Addition of metabolic model
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[#1145198] 2024/02/07 15:20:49 Booting image ubuntu/lts (default) on port 22521 [#1145198] 2024/02/07 15:20:50 Waiting for guest to settle [#1145198] 2024/02/07 15:20:58 Sending tasks [#1145198] 2024/02/07 15:21:00 Sending build environment [#1145198] 2024/02/07 15:21:00 Sending secrets [#1145198] 2024/02/07 15:21:00 Resolving secret 69332acb-b779-4bb2-ae8a-719f8e150ace [#1145198] 2024/02/07 15:21:01 Installing packages Warning: Permanently added '[localhost]:22521' (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 [110 kB] Get:3 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [119 kB] Get:4 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [109 kB] Get:5 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 Packages [1111 kB] Get:6 http://archive.ubuntu.com/ubuntu jammy-security/main Translation-en [208 kB] Get:7 http://archive.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [1317 kB] Get:8 http://archive.ubuntu.com/ubuntu jammy-security/restricted Translation-en [215 kB] Get:9 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [838 kB] Get:10 http://archive.ubuntu.com/ubuntu jammy-security/universe Translation-en [160 kB] Get:11 http://archive.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [37.1 kB] Get:12 http://archive.ubuntu.com/ubuntu jammy-security/multiverse Translation-en [7476 B] Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1362 kB] Get:14 http://archive.ubuntu.com/ubuntu jammy-updates/main Translation-en [271 kB] Get:15 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [1404 kB] Get:16 http://archive.ubuntu.com/ubuntu jammy-updates/restricted Translation-en [231 kB] Get:17 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1043 kB] Get:18 http://archive.ubuntu.com/ubuntu jammy-updates/universe Translation-en [235 kB] Get:19 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [42.1 kB] Get:20 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse Translation-en [10.1 kB] Get:21 http://archive.ubuntu.com/ubuntu jammy-backports/main amd64 Packages [41.7 kB] Get:22 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 Packages [24.2 kB] Fetched 8896 kB in 1s (8871 kB/s) Reading package lists... Warning: Permanently added '[localhost]:22521' (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 35 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 2.4.7-1ubuntu0.2 [147 kB] Get:3 http://archive.ubuntu.com/ubuntu jammy/main amd64 libjs-jquery all 3.6.0+dfsg+~3.5.13-1 [321 kB] Get:4 http://archive.ubuntu.com/ubuntu jammy/main amd64 libjs-underscore all 1.13.2~dfsg-2 [118 kB] Get:5 http://archive.ubuntu.com/ubuntu jammy/main amd64 libjs-sphinxdoc all 4.3.2-1 [139 kB] Get:6 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libpython3.10 amd64 3.10.12-1~22.04.3 [1948 kB] Get:7 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9.2 [164 kB] Get:8 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libpython3.10-dev amd64 3.10.12-1~22.04.3 [4762 kB] Get:9 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 libpython3-dev amd64 3.10.6-1~22.04 [7166 B] Get:10 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3.10-dev amd64 3.10.12-1~22.04.3 [507 kB] Get:11 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-lib2to3 all 3.10.8-1~22.04 [77.6 kB] Get:12 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-distutils all 3.10.8-1~22.04 [139 kB] Get:13 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-dev amd64 3.10.6-1~22.04 [26.0 kB] Get:14 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 python3-setuptools all 59.6.0-1.2ubuntu0.22.04.1 [339 kB] Get:15 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 python3-wheel all 0.37.1-2ubuntu0.22.04.1 [32.0 kB] Get:16 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 python3-pip all 22.0.2+dfsg-1ubuntu0.4 [1305 kB] Fetched 10.0 MB in 0s (24.6 MB/s) Selecting previously unselected package javascript-common. 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Setting up python3-wheel (0.37.1-2ubuntu0.22.04.1) ... Setting up libpython3.10-dev:amd64 (3.10.12-1~22.04.3) ... Setting up python3-pip (22.0.2+dfsg-1ubuntu0.4) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up python3.10-dev (3.10.12-1~22.04.3) ... Setting up libpython3-dev:amd64 (3.10.6-1~22.04) ... Setting up python3-dev (3.10.6-1~22.04) ... Processing triggers for libc-bin (2.35-0ubuntu3.5) ... [#1145198] 2024/02/07 15:21:06 Cloning repositories Cloning into 'OrgMatt'... + cd OrgMatt + git checkout -q 2d9cf68bf8f16ab507a9f64641d09e4ece3b214b + cd OrgMatt + git submodule update --init --recursive [#1145198] 2024/02/07 15:21:06 Running task path [#1145198] 2024/02/07 15:21:07 Running task check [#1145198] 2024/02/07 15:21:11 Running task setup [#1145198] 2024/02/07 15:21:30 Running task test [#1145198] 2024/02/07 15:21:38 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-3.0.1.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 boolean.py>=3.8
