0s autopkgtest [13:51:46]: starting date and time: 2025-01-09 13:51:46+0000 0s autopkgtest [13:51:46]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:51:46]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v3z1zm4c/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-arm64-12.secgroup --name adt-plucky-arm64-imexam-20250109-135146-juju-7f2275-prod-proposed-migration-environment-20-d125861e-681e-44ba-84ca-4be6cdc2d84a --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 153s autopkgtest [13:54:19]: testbed dpkg architecture: arm64 153s autopkgtest [13:54:19]: testbed apt version: 2.9.18 153s autopkgtest [13:54:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 154s autopkgtest [13:54:20]: testbed release detected to be: None 154s autopkgtest [13:54:20]: updating testbed package index (apt update) 155s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 155s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 155s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 155s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 155s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 155s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [126 kB] 155s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [769 kB] 156s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.6 kB] 156s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [242 kB] 156s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 156s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [976 kB] 156s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [22.4 kB] 156s Fetched 2295 kB in 1s (2218 kB/s) 157s Reading package lists... 157s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s Calculating upgrade... 159s The following packages will be upgraded: 159s libgpgme11t64 python3-oauthlib 159s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 232 kB of archives. 159s After this operation, 0 B of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgme11t64 arm64 1.24.1-2ubuntu1 [142 kB] 159s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-oauthlib all 3.2.2-3 [89.9 kB] 159s Fetched 232 kB in 0s (526 kB/s) 160s (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 ... 80185 files and directories currently installed.) 160s Preparing to unpack .../libgpgme11t64_1.24.1-2ubuntu1_arm64.deb ... 160s Unpacking libgpgme11t64:arm64 (1.24.1-2ubuntu1) over (1.24.0-2ubuntu1) ... 160s Preparing to unpack .../python3-oauthlib_3.2.2-3_all.deb ... 160s Unpacking python3-oauthlib (3.2.2-3) over (3.2.2-2) ... 160s Setting up python3-oauthlib (3.2.2-3) ... 160s Setting up libgpgme11t64:arm64 (1.24.1-2ubuntu1) ... 160s Processing triggers for libc-bin (2.40-4ubuntu1) ... 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s autopkgtest [13:54:27]: upgrading testbed (apt dist-upgrade and autopurge) 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 163s Entering ResolveByKeep 163s 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s autopkgtest [13:54:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 168s autopkgtest [13:54:34]: @@@@@@@@@@@@@@@@@@@@ apt-source imexam 174s Get:1 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (dsc) [2361 B] 174s Get:2 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (tar) [21.4 MB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky/universe imexam 0.9.1-6 (diff) [7756 B] 174s gpgv: Signature made Tue Nov 28 09:16:30 2023 UTC 174s gpgv: using RSA key BAFC6C85F7CB143FEEB6FB157115AFD07710DCF7 174s gpgv: Can't check signature: No public key 174s dpkg-source: warning: cannot verify inline signature for ./imexam_0.9.1-6.dsc: no acceptable signature found 174s autopkgtest [13:54:40]: testing package imexam version 0.9.1-6 175s autopkgtest [13:54:41]: build not needed 177s autopkgtest [13:54:43]: test command1: preparing testbed 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 178s The following NEW packages will be installed: 178s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx ipython3 178s libblas3 libdeflate0 liberfa1 libfontconfig1 libgfortran5 libgomp1 178s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 178s libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen 178s libjs-jquery-metadata libjs-jquery-tablesorter 178s libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc 178s libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 178s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 178s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwcs8 libwebp7 libwebpdemux2 178s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 178s python3-astropy python3-astropy-iers-data python3-asttokens python3-brotli 178s python3-contourpy python3-coverage python3-cycler python3-dateutil 178s python3-decorator python3-erfa python3-executing python3-fonttools 178s python3-fs python3-hypothesis python3-imexam python3-iniconfig 