2.1-cp39-cp39-linux_armv7l.whl#sha256=32d2163e9bc45f473bb9cd7022b5f7d459caa2ec784fcd56e25c186a47cb97ee (from https://www.piwheels.org/simple/pyemma/) 2024-04-26T15:45:50,035 Skipping link: No binaries permitted for pyemma: https://www.piwheels.org/simple/pyemma/pyEMMA-2.2-cp39-cp39-linux_armv6l.whl#sha256=99ea8563b6c5c5af380aebafdecf899b0573195e2fd0f2f271c4483f4534f5e0 (from https://www.piwheels.org/simple/pyemma/) 2024-04-26T15:45:50,035 Skipping link: No binaries permitted for pyemma: https://www.piwheels.org/simple/pyemma/pyEMMA-2.2-cp39-cp39-linux_armv7l.whl#sha256=99ea8563b6c5c5af380aebafdecf899b0573195e2fd0f2f271c4483f4534f5e0 (from https://www.piwheels.org/simple/pyemma/) 2024-04-26T15:45:50,035 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/) 2024-04-26T15:45:50,035 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/) 2024-04-26T15:45:50,036 Skipping link: not a file: https://www.piwheels.org/simple/pyemma/ 2024-04-26T15:45:50,036 Skipping link: not a file: https://pypi.org/simple/pyemma/ 2024-04-26T15:45:50,059 Given no hashes to check 1 links for project 'pyemma': discarding no candidates 2024-04-26T15:45:50,076 Collecting pyemma==2.2.3 2024-04-26T15:45:50,079 Created temporary directory: /tmp/pip-unpack-3nw0c5h0 2024-04-26T15:45:50,458 Downloading pyEMMA-2.2.3.tar.gz (1.0 MB) 2024-04-26T15:45:51,177 Added pyemma==2.2.3 from https://files.pythonhosted.org/packages/d4/85/6430704c7947a7b01c20f864ffffdbc32c22369c32258051219a6e780596/pyEMMA-2.2.3.tar.gz to build tracker '/tmp/pip-build-tracker-b0g6v2j2' 2024-04-26T15:45:51,179 Running setup.py (path:/tmp/pip-wheel-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/setup.py) egg_info for package pyemma 2024-04-26T15:45:51,180 Created temporary directory: /tmp/pip-pip-egg-info-l_ojklcn 2024-04-26T15:45:51,180 Preparing metadata (setup.py): started 2024-04-26T15:45:51,181 Running command python setup.py egg_info 2024-04-26T15:45:51,811 /tmp/pip-wheel-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T15:45:51,811 from pkg_resources import VersionConflict 2024-04-26T15:45:52,124 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T15:45:52,124 !! 2024-04-26T15:45:52,124 ******************************************************************************** 2024-04-26T15:45:52,124 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T15:45:52,124 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T15:45:52,125 ******************************************************************************** 2024-04-26T15:45:52,125 !! 2024-04-26T15:45:52,125 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T15:46:04,390 running egg_info 2024-04-26T15:46:04,392 creating /tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info 2024-04-26T15:46:04,459 writing /tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info/PKG-INFO 2024-04-26T15:46:04,464 writing dependency_links to /tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info/dependency_links.txt 2024-04-26T15:46:04,466 writing requirements to /tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info/requires.txt 2024-04-26T15:46:04,486 creating /tmp/hasfunction-sisjwy22/tmp 2024-04-26T15:46:04,487 creating /tmp/hasfunction-sisjwy22/tmp/hasfunction-sisjwy22 2024-04-26T15:46:04,488 cc -c /tmp/hasfunction-sisjwy22/funcname.c -o /tmp/hasfunction-sisjwy22/tmp/hasfunction-sisjwy22/funcname.o 2024-04-26T15:46:04,566 cc /tmp/hasfunction-sisjwy22/tmp/hasfunction-sisjwy22/funcname.o -o /tmp/hasfunction-sisjwy22/a.out 2024-04-26T15:46:04,668 creating /tmp/hasfunction-w65dyq2p/tmp 2024-04-26T15:46:04,669 creating /tmp/hasfunction-w65dyq2p/tmp/hasfunction-w65dyq2p 2024-04-26T15:46:04,670 cc -c /tmp/hasfunction-w65dyq2p/funcname.c -o /tmp/hasfunction-w65dyq2p/tmp/hasfunction-w65dyq2p/funcname.o 2024-04-26T15:46:04,742 cc /tmp/hasfunction-w65dyq2p/tmp/hasfunction-w65dyq2p/funcname.o -lgomp -o /tmp/hasfunction-w65dyq2p/a.out 2024-04-26T15:46:07,654 /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-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T15:46:07,655 tree = Parsing.p_module(s, pxd, full_module_name) 2024-04-26T15:46:08,601 Compiling pyemma/coordinates/estimators/covar/covar_c/covartools.pyx because it changed. 2024-04-26T15:46:08,602 [1/1] Cythonizing pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T15:46:08,602 /tmp/pip-wheel-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/setup.py:154: UserWarning: enabled openmp 2024-04-26T15:46:08,602 warnings.warn('enabled openmp') 2024-04-26T15:46:08,603 writing top-level names to /tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info/top_level.txt 2024-04-26T15:46:08,604 writing manifest file '/tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T15:46:08,766 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 2024-04-26T15:46:08,766 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 2024-04-26T15:46:08,766 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 2024-04-26T15:46:08,767 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 2024-04-26T15:46:08,767 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 2024-04-26T15:46:08,813 reading manifest file '/tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T15:46:08,815 reading manifest template 'MANIFEST.in' 2024-04-26T15:46:08,972 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T15:46:08,973 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T15:46:08,975 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T15:46:08,981 no previously-included directories found matching 'doc/build' 2024-04-26T15:46:08,982 no previously-included directories found matching 'doc/source/generated' 2024-04-26T15:46:08,983 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T15:46:08,984 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T15:46:08,986 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T15:46:09,227 no previously-included directories found matching '.eggs' 2024-04-26T15:46:09,228 adding license file 'LICENSE.txt' 2024-04-26T15:46:09,239 writing manifest file '/tmp/pip-pip-egg-info-l_ojklcn/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T15:46:09,593 Preparing metadata (setup.py): finished with status 'done' 2024-04-26T15:46:09,599 Source in /tmp/pip-wheel-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8 has version 2.2.3, which satisfies requirement pyemma==2.2.3 from https://files.pythonhosted.org/packages/d4/85/6430704c7947a7b01c20f864ffffdbc32c22369c32258051219a6e780596/pyEMMA-2.2.3.tar.gz 2024-04-26T15:46:09,600 Removed pyemma==2.2.3 from https://files.pythonhosted.org/packages/d4/85/6430704c7947a7b01c20f864ffffdbc32c22369c32258051219a6e780596/pyEMMA-2.2.3.tar.gz from build tracker '/tmp/pip-build-tracker-b0g6v2j2' 2024-04-26T15:46:09,605 Created temporary directory: /tmp/pip-unpack-vak1uy39 2024-04-26T15:46:09,606 Created temporary directory: /tmp/pip-unpack-3ibhduok 2024-04-26T15:46:09,624 Building wheels for collected packages: pyemma 2024-04-26T15:46:09,629 Created temporary directory: /tmp/pip-wheel-igdok4kh 2024-04-26T15:46:09,629 Building wheel for pyemma (setup.py): started 2024-04-26T15:46:09,630 Destination directory: /tmp/pip-wheel-igdok4kh 2024-04-26T15:46:09,630 Running command python setup.py bdist_wheel 2024-04-26T15:46:10,183 /tmp/pip-wheel-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T15:46:10,184 from pkg_resources import VersionConflict 2024-04-26T15:46:10,493 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T15:46:10,494 !! 2024-04-26T15:46:10,494 ******************************************************************************** 2024-04-26T15:46:10,494 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T15:46:10,494 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T15:46:10,494 ******************************************************************************** 2024-04-26T15:46:10,494 !! 2024-04-26T15:46:10,494 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T15:46:11,779 running bdist_wheel 2024-04-26T15:46:11,886 creating /tmp/hasfunction-t5mk5c3j/tmp 2024-04-26T15:46:11,887 creating /tmp/hasfunction-t5mk5c3j/tmp/hasfunction-t5mk5c3j 2024-04-26T15:46:11,888 cc -c /tmp/hasfunction-t5mk5c3j/funcname.c -o /tmp/hasfunction-t5mk5c3j/tmp/hasfunction-t5mk5c3j/funcname.o 2024-04-26T15:46:11,961 cc /tmp/hasfunction-t5mk5c3j/tmp/hasfunction-t5mk5c3j/funcname.o -o /tmp/hasfunction-t5mk5c3j/a.out 2024-04-26T15:46:12,064 creating /tmp/hasfunction-nasi0vl8/tmp 2024-04-26T15:46:12,065 creating /tmp/hasfunction-nasi0vl8/tmp/hasfunction-nasi0vl8 2024-04-26T15:46:12,066 cc -c /tmp/hasfunction-nasi0vl8/funcname.c -o /tmp/hasfunction-nasi0vl8/tmp/hasfunction-nasi0vl8/funcname.o 2024-04-26T15:46:12,138 cc /tmp/hasfunction-nasi0vl8/tmp/hasfunction-nasi0vl8/funcname.o -lgomp -o /tmp/hasfunction-nasi0vl8/a.out 2024-04-26T15:46:13,653 /tmp/pip-wheel-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/setup.py:154: UserWarning: enabled openmp 2024-04-26T15:46:13,653 warnings.warn('enabled openmp') 2024-04-26T15:46:13,745 running build 2024-04-26T15:46:13,745 running build_py 2024-04-26T15:46:13,751 creating build 2024-04-26T15:46:13,752 creating build/lib.linux-armv7l-cpython-39 2024-04-26T15:46:13,753 creating build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T15:46:13,754 copying pyemma/_version.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T15:46:13,756 copying pyemma/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T15:46:13,759 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T15:46:13,760 copying pyemma/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T15:46:13,762 copying pyemma/coordinates/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T15:46:13,766 copying pyemma/coordinates/acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T15:46:13,769 copying pyemma/coordinates/pipelines.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T15:46:13,773 creating build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T15:46:13,774 copying pyemma/datasets/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T15:46:13,778 copying pyemma/datasets/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T15:46:13,780 copying pyemma/datasets/double_well_discrete.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T15:46:13,783 creating build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,784 copying pyemma/util/units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,787 copying pyemma/util/numeric.