2024-04-26T14:26:29,331 Created temporary directory: /tmp/pip-build-tracker-ynlb_imd 2024-04-26T14:26:29,332 Initialized build tracking at /tmp/pip-build-tracker-ynlb_imd 2024-04-26T14:26:29,333 Created build tracker: /tmp/pip-build-tracker-ynlb_imd 2024-04-26T14:26:29,333 Entered build tracker: /tmp/pip-build-tracker-ynlb_imd 2024-04-26T14:26:29,333 Created temporary directory: /tmp/pip-wheel-13_siqhn 2024-04-26T14:26:29,337 Created temporary directory: /tmp/pip-ephem-wheel-cache-jl85m115 2024-04-26T14:26:29,361 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-26T14:26:29,365 2 location(s) to search for versions of pyemma: 2024-04-26T14:26:29,365 * https://pypi.org/simple/pyemma/ 2024-04-26T14:26:29,365 * https://www.piwheels.org/simple/pyemma/ 2024-04-26T14:26:29,365 Fetching project page and analyzing links: https://pypi.org/simple/pyemma/ 2024-04-26T14:26:29,366 Getting page https://pypi.org/simple/pyemma/ 2024-04-26T14:26:29,367 Found index url https://pypi.org/simple/ 2024-04-26T14:26:29,419 Fetched page https://pypi.org/simple/pyemma/ as application/vnd.pypi.simple.v1+json 2024-04-26T14:26:29,427 Found link https://files.pythonhosted.org/packages/8e/31/2c2e23bbc16b404c8808c1043ebaf3aebfdd31dd90b979f213caad01f5bf/pyEMMA-1.0a2.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a2 2024-04-26T14:26:29,428 Found link https://files.pythonhosted.org/packages/1c/e3/453e32e448baa4274c622c82c87862164a34939b5139f4660db1fd470e2c/pyEMMA-1.0a3.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0a3 2024-04-26T14:26:29,428 Found link https://files.pythonhosted.org/packages/9d/5a/d614dfaef84835bed7ec482b6fbaf1b94cc6fec0ca1e2f2ada7d3fdb9b7e/pyEMMA-1.0.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.0 2024-04-26T14:26:29,429 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 2024-04-26T14:26:29,429 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 2024-04-26T14:26:29,429 Found link https://files.pythonhosted.org/packages/c3/28/e677fb5d7f98e1fc80442da7fd5bd56b96738d7c63c5dee64321128d7223/pyEMMA-1.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 1.1 2024-04-26T14:26:29,429 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 2024-04-26T14:26:29,430 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 2024-04-26T14:26:29,430 Found link https://files.pythonhosted.org/packages/a9/f4/d6db0d7f70baf531ec67a59f85a31e1f0940fcea4a9389527ddb47c0ac8b/pyEMMA-1.2.zip (from https://pypi.org/simple/pyemma/), version: 1.2 2024-04-26T14:26:29,430 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 2024-04-26T14:26:29,430 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 2024-04-26T14:26:29,431 Found link https://files.pythonhosted.org/packages/88/aa/78bbf546f420dc9c54b8d71f23ab0e17a7f6860ac986f36303544d13c747/pyEMMA-2.0.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.0 2024-04-26T14:26:29,431 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 2024-04-26T14:26:29,431 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 2024-04-26T14:26:29,431 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 2024-04-26T14:26:29,432 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 2024-04-26T14:26:29,432 Found link https://files.pythonhosted.org/packages/92/75/afa9da7a4e730829b583eb1e0851397b9a4775d823721fc9d640cb1812a4/pyemma-2.1rc1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc1 2024-04-26T14:26:29,432 Found link https://files.pythonhosted.org/packages/3e/99/e330c14650f11a7660b41d209d75b7de8f92173216c2f6b61041006b9429/pyEMMA-2.1rc2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc2 2024-04-26T14:26:29,432 Found link https://files.pythonhosted.org/packages/43/59/2d2adbb91b148051a271b4b5ae7676313622c5427b62e552762bbf829790/pyEMMA-2.1rc3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1rc3 2024-04-26T14:26:29,433 Found link https://files.pythonhosted.org/packages/52/19/fc61cfeb577540e680beba38ee21fe917e5f2bd74fcd60e9347c24199739/pyEMMA-2.1.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.1 2024-04-26T14:26:29,433 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 2024-04-26T14:26:29,433 Found link https://files.pythonhosted.org/packages/ae/1f/61acb5b29f8bd8afd313d07a52ac91f47a4738c508b8a6e08cd2be82bc4b/pyEMMA-2.2.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.2 2024-04-26T14:26:29,434 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 2024-04-26T14:26:29,434 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 2024-04-26T14:26:29,434 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 2024-04-26T14:26:29,434 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 2024-04-26T14:26:29,435 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 2024-04-26T14:26:29,435 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 2024-04-26T14:26:29,435 Found link https://files.pythonhosted.org/packages/d6/51/799c7406a1b5d6433360be894123ad0e326fd0c2370752d8b386c35cbbb7/pyEMMA-2.3.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.3 2024-04-26T14:26:29,435 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 2024-04-26T14:26:29,436 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 2024-04-26T14:26:29,436 Found link https://files.pythonhosted.org/packages/45/d1/017a5298d6e67ab777268989c1793eb4d5d0869f366df7f1adf2a36a84e7/pyEMMA-2.4.tar.gz (from https://pypi.org/simple/pyemma/), version: 2.4 2024-04-26T14:26:29,436 Found link https://files.pythonhosted.org/packages/8e/f7/9e5573f5da3d5314dcc79a41e138c5c9a6891bd72b92f9d18b7f59e85ab6/pyEMMA-2.5.zip (from https://pypi.org/simple/pyemma/), version: 2.5 2024-04-26T14:26:29,436 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 2024-04-26T14:26:29,437 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 2024-04-26T14:26:29,437 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 2024-04-26T14:26:29,437 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 2024-04-26T14:26:29,437 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 2024-04-26T14:26:29,438 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 2024-04-26T14:26:29,438 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 2024-04-26T14:26:29,438 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 2024-04-26T14:26:29,439 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 2024-04-26T14:26:29,439 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 2024-04-26T14:26:29,439 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 2024-04-26T14:26:29,439 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 2024-04-26T14:26:29,440 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyemma/ 2024-04-26T14:26:29,440 Getting page https://www.piwheels.org/simple/pyemma/ 2024-04-26T14:26:29,441 Found index url https://www.piwheels.org/simple/ 2024-04-26T14:26:29,532 Fetched page https://www.piwheels.org/simple/pyemma/ as text/html 2024-04-26T14:26:29,534 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/) 2024-04-26T14:26:29,534 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/) 2024-04-26T14:26:29,535 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/) 2024-04-26T14:26:29,535 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/) 2024-04-26T14:26:29,535 Skipping link: not a file: https://www.piwheels.org/simple/pyemma/ 2024-04-26T14:26:29,535 Skipping link: not a file: https://pypi.org/simple/pyemma/ 2024-04-26T14:26:29,566 Given no hashes to check 1 links for project 'pyemma': discarding no candidates 2024-04-26T14:26:29,590 Collecting pyemma==2.2.1 2024-04-26T14:26:29,593 Created temporary directory: /tmp/pip-unpack-t26j64q2 2024-04-26T14:26:29,735 Downloading pyEMMA-2.2.1.zip (1.2 MB) 2024-04-26T14:26:30,458 Added pyemma==2.2.1 from https://files.pythonhosted.org/packages/8b/fa/5b40eb124d6c6862b4c51579bb71c0c78f076309869902f3fffb64d257b6/pyEMMA-2.2.1.zip to build tracker '/tmp/pip-build-tracker-ynlb_imd' 2024-04-26T14:26:30,459 Running setup.py (path:/tmp/pip-wheel-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/setup.py) egg_info for package pyemma 2024-04-26T14:26:30,460 Created temporary directory: /tmp/pip-pip-egg-info-sgdym2jx 2024-04-26T14:26:30,460 Preparing metadata (setup.py): started 2024-04-26T14:26:30,461 Running command python setup.py egg_info 2024-04-26T14:26:31,020 /tmp/pip-wheel-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T14:26:31,020 from pkg_resources import VersionConflict 2024-04-26T14:26:31,254 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T14:26:31,254 !! 2024-04-26T14:26:31,254 ******************************************************************************** 2024-04-26T14:26:31,254 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T14:26:31,254 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T14:26:31,255 ******************************************************************************** 2024-04-26T14:26:31,255 !! 2024-04-26T14:26:31,255 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T14:26:42,471 running egg_info 2024-04-26T14:26:42,473 creating /tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info 2024-04-26T14:26:42,503 writing /tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info/PKG-INFO 2024-04-26T14:26:42,508 writing dependency_links to /tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info/dependency_links.txt 2024-04-26T14:26:42,510 writing requirements to /tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info/requires.txt 2024-04-26T14:26:42,530 creating /tmp/hasfunction-6xbl_v99/tmp 2024-04-26T14:26:42,530 creating /tmp/hasfunction-6xbl_v99/tmp/hasfunction-6xbl_v99 2024-04-26T14:26:42,532 cc -c /tmp/hasfunction-6xbl_v99/funcname.c -o /tmp/hasfunction-6xbl_v99/tmp/hasfunction-6xbl_v99/funcname.o 2024-04-26T14:26:42,603 cc /tmp/hasfunction-6xbl_v99/tmp/hasfunction-6xbl_v99/funcname.o -o /tmp/hasfunction-6xbl_v99/a.out 2024-04-26T14:26:42,707 creating /tmp/hasfunction-r7bay8w1/tmp 2024-04-26T14:26:42,708 creating /tmp/hasfunction-r7bay8w1/tmp/hasfunction-r7bay8w1 2024-04-26T14:26:42,709 cc -c /tmp/hasfunction-r7bay8w1/funcname.c -o /tmp/hasfunction-r7bay8w1/tmp/hasfunction-r7bay8w1/funcname.o 2024-04-26T14:26:42,802 cc /tmp/hasfunction-r7bay8w1/tmp/hasfunction-r7bay8w1/funcname.o -lgomp -o /tmp/hasfunction-r7bay8w1/a.out 2024-04-26T14:26:46,066 /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-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T14:26:46,066 tree = Parsing.p_module(s, pxd, full_module_name) 2024-04-26T14:26:47,024 Compiling pyemma/coordinates/estimators/covar/covar_c/covartools.pyx because it changed. 