Support numpy 2 but wait for gt to update in tests
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[#1257143] 2024/06/21 15:01:01 Booting image ubuntu/lts (default) on port 22358 [#1257143] 2024/06/21 15:01:01 Waiting for guest to settle [#1257143] 2024/06/21 15:01:10 Sending tasks [#1257143] 2024/06/21 15:01:12 Sending build environment [#1257143] 2024/06/21 15:01:13 Sending secrets [#1257143] 2024/06/21 15:01:13 Resolving secret ceb490c3-68b4-41f7-9aa9-eb2e4b91d424 [#1257143] 2024/06/21 15:01:14 Resolving secret 0b249c79-8eaf-4b82-b1d1-f3c38c7eae4b [#1257143] 2024/06/21 15:01:15 Resolving secret 3a7c042a-24d8-4f53-b75c-f061f7517b65 [#1257143] 2024/06/21 15:01:15 Installing packages Warning: Permanently added '[localhost]:22358' (ED25519) to the list of known hosts. Hit:1 http://archive.ubuntu.com/ubuntu jammy InRelease Get:2 http://archive.ubuntu.com/ubuntu jammy-security InRelease [129 kB] Get:3 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [128 kB] Hit:4 http://archive.ubuntu.com/ubuntu jammy-backports InRelease Get:5 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 Packages [1526 kB] Get:6 http://archive.ubuntu.com/ubuntu jammy-security/main Translation-en [261 kB] Get:7 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [860 kB] Get:8 http://archive.ubuntu.com/ubuntu jammy-security/universe Translation-en [167 kB] Get:9 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1734 kB] Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1087 kB] Fetched 5892 kB in 2s (3542 kB/s) Reading package lists... Warning: Permanently added '[localhost]:22358' (ED25519) to the list of known hosts. Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: javascript-common libexpat1-dev libjs-jquery libjs-sphinxdoc libjs-underscore libpython3-dev libpython3.10 libpython3.10-dev python3-dev python3-distutils python3-lib2to3 python3-setuptools python3-wheel python3.10-dev zlib1g-dev Suggested packages: apache2 | lighttpd | httpd python-setuptools-doc The following NEW packages will be installed: javascript-common libexpat1-dev libjs-jquery libjs-sphinxdoc libjs-underscore libpython3-dev libpython3.10 libpython3.10-dev python3-dev python3-distutils python3-lib2to3 python3-pip python3-setuptools python3-wheel python3.10-dev zlib1g-dev 0 upgraded, 16 newly installed, 0 to remove and 3 not upgraded. Need to get 10.0 MB of archives. After this operation, 40.5 MB of additional disk space will be used. Get:1 http://archive.ubuntu.com/ubuntu jammy/main amd64 javascript-common all 11+nmu1 [5936 B] Get:2 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libexpat1-dev amd64 2.4.7-1ubuntu0.3 [147 kB] Get:3 http://archive.ubuntu.com/ubuntu jammy/main amd64 libjs-jquery all 3.6.0+dfsg+~3.5.13-1 [321 kB] Get:4 http://archive.ubuntu.com/ubuntu jammy/main amd64 libjs-underscore all 1.13.2~dfsg-2 [118 kB] Get:5 http://archive.ubuntu.com/ubuntu jammy/main amd64 libjs-sphinxdoc all 4.3.2-1 [139 kB] Get:6 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libpython3.10 amd64 3.10.12-1~22.04.3 [1948 kB] Get:7 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9.2 [164 kB] Get:8 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libpython3.10-dev amd64 3.10.12-1~22.04.3 [4762 kB] Get:9 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libpython3-dev amd64 3.10.6-1~22.04 [7166 B] Get:10 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3.10-dev amd64 3.10.12-1~22.04.3 [507 kB] Get:11 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-lib2to3 all 3.10.8-1~22.04 [77.6 kB] Get:12 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-distutils all 3.10.8-1~22.04 [139 kB] Get:13 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-dev amd64 3.10.6-1~22.04 [26.0 kB] Get:14 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-setuptools all 59.6.0-1.2ubuntu0.22.04.1 [339 kB] Get:15 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 python3-wheel all 0.37.1-2ubuntu0.22.04.1 [32.0 kB] Get:16 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 python3-pip all 22.0.2+dfsg-1ubuntu0.4 [1305 kB] Fetched 10.0 MB in 0s (50.2 MB/s) Selecting previously unselected package javascript-common. (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 ... 39171 files and directories currently installed.) Preparing to unpack .../00-javascript-common_11+nmu1_all.deb ... Unpacking javascript-common (11+nmu1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../01-libexpat1-dev_2.4.7-1ubuntu0.3_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.4.7-1ubuntu0.3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../02-libjs-jquery_3.6.0+dfsg+~3.5.13-1_all.deb ... Unpacking libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../03-libjs-underscore_1.13.2~dfsg-2_all.deb ... Unpacking libjs-underscore (1.13.2~dfsg-2) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../04-libjs-sphinxdoc_4.3.2-1_all.deb ... Unpacking libjs-sphinxdoc (4.3.2-1) ... Selecting previously unselected package libpython3.10:amd64. Preparing to unpack .../05-libpython3.10_3.10.12-1~22.04.3_amd64.deb ... Unpacking libpython3.10:amd64 (3.10.12-1~22.04.3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../06-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu9.2_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9.2) ... Selecting previously unselected package libpython3.10-dev:amd64. Preparing to unpack .../07-libpython3.10-dev_3.10.12-1~22.04.3_amd64.deb ... Unpacking libpython3.10-dev:amd64 (3.10.12-1~22.04.3) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../08-libpython3-dev_3.10.6-1~22.04_amd64.deb ... Unpacking libpython3-dev:amd64 (3.10.6-1~22.04) ... Selecting previously unselected package python3.10-dev. Preparing to unpack .../09-python3.10-dev_3.10.12-1~22.04.3_amd64.deb ... Unpacking python3.10-dev (3.10.12-1~22.04.3) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../10-python3-lib2to3_3.10.8-1~22.04_all.deb ... Unpacking python3-lib2to3 (3.10.8-1~22.04) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../11-python3-distutils_3.10.8-1~22.04_all.deb ... Unpacking python3-distutils (3.10.8-1~22.04) ... Selecting previously unselected package python3-dev. Preparing to unpack .../12-python3-dev_3.10.6-1~22.04_amd64.deb ... Unpacking python3-dev (3.10.6-1~22.04) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../13-python3-setuptools_59.6.0-1.2ubuntu0.22.04.1_all.deb ... Unpacking python3-setuptools (59.6.0-1.2ubuntu0.22.04.1) ... Selecting previously unselected package python3-wheel. Preparing to unpack .../14-python3-wheel_0.37.1-2ubuntu0.22.04.1_all.deb ... Unpacking python3-wheel (0.37.1-2ubuntu0.22.04.1) ... Selecting previously unselected package python3-pip. Preparing to unpack .../15-python3-pip_22.0.2+dfsg-1ubuntu0.4_all.deb ... Unpacking python3-pip (22.0.2+dfsg-1ubuntu0.4) ... Setting up javascript-common (11+nmu1) ... Setting up libpython3.10:amd64 (3.10.12-1~22.04.3) ... Setting up libexpat1-dev:amd64 (2.4.7-1ubuntu0.3) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9.2) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up python3-lib2to3 (3.10.8-1~22.04) ... Setting up libjs-underscore (1.13.2~dfsg-2) ... Setting up python3-distutils (3.10.8-1~22.04) ... Setting up python3-setuptools (59.6.0-1.2ubuntu0.22.04.1) ... Setting up python3-wheel (0.37.1-2ubuntu0.22.04.1) ... Setting up libpython3.10-dev:amd64 (3.10.12-1~22.04.3) ... Setting up python3-pip (22.0.2+dfsg-1ubuntu0.4) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up python3.10-dev (3.10.12-1~22.04.3) ... Setting up libpython3-dev:amd64 (3.10.6-1~22.04) ... Setting up python3-dev (3.10.6-1~22.04) ... Processing triggers for libc-bin (2.35-0ubuntu3.8) ... [#1257143] 2024/06/21 15:01:21 Cloning repositories Cloning into 'NNGT'... + cd NNGT + git checkout -q 8827d9b7a4aa1b1ee41a6ea19e963508ee2ec7c1 + cd NNGT + git submodule update --init --recursive Submodule 'nngt/geometry' (https://github.com/SENeC-Initiative/PyNCulture.git) registered for path 'nngt/geometry' Submodule 'nngt/plot/chord_diag' (https://codeberg.org/tfardet/mpl_chord_diagram.git) registered for path 'nngt/plot/chord_diag' Cloning into '/home/build/NNGT/nngt/geometry'... Cloning into '/home/build/NNGT/nngt/plot/chord_diag'... Submodule path 'nngt/geometry': checked out '98364e970315705ba32265e7d7bae90105b868c3' Submodule path 'nngt/plot/chord_diag': checked out '418e3ab73dad2f326e76d2bc13c7be9eb6a247b9' [#1257143] 2024/06/21 15:01:24 Running task check [#1257143] 2024/06/21 15:01:29 Running task setup [#1257143] 2024/06/21 15:03:51 Running task test [#1257143] 2024/06/21 15:04:07 Build failed. [#1257143] 2024/06/21 15:04:07 The build environment will be kept alive for 10 minutes. [#1257143] 2024/06/21 15:04:07 To log in with SSH and examine it, use the following command: [#1257143] 2024/06/21 15:04:07 [#1257143] 2024/06/21 15:04:07 ssh -t builds@fra01.builds.sr.ht connect 1257143 [#1257143] 2024/06/21 15:04:07 [#1257143] 2024/06/21 15:04:07 After logging in, the deadline is increased to your remaining build time. [#1257143] 2024/06/21 15:14:07 Deadline elapsed. Terminating build environment. [#1257143] 2024/06/21 15:14:07 Error: Running task on guest: exit status 1 |