178s python3-ipython python3-jedi python3-kiwisolver python3-lxml python3-lz4 178s python3-matplotlib python3-matplotlib-inline python3-mpmath python3-numpy 178s python3-packaging python3-parso python3-pexpect python3-pil 178s python3-pil.imagetk python3-platformdirs python3-pluggy python3-ply 178s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 178s python3-pytest-arraydiff python3-pytest-astropy 178s python3-pytest-astropy-header python3-pytest-cov python3-pytest-doctestplus 178s python3-pytest-filter-subpackage python3-pytest-mock 178s python3-pytest-remotedata python3-scipy python3-sortedcontainers 178s python3-stack-data python3-sympy python3-tk python3-traitlets 178s python3-typeshed python3-tz python3-ufolib2 python3-unicodedata2 178s python3-wcwidth python3.12-tk python3.13 python3.13-minimal python3.13-tk 178s tk8.6-blt2.5 unicode-data x11-common 179s 0 upgraded, 112 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 76.5 MB of archives. 179s After this operation, 390 MB of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.1-2 [879 kB] 179s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.1-2 [2262 kB] 179s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 179s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 179s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 179s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 179s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 180s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 180s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 180s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 180s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 180s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 180s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 180s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 180s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 180s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 180s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 180s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 180s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.4-1 [67.6 kB] 180s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 180s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 180s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 180s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 180s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 180s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 180s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 3.0.0-1 [20.4 kB] 180s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.1.0-0.1 [24.4 kB] 180s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 180s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 180s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 180s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-3 [48.1 kB] 180s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.30.0-2 [569 kB] 180s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 ipython3 all 8.30.0-2 [4936 B] 180s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 180s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 180s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 180s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-12ubuntu1 [145 kB] 180s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 180s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.1.0-1 [489 kB] 180s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 180s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 180s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 180s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-metadata all 12-4 [6582 B] 180s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 180s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 180s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 180s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 180s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-3 [30.9 kB] 180s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 180s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 180s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 180s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 180s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.1-2 [2061 kB] 180s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 180s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 180s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 180s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 180s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 180s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 180s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 libwcs8 arm64 8.4+ds-1 [262 kB] 181s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 181s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 