2024-04-26T14:26:47,024 [1/1] Cythonizing pyemma/coordinates/estimators/covar/covar_c/covartools.pyx 2024-04-26T14:26:47,025 /tmp/pip-wheel-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/setup.py:154: UserWarning: enabled openmp 2024-04-26T14:26:47,025 warnings.warn('enabled openmp') 2024-04-26T14:26:47,025 writing top-level names to /tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info/top_level.txt 2024-04-26T14:26:47,026 writing manifest file '/tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T14:26:47,155 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 2024-04-26T14:26:47,155 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 2024-04-26T14:26:47,155 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 2024-04-26T14:26:47,156 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 2024-04-26T14:26:47,156 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 2024-04-26T14:26:47,186 reading manifest file '/tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T14:26:47,187 reading manifest template 'MANIFEST.in' 2024-04-26T14:26:47,338 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T14:26:47,339 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T14:26:47,340 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T14:26:47,345 no previously-included directories found matching 'doc/build' 2024-04-26T14:26:47,346 no previously-included directories found matching 'doc/source/generated' 2024-04-26T14:26:47,347 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T14:26:47,348 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T14:26:47,349 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T14:26:47,574 no previously-included directories found matching '.eggs' 2024-04-26T14:26:47,574 adding license file 'LICENSE.txt' 2024-04-26T14:26:47,585 writing manifest file '/tmp/pip-pip-egg-info-sgdym2jx/pyEMMA.egg-info/SOURCES.txt' 2024-04-26T14:26:47,934 Preparing metadata (setup.py): finished with status 'done' 2024-04-26T14:26:47,940 Source in /tmp/pip-wheel-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400 has version 2.2.1, which satisfies requirement pyemma==2.2.1 from https://files.pythonhosted.org/packages/8b/fa/5b40eb124d6c6862b4c51579bb71c0c78f076309869902f3fffb64d257b6/pyEMMA-2.2.1.zip 2024-04-26T14:26:47,940 Removed pyemma==2.2.1 from https://files.pythonhosted.org/packages/8b/fa/5b40eb124d6c6862b4c51579bb71c0c78f076309869902f3fffb64d257b6/pyEMMA-2.2.1.zip from build tracker '/tmp/pip-build-tracker-ynlb_imd' 2024-04-26T14:26:47,945 Created temporary directory: /tmp/pip-unpack-hjspivrx 2024-04-26T14:26:47,946 Created temporary directory: /tmp/pip-unpack-q5edb_5q 2024-04-26T14:26:47,964 Building wheels for collected packages: pyemma 2024-04-26T14:26:47,968 Created temporary directory: /tmp/pip-wheel-9ysvmrfv 2024-04-26T14:26:47,968 Building wheel for pyemma (setup.py): started 2024-04-26T14:26:47,969 Destination directory: /tmp/pip-wheel-9ysvmrfv 2024-04-26T14:26:47,969 Running command python setup.py bdist_wheel 2024-04-26T14:26:48,535 /tmp/pip-wheel-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/setup.py:60: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-26T14:26:48,535 from pkg_resources import VersionConflict 2024-04-26T14:26:48,767 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-04-26T14:26:48,767 !! 2024-04-26T14:26:48,768 ******************************************************************************** 2024-04-26T14:26:48,768 Requirements should be satisfied by a PEP 517 installer. 2024-04-26T14:26:48,768 If you are using pip, you can try `pip install --use-pep517`. 2024-04-26T14:26:48,768 ******************************************************************************** 2024-04-26T14:26:48,768 !! 2024-04-26T14:26:48,768 dist.fetch_build_eggs(dist.setup_requires) 2024-04-26T14:26:49,776 running bdist_wheel 2024-04-26T14:26:49,853 creating /tmp/hasfunction-a983am4l/tmp 2024-04-26T14:26:49,854 creating /tmp/hasfunction-a983am4l/tmp/hasfunction-a983am4l 2024-04-26T14:26:49,855 cc -c /tmp/hasfunction-a983am4l/funcname.c -o /tmp/hasfunction-a983am4l/tmp/hasfunction-a983am4l/funcname.o 2024-04-26T14:26:49,926 cc /tmp/hasfunction-a983am4l/tmp/hasfunction-a983am4l/funcname.o -o /tmp/hasfunction-a983am4l/a.out 2024-04-26T14:26:50,026 creating /tmp/hasfunction-hauar65q/tmp 2024-04-26T14:26:50,026 creating /tmp/hasfunction-hauar65q/tmp/hasfunction-hauar65q 2024-04-26T14:26:50,027 cc -c /tmp/hasfunction-hauar65q/funcname.c -o /tmp/hasfunction-hauar65q/tmp/hasfunction-hauar65q/funcname.o 2024-04-26T14:26:50,098 cc /tmp/hasfunction-hauar65q/tmp/hasfunction-hauar65q/funcname.o -lgomp -o /tmp/hasfunction-hauar65q/a.out 2024-04-26T14:26:51,588 /tmp/pip-wheel-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/setup.py:154: UserWarning: enabled openmp 2024-04-26T14:26:51,588 warnings.warn('enabled openmp') 2024-04-26T14:26:51,651 running build 2024-04-26T14:26:51,651 running build_py 2024-04-26T14:26:51,656 creating build 2024-04-26T14:26:51,657 creating build/lib.linux-armv7l-cpython-39 2024-04-26T14:26:51,657 creating build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T14:26:51,659 copying pyemma/_version.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T14:26:51,660 copying pyemma/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T14:26:51,663 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T14:26:51,663 copying pyemma/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T14:26:51,665 copying pyemma/coordinates/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T14:26:51,669 copying pyemma/coordinates/acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T14:26:51,671 copying pyemma/coordinates/pipelines.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T14:26:51,674 creating build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T14:26:51,674 copying pyemma/datasets/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T14:26:51,676 copying pyemma/datasets/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T14:26:51,678 copying pyemma/datasets/double_well_discrete.py -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T14:26:51,681 creating build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,682 copying pyemma/util/units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,684 copying pyemma/util/numeric.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,686 copying pyemma/util/annotators.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,688 copying pyemma/util/linalg.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,690 copying pyemma/util/exceptions.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,692 copying pyemma/util/reflection.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,694 copying pyemma/util/discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,696 copying pyemma/util/debug.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,698 copying pyemma/util/contexts.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,700 copying pyemma/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,701 copying pyemma/util/config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,703 copying pyemma/util/types.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,706 copying pyemma/util/statistics.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,708 copying pyemma/util/indices.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,710 copying pyemma/util/files.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,712 copying pyemma/util/log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,714 copying pyemma/util/testing_tools.py -> build/lib.linux-armv7l-cpython-39/pyemma/util 2024-04-26T14:26:51,716 creating build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T14:26:51,717 copying pyemma/_base/estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T14:26:51,720 copying pyemma/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T14:26:51,722 copying pyemma/_base/model.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T14:26:51,724 copying pyemma/_base/logging.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base 2024-04-26T14:26:51,726 creating build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T14:26:51,727 copying pyemma/msm/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T14:26:51,729 copying pyemma/msm/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm 2024-04-26T14:26:51,734 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T14:26:51,735 copying pyemma/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext 2024-04-26T14:26:51,737 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T14:26:51,738 copying pyemma/thermo/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T14:26:51,740 copying pyemma/thermo/api.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo 2024-04-26T14:26:51,744 creating build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T14:26:51,745 copying pyemma/plots/thermoplots.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T14:26:51,747 copying pyemma/plots/plots2d.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T14:26:51,749 copying pyemma/plots/markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T14:26:51,751 copying pyemma/plots/timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T14:26:51,754 copying pyemma/plots/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T14:26:51,755 copying pyemma/plots/networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots 2024-04-26T14:26:51,759 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T14:26:51,760 copying pyemma/coordinates/util/patches.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T14:26:51,763 copying pyemma/coordinates/util/stat.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T14:26:51,764 copying pyemma/coordinates/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T14:26:51,766 copying pyemma/coordinates/util/change_notification.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util 2024-04-26T14:26:51,768 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T14:26:51,769 copying pyemma/coordinates/data/data_in_memory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T14:26:51,771 copying pyemma/coordinates/data/numpy_filereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T14:26:51,774 copying pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T14:26:51,776 copying pyemma/coordinates/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T14:26:51,778 copying pyemma/coordinates/data/feature_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T14:26:51,781 copying pyemma/coordinates/data/py_csv_reader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data 2024-04-26T14:26:51,785 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,786 copying pyemma/coordinates/tests/test_regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,788 copying pyemma/coordinates/tests/test_api_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,790 copying pyemma/coordinates/tests/test_source.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,792 copying pyemma/coordinates/tests/test_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,794 copying pyemma/coordinates/tests/test_traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,797 copying pyemma/coordinates/tests/test_save_trajs.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,799 copying pyemma/coordinates/tests/test_featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,802 copying pyemma/coordinates/tests/test_api_load.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,804 copying pyemma/coordinates/tests/test_datainmemory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,806 copying pyemma/coordinates/tests/test_coordinates_iterator.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,809 copying pyemma/coordinates/tests/test_frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,812 copying pyemma/coordinates/tests/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,814 copying pyemma/coordinates/tests/test_assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,816 copying pyemma/coordinates/tests/test_random_access_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,819 copying pyemma/coordinates/tests/test_pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,822 copying pyemma/coordinates/tests/test_csvreader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,824 copying pyemma/coordinates/tests/test_numpyfilereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,826 copying pyemma/coordinates/tests/test_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,829 copying pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,831 copying pyemma/coordinates/tests/test_featurereader.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,833 copying pyemma/coordinates/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,834 copying pyemma/coordinates/tests/test_acf.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,836 copying pyemma/coordinates/tests/test_discretizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,838 copying pyemma/coordinates/tests/test_cluster_samples.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,840 copying pyemma/coordinates/tests/test_save_traj.