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,789 copying pyemma/util/annotators.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,791 copying pyemma/util/linalg.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,794 copying pyemma/util/exceptions.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,796 copying pyemma/util/reflection.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,799 copying pyemma/util/discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,801 copying pyemma/util/debug.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,803 copying pyemma/util/contexts.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,805 copying pyemma/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,807 copying pyemma/util/config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,810 copying pyemma/util/types.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,813 copying pyemma/util/statistics.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,815 copying pyemma/util/indices.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,818 copying pyemma/util/files.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,819 copying pyemma/util/log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,822 copying pyemma/util/testing_tools.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T15:46:13,825 creating build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T15:46:13,826 copying pyemma/_base/estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T15:46:13,829 copying pyemma/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T15:46:13,831 copying pyemma/_base/model.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T15:46:13,834 copying pyemma/_base/logging.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T15:46:13,837 creating build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T15:46:13,838 copying pyemma/msm/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T15:46:13,841 copying pyemma/msm/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T15:46:13,846 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T15:46:13,847 copying pyemma/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T15:46:13,849 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T15:46:13,851 copying pyemma/thermo/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T15:46:13,853 copying pyemma/thermo/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T15:46:13,859 creating build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T15:46:13,861 copying pyemma/plots/thermoplots.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T15:46:13,865 copying pyemma/plots/plots2d.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T15:46:13,867 copying pyemma/plots/markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T15:46:13,870 copying pyemma/plots/timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T15:46:13,872 copying pyemma/plots/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T15:46:13,874 copying pyemma/plots/networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T15:46:13,878 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T15:46:13,879 copying pyemma/coordinates/util/patches.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T15:46:13,882 copying pyemma/coordinates/util/stat.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T15:46:13,884 copying pyemma/coordinates/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T15:46:13,886 copying pyemma/coordinates/util/change_notification.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T15:46:13,889 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T15:46:13,890 copying pyemma/coordinates/data/data_in_memory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T15:46:13,893 copying pyemma/coordinates/data/numpy_filereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T15:46:13,895 copying pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T15:46:13,899 copying pyemma/coordinates/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T15:46:13,901 copying pyemma/coordinates/data/feature_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T15:46:13,905 copying pyemma/coordinates/data/py_csv_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T15:46:13,909 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,910 copying pyemma/coordinates/tests/test_regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,913 copying pyemma/coordinates/tests/test_api_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,915 copying pyemma/coordinates/tests/test_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,918 copying pyemma/coordinates/tests/test_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,920 copying pyemma/coordinates/tests/test_traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,923 copying pyemma/coordinates/tests/test_save_trajs.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,926 copying pyemma/coordinates/tests/test_featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,929 copying pyemma/coordinates/tests/test_api_load.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,932 copying pyemma/coordinates/tests/test_datainmemory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,934 copying pyemma/coordinates/tests/test_coordinates_iterator.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,936 copying pyemma/coordinates/tests/test_frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,939 copying pyemma/coordinates/tests/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,941 copying pyemma/coordinates/tests/test_assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,944 copying pyemma/coordinates/tests/test_random_access_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,947 copying pyemma/coordinates/tests/test_pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,949 copying pyemma/coordinates/tests/test_csvreader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,952 copying pyemma/coordinates/tests/test_numpyfilereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,954 copying pyemma/coordinates/tests/test_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,956 copying pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,958 copying pyemma/coordinates/tests/test_featurereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,961 copying pyemma/coordinates/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,962 copying pyemma/coordinates/tests/test_acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,964 copying pyemma/coordinates/tests/test_discretizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,966 copying pyemma/coordinates/tests/test_cluster_samples.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,968 copying pyemma/coordinates/tests/test_save_traj.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,970 copying pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,972 copying pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,974 copying pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,976 copying pyemma/coordinates/tests/test_pipeline.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,978 copying pyemma/coordinates/tests/test_cluster.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,980 copying pyemma/coordinates/tests/test_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,982 copying pyemma/coordinates/tests/test_uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T15:46:13,984 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T15:46:13,985 copying pyemma/coordinates/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T15:46:13,987 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:13,988 copying pyemma/coordinates/clustering/assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:13,989 copying pyemma/coordinates/clustering/interface.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:13,992 copying pyemma/coordinates/clustering/uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:13,993 copying pyemma/coordinates/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:13,995 copying pyemma/coordinates/clustering/regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:13,997 copying pyemma/coordinates/clustering/kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:14,000 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T15:46:14,001 copying pyemma/coordinates/transform/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T15:46:14,002 copying pyemma/coordinates/transform/transformer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T15:46:14,005 copying pyemma/coordinates/transform/tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T15:46:14,007 copying pyemma/coordinates/transform/pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T15:46:14,010 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T15:46:14,011 copying pyemma/coordinates/data/util/traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T15:46:14,013 copying pyemma/coordinates/data/util/frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T15:46:14,015 copying pyemma/coordinates/data/util/reader_utils.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T15:46:14,018 copying pyemma/coordinates/data/util/traj_info_backends.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T15:46:14,020 copying pyemma/coordinates/data/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T15:46:14,022 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T15:46:14,023 copying pyemma/coordinates/data/_base/datasource.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T15:46:14,026 copying pyemma/coordinates/data/_base/iterable.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T15:46:14,028 copying pyemma/coordinates/data/_base/random_accessible.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T15:46:14,030 copying pyemma/coordinates/data/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T15:46:14,032 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,033 copying pyemma/coordinates/data/featurization/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,036 copying pyemma/coordinates/data/featurization/featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,038 copying pyemma/coordinates/data/featurization/_base.