0s autopkgtest [09:34:49]: starting date and time: 2024-12-03 09:34:49+0000 0s autopkgtest [09:34:49]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [09:34:49]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lpvcy09n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:astropy --apt-upgrade imexam --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=astropy/7.0.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-8.secgroup --name adt-plucky-arm64-imexam-20241203-093449-juju-7f2275-prod-proposed-migration-environment-20-b6cf7b3a-39bd-40a6-97d8-123126378cf4 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 260s autopkgtest [09:39:09]: testbed dpkg architecture: arm64 260s autopkgtest [09:39:09]: testbed apt version: 2.9.14ubuntu1 260s autopkgtest [09:39:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 261s autopkgtest [09:39:10]: testbed release detected to be: None 262s autopkgtest [09:39:11]: updating testbed package index (apt update) 262s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 262s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 262s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 262s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 262s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [65.3 kB] 262s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 262s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [781 kB] 262s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB] 262s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [145 kB] 263s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [58.2 kB] 263s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [669 kB] 263s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [21.3 kB] 263s Fetched 1838 kB in 1s (2030 kB/s) 264s Reading package lists... 264s Reading package lists... 264s Building dependency tree... 264s Reading state information... 265s Calculating upgrade... 265s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 265s Reading package lists... 266s Building dependency tree... 266s Reading state information... 266s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 266s autopkgtest [09:39:15]: upgrading testbed (apt dist-upgrade and autopurge) 267s Reading package lists... 267s Building dependency tree... 267s Reading state information... 267s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 267s Starting 2 pkgProblemResolver with broken count: 0 267s Done 268s Entering ResolveByKeep 268s 269s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 270s Starting pkgProblemResolver with broken count: 0 270s Starting 2 pkgProblemResolver with broken count: 0 270s Done 271s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 273s autopkgtest [09:39:22]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 273s autopkgtest [09:39:22]: @@@@@@@@@@@@@@@@@@@@ apt-source imexam 277s Get:1 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (dsc) [2361 B] 277s Get:2 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (tar) [21.4 MB] 277s Get:3 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (diff) [7756 B] 277s gpgv: Signature made Tue Nov 28 09:16:30 2023 UTC 277s gpgv: using RSA key BAFC6C85F7CB143FEEB6FB157115AFD07710DCF7 277s gpgv: Can't check signature: No public key 277s dpkg-source: warning: cannot verify inline signature for ./imexam_0.9.1-6.dsc: no acceptable signature found 278s autopkgtest [09:39:27]: testing package imexam version 0.9.1-6 278s autopkgtest [09:39:27]: build not needed 279s autopkgtest [09:39:28]: test command1: preparing testbed 280s Reading package lists... 280s Building dependency tree... 280s Reading state information... 280s Starting pkgProblemResolver with broken count: 0 280s Starting 2 pkgProblemResolver with broken count: 0 280s Done 281s The following NEW packages will be installed: 281s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx ipython3 281s libblas3 libdeflate0 liberfa1 libfontconfig1 libgfortran5 libgomp1 281s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 281s libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen 281s libjs-jquery-metadata libjs-jquery-tablesorter 281s libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc 281s libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 281s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 281s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwcs8 libwebp7 libwebpdemux2 281s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 281s python3-appdirs python3-astropy python3-astropy-iers-data python3-asttokens 281s python3-brotli python3-contourpy python3-coverage python3-cycler 281s python3-dateutil python3-decorator python3-erfa python3-executing 281s python3-fonttools python3-fs python3-hypothesis python3-imexam 281s python3-iniconfig python3-ipython python3-jedi python3-kiwisolver 281s python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline 281s python3-mpmath python3-numpy python3-packaging python3-parso python3-pexpect 281s python3-pil python3-pil.imagetk python3-pluggy python3-ply 281s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 281s python3-pytest-arraydiff python3-pytest-astropy 281s python3-pytest-astropy-header python3-pytest-cov python3-pytest-doctestplus 281s python3-pytest-filter-subpackage python3-pytest-mock 281s python3-pytest-remotedata python3-scipy python3-sortedcontainers 281s python3-stack-data python3-sympy python3-tk python3-traitlets 281s python3-typeshed python3-tz python3-ufolib2 python3-unicodedata2 281s python3-wcwidth python3.12-tk python3.13 python3.13-minimal python3.13-tk 281s tk8.6-blt2.5 unicode-data x11-common 281s 0 upgraded, 112 newly installed, 0 to remove and 0 not upgraded. 