destine_esa_gfts

Global Fish Tracking Service - DestinE DESP Use Case

https://github.com/destination-earth/destine_esa_gfts

Science Score: 44.0%

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
  • Committers with academic emails
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

destine esa fish pangeo
Last synced: 6 months ago · JSON representation ·

Repository

Global Fish Tracking Service - DestinE DESP Use Case

Basic Info
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 7
  • Open Issues: 14
  • Releases: 1
Topics
destine esa fish pangeo
Created over 2 years ago · Last pushed 8 months ago
Metadata Files
Readme License Code of conduct Citation Codemeta

README.md

Global Fish Tracking Service (GFTS)

A Destination Earth Platform use case.

GFTS Jupyter book

GFTS Jupyter Hub

This repository is the official content repository for the Gloabl FishTracking Service (GFTS), a Destination Earth Platform Use Case procured by ESA.

The GFTS in a nutshell

The lack of accurate modelling of fish movement, migration strategies, and site fidelity is a major challenge for policy-makers when they need to formulate effective conservation policies. By relying on the Pangeo infrastructure on the DestinatE Platform, the Use Case aims to predict the sea bass behavior and develop a Decision Support Tool (DST) for “what-if” scenario planning. As a result, the Use Case will help to obtain accurate insights into fish populations by introducing the Global Fish Tracking System (GFTS) and a Decision Support Tool into the DestinE Platform.

Documentation

Documentation can be viewed at https://destination-earth.github.io/DestinEESAGFTS.

RoHub

Build, Installation, and Execution Instructions

Prerequisites

  • Ensure you have Python 3.11 installed.

Supported Environments

This project is compatible with macOS and Linux distributions with Python 3.11 installed.

Build Instructions

To build this project, ensure you have Python 3 and all the necessary Python packages (see environmemt.yml) installed on your system.

Clone the github repository

To get a local copy of the GFTS repository, you can clone it on your local computer and/or server:

bash git clone https://github.com/destination-earth/DestinE_ESA_GFTS.git

Installation Instructions [local installation]

The sections below explain how to install and run DestinEESAGFTS jupyter notebooks locally from source. We assume you have already cloned the github repository.

Jupyter notebooks to showcase GFTS are in the docs folder and can be run after installing Python and the required packages listed in the .binder/environment.yml file.

Installation with Conda

To install Python, we recommend to install conda or miniconda and then create a new conda environment using .binder/environment.yml:

bash conda env create -f environment.yml

Do not forget to switch to the gfts conda environment prior to executing any Jupyter notebooks or programs from the GFTS repository.

bash conda activate gfts

To deactivate the gfts environment:

bash conda deactivate

Execution Instructions

The section below explains how to start JupyerLab and run the Jupyter notebooks.

Once all the required packages are installed, you can start JupyterLab and execute the jupyter notebooks from the docs folder:

bash jupyter lab

Installation instructions [using containers]

Before building the GFTS docker image, you would need to install docker.

Build docker container

Make sure you change directory to gfts-track-reconstruction/jupyterhub/images/user before executing the command below:

bash docker build -t gfts:latest .

Run GFTS from docker

bash docker run -p 7777:8888 -i -t gfts:latest jupyter lab --ip=0.0.0.0 --no-browser

Open your web browser and enter the following command:

bash http://127.0.0.1:7777/lab

Then you need to enter your token: it can be found at the bottom of the printout you got after running the docker run command given above.

Installation instruction [Deploy GFTS Hub on the cloud]

Instructions on how to build and deploy GFTS hub are described in ./gfts-track-reconstruction/jupyterhub/README.md.

The current Jupyterhub deployment is done on OVH cloud operator.

GFTS webapp

The webapp for this project is being developed in its own repository: github.com/developmentseed/gfts.

Authors

Active contributors

Contributing

Contributions are always welcome!

Tho contribute to DestinE Open Source SW collections please refer to Rule of Participation

Code of Conduct

DestinE open source community abide to this Code of Conduct## Deployment of GFTS Hub on the cloud

Instructions on how to build and deploy GFTS hub are described in ./gfts-track-reconstruction/jupyterhub/README.md.

The current Jupyterhub deployment is done on OVH cloud operator.

Feedback

If you have any feedback, please reach out to us by filling an issue.

Support

For support, please create a Github issue.

Used By

This project is used by the following companies:

🛠 Skills

Python, Jupyter Notebooks.

Citation

Please refer to the whole course as described in the CITATION.cff file

License

The content of this repository is made available under the Apache 2.0 license; for more details, see the LICENSE file.