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,040 copying pyemma/coordinates/data/featurization/angles.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,042 copying pyemma/coordinates/data/featurization/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,044 copying pyemma/coordinates/data/featurization/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,046 copying pyemma/coordinates/data/featurization/distances.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T15:46:14,049 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T15:46:14,049 copying pyemma/coordinates/estimators/covar/moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T15:46:14,052 copying pyemma/coordinates/estimators/covar/running_moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T15:46:14,055 copying pyemma/coordinates/estimators/covar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T15:46:14,057 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T15:46:14,057 copying pyemma/coordinates/estimators/covar/covar_c/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T15:46:14,060 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,060 copying pyemma/util/tests/test_log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,062 copying pyemma/util/tests/test_units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,064 copying pyemma/util/tests/test_config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,066 copying pyemma/util/tests/statistics_test.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,068 copying pyemma/util/tests/test_estimation_required_decorator.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,069 copying pyemma/util/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,071 copying pyemma/util/tests/test_discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,073 copying pyemma/util/tests/test_shortcut.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T15:46:14,075 creating build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T15:46:14,076 copying pyemma/util/_ext/shimmodule.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T15:46:14,078 copying pyemma/util/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T15:46:14,080 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T15:46:14,080 copying pyemma/_base/tests/test_progress.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T15:46:14,082 copying pyemma/_base/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T15:46:14,084 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T15:46:14,085 copying pyemma/_base/progress/reporter.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T15:46:14,087 copying pyemma/_base/progress/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T15:46:14,090 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T15:46:14,090 copying pyemma/_base/progress/bar/gui.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T15:46:14,093 copying pyemma/_base/progress/bar/_impl.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T15:46:14,095 copying pyemma/_base/progress/bar/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T15:46:14,097 copying pyemma/_base/progress/bar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T15:46:14,100 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,101 copying pyemma/msm/tests/test_bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,104 copying pyemma/msm/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,107 copying pyemma/msm/tests/test_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,110 copying pyemma/msm/tests/test_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,111 copying pyemma/msm/tests/test_reactive_flux.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,114 copying pyemma/msm/tests/test_msm_lowlevel_deprecation.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,116 copying pyemma/msm/tests/test_cktest.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,118 copying pyemma/msm/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,120 copying pyemma/msm/tests/test_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,122 copying pyemma/msm/tests/test_tpt.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,124 copying pyemma/msm/tests/test_bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,126 copying pyemma/msm/tests/birth_death_chain.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T15:46:14,129 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T15:46:14,130 copying pyemma/msm/models/reactive_flux.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T15:46:14,132 copying pyemma/msm/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T15:46:14,134 copying pyemma/msm/models/msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T15:46:14,136 copying pyemma/msm/models/hmsm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T15:46:14,138 copying pyemma/msm/models/msm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T15:46:14,140 copying pyemma/msm/models/hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T15:46:14,143 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,144 copying pyemma/msm/estimators/bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,147 copying pyemma/msm/estimators/bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,150 copying pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,153 copying pyemma/msm/estimators/maximum_likelihood_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,156 copying pyemma/msm/estimators/implied_timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,159 copying pyemma/msm/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,160 copying pyemma/msm/estimators/_dtraj_stats.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,163 copying pyemma/msm/estimators/lagged_model_validators.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T15:46:14,166 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T15:46:14,167 copying pyemma/_ext/sklearn/base.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T15:46:14,170 copying pyemma/_ext/sklearn/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T15:46:14,173 copying pyemma/_ext/sklearn/parameter_search.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T15:46:14,177 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T15:46:14,178 copying pyemma/thermo/util/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T15:46:14,182 copying pyemma/thermo/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T15:46:14,185 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T15:46:14,186 copying pyemma/thermo/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T15:46:14,188 copying pyemma/thermo/models/stationary.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T15:46:14,190 copying pyemma/thermo/models/multi_therm.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T15:46:14,192 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T15:46:14,193 copying pyemma/thermo/estimators/DTRAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T15:46:14,196 copying pyemma/thermo/estimators/_callback.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T15:46:14,197 copying pyemma/thermo/estimators/WHAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T15:46:14,199 copying pyemma/thermo/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T15:46:14,201 copying pyemma/thermo/estimators/MBAR_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T15:46:14,203 copying pyemma/thermo/estimators/TRAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T15:46:14,206 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T15:46:14,207 copying pyemma/plots/tests/test_markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T15:46:14,209 copying pyemma/plots/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T15:46:14,210 copying pyemma/plots/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T15:46:14,212 copying pyemma/plots/tests/test_networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T15:46:14,214 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T15:46:14,215 copying pyemma/plots/_ext/fruchterman_reingold.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T15:46:14,217 copying pyemma/plots/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T15:46:14,234 copying pyemma/pyemma.cfg -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T15:46:14,236 copying pyemma/logging.yml -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T15:46:14,238 copying pyemma/datasets/double_well_discrete.npz -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T15:46:14,242 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,243 copying pyemma/coordinates/tests/data/test.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,245 copying pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,248 copying pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,252 copying pyemma/coordinates/tests/data/bpti_mini.binpos -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,256 copying pyemma/coordinates/tests/data/bpti_mini.lh5 -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,260 copying pyemma/coordinates/tests/data/bpti_mini.trr -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,265 copying pyemma/coordinates/tests/data/bpti_ca.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,267 copying pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,270 copying pyemma/coordinates/tests/data/bpti_mini.h5 -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,274 copying pyemma/coordinates/tests/data/bpti_mini.dcd -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,278 copying pyemma/coordinates/tests/data/bpti_mini.netcdf -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,282 copying pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,285 copying pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,287 copying pyemma/coordinates/tests/data/bpti_mini.nc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,292 copying pyemma/coordinates/tests/data/bpti_mini.