281s Need to get 75.8 MB of archives. 281s After this operation, 383 MB of additional disk space will be used. 281s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 282s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 282s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 282s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 282s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 282s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 282s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 282s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 282s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 282s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 282s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 282s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 282s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 282s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 282s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 282s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 282s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 282s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 282s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 282s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 282s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 282s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 282s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 282s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 282s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 282s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 3.0.0-1 [20.4 kB] 282s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.1.0-0.1 [24.4 kB] 282s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 282s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 282s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 282s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 282s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.29.0-1 [569 kB] 282s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 ipython3 all 8.29.0-1 [4938 B] 282s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 282s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 282s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-9ubuntu1 [437 kB] 282s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-9ubuntu1 [145 kB] 282s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 282s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 282s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 282s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 282s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 282s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-metadata all 12-4 [6582 B] 282s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 282s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 282s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 282s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 282s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 282s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 283s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 283s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 283s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 283s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 283s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 283s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 283s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 283s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 283s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 283s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 283s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwcs8 arm64 8.4+ds-1 [262 kB] 283s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 283s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 283s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 283s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 283s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 283s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 283s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 283s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 283s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 283s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 283s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 283s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hypothesis all 6.119.3-1 [329 kB] 283s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 283s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-arraydiff all 0.6.1-3 [10.2 kB] 283s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-astropy-header all 0.2.2-2 [8620 B] 283s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 283s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.4.4+dfsg1-0ubuntu3 [150 kB] 283s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 283s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-cov all 5.0.0-1 [21.3 kB] 283s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-doctestplus all 1.3.0-1 [23.7 kB] 283s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-filter-subpackage all 0.2.0-1 [6094 B] 283s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 283s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-remotedata all 0.4.1-1 [8650 B] 283s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-astropy all 0.11.0-1 [5902 B] 283s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ply all 3.11-7 [45.4 kB] 