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+ export PATH=/home/build/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin + PATH=/home/build/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin + cd NNGT + python3 extra/check_headers.py + pip3 install reuse Defaulting to user installation because normal site-packages is not writeable Collecting reuse Downloading reuse-3.0.2.tar.gz (269 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 269.4/269.4 KB 15.3 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting license-expression>=1.0 Downloading license_expression-30.3.0-py3-none-any.whl (108 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 KB 19.7 MB/s eta 0:00:00 Collecting python-debian!=0.1.45,!=0.1.46,!=0.1.47,<0.2.0,>=0.1.34 Downloading python_debian-0.1.49-py3-none-any.whl (132 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.5/132.5 KB 60.6 MB/s eta 0:00:00 Collecting Jinja2<4.0.0,>=3.0.0 Downloading jinja2-3.1.4-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.3/133.3 KB 28.5 MB/s eta 0:00:00 Collecting boolean.py>=3.8 Downloading boolean.py-4.0-py3-none-any.whl (25 kB) Collecting binaryornot<0.5.0,>=0.4.4 Downloading binaryornot-0.4.4-py2.py3-none-any.whl (9.0 kB) Collecting chardet>=3.0.2 Downloading chardet-5.2.0-py3-none-any.whl (199 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 KB 38.0 MB/s eta 0:00:00 Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Building wheels for collected packages: reuse Building wheel for reuse (pyproject.toml): started Building wheel for reuse (pyproject.toml): finished with status 'done' Created wheel for reuse: filename=reuse-3.0.2-cp310-cp310-manylinux_2_35_x86_64.whl size=119657 sha256=91bebc3608eeea55875ac12fb9650ffa9738b8be4e8025014818adfddbb884c5 Stored in directory: /home/build/.cache/pip/wheels/2b/57/24/d43da4d2afa2378313e911ca8254dd24b3becb9e0ee2d57e0b Successfully built reuse Installing collected packages: boolean.py, MarkupSafe, license-expression, chardet, python-debian, Jinja2, binaryornot, reuse Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 binaryornot-0.4.4 boolean.py-4.0 chardet-5.2.0 license-expression-30.3.0 python-debian-0.1.49 reuse-3.0.2 + reuse lint # SUMMARY * Bad licenses: 0 * Deprecated licenses: 0 * Licenses without file extension: 0 * Missing licenses: 0 * Unused licenses: 0 * Used licenses: GPL-3.0-or-later, BSD-2-Clause, CC-BY-SA-4.0, Python-2.0, CC0-1.0 * Read errors: 0 * files with copyright information: 183 / 183 * files with license information: 183 / 183 Congratulations! Your project is compliant with version 3.0 of the REUSE Specification :-) |
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Get:137 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libopenblas-pthread-dev amd64 0.3.20+ds-1 [4634 kB] Get:138 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libopenblas-dev amd64 0.3.20+ds-1 [18.6 kB] Get:139 http://archive.ubuntu.com/ubuntu jammy/main amd64 libnuma-dev amd64 2.0.14-3ubuntu2 [35.9 kB] Get:140 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 libhwloc-dev amd64 2.7.0-2ubuntu1 [256 kB] Get:141 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libpmix-dev amd64 4.1.2-2ubuntu1 [805 kB] Get:142 http://archive.ubuntu.com/ubuntu jammy/universe amd64 proj-data all 8.2.1-1 [10.0 MB] Get:143 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libproj22 amd64 8.2.1-1 [1257 kB] Get:144 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libqhull-r8.0 amd64 2020.2-4 [196 kB] Get:145 http://archive.ubuntu.com/ubuntu jammy/main amd64 libraqm0 amd64 0.7.0-4ubuntu1 [11.7 kB] Get:146 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libsqlite3-dev amd64 3.37.2-2ubuntu0.3 [846 kB] Get:147 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libtbbmalloc2 amd64 2021.5.0-7ubuntu2 [49.6 kB] Get:148 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libtbb12 amd64 2021.5.0-7ubuntu2 [84.8 kB] Get:149 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libjbig-dev amd64 2.1-3.1ubuntu0.22.04.1 [27.4 kB] Get:150 http://archive.ubuntu.com/ubuntu jammy/main amd64 liblzma-dev amd64 5.2.5-2ubuntu1 [159 kB] Get:151 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libtiffxx5 amd64 4.3.0-6ubuntu0.9 [5726 B] Get:152 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libtiff-dev amd64 4.3.0-6ubuntu0.9 [316 kB] Get:153 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libtinfo-dev amd64 6.3-2ubuntu0.1 [780 B] Get:154 http://archive.ubuntu.com/ubuntu jammy/main amd64 libtool all 2.4.6-15build2 [164 kB] Get:155 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libwebpdemux2 amd64 1.2.2-2ubuntu0.22.04.2 [9964 B] Get:156 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libwebpmux3 amd64 1.2.2-2ubuntu0.22.04.2 [20.5 kB] Get:157 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libxml2-dev amd64 2.9.13+dfsg-1ubuntu0.4 [804 kB] Get:158 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libxsimd-dev amd64 7.6.0-2 [108 kB] Get:159 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libxslt1.1 amd64 1.1.34-4ubuntu0.22.04.1 [164 kB] Get:160 http://archive.ubuntu.com/ubuntu jammy/universe amd64 llvm-11-runtime amd64 1:11.1.0-6 [186 kB] Get:161 http://archive.ubuntu.com/ubuntu jammy/universe amd64 llvm-11-linker-tools amd64 1:11.1.0-6 [1275 kB] Get:162 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libpfm4 amd64 4.11.1+git32-gd0b85fb-1ubuntu0.1 [345 kB] Get:163 http://archive.ubuntu.com/ubuntu jammy/universe amd64 llvm-11 amd64 1:11.1.0-6 [9118 kB] Get:164 http://archive.ubuntu.com/ubuntu jammy/main amd64 libffi-dev amd64 3.4.2-4 [63.7 kB] Get:165 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-pygments all 2.11.2+dfsg-2 [750 kB] Get:166 http://archive.ubuntu.com/ubuntu jammy/universe amd64 llvm-11-tools amd64 1:11.1.0-6 [359 kB] Get:167 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libz3-4 amd64 4.8.12-1 [5766 kB] Get:168 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libz3-dev amd64 4.8.12-1 [72.2 kB] Get:169 http://archive.ubuntu.com/ubuntu jammy/universe amd64 llvm-11-dev amd64 1:11.1.0-6 [29.9 MB] Get:170 http://archive.ubuntu.com/ubuntu jammy/main amd64 mailcap all 3.70+nmu1ubuntu1 [23.8 kB] Get:171 http://archive.ubuntu.com/ubuntu jammy/main amd64 mime-support all 3.66 [3696 B] Get:172 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-numpy amd64 1:1.21.5-1ubuntu22.04.1 [3467 kB] Get:173 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-dateutil all 2.8.1-6 [78.4 kB] Get:174 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 python3-tz all 2022.1-1ubuntu0.22.04.1 [30.7 kB] Get:175 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-pandas-lib amd64 1.3.5+dfsg-3 [3735 kB] Get:176 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-pandas all 1.3.5+dfsg-3 [2680 kB] Get:177 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:178 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-gast all 0.5.2-2 [9394 B] Get:179 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-beniget all 0.4.1-2 [9904 B] Get:180 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-ply all 3.11-5 [47.5 kB] Get:181 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-pythran amd64 0.10.0+ds2-1 [423 kB] Get:182 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-scipy amd64 1.8.0-1exp2ubuntu1 [14.7 MB] Get:183 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python-matplotlib-data all 3.5.1-2build1 [2942 kB] Get:184 http://archive.ubuntu.com/ubuntu jammy/main amd64 libopenjp2-7 amd64 2.4.0-6 [158 kB] Get:185 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-pil amd64 9.0.1-1ubuntu0.3 [419 kB] Get:186 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-tk amd64 3.10.8-1~22.04 [110 kB] Get:187 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 python3-pil.imagetk amd64 9.0.1-1ubuntu0.3 [9616 B] Get:188 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-cycler all 0.11.0-1 [8156 B] Get:189 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-brotli amd64 1.0.9-2build6 [319 kB] Get:190 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-attr all 21.2.0-1 [44.0 kB] Get:191 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-ufolib2 all 0.13.1+dfsg1-1 [32.2 kB] Get:192 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-mpmath all 1.2.1-2 [419 kB] Get:193 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-sympy all 1.9-1 [4312 kB] Get:194 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-appdirs all 1.4.4-2 [11.4 kB] Get:195 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-fs all 2.4.12-1 [84.9 kB] Get:196 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-lxml amd64 4.8.0-1build1 [1150 kB] Get:197 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-lz4 amd64 3.1.3+dfsg-1build3 [33.3 kB] Get:198 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-unicodedata2 amd64 14.0.0+ds-8 [376 kB] Get:199 http://archive.ubuntu.com/ubuntu jammy/universe amd64 unicode-data all 14.0.0-1.1 [8206 kB] Get:200 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-fonttools amd64 4.29.1-2build1 [810 kB] Get:201 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-kiwisolver amd64 1.3.2-1build1 [48.0 kB] Get:202 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-packaging all 21.3-1 [30.7 kB] Get:203 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-matplotlib amd64 3.5.1-2build1 [5937 kB] Get:204 http://archive.ubuntu.com/ubuntu jammy/universe amd64 mpi-default-bin amd64 1.14 [2898 B] Get:205 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-mpi4py amd64 3.1.3-1build2 [465 kB] Get:206 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-h5py-serial amd64 3.6.0-2build1 [872 kB] Get:207 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-h5py all 3.6.0-2build1 [4740 B] Get:208 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-pydot all 1.4.2-1build1 [25.8 kB] Get:209 http://archive.ubuntu.com/ubuntu jammy/main amd64 sphinx-rtd-theme-common all 1.0.0+dfsg-1 [991 kB] Get:210 http://archive.ubuntu.com/ubuntu jammy/universe amd64 numba-doc all 0.55.1-0ubuntu2 [737 kB] Get:211 http://archive.ubuntu.com/ubuntu jammy/main amd64 python-babel-localedata all 2.8.0+dfsg.1-7 [4982 kB] Get:212 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python-odf-doc all 1.4.2-1 [222 kB] Get:213 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-defusedxml all 0.7.1-1 [43.2 kB] Get:214 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-odf all 1.4.2-1 [79.3 kB] Get:215 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python-odf-tools all 1.4.2-1 [27.3 kB] Get:216 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python-tables-data all 3.7.0-2build1 [47.6 kB] Get:217 