181s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 181s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 181s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 181s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 181s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 181s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB] 181s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 181s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 181s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hypothesis all 6.122.1-1 [330 kB] 181s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 181s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-arraydiff all 0.6.1-3 [10.2 kB] 181s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-astropy-header all 0.2.2-2 [8620 B] 181s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.1-2 [729 kB] 181s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.4.4+dfsg1-0ubuntu3 [150 kB] 181s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 181s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-cov all 5.0.0-1 [21.3 kB] 181s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-doctestplus all 1.3.0-1 [23.7 kB] 181s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-filter-subpackage all 0.2.0-1 [6094 B] 181s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 181s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-remotedata all 0.4.1-1 [8650 B] 181s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-astropy all 0.11.0-1 [5902 B] 181s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ply all 3.11-7 [45.4 kB] 181s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-astropy-iers-data all 0.2025.1.6.0.33.42-1 [1212 kB] 181s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 liberfa1 arm64 2.0.1-1build1 [136 kB] 181s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-erfa arm64 2.0.1.5+ds-1 [310 kB] 181s Get:88 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-astropy arm64 7.0.0-1 [3991 kB] 181s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 181s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1 [216 kB] 181s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 181s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.2-1 [31.5 kB] 181s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 181s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-5.1 [90.8 kB] 181s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1build1 [1591 kB] 181s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1 [27.3 kB] 181s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-3ubuntu1 [19.5 MB] 182s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 182s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 182s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 182s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 182s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 183s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.0-3 [1618 kB] 183s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu2 [182 kB] 183s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu2 [473 kB] 183s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.8-3 [115 kB] 183s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.1-2 [105 kB] 183s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 183s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu2 [9590 B] 183s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 183s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu1 [4612 kB] 183s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-imexam arm64 0.9.1-6 [50.5 kB] 184s Fetched 76.5 MB in 5s (16.0 MB/s) 184s Selecting previously unselected package libpython3.13-minimal:arm64. 184s (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 ... 80185 files and directories currently installed.) 184s Preparing to unpack .../000-libpython3.13-minimal_3.13.1-2_arm64.deb ... 184s Unpacking libpython3.13-minimal:arm64 (3.13.1-2) ... 184s Selecting previously unselected package python3.13-minimal. 184s Preparing to unpack .../001-python3.13-minimal_3.13.1-2_arm64.deb ... 184s Unpacking python3.13-minimal (3.13.1-2) ... 184s Selecting previously unselected package libjs-jquery. 184s Preparing to unpack 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package libdeflate0:arm64. 186s Preparing to unpack .../034-libdeflate0_1.22-1_arm64.deb ... 186s Unpacking libdeflate0:arm64 (1.22-1) ... 186s Selecting previously unselected package libgfortran5:arm64. 186s Preparing to unpack .../035-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 186s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 186s Selecting previously unselected package libgomp1:arm64. 186s Preparing to unpack .../036-libgomp1_14.2.0-12ubuntu1_arm64.deb ... 186s Unpacking libgomp1:arm64 (14.2.0-12ubuntu1) ... 