283s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-astropy-iers-data all 0.2024.07.22.00.34.13-1 [1198 kB] 283s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 liberfa1 arm64 2.0.1-1build1 [136 kB] 283s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-erfa arm64 2.0.1.5+ds-1 [310 kB] 283s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-astropy arm64 7.0.0-1 [3991 kB] 283s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 283s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2build1 [220 kB] 283s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 283s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 283s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-5 [90.7 kB] 283s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1build1 [1591 kB] 283s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build5 [27.5 kB] 283s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5ubuntu1 [19.1 MB] 284s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 284s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 284s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 284s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 284s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 285s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.0-3 [1618 kB] 285s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 285s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu2 [473 kB] 285s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 285s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 285s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 285s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu2 [9590 B] 285s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 285s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu1 [4612 kB] 285s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-imexam arm64 0.9.1-6 [50.5 kB] 286s Fetched 75.8 MB in 4s (17.1 MB/s) 286s Selecting previously unselected package libpython3.13-minimal:arm64. 286s (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 ... 80333 files and directories currently installed.) 286s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_arm64.deb ... 286s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 286s Selecting previously unselected package python3.13-minimal. 286s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_arm64.deb ... 286s Unpacking python3.13-minimal (3.13.0-2) ... 286s Selecting previously unselected package libjs-jquery. 286s Preparing to unpack .../002-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 286s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 286s Selecting previously unselected package libjs-jquery-hotkeys. 286s Preparing to unpack .../003-libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... 286s Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 287s Selecting previously unselected package libtcl8.6:arm64. 287s Preparing to unpack .../004-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 287s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 287s Selecting previously unselected package fonts-dejavu-mono. 287s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 287s Unpacking fonts-dejavu-mono (2.37-8) ... 287s Selecting previously unselected package fonts-dejavu-core. 287s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 287s Unpacking fonts-dejavu-core (2.37-8) ... 287s Selecting previously unselected package fontconfig-config. 287s Preparing to unpack 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unselected package python3-parso. 287s Preparing to unpack .../018-python3-parso_0.8.4-1_all.deb ... 287s Unpacking python3-parso (0.8.4-1) ... 287s Selecting previously unselected package python3-typeshed. 287s Preparing to unpack .../019-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 287s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 288s Selecting previously unselected package python3-jedi. 288s Preparing to unpack .../020-python3-jedi_0.19.1+ds1-1_all.deb ... 288s Unpacking python3-jedi (0.19.1+ds1-1) ... 288s Selecting previously unselected package python3-traitlets. 288s Preparing to unpack .../021-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 288s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 288s Selecting previously unselected package python3-matplotlib-inline. 288s Preparing to unpack .../022-python3-matplotlib-inline_0.1.6-2_all.deb ... 288s Unpacking python3-matplotlib-inline (0.1.6-2) ... 288s Selecting previously unselected package 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package libdeflate0:arm64. 289s Preparing to unpack .../034-libdeflate0_1.22-1_arm64.deb ... 289s Unpacking libdeflate0:arm64 (1.22-1) ... 289s Selecting previously unselected package libgfortran5:arm64. 289s Preparing to unpack .../035-libgfortran5_14.2.0-9ubuntu1_arm64.deb ... 289s Unpacking libgfortran5:arm64 (14.2.0-9ubuntu1) ... 289s Selecting previously unselected package libgomp1:arm64. 289s Preparing to unpack .../036-libgomp1_14.2.0-9ubuntu1_arm64.deb ... 289s Unpacking libgomp1:arm64 (14.2.0-9ubuntu1) ... 289s Selecting previously unselected package libgraphite2-3:arm64. 289s Preparing to unpack .../037-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 289s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 289s Selecting previously unselected package libharfbuzz0b:arm64. 289s Preparing to unpack .../038-libharfbuzz0b_10.0.1-1_arm64.deb ... 289s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 289s Selecting previously unselected package libimagequant0:arm64. 289s Preparing to unpack .../039-libimagequant0_2.18.0-1build1_arm64.deb ... 