Support numpy 2
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[#1256528] 2024/06/20 19:11:03 Booting image ubuntu/lts (default) on port 22050 [#1256528] 2024/06/20 19:11:03 Waiting for guest to settle [#1256528] 2024/06/20 19:11:12 Sending tasks [#1256528] 2024/06/20 19:11:15 Sending build environment [#1256528] 2024/06/20 19:11:15 Sending secrets [#1256528] 2024/06/20 19:11:15 Resolving secret 69332acb-b779-4bb2-ae8a-719f8e150ace [#1256528] 2024/06/20 19:11:16 Installing packages Warning: Permanently added '[localhost]:22050' (ED25519) to the list of known hosts. 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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 (49.9 MB/s) Selecting previously unselected package javascript-common. 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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) ... [#1256528] 2024/06/20 19:11:21 Cloning repositories Cloning into 'OrgMatt'... + cd OrgMatt + git checkout -q 5a68743ba20592de76ff1d6692550c83d413c29d + cd OrgMatt + git submodule update --init --recursive [#1256528] 2024/06/20 19:11:22 Running task path [#1256528] 2024/06/20 19:11:22 Running task check [#1256528] 2024/06/20 19:11:26 Running task setup [#1256528] 2024/06/20 19:11:44 Running task test [#1256528] 2024/06/20 19:11:57 Running task doc |
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+ echo 'export PATH=$PATH:/home/build/.local/bin' |
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+ 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)
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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'
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Preparing metadata (pyproject.toml): finished with status 'done'
Collecting boolean.py>=3.8
Downloading boolean.py-4.0-py3-none-any.whl (25 kB)
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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
+ cd OrgMatt
+ reuse lint
# SUMMARY
* Bad licenses: 0
* Deprecated licenses: 0
* Licenses without file extension: 0
* Missing licenses: 0
* Unused licenses: 0
* Used licenses: CC0-1.0, Python-2.0, GPL-3.0-or-later, CC-BY-4.0, CC-BY-SA-4.0, BSD-2-Clause
* Read errors: 0
* files with copyright information: 92 / 92
* files with license information: 92 / 92
Congratulations! Your project is compliant with version 3.0 of the REUSE Specification :-)
|
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+ cd OrgMatt
+ pip3 install --upgrade pip pytest 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-24.0-py3-none-any.whl (2.1 MB)
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Installing collected packages: tomli, setuptools, pluggy, pip, packaging, iniconfig, exceptiongroup, pytest
Successfully installed exceptiongroup-1.2.1 iniconfig-2.0.0 packaging-24.1 pip-24.0 pluggy-1.5.0 pytest-8.2.2 setuptools-70.1.0 tomli-2.0.1
+ pip install -r requirements.txt
Defaulting to user installation because normal site-packages is not writeable
Collecting numpy>=1.20 (from -r requirements.txt (line 5))
Downloading numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
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Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 7))
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Collecting matplotlib!=3.6.1,>=3.4 (from seaborn->-r requirements.txt (line 11))
Downloading matplotlib-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting contourpy>=1.0.1 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 11))
Downloading contourpy-1.2.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 11))
Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 11))
Downloading fonttools-4.53.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (162 kB)
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Requirement already satisfied: packaging>=20.0 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 11)) (24.1)
Collecting pillow>=8 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 11))
Downloading pillow-10.3.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (9.2 kB)
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Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->-r requirements.txt (line 7))
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Installing collected packages: pytz, globalwarmingpotentials, appdirs, tzdata, typing-extensions, six, pyparsing, pycountry, pillow, numpy, kiwisolver, fonttools, cycler, scipy, python-dateutil, flexparser, flexcache, contourpy, pint, pandas, matplotlib, seaborn, openscm-units
Successfully installed appdirs-1.4.4 contourpy-1.2.1 cycler-0.12.1 flexcache-0.3 flexparser-0.3.1 fonttools-4.53.0 globalwarmingpotentials-0.11.1 kiwisolver-1.4.5 matplotlib-3.9.0 numpy-2.0.0 openscm-units-0.6.0 pandas-2.2.2 pillow-10.3.0 pint-0.24 pycountry-24.6.1 pyparsing-3.1.2 python-dateutil-2.9.0.post0 pytz-2024.1 scipy-1.13.1 seaborn-0.13.2 six-1.16.0 typing-extensions-4.12.2 tzdata-2024.1
+ pip install coverage
Defaulting to user installation because normal site-packages is not writeable
Collecting coverage
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Installing collected packages: coverage
Successfully installed coverage-7.5.3
+ pip install .
