Added P part of the model
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[#1255414] 2024/06/19 20:30:22 Booting image ubuntu/lts (default) on port 22926 [#1255414] 2024/06/19 20:30:22 Waiting for guest to settle [#1255414] 2024/06/19 20:30:31 Sending tasks [#1255414] 2024/06/19 20:30:33 Sending build environment [#1255414] 2024/06/19 20:30:33 Sending secrets [#1255414] 2024/06/19 20:30:33 Resolving secret 69332acb-b779-4bb2-ae8a-719f8e150ace [#1255414] 2024/06/19 20:30:34 Installing packages Warning: Permanently added '[localhost]:22926' (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-updates/universe amd64 Packages [1087 kB] Fetched 1344 kB in 0s (3716 kB/s) Reading package lists... Warning: Permanently added '[localhost]:22926' (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 1s (8613 kB/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. 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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) ... [#1255414] 2024/06/19 20:30:39 Cloning repositories Cloning into 'OrgMatt'... + cd OrgMatt + git checkout -q 07bbdcab22bc9f1ae4976e23e9a01c9ce2182b62 + cd OrgMatt + git submodule update --init --recursive [#1255414] 2024/06/19 20:30:40 Running task path [#1255414] 2024/06/19 20:30:40 Running task check [#1255414] 2024/06/19 20:30:44 Running task setup [#1255414] 2024/06/19 20:31:00 Running task test [#1255414] 2024/06/19 20:31:12 Build failed. [#1255414] 2024/06/19 20:31:12 The build environment will be kept alive for 10 minutes. [#1255414] 2024/06/19 20:31:12 To log in with SSH and examine it, use the following command: [#1255414] 2024/06/19 20:31:12 [#1255414] 2024/06/19 20:31:12 ssh -t builds@fra02.builds.sr.ht connect 1255414 [#1255414] 2024/06/19 20:31:12 [#1255414] 2024/06/19 20:31:12 After logging in, the deadline is increased to your remaining build time. [#1255414] 2024/06/19 20:41:12 Deadline elapsed. Terminating build environment. [#1255414] 2024/06/19 20:41:12 Error: Running task on guest: exit status 1 |
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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'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting binaryornot<0.5.0,>=0.4.4
Downloading binaryornot-0.4.4-py2.py3-none-any.whl (9.0 kB)
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)
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Collecting Jinja2<4.0.0,>=3.0.0
Downloading jinja2-3.1.4-py3-none-any.whl (133 kB)
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Collecting license-expression>=1.0
Downloading license_expression-30.3.0-py3-none-any.whl (108 kB)
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Collecting boolean.py>=3.8
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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
+ cd OrgMatt
+ reuse lint
# SUMMARY
* Bad licenses: 0
* Deprecated licenses: 0
* Licenses without file extension: 0
* Missing licenses: 0
* Unused licenses: 0
* Used licenses: CC-BY-SA-4.0, BSD-2-Clause, CC-BY-4.0, GPL-3.0-or-later, Python-2.0, CC0-1.0
* Read errors: 0
* files with copyright information: 90 / 90
* files with license information: 90 / 90
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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Collecting pytest
Downloading pytest-8.2.2-py3-none-any.whl (339 kB)
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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)
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Collecting tomli>=1
Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting iniconfig
Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting pluggy<2.0,>=1.5
Downloading pluggy-1.5.0-py3-none-any.whl (20 kB)
Collecting packaging
Downloading packaging-24.1-py3-none-any.whl (53 kB)
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Collecting exceptiongroup>=1.0.0rc8
Downloading exceptiongroup-1.2.1-py3-none-any.whl (16 kB)
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 scipy (from -r requirements.txt (line 6))
Downloading scipy-1.13.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
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Collecting pandas (from -r requirements.txt (line 7))
Downloading pandas-2.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting pint>=0.19 (from -r requirements.txt (line 8))
Downloading Pint-0.24-py3-none-any.whl.metadata (8.5 kB)
Collecting pycountry (from -r requirements.txt (line 9))
Downloading pycountry-24.6.1-py3-none-any.whl.metadata (12 kB)
Collecting openscm-units (from -r requirements.txt (line 10))
Downloading openscm_units-0.6.0-py3-none-any.whl.metadata (3.9 kB)
Collecting seaborn (from -r requirements.txt (line 11))
Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting python-dateutil>=2.8.2 (from pandas->-r requirements.txt (line 7))
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 7))
Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas->-r requirements.txt (line 7))
