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https://github.com/consbio/trefoil

Geospatial operations for NetCDF and numpy

https://github.com/consbio/trefoil

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.8%) to scientific vocabulary

Keywords

geospatial netcdf numpy python rasterio

Keywords from Contributors

packaging interactive projection sequences archival embedded genomics observability autograding hacking
Last synced: 5 months ago · JSON representation

Repository

Geospatial operations for NetCDF and numpy

Basic Info
  • Host: GitHub
  • Owner: consbio
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Size: 1.29 MB
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 3
  • Open Issues: 25
  • Releases: 4
Topics
geospatial netcdf numpy python rasterio
Created almost 11 years ago · Last pushed 8 months ago
Metadata Files
Readme License

README.md

Trefoil (formerly Clover)

Because today might be your lucky day.

**(note: this was renamed from clover on 4/20/2018 due to name conflicts on pypi)

Geospatial operations with NetCDF files and numpy arrays.

Build Status Coverage Status

Why?

We needed a library to consolidate a series of utility scripts and general geospatial operations on NetCDF and numpy arrays. We found we were creating a lot of purpose built scripts for other projects involving lots of processing of NetCDF climate and model outputs. Where possible, we have been pulling out general patterns and placing them here. When we looked for existing work, we didn't find anything that quite met our needs, with a clean API and no strong assertions about data model or compliance with CF-conventions (we aspire to conventions, but not all data meet them).

Specifically, we want to provide:

  • simple and fast API for rendering numpy arrays to images
  • simple API to provide utility functions that make working with NetCDF data easier
  • simple command line interface to make common operations easy and portable
  • analysis operations to simplify using geometries alongside raster data
  • analysis operations to summarize across various dimensions of spatial and temporal-spatial datasets (anything more than 3 dimensions makes our heads hurt!)

We are trying to avoid reimplementing anything well-handled elsewhere. Where possible, we contribute functionality to other libraries (e.g., rasterio) where we think that the functionality is general enough not to depend on living within trefoil.

Where is it being used?

This is a core dependency for ncdjango, our Django-based NetCDF map server.

We are using this on a variety of internal projects within the Conservation Biology Institute.

Installation

Trefoil is available on PyPi. To install, use:

text $ pip install trefoil

Development

Poetry is used for managing dependencies in this project. To develop this project, install its dependencies with:

text $ poetry install

Command line interface

This is currently undergoing heavy development.
See CLI docs for more information.

Work in progress

This is still under active development, as we have time and need. All APIs are subject to change until we hit version 1.0.

Specifically, we need to work on:

  • standardizing API patterns
  • documentation
  • test coverage and correctness
  • roadmap

Contributors:

With inspiration from Tim Sheehan and Ken Ferschweiler.

See Also:

  • rasterio: Geospatial I/O and operations on rasters, done right.
  • OCGIS: Geoprocessing on CF compatible climate datasets.
  • scikit-image: Python image processing
  • python-rasterstats: Summary statistics of rasters using geometries

Owner

  • Name: Conservation Biology Institute
  • Login: consbio
  • Kind: organization
  • Location: Corvallis, OR

GitHub Events

Total
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 5
  • Member event: 1
  • Push event: 12
  • Pull request review event: 16
  • Pull request review comment event: 18
  • Pull request event: 3
  • Create event: 2
Last Year
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 5
  • Member event: 1
  • Push event: 12
  • Pull request review event: 16
  • Pull request review comment event: 18
  • Pull request event: 3
  • Create event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 115
  • Total Committers: 7
  • Avg Commits per committer: 16.429
  • Development Distribution Score (DDS): 0.278
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Brendan Ward b****d@c****g 83
Nik Molnar n****r@c****g 15
Brendan Ward b****d 10
Brendan Ward b****n@U****l 2
dependabot[bot] 4****] 2
Ken Ferschweiler k****f@g****m 2
Brendan C. Ward b****d@a****m 1
Committer Domains (Top 20 + Academic)
consbio.org: 2 astutespruce.com: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 41
  • Total pull requests: 27
  • Average time to close issues: 3 months
  • Average time to close pull requests: 28 days
  • Total issue authors: 4
  • Total pull request authors: 4
  • Average comments per issue: 1.22
  • Average comments per pull request: 1.11
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • brendan-ward (37)
  • TaylorMutch (2)
  • nikmolnar (1)
  • ghost (1)
Pull Request Authors
  • nikmolnar (13)
  • dependabot[bot] (8)
  • brendan-ward (4)
  • kennino (2)
  • klinkow (2)
Top Labels
Issue Labels
enhancement (15) bug (3)
Pull Request Labels
dependencies (8) enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 57 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 5
  • Total versions: 5
  • Total maintainers: 3
pypi.org: trefoil

Geospatial operations with NetCDF files and numpy arrays.

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 5
  • Downloads: 57 Last month
Rankings
Dependent repos count: 6.8%
Dependent packages count: 7.4%
Stargazers count: 15.6%
Forks count: 17.0%
Average: 19.3%
Downloads: 49.7%
Maintainers (3)
bcward databasin nikmolnar
Last synced: 6 months ago

Dependencies

Pipfile pypi
  • pytest * develop
  • pytest-cov * develop
  • twine * develop
  • wheel * develop
  • affine >=1.0
  • click *
  • fiona >=1.6.0
  • jinja2 *
  • netcdf4 >=1.1.1
  • numpy *
  • palettable *
  • pillow ==6.2.0
  • pyproj *
  • pytz *
  • rasterio >=1.0a12
Pipfile.lock pypi
  • attrs ==19.3.0 develop
  • certifi ==2019.9.11 develop
  • chardet ==3.0.4 develop
  • coverage ==4.5.4 develop
  • idna ==2.8 develop
  • more-itertools ==7.2.0 develop
  • pkginfo ==1.5.0.1 develop
  • pluggy ==0.6.0 develop
  • py ==1.8.0 develop
  • pytest ==3.5.0 develop
  • pytest-cov ==2.5.1 develop
  • requests ==2.22.0 develop
  • requests-toolbelt ==0.9.1 develop
  • six ==1.12.0 develop
  • tqdm ==4.36.1 develop
  • twine ==1.11.0 develop
  • urllib3 ==1.25.6 develop
  • wheel ==0.31.0 develop
  • affine ==2.2.0
  • attrs ==19.3.0
  • click ==6.7
  • click-plugins ==1.1.1
  • cligj ==0.5.0
  • enum34 ==1.1.6
  • fiona ==1.7.11.post1
  • jinja2 ==2.10
  • markupsafe ==1.1.1
  • munch ==2.3.2
  • netcdf4 ==1.3.1
  • numpy ==1.14.2
  • palettable ==3.1.0
  • pillow ==6.2.0
  • pyparsing ==2.4.2
  • pyproj ==1.9.5.1
  • pytz ==2018.4
  • rasterio ==1.0a12
  • six ==1.12.0
  • snuggs ==1.4.7
setup.py pypi
  • Numpy *
  • Pillow >=2.9.0
  • affine >=1.0
  • click *
  • fiona >=1.6.0
  • jinja2 *
  • netCDF4 >=1.1.1
  • palettable *
  • pyproj *
  • pytz *
  • rasterio >=1.0a12
  • six *