289s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 289s Selecting previously unselected package libjpeg-turbo8:arm64. 289s Preparing to unpack .../040-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 289s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 289s Selecting previously unselected package libjpeg8:arm64. 289s Preparing to unpack .../041-libjpeg8_8c-2ubuntu11_arm64.deb ... 289s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 289s Selecting previously unselected package libjs-jquery-metadata. 289s Preparing to unpack .../042-libjs-jquery-metadata_12-4_all.deb ... 289s Unpacking libjs-jquery-metadata (12-4) ... 289s Selecting previously unselected package libjs-jquery-tablesorter. 289s Preparing to unpack .../043-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-4_all.deb ... 289s Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 289s Selecting previously unselected package libjs-jquery-throttle-debounce. 289s Preparing to unpack .../044-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... 289s Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 289s Selecting previously unselected package libjs-jquery-ui. 289s Preparing to unpack .../045-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 289s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 289s Selecting previously unselected package libjs-underscore. 289s Preparing to unpack .../046-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 289s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 289s Selecting previously unselected package libjs-sphinxdoc. 289s Preparing to unpack .../047-libjs-sphinxdoc_7.4.7-4_all.deb ... 289s Unpacking libjs-sphinxdoc (7.4.7-4) ... 289s Selecting previously unselected package liblapack3:arm64. 289s Preparing to unpack .../048-liblapack3_3.12.0-4_arm64.deb ... 289s Unpacking liblapack3:arm64 (3.12.0-4) ... 289s Selecting previously unselected package liblbfgsb0:arm64. 289s Preparing to unpack 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(8.4+ds-1) ... 290s Selecting previously unselected package libwebpdemux2:arm64. 290s Preparing to unpack .../060-libwebpdemux2_1.4.0-0.1_arm64.deb ... 290s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 290s Selecting previously unselected package libwebpmux3:arm64. 290s Preparing to unpack .../061-libwebpmux3_1.4.0-0.1_arm64.deb ... 290s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 290s Selecting previously unselected package libxslt1.1:arm64. 290s Preparing to unpack .../062-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 290s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 290s Selecting previously unselected package python-matplotlib-data. 290s Preparing to unpack .../063-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 290s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 290s Selecting previously unselected package python3-appdirs. 290s Preparing to unpack .../064-python3-appdirs_1.4.4-4_all.deb ... 290s Unpacking python3-appdirs (1.4.4-4) ... 290s Selecting previously unselected package python3-iniconfig. 290s Preparing to unpack .../065-python3-iniconfig_1.1.1-2_all.deb ... 290s Unpacking python3-iniconfig (1.1.1-2) ... 290s Selecting previously unselected package python3-packaging. 290s Preparing to unpack .../066-python3-packaging_24.2-1_all.deb ... 290s Unpacking python3-packaging (24.2-1) ... 290s Selecting previously unselected package python3-pluggy. 290s Preparing to unpack .../067-python3-pluggy_1.5.0-1_all.deb ... 290s Unpacking python3-pluggy (1.5.0-1) ... 290s Selecting previously unselected package python3-pytest. 290s Preparing to unpack .../068-python3-pytest_8.3.3-1_all.deb ... 290s Unpacking python3-pytest (8.3.3-1) ... 290s Selecting previously unselected package python3-dateutil. 290s Preparing to unpack .../069-python3-dateutil_2.9.0-3_all.deb ... 290s Unpacking python3-dateutil (2.9.0-3) ... 290s Selecting previously unselected package python3-sortedcontainers. 290s Preparing to unpack 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.../085-python3-astropy-iers-data_0.2024.07.22.00.34.13-1_all.deb ... 291s Unpacking python3-astropy-iers-data (0.2024.07.22.00.34.13-1) ... 291s Selecting previously unselected package liberfa1:arm64. 291s Preparing to unpack .../086-liberfa1_2.0.1-1build1_arm64.deb ... 291s Unpacking liberfa1:arm64 (2.0.1-1build1) ... 291s Selecting previously unselected package python3-erfa. 291s Preparing to unpack .../087-python3-erfa_2.0.1.5+ds-1_arm64.deb ... 291s Unpacking python3-erfa (2.0.1.5+ds-1) ... 291s Selecting previously unselected package python3-astropy. 291s Preparing to unpack .../088-python3-astropy_7.0.0-1_arm64.deb ... 291s Unpacking python3-astropy (7.0.0-1) ... 291s Selecting previously unselected package python3-brotli. 291s Preparing to unpack .../089-python3-brotli_1.1.0-2build3_arm64.deb ... 291s Unpacking python3-brotli (1.1.0-2build3) ... 292s Selecting previously unselected package python3-contourpy. 292s Preparing to unpack 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arraydiff-0.6.1, typeguard-4.4.1, cov-5.0.0, astropy-header-0.2.2, remotedata-0.4.1, hypothesis-6.119.3 330s collected 21 items 330s 331s tests/test_imexamine.py ..sFFxFFs [ 42%] 331s tests/test_util.py ............ [100%] 331s 331s =================================== FAILURES =================================== 331s ________________________________ test_line_fit _________________________________ 331s 331s def test_line_fit(): 331s """Fit a Gaussian1D line to the data.""" 331s plots = Imexamine() 331s in_amp = 3. 