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T15:46:14,295 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T15:46:14,296 copying pyemma/util/tests/data/dtraj.dat -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T15:46:14,299 copying pyemma/util/tests/data/dtraj.npy -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T15:46:14,322 UPDATING build/lib.linux-armv7l-cpython-39/pyemma/_version.py 2024-04-26T15:46:14,323 set build/lib.linux-armv7l-cpython-39/pyemma/_version.py to '2.2.3' 2024-04-26T15:46:14,323 running build_ext 2024-04-26T15:46:14,327 building 'pyemma.coordinates.clustering.regspatial' extension 2024-04-26T15:46:14,328 creating build/temp.linux-armv7l-cpython-39 2024-04-26T15:46:14,328 creating build/temp.linux-armv7l-cpython-39/pyemma 2024-04-26T15:46:14,329 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T15:46:14,330 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T15:46:14,330 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src 2024-04-26T15:46:14,331 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-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/.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 2024-04-26T15:46:14,690 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T15:46:14,690 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T15:46:14,690 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T15:46:14,691 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T15:46:14,691 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T15:46:14,691 /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] 2024-04-26T15:46:14,691 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T15:46:14,691 | ^~~~~~~ 2024-04-26T15:46:14,721 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T15:46:14,721 pyemma/coordinates/clustering/src/clustering.c:81:23: warning: unused variable ‘trace_centers’ [-Wunused-variable] 2024-04-26T15:46:14,721 81 | float d, mindist, trace_centers; 2024-04-26T15:46:14,722 | ^~~~~~~~~~~~~ 2024-04-26T15:46:14,722 pyemma/coordinates/clustering/src/clustering.c:81:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T15:46:14,722 81 | float d, mindist, trace_centers; 2024-04-26T15:46:14,722 | ^ 2024-04-26T15:46:14,730 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T15:46:14,731 At top level: 2024-04-26T15:46:14,731 pyemma/coordinates/clustering/include/clustering.h:59:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T15:46:14,731 59 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T15:46:14,731 | ^~~~~~~~~~~~ 2024-04-26T15:46:14,733 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T15:46:14,734 pyemma/coordinates/clustering/src/clustering.c:94:7: warning: ‘debug’ is used uninitialized in this function [-Wuninitialized] 2024-04-26T15:46:14,734 94 | if(debug) printf("using openmp; n_threads=%i\n", n_threads); 2024-04-26T15:46:14,734 | ^ 2024-04-26T15:46:14,862 pyemma/coordinates/clustering/src/clustering.c:135:13: warning: ‘distance’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T15:46:14,863 135 | #pragma omp parallel private(buffer_a, buffer_b, i, j, chunk_p, mindist, argmin) 2024-04-26T15:46:14,863 | ^~~ 2024-04-26T15:46:15,005 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-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/.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 2024-04-26T15:46:15,318 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T15:46:15,318 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T15:46:15,318 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T15:46:15,318 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T15:46:15,318 from pyemma/coordinates/clustering/src/regspatial.c:19: 2024-04-26T15:46:15,318 /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] 2024-04-26T15:46:15,319 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T15:46:15,319 | ^~~~~~~ 2024-04-26T15:46:15,358 pyemma/coordinates/clustering/src/regspatial.c:177:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T15:46:15,358 177 | error_out(PyObject *m) { 2024-04-26T15:46:15,358 | ^~~~~~~~~ 2024-04-26T15:46:15,358 pyemma/coordinates/clustering/src/regspatial.c:127:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T15:46:15,359 127 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T15:46:15,359 | ^~~~~~~~~ 2024-04-26T15:46:15,632 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-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/.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 2024-04-26T15:46:15,763 building 'pyemma.coordinates.clustering.kmeans_clustering' extension 2024-04-26T15:46:15,764 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-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/.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 2024-04-26T15:46:16,083 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T15:46:16,083 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T15:46:16,083 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T15:46:16,084 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T15:46:16,084 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T15:46:16,084 /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] 2024-04-26T15:46:16,084 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T15:46:16,084 | ^~~~~~~ 2024-04-26T15:46:16,110 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T15:46:16,111 pyemma/coordinates/clustering/src/clustering.c:81:23: warning: unused variable ‘trace_centers’ [-Wunused-variable] 2024-04-26T15:46:16,111 81 | float d, mindist, trace_centers; 2024-04-26T15:46:16,111 | ^~~~~~~~~~~~~ 2024-04-26T15:46:16,111 pyemma/coordinates/clustering/src/clustering.c:81:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T15:46:16,111 81 | float d, mindist, trace_centers; 2024-04-26T15:46:16,111 | ^ 2024-04-26T15:46:16,120 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T15:46:16,120 At top level: 2024-04-26T15:46:16,120 pyemma/coordinates/clustering/include/clustering.h:59:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T15:46:16,120 59 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T15:46:16,120 | ^~~~~~~~~~~~ 2024-04-26T15:46:16,123 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T15:46:16,123 pyemma/coordinates/clustering/src/clustering.c:94:7: warning: ‘debug’ is used uninitialized in this function [-Wuninitialized] 2024-04-26T15:46:16,123 94 | if(debug) printf("using openmp; n_threads=%i\n", n_threads); 2024-04-26T15:46:16,123 | ^ 2024-04-26T15:46:16,247 pyemma/coordinates/clustering/src/clustering.c:135:13: warning: ‘distance’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T15:46:16,247 135 | #pragma omp parallel private(buffer_a, buffer_b, i, j, chunk_p, mindist, argmin) 2024-04-26T15:46:16,247 | ^~~ 2024-04-26T15:46:16,390 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-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/.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 2024-04-26T15:46:16,646 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T15:46:16,647 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T15:46:16,647 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T15:46:16,647 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T15:46:16,647 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T15:46:16,647 /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] 2024-04-26T15:46:16,647 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T15:46:16,647 | ^~~~~~~ 2024-04-26T15:46:16,672 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T15:46:16,672 pyemma/coordinates/clustering/src/kmeans.c:51:38: warning: variable ‘py_res’ set but not used [-Wunused-but-set-variable] 2024-04-26T15:46:16,672 51 | PyObject *py_centers, *py_item, *py_res; 2024-04-26T15:46:16,672 | ^~~~~~ 2024-04-26T15:46:16,673 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T15:46:16,674 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T15:46:16,674 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T15:46:16,674 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T15:46:16,674 pyemma/coordinates/clustering/src/kmeans.c: In function ‘costFunction’: 2024-04-26T15:46:16,675 pyemma/coordinates/clustering/src/kmeans.c:251:47: warning: passing argument 1 of ‘PyList_GetItem’ from incompatible pointer type [-Wincompatible-pointer-types] 2024-04-26T15:46:16,676 251 | centers = PyArray_DATA(PyList_GetItem(np_centers,r)); 2024-04-26T15:46:16,676 | ^~~~~~~~~~ 2024-04-26T15:46:16,676 | | 2024-04-26T15:46:16,676 | PyArrayObject * {aka struct tagPyArrayObject_fields *} 2024-04-26T15:46:16,676 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1605:62: note: in definition of macro ‘PyArray_DATA’ 2024-04-26T15:46:16,676 1605 | #define PyArray_DATA(obj) ((void *)((PyArrayObject_fields *)(obj))->data) 2024-04-26T15:46:16,676 | ^~~ 2024-04-26T15:46:16,677 In file included from /usr/include/python3.9/Python.h:106, 2024-04-26T15:46:16,677 from pyemma/coordinates/clustering/include/clustering.h:25, 2024-04-26T15:46:16,677 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T15:46:16,677 /usr/include/python3.9/listobject.h:31:39: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PyArrayObject *’ {aka ‘struct tagPyArrayObject_fields *’} 2024-04-26T15:46:16,678 31 | PyAPI_FUNC(PyObject *) PyList_GetItem(PyObject *, Py_ssize_t); 2024-04-26T15:46:16,678 | ^~~~~~~~~~ 2024-04-26T15:46:16,678 pyemma/coordinates/clustering/src/kmeans.c:217:18: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] 2024-04-26T15:46:16,679 217 | float value, d; 2024-04-26T15:46:16,679 | ^ 2024-04-26T15:46:16,679 pyemma/coordinates/clustering/src/kmeans.c:216:15: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 2024-04-26T15:46:16,679 216 | int k, i, j, r; 2024-04-26T15:46:16,679 | ^ 2024-04-26T15:46:16,697 At top level: 2024-04-26T15:46:16,698 pyemma/coordinates/clustering/src/kmeans.c:581:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T15:46:16,698 581 | error_out(PyObject *m) { 2024-04-26T15:46:16,698 | ^~~~~~~~~ 2024-04-26T15:46:16,698 pyemma/coordinates/clustering/src/kmeans.c:509:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T15:46:16,698 509 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T15:46:16,699 | ^~~~~~~~~ 2024-04-26T15:46:16,860 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T15:46:16,860 pyemma/coordinates/clustering/src/kmeans.c:171:50: warning: ‘closest_center_index’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T15:46:16,860 171 | new_centers[closest_center_index*dim+j] += chunk[i*dim+j]; 2024-04-26T15:46:16,861 | ^~ 2024-04-26T15:46:17,395 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-jk9pfoya/pyemma_2e998aff26bf42b482d79633773b9fc8/.