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-babel all 2.8.0+dfsg.1-7 [85.1 kB] Get:218 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-bottleneck amd64 1.3.2+ds1-2build1 [82.9 kB] Get:219 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-soupsieve all 2.3.1-1 [33.0 kB] Get:220 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-bs4 all 4.10.0-2 [79.1 kB] Get:221 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-chardet all 4.0.0-1 [98.0 kB] Get:222 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-et-xmlfile all 1.0.1-2.1 [9224 B] Get:223 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-webencodings all 0.5.1-4 [11.8 kB] Get:224 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-html5lib all 1.1-3 [87.0 kB] Get:225 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] Get:226 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-jdcal all 1.0-1.3 [7944 B] Get:227 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-markupsafe amd64 2.0.1-2build1 [12.7 kB] Get:228 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-jinja2 all 3.0.3-1ubuntu0.2 [108 kB] Get:229 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-llvmlite amd64 0.38.0-1 [126 kB] Get:230 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-numba amd64 0.55.1-0ubuntu2 [1588 kB] Get:231 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-numexpr amd64 2.8.1-1build1 [86.0 kB] Get:232 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-olefile all 0.46-3 [33.8 kB] Get:233 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-openpyxl all 3.0.9-1 [148 kB] Get:234 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-pluggy all 0.13.0-7.1 [19.0 kB] Get:235 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-py all 1.10.0-1 [71.9 kB] Get:236 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] Get:237 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-pytest all 6.2.5-1ubuntu2 [214 kB] Get:238 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-tables-lib amd64 3.7.0-2build1 [427 kB] Get:239 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-tables all 3.7.0-2build1 [333 kB] Get:240 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-xlwt all 1.3.0-3 [83.7 kB] Get:241 http://archive.ubuntu.com/ubuntu jammy/main amd64 libibverbs-dev amd64 39.0-1 [628 kB] Get:242 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libopenmpi-dev amd64 4.1.2-2ubuntu1 [867 kB] Get:243 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libproj-dev amd64 8.2.1-1 [1594 kB] Get:244 http://archive.ubuntu.com/ubuntu jammy/universe amd64 proj-bin amd64 8.2.1-1 [154 kB] debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 298 MB in 26s (11.4 MB/s) Selecting previously unselected package fonts-lato. (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 ... 41436 files and directories currently installed.) Preparing to unpack .../000-fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.41-3ubuntu0.1_amd64.deb ... Unpacking libmagic-mgc (1:5.41-3ubuntu0.1) ... Selecting previously unselected package libmagic1:amd64. 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Selecting previously unselected package python3-tables-lib. Preparing to unpack .../237-python3-tables-lib_3.7.0-2build1_amd64.deb ... Unpacking python3-tables-lib (3.7.0-2build1) ... Selecting previously unselected package python3-tables. Preparing to unpack .../238-python3-tables_3.7.0-2build1_all.deb ... Unpacking python3-tables (3.7.0-2build1) ... Selecting previously unselected package python3-xlwt. Preparing to unpack .../239-python3-xlwt_1.3.0-3_all.deb ... Unpacking python3-xlwt (1.3.0-3) ... Selecting previously unselected package libibverbs-dev:amd64. Preparing to unpack .../240-libibverbs-dev_39.0-1_amd64.deb ... Unpacking libibverbs-dev:amd64 (39.0-1) ... Selecting previously unselected package libopenmpi-dev:amd64. Preparing to unpack .../241-libopenmpi-dev_4.1.2-2ubuntu1_amd64.deb ... Unpacking libopenmpi-dev:amd64 (4.1.2-2ubuntu1) ... Selecting previously unselected package libproj-dev:amd64. Preparing to unpack .../242-libproj-dev_8.2.1-1_amd64.deb ... Unpacking libproj-dev:amd64 (8.2.1-1) ... Selecting previously unselected package proj-bin. Preparing to unpack .../243-proj-bin_8.2.1-1_amd64.deb ... Unpacking proj-bin (8.2.1-1) ... Setting up dh-python (5.20220403) ... Setting up libpipeline1:amd64 (1.5.5-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1build2) ... Setting up liblcms2-2:amd64 (2.12~rc1-2build2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libtbbmalloc2:amd64 (2021.5.0-7ubuntu2) ... Setting up libpixman-1-0:amd64 (0.40.0-1ubuntu0.22.04.1) ... Setting up python3-attr (21.2.0-1) ... Setting up libgeos3.10.2:amd64 (3.10.2-1) ... Setting up libpciaccess0:amd64 (0.16-3) ... Setting up fontconfig (2.13.1-4.2ubuntu5) ... Regenerating fonts cache... done. Setting up libjpeg-turbo8-dev:amd64 (2.1.2-0ubuntu1) ... Setting up libncurses-dev:amd64 (6.3-2ubuntu0.1) ... Setting up libboost1.74-dev:amd64 (1.74.0-14ubuntu3) ... Setting up fonts-lato (2.0-2.1) ... Setting up proj-data (8.2.1-1) ... Setting up hdf5-helpers (1.10.7+repack-4ubuntu2) ... Setting up libxrender1:amd64 (1:0.9.10-1build4) ... Setting up python3-py (1.10.0-1) ... Setting up libdatrie1:amd64 (0.2.13-2) ... Setting up python3-jdcal (1.0-1.3) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-3) ... Setting up libmagic-mgc (1:5.41-3ubuntu0.1) ... Setting up python3-lz4 (3.1.3+dfsg-1build3) ... Setting up libxcb-render0:amd64 (1.14-3ubuntu3) ... Setting up python3-defusedxml (0.7.1-1) ... Setting up python3-unicodedata2 (14.0.0+ds-8) ... Setting up fonts-lyx (2.3.6-1) ... Setting up python3-olefile (0.46-3) ... Setting up libwebpdemux2:amd64 (1.2.2-2ubuntu0.22.04.2) ... Setting up python3-ply (3.11-5) ... Setting up liblab-gamut1:amd64 (2.42.2-6) ... Setting up x11-common (1:7.7+23ubuntu2) ... debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline Setting up libmagic1:amd64 (1:5.41-3ubuntu0.1) ... Setting up python3-gast (0.5.2-2) ... Setting up libjbig-dev:amd64 (2.1-3.1ubuntu0.22.04.1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-3) ... Setting up libqhull-r8.0:amd64 (2020.2-4) ... Setting up liblzo2-2:amd64 (2.10-2build3) ... Setting up libtbb12:amd64 (2021.5.0-7ubuntu2) ... Setting up libxcb-shm0:amd64 (1.14-3ubuntu3) ... Setting up file (1:5.41-3ubuntu0.1) ... Setting up libproj22:amd64 (8.2.1-1) ... Setting up libcurl4-gnutls-dev:amd64 (7.81.0-1ubuntu1.16) ... Setting up libffi-dev:amd64 (3.4.2-4) ... Setting up python3-markupsafe (2.0.1-2build1) ... Setting up python3-webencodings (0.5.1-4) ... Setting up libcairo2:amd64 (1.16.0-5ubuntu2) ... Setting up libaec0:amd64 (1.0.6-1) ... Setting up python3-tz (2022.1-1ubuntu0.22.04.1) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up libsnappy1v5:amd64 (1.1.8-1build3) ... Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... Setting up unicode-data (14.0.0-1.1) ... Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-5) ... Setting up python3-beniget (0.4.1-2) ... Setting up libxsimd-dev:amd64 (7.6.0-2) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up autotools-dev (20220109.1) ... Setting up python3-pygments (2.11.2+dfsg-2) ... Setting up libz3-4:amd64 (4.8.12-1) ... Setting up libblas3:amd64 (3.10.0-2ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up python3-packaging (21.3-1) ... Setting up libgmpxx4ldbl:amd64 (2:6.2.1+dfsg-3ubuntu1) ... Setting up libpfm4:amd64 (4.11.1+git32-gd0b85fb-1ubuntu0.1) ... Setting up python3-chardet (4.0.0-1) ... Setting up libllvm11:amd64 (1:11.1.0-6) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up libsqlite3-dev:amd64 (3.37.2-2ubuntu0.3) ... Setting up libpathplan4:amd64 (2.42.2-6) ... Setting up python3-brotli (1.0.9-2build6) ... Setting up libann0 (1.1.2+doc-7build1) ... Setting up liblzf1:amd64 (3.6-3) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu3) ... Setting up python3-cycler (0.11.0-1) ... Setting up python-odf-doc (1.4.2-1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libssl-dev:amd64 (3.0.2-0ubuntu1.15) ... Setting up python3-kiwisolver (1.3.2-1build1) ... Setting up libhwloc15:amd64 (2.7.0-2ubuntu1) ... Setting up python3-xlwt (1.3.0-3) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-1build3) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-1build3) ... Setting up cython3 (0.29.28-1ubuntu3) ... Setting up libtcl8.6:amd64 (8.6.12+dfsg-1build1) ... Setting up binfmt-support (2.2.1-2) ... update-binfmts: warning: python3.10 already enabled in kernel. Created symlink /etc/systemd/system/multi-user.target.wants/binfmt-support.service → /lib/systemd/system/binfmt-support.service. Setting up icu-devtools (70.1-2) ... Setting up libgeos-c1v5:amd64 (3.10.2-1) ... Setting up python3-html5lib (1.1-3) ... Setting up libltdl7:amd64 (2.4.6-15build2) ... Setting up python3-toml (0.10.2-1) ... Setting up libgfortran5:amd64 (12.3.0-1ubuntu1~22.04) ... Setting up python3-pluggy (0.13.0-7.1) ... Setting up llvm-11-linker-tools (1:11.1.0-6) ... Setting up liblzma-dev:amd64 (5.2.5-2ubuntu1) ... Setting up libnuma1:amd64 (2.0.14-3ubuntu2) ... Setting up ocl-icd-libopencl1:amd64 (2.2.14-3) ... Setting up libxslt1.1:amd64 (1.1.34-4ubuntu0.22.04.1) ... Setting up libblosc1:amd64 (1.21.1+ds2-2) ... Setting up fonts-liberation (1:1.07.4-11) ... Setting up libnl-3-200:amd64 (3.5.0-0.1) ... Setting up python3-et-xmlfile (1.0.1-2.1) ... Setting up libpsm2-2 (11.2.185-1) ... Setting up openmpi-common (4.1.2-2ubuntu1) ... Setting up libopenjp2-7:amd64 (2.4.0-6) ... Setting up libharfbuzz0b:amd64 (2.7.4-1ubuntu3.1) ... Setting up libthai-data (0.1.29-1build1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libcdt5:amd64 (2.42.2-6) ... Setting up libcgraph6:amd64 (2.42.2-6) ... Setting up libboost-dev:amd64 (1.74.0.3ubuntu7) ... Setting up libxss1:amd64 (1:1.2.3-1build2) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjpeg8-dev:amd64 (8c-2ubuntu10) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python-matplotlib-data (3.5.1-2build1) ... Setting up libwebpmux3:amd64 (1.2.2-2ubuntu0.22.04.2) ... Setting up libdeflate-dev:amd64 (1.10-2) ... Setting up python3-appdirs (1.4.4-2) ... Setting up mailcap (3.70+nmu1ubuntu1) ... Setting up libicu-dev:amd64 (70.1-2) ... Setting up python3-soupsieve (2.3.1-1) ... Setting up python-tables-data (3.7.0-2build1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.0.0+dfsg-1) ... Setting up libonig5:amd64 (6.9.7.1-2build1) ... Setting up libsz2:amd64 (1.0.6-1) ... Setting up libtiffxx5:amd64 (4.3.0-6ubuntu0.9) ... Setting up python3-odf (1.4.2-1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1build3) ... Setting up python3-sympy (1.9-1) ... Setting up libtinfo-dev:amd64 (6.3-2ubuntu0.1) ... Setting up libgts-bin (0.7.6+darcs121130-5) ... Setting up libz3-dev:amd64 (4.8.12-1) ... Setting up libice6:amd64 (2:1.0.10-1build2) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-1build3) ... Setting up liblapack3:amd64 (3.10.0-2ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxft2:amd64 (2.3.4-1) ... Setting up llvm-11-runtime (1:11.1.0-6) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up libopenblas0-pthread:amd64 (0.3.20+ds-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libgmp-dev:amd64 (2:6.2.1+dfsg-3ubuntu1) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15build2) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libjq1:amd64 (1.6-2.1ubuntu3) ... Setting up llvm-11-tools (1:11.1.0-6) ... Setting up libgfortran-11-dev:amd64 (11.4.0-1ubuntu1~22.04) ... Setting up python3-pytest (6.2.5-1ubuntu2) ... Setting up libtk8.6:amd64 (8.6.12-1build1) ... Setting up libaec-dev:amd64 (1.0.6-1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu10) ... Setting up python-odf-tools (1.4.2-1) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-1build3) ... Setting up proj-bin (8.2.1-1) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up llvm-11 (1:11.1.0-6) ... Setting up libhwloc-plugins:amd64 (2.7.0-2ubuntu1) ... Setting up python3-bs4 (4.10.0-2) ... Setting up libnuma-dev:amd64 (2.0.14-3ubuntu2) ... Setting up libnl-route-3-200:amd64 (3.5.0-0.1) ... Setting up python3-fs (2.4.12-1) ... Setting up libclang-cpp11 (1:11.1.0-6) ... Setting up libthai0:amd64 (0.1.29-1build1) ... Setting up python3-llvmlite (0.38.0-1) ... Setting up python3-jinja2 (3.0.3-1ubuntu0.2) ... Setting up libxml2-dev:amd64 (2.9.13+dfsg-1ubuntu0.4) ... Setting up libtiff-dev:amd64 (4.3.0-6ubuntu0.9) ... Setting up libgeos-dev (3.10.2-1) ... Setting up libraqm0:amd64 (0.7.0-4ubuntu1) ... Setting up libevent-dev (2.1.12-stable-1build3) ... Setting up libproj-dev:amd64 (8.2.1-1) ... Setting up python3-numpy (1:1.21.5-1ubuntu22.04.1) ... Setting up gfortran-11 (11.4.0-1ubuntu1~22.04) ... Setting up autoconf (2.71-2) ... Setting up libgvpr2:amd64 (2.42.2-6) ... Setting up libhdf5-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libnl-3-dev:amd64 (3.5.0-0.1) ... Setting up libopenblas0:amd64 (0.3.20+ds-1) ... Setting up python3-lxml:amd64 (4.8.0-1build1) ... Setting up jq (1.6-2.1ubuntu3) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up numba-doc (0.55.1-0ubuntu2) ... Setting up libsm6:amd64 (2:1.2.3-1build2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-10) ... Setting up libhdf5-hl-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libopenblas-pthread-dev:amd64 (0.3.20+ds-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libibverbs1:amd64 (39.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Setting up llvm-11-dev (1:11.1.0-6) ... Setting up libpmix2:amd64 (4.1.2-2ubuntu1) ... Setting up ibverbs-providers:amd64 (39.0-1) ... Setting up python3-tables-lib (3.7.0-2build1) ... Setting up blt (2.5.3+dfsg-4.1build2) ... Setting up python3-pandas-lib:amd64 (1.3.5+dfsg-3) ... Setting up libpango-1.0-0:amd64 (1.50.6+ds-2ubuntu1) ... Setting up python3-h5py-serial (3.6.0-2build1) ... Setting up python3-tk:amd64 (3.10.8-1~22.04) ... Setting up gfortran (4:11.2.0-1ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libnl-route-3-dev:amd64 (3.5.0-0.1) ... Setting up libltdl-dev:amd64 (2.4.6-15build2) ... Setting up python3-pil:amd64 (9.0.1-1ubuntu0.3) ... Setting up libopenblas-dev:amd64 (0.3.20+ds-1) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up python3-pandas (1.3.5+dfsg-3) ... Setting up python3-pil.imagetk:amd64 (9.0.1-1ubuntu0.3) ... Setting up python3-openpyxl (3.0.9-1) ... Setting up python3-h5py (3.6.0-2build1) ... Setting up python3-bottleneck (1.3.2+ds1-2build1) ... Setting up libhdf5-fortran-102:amd64 (1.10.7+repack-4ubuntu2) ... Setting up python3-numexpr (2.8.1-1build1) ... Setting up libxt6:amd64 (1:1.2.1-1) ... Setting up python3-pythran (0.10.0+ds2-1) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhwloc-dev:amd64 (2.7.0-2ubuntu1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.6+ds-2ubuntu1) ... Setting up libpmix-dev:amd64 (4.1.2-2ubuntu1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.6+ds-2ubuntu1) ... Setting up librdmacm1:amd64 (39.0-1) ... Setting up libucx0:amd64 (1.12.1~rc2-1) ... Setting up libxmu6:amd64 (2:1.1.3-3) ... Setting up python3-scipy (1.8.0-1exp2ubuntu1) ... Setting up libcoarrays-dev:amd64 (2.9.2-3) ... Setting up libxaw7:amd64 (2:1.0.14-1) ... Setting up python3-tables (3.7.0-2build1) ... Setting up libibverbs-dev:amd64 (39.0-1) ... Setting up python3-numba (0.55.1-0ubuntu2) ... update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode Setting up libhdf5-dev (1.10.7+repack-4ubuntu2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libgvc6 (2.42.2-6) ... Setting up graphviz (2.42.2-6) ... Setting up libfabric1:amd64 (1.11.0-3) ... Setting up python3-pydot (1.4.2-1build1) ... Setting up libopenmpi3:amd64 (4.1.2-2ubuntu1) ... Setting up libcaf-openmpi-3:amd64 (2.9.2-3) ... Setting up openmpi-bin (4.1.2-2ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.14) ... Setting up python3-mpi4py (3.1.3-1build2) ... Setting up libcoarrays-openmpi-dev:amd64 (2.9.2-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/open-coarrays/openmpi/bin/caf to provide /usr/bin/caf.openmpi (caf-openmpi) in auto mode update-alternatives: using /usr/bin/caf.openmpi to provide /usr/bin/caf (caf) in auto mode Setting up libopenmpi-dev:amd64 (4.1.2-2ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up python3-fonttools (4.29.1-2build1) ... Setting up python3-ufolib2 (0.13.1+dfsg1-1) ... Setting up python3-matplotlib (3.5.1-2build1) ... Setting up nest (3.7-2ubuntu1ppa1-1641~202404150721~ubuntu22.04.1) ... Processing triggers for libc-bin (2.35-0ubuntu3.8) ... + sudo apt install -y python3-pip python3-tk libigraph-dev python3-graph-tool python3-cairo python3-cairocffi WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Reading package lists... Building dependency tree... Reading state information... python3-tk is already the newest version (3.10.8-1~22.04). python3-tk set to manually installed. python3-pip is already the newest version (22.0.2+dfsg-1ubuntu0.4). The following additional packages will be installed: adwaita-icon-theme at-spi2-core dbus-user-session dconf-gsettings-backend dconf-service gir1.2-atk-1.0 gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 gir1.2-gtk-3.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme libamd2 libarpack2 libatk-bridge2.0-0 libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libboost-context1.74.0 libboost-iostreams1.74.0 libboost-python1.74.0 libboost-regex1.74.0 libcairo-gobject2 libcairomm-1.0-1v5 libcolamd2 libcolord2 libcups2 libcxsparse3 libdconf1 libepoxy0 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-bin libgdk-pixbuf2.0-common libglpk40 libgtk-3-0 libgtk-3-bin libgtk-3-common libigraph2 libpangoxft-1.0-0 libplfit0 librsvg2-2 librsvg2-common libsigc++-2.0-0v5 libsuitesparseconfig5 libwayland-client0 libwayland-cursor0 libwayland-egl1 libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 libxkbcommon0 libxrandr2 libxtst6 python3-cffi python3-pycparser python3-xcffib session-migration ubuntu-mono Suggested packages: colord cups-common libiodbc2-dev default-libmysqlclient-dev gvfs libigraph-doc pkg-config plfit plfit-doc librsvg2-bin python-cairocffi-doc Recommended packages: libgv-python python-matplotlib python-cairo python-gi-cairo python-gi The following NEW packages will be installed: adwaita-icon-theme at-spi2-core dbus-user-session dconf-gsettings-backend dconf-service gir1.2-atk-1.0 gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 gir1.2-gtk-3.