331s in_mean = 50. 331s in_stddev = 2. 331s in_const = 20. 331s 331s # Set all the lines to be Gaussians 331s line_gauss = in_const + in_amp * np.exp(-0.5 * ((xx - in_mean) / in_stddev)**2) 331s plots.set_data(line_gauss) 331s > fit = plots.line_fit(50, 50, form='Gaussian1D', genplot=False) 331s 331s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:86: 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:765: in line_fit 331s amp, xout, yout, sigma, sigmay = self.gauss_center(xx, 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 331s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 331s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 331s results = fit(model, xx, yy, data) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 331s return func(self, model, x, y, z=z, **kwargs) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 331s init_values, fitparams, cov_x = self._run_fitter( 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 331s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:437: in leastsq 331s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:29: in _check_func 331s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s 331s params = array([ 3., 15., 15., 3., 3., 0., 20.]) 331s model = 331s weights = 1.0 331s x = array([[ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 331s 13., 14., 15., 16., 17., 18., 19., 20..., 10., 11., 12., 331s 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 331s 26., 27., 28., 29.]]) 331s y = array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 331s 0., 0., 0., 0., 0., 0., 0., 0..., 29., 29., 29., 331s 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 331s 29., 29., 29., 29.]]) 331s z = array([[20. , 20. , 20. , 20.00000005, 20.00000081, 331s 20.00001118, 20.0001202 , 20.00100639...2699, 20.00656247, 20.00100639, 20.0001202 , 331s 20.00001118, 20.00000081, 20.00000005, 20. , 20. ]]) 331s fit_param_indices = None 331s 331s @staticmethod 331s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 331s """ 331s Wraps the method calculating the Jacobian of the function to account 331s for model constraints. 331s `scipy.optimize.leastsq` expects the function derivative to have the 331s above signature (parlist, (argtuple)). In order to accommodate model 331s constraints, instead of using p directly, we set the parameter list in 331s this function. 331s """ 331s if weights is None: 331s weights = 1.0 331s 331s if model.has_fixed or model.has_tied: 331s # update the parameters with the current values from the fitter 331s fitter_to_model_params(model, params) 331s if z is None: 331s full = np.array(model.fit_deriv(x, *model.parameters)) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s else: 331s full = np.array( 331s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 331s ) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s 331s pars = [getattr(model, name) for name in model.param_names] 331s fixed = [par.fixed for par in pars] 331s tied = [par.tied for par in pars] 331s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 331s fix_and_tie = np.logical_or(fixed, tied) 331s ind = np.logical_not(fix_and_tie) 331s 331s if not model.col_fit_deriv: 331s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 331s else: 331s residues = full_deriv[np.nonzero(ind)] 331s 331s return [np.ravel(_) for _ in residues] 331s else: 331s if z is None: 331s fit_deriv = np.array(model.fit_deriv(x, *params)) 331s try: 331s output = np.array( 331s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 331s ) 331s if output.shape != fit_deriv.shape: 331s output = np.array( 331s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 331s ) 331s return output 331s except ValueError: 331s return np.array( 331s [ 331s np.ravel(_) 331s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 331s ] 331s ).transpose() 331s else: 331s if not model.col_fit_deriv: 331s return [ 331s np.ravel(_) 331s for _ in ( 331s np.ravel(weights) 331s * np.array(model.fit_deriv(x, y, *params)).T 331s ).T 331s ] 331s return [ 331s np.ravel(_) 331s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 331s ] 331s E ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (7,) + inhomogeneous part. 331s 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 331s ----------------------------- Captured stdout call ----------------------------- 331s using model: 331s Name: Gaussian1D 331s N_inputs: 1 331s N_outputs: 1 331s Fittable parameters: ('amplitude', 'mean', 'stddev') 331s ------------------------------ Captured log call ------------------------------- 331s INFO imexam.util:imexamine.py:749 using model: 331s Name: Gaussian1D 331s N_inputs: 1 331s N_outputs: 1 331s Fittable parameters: ('amplitude', 'mean', 'stddev') 331s _______________________________ test_column_fit ________________________________ 331s 331s def test_column_fit(): 331s """Fit a Gaussian1D column to the data.""" 331s plots = Imexamine() 331s in_amp = 3. 331s in_mean = 50. 331s in_stddev = 2. 331s in_const = 20. 