186s Selecting previously unselected package libgraphite2-3:arm64. 186s Preparing to unpack .../037-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 186s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 187s Selecting previously unselected package libharfbuzz0b:arm64. 187s Preparing to unpack .../038-libharfbuzz0b_10.1.0-1_arm64.deb ... 187s Unpacking libharfbuzz0b:arm64 (10.1.0-1) ... 187s Selecting previously unselected package libimagequant0:arm64. 187s Preparing to 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(0.17.0+dfsg1-1) ... 242s Setting up python3-matplotlib (3.8.3-3ubuntu1) ... 245s Setting up python3-imexam (0.9.1-6) ... 245s Processing triggers for libc-bin (2.40-4ubuntu1) ... 245s Processing triggers for systemd (257-2ubuntu1) ... 245s Processing triggers for man-db (2.13.0-1) ... 248s autopkgtest [13:55:54]: test command1: cd $AUTOPKGTEST_TMP && MPLBACKEND=Agg python3 -m pytest --pyargs imexam 248s autopkgtest [13:55:54]: test command1: [----------------------- 250s ============================= test session starts ============================== 250s platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 250s rootdir: /tmp/autopkgtest.4bTky8/autopkgtest_tmp 250s plugins: astropy-0.11.0, filter-subpackage-0.2.0, arraydiff-0.6.1, mock-3.14.0, astropy-header-0.2.2, cov-5.0.0, doctestplus-1.3.0, remotedata-0.4.1, hypothesis-6.122.1, typeguard-4.4.1 250s collected 21 items 250s 251s tests/test_imexamine.py ..sFFxFFs [ 42%] 251s tests/test_util.py ............ [100%] 251s 251s =================================== FAILURES =================================== 251s ________________________________ test_line_fit _________________________________ 251s 251s def test_line_fit(): 251s """Fit a Gaussian1D line to the data.""" 251s plots = Imexamine() 251s in_amp = 3. 251s in_mean = 50. 251s in_stddev = 2. 251s in_const = 20. 251s 251s # Set all the lines to be Gaussians 251s line_gauss = in_const + in_amp * np.exp(-0.5 * ((xx - in_mean) / in_stddev)**2) 251s plots.set_data(line_gauss) 251s > fit = plots.line_fit(50, 50, form='Gaussian1D', genplot=False) 251s 251s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:86: 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:765: in line_fit 251s amp, xout, yout, sigma, sigmay = self.gauss_center(xx, 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 251s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 251s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 251s results = fit(model, xx, yy, data) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 251s return func(self, model, x, y, z=z, **kwargs) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 251s init_values, fitparams, cov_x = self._run_fitter( 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 251s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 251s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 251s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s 251s params = array([ 3., 15., 15., 3., 3., 0., 20.]) 251s model = 251s weights = 1.0 251s x = array([[ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 251s 13., 14., 15., 16., 17., 18., 19., 20..., 10., 11., 12., 251s 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 251s 26., 27., 28., 29.]]) 251s y = array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 251s 0., 0., 0., 0., 0., 0., 0., 0..., 29., 29., 29., 251s 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 251s 29., 29., 29., 29.]]) 251s z = array([[20. , 20. , 20. , 20.00000005, 20.00000081, 251s 20.00001118, 20.0001202 , 20.00100639...2699, 20.00656247, 20.00100639, 20.0001202 , 251s 20.00001118, 20.00000081, 20.00000005, 20. , 20. ]]) 251s fit_param_indices = None 251s 251s @staticmethod 251s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 251s """ 251s Wraps the method calculating the Jacobian of the function to account 251s for model constraints. 251s `scipy.optimize.leastsq` expects the function derivative to have the 251s above signature (parlist, (argtuple)). In order to accommodate model 251s constraints, instead of using p directly, we set the parameter list in 251s this function. 