0s autopkgtest [13:18:20]: starting date and time: 2025-01-11 13:18:20+0000 0s autopkgtest [13:18:20]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:18:20]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ftzl3acz/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-7.secgroup --name adt-plucky-amd64-imexam-20250111-131820-juju-7f2275-prod-proposed-migration-environment-2-49e07ec6-7c41-401b-89ef-b652bd73e43b --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 55s autopkgtest [13:19:15]: testbed dpkg architecture: amd64 55s autopkgtest [13:19:15]: testbed apt version: 2.9.18 55s autopkgtest [13:19:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 56s autopkgtest [13:19:16]: testbed release detected to be: None 56s autopkgtest [13:19:16]: updating testbed package index (apt update) 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 57s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 58s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 58s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [131 kB] 58s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [778 kB] 58s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.7 kB] 58s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [164 kB] 58s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [296 kB] 58s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 58s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 58s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [979 kB] 58s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [380 kB] 58s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [13.0 kB] 58s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3516 B] 58s Fetched 2884 kB in 1s (2059 kB/s) 59s Reading package lists... 59s + lsb_release --codename --short 59s + RELEASE=plucky 59s + cat 59s + [ plucky != trusty ] 59s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 60s Reading package lists... 60s Building dependency tree...+ /usr/lib/apt/apt-helper analyze-pattern ?true 60s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ?obsolete 60s 60s Reading state information... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s + grep -q trusty /etc/lsb-release 60s + [ ! -d /usr/share/doc/unattended-upgrades ] 60s + [ ! -d /usr/share/doc/lxd ] 60s + [ ! -d /usr/share/doc/lxd-client ] 60s + [ ! -d /usr/share/doc/snapd ] 60s + type iptables 60s + cat 60s + chmod 755 /etc/rc.local 60s + . /etc/rc.local 60s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 60s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 60s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 60s + uname -m 60s + [ x86_64 = ppc64le ] 60s + [ -d /run/systemd/system ] 60s + systemd-detect-virt --quiet --vm 60s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 60s + cat 60s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 60s + echo COMPRESS=lz4 60s autopkgtest [13:19:20]: upgrading testbed (apt dist-upgrade and autopurge) 60s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 61s Starting 2 pkgProblemResolver with broken count: 0 61s Done 62s Entering ResolveByKeep 62s 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 63s Starting pkgProblemResolver with broken count: 0 63s Starting 2 pkgProblemResolver with broken count: 0 63s Done 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s autopkgtest [13:19:25]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 66s autopkgtest [13:19:26]: @@@@@@@@@@@@@@@@@@@@ apt-source imexam 69s Get:1 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (dsc) [2361 B] 69s Get:2 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (tar) [21.4 MB] 69s Get:3 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (diff) [7756 B] 69s gpgv: Signature made Tue Nov 28 09:16:30 2023 UTC 69s gpgv: using RSA key BAFC6C85F7CB143FEEB6FB157115AFD07710DCF7 69s gpgv: Can't check signature: No public key 69s dpkg-source: warning: cannot verify inline signature for ./imexam_0.9.1-6.dsc: no acceptable signature found 69s autopkgtest [13:19:29]: testing package imexam version 0.9.1-6 69s autopkgtest [13:19:29]: build not needed 71s autopkgtest [13:19:31]: test command1: preparing testbed 71s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Starting pkgProblemResolver with broken count: 0 72s Starting 2 pkgProblemResolver with broken count: 0 72s Done 72s The following NEW packages will be installed: 72s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx ipython3 72s libblas3 libdeflate0 liberfa1 libfontconfig1 libgfortran5 libgomp1 72s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 72s libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen 72s libjs-jquery-metadata libjs-jquery-tablesorter 72s libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc 72s libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 72s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 72s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwcs8 libwebp7 libwebpdemux2 72s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 72s python3-astropy python3-astropy-iers-data python3-asttokens python3-brotli 72s python3-contourpy python3-coverage python3-cycler python3-dateutil 72s python3-decorator python3-erfa python3-executing python3-fonttools 72s python3-fs python3-hypothesis python3-imexam python3-iniconfig 72s python3-ipython python3-jedi python3-kiwisolver python3-lxml python3-lz4 72s python3-matplotlib python3-matplotlib-inline