331s # Set all the columns to be Gaussians 331s col_gauss = in_const + in_amp * np.exp(-0.5 * ((yy - in_mean) / in_stddev)**2) 331s plots.set_data(col_gauss) 331s > fit = plots.column_fit(50, 50, form='Gaussian1D', genplot=False) 331s 331s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:104: 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:917: in column_fit 331s result = self.line_fit(x, y, data=data, form=form, 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:765: in line_fit 331s amp, xout, yout, sigma, sigmay = self.gauss_center(xx, 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 331s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 331s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 331s results = fit(model, xx, yy, data) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 331s return func(self, model, x, y, z=z, **kwargs) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 331s init_values, fitparams, cov_x = self._run_fitter( 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 331s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:437: in leastsq 331s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:29: in _check_func 331s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s 331s params = array([ 3., 15., 15., 3., 3., 0., 20.]) 331s model = 331s weights = 1.0 331s x = array([[ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 331s 13., 14., 15., 16., 17., 18., 19., 20..., 10., 11., 12., 331s 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 331s 26., 27., 28., 29.]]) 331s y = array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 331s 0., 0., 0., 0., 0., 0., 0., 0..., 29., 29., 29., 331s 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 331s 29., 29., 29., 29.]]) 331s z = array([[20. , 20. , 20. , 20. , 20. , 331s 20. , 20. , 20. ... , 20. , 20. , 20. , 331s 20. , 20. , 20. , 20. , 20. ]]) 331s fit_param_indices = None 331s 331s @staticmethod 331s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 331s """ 331s Wraps the method calculating the Jacobian of the function to account 331s for model constraints. 331s `scipy.optimize.leastsq` expects the function derivative to have the 331s above signature (parlist, (argtuple)). In order to accommodate model 331s constraints, instead of using p directly, we set the parameter list in 331s this function. 331s """ 331s if weights is None: 331s weights = 1.0 331s 331s if model.has_fixed or model.has_tied: 331s # update the parameters with the current values from the fitter 331s fitter_to_model_params(model, params) 331s if z is None: 331s full = np.array(model.fit_deriv(x, *model.parameters)) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s else: 331s full = np.array( 331s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 331s ) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s 331s pars = [getattr(model, name) for name in model.param_names] 331s fixed = [par.fixed for par in pars] 331s tied = [par.tied for par in pars] 331s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 331s fix_and_tie = np.logical_or(fixed, tied) 331s ind = np.logical_not(fix_and_tie) 331s 331s if not model.col_fit_deriv: 331s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 331s else: 331s residues = full_deriv[np.nonzero(ind)] 331s 331s return [np.ravel(_) for _ in residues] 331s else: 331s if z is None: 331s fit_deriv = np.array(model.fit_deriv(x, *params)) 331s try: 331s output = np.array( 331s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 331s ) 331s if output.shape != fit_deriv.shape: 331s output = np.array( 331s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 331s ) 331s return output 331s except ValueError: 331s return np.array( 331s [ 331s np.ravel(_) 331s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 331s ] 331s ).transpose() 331s else: 331s if not model.col_fit_deriv: 331s return [ 331s np.ravel(_) 331s for _ in ( 331s np.ravel(weights) 331s * np.array(model.fit_deriv(x, y, *params)).T 331s ).T 331s ] 331s return [ 331s np.ravel(_) 331s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 331s ] 331s E ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (7,) + inhomogeneous part. 331s 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 331s ----------------------------- Captured stdout call ----------------------------- 331s using model: 331s Name: Gaussian1D 331s N_inputs: 1 331s N_outputs: 1 331s Fittable parameters: ('amplitude', 'mean', 'stddev') 331s ------------------------------ Captured log call ------------------------------- 331s INFO imexam.util:imexamine.py:749 using model: 331s Name: Gaussian1D 331s N_inputs: 1 331s N_outputs: 1 331s Fittable parameters: ('amplitude', 'mean', 'stddev') 331s _____________________________ test_radial_profile ______________________________ 331s 331s def test_radial_profile(): 331s """Test the radial profile function 331s No background subtraction 331s individual pixel results used 331s """ 331s from astropy.convolution import Gaussian2DKernel 331s data = Gaussian2DKernel(1.5, x_size=25, y_size=25) 331s xx, yy = np.meshgrid(np.arange(25), np.arange(25)) 331s x0, y0 = np.where(data.array == data.array.max()) 331s 331s rad_in = np.sqrt((xx - x0)**2 + (yy - y0)**2) 331s rad_in = rad_in.ravel() 331s flux_in = data.array.ravel() 331s 331s order = np.argsort(rad_in) 331s rad_in = rad_in[order] 331s flux_in = flux_in[order] 331s 331s plots = Imexamine() 331s plots.set_data(data.array) 331s 331s plots.radial_profile_pars['pixels'][0] = True 331s plots.radial_profile_pars['background'][0] = False 331s plots.radial_profile_pars['clip'][0] = False 331s > rad_out, flux_out = plots.radial_profile(x0, y0, genplot=False) 331s 331s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:160: 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1102: in radial_profile 331s amp, centerx, centery, sigmax, sigmay = self.gauss_center(xx, yy, data, delta=datasize) 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 331s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 331s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 331s results = fit(model, xx, yy, data) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 331s return func(self, model, x, y, z=z, **kwargs) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 331s init_values, fitparams, cov_x = self._run_fitter( 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 331s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:437: in leastsq 331s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:29: in _check_func 331s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s 331s params = array([7.06778109e-02, 4.00000000e+00, 4.00000000e+00, 3.00000000e+00, 331s 3.00000000e+00, 0.00000000e+00, 5.77193322e-05]) 331s model = 331s weights = 1.0 331s x = array([[0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., ... [0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., 7.]]) 