Downloading tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting appdirs>=1.4.4 (from pint>=0.19->-r requirements.txt (line 8))
Downloading appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting typing-extensions (from pint>=0.19->-r requirements.txt (line 8))
Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting flexcache>=0.3 (from pint>=0.19->-r requirements.txt (line 8))
Downloading flexcache-0.3-py3-none-any.whl.metadata (7.0 kB)
Collecting flexparser>=0.3 (from pint>=0.19->-r requirements.txt (line 8))
Downloading flexparser-0.3.1-py3-none-any.whl.metadata (18 kB)
Collecting globalwarmingpotentials (from openscm-units->-r requirements.txt (line 10))
Downloading globalwarmingpotentials-0.11.1-py2.py3-none-any.whl.metadata (4.6 kB)
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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Collecting kiwisolver>=1.3.1 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 11))
Downloading kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB)
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)
Collecting pyparsing>=2.3.1 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 11))
Downloading pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->-r requirements.txt (line 7))
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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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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)
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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)
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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=116175 sha256=c1dff3d272f1c29849e9882bb022f17e16a5d3d5d9b2f8f2d1e167150d745018
Stored in directory: /tmp/pip-ephem-wheel-cache-iu7vsdhu/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 F. [ 34%]
tests/test_food.py ... [ 42%]
tests/test_impacts.py .. [ 47%]
tests/test_metabolism.py FF.F..FF [ 68%]
tests/test_nutrients.py ..F [ 76%]
tests/test_plots.py . [ 78%]
tests/test_units.py .... [ 89%]
tests/test_utils.py .F.. [100%]
=================================== FAILURES ===================================
____________________________ test_urine_production _____________________________
def test_urine_production():
'''
Check the urine production function
'''
# check errors
with pytest.raises(AssertionError):
urine_from_population(100, 100)
with pytest.raises(AssertionError):
urine_from_population(100, 100, plop=2)
# check that results are in the right range
assert 0.5*L < urine_from_population(1, 1*day) < 2*L
# check that the CI works
u_ref = urine_from_population(1, 1*day, ci=68)
> assert np.isnan(
urine_from_population(1, 1*day, ci=68, sex="mixed", region="Africa")
).all(), "Expected NaNs (urine production, sex=mixed, region=Africa)"
tests/test_excreta.py:31:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/units.py:148: in check_dim
res = f(*args, **kwargs)
orgmatt/excreta.py:76: in urine_from_population
res = _rval(df_Ur, "amount", pop, ci, q)
orgmatt/_utils/tools.py:160: in return_values
res = _val_from_arr(values, ci_value, q)
orgmatt/_utils/tools.py:57: in _val_from_arr
return np.full(len(q) + (ci > 0), np.NaN) * unit
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NaN'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards")
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards")
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr])
if attr in __expired_attributes__:
> raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}"
)
E AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.. Did you mean: 'nan'?
../.local/lib/python3.10/site-packages/numpy/__init__.py:397: AttributeError
____________________________ test_body_composition _____________________________
def test_body_composition():
''' Test results for body composition '''
for nut in "NKP":
default = body_composition(nut)
assert np.isclose(
default, body_composition(nut, group="adult"), rtol=0.05)
if nut != "P":
for g in ("kid", "teenager", "young adult"):
assert 0 < body_composition(nut, group=g) < 1
# test auto-correct
> assert np.isnan(body_composition(nut, age="8", region="Africa"))
tests/test_metabolism.py:41:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/metabolism/nutrient_flows.py:56: in body_composition
return 0.01*return_values(df, "content", 1, ci_value=ci, q=q)
orgmatt/_utils/tools.py:160: in return_values
res = _val_from_arr(values, ci_value, q)
orgmatt/_utils/tools.py:55: in _val_from_arr
return np.NaN * unit
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NaN'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards")
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards")
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr])
if attr in __expired_attributes__:
> raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}"
)
E AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.. Did you mean: 'nan'?
