Fix nutrient_from_population with kwargs
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[#1241868] 2024/06/04 14:01:05 Booting image ubuntu/lts (default) on port 22847 [#1241868] 2024/06/04 14:01:06 Waiting for guest to settle [#1241868] 2024/06/04 14:01:14 Sending tasks [#1241868] 2024/06/04 14:01:16 Sending build environment [#1241868] 2024/06/04 14:01:16 Sending secrets [#1241868] 2024/06/04 14:01:16 Resolving secret 69332acb-b779-4bb2-ae8a-719f8e150ace [#1241868] 2024/06/04 14:01:17 Installing packages Warning: Permanently added '[localhost]:22847' (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] Get:4 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [127 kB] Get:5 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 Packages [1475 kB] Get:6 http://archive.ubuntu.com/ubuntu jammy-security/main Translation-en [254 kB] Get:7 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [854 kB] Get:8 http://archive.ubuntu.com/ubuntu jammy-security/universe Translation-en [165 kB] Get:9 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1686 kB] Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/main Translation-en [313 kB] Get:11 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1076 kB] Get:12 http://archive.ubuntu.com/ubuntu jammy-updates/universe Translation-en [247 kB] Fetched 6454 kB in 2s (3722 kB/s) Reading package lists... Warning: Permanently added '[localhost]:22847' (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 6 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 (8212 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 ... 39103 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) ... [#1241868] 2024/06/04 14:01:23 Cloning repositories Cloning into 'OrgMatt'... + cd OrgMatt + git checkout -q b0842eee3bb1b2a38aa59878c916afee8dab7e07 + cd OrgMatt + git submodule update --init --recursive [#1241868] 2024/06/04 14:01:28 Running task path [#1241868] 2024/06/04 14:01:29 Running task check [#1241868] 2024/06/04 14:01:32 Running task setup [#1241868] 2024/06/04 14:01:47 Running task test [#1241868] 2024/06/04 14:02:02 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 269.4/269.4 KB 11.6 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.5/132.5 KB 21.5 MB/s eta 0:00:00 Collecting Jinja2<4.0.0,>=3.0.0 Downloading jinja2-3.1.4-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.3/133.3 KB 16.3 MB/s eta 0:00:00 Collecting boolean.py>=3.8 Downloading boolean.py-4.0-py3-none-any.whl (25 kB) Collecting license-expression>=1.0 Downloading license_expression-30.3.0-py3-none-any.whl (108 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 KB 28.2 MB/s eta 0:00:00 Collecting chardet>=3.0.2 Downloading chardet-5.2.0-py3-none-any.whl (199 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 KB 23.0 MB/s eta 0:00:00 Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Building wheels for collected packages: reuse Building wheel for reuse (pyproject.toml): started Building wheel for reuse (pyproject.toml): finished with status 'done' Created wheel for reuse: filename=reuse-3.0.2-cp310-cp310-manylinux_2_35_x86_64.whl size=119657 sha256=91bebc3608eeea55875ac12fb9650ffa9738b8be4e8025014818adfddbb884c5 Stored in directory: /home/build/.cache/pip/wheels/2b/57/24/d43da4d2afa2378313e911ca8254dd24b3becb9e0ee2d57e0b Successfully built reuse Installing collected packages: boolean.py, MarkupSafe, license-expression, chardet, python-debian, Jinja2, binaryornot, reuse Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 binaryornot-0.4.4 boolean.py-4.0 chardet-5.2.0 license-expression-30.3.0 python-debian-0.1.49 reuse-3.0.2 + 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, BSD-2-Clause, CC-BY-4.0, CC-BY-SA-4.0, GPL-3.0-or-later, Python-2.0 * Read errors: 0 * files with copyright information: 89 / 89 * files with license information: 89 / 89 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 91.4 MB/s eta 0:00:00 Collecting pytest Downloading pytest-8.2.2-py3-none-any.whl (339 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 339.9/339.9 KB 125.5 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 863.4/863.4 KB 160.4 MB/s eta 0:00:00 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) 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 packaging Downloading packaging-24.0-py3-none-any.whl (53 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.5/53.5 KB 37.2 MB/s eta 0:00:00 Installing collected packages: tomli, setuptools, pluggy, pip, packaging, iniconfig, exceptiongroup, pytest Successfully installed exceptiongroup-1.2.1 iniconfig-2.0.0 packaging-24.0 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 7.7 MB/s eta 0:00:00 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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typing-extensions (from pint>=0.19->-r requirements.txt (line 8)) Downloading typing_extensions-4.12.1-py3-none-any.whl.metadata (3.0 kB) Collecting globalwarmingpotentials (from openscm-units->-r requirements.txt (line 9)) Downloading globalwarmingpotentials-0.9.4-py2.py3-none-any.whl.metadata (4.1 kB) Collecting matplotlib!=3.6.1,>=3.4 (from seaborn->-r requirements.txt (line 10)) 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 10)) 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 10)) 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 10)) Downloading 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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) (0.23) 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: typing-extensions in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.4.1) (4.12.1) Requirement already satisfied: globalwarmingpotentials in /home/build/.local/lib/python3.10/site-packages (from openscm-units->OrgMatt==0.4.1) (0.9.4) 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) (24.0) 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=109428 sha256=7166a49173463dc1cafd4dac017759d7200c47c0abf86de5565996f086593dd9 Stored in directory: /tmp/pip-ephem-wheel-cache-tn4bnwm2/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 ....... [ 67%] tests/test_nutrients.py ... [ 75%] tests/test_plots.py . [ 78%] tests/test_units.py .... [ 89%] tests/test_utils.py .... [100%] ============================= 37 passed in 13.02s ============================== + coverage report -m Name Stmts Miss Cover Missing --------------------------------------------------------------------- orgmatt/__init__.py 26 0 100% orgmatt/_utils/__init__.py 3 0 100% orgmatt/_utils/logger.py 24 2 92% 37, 43 orgmatt/_utils/tools.py 259 9 97% 244, 265, 376-379, 387-388, 397, 409 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 3 0 100% orgmatt/metabolism/corrections.py 66 5 92% 142, 149-150, 156, 167 orgmatt/metabolism/metabolic_model.py 122 4 97% 151, 161, 324, 385 orgmatt/metabolism/nutrient_flows.py 72 2 97% 90, 184 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 125 9 93% 110-114, 117, 120, 123, 190, 209, 217 --------------------------------------------------------------------- TOTAL 1014 44 96% |
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+ cd OrgMatt ++ git show -s --pretty=%D HEAD ++ sed -n 2p ++ grep -v HEAD ++ tr -s ', /' '\n' + GIT_BRANCH=v0.4.1 + set +x |