destine_esa_gfts
Global Fish Tracking Service - DestinE DESP Use Case
Science Score: 44.0%
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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
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary
Keywords
Repository
Global Fish Tracking Service - DestinE DESP Use Case
Basic Info
- Host: GitHub
- Owner: destination-earth
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://destination-earth.github.io/DestinE_ESA_GFTS/
- Size: 25.1 MB
Statistics
- Stars: 13
- Watchers: 4
- Forks: 7
- Open Issues: 14
- Releases: 1
Topics
Metadata Files
README.md
Global Fish Tracking Service (GFTS)
A Destination Earth Platform use case.
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.
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
- Repositories: 1
- Profile: https://github.com/destination-earth
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
Top Committers
| Name | 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
Pull Request Labels
Dependencies
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- peaceiris/actions-gh-pages v3 composite
- quay.io/pangeo/pangeo-notebook 2024.01.23 build
- jupyterhub ==4.0.2
- chartpress *
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- actions/cache v4 composite
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- eccodes >=2.35.0
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