https://github.com/axiom-data-science/extract_model
Facilitates read-in and extraction for ocean model output.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 6 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.5%) to scientific vocabulary
Keywords from Contributors
Repository
Facilitates read-in and extraction for ocean model output.
Basic Info
- Host: GitHub
- Owner: axiom-data-science
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://extract-model.readthedocs.io/
- Size: 12.3 MB
Statistics
- Stars: 5
- Watchers: 4
- Forks: 4
- Open Issues: 5
- Releases: 37
Metadata Files
README.md
extract_model
Facilitates read-in and extraction for ocean model output. Most functions work on both structured and unstructured model output. Unstructured functionality has been tested with FVCOM and SELFE output.
In particular this package can:
- interpolate a model time series to a longitude, latitude location on a 2D grid, while bringing along the calculated z coordinates, with select()
- saves the weights of the interpolation to save time in the accessor if used, or allows user to input
- uses xESMF for fast interpolation that respects longitude/latitude grids
- find the nearest grid point to a longitude, latitude location on a horizontal grid (structured or unstructured) in sel2d() using xoak
- xoak saves the calculated index so that subsequent searches are faster
- select a sub-region of a structured or unstructured grid in two ways with sub_bbox() and sub_grid()
- has an xarray accessor for convenient access to methods
- uses cf-xarray to understand xarray Dataset metadata and allow for generic axis and coordinate names as well as calculate vertical coordinates
- can preprocess a variety of model output types (including ROMS, HYCOM, POM, and FVCOM) to improve metadata and ease of use
:warning: If you are using Windows: Horizontal interpolation currently will not work in
extract_modeluntilxESMFis installable on Windows. Other functions will work.
Project based on the cookiecutter science project template.
Installation
From conda-forge
This will install for all operating systems:
bash
conda install -c conda-forge extract_model
but it includes only minimal requirements. If you want to install packages to run the example docs notebooks and to make unstructured grid subsetting faster, you can additionally install for Windows:
bash
$ conda install --file conda-requirements-opt-win.txt
For running the example docs notebooks, horizontal interpolation (with xESMF), and to make horizontal subsetting faster, install additional packages for Mac and Linux:
bash
$ conda install --file conda-requirements-opt.txt
From PyPI
bash
pip install extract_model
With environment
Clone the repo:
bash
$ git clone https://github.com/axiom-data-science/extract_model.git
In the extract_model directory, install conda environment (for Mac or Linux):
bash
$ conda env create -f environment.yml
or for Windows:
bash
$ conda env create -f environment-win.yml
Local
For local package install, after cloning the repository, in the extract_model directory:
bash
$ pip install -e .
Development
To also develop this package, install additional packages with:
bash
$ conda install --file requirements-dev.txt
To then check code before committing and pushing it to github, locally run
bash
$ pre-commit run --all-files
Owner
- Name: Axiom Data Science
- Login: axiom-data-science
- Kind: organization
- Location: United States
- Website: https://www.axiomdatascience.com/
- Repositories: 64
- Profile: https://github.com/axiom-data-science
GitHub Events
Total
- Release event: 2
- Delete event: 1
- Issue comment event: 10
- Push event: 8
- Pull request event: 9
- Create event: 6
Last Year
- Release event: 2
- Delete event: 1
- Issue comment event: 10
- Push event: 8
- Pull request event: 9
- Create event: 6
Committers
Last synced: about 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Kristen Thyng | k****n@a****o | 152 |
| Kristen Thyng | k****g@g****m | 76 |
| Luke Campbell | l****e@a****m | 52 |
| dependabot[bot] | 4****]@u****m | 5 |
| Kyle Wilcox | k****e@a****m | 3 |
| Chris Barker | C****r@n****v | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 5
- Total pull requests: 99
- Average time to close issues: 3 months
- Average time to close pull requests: 1 day
- Total issue authors: 3
- Total pull request authors: 6
- Average comments per issue: 1.6
- Average comments per pull request: 0.73
- Merged pull requests: 96
- Bot issues: 0
- Bot pull requests: 12
Past Year
- Issues: 0
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: 8 days
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 3
Top Authors
Issue Authors
- ChrisBarker-NOAA (3)
- yosoyjay (1)
- kwilcox (1)
Pull Request Authors
- kthyng (70)
- dependabot[bot] (18)
- lukecampbell (16)
- kwilcox (1)
- yosoyjay (1)
- ChrisBarker-NOAA (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 88 last-month
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Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 4
(may contain duplicates) - Total versions: 21
- Total maintainers: 2
pypi.org: extract-model
Facilitates read-in and extraction for ocean model output.
- Homepage: https://github.com/axiom-data-science/extract_model
- Documentation: https://extract-model.readthedocs.io/
- License: MIT
-
Latest release: 1.4.3
published 11 months ago
Rankings
conda-forge.org: extract_model
- Homepage: https://github.com/axiom-data-science/extract_model
- License: MIT
-
Latest release: 0.9.0
published almost 4 years ago
Rankings
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pre-commit/action v3.0.0 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish master composite
- actions/cache v3 composite
- actions/checkout v3 composite
- codecov/codecov-action v3 composite
- conda-incubator/setup-miniconda v2 composite
- cmocean *
- matplotlib-base *
- numba *
- pooch *
- xcmocean *
- cmocean *
- matplotlib-base *
- numba *
- pooch *
- xcmocean *
- xesmf *
- black * development
- check-manifest * development
- doctr * development
- flake8 * development
- flake8-builtins * development
- flake8-comprehensions * development
- flake8-mutable * development
- flake8-print * development
- isort * development
- mypy * development
- nbsphinx * development
- pre-commit * development
- pylint * development
- pytest * development
- pytest-cov * development
- pytest-xdist * development
- setuptools_scm * development
- sphinx * development
- twine * development
- wheel * development
- zarr * development
- cf_xarray
- cmocean
- dask <=2022.05.0
- furo
- ipykernel
- ipython
- jinja2
- jupytext
- matplotlib-base
- myst-nb
- nbconvert
- nbformat
- netcdf4
- numba
- numpy <1.24
- numpydoc
- pandoc
- pip
- pooch
- python 3.8.*
- recommonmark
- requests
- scikit-learn
- sphinx
- sphinx_rtd_theme
- xarray
- xcmocean
- xesmf
- xoak