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme libamd2 libarpack2 libatk-bridge2.0-0 libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libboost-context1.74.0 libboost-iostreams1.74.0 libboost-python1.74.0 libboost-regex1.74.0 libcairo-gobject2 libcairomm-1.0-1v5 libcolamd2 libcolord2 libcups2 libcxsparse3 libdconf1 libepoxy0 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-bin libgdk-pixbuf2.0-common libglpk40 libgtk-3-0 libgtk-3-bin libgtk-3-common libigraph-dev libigraph2 libpangoxft-1.0-0 libplfit0 librsvg2-2 librsvg2-common libsigc++-2.0-0v5 libsuitesparseconfig5 libwayland-client0 libwayland-cursor0 libwayland-egl1 libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1 libxkbcommon0 libxrandr2 libxtst6 python3-cairo python3-cairocffi python3-cffi python3-graph-tool python3-pycparser python3-xcffib session-migration ubuntu-mono 0 upgraded, 71 newly installed, 0 to remove and 3 not upgraded. Need to get 67.4 MB of archives. After this operation, 423 MB of additional disk space will be used. Get:1 https://downloads.skewed.de/apt jammy/main amd64 python3-graph-tool amd64 2.70 [50.9 MB] Get:2 http://archive.ubuntu.com/ubuntu jammy/main amd64 hicolor-icon-theme all 0.17-2 [9976 B] Get:3 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libgdk-pixbuf2.0-common all 2.42.8+dfsg-1ubuntu0.3 [5630 B] Get:4 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.8+dfsg-1ubuntu0.3 [148 kB] Get:5 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 gtk-update-icon-cache amd64 3.24.33-1ubuntu2.1 [31.3 kB] Get:6 http://archive.ubuntu.com/ubuntu jammy/main amd64 humanity-icon-theme all 0.6.16 [1282 kB] Get:7 http://archive.ubuntu.com/ubuntu jammy/main amd64 ubuntu-mono all 20.10-0ubuntu2 [153 kB] Get:8 http://archive.ubuntu.com/ubuntu jammy/main amd64 adwaita-icon-theme all 41.0-1ubuntu1 [3444 kB] Get:9 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxi6 amd64 2:1.8-1build1 [32.6 kB] Get:10 http://archive.ubuntu.com/ubuntu jammy/main amd64 libatspi2.0-0 amd64 2.44.0-3 [80.9 kB] Get:11 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxtst6 amd64 2:1.2.3-1build4 [13.4 kB] Get:12 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 dbus-user-session amd64 1.12.20-2ubuntu4.1 [9442 B] Get:13 http://archive.ubuntu.com/ubuntu jammy/main amd64 libdconf1 amd64 0.40.0-3 [40.5 kB] Get:14 http://archive.ubuntu.com/ubuntu jammy/main amd64 dconf-service amd64 0.40.0-3 [28.5 kB] Get:15 http://archive.ubuntu.com/ubuntu jammy/main amd64 dconf-gsettings-backend amd64 0.40.0-3 [22.8 kB] Get:16 http://archive.ubuntu.com/ubuntu jammy/main amd64 session-migration amd64 0.3.6 [9774 B] Get:17 http://archive.ubuntu.com/ubuntu jammy/main amd64 gsettings-desktop-schemas all 42.0-1ubuntu1 [31.1 kB] Get:18 http://archive.ubuntu.com/ubuntu jammy/main amd64 at-spi2-core amd64 2.44.0-3 [54.4 kB] Get:19 http://archive.ubuntu.com/ubuntu jammy/main amd64 libatk1.0-data all 2.36.0-3build1 [2824 B] Get:20 http://archive.ubuntu.com/ubuntu jammy/main amd64 libatk1.0-0 amd64 2.36.0-3build1 [51.9 kB] Get:21 http://archive.ubuntu.com/ubuntu jammy/main amd64 gir1.2-atk-1.0 amd64 2.36.0-3build1 [21.0 kB] Get:22 http://archive.ubuntu.com/ubuntu jammy/main amd64 gir1.2-freedesktop amd64 1.72.0-1 [22.3 kB] Get:23 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 gir1.2-gdkpixbuf-2.0 amd64 2.42.8+dfsg-1ubuntu0.3 [9486 B] Get:24 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 gir1.2-harfbuzz-0.0 amd64 2.7.4-1ubuntu3.1 [31.6 kB] Get:25 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libpangoxft-1.0-0 amd64 1.50.6+ds-2ubuntu1 [31.0 kB] Get:26 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 gir1.2-pango-1.0 amd64 1.50.6+ds-2ubuntu1 [44.0 kB] Get:27 http://archive.ubuntu.com/ubuntu jammy/main amd64 libatk-bridge2.0-0 amd64 2.38.0-3 [66.6 kB] Get:28 http://archive.ubuntu.com/ubuntu jammy/main amd64 libcairo-gobject2 amd64 1.16.0-5ubuntu2 [19.4 kB] Get:29 http://archive.ubuntu.com/ubuntu jammy/main amd64 libcolord2 amd64 1.4.6-1 [155 kB] Get:30 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libavahi-common-data amd64 0.8-5ubuntu5.2 [23.8 kB] Get:31 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libavahi-common3 amd64 0.8-5ubuntu5.2 [23.9 kB] Get:32 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libavahi-client3 amd64 0.8-5ubuntu5.2 [28.0 kB] Get:33 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libcups2 amd64 2.4.1op1-1ubuntu4.8 [264 kB] Get:34 http://archive.ubuntu.com/ubuntu jammy/main amd64 libepoxy0 amd64 1.5.10-1 [237 kB] Get:35 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libwayland-client0 amd64 1.20.0-1ubuntu0.1 [25.9 kB] Get:36 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libwayland-cursor0 amd64 1.20.0-1ubuntu0.1 [10.7 kB] Get:37 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libwayland-egl1 amd64 1.20.0-1ubuntu0.1 [5582 B] Get:38 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcomposite1 amd64 1:0.4.5-1build2 [7192 B] Get:39 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxfixes3 amd64 1:6.0.0-1 [11.7 kB] Get:40 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcursor1 amd64 1:1.2.0-2build4 [20.9 kB] Get:41 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxdamage1 amd64 1:1.1.5-2build2 [7154 B] Get:42 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxinerama1 amd64 2:1.1.4-3 [7382 B] Get:43 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxkbcommon0 amd64 1.4.0-1 [125 kB] Get:44 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxrandr2 amd64 2:1.5.2-1build1 [20.4 kB] Get:45 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libgtk-3-common all 3.24.33-1ubuntu2.1 [239 kB] Get:46 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libgtk-3-0 amd64 3.24.33-1ubuntu2.1 [3053 kB] Get:47 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 gir1.2-gtk-3.0 amd64 3.24.33-1ubuntu2.1 [240 kB] Get:48 http://archive.ubuntu.com/ubuntu jammy/main amd64 libsuitesparseconfig5 amd64 1:5.10.1+dfsg-4build1 [10.4 kB] Get:49 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libamd2 amd64 1:5.10.1+dfsg-4build1 [21.6 kB] Get:50 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libarpack2 amd64 3.8.0-1 [92.4 kB] Get:51 http://archive.ubuntu.com/ubuntu jammy/main amd64 libboost-context1.74.0 amd64 1.74.0-14ubuntu3 [223 kB] Get:52 http://archive.ubuntu.com/ubuntu jammy/main amd64 libboost-iostreams1.74.0 amd64 1.74.0-14ubuntu3 [245 kB] Get:53 http://archive.ubuntu.com/ubuntu jammy/main amd64 libboost-python1.74.0 amd64 1.74.0-14ubuntu3 [299 kB] Get:54 http://archive.ubuntu.com/ubuntu jammy/main amd64 libboost-regex1.74.0 amd64 1.74.0-14ubuntu3 [511 kB] Get:55 http://archive.ubuntu.com/ubuntu jammy/main amd64 libsigc++-2.0-0v5 amd64 2.10.4-2ubuntu3 [12.1 kB] Get:56 http://archive.ubuntu.com/ubuntu jammy/main amd64 libcairomm-1.0-1v5 amd64 1.12.2-4build3 [45.1 kB] Get:57 http://archive.ubuntu.com/ubuntu jammy/main amd64 libcolamd2 amd64 1:5.10.1+dfsg-4build1 [18.0 kB] Get:58 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libcxsparse3 amd64 1:5.10.1+dfsg-4build1 [70.8 kB] Get:59 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libgdk-pixbuf2.0-bin amd64 2.42.8+dfsg-1ubuntu0.3 [14.2 kB] Get:60 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libglpk40 amd64 5.0-1 [361 kB] Get:61 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libgtk-3-bin amd64 3.24.33-1ubuntu2.1 [69.6 kB] Get:62 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libplfit0 amd64 0.9.3+ds-1ubuntu1 [28.7 kB] Get:63 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libigraph2 amd64 0.9.6+ds-2ubuntu1 [823 kB] Get:64 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libigraph-dev amd64 0.9.6+ds-2ubuntu1 [69.4 kB] Get:65 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 librsvg2-2 amd64 2.52.5+dfsg-3ubuntu0.2 [2974 kB] Get:66 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 librsvg2-common amd64 2.52.5+dfsg-3ubuntu0.2 [17.7 kB] Get:67 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-cairo amd64 1.20.1-3build1 [73.7 kB] Get:68 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-pycparser all 2.21-1 [76.9 kB] Get:69 http://archive.ubuntu.com/ubuntu jammy/main amd64 python3-cffi all 1.15.0-1build2 [72.6 kB] Get:70 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-xcffib all 0.11.1-2 [63.3 kB] Get:71 http://archive.ubuntu.com/ubuntu jammy/universe amd64 python3-cairocffi all 1.2.0-2 [70.3 kB] debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 67.4 MB in 2s (43.9 MB/s) Selecting previously unselected package hicolor-icon-theme. 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Preparing to unpack .../70-python3-graph-tool_2.70_amd64.deb ... Unpacking python3-graph-tool (2.70) ... Setting up session-migration (0.3.6) ... Created symlink /etc/systemd/user/graphical-session-pre.target.wants/session-migration.service → /usr/lib/systemd/user/session-migration.service. Setting up gir1.2-freedesktop:amd64 (1.72.0-1) ... Setting up libxdamage1:amd64 (1:1.1.5-2build2) ... Setting up python3-cairo:amd64 (1.20.1-3build1) ... Setting up libpangoxft-1.0-0:amd64 (1.50.6+ds-2ubuntu1) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libxi6:amd64 (2:1.8-1build1) ... Setting up libboost-iostreams1.74.0:amd64 (1.74.0-14ubuntu3) ... Setting up libxtst6:amd64 (2:1.2.3-1build4) ... Setting up libgdk-pixbuf2.0-common (2.42.8+dfsg-1ubuntu0.3) ... Setting up libarpack2:amd64 (3.8.0-1) ... Setting up libatspi2.0-0:amd64 (2.44.0-3) ... Setting up gir1.2-harfbuzz-0.0:amd64 (2.7.4-1ubuntu3.1) ... Setting up libcolord2:amd64 (1.4.6-1) ... 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Setting up libwayland-egl1:amd64 (1.20.0-1ubuntu0.1) ... Setting up libboost-python1.74.0 (1.74.0-14ubuntu3) ... Setting up libxcomposite1:amd64 (1:0.4.5-1build2) ... Setting up libsuitesparseconfig5:amd64 (1:5.10.1+dfsg-4build1) ... Setting up libxkbcommon0:amd64 (1.4.0-1) ... Setting up libwayland-client0:amd64 (1.20.0-1ubuntu0.1) ... Setting up libamd2:amd64 (1:5.10.1+dfsg-4build1) ... Setting up gtk-update-icon-cache (3.24.33-1ubuntu2.1) ... Setting up libcolamd2:amd64 (1:5.10.1+dfsg-4build1) ... Setting up gir1.2-gdkpixbuf-2.0:amd64 (2.42.8+dfsg-1ubuntu0.3) ... Setting up gir1.2-atk-1.0:amd64 (2.36.0-3build1) ... Setting up libxcursor1:amd64 (1:1.2.0-2build4) ... Setting up python3-cffi (1.15.0-1build2) ... Setting up libavahi-common3:amd64 (0.8-5ubuntu5.2) ... Setting up dconf-service (0.40.0-3) ... Setting up librsvg2-2:amd64 (2.52.5+dfsg-3ubuntu0.2) ... Setting up libcairomm-1.0-1v5:amd64 (1.12.2-4build3) ... Setting up libatk-bridge2.0-0:amd64 (2.38.0-3) ... Setting up libglpk40:amd64 (5.0-1) ... Setting up libigraph2:amd64 (0.9.6+ds-2ubuntu1) ... Setting up librsvg2-common:amd64 (2.52.5+dfsg-3ubuntu0.2) ... Setting up python3-xcffib (0.11.1-2) ... Setting up libgdk-pixbuf2.0-bin (2.42.8+dfsg-1ubuntu0.3) ... Setting up libwayland-cursor0:amd64 (1.20.0-1ubuntu0.1) ... Setting up libavahi-client3:amd64 (0.8-5ubuntu5.2) ... Setting up libigraph-dev:amd64 (0.9.6+ds-2ubuntu1) ... Setting up python3-graph-tool (2.70) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-3) ... Setting up python3-cairocffi (1.2.0-2) ... Setting up libcups2:amd64 (2.4.1op1-1ubuntu4.8) ... Setting up libgtk-3-common (3.24.33-1ubuntu2.1) ... Setting up gsettings-desktop-schemas (42.0-1ubuntu1) ... Setting up adwaita-icon-theme (41.0-1ubuntu1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up humanity-icon-theme (0.6.16) ... Setting up ubuntu-mono (20.10-0ubuntu2) ... Processing triggers for libglib2.0-0:amd64 (2.72.4-0ubuntu2.3) ... Setting up libgtk-3-0:amd64 (3.24.33-1ubuntu2.1) ... Processing triggers for libc-bin (2.35-0ubuntu3.8) ... Setting up gir1.2-gtk-3.0:amd64 (3.24.33-1ubuntu2.1) ... Setting up libgtk-3-bin (3.24.33-1ubuntu2.1) ... Setting up at-spi2-core (2.44.0-3) ... Processing triggers for libgdk-pixbuf-2.0-0:amd64 (2.42.8+dfsg-1ubuntu0.3) ... + pip3 install --upgrade pip setuptools Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: pip in /usr/lib/python3/dist-packages (22.0.2) Collecting pip Downloading pip-24.