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,842 copying pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,844 copying pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,846 copying pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,848 copying pyemma/coordinates/tests/test_pipeline.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,850 copying pyemma/coordinates/tests/test_cluster.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,852 copying pyemma/coordinates/tests/test_stride.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,854 copying pyemma/coordinates/tests/test_uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests 2024-04-26T14:26:51,856 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T14:26:51,857 copying pyemma/coordinates/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T14:26:51,859 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:51,860 copying pyemma/coordinates/clustering/assign.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:51,862 copying pyemma/coordinates/clustering/interface.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:51,865 copying pyemma/coordinates/clustering/uniform_time.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:51,867 copying pyemma/coordinates/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:51,869 copying pyemma/coordinates/clustering/regspace.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:51,872 copying pyemma/coordinates/clustering/kmeans.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:51,875 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T14:26:51,876 copying pyemma/coordinates/transform/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T14:26:51,878 copying pyemma/coordinates/transform/transformer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T14:26:51,880 copying pyemma/coordinates/transform/tica.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T14:26:51,884 copying pyemma/coordinates/transform/pca.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform 2024-04-26T14:26:51,887 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T14:26:51,888 copying pyemma/coordinates/data/util/traj_info_cache.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T14:26:51,891 copying pyemma/coordinates/data/util/frames_from_file.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T14:26:51,893 copying pyemma/coordinates/data/util/reader_utils.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T14:26:51,896 copying pyemma/coordinates/data/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util 2024-04-26T14:26:51,898 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T14:26:51,899 copying pyemma/coordinates/data/_base/datasource.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T14:26:51,901 copying pyemma/coordinates/data/_base/iterable.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T14:26:51,904 copying pyemma/coordinates/data/_base/random_accessible.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T14:26:51,906 copying pyemma/coordinates/data/_base/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base 2024-04-26T14:26:51,908 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,909 copying pyemma/coordinates/data/featurization/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,912 copying pyemma/coordinates/data/featurization/featurizer.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,915 copying pyemma/coordinates/data/featurization/_base.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,917 copying pyemma/coordinates/data/featurization/angles.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,919 copying pyemma/coordinates/data/featurization/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,922 copying pyemma/coordinates/data/featurization/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,923 copying pyemma/coordinates/data/featurization/distances.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization 2024-04-26T14:26:51,926 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T14:26:51,927 copying pyemma/coordinates/estimators/covar/moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T14:26:51,930 copying pyemma/coordinates/estimators/covar/running_moments.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T14:26:51,932 copying pyemma/coordinates/estimators/covar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T14:26:51,934 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T14:26:51,935 copying pyemma/coordinates/estimators/covar/covar_c/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T14:26:51,937 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,938 copying pyemma/util/tests/test_log.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,940 copying pyemma/util/tests/test_units.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,941 copying pyemma/util/tests/test_config.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,943 copying pyemma/util/tests/statistics_test.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,945 copying pyemma/util/tests/test_estimation_required_decorator.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,947 copying pyemma/util/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,949 copying pyemma/util/tests/test_discrete_trajectories.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,951 copying pyemma/util/tests/test_shortcut.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests 2024-04-26T14:26:51,953 creating build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T14:26:51,954 copying pyemma/util/_ext/shimmodule.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T14:26:51,956 copying pyemma/util/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/util/_ext 2024-04-26T14:26:51,958 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T14:26:51,959 copying pyemma/_base/tests/test_progress.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T14:26:51,961 copying pyemma/_base/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/tests 2024-04-26T14:26:51,963 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T14:26:51,964 copying pyemma/_base/progress/reporter.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T14:26:51,967 copying pyemma/_base/progress/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress 2024-04-26T14:26:51,969 creating build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T14:26:51,970 copying pyemma/_base/progress/bar/gui.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T14:26:51,973 copying pyemma/_base/progress/bar/_impl.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T14:26:51,976 copying pyemma/_base/progress/bar/misc.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T14:26:51,979 copying pyemma/_base/progress/bar/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar 2024-04-26T14:26:51,982 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:51,983 copying pyemma/msm/tests/test_bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:51,986 copying pyemma/msm/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:51,988 copying pyemma/msm/tests/test_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:51,992 copying pyemma/msm/tests/test_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:51,994 copying pyemma/msm/tests/test_reactive_flux.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:51,996 copying pyemma/msm/tests/test_msm_lowlevel_deprecation.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:51,998 copying pyemma/msm/tests/test_cktest.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:52,000 copying pyemma/msm/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:52,002 copying pyemma/msm/tests/test_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:52,004 copying pyemma/msm/tests/test_tpt.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:52,007 copying pyemma/msm/tests/test_bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:52,009 copying pyemma/msm/tests/birth_death_chain.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/tests 2024-04-26T14:26:52,012 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T14:26:52,013 copying pyemma/msm/models/reactive_flux.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T14:26:52,015 copying pyemma/msm/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T14:26:52,017 copying pyemma/msm/models/msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T14:26:52,021 copying pyemma/msm/models/hmsm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T14:26:52,023 copying pyemma/msm/models/msm_sampled.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T14:26:52,025 copying pyemma/msm/models/hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/models 2024-04-26T14:26:52,029 creating build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,030 copying pyemma/msm/estimators/bayesian_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,032 copying pyemma/msm/estimators/bayesian_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,035 copying pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,038 copying pyemma/msm/estimators/maximum_likelihood_msm.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,042 copying pyemma/msm/estimators/implied_timescales.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,044 copying pyemma/msm/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,045 copying pyemma/msm/estimators/_dtraj_stats.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,048 copying pyemma/msm/estimators/lagged_model_validators.py -> build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators 2024-04-26T14:26:52,050 creating build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T14:26:52,051 copying pyemma/_ext/sklearn/base.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T14:26:52,054 copying pyemma/_ext/sklearn/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T14:26:52,055 copying pyemma/_ext/sklearn/parameter_search.py -> build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn 2024-04-26T14:26:52,057 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T14:26:52,058 copying pyemma/thermo/util/util.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T14:26:52,061 copying pyemma/thermo/util/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/util 2024-04-26T14:26:52,063 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T14:26:52,064 copying pyemma/thermo/models/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T14:26:52,066 copying pyemma/thermo/models/stationary.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T14:26:52,068 copying pyemma/thermo/models/multi_therm.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/models 2024-04-26T14:26:52,070 creating build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T14:26:52,071 copying pyemma/thermo/estimators/DTRAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T14:26:52,074 copying pyemma/thermo/estimators/_callback.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T14:26:52,076 copying pyemma/thermo/estimators/WHAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T14:26:52,078 copying pyemma/thermo/estimators/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T14:26:52,080 copying pyemma/thermo/estimators/TRAM_estimator.py -> build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators 2024-04-26T14:26:52,084 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T14:26:52,085 copying pyemma/plots/tests/test_markovtests.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T14:26:52,087 copying pyemma/plots/tests/test_its.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T14:26:52,088 copying pyemma/plots/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T14:26:52,090 copying pyemma/plots/tests/test_networks.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/tests 2024-04-26T14:26:52,092 creating build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T14:26:52,093 copying pyemma/plots/_ext/fruchterman_reingold.