python3-mpmath python3-numpy 72s python3-packaging python3-parso python3-pexpect python3-pil 72s python3-pil.imagetk python3-platformdirs python3-pluggy python3-ply 72s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 72s python3-pytest-arraydiff python3-pytest-astropy 72s python3-pytest-astropy-header python3-pytest-cov python3-pytest-doctestplus 72s python3-pytest-filter-subpackage python3-pytest-mock 72s python3-pytest-remotedata python3-scipy python3-sortedcontainers 72s python3-stack-data python3-sympy python3-tk python3-traitlets 72s python3-typeshed python3-tz python3-ufolib2 python3-unicodedata2 72s python3-wcwidth python3.12-tk python3.13 python3.13-minimal python3.13-tk 72s tk8.6-blt2.5 unicode-data x11-common 72s 0 upgraded, 112 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 83.5 MB of archives. 72s After this operation, 419 MB of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.1-2 [881 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.1-2 [2358 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 73s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 73s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 73s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 73s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 73s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 73s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 73s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 73s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 73s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 73s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 73s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 73s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 73s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 73s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.4-1 [67.6 kB] 73s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 73s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 73s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 73s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 73s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 73s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 73s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 3.0.0-1 [20.4 kB] 73s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.1.0-0.1 [24.4 kB] 73s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 73s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 73s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 73s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-3 [48.1 kB] 73s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.30.0-2 [569 kB] 73s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 ipython3 all 8.30.0-2 [4936 B] 73s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 73s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 73s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-12ubuntu1 [909 kB] 73s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-12ubuntu1 [148 kB] 73s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 73s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.1.0-1 [541 kB] 73s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 73s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 73s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 73s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-metadata all 12-4 [6582 B] 73s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 73s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 73s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 73s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 73s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 8.1.3-3 [30.9 kB] 73s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 74s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 74s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 74s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 74s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [2088 kB] 74s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 74s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 74s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 74s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 74s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 74s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 74s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 libwcs8 amd64 8.4+ds-1 [310 kB] 74s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 74s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 74s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 74s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 74s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 74s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 74s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 74s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 74s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 74s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 74s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hypothesis all 6.122.1-1 [330 kB] 74s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [5319 kB] 74s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-arraydiff all 0.6.1-3 [10.2 kB] 74s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-astropy-header all 0.2.2-2 [8620 B] 74s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.1-2 [729 kB] 74s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coverage amd64 7.4.4+dfsg1-0ubuntu3 [150 kB] 74s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 74s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-cov all 5.0.0-1 [21.3 kB] 74s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-doctestplus all 1.3.0-1 [23.7 kB] 74s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-filter-subpackage all 0.2.0-1 [6094 B] 74s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 74s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-remotedata all 0.4.1-1 [8650 B] 74s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-astropy all 0.11.0-1 [5902 B] 74s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ply all 3.11-7 [45.4 kB] 74s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-astropy-iers-data all 0.2025.1.6.0.33.42-1 [1212 kB] 74s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 liberfa1 amd64 2.0.1-1build1 [139 kB] 74s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-erfa amd64 2.0.1.5+ds-1 [321 kB] 74s Get:88 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-astropy amd64 7.0.0-1 [4108 kB] 75s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 75s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1 [271 kB] 75s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 75s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.2-1 [31.5 kB] 75s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 75s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-5.1 [90.8 kB] 75s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1build1 [1834 kB] 75s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1 [27.4 kB] 75s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-3ubuntu1 [22.3 MB] 76s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 76s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 76s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 76s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 76s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 77s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.0-3 [1759 kB] 77s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu2 [217 kB] 77s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu2 [580 kB] 77s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.8-3 [116 kB] 77s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.1-2 [107 kB] 77s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 77s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu2 [9568 B] 77s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 77s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu1 [4691 kB] 77s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-imexam amd64 0.9.1-6 [50.5 kB] 77s Fetched 83.5 MB in 5s (17.1 MB/s) 77s Selecting previously unselected package libpython3.13-minimal:amd64. 78s (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 ... 75820 files and directories currently installed.) 78s Preparing to unpack .../000-libpython3.13-minimal_3.13.1-2_amd64.deb ... 78s Unpacking libpython3.13-minimal:amd64 (3.13.1-2) ... 78s Selecting previously unselected package python3.13-minimal. 78s Preparing to unpack .../001-python3.13-minimal_3.13.1-2_amd64.deb ... 78s Unpacking python3.13-minimal (3.13.1-2) ... 78s Selecting previously unselected package libjs-jquery. 78s Preparing to unpack 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78s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 78s Selecting previously unselected package libtk8.6:amd64. 78s Preparing to unpack .../013-libtk8.6_8.6.15-1_amd64.deb ... 78s Unpacking libtk8.6:amd64 (8.6.15-1) ... 78s Selecting previously unselected package tk8.6-blt2.5. 78s Preparing to unpack .../014-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 78s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 78s Selecting previously unselected package blt. 78s Preparing to unpack .../015-blt_2.5.3+dfsg-7build1_amd64.deb ... 78s Unpacking blt (2.5.3+dfsg-7build1) ... 78s Selecting previously unselected package fonts-lyx. 78s Preparing to unpack .../016-fonts-lyx_2.4.2.1-1_all.deb ... 78s Unpacking fonts-lyx (2.4.2.1-1) ... 79s Selecting previously unselected package python3-decorator. 79s Preparing to unpack .../017-python3-decorator_5.1.1-5_all.deb ... 79s Unpacking python3-decorator (5.1.1-5) ... 79s Selecting previously unselected package python3-parso. 79s Preparing to unpack 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81s Selecting previously unselected package libwebpmux3:amd64. 81s Preparing to unpack .../061-libwebpmux3_1.4.0-0.1_amd64.deb ... 81s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 81s Selecting previously unselected package libxslt1.1:amd64. 81s Preparing to unpack .../062-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 81s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 81s Selecting previously unselected package python-matplotlib-data. 81s Preparing to unpack .../063-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 81s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 81s Selecting previously unselected package python3-iniconfig. 81s Preparing to unpack .../064-python3-iniconfig_1.1.1-2_all.deb ... 81s Unpacking python3-iniconfig (1.1.1-2) ... 81s Selecting previously unselected package python3-packaging. 81s Preparing to unpack .../065-python3-packaging_24.2-1_all.deb ... 81s Unpacking python3-packaging (24.2-1) ... 