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 77.0 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /usr/lib/python3/dist-packages (59.6.0) Collecting setuptools Downloading setuptools-70.1.0-py3-none-any.whl (882 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 882.6/882.6 KB 121.4 MB/s eta 0:00:00 Installing collected packages: setuptools, pip WARNING: The scripts pip, pip3 and pip3.10 are installed in '/home/build/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed pip-24.1 setuptools-70.1.0 + pip install --upgrade 'numpy<2' scipy cython mpi4py Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: numpy<2 in /usr/lib/python3/dist-packages (1.21.5) Collecting numpy<2 Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 15.3 MB/s eta 0:00:00 Requirement already satisfied: scipy in /usr/lib/python3/dist-packages (1.8.0) Collecting scipy Downloading scipy-1.13.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 20.7 MB/s eta 0:00:00 Requirement already satisfied: cython in /usr/lib/python3/dist-packages (0.29.28) Collecting cython Downloading Cython-3.0.10-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.2 kB) Requirement already satisfied: mpi4py in /usr/lib/python3/dist-packages (3.1.3) Collecting mpi4py Downloading mpi4py-3.1.6.tar.gz (2.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 129.1 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 106.4 MB/s eta 0:00:00 Downloading scipy-1.13.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.6/38.6 MB 93.2 MB/s eta 0:00:00 Downloading Cython-3.0.10-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 141.2 MB/s eta 0:00:00 Building wheels for collected packages: mpi4py Building wheel for mpi4py (pyproject.toml): started Building wheel for mpi4py (pyproject.toml): finished with status 'done' Created wheel for mpi4py: filename=mpi4py-3.1.6-cp310-cp310-linux_x86_64.whl size=2746315 sha256=6da8824e272fe934a55874ef09268f02378995cb1624cac8ab8525e7daecdbb3 Stored in directory: /home/build/.cache/pip/wheels/4c/ca/89/8fc1fb1c620afca13bb41c630b1f948bbf446e0aaa4b762e10 Successfully built mpi4py Installing collected packages: numpy, mpi4py, cython, scipy WARNING: The script f2py is installed in '/home/build/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. WARNING: The scripts cygdb, cython and cythonize are installed in '/home/build/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed cython-3.0.10 mpi4py-3.1.6 numpy-1.26.4 scipy-1.13.1 + pip install --upgrade 'networkx>=2.4' python-igraph Defaulting to user installation because normal site-packages is not writeable Collecting networkx>=2.4 Downloading networkx-3.3-py3-none-any.whl.metadata (5.1 kB) Collecting python-igraph Downloading python_igraph-0.11.5-py3-none-any.whl.metadata (2.8 kB) Collecting igraph==0.11.5 (from python-igraph) Downloading igraph-0.11.5-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB) Collecting texttable>=1.6.2 (from igraph==0.11.5->python-igraph) Downloading texttable-1.7.0-py2.py3-none-any.whl.metadata (9.8 kB) Downloading networkx-3.3-py3-none-any.whl (1.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 111.6 MB/s eta 0:00:00 Downloading python_igraph-0.11.5-py3-none-any.whl (9.1 kB) Downloading igraph-0.11.5-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 154.1 MB/s eta 0:00:00 Downloading texttable-1.7.0-py2.py3-none-any.whl (10 kB) Installing collected packages: texttable, networkx, igraph, python-igraph WARNING: The script igraph is installed in '/home/build/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed igraph-0.11.5 networkx-3.3 python-igraph-0.11.5 texttable-1.7.0 + pip install --upgrade 'matplotlib<3.7' seaborn shapely svg.path dxfgrabber cartopy geopandas descartes lxml Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: matplotlib<3.7 in /usr/lib/python3/dist-packages (3.5.1) Collecting matplotlib<3.7 Downloading matplotlib-3.6.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.8 kB) Collecting seaborn Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting shapely Downloading shapely-2.0.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.0 kB) Collecting svg.path Downloading svg.path-6.3-py2.py3-none-any.whl.metadata (13 kB) Collecting dxfgrabber Downloading dxfgrabber-1.0.1-py2.py3-none-any.whl.metadata (7.5 kB) Collecting cartopy Downloading Cartopy-0.23.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.0 kB) Collecting geopandas Downloading geopandas-0.14.4-py3-none-any.whl.metadata (1.5 kB) Collecting descartes Downloading descartes-1.1.0-py3-none-any.whl.metadata (2.4 kB) Requirement already satisfied: lxml in /usr/lib/python3/dist-packages (4.8.0) Collecting lxml Downloading lxml-5.2.2-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (3.4 kB) Collecting contourpy>=1.0.1 (from matplotlib<3.7) Downloading contourpy-1.2.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Requirement already satisfied: cycler>=0.10 in /usr/lib/python3/dist-packages (from matplotlib<3.7) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in /usr/lib/python3/dist-packages (from matplotlib<3.7) (4.29.1) Requirement already satisfied: kiwisolver>=1.0.1 in /usr/lib/python3/dist-packages (from matplotlib<3.7) (1.3.2) Requirement already satisfied: numpy>=1.19 in ./.local/lib/python3.10/site-packages (from matplotlib<3.7) (1.26.4) Requirement already satisfied: packaging>=20.0 in 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0:00:00 Collecting pandas>=1.2 (from seaborn) Downloading pandas-2.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB) Requirement already satisfied: attrs>=19.2.0 in /usr/lib/python3/dist-packages (from fiona>=1.8.21->geopandas) (21.2.0) Collecting certifi (from fiona>=1.8.21->geopandas) Downloading certifi-2024.6.2-py3-none-any.whl.metadata (2.2 kB) Collecting click~=8.0 (from fiona>=1.8.21->geopandas) Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting click-plugins>=1.0 (from fiona>=1.8.21->geopandas) Downloading click_plugins-1.1.1-py2.py3-none-any.whl.metadata (6.4 kB) Collecting cligj>=0.5 (from fiona>=1.8.21->geopandas) Downloading cligj-0.7.2-py3-none-any.whl.metadata (5.0 kB) Requirement already satisfied: six in /usr/lib/python3/dist-packages (from fiona>=1.8.21->geopandas) (1.16.0) Collecting python-dateutil>=2.7 (from matplotlib<3.7) Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Requirement already satisfied: pytz>=2020.1 in /usr/lib/python3/dist-packages (from pandas>=1.2->seaborn) (2022.1) Collecting tzdata>=2022.7 (from pandas>=1.2->seaborn) Downloading tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB) Downloading matplotlib-3.6.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.8/11.8 MB 169.3 MB/s eta 0:00:00 Downloading seaborn-0.13.2-py3-none-any.whl (294 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 108.9 MB/s eta 0:00:00 Downloading shapely-2.0.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 151.1 MB/s eta 0:00:00 Downloading svg.path-6.3-py2.py3-none-any.whl (16 kB) Downloading dxfgrabber-1.0.1-py2.py3-none-any.whl (34 kB) Downloading Cartopy-0.23.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 173.9 MB/s eta 0:00:00 Downloading 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pyshp-2.3.1-py2.py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.5/46.5 kB 26.4 MB/s eta 0:00:00 Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 229.9/229.9 kB 85.9 MB/s eta 0:00:00 Downloading click-8.1.7-py3-none-any.whl (97 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 51.2 MB/s eta 0:00:00 Downloading click_plugins-1.1.1-py2.py3-none-any.whl (7.5 kB) Downloading cligj-0.7.2-py3-none-any.whl (7.1 kB) Downloading tzdata-2024.1-py2.py3-none-any.whl (345 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 345.4/345.4 kB 111.9 MB/s eta 0:00:00 Downloading certifi-2024.6.2-py3-none-any.whl (164 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 164.4/164.4 kB 73.2 MB/s eta 0:00:00 Installing collected packages: dxfgrabber, tzdata, svg.path, shapely, python-dateutil, pyshp, lxml, contourpy, click, certifi, pyproj, pandas, matplotlib, cligj, click-plugins, seaborn, fiona, descartes, cartopy, geopandas WARNING: The script pyproj is installed in '/home/build/.local/bin' which is not on PATH. 