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T14:26:52,095 copying pyemma/plots/_ext/__init__.py -> build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext 2024-04-26T14:26:52,112 copying pyemma/pyemma.cfg -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T14:26:52,114 copying pyemma/logging.yml -> build/lib.linux-armv7l-cpython-39/pyemma 2024-04-26T14:26:52,116 copying pyemma/datasets/double_well_discrete.npz -> build/lib.linux-armv7l-cpython-39/pyemma/datasets 2024-04-26T14:26:52,121 creating build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,121 copying pyemma/coordinates/tests/data/test.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,123 copying pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,126 copying pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,131 copying pyemma/coordinates/tests/data/bpti_mini.binpos -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,135 copying pyemma/coordinates/tests/data/bpti_mini.lh5 -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,140 copying pyemma/coordinates/tests/data/bpti_mini.trr -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,144 copying pyemma/coordinates/tests/data/bpti_ca.pdb -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,147 copying pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,149 copying pyemma/coordinates/tests/data/bpti_mini.h5 -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,154 copying pyemma/coordinates/tests/data/bpti_mini.dcd -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,159 copying pyemma/coordinates/tests/data/bpti_mini.netcdf -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,163 copying pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,165 copying pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,168 copying pyemma/coordinates/tests/data/bpti_mini.nc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,172 copying pyemma/coordinates/tests/data/bpti_mini.xtc -> build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data 2024-04-26T14:26:52,175 creating build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T14:26:52,176 copying pyemma/util/tests/data/dtraj.dat -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T14:26:52,179 copying pyemma/util/tests/data/dtraj.npy -> build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data 2024-04-26T14:26:52,205 UPDATING build/lib.linux-armv7l-cpython-39/pyemma/_version.py 2024-04-26T14:26:52,207 set build/lib.linux-armv7l-cpython-39/pyemma/_version.py to '2.2.1' 2024-04-26T14:26:52,207 running build_ext 2024-04-26T14:26:52,211 building 'pyemma.coordinates.clustering.regspatial' extension 2024-04-26T14:26:52,211 creating build/temp.linux-armv7l-cpython-39 2024-04-26T14:26:52,212 creating build/temp.linux-armv7l-cpython-39/pyemma 2024-04-26T14:26:52,213 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates 2024-04-26T14:26:52,213 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering 2024-04-26T14:26:52,214 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/clustering/src 2024-04-26T14:26:52,215 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-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/.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 2024-04-26T14:26:52,530 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T14:26:52,530 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T14:26:52,530 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T14:26:52,531 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T14:26:52,531 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T14:26:52,531 /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] 2024-04-26T14:26:52,531 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T14:26:52,531 | ^~~~~~~ 2024-04-26T14:26:52,561 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T14:26:52,561 pyemma/coordinates/clustering/src/clustering.c:81:23: warning: unused variable ‘trace_centers’ [-Wunused-variable] 2024-04-26T14:26:52,561 81 | float d, mindist, trace_centers; 2024-04-26T14:26:52,562 | ^~~~~~~~~~~~~ 2024-04-26T14:26:52,562 pyemma/coordinates/clustering/src/clustering.c:81:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T14:26:52,562 81 | float d, mindist, trace_centers; 2024-04-26T14:26:52,562 | ^ 2024-04-26T14:26:52,571 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T14:26:52,572 At top level: 2024-04-26T14:26:52,572 pyemma/coordinates/clustering/include/clustering.h:53:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T14:26:52,572 53 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T14:26:52,573 | ^~~~~~~~~~~~ 2024-04-26T14:26:52,575 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T14:26:52,576 pyemma/coordinates/clustering/src/clustering.c:94:7: warning: ‘debug’ is used uninitialized in this function [-Wuninitialized] 2024-04-26T14:26:52,576 94 | if(debug) printf("using openmp; n_threads=%i\n", n_threads); 2024-04-26T14:26:52,576 | ^ 2024-04-26T14:26:52,706 pyemma/coordinates/clustering/src/clustering.c:135:13: warning: ‘distance’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T14:26:52,707 135 | #pragma omp parallel private(buffer_a, buffer_b, i, j, chunk_p, mindist, argmin) 2024-04-26T14:26:52,707 | ^~~ 2024-04-26T14:26:52,848 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-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/.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 2024-04-26T14:26:53,152 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T14:26:53,153 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T14:26:53,153 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T14:26:53,153 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T14:26:53,153 from pyemma/coordinates/clustering/src/regspatial.c:19: 2024-04-26T14:26:53,153 /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] 2024-04-26T14:26:53,153 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T14:26:53,153 | ^~~~~~~ 2024-04-26T14:26:53,190 pyemma/coordinates/clustering/src/regspatial.c:177:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T14:26:53,190 177 | error_out(PyObject *m) { 2024-04-26T14:26:53,190 | ^~~~~~~~~ 2024-04-26T14:26:53,190 pyemma/coordinates/clustering/src/regspatial.c:127:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T14:26:53,190 127 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T14:26:53,191 | ^~~~~~~~~ 2024-04-26T14:26:53,464 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-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/.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 2024-04-26T14:26:53,591 building 'pyemma.coordinates.clustering.kmeans_clustering' extension 2024-04-26T14:26:53,592 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-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/.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 2024-04-26T14:26:53,916 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T14:26:53,917 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T14:26:53,917 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T14:26:53,917 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T14:26:53,917 from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T14:26:53,917 /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] 2024-04-26T14:26:53,917 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T14:26:53,917 | ^~~~~~~ 2024-04-26T14:26:53,944 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T14:26:53,944 pyemma/coordinates/clustering/src/clustering.c:81:23: warning: unused variable ‘trace_centers’ [-Wunused-variable] 2024-04-26T14:26:53,944 81 | float d, mindist, trace_centers; 2024-04-26T14:26:53,944 | ^~~~~~~~~~~~~ 2024-04-26T14:26:53,945 pyemma/coordinates/clustering/src/clustering.c:81:11: warning: unused variable ‘d’ [-Wunused-variable] 2024-04-26T14:26:53,945 81 | float d, mindist, trace_centers; 2024-04-26T14:26:53,945 | ^ 2024-04-26T14:26:53,954 In file included from pyemma/coordinates/clustering/src/clustering.c:20: 2024-04-26T14:26:53,955 At top level: 2024-04-26T14:26:53,955 pyemma/coordinates/clustering/include/clustering.h:53:13: warning: ‘ASSIGN_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T14:26:53,955 53 | static char ASSIGN_USAGE[] = "assign(chunk, centers, dtraj, metric)\n"\ 2024-04-26T14:26:53,956 | ^~~~~~~~~~~~ 2024-04-26T14:26:53,958 pyemma/coordinates/clustering/src/clustering.c: In function ‘c_assign’: 2024-04-26T14:26:53,959 pyemma/coordinates/clustering/src/clustering.c:94:7: warning: ‘debug’ is used uninitialized in this function [-Wuninitialized] 2024-04-26T14:26:53,959 94 | if(debug) printf("using openmp; n_threads=%i\n", n_threads); 2024-04-26T14:26:53,959 | ^ 2024-04-26T14:26:54,084 pyemma/coordinates/clustering/src/clustering.c:135:13: warning: ‘distance’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T14:26:54,087 135 | #pragma omp parallel private(buffer_a, buffer_b, i, j, chunk_p, mindist, argmin) 2024-04-26T14:26:54,087 | ^~~ 2024-04-26T14:26:54,261 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-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/.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 2024-04-26T14:26:54,910 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T14:26:54,911 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T14:26:54,911 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T14:26:54,911 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T14:26:54,911 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T14:26:54,911 /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] 2024-04-26T14:26:54,911 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T14:26:54,911 | ^~~~~~~ 2024-04-26T14:26:54,939 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T14:26:54,939 pyemma/coordinates/clustering/src/kmeans.c:51:38: warning: variable ‘py_res’ set but not used [-Wunused-but-set-variable] 2024-04-26T14:26:54,939 51 | PyObject *py_centers, *py_item, *py_res; 2024-04-26T14:26:54,939 | ^~~~~~ 2024-04-26T14:26:54,940 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T14:26:54,940 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T14:26:54,940 from pyemma/coordinates/clustering/include/clustering.h:27, 2024-04-26T14:26:54,940 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T14:26:54,940 pyemma/coordinates/clustering/src/kmeans.c: In function ‘costFunction’: 2024-04-26T14:26:54,942 pyemma/coordinates/clustering/src/kmeans.c:251:47: warning: passing argument 1 of ‘PyList_GetItem’ from incompatible pointer type [-Wincompatible-pointer-types] 2024-04-26T14:26:54,942 251 | centers = PyArray_DATA(PyList_GetItem(np_centers,r)); 2024-04-26T14:26:54,943 | ^~~~~~~~~~ 2024-04-26T14:26:54,943 | | 2024-04-26T14:26:54,943 | PyArrayObject * {aka struct tagPyArrayObject_fields *} 2024-04-26T14:26:54,943 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1605:62: note: in definition of macro ‘PyArray_DATA’ 2024-04-26T14:26:54,943 1605 | #define PyArray_DATA(obj) ((void *)((PyArrayObject_fields *)(obj))->data) 2024-04-26T14:26:54,943 | ^~~ 2024-04-26T14:26:54,945 In file included from /usr/include/python3.9/Python.h:106, 2024-04-26T14:26:54,945 from pyemma/coordinates/clustering/include/clustering.h:25, 2024-04-26T14:26:54,945 from pyemma/coordinates/clustering/src/kmeans.c:20: 2024-04-26T14:26:54,945 /usr/include/python3.9/listobject.h:31:39: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PyArrayObject *’ {aka ‘struct tagPyArrayObject_fields *’} 2024-04-26T14:26:54,945 31 | PyAPI_FUNC(PyObject *) PyList_GetItem(PyObject *, Py_ssize_t); 2024-04-26T14:26:54,945 | ^~~~~~~~~~ 2024-04-26T14:26:54,946 pyemma/coordinates/clustering/src/kmeans.c:217:18: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] 2024-04-26T14:26:54,946 217 | float value, d; 2024-04-26T14:26:54,946 | ^ 2024-04-26T14:26:54,946 pyemma/coordinates/clustering/src/kmeans.c:216:15: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 2024-04-26T14:26:54,946 216 | int k, i, j, r; 2024-04-26T14:26:54,946 | ^ 2024-04-26T14:26:54,965 At top level: 2024-04-26T14:26:54,965 pyemma/coordinates/clustering/src/kmeans.c:581:1: warning: ‘error_out’ defined but not used [-Wunused-function] 2024-04-26T14:26:54,965 581 | error_out(PyObject *m) { 2024-04-26T14:26:54,965 | ^~~~~~~~~ 2024-04-26T14:26:54,965 pyemma/coordinates/clustering/src/kmeans.c:509:13: warning: ‘MOD_USAGE’ defined but not used [-Wunused-variable] 2024-04-26T14:26:54,966 509 | static char MOD_USAGE[] = "Chunked regular spatial clustering"; 2024-04-26T14:26:54,966 | ^~~~~~~~~ 2024-04-26T14:26:55,126 pyemma/coordinates/clustering/src/kmeans.c: In function ‘cluster’: 2024-04-26T14:26:55,127 pyemma/coordinates/clustering/src/kmeans.c:171:50: warning: ‘closest_center_index’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-04-26T14:26:55,127 171 | new_centers[closest_center_index*dim+j] += chunk[i*dim+j]; 2024-04-26T14:26:55,127 | ^~ 2024-04-26T14:26:55,654 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-13_siqhn/pyemma_310ad32f4c1643329c4b9bcb8e6ea400/.