~tfardet/#1196327

success

5fda53bTanguy Fardet

Improved corrections (metabolism), flow_fractions

Owner
~tfardet
Created
7 months ago
Updated
7 months ago
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[#1196327] 2024/04/15 11:34:09 Booting image ubuntu/lts (default) on port 22651
[#1196327] 2024/04/15 11:34:09 Waiting for guest to settle
[#1196327] 2024/04/15 11:34:17 Sending tasks
[#1196327] 2024/04/15 11:34:19 Sending build environment
[#1196327] 2024/04/15 11:34:20 Sending secrets
[#1196327] 2024/04/15 11:34:20 Resolving secret 69332acb-b779-4bb2-ae8a-719f8e150ace
[#1196327] 2024/04/15 11:34:20 Installing packages
Warning: Permanently added '[localhost]:22651' (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]
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Hit:4 http://archive.ubuntu.com/ubuntu jammy-backports InRelease
Get:5 http://archive.ubuntu.com/ubuntu jammy-security/main amd64 Packages [1343 kB]
Get:6 http://archive.ubuntu.com/ubuntu jammy-security/main Translation-en [237 kB]
Get:7 http://archive.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [1670 kB]
Get:8 http://archive.ubuntu.com/ubuntu jammy-security/restricted Translation-en [280 kB]
Get:9 http://archive.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [853 kB]
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Get:11 http://archive.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [37.2 kB]
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Get:20 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse Translation-en [12.1 kB]
Fetched 10.0 MB in 2s (5363 kB/s)
Reading package lists...
Warning: Permanently added '[localhost]:22651' (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 13 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]
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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 (8327 kB/s)
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(Reading database ... 39101 files and directories currently installed.)
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Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ...
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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 (2.35-0ubuntu3.6) ...
[#1196327] 2024/04/15 11:34:26 Cloning repositories
Cloning into 'OrgMatt'...
+ cd OrgMatt
+ git checkout -q 5fda53bca29e3b1a01043fe9a41699de36ed3e50
+ cd OrgMatt
+ git submodule update --init --recursive
[#1196327] 2024/04/15 11:34:27 Running task path
[#1196327] 2024/04/15 11:34:28 Running task check
[#1196327] 2024/04/15 11:34:31 Running task setup
[#1196327] 2024/04/15 11:34:46 Running task test
[#1196327] 2024/04/15 11:34:59 Running task doc
path
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+ echo 'export PATH=$PATH:/home/build/.local/bin'
check
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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 15.5 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 Jinja2<4.0.0,>=3.0.0
  Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 KB 48.0 MB/s eta 0:00:00
Collecting license-expression>=1.0
  Downloading license_expression-30.3.0-py3-none-any.whl (108 kB)
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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 binaryornot<0.5.0,>=0.4.4
  Downloading binaryornot-0.4.4-py2.py3-none-any.whl (9.0 kB)
Collecting boolean.py>=3.8
  Downloading boolean.py-4.0-py3-none-any.whl (25 kB)
Collecting chardet>=3.0.2
  Downloading chardet-5.2.0-py3-none-any.whl (199 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 KB 58.4 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 Jinja2-3.1.3 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: BSD-2-Clause, Python-2.0, CC-BY-SA-4.0, CC0-1.0, GPL-3.0-or-later, CC-BY-4.0
* 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)
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Collecting pytest
  Downloading pytest-8.1.1-py3-none-any.whl (337 kB)
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Requirement already satisfied: setuptools in /usr/lib/python3/dist-packages (59.6.0)
Collecting setuptools
  Downloading setuptools-69.5.1-py3-none-any.whl (894 kB)
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Collecting iniconfig
  Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting tomli>=1
  Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting exceptiongroup>=1.0.0rc8
  Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB)
Collecting pluggy<2.0,>=1.4
  Downloading pluggy-1.4.0-py3-none-any.whl (20 kB)
Collecting packaging
  Downloading packaging-24.0-py3-none-any.whl (53 kB)
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Installing collected packages: tomli, setuptools, pluggy, pip, packaging, iniconfig, exceptiongroup, pytest
Successfully installed exceptiongroup-1.2.0 iniconfig-2.0.0 packaging-24.0 pip-24.0 pluggy-1.4.0 pytest-8.1.1 setuptools-69.5.1 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-1.13.0-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))
  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-0.23-py3-none-any.whl.metadata (8.1 kB)
Collecting openscm-units (from -r requirements.txt (line 9))
  Downloading openscm_units-0.5.4-py3-none-any.whl.metadata (3.9 kB)
Collecting seaborn (from -r requirements.txt (line 10))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