../.local/lib/python3.10/site-packages/numpy/__init__.py:397: AttributeError
___________________________ test_nutrient_fractions ____________________________
def test_nutrient_fractions():
'''
Check the function to compute the fraction of nutrients that is kept
within the body or excreted in urine and feces.
'''
for nut in "NKP":
> res = fraction_nutrient_excreta(nut, age="8")
tests/test_metabolism.py:56:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/metabolism/nutrient_flows.py:177: in fraction_nutrient_excreta
frac -= fraction_nutrient_retention(nutrient, ci=ci, q=q, **kwargs)
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/metabolism/nutrient_flows.py:117: in fraction_nutrient_retention
frac = 0.01*return_values(df, "amount", 1, ci_value=ci, q=q)
orgmatt/_utils/tools.py:160: in return_values
res = _val_from_arr(values, ci_value, q)
orgmatt/_utils/tools.py:55: in _val_from_arr
return np.NaN * unit
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NaN'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards")
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards")
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr])
if attr in __expired_attributes__:
> raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}"
)
E AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.. Did you mean: 'nan'?
../.local/lib/python3.10/site-packages/numpy/__init__.py:397: AttributeError
____________________________ test_unavailable_data _____________________________
def test_unavailable_data():
''' Check corrections when data is unavailable '''
kwargs = {"sex": "female", "diet": "vegan", "country": "DEU"}
m = DataBasedMetabolicModel(age_group="senior", **kwargs)
# for intake
> assert np.isnan(nutrient_intake(1, 1*day, "N", group="senior", **kwargs).m)
tests/test_metabolism.py:118:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/units.py:148: in check_dim
res = f(*args, **kwargs)
orgmatt/agrifood/human_consumption.py:142: in nutrient_intake
nintake = return_values(df, "intake", pop, ci, q)
orgmatt/_utils/tools.py:160: in return_values
res = _val_from_arr(values, ci_value, q)
orgmatt/_utils/tools.py:55: in _val_from_arr
return np.NaN * unit
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NaN'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards")
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards")
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr])
if attr in __expired_attributes__:
> raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}"
)
E AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.. Did you mean: 'nan'?
../.local/lib/python3.10/site-packages/numpy/__init__.py:397: AttributeError
______________________________ test_flow_fraction ______________________________
def test_flow_fraction():
''' Check data and models for flow fractions '''
kwargs = {"sex": "female", "diet": "omnivorous"}
m = DataBasedMetabolicModel(age_group="adult", **kwargs)
# check that results are identical when data is available
res_model = m.flow_fraction("N", flow="urine")
assert m.last_correction_status == 0
res_urine = fraction_nutrient_excreta(
"N", "urine", sex="female", diet="omnivorous", group="adult")
assert np.isclose(res_model, res_urine, rtol=0.05)
res_feces = m.flow_fraction("N", flow="feces")
res_ffunc = fraction_nutrient_excreta(
"N", "feces", sex="female", diet="omnivorous", group="adult")
> res_ffunc2 = fraction_nutrient_excreta(
"N", "feces", sex="female", diet="omnivorous", age="33-34")
tests/test_metabolism.py:419:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/metabolism/nutrient_flows.py:193: in fraction_nutrient_excreta
frac = 0.01*return_values(df, "amount", 1, ci, q)
orgmatt/_utils/tools.py:160: in return_values
res = _val_from_arr(values, ci_value, q)
orgmatt/_utils/tools.py:55: in _val_from_arr
return np.NaN * unit
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NaN'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards")
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards")
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr])
if attr in __expired_attributes__:
> raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}"
)
E AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.. Did you mean: 'nan'?