Downloading boolean.py-4.0-py3-none-any.whl (25 kB)
Collecting binaryornot<0.5.0,>=0.4.4
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Collecting Jinja2<4.0.0,>=3.0.0
Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
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Building wheels for collected packages: reuse
Building wheel for reuse (pyproject.toml): started
Building wheel for reuse (pyproject.toml): finished with status 'done'
Created wheel for reuse: filename=reuse-3.0.1-cp310-cp310-manylinux_2_35_x86_64.whl size=119651 sha256=0e6cfb692dc3bf53322122460456bf777c4f0a0b69fddf68ca53723ee29870c8
Stored in directory: /home/build/.cache/pip/wheels/55/f8/83/e60ce3c9e2ef3fe37c4343c66e0c40f8655055d5fff168d337
Successfully built reuse
Installing collected packages: boolean.py, MarkupSafe, license-expression, chardet, python-debian, Jinja2, binaryornot, reuse
Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.5 binaryornot-0.4.4 boolean.py-4.0 chardet-5.2.0 license-expression-30.2.0 python-debian-0.1.49 reuse-3.0.1
+ cd OrgMatt
+ reuse lint
# SUMMARY
* Bad licenses: 0
* Deprecated licenses: 0
* Licenses without file extension: 0
* Missing licenses: 0
* Unused licenses: 0
* Used licenses: BSD-2-Clause, CC-BY-SA-4.0, GPL-3.0-or-later, CC0-1.0, CC-BY-4.0, Python-2.0
* Read errors: 0
* files with copyright information: 82 / 82
* files with license information: 82 / 82
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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Downloading pytest-8.0.0-py3-none-any.whl (334 kB)
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Collecting packaging
Downloading packaging-23.2-py3-none-any.whl (53 kB)
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Collecting iniconfig
Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Installing collected packages: tomli, setuptools, pluggy, pip, packaging, iniconfig, exceptiongroup, pytest
Successfully installed exceptiongroup-1.2.0 iniconfig-2.0.0 packaging-23.2 pip-24.0 pluggy-1.4.0 pytest-8.0.0 setuptools-69.0.3 tomli-2.0.1
+ pip install -r requirements.txt
Defaulting to user installation because normal site-packages is not writeable
Collecting numpy (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-1.12.0-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))
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Collecting pint>=0.19 (from -r requirements.txt (line 8))
Downloading Pint-0.23-py3-none-any.whl.metadata (8.1 kB)
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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-2.8.2-py2.py3-none-any.whl (247 kB)
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Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 7))
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Collecting matplotlib!=3.6.1,>=3.4 (from seaborn->-r requirements.txt (line 10))
Downloading matplotlib-3.8.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting contourpy>=1.0.1 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 10))
Downloading contourpy-1.2.0-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 fonttools-4.48.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (158 kB)
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Collecting kiwisolver>=1.3.1 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 10))
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 10)) (23.2)
Collecting pillow>=8 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 10))
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Installing collected packages: pytz, globalwarmingpotentials, tzdata, typing-extensions, six, pyparsing, pillow, numpy, kiwisolver, fonttools, cycler, scipy, python-dateutil, pint, contourpy, pandas, matplotlib, seaborn, openscm-units
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+ pip install coverage
Defaulting to user installation because normal site-packages is not writeable
Collecting coverage
Downloading coverage-7.4.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Downloading coverage-7.4.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (233 kB)
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Installing collected packages: coverage
Successfully installed coverage-7.4.1
+ 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 in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.3.0) (1.26.4)
Requirement already satisfied: scipy in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.3.0) (1.12.0)
Requirement already satisfied: pandas in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.3.0) (2.2.0)