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Collecting pillow>=8 (from matplotlib!=3.6.1,>=3.4->seaborn->-r requirements.txt (line 10))
  Downloading pillow-10.3.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (9.2 kB)
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Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->-r requirements.txt (line 7))
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Installing collected packages: pytz, globalwarmingpotentials, tzdata, typing-extensions, six, pyparsing, pillow, numpy, kiwisolver, fonttools, cycler, scipy, python-dateutil, pint, contourpy, pandas, matplotlib, seaborn, openscm-units
Successfully installed contourpy-1.2.1 cycler-0.12.1 fonttools-4.51.0 globalwarmingpotentials-0.9.4 kiwisolver-1.4.5 matplotlib-3.8.4 numpy-1.26.4 openscm-units-0.5.4 pandas-2.2.2 pillow-10.3.0 pint-0.23 pyparsing-3.1.2 python-dateutil-2.9.0.post0 pytz-2024.1 scipy-1.13.0 seaborn-0.13.2 six-1.16.0 typing-extensions-4.11.0 tzdata-2024.1
+ pip install coverage
Defaulting to user installation because normal site-packages is not writeable
Collecting coverage
  Downloading coverage-7.4.4-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-7.4.4-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-7.4.4
+ 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==0.4.0) (1.26.4)
Requirement already satisfied: scipy in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.0) (1.13.0)
Requirement already satisfied: pandas in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.0) (2.2.2)
Requirement already satisfied: pint>=0.19 in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.0) (0.23)
Requirement already satisfied: openscm-units in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.0) (0.5.4)
Requirement already satisfied: seaborn in /home/build/.local/lib/python3.10/site-packages (from OrgMatt==0.4.0) (0.13.2)
Requirement already satisfied: typing-extensions in /home/build/.local/lib/python3.10/site-packages (from pint>=0.19->OrgMatt==0.4.0) (4.11.0)
Requirement already satisfied: globalwarmingpotentials in /home/build/.local/lib/python3.10/site-packages (from openscm-units->OrgMatt==0.4.0) (0.9.4)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.4.0) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.4.0) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in /home/build/.local/lib/python3.10/site-packages (from pandas->OrgMatt==0.4.0) (2024.1)
Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /home/build/.local/lib/python3.10/site-packages (from seaborn->OrgMatt==0.4.0) (3.8.4)
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==0.4.0) (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==0.4.0) (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==0.4.0) (4.51.0)
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==0.4.0) (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==0.4.0) (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==0.4.0) (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==0.4.0) (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==0.4.0) (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-0.4.0-py3-none-any.whl size=109414 sha256=50ab8e1aa251a2701ac3c790fe8f228eb0aa037901495e0b73fa00864ede0200
  Stored in directory: /tmp/pip-ephem-wheel-cache-bognudya/wheels/fa/c8/54/6668a436f152ec271fbc43c4d4817e40063b0c2195101cffa1
Successfully built OrgMatt
Installing collected packages: OrgMatt
Successfully installed OrgMatt-0.4.0
test
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+ cd OrgMatt
+ coverage run -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.10.12, pytest-8.1.1, pluggy-1.4.0
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 12.17s ==============================
+ coverage report -m
Name                                    Stmts   Miss  Cover   Missing
---------------------------------------------------------------------
orgmatt/__init__.py                        26      0   100%
orgmatt/_utils/__init__.py                  4      0   100%
orgmatt/_utils/logger.py                   24      2    92%   37, 43
orgmatt/_utils/tools.py                   260      9    97%   245, 266, 377-380, 388-389, 398, 410
orgmatt/agrifood/__init__.py                3      0   100%
orgmatt/agrifood/biowaste.py               22      2    91%   80, 83
orgmatt/agrifood/human_consumption.py      26      0   100%
orgmatt/data/__init__.py                   45      0   100%
orgmatt/excreta.py                         24      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              4      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%   159, 229
orgmatt/nutrients/nitrogen.py              12      0   100%
orgmatt/nutrients/phosphorus.py            12      0   100%
orgmatt/plot/__init__.py                    3      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                                    1022     44    96%
doc
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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
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   126  100    66  100    60     94     86 --:--:-- --:--:-- --:--:--   181
100   126  100    66  100    60     94     86 --:--:-- --:--:-- --:--:--   181
{"build_triggered":true,"project":"orgmatt","versions":["latest"]}
Build complete: success 7 months ago (took 51 seconds)