331s y = array([[0., 0., 0., 0., 0., 0., 0., 0.], 331s [1., 1., 1., 1., 1., 1., 1., 1.], 331s [2., 2., 2., 2., 2., 2., 2., ... [5., 5., 5., 5., 5., 5., 5., 5.], 331s [6., 6., 6., 6., 6., 6., 6., 6.], 331s [7., 7., 7., 7., 7., 7., 7., 7.]]) 331s z = array([[5.77193322e-05, 2.73457911e-04, 8.30691786e-04, 1.61796667e-03, 331s 2.02059585e-03, 1.61796667e-03, 8.3069...29556643e-03, 3.93558331e-03, 7.66546959e-03, 331s 9.57301302e-03, 7.66546959e-03, 3.93558331e-03, 1.29556643e-03]]) 331s fit_param_indices = None 331s 331s @staticmethod 331s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 331s """ 331s Wraps the method calculating the Jacobian of the function to account 331s for model constraints. 331s `scipy.optimize.leastsq` expects the function derivative to have the 331s above signature (parlist, (argtuple)). In order to accommodate model 331s constraints, instead of using p directly, we set the parameter list in 331s this function. 331s """ 331s if weights is None: 331s weights = 1.0 331s 331s if model.has_fixed or model.has_tied: 331s # update the parameters with the current values from the fitter 331s fitter_to_model_params(model, params) 331s if z is None: 331s full = np.array(model.fit_deriv(x, *model.parameters)) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s else: 331s full = np.array( 331s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 331s ) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s 331s pars = [getattr(model, name) for name in model.param_names] 331s fixed = [par.fixed for par in pars] 331s tied = [par.tied for par in pars] 331s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 331s fix_and_tie = np.logical_or(fixed, tied) 331s ind = np.logical_not(fix_and_tie) 331s 331s if not model.col_fit_deriv: 331s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 331s else: 331s residues = full_deriv[np.nonzero(ind)] 331s 331s return [np.ravel(_) for _ in residues] 331s else: 331s if z is None: 331s fit_deriv = np.array(model.fit_deriv(x, *params)) 331s try: 331s output = np.array( 331s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 331s ) 331s if output.shape != fit_deriv.shape: 331s output = np.array( 331s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 331s ) 331s return output 331s except ValueError: 331s return np.array( 331s [ 331s np.ravel(_) 331s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 331s ] 331s ).transpose() 331s else: 331s if not model.col_fit_deriv: 331s return [ 331s np.ravel(_) 331s for _ in ( 331s np.ravel(weights) 331s * np.array(model.fit_deriv(x, y, *params)).T 331s ).T 331s ] 331s return [ 331s np.ravel(_) 331s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 331s ] 331s E ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (7,) + inhomogeneous part. 331s 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 331s ________________________ test_radial_profile_cumulative ________________________ 331s 331s def test_radial_profile_cumulative(): 331s """Test the radial profile function 331s without background subtraction 331s with each pixel integer binned 331s """ 331s from astropy.convolution import Gaussian2DKernel 331s ksize = 25 331s data = Gaussian2DKernel(1.5, x_size=ksize, y_size=ksize) 331s xx, yy = np.meshgrid(np.arange(ksize), np.arange(ksize)) 331s x0, y0 = np.where(data.array == data.array.max()) 331s rad_in = np.sqrt((xx - x0)**2 + (yy - y0)**2) 331s 331s rad_in = rad_in.ravel() 331s flux_in = data.array.ravel() 331s 331s indices = np.argsort(rad_in) 331s rad_in = rad_in[indices] 331s flux_in = flux_in[indices] 331s 331s # now bin the radflux like we expect 331s rad_in = rad_in.astype(int) 331s flux_in = np.bincount(rad_in, flux_in) / np.bincount(rad_in) 331s rad_in = np.arange(len(flux_in)) 331s assert (data.array[x0, y0] == flux_in[0]) 331s 331s # check the binned results 331s plots = Imexamine() 331s plots.set_data(data.array) 331s plots.radial_profile_pars['pixels'][0] = False 331s plots.radial_profile_pars['background'][0] = False 331s plots.radial_profile_pars['clip'][0] = False 331s > rad_out, flux_out = plots.radial_profile(x0, y0, genplot=False) 331s 331s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:206: 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1102: in radial_profile 331s amp, centerx, centery, sigmax, sigmay = self.gauss_center(xx, yy, data, delta=datasize) 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 331s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 331s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 331s results = fit(model, xx, yy, data) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 331s return func(self, model, x, y, z=z, **kwargs) 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 331s init_values, fitparams, cov_x = self._run_fitter( 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 331s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:437: in leastsq 331s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 331s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:29: in _check_func 331s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 331s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 331s 331s params = array([7.06778109e-02, 4.00000000e+00, 4.00000000e+00, 3.00000000e+00, 331s 3.00000000e+00, 0.00000000e+00, 5.77193322e-05]) 331s model = 331s weights = 1.0 331s x = array([[0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., ... [0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., 7.], 331s [0., 1., 2., 3., 4., 5., 6., 7.]]) 