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geograph

GeoGraph provides a tool for analysing habitat fragmentation and related problems in landscape ecology. GeoGraph builds a geospatially referenced graph from land cover or field survey data and enables graph-based landscape ecology analysis as well as interactive visualizations.

https://github.com/ai4er-cdt/geograph

Science Score: 72.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    7 of 16 committers (43.8%) from academic institutions
  • ✓
    Institutional organization owner
    Organization ai4er-cdt has institutional domain (ai4er-cdt.esc.cam.ac.uk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary

Keywords

biodiversity biodiversity-informatics landcover landscape-connectivity landscape-ecology landscape-evolution python remote-sensing

Keywords from Contributors

mesh interactive
Last synced: 6 months ago · JSON representation ·

Repository

GeoGraph provides a tool for analysing habitat fragmentation and related problems in landscape ecology. GeoGraph builds a geospatially referenced graph from land cover or field survey data and enables graph-based landscape ecology analysis as well as interactive visualizations.

Basic Info
Statistics
  • Stars: 40
  • Watchers: 8
  • Forks: 10
  • Open Issues: 14
  • Releases: 2
Topics
biodiversity biodiversity-informatics landcover landscape-connectivity landscape-ecology landscape-evolution python remote-sensing
Created about 5 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License Citation

README.md

GeoGraph

Binder License: MIT Code style: black Documentation Status PyPI version DOI

GeoGraphViewer demo gif

Table of contents: 1. Description 1. Installation 1. Requirements 1. Documentation

1. Description

GeoGraph provides a tool for analysing habitat fragmentation, related problems in landscape ecology. GeoGraph builds a geospatially referenced graph from land cover or field survey data and enables graph-based landscape ecology analysis as well as interactive visualizations. Beyond the graph-based features, GeoGraph also enables the computation of common landscape metrics.

2. Installation

GeoGraph is available via pip, so you can install it using

pip install geograph

Done, you're ready to go!

See the documentation for a full getting started guide.

3. Requirements

GeoGraph is written in Python 3.8 and builds on NetworkX, ipyleaflet and many more packages. See the requirements directory for a full list of dependencies.

4. Documentation

Our documentation is available at geograph.readthedocs.io.

Owner

  • Name: AI for Environmental Risk
  • Login: ai4er-cdt
  • Kind: organization
  • Location: Cambridge, UK

UKRI Centre for Doctoral Training in the Application of AI to the study of Environmental Risks, University of Cambridge and British Antarctic Survey

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Bradley"
    given-names: "Herbie"
    orcid: "https://orcid.org/0000-0001-5390-1257"
  - family-names: "Mathis"
    given-names: "Simon Valentin"
    orcid: "https://orcid.org/0000-0002-5246-6481"
  - family-names: "Findeis"
    given-names: "Arduin"
    orcid: "https://orcid.org/0000-0003-2163-3854"
  - family-names: "Thomas"
    given-names: "Simon D.A."
    orcid: "https://orcid.org/0000-0001-7911-1659"
  - family-names: "Li"
    given-names: "Yilin"
    orcid: "https://orcid.org/0000-0002-7378-8615"
  - family-names: "Green"
    given-names: "Katherine"
    orcid: "https://orcid.org/0000-0003-4664-3354"
  - family-names: "Ashton-Butt"
    given-names: "Adham"
    orcid: "https://orcid.org/0000-0002-6926-6099"
  - family-names: "Rogers"
    given-names: "Martin"
    orcid: "https://orcid.org/0000-0003-0056-2030"
  - family-names: "Dowling"
    given-names: "Tom"
    orcid: "https://orcid.org/0000-0003-0569-4462"
title: "Geograph"
version: 0.0.2
doi: 10.5281/zenodo.4774141
date-released: 2021-05-19
url: "https://github.com/ai4er-cdt/geograph"