251s """ 251s if weights is None: 251s weights = 1.0 251s 251s if model.has_fixed or model.has_tied: 251s # update the parameters with the current values from the fitter 251s fitter_to_model_params(model, params) 251s if z is None: 251s full = np.array(model.fit_deriv(x, *model.parameters)) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s else: 251s full = np.array( 251s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 251s ) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s 251s pars = [getattr(model, name) for name in model.param_names] 251s fixed = [par.fixed for par in pars] 251s tied = [par.tied for par in pars] 251s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 251s fix_and_tie = np.logical_or(fixed, tied) 251s ind = np.logical_not(fix_and_tie) 251s 251s if not model.col_fit_deriv: 251s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 251s else: 251s residues = full_deriv[np.nonzero(ind)] 251s 251s return [np.ravel(_) for _ in residues] 251s else: 251s if z is None: 251s fit_deriv = np.array(model.fit_deriv(x, *params)) 251s try: 251s output = np.array( 251s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 251s ) 251s if output.shape != fit_deriv.shape: 251s output = np.array( 251s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 251s ) 251s return output 251s except ValueError: 251s return np.array( 251s [ 251s np.ravel(_) 251s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 251s ] 251s ).transpose() 251s else: 251s if not model.col_fit_deriv: 251s return [ 251s np.ravel(_) 251s for _ in ( 251s np.ravel(weights) 251s * np.array(model.fit_deriv(x, y, *params)).T 251s ).T 251s ] 251s return [ 251s np.ravel(_) 251s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 251s ] 251s 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. 251s 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 251s ----------------------------- Captured stdout call ----------------------------- 251s using model: 251s Name: Gaussian1D 251s N_inputs: 1 251s N_outputs: 1 251s Fittable parameters: ('amplitude', 'mean', 'stddev') 251s ------------------------------ Captured log call ------------------------------- 251s INFO imexam.util:imexamine.py:749 using model: 251s Name: Gaussian1D 251s N_inputs: 1 251s N_outputs: 1 251s Fittable parameters: ('amplitude', 'mean', 'stddev') 251s _______________________________ test_column_fit ________________________________ 251s 251s def test_column_fit(): 251s """Fit a Gaussian1D column to the data.""" 251s plots = Imexamine() 251s in_amp = 3. 251s in_mean = 50. 251s in_stddev = 2. 251s in_const = 20. 251s # Set all the columns to be Gaussians 251s col_gauss = in_const + in_amp * np.exp(-0.5 * ((yy - in_mean) / in_stddev)**2) 251s plots.set_data(col_gauss) 251s > fit = plots.column_fit(50, 50, form='Gaussian1D', genplot=False) 251s 251s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:104: 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:917: in column_fit 251s result = self.line_fit(x, y, data=data, form=form, 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:765: in line_fit 251s amp, xout, yout, sigma, sigmay = self.gauss_center(xx, 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 251s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 251s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 251s results = fit(model, xx, yy, data) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 251s return func(self, model, x, y, z=z, **kwargs) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 251s init_values, fitparams, cov_x = self._run_fitter( 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 251s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 251s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 251s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s 251s params = array([ 3., 15., 15., 3., 3., 0., 20.]) 251s model = 251s weights = 1.0 251s x = array([[ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 251s 13., 14., 15., 16., 17., 18., 19., 20..., 10., 11., 12., 251s 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 251s 26., 27., 28., 29.]]) 251s y = array([[ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 251s 0., 0., 0., 0., 0., 0., 0., 0..., 29., 29., 29., 251s 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 29., 251s 29., 29., 29., 29.]]) 251s z = array([[20. , 20. , 20. , 20. , 20. , 251s 20. , 20. , 20. ... , 20. , 20. , 20. , 251s 20. , 20. , 20. , 20. , 20. ]]) 251s fit_param_indices = None 251s 251s @staticmethod 251s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 251s """ 251s Wraps the method calculating the Jacobian of the function to account 251s for model constraints. 251s `scipy.optimize.leastsq` expects the function derivative to have the 251s above signature (parlist, (argtuple)). In order to accommodate model 251s constraints, instead of using p directly, we set the parameter list in 251s this function. 