Add geographic support with pycountry
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[#1251627] 2024/06/15 08:36:25 Booting image ubuntu/lts (default) on port 22729 [#1251627] 2024/06/15 08:36:26 Waiting for guest to settle [#1251627] 2024/06/15 08:36:33 Sending tasks [#1251627] 2024/06/15 08:36:36 Sending build environment [#1251627] 2024/06/15 08:36:37 Sending secrets [#1251627] 2024/06/15 08:36:37 Resolving secret 69332acb-b779-4bb2-ae8a-719f8e150ace [#1251627] 2024/06/15 08:36:38 Installing packages Warning: Permanently added '[localhost]:22729' (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 [1517 kB] Get:6 http://archive.ubuntu.com/ubuntu jammy-security/main Translation-en [259 kB] Get:7 http://archive.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [1933 kB] Get:8 http://archive.ubuntu.com/ubuntu jammy-security/restricted Translation-en [329 kB] Get:9 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [858 kB] Get:10 http://archive.ubuntu.com/ubuntu jammy-security/universe Translation-en [166 kB] Get:11 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1731 kB] Get:12 http://archive.ubuntu.com/ubuntu jammy-updates/main Translation-en [318 kB] Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [1990 kB] Get:14 http://archive.ubuntu.com/ubuntu jammy-updates/restricted Translation-en [338 kB] Get:15 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1086 kB] Fetched 10.8 MB in 1s (8328 kB/s) Reading package lists... Warning: Permanently added '[localhost]:22729' (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 4 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 (7993 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 ... 39100 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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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) ... [#1251627] 2024/06/15 08:36:45 Cloning repositories Cloning into 'OrgMatt'... + cd OrgMatt + git checkout -q ce759f53cda14361c1586deb3bc98228878652b7 + cd OrgMatt + git submodule update --init --recursive [#1251627] 2024/06/15 08:36:46 Running task path [#1251627] 2024/06/15 08:36:47 Running task check [#1251627] 2024/06/15 08:36:51 Running task setup [#1251627] 2024/06/15 08:37:15 Running task test [#1251627] 2024/06/15 08:37:30 Build failed. [#1251627] 2024/06/15 08:37:30 The build environment will be kept alive for 10 minutes. [#1251627] 2024/06/15 08:37:30 To log in with SSH and examine it, use the following command: [#1251627] 2024/06/15 08:37:30 [#1251627] 2024/06/15 08:37:30 ssh -t builds@fra01.builds.sr.ht connect 1251627 [#1251627] 2024/06/15 08:37:30 [#1251627] 2024/06/15 08:37:30 After logging in, the deadline is increased to your remaining build time. [#1251627] 2024/06/15 08:47:30 Deadline elapsed. Terminating build environment. [#1251627] 2024/06/15 08:47:30 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 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 binaryornot<0.5.0,>=0.4.4
Downloading binaryornot-0.4.4-py2.py3-none-any.whl (9.0 kB)
Collecting Jinja2<4.0.0,>=3.0.0
Downloading jinja2-3.1.4-py3-none-any.whl (133 kB)
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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: Python-2.0, CC-BY-SA-4.0, CC-BY-4.0, CC0-1.0, GPL-3.0-or-later, BSD-2-Clause
* 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-70.0.0-py3-none-any.whl (863 kB)
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Collecting packaging
Downloading packaging-24.1-py3-none-any.whl (53 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 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-70.0.0 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-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 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-0.5.4-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)
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Downloading globalwarmingpotentials-0.10.1-py2.py3-none-any.whl.metadata (4.5 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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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-0.10.1 kiwisolver-1.4.5 matplotlib-3.9.0 numpy-1.26.4 openscm-units-0.5.4 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'