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 678
  • Total Committers: 16
  • Avg Commits per committer: 42.375
  • Development Distribution Score (DDS): 0.671
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Simon Mathis s****4@c****k 223
rdnfn 7****n 198
Herbie Bradley m****l@h****m 96
Simon Thomas s****2@c****k 57
Simon Mathis (WSL Ubuntu 18.04) s****s@g****m 42
Simon D.A. Thomas 3****2 18
KMacfarlaneGreen k****2@c****k 17
Crystallee1104 l****4@1****m 13
Simon Thomas s****n@u****k 3
Simon Thomas s****n@u****k 3
Simon Thomas s****n@s****l 2
Yilin Li l****4@s****k 2
Katie Green k****n@s****k 1
ai4er-cookiecutter c****r@h****g 1
Crystallee1104 7****4 1
dependabot[bot] 4****] 1
Committer Domains (Top 20 + Academic)
cam.ac.uk: 3 has-no-mail.org: 1 sci2.jasmin.ac.uk: 1 sci1.jasmin.ac.uk: 1 user-32-234.vpn.net.private.cam.ac.uk: 1 user-32-199.vpn.net.private.cam.ac.uk: 1 163.com: 1 herbiebradley.com: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 38
  • Total pull requests: 56
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Total issue authors: 6
  • Total pull request authors: 8
  • Average comments per issue: 1.89
  • Average comments per pull request: 1.23
  • Merged pull requests: 46
  • Bot issues: 0
  • Bot pull requests: 1
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
  • rdnfn (17)
  • Croydon-Brixton (8)
  • sdat2 (6)
  • herbiebradley (3)
  • CWen001 (2)
  • rockbusteriitk (2)
Pull Request Authors
  • Croydon-Brixton (16)
  • rdnfn (15)
  • herbiebradley (11)
  • sdat2 (9)
  • lucbettaieb (2)
  • Crystallee1104 (2)
  • kenzaxtazi (1)
  • dependabot[bot] (1)
Top Labels
Issue Labels
concerns: GeoGraph (15) kind: feature (12) kind: enhancement (7) kind: documentation (5) concerns: model (4) concerns: user-interface (4) kind: bug (4) concerns: metrics (4) concerns: distribution (3) kind: performance (3) concerns: report (3) concerns: case study (2) concerns: evaluation (2) action: duplicate (2) concerns: architecture (1) concerns: preprocessing (1) requires: benchmarks (1) action: good first issue (1) kind: question (1)
Pull Request Labels
kind: feature (12) concerns: GeoGraph (8) kind: enhancement (6) concerns: model (5) kind: documentation (4) concerns: user-interface (3) kind: performance (2) concerns: metrics (2) dependencies (1) kind: bug (1) concerns: case study (1) concerns: preprocessing (1) concerns: evaluation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 16 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 3
pypi.org: geograph

Group Team Challenge 2021 - Biodiversity Team

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 16 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Average: 24.0%
Downloads: 40.3%
Maintainers (3)
herbiebradley rdnfn Croydon-Brixton
Last synced: 7 months ago

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/python-package.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
binder/environment.yml pypi
binder/requirements.txt pypi
  • descartes ==1.1.0
  • folium ==0.12.1
  • geopandas ==0.9.0
  • ipyleaflet ==0.13.6
  • jupyter ==1.0.0
  • matplotlib ==3.3.4
  • netcdf4 *
  • networkx ==2.5
  • numpy ==1.22.0
  • pandas ==1.2.3
  • pylandstats ==2.2.1
  • rasterio ==1.1.8
  • rioxarray ==0.3.1
  • rtree ==0.9.7
  • seaborn ==0.11.1
  • shapely ==1.7.1
  • tqdm ==4.59.0
  • xarray ==0.17.0
requirements/dev-requirements.txt pypi
  • black * development
  • bottleneck * development
  • dask * development
  • descartes * development
  • fiona * development
  • folium * development
  • geopandas * development
  • geopy * development
  • google-api-python-client * development
  • google-auth-httplib2 * development
  • google-auth-oauthlib * development
  • graphviz * development
  • hydra-core * development
  • imageio * development
  • imageio-ffmpeg * development
  • ipyleaflet * development
  • isort * development
  • jupyterlab * development
  • matplotlib * development
  • mypy * development
  • netCDF4 * development
  • networkx * development
  • numba * development
  • numpy * development
  • pandas * development
  • pillow * development
  • pre-commit * development
  • pycrs * development
  • pydocstyle * development
  • pylint * development
  • python-dotenv * development
  • pytorch-lightning * development
  • rasterio * development
  • rioxarray * development
  • rtree * development
  • scipy * development
  • seaborn * development
  • shapely * development
  • sklearn * development
  • torch ==1.8 development
  • torchvision * development
  • tqdm * development
  • twine * development
  • wandb * development
  • xarray * development
  • xgboost * development
requirements/doc-requirements.txt pypi
  • black *
  • bottleneck *
  • dask *
  • descartes *
  • fiona *
  • folium *
  • geopandas *
  • geopy *
  • google-api-python-client *
  • google-auth-httplib2 *
  • google-auth-oauthlib *
  • graphviz *
  • hydra-core *
  • imageio *
  • imageio-ffmpeg *
  • ipyleaflet *
  • isort *
  • jupyterlab *
  • matplotlib *
  • mypy *
  • nbsphinx *
  • nbsphinx-link *
  • netCDF4 *
  • networkx *
  • numba *
  • numpy *
  • pandas *
  • pillow *
  • pre-commit *
  • pycrs *
  • pydocstyle *
  • pylint *
  • python-dotenv *
  • pytorch-lightning *
  • rasterio *
  • rioxarray *
  • rtree *
  • scipy *
  • seaborn *
  • shapely *
  • sklearn *
  • sphinx *
  • sphinx-autodoc-typehints *
  • torch ==1.8
  • torchvision *
  • tqdm *
  • wandb *
  • xarray *
  • xgboost *
requirements/environment.yml pypi
requirements/requirements.txt pypi
  • folium *
  • geopandas *
  • ipyleaflet *
  • networkx *
  • numpy *
  • pandas *
  • rasterio ==1.1.8
  • rtree *
  • shapely *
  • tqdm *
  • xarray *
requirements/test-requirements.txt pypi
  • click * test
  • coverage * test
  • flake8 * test
  • python-dotenv * test
  • sphinx * test
  • virtualenv * test
setup.py pypi