Requirement already satisfied: pint>=0.19 in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.3.0) (0.23)
Requirement already satisfied: openscm-units in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.3.0) (0.5.4)
Requirement already satisfied: seaborn in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.3.0) (0.13.2)
Requirement already satisfied: typing-extensions in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.3.0) (4.9.0)
Requirement already satisfied: globalwarmingpotentials in /home/build/.local/lib/python3.10/site-packages (from openscm-units->OrgMatt==0.3.0) (0.9.4)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.3.0) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.3.0) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.3.0) (2023.4)
Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /home/build/.local/lib/python3.10/site-packages (from seaborn->OrgMatt==0.3.0) (3.8.2)
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==0.3.0) (1.2.0)
Requirement already satisfied: cycler>=0.10 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.3.0) (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==0.3.0) (4.48.1)
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==0.3.0) (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==0.3.0) (23.2)
Requirement already satisfied: pillow>=8 in /home/build/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->OrgMatt==0.3.0) (10.2.0)
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==0.3.0) (3.1.1)
Requirement already satisfied: six>=1.5 in /home/build/.local/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas->OrgMatt==0.3.0) (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-0.3.0-py3-none-any.whl size=99439 sha256=1a79633387bdaff69590d6ebbbca886cb3c9badf215bb01b4df5dc0da9165b3f
Stored in directory: /tmp/pip-ephem-wheel-cache-iyzhd0g1/wheels/fa/c8/54/6668a436f152ec271fbc43c4d4817e40063b0c2195101cffa1
Successfully built OrgMatt
Installing collected packages: OrgMatt
Successfully installed OrgMatt-0.3.0
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+ cd OrgMatt + coverage run -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.10.12, pytest-8.0.0, pluggy-1.4.0 rootdir: /home/build/OrgMatt collected 28 items tests/test_data.py ......... [ 32%] tests/test_excreta.py .. [ 39%] tests/test_food.py .. [ 46%] tests/test_impacts.py .. [ 53%] tests/test_metabolism.py ... [ 64%] tests/test_nutrients.py ... [ 75%] tests/test_plots.py . [ 78%] tests/test_units.py .... [ 92%] tests/test_utils.py .. [100%] =============================== warnings summary =============================== orgmatt/_utils/tools.py:19 /home/build/OrgMatt/orgmatt/_utils/tools.py:19: DeprecationWarning: Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0), (to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries) but was not found to be installed on your system. If this would cause problems for you, please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466 from pandas import DataFrame -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================== 28 passed, 1 warning in 6.38s ========================= + coverage report -m Name Stmts Miss Cover Missing --------------------------------------------------------------------- orgmatt/__init__.py 25 0 100% orgmatt/_utils/__init__.py 4 0 100% orgmatt/_utils/logger.py 24 2 92% 37, 43 orgmatt/_utils/tools.py 144 2 99% 83, 184 orgmatt/agrifood/__init__.py 3 0 100% orgmatt/agrifood/biowaste.py 21 2 90% 71, 74 orgmatt/agrifood/human_consumption.py 25 4 84% 42-55 orgmatt/data/__init__.py 42 0 100% orgmatt/excreta.py 21 0 100% orgmatt/impacts/__init__.py 2 0 100% orgmatt/impacts/fertilizers.py 14 0 100% orgmatt/impacts/water.py 20 1 95% 65 orgmatt/metabolism/__init__.py 3 0 100% orgmatt/metabolism/corrections.py 47 6 87% 78-84, 122 orgmatt/metabolism/metabolic_model.py 89 13 85% 96-97, 123, 128, 133, 138, 143, 189, 228-229, 248, 259, 264 orgmatt/metabolism/nutrient_flows.py 23 6 74% 29, 43, 47-50 orgmatt/nutrients/__init__.py 3 0 100% orgmatt/nutrients/all_nutrients.py 56 2 96% 147, 201 orgmatt/nutrients/nitrogen.py 44 1 98% 173 orgmatt/nutrients/phosphorus.py 44 2 95% 169, 175 orgmatt/plot/__init__.py 3 0 100% orgmatt/plot/distributions.py 66 8 88% 72, 81-82, 89, 127, 180, 195, 198 orgmatt/units.py 124 9 93% 108-112, 115, 118, 121, 188, 207, 215 --------------------------------------------------------------------- TOTAL 847 58 93% |
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+ cd OrgMatt
++ git show -s --pretty=%D HEAD
++ grep -v HEAD
++ tr -s ', /' '\n'
++ sed -n 2p
+ GIT_BRANCH=main
+ set +x
% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 126 100 66 100 60 133 121 --:--:-- --:--:-- --:--:-- 255
{"build_triggered":true,"project":"orgmatt","versions":["latest"]} |