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 2024-04-26T14:26:55,778 building 'pyemma.coordinates.estimators.covar.covar_c.covartools' extension 2024-04-26T14:26:55,779 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators 2024-04-26T14:26:55,779 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar 2024-04-26T14:26:55,780 creating build/temp.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T14:26:55,781 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 2024-04-26T14:26:56,209 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 2024-04-26T14:26:56,525 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-26T14:26:56,525 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-26T14:26:56,525 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-26T14:26:56,525 from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1257: 2024-04-26T14:26:56,525 /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] 2024-04-26T14:26:56,525 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-26T14:26:56,526 | ^~~~~~~ 2024-04-26T14:26:56,635 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_12subtract_row_float’: 2024-04-26T14:26:56,638 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] 2024-04-26T14:26:56,638 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T14:26:56,638 | ^~~~~~~~~~ 2024-04-26T14:26:56,638 | | 2024-04-26T14:26:56,638 | float * 2024-04-26T14:26:56,639 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T14:26:56,639 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:34: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T14:26:56,639 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T14:26:56,639 | ~~~~~~~~^ 2024-04-26T14:26:56,642 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] 2024-04-26T14:26:56,642 6712 | _subtract_row_float(__pyx_v_pX, __pyx_v_prow, __pyx_t_1, __pyx_t_2); 2024-04-26T14:26:56,642 | ^~~~~~~~~~~~ 2024-04-26T14:26:56,642 | | 2024-04-26T14:26:56,643 | float * 2024-04-26T14:26:56,643 In file included from pyemma/coordinates/estimators/covar/covar_c/covartools.c:1262: 2024-04-26T14:26:56,643 pyemma/coordinates/estimators/covar/covar_c/_covartools.h:21:45: note: expected ‘double *’ but argument is of type ‘float *’ 2024-04-26T14:26:56,643 21 | void _subtract_row_float(double* X, double* row, int M, int N); 2024-04-26T14:26:56,643 | ~~~~~~~~^~~ 2024-04-26T14:26:56,682 pyemma/coordinates/estimators/covar/covar_c/covartools.c: In function ‘__pyx_pf_6pyemma_11coordinates_10estimators_5covar_7covar_c_10covartools_18subtract_row_float_copy’: 2024-04-26T14:26:56,688 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] 2024-04-26T14:26:56,688 7472 | _subtract_row_float_copy(__pyx_v_pX0, __pyx_v_pX, __pyx_v_prow, __pyx_t_6, __pyx_t_7); 2024-04-26T14:26:56,688 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2024-04-26T14:26:56,688 | _subtract_row_float 2024-04-26T14:27:07,771 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 2024-04-26T14:27:07,941 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-04-26T14:27:07,942 !! 2024-04-26T14:27:07,942 ******************************************************************************** 2024-04-26T14:27:07,942 Please avoid running ``setup.py`` directly. 2024-04-26T14:27:07,942 Instead, use pypa/build, pypa/installer or other 2024-04-26T14:27:07,943 standards-based tools. 2024-04-26T14:27:07,943 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-04-26T14:27:07,943 ******************************************************************************** 2024-04-26T14:27:07,943 !! 2024-04-26T14:27:07,943 self.initialize_options() 2024-04-26T14:27:07,971 installing to build/bdist.linux-armv7l/wheel 2024-04-26T14:27:07,971 running install 2024-04-26T14:27:07,996 running install_lib 2024-04-26T14:27:08,026 creating build/bdist.linux-armv7l 2024-04-26T14:27:08,026 creating build/bdist.linux-armv7l/wheel 2024-04-26T14:27:08,028 creating build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T14:27:08,030 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T14:27:08,031 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T14:27:08,032 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/patches.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T14:27:08,034 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/stat.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T14:27:08,036 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T14:27:08,037 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/util/change_notification.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/util 2024-04-26T14:27:08,040 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T14:27:08,041 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/data_in_memory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T14:27:08,043 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/numpy_filereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T14:27:08,047 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T14:27:08,047 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T14:27:08,050 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T14:27:08,052 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/reader_utils.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T14:27:08,055 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/util 2024-04-26T14:27:08,057 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T14:27:08,058 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/datasource.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T14:27:08,061 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/iterable.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T14:27:08,063 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/random_accessible.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T14:27:08,065 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/_base 2024-04-26T14:27:08,067 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/fragmented_trajectory_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T14:27:08,069 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T14:27:08,073 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,074 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/util.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,077 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,081 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/_base.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,083 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/angles.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,086 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,089 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,092 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/featurization/distances.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data/featurization 2024-04-26T14:27:08,095 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/feature_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T14:27:08,098 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/data/py_csv_reader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/data 2024-04-26T14:27:08,101 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,102 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,104 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,107 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_source.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,110 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,112 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_traj_info_cache.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,114 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_trajs.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,117 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,120 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_api_load.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,122 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_datainmemory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,124 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_coordinates_iterator.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,126 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_frames_from_file.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,129 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/util.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,131 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,134 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_random_access_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,138 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,139 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/test.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,141 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_067-100.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,143 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 2024-04-26T14:27:08,147 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.binpos -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,150 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.lh5 -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,153 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.trr -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,157 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_ca.pdb -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,159 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_034-066.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,162 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.h5 -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,166 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.dcd -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,171 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.netcdf -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,174 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 2024-04-26T14:27:08,176 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_001-033.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,178 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.nc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,182 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/data/bpti_mini.xtc -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests/data 2024-04-26T14:27:08,185 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,187 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_csvreader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,190 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_numpyfilereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,192 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,194 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_fragmented_trajectory.