0s autopkgtest [00:49:12]: starting date and time: 2024-06-08 00:49:12+0000 0s autopkgtest [00:49:12]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [00:49:12]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yo3ppkn0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade python-pymbar --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-6.secgroup --name adt-oracular-amd64-python-pymbar-20240608-004912-juju-7f2275-prod-proposed-migration-environment-3-9a808e79-85f7-4e6f-bd88-17ede75a19c9 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 269s autopkgtest [00:53:41]: testbed dpkg architecture: amd64 269s autopkgtest [00:53:41]: testbed apt version: 2.9.3 269s autopkgtest [00:53:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 270s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 270s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 270s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2852 B] 270s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 270s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 270s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [37.8 kB] 270s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [65.6 kB] 270s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 270s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 270s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [124 kB] 270s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [300 kB] 270s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 270s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [9280 B] 270s Fetched 1081 kB in 0s (4182 kB/s) 270s Reading package lists... 271s Reading package lists... 272s Building dependency tree... 272s Reading state information... 272s Calculating upgrade... 272s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 272s Reading package lists... 272s Building dependency tree... 272s Reading state information... 273s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 273s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 273s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 273s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 273s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 274s Reading package lists... 274s Reading package lists... 275s Building dependency tree... 275s Reading state information... 275s Calculating upgrade... 275s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 275s Reading package lists... 276s Building dependency tree... 276s Reading state information... 276s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 277s autopkgtest [00:53:49]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 277s autopkgtest [00:53:49]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 278s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (dsc) [2363 B] 278s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (tar) [17.1 MB] 278s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (diff) [3916 B] 278s gpgv: Signature made Wed Feb 1 21:01:41 2023 UTC 278s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 278s gpgv: issuer "emollier@debian.org" 278s gpgv: Can't check signature: No public key 278s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_3.1.0-4.dsc: no acceptable signature found 279s autopkgtest [00:53:51]: testing package python-pymbar version 3.1.0-4 279s autopkgtest [00:53:51]: build not needed 280s autopkgtest [00:53:52]: test command1: preparing testbed 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 281s Starting pkgProblemResolver with broken count: 0 281s Starting 2 pkgProblemResolver with broken count: 0 281s Done 282s The following additional packages will be installed: 282s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-decorator 282s python3-iniconfig python3-numpy python3-packaging python3-pluggy 282s python3-pymbar python3-pytest python3-scipy 282s Suggested packages: 282s gcc gfortran python-numpy-doc python3-dev python-scipy-doc 282s Recommended packages: 282s g++ | c++-compiler python3-pil 282s The following NEW packages will be installed: 282s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 282s python3-decorator python3-iniconfig python3-numpy python3-packaging 282s python3-pluggy python3-pymbar python3-pytest python3-scipy 282s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 282s Need to get 24.2 MB/24.2 MB of archives. 282s After this operation, 98.9 MB of additional disk space will be used. 282s Get:1 /tmp/autopkgtest.G9HynV/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 282s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 282s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 282s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 282s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 282s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 282s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 282s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 282s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 282s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 282s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.11.4-10 [15.5 MB] 282s Get:12 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pymbar all 3.1.0-4 [67.8 kB] 282s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 282s Fetched 24.2 MB in 0s (82.8 MB/s) 282s Selecting previously unselected package libblas3:amd64. 283s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74365 files and directories currently installed.) 283s Preparing to unpack .../00-libblas3_3.12.0-3build1_amd64.deb ... 