../.local/lib/python3.10/site-packages/numpy/__init__.py:397: AttributeError
__________________________ test_consistent_metabolism __________________________
def test_consistent_metabolism():
''' Check the consistent metabolic model '''
kwargs = {"sex": "female", "diet": "vegan", "country": "URY"}
m = ConsistentMetabolicModel(age_group="kid", **kwargs)
for nutrient in ("N", "P", "K"):
> loss = m.flow_fraction(nutrient, flow="loss", ci=90)
tests/test_metabolism.py:474:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/metabolism/metabolic_model.py:456: in flow_fraction
if len(self._get_flow("urine", nutrient)) == 0:
orgmatt/metabolism/metabolic_model.py:310: in _get_flow
unit = ureg("g{nutrient}")
../.local/lib/python3.10/site-packages/pint/facets/plain/registry.py:1398: in parse_expression
return build_eval_tree(gen).evaluate(_define_op)
../.local/lib/python3.10/site-packages/pint/pint_eval.py:384: in evaluate
self.right.evaluate(define_op, bin_op, un_op),
../.local/lib/python3.10/site-packages/pint/pint_eval.py:395: in evaluate
return define_op(self.left)
../.local/lib/python3.10/site-packages/pint/facets/plain/registry.py:1396: in _define_op
return self._eval_token(s, case_sensitive=case_sensitive, **values)
../.local/lib/python3.10/site-packages/pint/facets/plain/registry.py:1305: in _eval_token
{self.get_name(token_text, case_sensitive=case_sensitive): 1}
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pint.registry.UnitRegistry object at 0x7f2790a04100>
name_or_alias = 'nutrient', case_sensitive = None
def get_name(self, name_or_alias: str, case_sensitive: bool | None = None) -> str:
"""Return the canonical name of a unit."""
if name_or_alias == "dimensionless":
return ""
try:
return self._units[name_or_alias].name
except KeyError:
pass
candidates = self.parse_unit_name(name_or_alias, case_sensitive)
if not candidates:
> raise UndefinedUnitError(name_or_alias)
E pint.errors.UndefinedUnitError: 'nutrient' is not defined in the unit registry
../.local/lib/python3.10/site-packages/pint/facets/plain/registry.py:658: UndefinedUnitError
____________________________ test_nutrient_content _____________________________
def test_nutrient_content():
''' Check the nutrient content of urine and feces '''
nitrogen_from_feces(1*kg, wet=False)
# check that results are in the right range
Nf = nitrogen_from_feces(1*kg)
Nu = nitrogen_from_urine(1*L)
Pu = phosphorus_from_urine(1*L)
Pf = phosphorus_from_feces(1*kg)
Nw = nutrient_from_biowaste(1*kg, "N")
Pw = nutrient_from_biowaste(1*kg, "P")
Kw = nutrient_from_biowaste(1*kg, "K")
assert 10*gN < Nf < 30*gN
assert 5*gN < Nu < 15*gN
assert 1*gP < Pu < 2.5*gP
assert 3*gP < Pf < 8*gP
assert 2.9*gN < Nw < 10*gN
assert 0.5*gP < Pw < 2*gP
assert 2*gK < Kw < 10*gK
# check that compound gives the same results
Nf2 = nutrient_from_compound(1*kg, "N", "feces", group="adult")
Pu2 = nutrient_from_compound(1*L, "P", "urine", group="adult")
Pw2 = nutrient_from_compound(1*kg, "P", "biowaste")
assert np.isclose(Nf, Nf2, rtol=0.05)
assert np.isclose(Pu, Pu2, rtol=0.05)
assert np.isclose(Pw, Pw2, rtol=0.05)
# check that the CI works
nitrogen_from_feces(1*kg, ci=68, group=None)
nitrogen_from_urine(1*L, ci=68)
phosphorus_from_urine(1*L, ci=68)
nutrient_from_biowaste(1*kg, "N", waste_type="FoodResidues", ci=68)
# check vector
val = [1, 2, 5, 10]
Nf_vec = nitrogen_from_feces(val*kg)
for v, res in zip(val, Nf_vec):
assert np.isclose(v*Nf, res, rtol=0.05)
Nf_vec = nitrogen_from_feces(val*kg, ci=68)
assert Nf_vec.shape == (len(val), 3)
for v, res in zip(val, Nf_vec):
assert np.isclose(v*Nf, res[1], rtol=0.05)
# check kwargs
> nutrient_from_biowaste(1*kg, "N", location="home", region="Europe")
tests/test_nutrients.py:158:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/units.py:148: in check_dim
res = f(*args, **kwargs)
orgmatt/nutrients/all_nutrients.py:164: in nutrient_from_biowaste
return ureg(unit) * return_values(df, "value", mass, ci, q)
orgmatt/_utils/tools.py:160: in return_values
res = _val_from_arr(values, ci_value, q)
orgmatt/_utils/tools.py:55: in _val_from_arr
return np.NaN * unit
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NaN'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards")
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards")
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr])
if attr in __expired_attributes__:
> raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}"
)
E AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.. Did you mean: 'nan'?