81s Selecting previously unselected package python3-pluggy. 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python3-numpy (1:1.26.4+ds-12) ... 81s Selecting previously unselected package python3-pytest-arraydiff. 81s Preparing to unpack .../072-python3-pytest-arraydiff_0.6.1-3_all.deb ... 81s Unpacking python3-pytest-arraydiff (0.6.1-3) ... 81s Selecting previously unselected package python3-pytest-astropy-header. 81s Preparing to unpack .../073-python3-pytest-astropy-header_0.2.2-2_all.deb ... 81s Unpacking python3-pytest-astropy-header (0.2.2-2) ... 81s Selecting previously unselected package python3.13. 81s Preparing to unpack .../074-python3.13_3.13.1-2_amd64.deb ... 81s Unpacking python3.13 (3.13.1-2) ... 81s Selecting previously unselected package python3-coverage. 81s Preparing to unpack .../075-python3-coverage_7.4.4+dfsg1-0ubuntu3_amd64.deb ... 81s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 81s Selecting previously unselected package libjs-jquery-isonscreen. 81s Preparing to unpack .../076-libjs-jquery-isonscreen_1.2.0-1.1_all.deb ... 81s Unpacking libjs-jquery-isonscreen (1.2.0-1.1) ... 81s Selecting previously unselected package python3-pytest-cov. 81s Preparing to unpack .../077-python3-pytest-cov_5.0.0-1_all.deb ... 81s Unpacking python3-pytest-cov (5.0.0-1) ... 81s Selecting previously unselected package python3-pytest-doctestplus. 81s Preparing to unpack .../078-python3-pytest-doctestplus_1.3.0-1_all.deb ... 81s Unpacking python3-pytest-doctestplus (1.3.0-1) ... 81s Selecting previously unselected package python3-pytest-filter-subpackage. 81s Preparing to unpack .../079-python3-pytest-filter-subpackage_0.2.0-1_all.deb ... 81s Unpacking python3-pytest-filter-subpackage (0.2.0-1) ... 81s Selecting previously unselected package python3-pytest-mock. 81s Preparing to unpack .../080-python3-pytest-mock_3.14.0-2_all.deb ... 81s Unpacking python3-pytest-mock (3.14.0-2) ... 81s Selecting previously unselected package python3-pytest-remotedata. 81s Preparing to unpack .../081-python3-pytest-remotedata_0.4.1-1_all.deb ... 81s Unpacking python3-pytest-remotedata (0.4.1-1) ... 81s Selecting previously unselected package python3-pytest-astropy. 81s Preparing to unpack .../082-python3-pytest-astropy_0.11.0-1_all.deb ... 81s Unpacking python3-pytest-astropy (0.11.0-1) ... 82s Selecting previously unselected package python3-ply. 82s Preparing to unpack .../083-python3-ply_3.11-7_all.deb ... 82s Unpacking python3-ply (3.11-7) ... 82s Selecting previously unselected package python3-astropy-iers-data. 82s Preparing to unpack .../084-python3-astropy-iers-data_0.2025.1.6.0.33.42-1_all.deb ... 82s Unpacking python3-astropy-iers-data (0.2025.1.6.0.33.42-1) ... 82s Selecting previously unselected package liberfa1:amd64. 82s Preparing to unpack .../085-liberfa1_2.0.1-1build1_amd64.deb ... 82s Unpacking liberfa1:amd64 (2.0.1-1build1) ... 82s Selecting previously unselected package python3-erfa. 82s Preparing to unpack .../086-python3-erfa_2.0.1.5+ds-1_amd64.deb ... 82s Unpacking python3-erfa (2.0.1.5+ds-1) ... 82s Selecting previously unselected package python3-astropy. 82s Preparing to unpack .../087-python3-astropy_7.0.0-1_amd64.deb ... 82s Unpacking python3-astropy (7.0.0-1) ... 82s Selecting previously unselected package python3-brotli. 82s Preparing to unpack .../088-python3-brotli_1.1.0-2build3_amd64.deb ... 82s Unpacking python3-brotli (1.1.0-2build3) ... 82s Selecting previously unselected package python3-contourpy. 82s Preparing to unpack .../089-python3-contourpy_1.3.1-1_amd64.deb ... 82s Unpacking python3-contourpy (1.3.1-1) ... 82s Selecting previously unselected package python3-cycler. 82s Preparing to unpack .../090-python3-cycler_0.12.1-1_all.deb ... 82s Unpacking python3-cycler (0.12.1-1) ... 82s Selecting previously unselected package python3-tz. 82s Preparing to unpack .../091-python3-tz_2024.2-1_all.deb ... 82s Unpacking python3-tz (2024.2-1) ... 82s Selecting previously unselected package python3-platformdirs. 82s Preparing to unpack .../092-python3-platformdirs_4.3.6-1_all.deb ... 82s 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[----------------------- 126s ============================= test session starts ============================== 126s platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 126s rootdir: /tmp/autopkgtest.0xVIOO/autopkgtest_tmp 126s plugins: remotedata-0.4.1, cov-5.0.0, hypothesis-6.122.1, mock-3.14.0, astropy-header-0.2.2, arraydiff-0.6.1, typeguard-4.4.1, filter-subpackage-0.2.0, doctestplus-1.3.0, astropy-0.11.0 126s collected 21 items 126s 126s tests/test_imexamine.py ..sFFxFFs [ 42%] 126s tests/test_util.py ............ [100%] 126s 126s =================================== FAILURES =================================== 126s ________________________________ test_line_fit _________________________________ 126s 126s def test_line_fit(): 126s """Fit a Gaussian1D line to the data.""" 126s plots = Imexamine() 126s in_amp = 3. 126s in_mean = 50. 126s in_stddev = 2. 126s in_const = 20. 