251s """ 251s if weights is None: 251s weights = 1.0 251s 251s if model.has_fixed or model.has_tied: 251s # update the parameters with the current values from the fitter 251s fitter_to_model_params(model, params) 251s if z is None: 251s full = np.array(model.fit_deriv(x, *model.parameters)) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s else: 251s full = np.array( 251s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 251s ) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s 251s pars = [getattr(model, name) for name in model.param_names] 251s fixed = [par.fixed for par in pars] 251s tied = [par.tied for par in pars] 251s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 251s fix_and_tie = np.logical_or(fixed, tied) 251s ind = np.logical_not(fix_and_tie) 251s 251s if not model.col_fit_deriv: 251s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 251s else: 251s residues = full_deriv[np.nonzero(ind)] 251s 251s return [np.ravel(_) for _ in residues] 251s else: 251s if z is None: 251s fit_deriv = np.array(model.fit_deriv(x, *params)) 251s try: 251s output = np.array( 251s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 251s ) 251s if output.shape != fit_deriv.shape: 251s output = np.array( 251s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 251s ) 251s return output 251s except ValueError: 251s return np.array( 251s [ 251s np.ravel(_) 251s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 251s ] 251s ).transpose() 251s else: 251s if not model.col_fit_deriv: 251s return [ 251s np.ravel(_) 251s for _ in ( 251s np.ravel(weights) 251s * np.array(model.fit_deriv(x, y, *params)).T 251s ).T 251s ] 251s return [ 251s np.ravel(_) 251s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 251s ] 251s 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. 251s 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 251s ----------------------------- Captured stdout call ----------------------------- 251s using model: 251s Name: Gaussian1D 251s N_inputs: 1 251s N_outputs: 1 251s Fittable parameters: ('amplitude', 'mean', 'stddev') 251s ------------------------------ Captured log call ------------------------------- 251s INFO imexam.util:imexamine.py:749 using model: 251s Name: Gaussian1D 251s N_inputs: 1 251s N_outputs: 1 251s Fittable parameters: ('amplitude', 'mean', 'stddev') 251s _____________________________ test_radial_profile ______________________________ 251s 251s def test_radial_profile(): 251s """Test the radial profile function 251s No background subtraction 251s individual pixel results used 251s """ 251s from astropy.convolution import Gaussian2DKernel 251s data = Gaussian2DKernel(1.5, x_size=25, y_size=25) 251s xx, yy = np.meshgrid(np.arange(25), np.arange(25)) 251s x0, y0 = np.where(data.array == data.array.max()) 251s 251s rad_in = np.sqrt((xx - x0)**2 + (yy - y0)**2) 251s rad_in = rad_in.ravel() 251s flux_in = data.array.ravel() 251s 251s order = np.argsort(rad_in) 251s rad_in = rad_in[order] 251s flux_in = flux_in[order] 251s 251s plots = Imexamine() 251s plots.set_data(data.array) 251s 251s plots.radial_profile_pars['pixels'][0] = True 251s plots.radial_profile_pars['background'][0] = False 251s plots.radial_profile_pars['clip'][0] = False 251s > rad_out, flux_out = plots.radial_profile(x0, y0, genplot=False) 251s 251s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:160: 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:1102: in radial_profile 251s amp, centerx, centery, sigmax, sigmay = self.gauss_center(xx, yy, data, delta=datasize) 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 251s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 251s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 251s results = fit(model, xx, yy, data) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 251s return func(self, model, x, y, z=z, **kwargs) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 251s init_values, fitparams, cov_x = self._run_fitter( 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 251s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 251s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 251s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s 251s params = array([7.06778109e-02, 4.00000000e+00, 4.00000000e+00, 3.00000000e+00, 251s 3.00000000e+00, 0.00000000e+00, 5.77193322e-05]) 251s model = 251s weights = 1.0 251s x = array([[0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., ... [0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., 7.]]) 251s y = array([[0., 0., 0., 0., 0., 0., 0., 0.], 251s [1., 1., 1., 1., 1., 1., 1., 1.], 251s [2., 2., 2., 2., 2., 2., 2., ... [5., 5., 5., 5., 5., 5., 5., 5.], 251s [6., 6., 6., 6., 6., 6., 6., 6.], 251s [7., 7., 7., 7., 7., 7., 7., 7.]]) 251s z = array([[5.77193322e-05, 2.73457911e-04, 8.30691786e-04, 1.61796667e-03, 251s 2.02059585e-03, 1.61796667e-03, 8.3069...29556643e-03, 3.93558331e-03, 7.66546959e-03, 251s 9.57301302e-03, 7.66546959e-03, 3.93558331e-03, 1.29556643e-03]]) 251s fit_param_indices = None 251s 251s @staticmethod 251s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 251s """ 251s Wraps the method calculating the Jacobian of the function to account 251s for model constraints. 251s `scipy.optimize.leastsq` expects the function derivative to have the 251s above signature (parlist, (argtuple)). In order to accommodate model 251s constraints, instead of using p directly, we set the parameter list in 251s this function. 