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 2024-04-26T15:46:17,520 building 'pyemma.coordinates.estimators.covar.covar_c.covartools' extension 2024-04-26T15:46:17,521 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T15:46:17,522 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T15:46:17,522 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T15:46:17,523 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 2024-04-26T15:46:17,953 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 2024-04-26T15:46:18,272 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T15:46:18,272 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T15:46:18,272 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T15:46:18,272 from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1257: 2024-04-26T15:46:18,272 /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] 2024-04-26T15:46:18,273 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T15:46:18,273 | ^~~~~~~ 2024-04-26T15:46:18,381 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_12subtract_row_float’: 2024-04-26T15:46:18,384 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] 2024-04-26T15:46:18,385 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T15:46:18,385 | ^~~~~~~~~~ 2024-04-26T15:46:18,385 | | 2024-04-26T15:46:18,385 | float * 2024-04-26T15:46:18,385 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T15:46:18,385 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:34: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T15:46:18,385 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T15:46:18,386 | ~~~~~~~~^ 2024-04-26T15:46:18,389 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] 2024-04-26T15:46:18,389 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T15:46:18,389 | ^~~~~~~~~~~~ 2024-04-26T15:46:18,389 | | 2024-04-26T15:46:18,389 | float * 2024-04-26T15:46:18,389 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T15:46:18,390 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:45: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T15:46:18,390 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T15:46:18,390 | ~~~~~~~~^~~ 2024-04-26T15:46:18,428 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_18subtract_row_float_copy’: 2024-04-26T15:46:18,435 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] 2024-04-26T15:46:18,435 7472 | _subtract_row_float_copy(__pyx_v_pX0, __pyx_v_pX, __pyx_v_prow, __pyx_t_6, __pyx_t_7); 2024-04-26T15:46:18,435 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2024-04-26T15:46:18,435 | _subtract_row_float 2024-04-26T15:46:29,533 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 2024-04-26T15:46:29,718 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-04-26T15:46:29,718 !! 2024-04-26T15:46:29,719 ******************************************************************************** 2024-04-26T15:46:29,719 Please avoid running ``setup.py`` directly. 2024-04-26T15:46:29,719 Instead, use pypa/build, pypa/installer or other 2024-04-26T15:46:29,719 standards-based tools. 2024-04-26T15:46:29,719 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-04-26T15:46:29,720 ******************************************************************************** 2024-04-26T15:46:29,720 !! 2024-04-26T15:46:29,720 self.initialize_options() 2024-04-26T15:46:29,765 installing to build/bdist.linux-armv7l/wheel 2024-04-26T15:46:29,765 running install 2024-04-26T15:46:29,790 running install_lib 2024-04-26T15:46:29,835 creating build/bdist.linux-armv7l 2024-04-26T15:46:29,836 creating build/bdist.linux-armv7l/wheel 2024-04-26T15:46:29,838 creating build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T15:46:29,839 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T15:46:29,841 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T15:46:29,842 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/patches.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T15:46:29,845 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/stat.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T15:46:29,847 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T15:46:29,849 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/change_notification.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T15:46:29,851 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T15:46:29,852 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/data_in_memory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T15:46:29,855 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/numpy_filereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T15:46:29,858 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T15:46:29,859 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T15:46:29,862 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T15:46:29,864 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/reader_utils.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T15:46:29,867 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/traj_info_backends.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T15:46:29,870 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T15:46:29,872 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T15:46:29,873 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/datasource.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T15:46:29,876 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/iterable.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T15:46:29,879 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/random_accessible.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T15:46:29,881 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T15:46:29,883 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T15:46:29,885 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T15:46:29,888 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,889 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/util.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,892 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,895 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/_base.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,897 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/angles.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,899 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,902 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,903 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/distances.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T15:46:29,905 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/feature_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T15:46:29,908 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/py_csv_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T15:46:29,911 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,912 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,915 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,918 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,920 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,922 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,925 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_trajs.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,927 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,930 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_load.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,932 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_datainmemory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,935 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_coordinates_iterator.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,937 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,940 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/util.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,942 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,944 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_random_access_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:29,947 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,948 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/test.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,950 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,952 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 2024-04-26T15:46:29,957 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.binpos -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,961 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.lh5 -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,965 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.trr -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,970 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_ca.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,973 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,975 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.h5 -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,979 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.dcd -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,984 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.netcdf -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,988 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 2024-04-26T15:46:29,990 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,992 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.nc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,996 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T15:46:29,999 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,001 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_csvreader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,004 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_numpyfilereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,006 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,009 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,011 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,014 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,015 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,018 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_discretizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,020 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster_samples.