126s 126s # Set all the lines to be Gaussians 126s line_gauss = in_const + in_amp * np.exp(-0.5 * ((xx - in_mean) / in_stddev)**2) 126s plots.set_data(line_gauss) 126s > fit = plots.line_fit(50, 50, form='Gaussian1D', genplot=False) 126s 126s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:86: 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:765: in line_fit 126s amp, xout, yout, sigma, sigmay = self.gauss_center(xx, 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 126s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 126s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 126s results = fit(model, xx, yy, data) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 126s return func(self, model, x, y, z=z, **kwargs) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 126s init_values, fitparams, cov_x = self._run_fitter( 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 126s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 126s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 126s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s 126s params = array([ 3., 15., 15., 3., 3., 0., 20.]) 126s model = 126s weights = 1.0 126s x = array([[ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 126s 13., 14., 15., 16., 17., 18., 19., 20..., 10., 11., 12., 126s 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 126s 26., 27., 28., 29.]]) 126s y = array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 126s 0., 0., 0., 0., 0., 0., 0., 0..., 29., 29., 29., 126s 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 126s 29., 29., 29., 29.]]) 126s z = array([[20. , 20. , 20. , 20.00000005, 20.00000081, 126s 20.00001118, 20.0001202 , 20.00100639...2699, 20.00656247, 20.00100639, 20.0001202 , 126s 20.00001118, 20.00000081, 20.00000005, 20. , 20. ]]) 126s fit_param_indices = None 126s 126s @staticmethod 126s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 126s """ 126s Wraps the method calculating the Jacobian of the function to account 126s for model constraints. 126s `scipy.optimize.leastsq` expects the function derivative to have the 126s above signature (parlist, (argtuple)). In order to accommodate model 126s constraints, instead of using p directly, we set the parameter list in 126s this function. 126s """ 126s if weights is None: 126s weights = 1.0 126s 126s if model.has_fixed or model.has_tied: 126s # update the parameters with the current values from the fitter 126s fitter_to_model_params(model, params) 126s if z is None: 126s full = np.array(model.fit_deriv(x, *model.parameters)) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s else: 126s full = np.array( 126s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 126s ) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s 126s pars = [getattr(model, name) for name in model.param_names] 126s fixed = [par.fixed for par in pars] 126s tied = [par.tied for par in pars] 126s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 126s fix_and_tie = np.logical_or(fixed, tied) 126s ind = np.logical_not(fix_and_tie) 126s 126s if not model.col_fit_deriv: 126s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 126s else: 126s residues = full_deriv[np.nonzero(ind)] 126s 126s return [np.ravel(_) for _ in residues] 126s else: 126s if z is None: 126s fit_deriv = np.array(model.fit_deriv(x, *params)) 126s try: 126s output = np.array( 126s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 126s ) 126s if output.shape != fit_deriv.shape: 126s output = np.array( 126s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 126s ) 126s return output 126s except ValueError: 126s return np.array( 126s [ 126s np.ravel(_) 126s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 126s ] 126s ).transpose() 126s else: 126s if not model.col_fit_deriv: 126s return [ 126s np.ravel(_) 126s for _ in ( 126s np.ravel(weights) 126s * np.array(model.fit_deriv(x, y, *params)).T 126s ).T 126s ] 126s return [ 126s np.ravel(_) 126s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 126s ] 126s 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. 126s 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 126s ----------------------------- Captured stdout call ----------------------------- 126s using model: 126s Name: Gaussian1D 126s N_inputs: 1 126s N_outputs: 1 126s Fittable parameters: ('amplitude', 'mean', 'stddev') 126s ------------------------------ Captured log call ------------------------------- 126s INFO imexam.util:imexamine.py:749 using model: 126s Name: Gaussian1D 126s N_inputs: 1 126s N_outputs: 1 126s Fittable parameters: ('amplitude', 'mean', 'stddev') 126s _______________________________ test_column_fit ________________________________ 126s 126s def test_column_fit(): 126s """Fit a Gaussian1D column to the data.""" 126s plots = Imexamine() 126s in_amp = 3. 126s in_mean = 50. 126s in_stddev = 2. 126s in_const = 20. 126s # Set all the columns to be Gaussians 126s col_gauss = in_const + in_amp * np.exp(-0.5 * ((yy - in_mean) / in_stddev)**2) 126s plots.set_data(col_gauss) 126s > fit = plots.column_fit(50, 50, form='Gaussian1D', genplot=False) 126s 126s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:104: 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:917: in column_fit 126s result = self.line_fit(x, y, data=data, form=form, 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:765: in line_fit 126s amp, xout, yout, sigma, sigmay = self.gauss_center(xx, 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 126s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 126s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 126s results = fit(model, xx, yy, data) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 126s return func(self, model, x, y, z=z, **kwargs) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 126s init_values, fitparams, cov_x = self._run_fitter( 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 126s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 126s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 126s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s 126s params = array([ 3., 15., 15., 3., 3., 0., 20.]) 