331s y = array([[0., 0., 0., 0., 0., 0., 0., 0.], 331s [1., 1., 1., 1., 1., 1., 1., 1.], 331s [2., 2., 2., 2., 2., 2., 2., ... [5., 5., 5., 5., 5., 5., 5., 5.], 331s [6., 6., 6., 6., 6., 6., 6., 6.], 331s [7., 7., 7., 7., 7., 7., 7., 7.]]) 331s z = array([[5.77193322e-05, 2.73457911e-04, 8.30691786e-04, 1.61796667e-03, 331s 2.02059585e-03, 1.61796667e-03, 8.3069...29556643e-03, 3.93558331e-03, 7.66546959e-03, 331s 9.57301302e-03, 7.66546959e-03, 3.93558331e-03, 1.29556643e-03]]) 331s fit_param_indices = None 331s 331s @staticmethod 331s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 331s """ 331s Wraps the method calculating the Jacobian of the function to account 331s for model constraints. 331s `scipy.optimize.leastsq` expects the function derivative to have the 331s above signature (parlist, (argtuple)). In order to accommodate model 331s constraints, instead of using p directly, we set the parameter list in 331s this function. 331s """ 331s if weights is None: 331s weights = 1.0 331s 331s if model.has_fixed or model.has_tied: 331s # update the parameters with the current values from the fitter 331s fitter_to_model_params(model, params) 331s if z is None: 331s full = np.array(model.fit_deriv(x, *model.parameters)) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s else: 331s full = np.array( 331s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 331s ) 331s if not model.col_fit_deriv: 331s full_deriv = np.ravel(weights) * full.T 331s else: 331s full_deriv = np.ravel(weights) * full 331s 331s pars = [getattr(model, name) for name in model.param_names] 331s fixed = [par.fixed for par in pars] 331s tied = [par.tied for par in pars] 331s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 331s fix_and_tie = np.logical_or(fixed, tied) 331s ind = np.logical_not(fix_and_tie) 331s 331s if not model.col_fit_deriv: 331s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 331s else: 331s residues = full_deriv[np.nonzero(ind)] 331s 331s return [np.ravel(_) for _ in residues] 331s else: 331s if z is None: 331s fit_deriv = np.array(model.fit_deriv(x, *params)) 331s try: 331s output = np.array( 331s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 331s ) 331s if output.shape != fit_deriv.shape: 331s output = np.array( 331s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 331s ) 331s return output 331s except ValueError: 331s return np.array( 331s [ 331s np.ravel(_) 331s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 331s ] 331s ).transpose() 331s else: 331s if not model.col_fit_deriv: 331s return [ 331s np.ravel(_) 331s for _ in ( 331s np.ravel(weights) 331s * np.array(model.fit_deriv(x, y, *params)).T 331s ).T 331s ] 331s return [ 331s np.ravel(_) 331s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 331s ] 331s E ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (7,) + inhomogeneous part. 331s 331s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 331s =============================== warnings summary =============================== 331s ../../../usr/lib/python3/dist-packages/imexam/__init__.py:12 331s /usr/lib/python3/dist-packages/imexam/__init__.py:12: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 331s from pkg_resources import get_distribution, DistributionNotFound 331s 331s tests/test_imexamine.py::test_radial_profile 331s tests/test_imexamine.py::test_radial_profile_cumulative 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1097: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 331s xx = int(x) 331s 331s tests/test_imexamine.py::test_radial_profile 331s tests/test_imexamine.py::test_radial_profile_cumulative 331s /usr/lib/python3/dist-packages/imexam/imexamine.py:1098: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 331s yy = int(y) 331s 331s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 331s =========================== short test summary info ============================ 331s FAILED tests/test_imexamine.py::test_line_fit - ValueError: setting an array ... 331s FAILED tests/test_imexamine.py::test_column_fit - ValueError: setting an arra... 331s FAILED tests/test_imexamine.py::test_radial_profile - ValueError: setting an ... 331s FAILED tests/test_imexamine.py::test_radial_profile_cumulative - ValueError: ... 331s ======== 4 failed, 14 passed, 2 skipped, 1 xfailed, 5 warnings in 3.15s ======== 332s autopkgtest [09:40:21]: test command1: -----------------------] 332s autopkgtest [09:40:21]: test command1: - - - - - - - - - - results - - - - - - - - - - 332s command1 FAIL non-zero exit status 1 333s autopkgtest [09:40:22]: @@@@@@@@@@@@@@@@@@@@ summary 333s command1 FAIL non-zero exit status 1 354s nova [W] Using flock in prodstack6-arm64 354s flock: timeout while waiting to get lock 354s Creating nova instance adt-plucky-arm64-imexam-20241203-093449-juju-7f2275-prod-proposed-migration-environment-20-b6cf7b3a-39bd-40a6-97d8-123126378cf4 from image adt/ubuntu-plucky-arm64-server-20241203.img (UUID b9293590-1195-42ea-ba16-5ab4b1e94eab)...