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,022 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_traj.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,024 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,027 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,029 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,031 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pipeline.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,033 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,035 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,038 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T15:46:30,040 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T15:46:30,042 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/api.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T15:46:30,045 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T15:46:30,048 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T15:46:30,049 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T15:46:30,051 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T15:46:30,053 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T15:46:30,054 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 2024-04-26T15:46:30,069 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 2024-04-26T15:46:30,071 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T15:46:30,074 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/running_moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T15:46:30,077 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T15:46:30,079 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T15:46:30,080 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 2024-04-26T15:46:30,085 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T15:46:30,087 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/interface.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T15:46:30,090 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T15:46:30,092 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T15:46:30,094 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T15:46:30,096 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 2024-04-26T15:46:30,104 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T15:46:30,107 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T15:46:30,108 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T15:46:30,110 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/transformer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T15:46:30,113 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T15:46:30,115 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T15:46:30,118 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/pipelines.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T15:46:30,121 creating build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T15:46:30,121 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.npz -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T15:46:30,125 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T15:46:30,127 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/api.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T15:46:30,129 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T15:46:30,131 creating build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,132 copying build/lib.linux-armv7l-cpython-39/pyemma/util/units.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,135 copying build/lib.linux-armv7l-cpython-39/pyemma/util/numeric.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,137 copying build/lib.linux-armv7l-cpython-39/pyemma/util/annotators.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,139 copying build/lib.linux-armv7l-cpython-39/pyemma/util/linalg.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,141 copying build/lib.linux-armv7l-cpython-39/pyemma/util/exceptions.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,143 copying build/lib.linux-armv7l-cpython-39/pyemma/util/reflection.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,145 copying build/lib.linux-armv7l-cpython-39/pyemma/util/discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,149 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,150 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_log.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,152 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_units.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,154 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_config.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,156 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/statistics_test.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,158 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_estimation_required_decorator.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,160 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T15:46:30,161 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.dat -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T15:46:30,164 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.npy -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T15:46:30,169 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,171 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,173 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_shortcut.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T15:46:30,175 copying build/lib.linux-armv7l-cpython-39/pyemma/util/debug.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,177 creating build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T15:46:30,178 copying build/lib.linux-armv7l-cpython-39/pyemma/util/_ext/shimmodule.py -> build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T15:46:30,180 copying build/lib.linux-armv7l-cpython-39/pyemma/util/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T15:46:30,182 copying build/lib.linux-armv7l-cpython-39/pyemma/util/contexts.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,184 copying build/lib.linux-armv7l-cpython-39/pyemma/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,185 copying build/lib.linux-armv7l-cpython-39/pyemma/util/config.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,188 copying build/lib.linux-armv7l-cpython-39/pyemma/util/types.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,190 copying build/lib.linux-armv7l-cpython-39/pyemma/util/statistics.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,192 copying build/lib.linux-armv7l-cpython-39/pyemma/util/indices.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,194 copying build/lib.linux-armv7l-cpython-39/pyemma/util/files.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,196 copying build/lib.linux-armv7l-cpython-39/pyemma/util/log.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,198 copying build/lib.linux-armv7l-cpython-39/pyemma/util/testing_tools.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T15:46:30,200 copying build/lib.linux-armv7l-cpython-39/pyemma/pyemma.cfg -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T15:46:30,202 creating build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T15:46:30,203 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T15:46:30,206 creating build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T15:46:30,207 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/test_progress.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T15:46:30,209 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T15:46:30,210 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T15:46:30,213 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T15:46:30,213 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/reporter.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T15:46:30,216 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T15:46:30,217 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/gui.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T15:46:30,219 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/_impl.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T15:46:30,221 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T15:46:30,224 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T15:46:30,225 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T15:46:30,227 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/model.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T15:46:30,230 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/logging.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T15:46:30,232 creating build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T15:46:30,233 creating build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,234 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,237 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,239 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,242 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,243 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_reactive_flux.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,246 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_msm_lowlevel_deprecation.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,248 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_cktest.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,250 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,252 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,255 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_tpt.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,257 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,259 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/birth_death_chain.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T15:46:30,262 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T15:46:30,264 creating build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T15:46:30,265 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/reactive_flux.