Funding

This project is funded by the European Space Agency through the Destination Earth Use Case initiative.

Project Status

The project is currently work in progress

Owner

  • Name: destination-earth
  • Login: destination-earth
  • Kind: organization

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: GFTS
message: Global Fish Tracking System
type: software
authors:
  - given-names: Benjamin
    family-names: Ragan-Kelley
    email: minrk@simula.no
    affiliation: "Simula Research Laboratory, Norway"
    orcid: "https://orcid.org/0000-0002-1023-7082"
    credit: "Deployment of the GFTS JupyterHub for the DestinE platform"
    role: Developer
  - given-names: Daniel
    family-names: Wiesmann
    email: danielwiesmann@developmentseed.org
    affiliation: "Development Seed, Portugal"
    orcid: "https://orcid.org/0000-0002-3190-4278"
    credit: "Project coordination; Visualisation"
    role: Project coordinator
  - orcid: "https://orcid.org/0000-0002-1500-0156"
    affiliation: "IFREMER, France"
    given-names: Tina
    family-names: Odaka
    email: tina.odaka@ifremer.fr
    credit: "Develop and run of Pangeo-Fish"
    role: Developer
  - orcid: "https://orcid.org/0000-0002-1784-2920"
    affiliation: "Simula Research Laboratory, France"
    email: annef@simula.no
    family-names: Fouilloux
    given-names: Anne
    credit: "Data-related development; Open Science compliance"
    role: Developer
  - orcid: "https://orcid.org/0000-0002-1032-2105"
    affiliation: "IFREMER, France"
    email: mathieu.woillez@ifremer.fr
    family-names: Woillez
    given-names: Mathieu
    credit: "Scientific advisor; Domain expertise"
    role: Scientific Advisor
identifiers:
  - type: other
    value: >-
      https://w3id.org/ro-id/2edcfa66-0f59-42f4-aa29-1c5681466424
    description: Persistent identifier of the associated RO-Crate
  - type: url
    value: >-
      https://destination-earth.eu/use-cases/global-fish-tracking-system-gfts/
    description: GFTS website.
repository-code: "https://github.com/destination-earth/DestinE_ESA_GFTS"
url: >-
  https://destination-earth.github.io/DestinE_ESA_GFTS/intro.html
abstract: >-
  This project entails the implementation of an advanced
  fish tracking system utilizing biologging data and
  high-resolution ocean temperature and bathymetry.
  Employing state-of-the-art modeling techniques and
  large-scale cloud computing, the initiative focuses on
  accurately estimating the movement of tagged fish.
  Additionally, a Decision Support Tool will be developed to
  present modeling outputs in an intuitive manner, catering
  to the needs of decision-makers in fisheries management.
keywords:
  - fisheries
  - Pangeo
  - ESA
  - DestinE
license: Apache-2.0
commit: c7ba7c1bf0afdc1e5b290644631de5c46fb67b0d
date-released: "2024-06-23"

CodeMeta (codemeta.json)