126s model = 126s weights = 1.0 126s x = array([[ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 126s 13., 14., 15., 16., 17., 18., 19., 20..., 10., 11., 12., 126s 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 126s 26., 27., 28., 29.]]) 126s y = array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 126s 0., 0., 0., 0., 0., 0., 0., 0..., 29., 29., 29., 126s 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 126s 29., 29., 29., 29.]]) 126s z = array([[20. , 20. , 20. , 20. , 20. , 126s 20. , 20. , 20. ... , 20. , 20. , 20. , 126s 20. , 20. , 20. , 20. , 20. ]]) 126s fit_param_indices = None 126s 126s @staticmethod 126s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 126s """ 126s Wraps the method calculating the Jacobian of the function to account 126s for model constraints. 126s `scipy.optimize.leastsq` expects the function derivative to have the 126s above signature (parlist, (argtuple)). In order to accommodate model 126s constraints, instead of using p directly, we set the parameter list in 126s this function. 126s """ 126s if weights is None: 126s weights = 1.0 126s 126s if model.has_fixed or model.has_tied: 126s # update the parameters with the current values from the fitter 126s fitter_to_model_params(model, params) 126s if z is None: 126s full = np.array(model.fit_deriv(x, *model.parameters)) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s else: 126s full = np.array( 126s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 126s ) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s 126s pars = [getattr(model, name) for name in model.param_names] 126s fixed = [par.fixed for par in pars] 126s tied = [par.tied for par in pars] 126s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 126s fix_and_tie = np.logical_or(fixed, tied) 126s ind = np.logical_not(fix_and_tie) 126s 126s if not model.col_fit_deriv: 126s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 126s else: 126s residues = full_deriv[np.nonzero(ind)] 126s 126s return [np.ravel(_) for _ in residues] 126s else: 126s if z is None: 126s fit_deriv = np.array(model.fit_deriv(x, *params)) 126s try: 126s output = np.array( 126s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 126s ) 126s if output.shape != fit_deriv.shape: 126s output = np.array( 126s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 126s ) 126s return output 126s except ValueError: 126s return np.array( 126s [ 126s np.ravel(_) 126s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 126s ] 126s ).transpose() 126s else: 126s if not model.col_fit_deriv: 126s return [ 126s np.ravel(_) 126s for _ in ( 126s np.ravel(weights) 126s * np.array(model.fit_deriv(x, y, *params)).T 126s ).T 126s ] 126s return [ 126s np.ravel(_) 126s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 126s ] 126s 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. 126s 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 126s ----------------------------- Captured stdout call ----------------------------- 126s using model: 126s Name: Gaussian1D 126s N_inputs: 1 126s N_outputs: 1 126s Fittable parameters: ('amplitude', 'mean', 'stddev') 126s ------------------------------ Captured log call ------------------------------- 126s INFO imexam.util:imexamine.py:749 using model: 126s Name: Gaussian1D 126s N_inputs: 1 126s N_outputs: 1 126s Fittable parameters: ('amplitude', 'mean', 'stddev') 126s _____________________________ test_radial_profile ______________________________ 126s 126s def test_radial_profile(): 126s """Test the radial profile function 126s No background subtraction 126s individual pixel results used 126s """ 126s from astropy.convolution import Gaussian2DKernel 126s data = Gaussian2DKernel(1.5, x_size=25, y_size=25) 126s xx, yy = np.meshgrid(np.arange(25), np.arange(25)) 126s x0, y0 = np.where(data.array == data.array.max()) 126s 126s rad_in = np.sqrt((xx - x0)**2 + (yy - y0)**2) 126s rad_in = rad_in.ravel() 126s flux_in = data.array.ravel() 126s 126s order = np.argsort(rad_in) 126s rad_in = rad_in[order] 126s flux_in = flux_in[order] 126s 126s plots = Imexamine() 126s plots.set_data(data.array) 126s 126s plots.radial_profile_pars['pixels'][0] = True 126s plots.radial_profile_pars['background'][0] = False 126s plots.radial_profile_pars['clip'][0] = False 126s > rad_out, flux_out = plots.radial_profile(x0, y0, genplot=False) 126s 126s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:160: 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:1102: in radial_profile 126s amp, centerx, centery, sigmax, sigmay = self.gauss_center(xx, yy, data, delta=datasize) 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 126s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 126s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 126s results = fit(model, xx, yy, data) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 126s return func(self, model, x, y, z=z, **kwargs) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 126s init_values, fitparams, cov_x = self._run_fitter( 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 126s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 126s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 126s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s 126s params = array([7.06778109e-02, 4.00000000e+00, 4.00000000e+00, 3.00000000e+00, 126s 3.00000000e+00, 0.00000000e+00, 5.77193322e-05]) 126s model = 126s weights = 1.0 126s x = array([[0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., ... [0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., 7.]]) 