../.local/lib/python3.10/site-packages/numpy/__init__.py:397: AttributeError
______________________________ test_auto_correct _______________________________
def test_auto_correct():
''' Test autocorrect features '''
> res_basic = nitrogen_from_population(1, 1*year, age="12")
tests/test_utils.py:45:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
orgmatt/nutrients/nitrogen.py:64: in nitrogen_from_population
return nutrient_from_population(
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/units.py:148: in check_dim
res = f(*args, **kwargs)
orgmatt/nutrients/all_nutrients.py:83: in nutrient_from_population
return factor * nutrient_intake(
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:331: in auto_format
raise exception
orgmatt/_utils/tools.py:274: in auto_format
res = f(*args, **local_kwargs)
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/units.py:148: in check_dim
res = f(*args, **kwargs)
orgmatt/agrifood/human_consumption.py:142: in nutrient_intake
nintake = return_values(df, "intake", pop, ci, q)
orgmatt/_utils/tools.py:160: in return_values
res = _val_from_arr(values, ci_value, q)
orgmatt/_utils/tools.py:55: in _val_from_arr
return np.NaN * unit
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NaN'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards")
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards")
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr])
if attr in __expired_attributes__:
> raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}"
)
E AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead.. Did you mean: 'nan'?
../.local/lib/python3.10/site-packages/numpy/__init__.py:397: AttributeError
----------------------------- Captured stderr call -----------------------------
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'age': '12'} from `kwargs` in function `fraction_nutrient_excreta`.
Final arguments used were: {'group': 'teenager'}.
------------------------------ Captured log call -------------------------------
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'age': '12'} from `kwargs` in function `fraction_nutrient_excreta`.
Final arguments used were: {'group': 'teenager'}.
=============================== warnings summary ===============================
orgmatt/units.py:23
/home/build/OrgMatt/orgmatt/units.py:23: DeprecationWarning: This function will be removed in future versions of pint.
Use ureg.formatter.default_format
ureg.default_format = "~" # abbreviated unit names
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_excreta.py::test_urine_production - AttributeError: `np.NaN...
FAILED tests/test_metabolism.py::test_body_composition - AttributeError: `np....
FAILED tests/test_metabolism.py::test_nutrient_fractions - AttributeError: `n...
FAILED tests/test_metabolism.py::test_unavailable_data - AttributeError: `np....
FAILED tests/test_metabolism.py::test_flow_fraction - AttributeError: `np.NaN...
FAILED tests/test_metabolism.py::test_consistent_metabolism - pint.errors.Und...
FAILED tests/test_nutrients.py::test_nutrient_content - AttributeError: `np.N...
FAILED tests/test_utils.py::test_auto_correct - AttributeError: `np.NaN` was ...
=================== 8 failed, 30 passed, 1 warning in 11.29s ===================
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