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Successfully installed cartopy-0.23.0 certifi-2024.6.2 click-8.1.7 click-plugins-1.1.1 cligj-0.7.2 contourpy-1.2.1 descartes-1.1.0 dxfgrabber-1.0.1 fiona-1.9.6 geopandas-0.14.4 lxml-5.2.2 matplotlib-3.6.3 pandas-2.2.2 pyproj-3.6.1 pyshp-2.3.1 python-dateutil-2.9.0.post0 seaborn-0.13.2 shapely-2.0.4 svg.path-6.3 tzdata-2024.1 + pip install --upgrade pytest pytest-mpi cov-core coverage 'coveralls[yaml]' Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: pytest in /usr/lib/python3/dist-packages (6.2.5) Collecting pytest Downloading pytest-8.2.2-py3-none-any.whl.metadata (7.6 kB) Collecting pytest-mpi Downloading pytest_mpi-0.6-py2.py3-none-any.whl.metadata (1.7 kB) Collecting cov-core Downloading cov-core-1.15.0.tar.gz (5.9 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting coverage Downloading coverage-7.5.3-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB) Collecting coveralls[yaml] Downloading coveralls-4.0.1-py3-none-any.whl.metadata (5.3 kB) Requirement already satisfied: iniconfig in /usr/lib/python3/dist-packages (from pytest) (1.1.1) Requirement already satisfied: packaging in /usr/lib/python3/dist-packages (from pytest) (21.3) Collecting pluggy<2.0,>=1.5 (from pytest) Downloading pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB) Collecting exceptiongroup>=1.0.0rc8 (from pytest) Downloading exceptiongroup-1.2.1-py3-none-any.whl.metadata (6.6 kB) Collecting tomli>=1 (from pytest) Downloading tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB) Collecting docopt<0.7.0,>=0.6.1 (from coveralls[yaml]) Downloading docopt-0.6.2.tar.gz (25 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting requests<3.0.0,>=1.0.0 (from coveralls[yaml]) Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) Requirement already satisfied: pyyaml<7.0,>=3.10 in /usr/lib/python3/dist-packages (from coveralls[yaml]) (5.4.1) Collecting charset-normalizer<4,>=2 (from requests<3.0.0,>=1.0.0->coveralls[yaml]) Downloading charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests<3.0.0,>=1.0.0->coveralls[yaml]) Downloading idna-3.7-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<3,>=1.21.1 (from requests<3.0.0,>=1.0.0->coveralls[yaml]) Downloading urllib3-2.2.2-py3-none-any.whl.metadata (6.4 kB) Requirement already satisfied: certifi>=2017.4.17 in ./.local/lib/python3.10/site-packages (from requests<3.0.0,>=1.0.0->coveralls[yaml]) (2024.6.2) Downloading pytest-8.2.2-py3-none-any.whl (339 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 339.9/339.9 kB 53.4 MB/s eta 0:00:00 Downloading pytest_mpi-0.6-py2.py3-none-any.whl (5.9 kB) Downloading coverage-7.5.3-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (231 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 231.6/231.6 kB 90.6 MB/s eta 0:00:00 Downloading exceptiongroup-1.2.1-py3-none-any.whl (16 kB) Downloading pluggy-1.5.0-py3-none-any.whl (20 kB) Downloading requests-2.32.3-py3-none-any.whl (64 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.9/64.9 kB 26.7 MB/s eta 0:00:00 Downloading tomli-2.0.1-py3-none-any.whl (12 kB) Downloading coveralls-4.0.1-py3-none-any.whl (13 kB) Downloading charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.1/142.1 kB 52.8 MB/s eta 0:00:00 Downloading idna-3.7-py3-none-any.whl (66 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 27.5 MB/s eta 0:00:00 Downloading urllib3-2.2.2-py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.4/121.4 kB 46.9 MB/s eta 0:00:00 Building wheels for collected packages: cov-core, docopt Building wheel for cov-core (setup.py): started Building wheel for cov-core (setup.py): finished with status 'done' Created wheel for cov-core: filename=cov_core-1.15.0-py3-none-any.whl size=6006 sha256=bf72fffe92c3866c479287a568e6c7c412a042bb4390194e12859b08f3dcdadf Stored in directory: /home/build/.cache/pip/wheels/80/73/f2/6e7f18d4d52855e20db9463f7a23679627c90d9e0c46fb9046 Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13706 sha256=95161bb058feb4322aee20a983d7057c35e2cea19bd5e923e70f561c762f5656 Stored in directory: /home/build/.cache/pip/wheels/fc/ab/d4/5da2067ac95b36618c629a5f93f809425700506f72c9732fac Successfully built cov-core docopt Installing collected packages: docopt, urllib3, tomli, pluggy, idna, exceptiongroup, coverage, charset-normalizer, requests, pytest, cov-core, pytest-mpi, coveralls WARNING: The scripts coverage, coverage-3.10 and coverage3 are installed in '/home/build/.local/bin' which is not on PATH. 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Successfully installed charset-normalizer-3.3.2 cov-core-1.15.0 coverage-7.5.3 coveralls-4.0.1 docopt-0.6.2 exceptiongroup-1.2.1 idna-3.7 pluggy-1.5.0 pytest-8.2.2 pytest-mpi-0.6 requests-2.32.3 tomli-2.0.1 urllib3-2.2.2 + mv .coveralls.yml NNGT/.coveralls.yml + cd NNGT + pip install . Defaulting to user installation because normal site-packages is not writeable Processing /home/build/NNGT Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: cython in /home/build/.local/lib/python3.10/site-packages (from NNGT==2.7.3) (3.0.10) Collecting platformdirs (from NNGT==2.7.3) Downloading platformdirs-4.2.2-py3-none-any.whl.metadata (11 kB) Requirement already satisfied: numpy>=1.17 in /home/build/.local/lib/python3.10/site-packages (from NNGT==2.7.3) (1.26.4) Requirement already satisfied: scipy>=0.11 in /home/build/.local/lib/python3.10/site-packages (from NNGT==2.7.3) (1.13.1) Downloading platformdirs-4.2.2-py3-none-any.whl (18 kB) Building wheels for collected packages: NNGT Building wheel for NNGT (pyproject.toml): started Building wheel for NNGT (pyproject.toml): finished with status 'done' Created wheel for NNGT: filename=NNGT-2.7.3-cp310-cp310-linux_x86_64.whl size=1625695 sha256=af61335271b91d09724d5261cf0957fe7d62f83a38b26dbea8bd52d3afa8f8e0 Stored in directory: /tmp/pip-ephem-wheel-cache-3heeis2d/wheels/92/fa/40/bf3cd25b985bea2c1c5a04b1b799a3c432eded83a10407205a Successfully built NNGT Installing collected packages: platformdirs, NNGT Successfully installed NNGT-2.7.3 platformdirs-4.2.2 + echo 'export PATH=/home/build/.local/bin:$PATH' |
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+ cd NNGT + GL=all + coverage run -p -m pytest testing/library_compatibility.py ============================= test session starts ============================== platform linux -- Python 3.10.12, pytest-8.2.2, pluggy-1.5.0 rootdir: /home/build/NNGT configfile: pyproject.toml plugins: mpi-0.6 collected 11 items testing/library_compatibility.py FFFFFFFFFF. [100%] =================================== FAILURES =================================== _____________________ test_weighted_undirected_clustering ______________________ def test_weighted_undirected_clustering(): ''' Compare the onnela implementation with networkx and Barrat with igraph. ''' # import networkx and igraph import networkx as nx import igraph as ig # create a pre-defined graph num_nodes = 5 edge_list = [ (0, 3), (1, 0), (1, 2), (2, 4), (4, 1), (4, 3), (4, 0) ] weights = [0.53, 0.45, 0.8, 0.125, 0.66, 0.31, 0.78] # create nx graph and compute reference onnela clustering nx_graph = nx.Graph() nx_graph.add_nodes_from(range(num_nodes)) arr_edges = [e + (w,) for e, w in zip(edge_list, weights)] nx_graph.add_weighted_edges_from(arr_edges, weight="weight") onnela = list(nx.clustering(nx_graph, weight="weight").values()) triplets = [3, 3, 1, 1, 6] gc_onnela = np.sum(np.multiply(onnela, triplets)) / np.sum(triplets) # create ig graph and compute reference Barrat clustering ig_graph = ig.Graph(num_nodes, directed=False) ig_graph.add_edges(edge_list) ig_graph.es["weight"] = weights barrat = ig_graph.transitivity_local_undirected(mode="zero", weights="weight") strength = np.array(ig_graph.strength(weights='weight')) degree = np.array(ig_graph.degree()) triplets = strength*(degree - 1) gc_barrat = np.sum(np.multiply(barrat, triplets)) / np.sum(triplets) # check for all backends for bckd in all_backends: > nngt.set_config("backend", bckd) testing/library_compatibility.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:176: in set_config nngt.use_backend(val) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: networkx 3.3 Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: igraph 0.11. Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True ______________________________ test_assortativity ______________________________ def test_assortativity(): ''' Check assortativity result for all backends ''' # DIRECTED num_nodes = 5 edge_list = [(0, 3), (1, 0), (1, 2), (2, 4), (4, 1), (4, 3), (4, 2)] weights = [0.53, 0.45, 0.8, 0.125, 0.66, 0.31, 0.78] # expected results assort_unweighted = -0.47140452079103046 assort_weighted = -0.5457956719785911 for bckd in backends: > nngt.set_config("backend", bckd) testing/library_compatibility.py:129: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:176: in set_config nngt.use_backend(val) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: networkx 3.3 Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: igraph 0.11. Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True ________________________________ test_closeness ________________________________ def test_closeness(): ''' Check closeness results for all backends ''' num_nodes = 5 edge_list = [(0, 1), (0, 3), (1, 3), (2, 0), (3, 2), (3, 4), (4, 2)] weights = [0.54881, 0.71518, 0.60276, 0.54488, 0.42365, 0.64589, 0.43758] expected = [2/3, 0.5, 0.5, 0.5714285714285714, 0.4444444444444444] weighted = [1.06273031, 0.89905622, 0.83253895, 1.12504606, 0.86040934] for bckd in backends: > nngt.set_config("backend", bckd) testing/library_compatibility.py:177: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:176: in set_config nngt.use_backend(val) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: networkx 3.3 Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: igraph 0.11. Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True _______________________________ test_betweenness _______________________________ def test_betweenness(): ''' Check betweenness results for all backends ''' num_nodes = 5 # UNDIRECTED edge_list = [(0, 1), (0, 2), (0, 3), (1, 3), (2, 3), (2, 4), (3, 4)] weights = [0.1, 0.3, 1.5, 0.8, 5.6, 4., 2.3] nb_expect = [0.083333, 0.0, 0.083333, 0.3333333, 0.0] eb_expect = [0.15, 0.2, 0.15, 0.25, 0.15, 0.15, 0.25] nb_exp_wght = [0.5, 2/3, 0, 0.5, 0] eb_exp_wght = [0.6, 0.4, 0, 0.6, 0, 0, 0.4] for bckd in backends: > nngt.set_config("backend", bckd) testing/library_compatibility.py:278: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:176: in set_config nngt.use_backend(val) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: networkx 3.3 Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: igraph 0.11. Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True _______________________________ test_components ________________________________ def test_components(): ''' Check connected components for all backends ''' num_nodes = 8 edge_list = [(0, 1), (0, 2), (1, 2)] for i in range(3, num_nodes - 1): edge_list.append((i, i+1)) edge_list.append((7, 3)) for bckd in all_backends: > nngt.set_config("backend", bckd) testing/library_compatibility.py:336: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:176: in set_config nngt.use_backend(val) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: networkx 3.3 Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: igraph 0.11. Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True ________________________________ test_diameter _________________________________ def test_diameter(): ''' Check connected components for all backends ''' # unconnected num_nodes = 8 edge_list = [(0, 1), (0, 2), (1, 2)] for i in range(3, num_nodes - 1): edge_list.append((i, i+1)) edge_list.append((7, 3)) weights = [0.58, 0.59, 0.88, 0.8, 0.61, 0.66, 0.62, 0.28] for bckd in backends: > nngt.set_config("backend", bckd) testing/library_compatibility.py:398: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:176: in set_config nngt.use_backend(val) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: networkx 3.3 Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. INFO nngt.lib.nngt_config:nngt_config.py:386 # ----------- # # NNGT config # # ----------- # Graph library: igraph 0.11. Multithreading: True (2 threads) MPI: False Plotting: True NEST support: False Shapely: 2.0.4 SVG support: True DXF support: True Database: False Geo support: True ________________________ test_binary_shortest_distance _________________________ def test_binary_shortest_distance(): ''' Check shortest distance ''' num_nodes = 5 for bckd in backends: > nngt.use_backend(bckd) testing/library_compatibility.py:432: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. _______________________ test_weighted_shortest_distance ________________________ def test_weighted_shortest_distance(): ''' Check shortest distance ''' for bckd in backends: > nngt.use_backend(bckd) testing/library_compatibility.py:508: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. __________________________ test_binary_shortest_paths __________________________ def test_binary_shortest_paths(): ''' Test shortests paths with BFS algorithm ''' for bckd in backends: > nngt.use_backend(bckd) testing/library_compatibility.py:589: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. _________________________ test_weighted_shortest_paths _________________________ def test_weighted_shortest_paths(): ''' Test shortest paths with Dijsktra algorithm ''' for bckd in backends: > nngt.use_backend(bckd) testing/library_compatibility.py:653: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/graph_backends.py:120: in use_backend nngt.set_config(old_config, silent=True) nngt/lib/decorator.py:208: in fun return caller(func, *(extras + args), **kw) nngt/lib/test_functions.py:92: in wrapper return func(*args, **kwargs) nngt/lib/nngt_config.py:198: in set_config _post_update_parallelism(new_config, old_gl, old_msd, old_mt, old_mpi) nngt/lib/nngt_config.py:515: in _post_update_parallelism _set_gt_config(old_gl, new_config) nngt/lib/nngt_config.py:401: in _set_gt_config gt.openmp_set_num_threads(nngt._config["omp"]) /usr/local/lib/python3.10/dist-packages/graph_tool/openmp.py:38: in openmp_set_num_threads from graph_tool.inference import libinference /usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py:330: in <module> from . base_states import * /usr/local/lib/python3.10/dist-packages/graph_tool/inference/base_states.py:33: in <module> import graph_tool.draw _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ #! /usr/bin/env python # -*- coding: utf-8 -*- # # graph_tool -- a general graph manipulation python module # # Copyright (C) 2006-2024 Tiago de Paula Peixoto <tiago@skewed.de> # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 3 of the License, or (at your option) any # later version. # # This program is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. """ ``graph_tool.draw`` ------------------- This module contains functions for graph drawing and layout. Layout algorithms ================= .. autosummary:: :nosignatures: :toctree: autosummary sfdp_layout fruchterman_reingold_layout arf_layout radial_tree_layout planar_layout random_layout Graph drawing ============= .. autosummary:: :nosignatures: :toctree: autosummary graph_draw draw_hierarchy graphviz_draw prop_to_size get_hierarchy_control_points Low-level graph drawing ^^^^^^^^^^^^^^^^^^^^^^^ .. autosummary:: :nosignatures: :toctree: autosummary cairo_draw interactive_window .. autosummary:: :nosignatures: :toctree: autosummary :template: class-no-inherit.rst GraphWidget GraphWindow .. autosummary:: :nosignatures: :toctree: autosummary GraphArtist """ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \ group_vector_property, ungroup_vector_property, infect_vertex_property, \ _prop, _get_rng, VertexPropertyMap from .. topology import max_cardinality_matching, max_independent_vertex_set, \ label_components, shortest_distance, make_maximal_planar, is_planar from .. generation import predecessor_tree, condensation_graph > from .. inference import minimize_blockmodel_dl, BlockState, ModularityState E ImportError: cannot import name 'minimize_blockmodel_dl' from partially initialized module 'graph_tool.inference' (most likely due to a circular import) (/usr/local/lib/python3.10/dist-packages/graph_tool/inference/__init__.py) /usr/local/lib/python3.10/dist-packages/graph_tool/draw/__init__.py:87: ImportError ------------------------------ Captured log call ------------------------------- INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to networkx. INFO nngt.lib.graph_backends:logger.py:96 from coverage (L8) - Successfuly switched to igraph. =============================== warnings summary =============================== ../../../usr/lib/python3/dist-packages/pythran/config.py:8 /usr/lib/python3/dist-packages/pythran/config.py:8: DeprecationWarning: `numpy.distutils` is deprecated since NumPy 1.23.0, as a result of the deprecation of `distutils` itself. It will be removed for Python >= 3.12. For older Python versions it will remain present. It is recommended to use `setuptools < 60.0` for those Python versions. For more details, see: https://numpy.org/devdocs/reference/distutils_status_migration.html import numpy.distutils.system_info as numpy_sys ../.local/lib/python3.10/site-packages/setuptools/_distutils/msvccompiler.py:67 /home/build/.local/lib/python3.10/site-packages/setuptools/_distutils/msvccompiler.py:67: DeprecationWarning: msvccompiler is deprecated and slated to be removed in the future. Please discontinue use or file an issue with pypa/distutils describing your use case. warnings.warn( ../../../usr/lib/python3/dist-packages/pythran/tables.py:4520 /usr/lib/python3/dist-packages/pythran/tables.py:4520: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): ../../../usr/lib/python3/dist-packages/pythran/tables.py:4553 /usr/lib/python3/dist-packages/pythran/tables.py:4553: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) ../.local/lib/python3.10/site-packages/setuptools/sandbox.py:15 /home/build/.local/lib/python3.10/site-packages/setuptools/sandbox.py:15: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources ../.local/lib/python3.10/site-packages/pkg_resources/__init__.py:2976 /home/build/.local/lib/python3.10/site-packages/pkg_resources/__init__.py:2976: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(pkg) ../.local/lib/python3.10/site-packages/numpy/distutils/command/build_ext.py:8 /home/build/.local/lib/python3.10/site-packages/numpy/distutils/command/build_ext.py:8: DeprecationWarning: dep_util is Deprecated. Use functions from setuptools instead. from distutils.dep_util import newer_group ../.local/lib/python3.10/site-packages/numpy/distutils/command/build_clib.py:11 /home/build/.local/lib/python3.10/site-packages/numpy/distutils/command/build_clib.py:11: DeprecationWarning: dep_util is Deprecated. Use functions from setuptools instead. from distutils.dep_util import newer_group ../.local/lib/python3.10/site-packages/numpy/distutils/command/build_src.py:10 ../.local/lib/python3.10/site-packages/numpy/distutils/command/build_src.py:10 /home/build/.local/lib/python3.10/site-packages/numpy/distutils/command/build_src.py:10: DeprecationWarning: dep_util is Deprecated. Use functions from setuptools instead. from distutils.dep_util import newer_group, newer testing/library_compatibility.py::test_binary_shortest_paths /home/build/NNGT/nngt/analysis/ig_functions.py:351: RuntimeWarning: Couldn't reach some vertices at src/paths/unweighted.c:444 path = graph.get_shortest_paths(source, target, mode="out", weights=w)[0] testing/library_compatibility.py::test_weighted_shortest_paths /home/build/NNGT/nngt/analysis/ig_functions.py:351: RuntimeWarning: Couldn't reach some vertices. at src/paths/dijkstra.c:534 path = graph.get_shortest_paths(source, target, mode="out", weights=w)[0] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED testing/library_compatibility.py::test_weighted_undirected_clustering FAILED testing/library_compatibility.py::test_assortativity - ImportError: ca... FAILED testing/library_compatibility.py::test_closeness - ImportError: cannot... FAILED testing/library_compatibility.py::test_betweenness - ImportError: cann... FAILED testing/library_compatibility.py::test_components - ImportError: canno... FAILED testing/library_compatibility.py::test_diameter - ImportError: cannot ... FAILED testing/library_compatibility.py::test_binary_shortest_distance - Impo... FAILED testing/library_compatibility.py::test_weighted_shortest_distance - Im... FAILED testing/library_compatibility.py::test_binary_shortest_paths - ImportE... FAILED testing/library_compatibility.py::test_weighted_shortest_paths - Impor... ================== 10 failed, 1 passed, 12 warnings in 14.13s ================== |