126s y = array([[0., 0., 0., 0., 0., 0., 0., 0.], 126s [1., 1., 1., 1., 1., 1., 1., 1.], 126s [2., 2., 2., 2., 2., 2., 2., ... [5., 5., 5., 5., 5., 5., 5., 5.], 126s [6., 6., 6., 6., 6., 6., 6., 6.], 126s [7., 7., 7., 7., 7., 7., 7., 7.]]) 126s z = array([[5.77193322e-05, 2.73457911e-04, 8.30691786e-04, 1.61796667e-03, 126s 2.02059585e-03, 1.61796667e-03, 8.3069...29556643e-03, 3.93558331e-03, 7.66546959e-03, 126s 9.57301302e-03, 7.66546959e-03, 3.93558331e-03, 1.29556643e-03]]) 126s fit_param_indices = None 126s 126s @staticmethod 126s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 126s """ 126s Wraps the method calculating the Jacobian of the function to account 126s for model constraints. 126s `scipy.optimize.leastsq` expects the function derivative to have the 126s above signature (parlist, (argtuple)). In order to accommodate model 126s constraints, instead of using p directly, we set the parameter list in 126s this function. 126s """ 126s if weights is None: 126s weights = 1.0 126s 126s if model.has_fixed or model.has_tied: 126s # update the parameters with the current values from the fitter 126s fitter_to_model_params(model, params) 126s if z is None: 126s full = np.array(model.fit_deriv(x, *model.parameters)) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s else: 126s full = np.array( 126s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 126s ) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s 126s pars = [getattr(model, name) for name in model.param_names] 126s fixed = [par.fixed for par in pars] 126s tied = [par.tied for par in pars] 126s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 126s fix_and_tie = np.logical_or(fixed, tied) 126s ind = np.logical_not(fix_and_tie) 126s 126s if not model.col_fit_deriv: 126s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 126s else: 126s residues = full_deriv[np.nonzero(ind)] 126s 126s return [np.ravel(_) for _ in residues] 126s else: 126s if z is None: 126s fit_deriv = np.array(model.fit_deriv(x, *params)) 126s try: 126s output = np.array( 126s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 126s ) 126s if output.shape != fit_deriv.shape: 126s output = np.array( 126s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 126s ) 126s return output 126s except ValueError: 126s return np.array( 126s [ 126s np.ravel(_) 126s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 126s ] 126s ).transpose() 126s else: 126s if not model.col_fit_deriv: 126s return [ 126s np.ravel(_) 126s for _ in ( 126s np.ravel(weights) 126s * np.array(model.fit_deriv(x, y, *params)).T 126s ).T 126s ] 126s return [ 126s np.ravel(_) 126s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 126s ] 126s 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. 126s 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 126s ________________________ test_radial_profile_cumulative ________________________ 126s 126s def test_radial_profile_cumulative(): 126s """Test the radial profile function 126s without background subtraction 126s with each pixel integer binned 126s """ 126s from astropy.convolution import Gaussian2DKernel 126s ksize = 25 126s data = Gaussian2DKernel(1.5, x_size=ksize, y_size=ksize) 126s xx, yy = np.meshgrid(np.arange(ksize), np.arange(ksize)) 126s x0, y0 = np.where(data.array == data.array.max()) 126s rad_in = np.sqrt((xx - x0)**2 + (yy - y0)**2) 126s 126s rad_in = rad_in.ravel() 126s flux_in = data.array.ravel() 126s 126s indices = np.argsort(rad_in) 126s rad_in = rad_in[indices] 126s flux_in = flux_in[indices] 126s 126s # now bin the radflux like we expect 126s rad_in = rad_in.astype(int) 126s flux_in = np.bincount(rad_in, flux_in) / np.bincount(rad_in) 126s rad_in = np.arange(len(flux_in)) 126s assert (data.array[x0, y0] == flux_in[0]) 126s 126s # check the binned results 126s plots = Imexamine() 126s plots.set_data(data.array) 126s plots.radial_profile_pars['pixels'][0] = False 126s plots.radial_profile_pars['background'][0] = False 126s plots.radial_profile_pars['clip'][0] = False 126s > rad_out, flux_out = plots.radial_profile(x0, y0, genplot=False) 126s 126s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:206: 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:1102: in radial_profile 126s amp, centerx, centery, sigmax, sigmay = self.gauss_center(xx, yy, data, delta=datasize) 126s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 126s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 126s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 126s results = fit(model, xx, yy, data) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 126s return func(self, model, x, y, z=z, **kwargs) 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 126s init_values, fitparams, cov_x = self._run_fitter( 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 126s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 126s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 126s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 126s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 126s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 126s 126s params = array([7.06778109e-02, 4.00000000e+00, 4.00000000e+00, 3.00000000e+00, 126s 3.00000000e+00, 0.00000000e+00, 5.77193322e-05]) 126s model = 126s weights = 1.0 126s x = array([[0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., ... [0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., 7.], 126s [0., 1., 2., 3., 4., 5., 6., 7.]]) 