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T15:46:30,267 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T15:46:30,269 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T15:46:30,272 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T15:46:30,274 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T15:46:30,275 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T15:46:30,278 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/api.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T15:46:30,282 creating build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,282 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,285 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,287 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,290 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,293 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/implied_timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,296 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,297 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/_dtraj_stats.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,300 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/lagged_model_validators.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T15:46:30,302 creating build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T15:46:30,303 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T15:46:30,305 creating build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T15:46:30,306 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/base.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T15:46:30,310 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T15:46:30,312 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/parameter_search.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T15:46:30,315 copying build/lib.linux-armv7l-cpython-39/pyemma/_version.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T15:46:30,317 copying build/lib.linux-armv7l-cpython-39/pyemma/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T15:46:30,320 copying build/lib.linux-armv7l-cpython-39/pyemma/logging.yml -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T15:46:30,322 creating build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T15:46:30,323 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T15:46:30,324 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/util.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T15:46:30,327 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T15:46:30,329 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T15:46:30,331 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T15:46:30,332 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T15:46:30,334 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/stationary.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T15:46:30,336 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/multi_therm.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T15:46:30,338 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/api.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T15:46:30,342 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T15:46:30,343 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/DTRAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T15:46:30,345 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/_callback.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T15:46:30,347 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/WHAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T15:46:30,349 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T15:46:30,351 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/MBAR_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T15:46:30,353 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/TRAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T15:46:30,357 creating build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T15:46:30,358 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/thermoplots.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T15:46:30,360 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/plots2d.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T15:46:30,362 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T15:46:30,365 creating build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T15:46:30,365 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T15:46:30,367 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T15:46:30,369 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T15:46:30,371 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T15:46:30,373 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T15:46:30,376 creating build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T15:46:30,377 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/fruchterman_reingold.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T15:46:30,379 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T15:46:30,380 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T15:46:30,382 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T15:46:30,386 running install_egg_info 2024-04-26T15:46:30,479 running egg_info 2024-04-26T15:46:30,524 writing pyEMMA.egg-info/PKG-INFO 2024-04-26T15:46:30,529 writing dependency_links to pyEMMA.egg-info/dependency_links.txt 2024-04-26T15:46:30,531 writing requirements to pyEMMA.egg-info/requires.txt 2024-04-26T15:46:30,532 writing top-level names to pyEMMA.egg-info/top_level.txt 2024-04-26T15:46:30,595 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 2024-04-26T15:46:30,595 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 2024-04-26T15:46:30,595 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 2024-04-26T15:46:30,596 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 2024-04-26T15:46:30,596 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 2024-04-26T15:46:30,641 reading manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T15:46:30,654 reading manifest template 'MANIFEST.in' 2024-04-26T15:46:30,806 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T15:46:30,808 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T15:46:30,809 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T15:46:30,813 no previously-included directories found matching 'doc/build' 2024-04-26T15:46:30,814 no previously-included directories found matching 'doc/source/generated' 2024-04-26T15:46:30,815 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T15:46:30,817 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T15:46:30,818 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T15:46:31,056 no previously-included directories found matching '.eggs' 2024-04-26T15:46:31,057 adding license file 'LICENSE.txt' 2024-04-26T15:46:31,072 writing manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T15:46:31,074 Copying pyEMMA.egg-info to build/bdist.linux-armv7l/wheel/pyEMMA-2.2.3-py3.9.egg-info 2024-04-26T15:46:31,088 running install_scripts 2024-04-26T15:46:31,112 adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") 2024-04-26T15:46:31,119 creating build/bdist.linux-armv7l/wheel/pyEMMA-2.2.3.dist-info/WHEEL 2024-04-26T15:46:31,122 creating '/tmp/pip-wheel-igdok4kh/pyEMMA-2.2.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-04-26T15:46:31,126 adding 'pyemma/__init__.py' 2024-04-26T15:46:31,127 adding 'pyemma/_version.py' 2024-04-26T15:46:31,128 adding 'pyemma/logging.yml' 2024-04-26T15:46:31,129 adding 'pyemma/pyemma.cfg' 2024-04-26T15:46:31,131 adding 'pyemma/_base/__init__.py' 2024-04-26T15:46:31,134 adding 'pyemma/_base/estimator.py' 2024-04-26T15:46:31,135 adding 'pyemma/_base/logging.py' 2024-04-26T15:46:31,137 adding 'pyemma/_base/model.py' 2024-04-26T15:46:31,139 adding 'pyemma/_base/progress/__init__.py' 2024-04-26T15:46:31,141 adding 'pyemma/_base/progress/reporter.py' 2024-04-26T15:46:31,142 adding 'pyemma/_base/progress/bar/__init__.py' 2024-04-26T15:46:31,145 adding 'pyemma/_base/progress/bar/_impl.py' 2024-04-26T15:46:31,147 adding 'pyemma/_base/progress/bar/gui.py' 2024-04-26T15:46:31,149 adding 'pyemma/_base/progress/bar/misc.py' 2024-04-26T15:46:31,150 adding 'pyemma/_base/tests/__init__.py' 2024-04-26T15:46:31,152 adding 'pyemma/_base/tests/test_progress.py' 2024-04-26T15:46:31,154 adding 'pyemma/_ext/__init__.py' 2024-04-26T15:46:31,155 adding 'pyemma/_ext/sklearn/__init__.py' 2024-04-26T15:46:31,158 adding 'pyemma/_ext/sklearn/base.py' 2024-04-26T15:46:31,159 adding 'pyemma/_ext/sklearn/parameter_search.py' 2024-04-26T15:46:31,161 adding 'pyemma/coordinates/__init__.py' 2024-04-26T15:46:31,163 adding 'pyemma/coordinates/acf.py' 2024-04-26T15:46:31,171 adding 'pyemma/coordinates/api.py' 2024-04-26T15:46:31,174 adding 'pyemma/coordinates/pipelines.py' 2024-04-26T15:46:31,176 adding 'pyemma/coordinates/clustering/__init__.py' 2024-04-26T15:46:31,177 adding 'pyemma/coordinates/clustering/assign.py' 2024-04-26T15:46:31,180 adding 'pyemma/coordinates/clustering/interface.py' 2024-04-26T15:46:31,182 adding 'pyemma/coordinates/clustering/kmeans.py' 2024-04-26T15:46:31,205 adding 'pyemma/coordinates/clustering/kmeans_clustering.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T15:46:31,207 adding 'pyemma/coordinates/clustering/regspace.py' 2024-04-26T15:46:31,226 adding 'pyemma/coordinates/clustering/regspatial.