283s Unpacking libblas3:amd64 (3.12.0-3build1) ... 283s Selecting previously unselected package libgfortran5:amd64. 283s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 283s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 283s Selecting previously unselected package liblapack3:amd64. 283s Preparing to unpack .../02-liblapack3_3.12.0-3build1_amd64.deb ... 283s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 283s Selecting previously unselected package liblbfgsb0:amd64. 283s Preparing to unpack .../03-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 283s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 283s Selecting previously unselected package python3-decorator. 283s Preparing to unpack .../04-python3-decorator_5.1.1-5_all.deb ... 283s Unpacking python3-decorator (5.1.1-5) ... 283s Selecting previously unselected package python3-iniconfig. 283s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 283s Unpacking python3-iniconfig (1.1.1-2) ... 283s Selecting previously unselected package python3-numpy. 283s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 283s Unpacking python3-numpy (1:1.26.4+ds-10) ... 283s Selecting previously unselected package python3-packaging. 283s Preparing to unpack .../07-python3-packaging_24.0-1_all.deb ... 283s Unpacking python3-packaging (24.0-1) ... 283s Selecting previously unselected package python3-pluggy. 283s Preparing to unpack .../08-python3-pluggy_1.5.0-1_all.deb ... 283s Unpacking python3-pluggy (1.5.0-1) ... 283s Selecting previously unselected package python3-scipy. 283s Preparing to unpack .../09-python3-scipy_1.11.4-10_amd64.deb ... 283s Unpacking python3-scipy (1.11.4-10) ... 284s Selecting previously unselected package python3-pymbar. 284s Preparing to unpack .../10-python3-pymbar_3.1.0-4_all.deb ... 284s Unpacking python3-pymbar (3.1.0-4) ... 284s Selecting previously unselected package python3-pytest. 284s Preparing to unpack .../11-python3-pytest_8.2.2-1ubuntu1_all.deb ... 284s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 284s Selecting previously unselected package autopkgtest-satdep. 284s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 284s Unpacking autopkgtest-satdep (0) ... 284s Setting up python3-iniconfig (1.1.1-2) ... 284s Setting up python3-decorator (5.1.1-5) ... 284s Setting up libblas3:amd64 (3.12.0-3build1) ... 284s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 284s Setting up python3-packaging (24.0-1) ... 284s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 284s Setting up python3-pluggy (1.5.0-1) ... 284s Setting up liblapack3:amd64 (3.12.0-3build1) ... 284s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 284s Setting up python3-pytest (8.2.2-1ubuntu1) ... 285s Setting up python3-numpy (1:1.26.4+ds-10) ... 287s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 287s Setting up python3-scipy (1.11.4-10) ... 290s Setting up python3-pymbar (3.1.0-4) ... 290s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 290s """A function that when zeroed is equivalent to the solution of 290s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 290s """ 290s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 290s """ 290s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 290s """ 290s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 290s """ 290s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 290s """ 290s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 290s """Compute estimate of overlap matrix between the states. 290s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 290s """Compute the free energy of occupying a number of bins. 290s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 290s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 290s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 290s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 290s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 290s """ 290s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 290s """Generate samples from forward and reverse Gaussian work distributions. 290s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 290s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 290s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 290s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 290s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 290s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 290s Setting up autopkgtest-satdep (0) ... 290s Processing triggers for man-db (2.12.1-1) ... 291s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 293s (Reading database ... 76839 files and directories currently installed.) 293s Removing autopkgtest-satdep (0) ... 294s autopkgtest [00:54:06]: test command1: rm pymbar/*.py && pytest-3 294s autopkgtest [00:54:06]: test command1: [----------------------- 295s ============================= test session starts ============================== 295s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 295s rootdir: /tmp/autopkgtest.G9HynV/build.caG/src 295s collected 37 items 295s 295s pymbar/tests/test_bar.py .. [ 5%] 411s pymbar/tests/test_covariance.py ... [ 13%] 433s pymbar/tests/test_mbar.py ................ [ 56%] 457s pymbar/tests/test_mbar_solvers.py .... [ 67%] 462s pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] 462s pymbar/tests/test_utils.py ... [100%] 462s 462s =============================== warnings summary =============================== 462s ../../../../usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29 462s /usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 462s from pkg_resources import resource_filename 462s 462s pymbar/tests/test_bar.py: 4 warnings 462s pymbar/tests/test_covariance.py: 9 warnings 462s pymbar/tests/test_mbar.py: 8 warnings 462s pymbar/tests/test_mbar_solvers.py: 11 warnings 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:561: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s f_i = np.matrix(self.f_k) 462s 462s pymbar/tests/test_bar.py: 4 warnings 462s pymbar/tests/test_covariance.py: 3 warnings 462s pymbar/tests/test_mbar.py: 29 warnings 462s pymbar/tests/test_mbar_solvers.py: 11 warnings 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1772: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 462s 462s pymbar/tests/test_bar.py: 4 warnings 462s pymbar/tests/test_covariance.py: 3 warnings 462s pymbar/tests/test_mbar.py: 29 warnings 462s pymbar/tests/test_mbar_solvers.py: 11 warnings 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1773: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s W = np.matrix(W, dtype=np.float64) 462s 462s pymbar/tests/test_bar.py: 40 warnings 462s pymbar/tests/test_covariance.py: 78 warnings 462s pymbar/tests/test_mbar.py: 287 warnings 462s pymbar/tests/test_mbar_solvers.py: 99 warnings 462s /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s return matrix(data, dtype=dtype, copy=False) 462s 462s pymbar/tests/test_bar.py: 4 warnings 462s pymbar/tests/test_covariance.py: 3 warnings 462s pymbar/tests/test_mbar.py: 29 warnings 462s pymbar/tests/test_mbar_solvers.py: 11 warnings 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1783: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Sigma = np.matrix(np.diag(np.sqrt(S2))) 462s 462s pymbar/tests/test_bar.py: 4 warnings 462s pymbar/tests/test_covariance.py: 3 warnings 462s pymbar/tests/test_mbar.py: 29 warnings 462s pymbar/tests/test_mbar_solvers.py: 11 warnings 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1784: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s V = np.matrix(V) 462s 462s pymbar/tests/test_bar.py: 4 warnings 462s pymbar/tests/test_covariance.py: 9 warnings 462s pymbar/tests/test_mbar.py: 23 warnings 462s pymbar/tests/test_mbar_solvers.py: 11 warnings 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1636: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s diag = np.matrix(cov.diagonal()) 462s 462s pymbar/tests/test_bar.py::test_bar_computeOverlap 462s pymbar/tests/test_bar.py::test_bar_computeOverlap 462s /usr/lib/python3/dist-packages/pymbar/bar.py:527: FutureWarning: Warning: This API is experimental and subject to change in future releases 462s warnings.warn("Warning: This API is experimental and subject to change in future releases", FutureWarning) 462s 462s pymbar/tests/test_bar.py::test_bar_computeOverlap 462s pymbar/tests/test_bar.py::test_bar_computeOverlap 462s pymbar/tests/test_bar.py::test_bar_computeOverlap 462s pymbar/tests/test_bar.py::test_bar_computeOverlap 462s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 462s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 462s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 462s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:485: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s W = np.matrix(self.getWeights(), np.float64) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1753: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1754: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s W = np.matrix(W, dtype=np.float64) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1759: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Sigma = np.matrix(np.diag(S)) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1760: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s V = np.matrix(Vt).T 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:385: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s f_i = np.matrix(self.f_k) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1925: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1926: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s W = np.matrix(W, dtype=np.float64) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1931: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Sigma = np.matrix(np.diag(S)) 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1932: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s V = np.matrix(Vt).T 462s 462s pymbar/tests/test_covariance.py::test_100x100_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_oscillators 462s pymbar/tests/test_covariance.py::test_200x50_exponentials 462s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1784: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Ainv = np.matrix(np.zeros([M, M], dtype=np.float64)) 462s 462s pymbar/tests/test_mbar.py: 560 warnings 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:579: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s diffm[:,:,b] = np.matrix(self.f_k_boots[b,:]) - np.matrix(self.f_k_boots[b,:]).transpose() 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 462s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1088: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s A_im = np.matrix(inner_results['observables']) 462s 462s pymbar/tests/test_mbar.py: 16 warnings 462s /tmp/autopkgtest.G9HynV/build.caG/src/pymbar/tests/test_mbar.py:23: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s xa_ij = np.array(np.matrix(xa) - np.matrix(xa).transpose()) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1377: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s Adiag = np.matrix(np.zeros([3*K,3*K],dtype=np.float64)) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1382: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s f_k = np.matrix(inner_results['f']) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1389: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s u_k = np.matrix(inner_results['observables']) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s /tmp/autopkgtest.G9HynV/build.caG/src/pymbar/tests/test_mbar.py:253: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s fa_ij = np.array(np.matrix(fa) - np.matrix(fa).transpose()) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s /tmp/autopkgtest.G9HynV/build.caG/src/pymbar/tests/test_mbar.py:254: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s ua_ij = np.array(np.matrix(ua) - np.matrix(ua).transpose()) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 462s /tmp/autopkgtest.G9HynV/build.caG/src/pymbar/tests/test_mbar.py:255: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s sa_ij = np.array(np.matrix(sa) - np.matrix(sa).transpose()) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 462s /tmp/autopkgtest.G9HynV/build.caG/src/pymbar/tests/test_mbar.py:301: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s reference_matrix = np.matrix((1.0/d)*np.ones([d,d])) 462s 462s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 462s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 462s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 462s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 462s /usr/lib/python3/dist-packages/pymbar/mbar.py:1280: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 462s f_k = np.matrix(inner_results['f']) 462s 462s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 462s =========== 33 passed, 4 skipped, 1431 warnings in 167.76s (0:02:47) =========== 462s autopkgtest [00:56:54]: test command1: -----------------------] 463s command1 PASS 463s autopkgtest [00:56:55]: test command1: - - - - - - - - - - results - - - - - - - - - - 463s autopkgtest [00:56:55]: test autodep8-python3: preparing testbed 593s autopkgtest [00:59:05]: testbed dpkg architecture: amd64 593s autopkgtest [00:59:05]: testbed apt version: 2.9.3 593s autopkgtest [00:59:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 594s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 594s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 594s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 594s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 594s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 594s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [38.1 kB] 594s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [66.4 kB] 594s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 594s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 594s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [126 kB] 594s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [315 kB] 594s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 594s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [11.7 kB] 594s Fetched 1102 kB in 0s (4213 kB/s) 594s Reading package lists... 596s Reading package lists... 597s Building dependency tree... 597s Reading state information... 597s Calculating upgrade... 597s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 597s Reading package lists... 598s Building dependency tree... 598s Reading state information... 598s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 599s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 599s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 599s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 599s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 600s Reading package lists... 600s Reading package lists... 600s Building dependency tree... 600s Reading state information... 601s Calculating upgrade... 601s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 601s Reading package lists... 601s Building dependency tree... 601s Reading state information... 602s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 604s Reading package lists... 604s Building dependency tree... 604s Reading state information... 604s Starting pkgProblemResolver with broken count: 0 604s Starting 2 pkgProblemResolver with broken count: 0 604s Done 605s The following additional packages will be installed: 605s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all python3-decorator 605s python3-numpy python3-pymbar python3-scipy 605s Suggested packages: 605s gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 605s Recommended packages: 605s g++ | c++-compiler python3-pil 605s The following NEW packages will be installed: 605s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all 605s python3-decorator python3-numpy python3-pymbar python3-scipy 605s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 605s Need to get 23.9 MB/23.9 MB of archives. 605s After this operation, 97.4 MB of additional disk space will be used. 605s Get:1 /tmp/autopkgtest.G9HynV/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 605s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 605s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 605s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 605s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 605s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-all amd64 3.12.3-0ubuntu1 [888 B] 605s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 605s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 605s Get:9 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.11.4-10 [15.5 MB] 605s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pymbar all 3.1.0-4 [67.8 kB] 606s Fetched 23.9 MB in 0s (94.9 MB/s) 606s Selecting previously unselected package libblas3:amd64. 