251s """ 251s if weights is None: 251s weights = 1.0 251s 251s if model.has_fixed or model.has_tied: 251s # update the parameters with the current values from the fitter 251s fitter_to_model_params(model, params) 251s if z is None: 251s full = np.array(model.fit_deriv(x, *model.parameters)) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s else: 251s full = np.array( 251s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 251s ) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s 251s pars = [getattr(model, name) for name in model.param_names] 251s fixed = [par.fixed for par in pars] 251s tied = [par.tied for par in pars] 251s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 251s fix_and_tie = np.logical_or(fixed, tied) 251s ind = np.logical_not(fix_and_tie) 251s 251s if not model.col_fit_deriv: 251s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 251s else: 251s residues = full_deriv[np.nonzero(ind)] 251s 251s return [np.ravel(_) for _ in residues] 251s else: 251s if z is None: 251s fit_deriv = np.array(model.fit_deriv(x, *params)) 251s try: 251s output = np.array( 251s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 251s ) 251s if output.shape != fit_deriv.shape: 251s output = np.array( 251s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 251s ) 251s return output 251s except ValueError: 251s return np.array( 251s [ 251s np.ravel(_) 251s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 251s ] 251s ).transpose() 251s else: 251s if not model.col_fit_deriv: 251s return [ 251s np.ravel(_) 251s for _ in ( 251s np.ravel(weights) 251s * np.array(model.fit_deriv(x, y, *params)).T 251s ).T 251s ] 251s return [ 251s np.ravel(_) 251s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 251s ] 251s 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. 251s 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 251s ________________________ test_radial_profile_cumulative ________________________ 251s 251s def test_radial_profile_cumulative(): 251s """Test the radial profile function 251s without background subtraction 251s with each pixel integer binned 251s """ 251s from astropy.convolution import Gaussian2DKernel 251s ksize = 25 251s data = Gaussian2DKernel(1.5, x_size=ksize, y_size=ksize) 251s xx, yy = np.meshgrid(np.arange(ksize), np.arange(ksize)) 251s x0, y0 = np.where(data.array == data.array.max()) 251s rad_in = np.sqrt((xx - x0)**2 + (yy - y0)**2) 251s 251s rad_in = rad_in.ravel() 251s flux_in = data.array.ravel() 251s 251s indices = np.argsort(rad_in) 251s rad_in = rad_in[indices] 251s flux_in = flux_in[indices] 251s 251s # now bin the radflux like we expect 251s rad_in = rad_in.astype(int) 251s flux_in = np.bincount(rad_in, flux_in) / np.bincount(rad_in) 251s rad_in = np.arange(len(flux_in)) 251s assert (data.array[x0, y0] == flux_in[0]) 251s 251s # check the binned results 251s plots = Imexamine() 251s plots.set_data(data.array) 251s plots.radial_profile_pars['pixels'][0] = False 251s plots.radial_profile_pars['background'][0] = False 251s plots.radial_profile_pars['clip'][0] = False 251s > rad_out, flux_out = plots.radial_profile(x0, y0, genplot=False) 251s 251s /usr/lib/python3/dist-packages/imexam/tests/test_imexamine.py:206: 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:1102: in radial_profile 251s amp, centerx, centery, sigmax, sigmay = self.gauss_center(xx, yy, data, delta=datasize) 251s /usr/lib/python3/dist-packages/imexam/imexamine.py:1007: in gauss_center 251s fit = math_helper.fit_gaussian_2d(chunk, sigma_factor=sigma_factor) 251s /usr/lib/python3/dist-packages/imexam/math_helper.py:254: in fit_gaussian_2d 251s results = fit(model, xx, yy, data) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:303: in wrapper 251s return func(self, model, x, y, z=z, **kwargs) 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1434: in __call__ 251s init_values, fitparams, cov_x = self._run_fitter( 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1509: in _run_fitter 251s fitparams, cov_x, dinfo, mess, ierr = optimize.leastsq( 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:443: in leastsq 251s _check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n, m)) 251s /usr/lib/python3/dist-packages/scipy/optimize/_minpack_py.py:23: in _check_func 251s res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) 251s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 251s 251s params = array([7.06778109e-02, 4.00000000e+00, 4.00000000e+00, 3.00000000e+00, 251s 3.00000000e+00, 0.00000000e+00, 5.77193322e-05]) 251s model = 251s weights = 1.0 251s x = array([[0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., ... [0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., 7.], 251s [0., 1., 2., 3., 4., 5., 6., 7.]]) 