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,196 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,199 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,200 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,202 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_discretizer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,204 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster_samples.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,206 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_save_traj.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,208 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,210 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_mini_batch_kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,212 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_featurereader_and_tica_projection.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,214 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_pipeline.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,217 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_cluster.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,218 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_stride.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,221 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/tests/test_uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/tests 2024-04-26T14:27:08,223 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T14:27:08,225 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/api.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T14:27:08,229 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/acf.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T14:27:08,231 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T14:27:08,232 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators 2024-04-26T14:27:08,234 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T14:27:08,236 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar/covar_c 2024-04-26T14:27:08,237 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 2024-04-26T14:27:08,260 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 2024-04-26T14:27:08,263 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T14:27:08,268 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/running_moments.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T14:27:08,270 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/estimators/covar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/estimators/covar 2024-04-26T14:27:08,272 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T14:27:08,273 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 2024-04-26T14:27:08,278 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/assign.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T14:27:08,280 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/interface.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T14:27:08,282 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/uniform_time.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T14:27:08,284 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T14:27:08,286 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/regspace.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T14:27:08,288 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 2024-04-26T14:27:08,296 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/clustering/kmeans.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/clustering 2024-04-26T14:27:08,301 creating build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T14:27:08,302 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T14:27:08,304 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/transformer.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T14:27:08,306 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/tica.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T14:27:08,309 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/transform/pca.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates/transform 2024-04-26T14:27:08,311 copying build/lib.linux-armv7l-cpython-39/pyemma/coordinates/pipelines.py -> build/bdist.linux-armv7l/wheel/pyemma/coordinates 2024-04-26T14:27:08,314 creating build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T14:27:08,314 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.npz -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T14:27:08,318 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T14:27:08,320 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/api.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T14:27:08,321 copying build/lib.linux-armv7l-cpython-39/pyemma/datasets/double_well_discrete.py -> build/bdist.linux-armv7l/wheel/pyemma/datasets 2024-04-26T14:27:08,324 creating build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,325 copying build/lib.linux-armv7l-cpython-39/pyemma/util/units.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,327 copying build/lib.linux-armv7l-cpython-39/pyemma/util/numeric.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,329 copying build/lib.linux-armv7l-cpython-39/pyemma/util/annotators.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,331 copying build/lib.linux-armv7l-cpython-39/pyemma/util/linalg.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,333 copying build/lib.linux-armv7l-cpython-39/pyemma/util/exceptions.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,335 copying build/lib.linux-armv7l-cpython-39/pyemma/util/reflection.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,337 copying build/lib.linux-armv7l-cpython-39/pyemma/util/discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,340 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,341 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_log.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,343 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_units.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,344 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_config.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,347 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/statistics_test.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,348 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_estimation_required_decorator.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,350 creating build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T14:27:08,351 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.dat -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T14:27:08,354 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/data/dtraj.npy -> build/bdist.linux-armv7l/wheel/pyemma/util/tests/data 2024-04-26T14:27:08,357 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,359 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_discrete_trajectories.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,361 copying build/lib.linux-armv7l-cpython-39/pyemma/util/tests/test_shortcut.py -> build/bdist.linux-armv7l/wheel/pyemma/util/tests 2024-04-26T14:27:08,363 copying build/lib.linux-armv7l-cpython-39/pyemma/util/debug.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,365 creating build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T14:27:08,366 copying build/lib.linux-armv7l-cpython-39/pyemma/util/_ext/shimmodule.py -> build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T14:27:08,368 copying build/lib.linux-armv7l-cpython-39/pyemma/util/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util/_ext 2024-04-26T14:27:08,370 copying build/lib.linux-armv7l-cpython-39/pyemma/util/contexts.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,372 copying build/lib.linux-armv7l-cpython-39/pyemma/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,374 copying build/lib.linux-armv7l-cpython-39/pyemma/util/config.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,377 copying build/lib.linux-armv7l-cpython-39/pyemma/util/types.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,380 copying build/lib.linux-armv7l-cpython-39/pyemma/util/statistics.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,382 copying build/lib.linux-armv7l-cpython-39/pyemma/util/indices.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,385 copying build/lib.linux-armv7l-cpython-39/pyemma/util/files.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,387 copying build/lib.linux-armv7l-cpython-39/pyemma/util/log.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,389 copying build/lib.linux-armv7l-cpython-39/pyemma/util/testing_tools.py -> build/bdist.linux-armv7l/wheel/pyemma/util 2024-04-26T14:27:08,391 copying build/lib.linux-armv7l-cpython-39/pyemma/pyemma.cfg -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T14:27:08,394 creating build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T14:27:08,395 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T14:27:08,399 creating build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T14:27:08,400 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/test_progress.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T14:27:08,403 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/tests 2024-04-26T14:27:08,405 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T14:27:08,408 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T14:27:08,409 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/reporter.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T14:27:08,412 creating build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T14:27:08,413 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/gui.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T14:27:08,416 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/_impl.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T14:27:08,420 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/misc.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T14:27:08,423 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/bar/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress/bar 2024-04-26T14:27:08,425 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/progress/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_base/progress 2024-04-26T14:27:08,427 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/model.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T14:27:08,430 copying build/lib.linux-armv7l-cpython-39/pyemma/_base/logging.py -> build/bdist.linux-armv7l/wheel/pyemma/_base 2024-04-26T14:27:08,433 creating build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T14:27:08,435 creating build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,436 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,439 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,442 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,445 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,448 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_reactive_flux.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,451 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_msm_lowlevel_deprecation.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,453 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_cktest.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,456 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,459 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,463 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_tpt.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,467 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/test_bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,470 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/tests/birth_death_chain.