606s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74365 files and directories currently installed.) 606s Preparing to unpack .../0-libblas3_3.12.0-3build1_amd64.deb ... 606s Unpacking libblas3:amd64 (3.12.0-3build1) ... 606s Selecting previously unselected package libgfortran5:amd64. 606s Preparing to unpack .../1-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 606s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 606s Selecting previously unselected package liblapack3:amd64. 606s Preparing to unpack .../2-liblapack3_3.12.0-3build1_amd64.deb ... 606s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 606s Selecting previously unselected package liblbfgsb0:amd64. 606s Preparing to unpack .../3-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 606s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 606s Selecting previously unselected package python3-all. 606s Preparing to unpack .../4-python3-all_3.12.3-0ubuntu1_amd64.deb ... 606s Unpacking python3-all (3.12.3-0ubuntu1) ... 606s Selecting previously unselected package python3-decorator. 606s Preparing to unpack .../5-python3-decorator_5.1.1-5_all.deb ... 606s Unpacking python3-decorator (5.1.1-5) ... 606s Selecting previously unselected package python3-numpy. 606s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 606s Unpacking python3-numpy (1:1.26.4+ds-10) ... 607s Selecting previously unselected package python3-scipy. 607s Preparing to unpack .../7-python3-scipy_1.11.4-10_amd64.deb ... 607s Unpacking python3-scipy (1.11.4-10) ... 607s Selecting previously unselected package python3-pymbar. 607s Preparing to unpack .../8-python3-pymbar_3.1.0-4_all.deb ... 607s Unpacking python3-pymbar (3.1.0-4) ... 607s Selecting previously unselected package autopkgtest-satdep. 607s Preparing to unpack .../9-2-autopkgtest-satdep.deb ... 607s Unpacking autopkgtest-satdep (0) ... 607s Setting up python3-all (3.12.3-0ubuntu1) ... 607s Setting up python3-decorator (5.1.1-5) ... 607s Setting up libblas3:amd64 (3.12.0-3build1) ... 607s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 607s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 607s Setting up liblapack3:amd64 (3.12.0-3build1) ... 607s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 607s Setting up python3-numpy (1:1.26.4+ds-10) ... 610s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 610s Setting up python3-scipy (1.11.4-10) ... 613s Setting up python3-pymbar (3.1.0-4) ... 613s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 613s """A function that when zeroed is equivalent to the solution of 613s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 613s """ 613s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 613s """ 613s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 613s """ 613s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 613s """ 613s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 613s """ 613s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 613s """Compute estimate of overlap matrix between the states. 613s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 613s """Compute the free energy of occupying a number of bins. 613s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 613s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 613s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 613s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 613s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 613s """ 613s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 613s """Generate samples from forward and reverse Gaussian work distributions. 613s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 613s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 613s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 613s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 613s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 613s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 613s Setting up autopkgtest-satdep (0) ... 613s Processing triggers for man-db (2.12.1-1) ... 614s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 616s (Reading database ... 76676 files and directories currently installed.) 616s Removing autopkgtest-satdep (0) ... 618s autopkgtest [00:59:30]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pymbar; print(pymbar)" ; done 618s autopkgtest [00:59:30]: test autodep8-python3: [----------------------- 618s Testing with python3.12: 618s 619s autopkgtest [00:59:31]: test autodep8-python3: -----------------------] 619s autopkgtest [00:59:31]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 619s autodep8-python3 PASS (superficial) 619s autopkgtest [00:59:31]: @@@@@@@@@@@@@@@@@@@@ summary 619s command1 PASS 619s autodep8-python3 PASS (superficial) 630s nova [W] Skipping flock for amd64 630s Creating nova instance adt-oracular-amd64-python-pymbar-20240608-004912-juju-7f2275-prod-proposed-migration-environment-3-9a808e79-85f7-4e6f-bd88-17ede75a19c9 from image adt/ubuntu-oracular-amd64-server-20240607.img (UUID d996b44c-1e10-4875-aeab-5b4c434d75a2)... 630s nova [W] Skipping flock for amd64 630s Creating nova instance adt-oracular-amd64-python-pymbar-20240608-004912-juju-7f2275-prod-proposed-migration-environment-3-9a808e79-85f7-4e6f-bd88-17ede75a19c9 from image adt/ubuntu-oracular-amd64-server-20240607.img (UUID d996b44c-1e10-4875-aeab-5b4c434d75a2)...