251s y = array([[0., 0., 0., 0., 0., 0., 0., 0.], 251s [1., 1., 1., 1., 1., 1., 1., 1.], 251s [2., 2., 2., 2., 2., 2., 2., ... [5., 5., 5., 5., 5., 5., 5., 5.], 251s [6., 6., 6., 6., 6., 6., 6., 6.], 251s [7., 7., 7., 7., 7., 7., 7., 7.]]) 251s z = array([[5.77193322e-05, 2.73457911e-04, 8.30691786e-04, 1.61796667e-03, 251s 2.02059585e-03, 1.61796667e-03, 8.3069...29556643e-03, 3.93558331e-03, 7.66546959e-03, 251s 9.57301302e-03, 7.66546959e-03, 3.93558331e-03, 1.29556643e-03]]) 251s fit_param_indices = None 251s 251s @staticmethod 251s def _wrap_deriv(params, model, weights, x, y, z=None, fit_param_indices=None): 251s """ 251s Wraps the method calculating the Jacobian of the function to account 251s for model constraints. 251s `scipy.optimize.leastsq` expects the function derivative to have the 251s above signature (parlist, (argtuple)). In order to accommodate model 251s constraints, instead of using p directly, we set the parameter list in 251s this function. 251s """ 251s if weights is None: 251s weights = 1.0 251s 251s if model.has_fixed or model.has_tied: 251s # update the parameters with the current values from the fitter 251s fitter_to_model_params(model, params) 251s if z is None: 251s full = np.array(model.fit_deriv(x, *model.parameters)) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s else: 251s full = np.array( 251s [np.ravel(_) for _ in model.fit_deriv(x, y, *model.parameters)] 251s ) 251s if not model.col_fit_deriv: 251s full_deriv = np.ravel(weights) * full.T 251s else: 251s full_deriv = np.ravel(weights) * full 251s 251s pars = [getattr(model, name) for name in model.param_names] 251s fixed = [par.fixed for par in pars] 251s tied = [par.tied for par in pars] 251s tied = list(np.where([par.tied is not False for par in pars], True, tied)) 251s fix_and_tie = np.logical_or(fixed, tied) 251s ind = np.logical_not(fix_and_tie) 251s 251s if not model.col_fit_deriv: 251s residues = np.asarray(full_deriv[np.nonzero(ind)]).T 251s else: 251s residues = full_deriv[np.nonzero(ind)] 251s 251s return [np.ravel(_) for _ in residues] 251s else: 251s if z is None: 251s fit_deriv = np.array(model.fit_deriv(x, *params)) 251s try: 251s output = np.array( 251s [np.ravel(_) for _ in np.array(weights) * fit_deriv] 251s ) 251s if output.shape != fit_deriv.shape: 251s output = np.array( 251s [np.ravel(_) for _ in np.atleast_2d(weights).T * fit_deriv] 251s ) 251s return output 251s except ValueError: 251s return np.array( 251s [ 251s np.ravel(_) 251s for _ in np.array(weights) * np.moveaxis(fit_deriv, -1, 0) 251s ] 251s ).transpose() 251s else: 251s if not model.col_fit_deriv: 251s return [ 251s np.ravel(_) 251s for _ in ( 251s np.ravel(weights) 251s * np.array(model.fit_deriv(x, y, *params)).T 251s ).T 251s ] 251s return [ 251s np.ravel(_) 251s > for _ in weights * np.array(model.fit_deriv(x, y, *params)) 251s ] 251s 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. 251s 251s /usr/lib/python3/dist-packages/astropy/modeling/fitting.py:1287: ValueError 251s =============================== warnings summary =============================== 251s ../../../usr/lib/python3/dist-packages/imexam/__init__.py:12 251s /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 251s from pkg_resources import get_distribution, DistributionNotFound 251s 251s tests/test_imexamine.py::test_radial_profile 251s tests/test_imexamine.py::test_radial_profile_cumulative 251s /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.) 251s xx = int(x) 251s 251s tests/test_imexamine.py::test_radial_profile 251s tests/test_imexamine.py::test_radial_profile_cumulative 251s /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.) 251s yy = int(y) 251s 251s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 251s =========================== short test summary info ============================ 251s FAILED tests/test_imexamine.py::test_line_fit - ValueError: setting an array ... 251s FAILED tests/test_imexamine.py::test_column_fit - ValueError: setting an arra... 251s FAILED tests/test_imexamine.py::test_radial_profile - ValueError: setting an ... 251s FAILED tests/test_imexamine.py::test_radial_profile_cumulative - ValueError: ... 251s ======== 4 failed, 14 passed, 2 skipped, 1 xfailed, 5 warnings in 2.89s ======== 252s autopkgtest [13:55:58]: test command1: -----------------------] 253s command1 FAIL non-zero exit status 1 253s autopkgtest [13:55:59]: test command1: - - - - - - - - - - results - - - - - - - - - - 253s autopkgtest [13:55:59]: @@@@@@@@@@@@@@@@@@@@ summary 253s command1 FAIL non-zero exit status 1 270s nova [W] Using flock in prodstack6-arm64 270s Creating nova instance adt-plucky-arm64-imexam-20250109-135146-juju-7f2275-prod-proposed-migration-environment-20-d125861e-681e-44ba-84ca-4be6cdc2d84a from image adt/ubuntu-plucky-arm64-server-20250108.img (UUID 053f5e9f-d810-4aac-9e57-cf8ac63865d2)... 270s nova [W] Timed out waiting for cc450d25-433b-4816-801a-210631a9b97c to get deleted.