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T15:46:31,229 adding 'pyemma/coordinates/clustering/uniform_time.py' 2024-04-26T15:46:31,231 adding 'pyemma/coordinates/data/__init__.py' 2024-04-26T15:46:31,233 adding 'pyemma/coordinates/data/data_in_memory.py' 2024-04-26T15:46:31,235 adding 'pyemma/coordinates/data/feature_reader.py' 2024-04-26T15:46:31,238 adding 'pyemma/coordinates/data/fragmented_trajectory_reader.py' 2024-04-26T15:46:31,240 adding 'pyemma/coordinates/data/numpy_filereader.py' 2024-04-26T15:46:31,242 adding 'pyemma/coordinates/data/py_csv_reader.py' 2024-04-26T15:46:31,244 adding 'pyemma/coordinates/data/_base/__init__.py' 2024-04-26T15:46:31,247 adding 'pyemma/coordinates/data/_base/datasource.py' 2024-04-26T15:46:31,249 adding 'pyemma/coordinates/data/_base/iterable.py' 2024-04-26T15:46:31,251 adding 'pyemma/coordinates/data/_base/random_accessible.py' 2024-04-26T15:46:31,253 adding 'pyemma/coordinates/data/featurization/__init__.py' 2024-04-26T15:46:31,254 adding 'pyemma/coordinates/data/featurization/_base.py' 2024-04-26T15:46:31,256 adding 'pyemma/coordinates/data/featurization/angles.py' 2024-04-26T15:46:31,257 adding 'pyemma/coordinates/data/featurization/distances.py' 2024-04-26T15:46:31,261 adding 'pyemma/coordinates/data/featurization/featurizer.py' 2024-04-26T15:46:31,263 adding 'pyemma/coordinates/data/featurization/misc.py' 2024-04-26T15:46:31,265 adding 'pyemma/coordinates/data/featurization/util.py' 2024-04-26T15:46:31,267 adding 'pyemma/coordinates/data/util/__init__.py' 2024-04-26T15:46:31,269 adding 'pyemma/coordinates/data/util/frames_from_file.py' 2024-04-26T15:46:31,270 adding 'pyemma/coordinates/data/util/reader_utils.py' 2024-04-26T15:46:31,273 adding 'pyemma/coordinates/data/util/traj_info_backends.py' 2024-04-26T15:46:31,275 adding 'pyemma/coordinates/data/util/traj_info_cache.py' 2024-04-26T15:46:31,276 adding 'pyemma/coordinates/estimators/__init__.py' 2024-04-26T15:46:31,278 adding 'pyemma/coordinates/estimators/covar/__init__.py' 2024-04-26T15:46:31,281 adding 'pyemma/coordinates/estimators/covar/moments.py' 2024-04-26T15:46:31,284 adding 'pyemma/coordinates/estimators/covar/running_moments.py' 2024-04-26T15:46:31,285 adding 'pyemma/coordinates/estimators/covar/covar_c/__init__.py' 2024-04-26T15:46:31,403 adding 'pyemma/coordinates/estimators/covar/covar_c/covartools.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T15:46:31,412 adding 'pyemma/coordinates/tests/__init__.py' 2024-04-26T15:46:31,415 adding 'pyemma/coordinates/tests/test_acf.py' 2024-04-26T15:46:31,417 adding 'pyemma/coordinates/tests/test_api_load.py' 2024-04-26T15:46:31,420 adding 'pyemma/coordinates/tests/test_api_source.py' 2024-04-26T15:46:31,422 adding 'pyemma/coordinates/tests/test_assign.py' 2024-04-26T15:46:31,424 adding 'pyemma/coordinates/tests/test_cluster.py' 2024-04-26T15:46:31,425 adding 'pyemma/coordinates/tests/test_cluster_samples.py' 2024-04-26T15:46:31,427 adding 'pyemma/coordinates/tests/test_coordinates_iterator.py' 2024-04-26T15:46:31,429 adding 'pyemma/coordinates/tests/test_csvreader.py' 2024-04-26T15:46:31,431 adding 'pyemma/coordinates/tests/test_datainmemory.py' 2024-04-26T15:46:31,433 adding 'pyemma/coordinates/tests/test_discretizer.py' 2024-04-26T15:46:31,434 adding 'pyemma/coordinates/tests/test_featurereader.py' 2024-04-26T15:46:31,436 adding 'pyemma/coordinates/tests/test_featurereader_and_tica.py' 2024-04-26T15:46:31,438 adding 'pyemma/coordinates/tests/test_featurereader_and_tica_projection.py' 2024-04-26T15:46:31,441 adding 'pyemma/coordinates/tests/test_featurizer.py' 2024-04-26T15:46:31,443 adding 'pyemma/coordinates/tests/test_fragmented_trajectory.py' 2024-04-26T15:46:31,445 adding 'pyemma/coordinates/tests/test_frames_from_file.py' 2024-04-26T15:46:31,446 adding 'pyemma/coordinates/tests/test_kmeans.py' 2024-04-26T15:46:31,448 adding 'pyemma/coordinates/tests/test_mini_batch_kmeans.py' 2024-04-26T15:46:31,449 adding 'pyemma/coordinates/tests/test_numpyfilereader.py' 2024-04-26T15:46:31,451 adding 'pyemma/coordinates/tests/test_pca.py' 2024-04-26T15:46:31,453 adding 'pyemma/coordinates/tests/test_pipeline.py' 2024-04-26T15:46:31,455 adding 'pyemma/coordinates/tests/test_random_access_stride.py' 2024-04-26T15:46:31,457 adding 'pyemma/coordinates/tests/test_regspace.py' 2024-04-26T15:46:31,459 adding 'pyemma/coordinates/tests/test_save_traj.py' 2024-04-26T15:46:31,460 adding 'pyemma/coordinates/tests/test_save_trajs.py' 2024-04-26T15:46:31,462 adding 'pyemma/coordinates/tests/test_source.py' 2024-04-26T15:46:31,463 adding 'pyemma/coordinates/tests/test_stride.py' 2024-04-26T15:46:31,466 adding 'pyemma/coordinates/tests/test_tica.py' 2024-04-26T15:46:31,468 adding 'pyemma/coordinates/tests/test_traj_info_cache.py' 2024-04-26T15:46:31,469 adding 'pyemma/coordinates/tests/test_uniform_time.py' 2024-04-26T15:46:31,470 adding 'pyemma/coordinates/tests/util.py' 2024-04-26T15:46:31,473 adding 'pyemma/coordinates/tests/data/bpti_001-033.xtc' 2024-04-26T15:46:31,475 adding 'pyemma/coordinates/tests/data/bpti_034-066.xtc' 2024-04-26T15:46:31,477 adding 'pyemma/coordinates/tests/data/bpti_067-100.xtc' 2024-04-26T15:46:31,479 adding 'pyemma/coordinates/tests/data/bpti_ca.pdb' 2024-04-26T15:46:31,496 adding 'pyemma/coordinates/tests/data/bpti_mini.binpos' 2024-04-26T15:46:31,513 adding 'pyemma/coordinates/tests/data/bpti_mini.dcd' 2024-04-26T15:46:31,521 adding 'pyemma/coordinates/tests/data/bpti_mini.h5' 2024-04-26T15:46:31,528 adding 'pyemma/coordinates/tests/data/bpti_mini.lh5' 2024-04-26T15:46:31,549 adding 'pyemma/coordinates/tests/data/bpti_mini.nc' 2024-04-26T15:46:31,571 adding 'pyemma/coordinates/tests/data/bpti_mini.netcdf' 2024-04-26T15:46:31,588 adding 'pyemma/coordinates/tests/data/bpti_mini.trr' 2024-04-26T15:46:31,592 adding 'pyemma/coordinates/tests/data/bpti_mini.xtc' 2024-04-26T15:46:31,594 adding 'pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz' 2024-04-26T15:46:31,604 adding 'pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz' 2024-04-26T15:46:31,605 adding 'pyemma/coordinates/tests/data/test.pdb' 2024-04-26T15:46:31,607 adding 'pyemma/coordinates/transform/__init__.py' 2024-04-26T15:46:31,609 adding 'pyemma/coordinates/transform/pca.py' 2024-04-26T15:46:31,612 adding 'pyemma/coordinates/transform/tica.py' 2024-04-26T15:46:31,614 adding 'pyemma/coordinates/transform/transformer.py' 2024-04-26T15:46:31,615 adding 'pyemma/coordinates/util/__init__.py' 2024-04-26T15:46:31,617 adding 'pyemma/coordinates/util/change_notification.py' 2024-04-26T15:46:31,619 adding 'pyemma/coordinates/util/patches.py' 2024-04-26T15:46:31,620 adding 'pyemma/coordinates/util/stat.py' 2024-04-26T15:46:31,622 adding 'pyemma/datasets/__init__.py' 2024-04-26T15:46:31,623 adding 'pyemma/datasets/api.py' 2024-04-26T15:46:31,631 adding 'pyemma/datasets/double_well_discrete.npz' 2024-04-26T15:46:31,633 adding 'pyemma/datasets/double_well_discrete.py' 2024-04-26T15:46:31,635 adding 'pyemma/msm/__init__.py' 2024-04-26T15:46:31,641 adding 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'pyemma/msm/models/reactive_flux.py' 2024-04-26T15:46:31,680 adding 'pyemma/msm/tests/__init__.py' 2024-04-26T15:46:31,681 adding 'pyemma/msm/tests/birth_death_chain.py' 2024-04-26T15:46:31,683 adding 'pyemma/msm/tests/test_bayesian_hmsm.py' 2024-04-26T15:46:31,685 adding 'pyemma/msm/tests/test_bayesian_msm.py' 2024-04-26T15:46:31,687 adding 'pyemma/msm/tests/test_cktest.py' 2024-04-26T15:46:31,689 adding 'pyemma/msm/tests/test_estimator.py' 2024-04-26T15:46:31,691 adding 'pyemma/msm/tests/test_hmsm.py' 2024-04-26T15:46:31,693 adding 'pyemma/msm/tests/test_its.py' 2024-04-26T15:46:31,697 adding 'pyemma/msm/tests/test_msm.py' 2024-04-26T15:46:31,698 adding 'pyemma/msm/tests/test_msm_lowlevel_deprecation.py' 2024-04-26T15:46:31,700 adding 'pyemma/msm/tests/test_reactive_flux.py' 2024-04-26T15:46:31,702 adding 'pyemma/msm/tests/test_tpt.py' 2024-04-26T15:46:31,705 adding 'pyemma/plots/__init__.py' 2024-04-26T15:46:31,707 adding 'pyemma/plots/markovtests.py' 2024-04-26T15:46:31,710 adding 'pyemma/plots/networks.py' 2024-04-26T15:46:31,712 adding 'pyemma/plots/plots2d.py' 2024-04-26T15:46:31,714 adding 'pyemma/plots/thermoplots.py' 2024-04-26T15:46:31,715 adding 'pyemma/plots/timescales.py' 2024-04-26T15:46:31,717 adding 'pyemma/plots/_ext/__init__.py' 2024-04-26T15:46:31,719 adding 'pyemma/plots/_ext/fruchterman_reingold.py' 2024-04-26T15:46:31,721 adding 'pyemma/plots/tests/__init__.py' 2024-04-26T15:46:31,722 adding 'pyemma/plots/tests/test_its.py' 2024-04-26T15:46:31,723 adding 'pyemma/plots/tests/test_markovtests.py' 2024-04-26T15:46:31,725 adding 'pyemma/plots/tests/test_networks.py' 2024-04-26T15:46:31,727 adding 'pyemma/thermo/__init__.py' 2024-04-26T15:46:31,731 adding 'pyemma/thermo/api.py' 2024-04-26T15:46:31,734 adding 'pyemma/thermo/estimators/DTRAM_estimator.py' 2024-04-26T15:46:31,735 adding 'pyemma/thermo/estimators/MBAR_estimator.py' 2024-04-26T15:46:31,738 adding 'pyemma/thermo/estimators/TRAM_estimator.py' 2024-04-26T15:46:31,740 adding 'pyemma/thermo/estimators/WHAM_estimator.py' 2024-04-26T15:46:31,741 adding 'pyemma/thermo/estimators/__init__.py' 2024-04-26T15:46:31,742 adding 'pyemma/thermo/estimators/_callback.py' 2024-04-26T15:46:31,745 adding 'pyemma/thermo/models/__init__.py' 2024-04-26T15:46:31,746 adding 'pyemma/thermo/models/multi_therm.py' 2024-04-26T15:46:31,748 adding 'pyemma/thermo/models/stationary.py' 2024-04-26T15:46:31,750 adding 'pyemma/thermo/util/__init__.py' 2024-04-26T15:46:31,752 adding 'pyemma/thermo/util/util.py' 2024-04-26T15:46:31,754 adding 'pyemma/util/__init__.py' 2024-04-26T15:46:31,756 adding 'pyemma/util/annotators.py' 2024-04-26T15:46:31,759 adding 'pyemma/util/config.py' 2024-04-26T15:46:31,760 adding 'pyemma/util/contexts.py' 2024-04-26T15:46:31,761 adding 'pyemma/util/debug.py' 2024-04-26T15:46:31,763 adding 'pyemma/util/discrete_trajectories.py' 2024-04-26T15:46:31,765 adding 'pyemma/util/exceptions.py' 2024-04-26T15:46:31,766 adding 'pyemma/util/files.py' 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'pyemma/util/tests/test_estimation_required_decorator.py' 2024-04-26T15:46:31,794 adding 'pyemma/util/tests/test_log.py' 2024-04-26T15:46:31,795 adding 'pyemma/util/tests/test_shortcut.py' 2024-04-26T15:46:31,796 adding 'pyemma/util/tests/test_units.py' 2024-04-26T15:46:31,803 adding 'pyemma/util/tests/data/dtraj.dat' 2024-04-26T15:46:31,812 adding 'pyemma/util/tests/data/dtraj.npy' 2024-04-26T15:46:31,814 adding 'pyEMMA-2.2.3.dist-info/LICENSE.txt' 2024-04-26T15:46:31,816 adding 'pyEMMA-2.2.3.dist-info/METADATA' 2024-04-26T15:46:31,817 adding 'pyEMMA-2.2.3.dist-info/WHEEL' 2024-04-26T15:46:31,818 adding 'pyEMMA-2.2.3.dist-info/pbr.json' 2024-04-26T15:46:31,819 adding 'pyEMMA-2.2.3.dist-info/top_level.txt' 2024-04-26T15:46:31,822 adding 'pyEMMA-2.2.3.dist-info/RECORD' 2024-04-26T15:46:31,860 removing build/bdist.linux-armv7l/wheel 2024-04-26T15:46:32,164 Building wheel for pyemma (setup.py): finished with status 'done' 2024-04-26T15:46:32,181 Created wheel for pyemma: filename=pyEMMA-2.2.3-cp39-cp39-linux_armv7l.whl size=1332887 sha256=c643ee36812f31eb86e608115dd78c33ea1d987242f636f4fe0f341f49c221a5 2024-04-26T15:46:32,182 Stored in directory: /tmp/pip-ephem-wheel-cache-du3ufbmq/wheels/5e/1d/cd/cd6baac11e9f6b623382499f2095bf6218912588961e3a3af0 2024-04-26T15:46:32,200 Successfully built pyemma 2024-04-26T15:46:32,254 Removed build tracker: '/tmp/pip-build-tracker-b0g6v2j2'