126s y = array([[0., 0., 0., 0., 0., 0., 0., 0.], 126s [1., 1., 1., 1., 1., 1., 1., 1.], 126s [2., 2., 2., 2., 2., 2., 2., ... [5., 5., 5., 5., 5., 5., 5., 5.], 126s [6., 6., 6., 6., 6., 6., 6., 6.], 126s [7., 7., 7., 7., 7., 7., 7., 7.]]) 126s z = array([[5.77193322e-05, 2.73457911e-04, 8.30691786e-04, 1.61796667e-03, 126s 2.02059585e-03, 1.61796667e-03, 8.3069...29556643e-03, 3.93558331e-03, 7.66546959e-03, 126s 9.57301302e-03, 7.66546959e-03, 3.93558331e-03, 1.29556643e-03]]) 126s fit_param_indices = None 126s 126s @staticmethod 126s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 126s """ 126s Wraps the method calculating the Jacobian of the function to account 126s for model constraints. 126s `scipy.optimize.leastsq` expects the function derivative to have the 126s above signature (parlist, (argtuple)). In order to accommodate model 126s constraints, instead of using p directly, we set the parameter list in 126s this function. 126s """ 126s if weights is None: 126s weights = 1.0 126s 126s if model.has_fixed or model.has_tied: 126s # update the parameters with the current values from the fitter 126s fitter_to_model_params(model, params) 126s if z is None: 126s full = np.array(model.fit_deriv(x, *model.parameters)) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s else: 126s full = np.array( 126s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 126s ) 126s if not model.col_fit_deriv: 126s full_deriv = np.ravel(weights) * full.T 126s else: 126s full_deriv = np.ravel(weights) * full 126s 126s pars = [getattr(model, name) for name in model.param_names] 126s fixed = [par.fixed for par in pars] 126s tied = [par.tied for par in pars] 126s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 126s fix_and_tie = np.logical_or(fixed, tied) 126s ind = np.logical_not(fix_and_tie) 126s 126s if not model.col_fit_deriv: 126s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 126s else: 126s residues = full_deriv[np.nonzero(ind)] 126s 126s return [np.ravel(_) for _ in residues] 126s else: 126s if z is None: 126s fit_deriv = np.array(model.fit_deriv(x, *params)) 126s try: 126s output = np.array( 126s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 126s ) 126s if output.shape != fit_deriv.shape: 126s output = np.array( 126s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 126s ) 126s return output 126s except ValueError: 126s return np.array( 126s [ 126s np.ravel(_) 126s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 126s ] 126s ).transpose() 126s else: 126s if not model.col_fit_deriv: 126s return [ 126s np.ravel(_) 126s for _ in ( 126s np.ravel(weights) 126s * np.array(model.fit_deriv(x, y, *params)).T 126s ).T 126s ] 126s return [ 126s np.ravel(_) 126s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 126s ] 126s 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. 126s 126s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 126s =============================== warnings summary =============================== 126s ../../../usr/lib/python3/dist-packages/imexam/__init__.py:12 126s /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 126s from pkg_resources import get_distribution, DistributionNotFound 126s 126s tests/test_imexamine.py::test_radial_profile 126s tests/test_imexamine.py::test_radial_profile_cumulative 126s /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.) 126s xx = int(x) 126s 126s tests/test_imexamine.py::test_radial_profile 126s tests/test_imexamine.py::test_radial_profile_cumulative 126s /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.) 126s yy = int(y) 126s 126s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 126s =========================== short test summary info ============================ 126s FAILED tests/test_imexamine.py::test_line_fit - ValueError: setting an array ... 126s FAILED tests/test_imexamine.py::test_column_fit - ValueError: setting an arra... 126s FAILED tests/test_imexamine.py::test_radial_profile - ValueError: setting an ... 126s FAILED tests/test_imexamine.py::test_radial_profile_cumulative - ValueError: ... 126s ======== 4 failed, 14 passed, 2 skipped, 1 xfailed, 5 warnings in 2.16s ======== 127s autopkgtest [13:20:27]: test command1: -----------------------] 127s autopkgtest [13:20:27]: test command1: - - - - - - - - - - results - - - - - - - - - - 127s command1 FAIL non-zero exit status 1 128s autopkgtest [13:20:28]: @@@@@@@@@@@@@@@@@@@@ summary 128s command1 FAIL non-zero exit status 1 145s nova [W] Skipping flock for amd64 145s Creating nova instance adt-plucky-amd64-imexam-20250111-131820-juju-7f2275-prod-proposed-migration-environment-2-49e07ec6-7c41-401b-89ef-b652bd73e43b from image adt/ubuntu-plucky-amd64-server-20250111.img (UUID 583b1e24-63f4-4305-9a48-aa6a34658dc0)... 145s nova [W] Timed out waiting for 0a0f0784-6814-4e51-8835-9638858fbcc8 to get deleted.