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/tests 2024-04-26T14:27:08,473 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T14:27:08,476 creating build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T14:27:08,477 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/reactive_flux.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T14:27:08,480 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T14:27:08,482 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T14:27:08,486 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T14:27:08,488 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/msm_sampled.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T14:27:08,490 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/models/hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/models 2024-04-26T14:27:08,492 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/api.py -> build/bdist.linux-armv7l/wheel/pyemma/msm 2024-04-26T14:27:08,496 creating build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,497 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,500 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/bayesian_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,503 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_hmsm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,506 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/maximum_likelihood_msm.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,508 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/implied_timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,511 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,513 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/_dtraj_stats.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,516 copying build/lib.linux-armv7l-cpython-39/pyemma/msm/estimators/lagged_model_validators.py -> build/bdist.linux-armv7l/wheel/pyemma/msm/estimators 2024-04-26T14:27:08,519 creating build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T14:27:08,519 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext 2024-04-26T14:27:08,522 creating build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T14:27:08,522 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/base.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T14:27:08,525 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T14:27:08,526 copying build/lib.linux-armv7l-cpython-39/pyemma/_ext/sklearn/parameter_search.py -> build/bdist.linux-armv7l/wheel/pyemma/_ext/sklearn 2024-04-26T14:27:08,529 copying build/lib.linux-armv7l-cpython-39/pyemma/_version.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T14:27:08,530 copying build/lib.linux-armv7l-cpython-39/pyemma/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T14:27:08,532 copying build/lib.linux-armv7l-cpython-39/pyemma/logging.yml -> build/bdist.linux-armv7l/wheel/pyemma 2024-04-26T14:27:08,534 creating build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T14:27:08,535 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T14:27:08,536 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/util.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T14:27:08,539 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/util/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/util 2024-04-26T14:27:08,541 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T14:27:08,543 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T14:27:08,544 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T14:27:08,546 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/stationary.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T14:27:08,548 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/models/multi_therm.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/models 2024-04-26T14:27:08,550 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/api.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo 2024-04-26T14:27:08,553 creating build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T14:27:08,554 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/DTRAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T14:27:08,557 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/_callback.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T14:27:08,558 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/WHAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T14:27:08,561 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T14:27:08,562 copying build/lib.linux-armv7l-cpython-39/pyemma/thermo/estimators/TRAM_estimator.py -> build/bdist.linux-armv7l/wheel/pyemma/thermo/estimators 2024-04-26T14:27:08,565 creating build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T14:27:08,566 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/thermoplots.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T14:27:08,569 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/plots2d.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T14:27:08,571 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T14:27:08,573 creating build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T14:27:08,574 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_markovtests.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T14:27:08,576 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_its.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T14:27:08,577 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T14:27:08,579 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/tests/test_networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/tests 2024-04-26T14:27:08,581 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/timescales.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T14:27:08,583 creating build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T14:27:08,584 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/fruchterman_reingold.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T14:27:08,587 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/_ext/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots/_ext 2024-04-26T14:27:08,589 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/__init__.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T14:27:08,591 copying build/lib.linux-armv7l-cpython-39/pyemma/plots/networks.py -> build/bdist.linux-armv7l/wheel/pyemma/plots 2024-04-26T14:27:08,593 running install_egg_info 2024-04-26T14:27:08,659 running egg_info 2024-04-26T14:27:08,689 writing pyEMMA.egg-info/PKG-INFO 2024-04-26T14:27:08,693 writing dependency_links to pyEMMA.egg-info/dependency_links.txt 2024-04-26T14:27:08,696 writing requirements to pyEMMA.egg-info/requires.txt 2024-04-26T14:27:08,698 writing top-level names to pyEMMA.egg-info/top_level.txt 2024-04-26T14:27:08,772 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 2024-04-26T14:27:08,773 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 2024-04-26T14:27:08,773 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 2024-04-26T14:27:08,773 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 2024-04-26T14:27:08,773 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 2024-04-26T14:27:08,804 reading manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T14:27:08,816 reading manifest template 'MANIFEST.in' 2024-04-26T14:27:08,982 warning: no files found matching 'testfiles/*' under directory 'pyemma' 2024-04-26T14:27:08,984 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2024-04-26T14:27:08,986 warning: no previously-included files matching '*.orig' found anywhere in distribution 2024-04-26T14:27:08,989 no previously-included directories found matching 'doc/build' 2024-04-26T14:27:08,990 no previously-included directories found matching 'doc/source/generated' 2024-04-26T14:27:08,991 no previously-included directories found matching 'doc/source/api/generated' 2024-04-26T14:27:08,993 warning: no previously-included files matching 'git' found under directory '*' 2024-04-26T14:27:08,994 warning: no previously-included files matching '.git*' found under directory '*' 2024-04-26T14:27:09,251 no previously-included directories found matching '.eggs' 2024-04-26T14:27:09,251 adding license file 'LICENSE.txt' 2024-04-26T14:27:09,266 writing manifest file 'pyEMMA.egg-info/SOURCES.txt' 2024-04-26T14:27:09,268 Copying pyEMMA.egg-info to build/bdist.linux-armv7l/wheel/pyEMMA-2.2.1-py3.9.egg-info 2024-04-26T14:27:09,282 running install_scripts 2024-04-26T14:27:09,304 adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") 2024-04-26T14:27:09,309 creating build/bdist.linux-armv7l/wheel/pyEMMA-2.2.1.dist-info/WHEEL 2024-04-26T14:27:09,312 creating '/tmp/pip-wheel-9ysvmrfv/pyEMMA-2.2.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-04-26T14:27:09,315 adding 'pyemma/__init__.py' 2024-04-26T14:27:09,317 adding 'pyemma/_version.py' 2024-04-26T14:27:09,318 adding 'pyemma/logging.yml' 2024-04-26T14:27:09,319 adding 'pyemma/pyemma.cfg' 2024-04-26T14:27:09,321 adding 'pyemma/_base/__init__.py' 2024-04-26T14:27:09,323 adding 'pyemma/_base/estimator.py' 2024-04-26T14:27:09,325 adding 'pyemma/_base/logging.py' 2024-04-26T14:27:09,326 adding 'pyemma/_base/model.py' 2024-04-26T14:27:09,328 adding 'pyemma/_base/progress/__init__.py' 2024-04-26T14:27:09,330 adding 'pyemma/_base/progress/reporter.py' 2024-04-26T14:27:09,332 adding 'pyemma/_base/progress/bar/__init__.py' 2024-04-26T14:27:09,335 adding 'pyemma/_base/progress/bar/_impl.py' 2024-04-26T14:27:09,337 adding 'pyemma/_base/progress/bar/gui.py' 2024-04-26T14:27:09,339 adding 'pyemma/_base/progress/bar/misc.py' 2024-04-26T14:27:09,340 adding 'pyemma/_base/tests/__init__.py' 2024-04-26T14:27:09,342 adding 'pyemma/_base/tests/test_progress.py' 2024-04-26T14:27:09,343 adding 'pyemma/_ext/__init__.py' 2024-04-26T14:27:09,345 adding 'pyemma/_ext/sklearn/__init__.py' 2024-04-26T14:27:09,348 adding 'pyemma/_ext/sklearn/base.py' 2024-04-26T14:27:09,349 adding 'pyemma/_ext/sklearn/parameter_search.py' 2024-04-26T14:27:09,351 adding 'pyemma/coordinates/__init__.py' 2024-04-26T14:27:09,353 adding 'pyemma/coordinates/acf.py' 2024-04-26T14:27:09,361 adding 'pyemma/coordinates/api.py' 2024-04-26T14:27:09,364 adding 'pyemma/coordinates/pipelines.py' 2024-04-26T14:27:09,366 adding 'pyemma/coordinates/clustering/__init__.py' 2024-04-26T14:27:09,367 adding 'pyemma/coordinates/clustering/assign.py' 2024-04-26T14:27:09,370 adding 'pyemma/coordinates/clustering/interface.py' 2024-04-26T14:27:09,372 adding 'pyemma/coordinates/clustering/kmeans.py' 2024-04-26T14:27:09,395 adding 'pyemma/coordinates/clustering/kmeans_clustering.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T14:27:09,397 adding 'pyemma/coordinates/clustering/regspace.py' 2024-04-26T14:27:09,416 adding 'pyemma/coordinates/clustering/regspatial.