Installing backend dependencies: started
Installing backend dependencies: 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==0.4.1) (1.26.4)
Requirement already satisfied: scipy in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.1) (1.13.1)
Requirement already satisfied: pandas in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.1) (2.2.2)
Requirement already satisfied: pint>=0.19 in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.1) (0.24)
Requirement already satisfied: pycountry in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.1) (24.6.1)
Requirement already satisfied: openscm-units in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.1) (0.5.4)
Requirement already satisfied: seaborn in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.1) (0.13.2)
Requirement already satisfied: appdirs>=1.4.4 in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.4.1) (1.4.4)
Requirement already satisfied: typing-extensions in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.4.1) (4.12.2)
Requirement already satisfied: flexcache>=0.3 in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.4.1) (0.3)
Requirement already satisfied: flexparser>=0.3 in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.4.1) (0.3.1)
Requirement already satisfied: globalwarmingpotentials in /home/build/.local/lib/python3.10/site-packages (from openscm-units->OrgMatt==0.4.1) (0.10.1)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.4.1) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.4.1) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.4.1) (2024.1)
Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /home/build/.local/lib/python3.10/site-packages (from seaborn->OrgMatt==0.4.1) (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==0.4.1) (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==0.4.1) (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==0.4.1) (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==0.4.1) (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==0.4.1) (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==0.4.1) (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==0.4.1) (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==0.4.1) (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-0.4.1-py3-none-any.whl size=111560 sha256=aeb2f0ed2baade3dc75fbf2940a0641514a2c5c500f94674531351e2b2b21ab6
Stored in directory: /tmp/pip-ephem-wheel-cache-5cmyxw0o/wheels/fa/c8/54/6668a436f152ec271fbc43c4d4817e40063b0c2195101cffa1
Successfully built OrgMatt
Installing collected packages: OrgMatt
Successfully installed OrgMatt-0.4.1
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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 37 items
tests/test_data.py ........... [ 29%]
tests/test_excreta.py .. [ 35%]
tests/test_food.py ... [ 43%]
tests/test_impacts.py .. [ 48%]
tests/test_metabolism.py ...F... [ 67%]
tests/test_nutrients.py ... [ 75%]
tests/test_plots.py . [ 78%]
tests/test_units.py .... [ 89%]
tests/test_utils.py .... [100%]
=================================== FAILURES ===================================
____________________________ test_unavailable_data _____________________________
def test_unavailable_data():
''' Check corrections when data is unavailable '''
kwargs = {"sex": "female", "diet": "vegan", "country": "DEU"}
m = MetabolicDataModel(age_group="senior", **kwargs)
# for intake
assert np.isnan(nutrient_intake(1, 1*day, "N", group="senior", **kwargs).m)
res_func = nutrient_intake(
1, 1*day, "N", group="senior", auto_correct=True, **kwargs)
res_model = m.nutrient_intake(1*day, "N")
assert m.last_correction_status >= 1
assert res_func != res_model
# for excreta
kwargs = {"sex": "male", "country": "SWE"}
age_range = "31-38"
m = MetabolicDataModel(age_group=age_range, **kwargs)
assert m.age == age_range
assert np.isnan(
nutrient_from_population(
1, 1*day, "N", age=age_range, excreta="urine", **kwargs).m)
skipped = []
res_func = nutrient_from_population(
1, 1*day, "N", age=age_range, excreta="urine", auto_correct=True,
skipped_constraints=skipped, **kwargs)
assert "sex" in skipped, "This test should check correction for `sex`."