Defaulting to user installation because normal site-packages is not writeable
Processing /home/build/OrgMatt
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: numpy>=1.20 in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.5.0) (2.0.0)
Requirement already satisfied: scipy in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.5.0) (1.13.1)
Requirement already satisfied: pandas in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.5.0) (2.2.2)
Requirement already satisfied: pint>=0.19 in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.5.0) (0.24)
Requirement already satisfied: pycountry in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.5.0) (24.6.1)
Requirement already satisfied: openscm-units in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.5.0) (0.6.0)
Requirement already satisfied: seaborn in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.5.0) (0.13.2)
Requirement already satisfied: appdirs>=1.4.4 in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.5.0) (1.4.4)
Requirement already satisfied: typing-extensions in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.5.0) (4.12.2)
Requirement already satisfied: flexcache>=0.3 in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.5.0) (0.3)
Requirement already satisfied: flexparser>=0.3 in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.5.0) (0.3.1)
Requirement already satisfied: globalwarmingpotentials in /home/build/.local/lib/python3.10/site-packages (from openscm-units->OrgMatt==0.5.0) (0.11.1)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.5.0) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.5.0) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.5.0) (2024.1)
Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /home/build/.local/lib/python3.10/site-packages (from seaborn->OrgMatt==0.5.0) (3.9.0)
Requirement already satisfied: contourpy>=1.0.1 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.5.0) (1.2.1)
Requirement already satisfied: cycler>=0.10 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.5.0) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.5.0) (4.53.0)
Requirement already satisfied: kiwisolver>=1.3.1 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.5.0) (1.4.5)
Requirement already satisfied: packaging>=20.0 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.5.0) (24.1)
Requirement already satisfied: pillow>=8 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.5.0) (10.3.0)
Requirement already satisfied: pyparsing>=2.3.1 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.5.0) (3.1.2)
Requirement already satisfied: six>=1.5 in /home/build/.local/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas->OrgMatt==0.5.0) (1.16.0)
Building wheels for collected packages: OrgMatt
Building wheel for OrgMatt (pyproject.toml): started
Building wheel for OrgMatt (pyproject.toml): finished with status 'done'
Created wheel for OrgMatt: filename=OrgMatt-0.5.0-py3-none-any.whl size=120845 sha256=269361663f8f82270fb6230ef2d3e0af190c733b5f5153240d54f6ee2751eadb
Stored in directory: /tmp/pip-ephem-wheel-cache-io5p6tgu/wheels/fa/c8/54/6668a436f152ec271fbc43c4d4817e40063b0c2195101cffa1
Successfully built OrgMatt
Installing collected packages: OrgMatt
Successfully installed OrgMatt-0.5.0
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+ cd OrgMatt + coverage run -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.10.12, pytest-8.2.2, pluggy-1.5.0 rootdir: /home/build/OrgMatt configfile: pyproject.toml collected 38 items tests/test_data.py ........... [ 28%] tests/test_excreta.py .. [ 34%] tests/test_food.py ... [ 42%] tests/test_impacts.py .. [ 47%] tests/test_metabolism.py ........ [ 68%] tests/test_nutrients.py ... [ 76%] tests/test_plots.py . [ 78%] tests/test_units.py .... [ 89%] tests/test_utils.py .... [100%] ============================= 38 passed in 12.04s ============================== + coverage report -m Name Stmts Miss Cover Missing ------------------------------------------------------------------------------ orgmatt/__init__.py 26 0 100% orgmatt/_utils/__init__.py 3 0 100% orgmatt/_utils/countries.py 28 4 86% 20-25, 54, 67 orgmatt/_utils/logger.py 24 2 92% 37, 43 orgmatt/_utils/tools.py 301 9 97% 310, 333, 444-447, 455-456, 465, 477 orgmatt/agrifood/__init__.py 2 0 100% orgmatt/agrifood/biowaste.py 21 2 90% 80, 83 orgmatt/agrifood/human_consumption.py 26 0 100% orgmatt/data/__init__.py 44 0 100% orgmatt/excreta.py 23 0 100% orgmatt/impacts/__init__.py 2 0 100% orgmatt/impacts/fertilizers.py 17 0 100% orgmatt/impacts/water.py 21 1 95% 68 orgmatt/metabolism/__init__.py 5 0 100% orgmatt/metabolism/base_metabolic_model.py 134 7 95% 88, 98, 175, 407, 474, 489-492 orgmatt/metabolism/constant_metabolic_model.py 89 10 89% 116-117, 207, 210, 213, 270-272, 277, 289 orgmatt/metabolism/corrections.py 67 3 96% 144, 158, 169 orgmatt/metabolism/linear_metabolic_model.py 101 87 14% 52-65, 73-147, 181-190, 215-242, 287-310 orgmatt/metabolism/nutrient_flows.py 72 2 97% 91, 185 orgmatt/nutrients/__init__.py 3 0 100% orgmatt/nutrients/all_nutrients.py 56 2 96% 160, 230 orgmatt/nutrients/nitrogen.py 12 0 100% orgmatt/nutrients/phosphorus.py 12 0 100% orgmatt/plot/__init__.py 2 0 100% orgmatt/plot/distributions.py 66 8 88% 72, 81-82, 89, 127, 180, 195, 198 orgmatt/typing.py 7 0 100% orgmatt/units.py 128 11 91% 26-27, 114-118, 121, 124, 127, 194, 213, 221 ------------------------------------------------------------------------------ TOTAL 1292 148 89% |
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+ cd OrgMatt ++ git show -s --pretty=%D HEAD ++ sed -n 2p ++ grep -v HEAD ++ tr -s ', /' '\n' + GIT_BRANCH=linear-model + set +x |