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "Oceanography",
  "author": [
    {
      "id": "https://orcid.org/0000-0002-1023-7082",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Simula Research Laboratory, Norway"
      },
      "email": "minrk@simula.no",
      "familyName": "Ragan-Kelley",
      "givenName": "Benjamin"
    },
    {
      "type": "Role",
      "schema:author": "https://orcid.org/0000-0002-1023-7082",
      "roleName": "Developer"
    },
    {
      "id": "https://orcid.org/0000-0002-3190-4278",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Development Seed, Portugal"
      },
      "email": "danielwiesmann@developmentseed.org",
      "familyName": "Wiesmann",
      "givenName": "Daniel"
    },
    {
      "type": "Role",
      "schema:author": "https://orcid.org/0000-0002-3190-4278",
      "roleName": "coordinator"
    },
    {
      "id": "https://orcid.org/0000-0002-1500-0156",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "IFREMER, France"
      },
      "email": "tina.odaka@ifremer.fr",
      "familyName": "Odaka",
      "givenName": "Tina"
    },
    {
      "type": "Role",
      "schema:author": "https://orcid.org/0000-0002-1500-0156",
      "roleName": "Developer"
    },
    {
      "id": "https://orcid.org/0000-0002-1784-2920",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Simula Research Laboratory, Norway"
      },
      "email": "annef@simula.no",
      "familyName": "Fouilloux",
      "givenName": "Anne"
    },
    {
      "type": "Role",
      "schema:author": "https://orcid.org/0000-0002-1784-2920",
      "roleName": "Developer"
    },
    {
      "id": "https://orcid.org/0000-0002-1032-2105",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "IFREMER, France"
      },
      "email": "mathieu.woillez@ifremer.fr",
      "familyName": "Woillez",
      "givenName": "Mathieu"
    }
  ],
  "codeRepository": "git+https://github.com/destination-earth/DestinE_ESA_GFTS",
  "dateCreated": "2023-11-16",
  "description": "The Global Fish Tracking System (GFTS) is a Destination Earth Platform use case. The lack of accurate modelling of fish movement, migration strategies, and site fidelity is a major challenge for policy-makers when they need to formulate effective conservation policies. By relying on the Pangeo infrastructure on the DestinatE Platform, the Use Case aims to predict the sea bass behavior and develop a Decision Support Tool (DST) for what-if scenario planning. As a result, the Use Case will help to obtain accurate insights into fish populations by introducing the Global Fish Tracking System (GFTS) and a Decision Support Tool into the DestinE Platform.",
  "funder": {
    "type": "Organization",
    "name": "ESA"
  },
  "keywords": [
    "Fish",
    "ESA",
    "DestinE",
    "Pangeo",
    "Climate"
  ],
  "license": "https://spdx.org/licenses/Apache-2.0",
  "name": "GFTS",
  "operatingSystem": "Linux",
  "programmingLanguage": "Python 3",
  "relatedLink": [
    "https://destination-earth.eu/use-cases/global-fish-tracking-system-gfts/",
    "https://w3id.org/ro-id/2edcfa66-0f59-42f4-aa29-1c5681466424"
  ],
  "softwareRequirements": "https://github.com/destination-earth/DestinE_ESA_GFTS/blob/main/.binder/environment.yml",
  "developmentStatus": "active",
  "funding": "Destination Earth ESA use case",
  "issueTracker": "https://github.com/destination-earth/DestinE_ESA_GFTS/issues"
}

GitHub Events

Total
  • Create event: 39
  • Release event: 1
  • Issues event: 32
  • Watch event: 4
  • Delete event: 33
  • Member event: 2
  • Issue comment event: 82
  • Push event: 211
  • Pull request review comment event: 3
  • Pull request review event: 15
  • Pull request event: 101
Last Year
  • Create event: 39
  • Release event: 1
  • Issues event: 32
  • Watch event: 4
  • Delete event: 33
  • Member event: 2
  • Issue comment event: 82
  • Push event: 211
  • Pull request review comment event: 3
  • Pull request review event: 15
  • Pull request event: 101

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 8
  • Total Committers: 3
  • Avg Commits per committer: 2.667
  • Development Distribution Score (DDS): 0.375
Past Year
  • Commits: 8
  • Committers: 3
  • Avg Commits per committer: 2.667
  • Development Distribution Score (DDS): 0.375
Top Committers
Name Email Commits
Anne Fouilloux a****f@s****o 5
Daniel Wiesmann y****p 2
Daniel Wiesmann d****l@w****t 1
Committer Domains (Top 20 + Academic)

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 10
  • Total pull requests: 36
  • Average time to close issues: 5 months
  • Average time to close pull requests: 14 days
  • Total issue authors: 4
  • Total pull request authors: 6
  • Average comments per issue: 2.2
  • Average comments per pull request: 0.72
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 36
  • Average time to close issues: 5 months
  • Average time to close pull requests: 14 days
  • Issue authors: 4
  • Pull request authors: 6
  • Average comments per issue: 2.2
  • Average comments per pull request: 0.72
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
  • yellowcap (11)
  • tinaok (5)
  • pantierra (4)
  • QuentinMaz (2)
  • minrk (2)
  • keewis (1)
  • annefou (1)
Pull Request Authors
  • minrk (49)
  • annefou (29)
  • yellowcap (17)
  • pantierra (10)
  • tinaok (7)
  • QuentinMaz (5)
  • aderrien7 (4)
  • danielfdsilva (1)
Top Labels
Issue Labels
enhancement (1) help wanted (1)
Pull Request Labels
documentation (1)

Dependencies

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.github/workflows/deploy.yml actions
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jupyterhub/images/user/Dockerfile docker
  • quay.io/pangeo/pangeo-notebook 2024.01.23 build
jupyterhub/images/user/requirements.txt pypi
  • jupyterhub ==4.0.2
jupyterhub/requirements.txt pypi
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pyproject.toml pypi
.github/workflows/pre-commit.yaml actions
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.github/workflows/test-image.yaml actions
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.binder/environment.yml conda
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jupyterhub/images/user/conda-requirements.txt pypi
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