res_model = m.nutrient_excretion(1*day, "N", excreta="urine")
assert res_func != res_model
# check that corrections are consistent
diet = "vegan"
kwargs = {"sex": "female", "diet": diet, "country": "DEU"}
res_intake = {}
res_excreta = {}
res_urine = {}
for g in ("kid", "adult"):
assert np.isnan(nutrient_intake(1, 1*day, "N", group=g, **kwargs).m)
m = MetabolicDataModel(age_group=g, **kwargs)
assert m.diet == diet
res_intake[g] = m.nutrient_intake(1*day, "N")
res_excreta[g] = m.nutrient_excretion(1*day, "N", excreta="all")
res_urine[g] = m.nutrient_excretion(1*day, "N", excreta="urine")
# NB: data-based model is not fully consistent, urine excretion may be
# higher than intake
assert res_intake["kid"] < res_intake["adult"]
assert res_urine["kid"] < res_urine["adult"]
assert res_excreta["kid"] < res_excreta["adult"]
assert res_excreta["kid"] < res_intake["kid"]
assert res_excreta["adult"] <= res_intake["adult"]
# check error unavailable corrections
kwargs = {"sex": "female", "diet": diet, "country": "nonexistent"}
m = MetabolicDataModel(age_group="adult", **kwargs)
> m.nutrient_intake(1*day, "N")
tests/test_metabolism.py:183:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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/metabolism/metabolic_model.py:204: in nutrient_intake
res = nutrient_intake(
orgmatt/_utils/decorator.py:208: in fun
return caller(func, *(extras + args), **kw)
orgmatt/_utils/tools.py:174: in auto_format
ca3 = get_country_iso(base_kwargs["country"], alpha=3)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
country = 'nonexistent', alpha = 3
@cache
def get_country_iso(country: str, alpha: int = 2) -> str:
'''
Returns a country's ISO 3366-1 code.
Parameters
----------
country : str
Country for which the ISO code should be returned.
alpha : int, optional (default: 2)
Type of ISO code to return: either a 2 (alpha 2) or 3-letter (alpha 3)
code. E.g. "France" is designated by "FR" in alpha 2 and "FRA" in alpha
3.
'''
country = normalize(country)
cntry = None
if len(country) == 3:
cntry = pc.countries.get(alpha_3=country)
elif len(country) == 2:
cntry = pc.countries.get(alpha_2=country)
else:
cntry = pc.countries.get(name=country)
if cntry is None:
> raise ValueError(f"No such country '{country}'.")
E ValueError: No such country 'nonexistent'.
orgmatt/_utils/countries.py:59: ValueError
----------------------------- Captured stderr call -----------------------------
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'senior', 'sex': 'female'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'senior', 'sex': 'female'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'age', 'sex'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'country': 'SWE'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'sex'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'country': 'SWE', 'group': 'adult'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'kid', 'sex': 'female'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'group'} from `kwargs` in function `fraction_nutrient_excreta`.
Final arguments used were: {'region': 'Europe', 'diet': 'vegan', 'sex': 'female', 'country': 'DEU'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'kid', 'sex': 'female'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'diet', 'country', 'group'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'sex': 'female'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'diet': 'vegan', 'sex': 'female'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'diet': 'vegan', 'sex': 'female'}.
[INFO @ orgmatt._utils.tools]: from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'sex': 'female'}.
------------------------------ Captured log call -------------------------------
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'senior', 'sex': 'female'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'senior', 'sex': 'female'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'age', 'sex'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'country': 'SWE'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'sex'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'country': 'SWE', 'group': 'adult'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'kid', 'sex': 'female'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'group'} from `kwargs` in function `fraction_nutrient_excreta`.
Final arguments used were: {'region': 'Europe', 'diet': 'vegan', 'sex': 'female', 'country': 'DEU'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'kid', 'sex': 'female'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'diet', 'country', 'group'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'sex': 'female'}.
WARNING root:logger.py:39 from coverage (L8) - Could not autocorrect missing field: 'diet=vegan'.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'diet': 'vegan', 'sex': 'female'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'country'} from `kwargs` in function `nutrient_intake`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'diet': 'vegan', 'sex': 'female'}.
INFO orgmatt._utils.tools:logger.py:41 from coverage (L8) - Removed {'diet', 'country'} from `kwargs` in function `nutrient_from_population`.
Final arguments used were: {'region': 'Europe', 'group': 'adult', 'sex': 'female'}.
WARNING root:logger.py:39 from coverage (L8) - Could not autocorrect missing field: 'diet=vegan'.
=============================== 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_metabolism.py::test_unavailable_data - ValueError: No such ...
=================== 1 failed, 36 passed, 1 warning in 14.54s ===================
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