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T14:27:09,418 adding 'pyemma/coordinates/clustering/uniform_time.py' 2024-04-26T14:27:09,420 adding 'pyemma/coordinates/data/__init__.py' 2024-04-26T14:27:09,422 adding 'pyemma/coordinates/data/data_in_memory.py' 2024-04-26T14:27:09,425 adding 'pyemma/coordinates/data/feature_reader.py' 2024-04-26T14:27:09,428 adding 'pyemma/coordinates/data/fragmented_trajectory_reader.py' 2024-04-26T14:27:09,429 adding 'pyemma/coordinates/data/numpy_filereader.py' 2024-04-26T14:27:09,432 adding 'pyemma/coordinates/data/py_csv_reader.py' 2024-04-26T14:27:09,435 adding 'pyemma/coordinates/data/_base/__init__.py' 2024-04-26T14:27:09,438 adding 'pyemma/coordinates/data/_base/datasource.py' 2024-04-26T14:27:09,440 adding 'pyemma/coordinates/data/_base/iterable.py' 2024-04-26T14:27:09,442 adding 'pyemma/coordinates/data/_base/random_accessible.py' 2024-04-26T14:27:09,443 adding 'pyemma/coordinates/data/featurization/__init__.py' 2024-04-26T14:27:09,445 adding 'pyemma/coordinates/data/featurization/_base.py' 2024-04-26T14:27:09,446 adding 'pyemma/coordinates/data/featurization/angles.py' 2024-04-26T14:27:09,448 adding 'pyemma/coordinates/data/featurization/distances.py' 2024-04-26T14:27:09,451 adding 'pyemma/coordinates/data/featurization/featurizer.py' 2024-04-26T14:27:09,453 adding 'pyemma/coordinates/data/featurization/misc.py' 2024-04-26T14:27:09,455 adding 'pyemma/coordinates/data/featurization/util.py' 2024-04-26T14:27:09,457 adding 'pyemma/coordinates/data/util/__init__.py' 2024-04-26T14:27:09,459 adding 'pyemma/coordinates/data/util/frames_from_file.py' 2024-04-26T14:27:09,461 adding 'pyemma/coordinates/data/util/reader_utils.py' 2024-04-26T14:27:09,463 adding 'pyemma/coordinates/data/util/traj_info_cache.py' 2024-04-26T14:27:09,464 adding 'pyemma/coordinates/estimators/__init__.py' 2024-04-26T14:27:09,466 adding 'pyemma/coordinates/estimators/covar/__init__.py' 2024-04-26T14:27:09,469 adding 'pyemma/coordinates/estimators/covar/moments.py' 2024-04-26T14:27:09,472 adding 'pyemma/coordinates/estimators/covar/running_moments.py' 2024-04-26T14:27:09,473 adding 'pyemma/coordinates/estimators/covar/covar_c/__init__.py' 2024-04-26T14:27:09,590 adding 'pyemma/coordinates/estimators/covar/covar_c/covartools.cpython-39-arm-linux-gnueabihf.so' 2024-04-26T14:27:09,596 adding 'pyemma/coordinates/tests/__init__.py' 2024-04-26T14:27:09,598 adding 'pyemma/coordinates/tests/test_acf.py' 2024-04-26T14:27:09,599 adding 'pyemma/coordinates/tests/test_api_load.py' 2024-04-26T14:27:09,601 adding 'pyemma/coordinates/tests/test_api_source.py' 2024-04-26T14:27:09,603 adding 'pyemma/coordinates/tests/test_assign.py' 2024-04-26T14:27:09,604 adding 'pyemma/coordinates/tests/test_cluster.py' 2024-04-26T14:27:09,606 adding 'pyemma/coordinates/tests/test_cluster_samples.py' 2024-04-26T14:27:09,607 adding 'pyemma/coordinates/tests/test_coordinates_iterator.py' 2024-04-26T14:27:09,609 adding 'pyemma/coordinates/tests/test_csvreader.py' 2024-04-26T14:27:09,611 adding 'pyemma/coordinates/tests/test_datainmemory.py' 2024-04-26T14:27:09,613 adding 'pyemma/coordinates/tests/test_discretizer.py' 2024-04-26T14:27:09,615 adding 'pyemma/coordinates/tests/test_featurereader.py' 2024-04-26T14:27:09,616 adding 'pyemma/coordinates/tests/test_featurereader_and_tica.py' 2024-04-26T14:27:09,618 adding 'pyemma/coordinates/tests/test_featurereader_and_tica_projection.py' 2024-04-26T14:27:09,621 adding 'pyemma/coordinates/tests/test_featurizer.py' 2024-04-26T14:27:09,623 adding 'pyemma/coordinates/tests/test_fragmented_trajectory.py' 2024-04-26T14:27:09,625 adding 'pyemma/coordinates/tests/test_frames_from_file.py' 2024-04-26T14:27:09,627 adding 'pyemma/coordinates/tests/test_kmeans.py' 2024-04-26T14:27:09,628 adding 'pyemma/coordinates/tests/test_mini_batch_kmeans.py' 2024-04-26T14:27:09,630 adding 'pyemma/coordinates/tests/test_numpyfilereader.py' 2024-04-26T14:27:09,631 adding 'pyemma/coordinates/tests/test_pca.py' 2024-04-26T14:27:09,633 adding 'pyemma/coordinates/tests/test_pipeline.py' 2024-04-26T14:27:09,635 adding 'pyemma/coordinates/tests/test_random_access_stride.py' 2024-04-26T14:27:09,637 adding 'pyemma/coordinates/tests/test_regspace.py' 2024-04-26T14:27:09,639 adding 'pyemma/coordinates/tests/test_save_traj.py' 2024-04-26T14:27:09,640 adding 'pyemma/coordinates/tests/test_save_trajs.py' 2024-04-26T14:27:09,642 adding 'pyemma/coordinates/tests/test_source.py' 2024-04-26T14:27:09,643 adding 'pyemma/coordinates/tests/test_stride.py' 2024-04-26T14:27:09,646 adding 'pyemma/coordinates/tests/test_tica.py' 2024-04-26T14:27:09,647 adding 'pyemma/coordinates/tests/test_traj_info_cache.py' 2024-04-26T14:27:09,649 adding 'pyemma/coordinates/tests/test_uniform_time.py' 2024-04-26T14:27:09,650 adding 'pyemma/coordinates/tests/util.py' 2024-04-26T14:27:09,653 adding 'pyemma/coordinates/tests/data/bpti_001-033.xtc' 2024-04-26T14:27:09,655 adding 'pyemma/coordinates/tests/data/bpti_034-066.xtc' 2024-04-26T14:27:09,657 adding 'pyemma/coordinates/tests/data/bpti_067-100.xtc' 2024-04-26T14:27:09,659 adding 'pyemma/coordinates/tests/data/bpti_ca.pdb' 2024-04-26T14:27:09,676 adding 'pyemma/coordinates/tests/data/bpti_mini.binpos' 2024-04-26T14:27:09,693 adding 'pyemma/coordinates/tests/data/bpti_mini.dcd' 2024-04-26T14:27:09,700 adding 'pyemma/coordinates/tests/data/bpti_mini.h5' 2024-04-26T14:27:09,707 adding 'pyemma/coordinates/tests/data/bpti_mini.lh5' 2024-04-26T14:27:09,728 adding 'pyemma/coordinates/tests/data/bpti_mini.nc' 2024-04-26T14:27:09,750 adding 'pyemma/coordinates/tests/data/bpti_mini.netcdf' 2024-04-26T14:27:09,766 adding 'pyemma/coordinates/tests/data/bpti_mini.trr' 2024-04-26T14:27:09,771 adding 'pyemma/coordinates/tests/data/bpti_mini.xtc' 2024-04-26T14:27:09,773 adding 'pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz' 2024-04-26T14:27:09,782 adding 'pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz' 2024-04-26T14:27:09,784 adding 'pyemma/coordinates/tests/data/test.pdb' 2024-04-26T14:27:09,785 adding 'pyemma/coordinates/transform/__init__.py' 2024-04-26T14:27:09,787 adding 'pyemma/coordinates/transform/pca.py' 2024-04-26T14:27:09,794 adding 'pyemma/coordinates/transform/tica.py' 2024-04-26T14:27:09,796 adding 'pyemma/coordinates/transform/transformer.py' 2024-04-26T14:27:09,798 adding 'pyemma/coordinates/util/__init__.py' 2024-04-26T14:27:09,799 adding 'pyemma/coordinates/util/change_notification.py' 2024-04-26T14:27:09,801 adding 'pyemma/coordinates/util/patches.py' 2024-04-26T14:27:09,803 adding 'pyemma/coordinates/util/stat.py' 2024-04-26T14:27:09,805 adding 'pyemma/datasets/__init__.py' 2024-04-26T14:27:09,806 adding 'pyemma/datasets/api.py' 2024-04-26T14:27:09,814 adding 'pyemma/datasets/double_well_discrete.npz' 2024-04-26T14:27:09,816 adding 'pyemma/datasets/double_well_discrete.py' 2024-04-26T14:27:09,818 adding 'pyemma/msm/__init__.py' 2024-04-26T14:27:09,825 adding 'pyemma/msm/api.py' 2024-04-26T14:27:09,827 adding 'pyemma/msm/estimators/__init__.py' 2024-04-26T14:27:09,829 adding 'pyemma/msm/estimators/_dtraj_stats.py' 2024-04-26T14:27:09,831 adding 'pyemma/msm/estimators/bayesian_hmsm.py' 2024-04-26T14:27:09,833 adding 'pyemma/msm/estimators/bayesian_msm.py' 2024-04-26T14:27:09,835 adding 'pyemma/msm/estimators/implied_timescales.py' 2024-04-26T14:27:09,838 adding 'pyemma/msm/estimators/lagged_model_validators.py' 2024-04-26T14:27:09,841 adding 'pyemma/msm/estimators/maximum_likelihood_hmsm.py' 2024-04-26T14:27:09,846 adding 'pyemma/msm/estimators/maximum_likelihood_msm.py' 2024-04-26T14:27:09,848 adding 'pyemma/msm/models/__init__.py' 2024-04-26T14:27:09,851 adding 'pyemma/msm/models/hmsm.py' 2024-04-26T14:27:09,852 adding 'pyemma/msm/models/hmsm_sampled.py' 2024-04-26T14:27:09,857 adding 'pyemma/msm/models/msm.py' 2024-04-26T14:27:09,859 adding 'pyemma/msm/models/msm_sampled.py' 2024-04-26T14:27:09,861 adding 'pyemma/msm/models/reactive_flux.py' 2024-04-26T14:27:09,863 adding 'pyemma/msm/tests/__init__.py' 2024-04-26T14:27:09,865 adding 'pyemma/msm/tests/birth_death_chain.py' 2024-04-26T14:27:09,866 adding 'pyemma/msm/tests/test_bayesian_hmsm.py' 2024-04-26T14:27:09,868 adding 'pyemma/msm/tests/test_bayesian_msm.py' 2024-04-26T14:27:09,870 adding 'pyemma/msm/tests/test_cktest.py' 2024-04-26T14:27:09,872 adding 'pyemma/msm/tests/test_estimator.py' 2024-04-26T14:27:09,874 adding 'pyemma/msm/tests/test_hmsm.py' 2024-04-26T14:27:09,876 adding 'pyemma/msm/tests/test_its.py' 2024-04-26T14:27:09,879 adding 'pyemma/msm/tests/test_msm.py' 2024-04-26T14:27:09,881 adding 'pyemma/msm/tests/test_msm_lowlevel_deprecation.py' 2024-04-26T14:27:09,883 adding 'pyemma/msm/tests/test_reactive_flux.py' 2024-04-26T14:27:09,885 adding 'pyemma/msm/tests/test_tpt.py' 2024-04-26T14:27:09,887 adding 'pyemma/plots/__init__.py' 2024-04-26T14:27:09,888 adding 'pyemma/plots/markovtests.py' 2024-04-26T14:27:09,891 adding 'pyemma/plots/networks.py' 2024-04-26T14:27:09,893 adding 'pyemma/plots/plots2d.py' 2024-04-26T14:27:09,895 adding 'pyemma/plots/thermoplots.py' 2024-04-26T14:27:09,896 adding 'pyemma/plots/timescales.py' 2024-04-26T14:27:09,898 adding 'pyemma/plots/_ext/__init__.py' 2024-04-26T14:27:09,900 adding 'pyemma/plots/_ext/fruchterman_reingold.py' 2024-04-26T14:27:09,901 adding 'pyemma/plots/tests/__init__.py' 2024-04-26T14:27:09,903 adding 'pyemma/plots/tests/test_its.py' 2024-04-26T14:27:09,904 adding 'pyemma/plots/tests/test_markovtests.py' 2024-04-26T14:27:09,905 adding 'pyemma/plots/tests/test_networks.py' 2024-04-26T14:27:09,907 adding 'pyemma/thermo/__init__.py' 2024-04-26T14:27:09,911 adding 'pyemma/thermo/api.py' 2024-04-26T14:27:09,914 adding 'pyemma/thermo/estimators/DTRAM_estimator.py' 2024-04-26T14:27:09,917 adding 'pyemma/thermo/estimators/TRAM_estimator.py' 2024-04-26T14:27:09,918 adding 'pyemma/thermo/estimators/WHAM_estimator.py' 2024-04-26T14:27:09,920 adding 'pyemma/thermo/estimators/__init__.py' 2024-04-26T14:27:09,921 adding 'pyemma/thermo/estimators/_callback.py' 2024-04-26T14:27:09,923 adding 'pyemma/thermo/models/__init__.py' 2024-04-26T14:27:09,925 adding 'pyemma/thermo/models/multi_therm.py' 2024-04-26T14:27:09,926 adding 'pyemma/thermo/models/stationary.py' 2024-04-26T14:27:09,929 adding 'pyemma/thermo/util/__init__.py' 2024-04-26T14:27:09,931 adding 'pyemma/thermo/util/util.py' 2024-04-26T14:27:09,934 adding 'pyemma/util/__init__.py' 2024-04-26T14:27:09,935 adding 'pyemma/util/annotators.py' 2024-04-26T14:27:09,938 adding 'pyemma/util/config.py' 2024-04-26T14:27:09,939 adding 'pyemma/util/contexts.py' 2024-04-26T14:27:09,941 adding 'pyemma/util/debug.py' 2024-04-26T14:27:09,943 adding 'pyemma/util/discrete_trajectories.py' 2024-04-26T14:27:09,944 adding 'pyemma/util/exceptions.py' 2024-04-26T14:27:09,946 adding 'pyemma/util/files.py' 2024-04-26T14:27:09,947 adding 'pyemma/util/indices.py' 2024-04-26T14:27:09,949 adding 'pyemma/util/linalg.py' 2024-04-26T14:27:09,950 adding 'pyemma/util/log.py' 2024-04-26T14:27:09,952 adding 'pyemma/util/numeric.py' 2024-04-26T14:27:09,953 adding 'pyemma/util/reflection.py' 2024-04-26T14:27:09,955 adding 'pyemma/util/statistics.py' 2024-04-26T14:27:09,956 adding 'pyemma/util/testing_tools.py' 2024-04-26T14:27:09,958 adding 'pyemma/util/types.py' 2024-04-26T14:27:09,960 adding 'pyemma/util/units.py' 2024-04-26T14:27:09,962 adding 'pyemma/util/_ext/__init__.py' 2024-04-26T14:27:09,963 adding 'pyemma/util/_ext/shimmodule.py' 2024-04-26T14:27:09,965 adding 'pyemma/util/tests/__init__.py' 2024-04-26T14:27:09,966 adding 'pyemma/util/tests/statistics_test.py' 2024-04-26T14:27:09,968 adding 'pyemma/util/tests/test_config.py' 2024-04-26T14:27:09,969 adding 'pyemma/util/tests/test_discrete_trajectories.py' 2024-04-26T14:27:09,971 adding 'pyemma/util/tests/test_estimation_required_decorator.py' 2024-04-26T14:27:09,972 adding 'pyemma/util/tests/test_log.py' 2024-04-26T14:27:09,974 adding 'pyemma/util/tests/test_shortcut.py' 2024-04-26T14:27:09,975 adding 'pyemma/util/tests/test_units.py' 2024-04-26T14:27:09,982 adding 'pyemma/util/tests/data/dtraj.dat' 2024-04-26T14:27:09,991 adding 'pyemma/util/tests/data/dtraj.npy' 2024-04-26T14:27:09,993 adding 'pyEMMA-2.2.1.dist-info/LICENSE.txt' 2024-04-26T14:27:09,995 adding 'pyEMMA-2.2.1.dist-info/METADATA' 2024-04-26T14:27:09,996 adding 'pyEMMA-2.2.1.dist-info/WHEEL' 2024-04-26T14:27:09,997 adding 'pyEMMA-2.2.1.dist-info/pbr.json' 2024-04-26T14:27:09,998 adding 'pyEMMA-2.2.1.dist-info/top_level.txt' 2024-04-26T14:27:10,001 adding 'pyEMMA-2.2.1.dist-info/RECORD' 2024-04-26T14:27:10,025 removing build/bdist.linux-armv7l/wheel 2024-04-26T14:27:10,318 Building wheel for pyemma (setup.py): finished with status 'done' 2024-04-26T14:27:10,334 Created wheel for pyemma: filename=pyEMMA-2.2.1-cp39-cp39-linux_armv7l.whl size=1324934 sha256=32d2163e9bc45f473bb9cd7022b5f7d459caa2ec784fcd56e25c186a47cb97ee 2024-04-26T14:27:10,335 Stored in directory: /tmp/pip-ephem-wheel-cache-jl85m115/wheels/d0/d1/a6/cbc87b350a171143178454d46d2c7f76f8a6c7c0e6afaa3891 2024-04-26T14:27:10,352 Successfully built pyemma 2024-04-26T14:27:10,407 Removed build tracker: '/tmp/pip-build-tracker-ynlb_imd'