Science Score: 39.0%
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✓DOI references
Found 5 DOI reference(s) in README -
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Low similarity (15.6%) to scientific vocabulary
Keywords
Repository
Marine carbonate system calculations in Python
Basic Info
- Host: GitHub
- Owner: mvdh7
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Homepage: https://pyco2sys.readthedocs.io
- Size: 137 MB
Statistics
- Stars: 56
- Watchers: 7
- Forks: 15
- Open Issues: 3
- Releases: 30
Topics
Metadata Files
README.md
PyCO2SYS
Public beta testing for PyCO2SYS v2 is now live!
See the v2 docs at mvdh.xyz/PyCO2SYS for instructions and please provide feedback!
Introduction
PyCO2SYS is a Python implementation of CO2SYS, based on the MATLAB v2.0.5 but also including the updates made for MATLAB CO2SYS v3 as well as some additional related calculations. PyCO2SYS solves the full marine carbonate system from the values of any two of its parameters.
Every combination of input parameters has been tested, with differences in the results small enough to be attributable to floating point errors and iterative solver endpoint differences (i.e. negligible). See the scripts in validate to see how and check this for yourself, and their discussion in the online docs. Please let us know ASAP if you discover a discrepancy that we have not spotted!
Documentation is available online at PyCO2SYS.readthedocs.io.
There are also some usage examples that you can either download or run live in your web browser (with no Python installation required) at PyCO2SYS-examples.
Citation
A paper describing PyCO2SYS is freely available:
Humphreys, M. P., Lewis, E. R., Sharp, J. D., and Pierrot, D. (2022). PyCO2SYS v1.8: marine carbonate system calculations in Python. Geoscientific Model Development 15, 15-43. doi:10.5194/gmd-15-15-2022.
Please also specify the full version number that you used. You can find this in Python with:
python
import PyCO2SYS as pyco2
pyco2.hello()
As per the instructions in the the CO2SYS-MATLAB repo, you should also consider citing the original work by Lewis and Wallace (1998).
Installation
If you manage Python with conda, we recommend that you first install NumPy, pandas and xarray into the environment where PyCO2SYS is to be installed with conda.
With pip
Install from the Python Package Index:
pip install PyCO2SYS
Update an existing installation:
pip install PyCO2SYS --upgrade --no-cache-dir
With conda/mamba
Install from the conda-forge channel:
conda install PyCO2SYS -c conda-forge
Documentation
Documentation for the current release, based on the main branch, is available at PyCO2SYS.readthedocs.io and at mvdh.xyz/PyCO2SYS.
Basic use
The only function you need is pyco2.sys. To solve the marine carbonate system from two of its parameters (par1 and par2), just use:
python
import PyCO2SYS as pyco2
results = pyco2.sys(par1, par2, par1_type, par2_type, **kwargs)
The keys to the results dict are described in the documentation. Arguments should be provided as scalars or NumPy arrays in any mutually broadcastable combination. A large number of optional kwargs can be provided to specify everything beyond the carbonate system parameters — read the docs!.
You can also look at the examples Notebooks that you can try out without needing to install anything on your computer.
About
PyCO2SYS is maintained by Dr Matthew Humphreys at the NIOZ (Royal Netherlands Institute for Sea Research) with the support of the main developers of all previous versions of CO2SYS.
Contributions are welcome - please check the guidelines before setting to work.
License
PyCO2SYS is licensed under the GNU General Public License version 3 (GPLv3).
Owner
- Name: Matthew Humphreys
- Login: mvdh7
- Kind: user
- Location: Texel, the Netherlands
- Company: NIOZ
- Website: seaco2.group
- Repositories: 53
- Profile: https://github.com/mvdh7
Marine carbon cyclist at the Royal Netherlands Institute for Sea Research
GitHub Events
Total
- Create event: 17
- Release event: 4
- Issues event: 10
- Watch event: 7
- Delete event: 7
- Issue comment event: 9
- Push event: 175
- Pull request event: 26
- Pull request review event: 1
- Pull request review comment event: 3
- Fork event: 7
Last Year
- Create event: 17
- Release event: 4
- Issues event: 10
- Watch event: 7
- Delete event: 7
- Issue comment event: 9
- Push event: 175
- Pull request event: 26
- Pull request review event: 1
- Pull request review comment event: 3
- Fork event: 7
Committers
Last synced: 6 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Matthew Humphreys | m****s@i****m | 932 |
| Matthew Humphreys | m****s@g****m | 30 |
| Luke Gregor | l****e@g****m | 5 |
| d-sandborn | d****e@g****m | 4 |
| Ben Cala | 1****1 | 2 |
| AJSchiller | 5****r | 2 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 30
- Total pull requests: 69
- Average time to close issues: 8 months
- Average time to close pull requests: 1 day
- Total issue authors: 9
- Total pull request authors: 6
- Average comments per issue: 1.6
- Average comments per pull request: 0.13
- Merged pull requests: 62
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 24
- Average time to close issues: 4 days
- Average time to close pull requests: 1 day
- Issue authors: 3
- Pull request authors: 3
- Average comments per issue: 1.5
- Average comments per pull request: 0.17
- Merged pull requests: 20
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mvdh7 (19)
- VeckoTheGecko (2)
- d-sandborn (2)
- uliw (2)
- gmacgilchrist (1)
- davidclemens (1)
- pfheiter (1)
- lukegre (1)
- rossidae (1)
Pull Request Authors
- mvdh7 (52)
- bcala1 (6)
- VeckoTheGecko (5)
- AJSchiller (3)
- d-sandborn (2)
- lukegre (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
- Total downloads: unknown
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 50
proxy.golang.org: github.com/mvdh7/PyCO2SYS
- Documentation: https://pkg.go.dev/github.com/mvdh7/PyCO2SYS#section-documentation
- License: gpl-3.0
-
Latest release: v1.8.3
published about 2 years ago
Rankings
proxy.golang.org: github.com/mvdh7/pyco2sys
- Documentation: https://pkg.go.dev/github.com/mvdh7/pyco2sys#section-documentation
- License: gpl-3.0
-
Latest release: v1.8.3
published about 2 years ago
Rankings
Dependencies
- mkdocs-material ==7.1.4
- actions/checkout v3 composite
- actions/setup-python v4 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- PyCO2SYS *
- autograd *
- numpy *