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‎.github/workflows/build-and-push-jupyterlab-image.yml‎

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name: build-and-push-jupyterlab-image
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on:
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workflow_dispatch: # This allows you to manually trigger the action from GitHub UI.
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v3
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- name: Login to dockerhub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_PASSWORD }}
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- name: Get lowercase repo name (for dynamic tags)
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id: repo_name
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run: |
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lowercase_name=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]')
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echo "repo_name=${lowercase_name}" >> "$GITHUB_OUTPUT"
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- name: Build and push latest
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id: docker_build_jupyterlab
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uses: docker/build-push-action@v5
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with:
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context: containers/jupyterlab
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file: containers/jupyterlab/Dockerfile
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builder: ${{ steps.buildx.outputs.name }}
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push: true
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tags: |
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esiil/${{ steps.repo_name.outputs.repo_name }}_jupyterlab:latest
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- name: Image digest
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run: echo ${{ steps.docker_build_jupyterlab.outputs.digest }}

‎.github/workflows/fetch-template.yml‎

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name: Sync with Template Repository
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on:
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workflow_dispatch:
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jobs:
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sync_template:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout main repository
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uses: actions/checkout@v4
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- name: Configure Git for merge
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run: |
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git config --global user.name "github-actions"
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git config --global user.email "actions@users.noreply.github.com"
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- name: Fetch template repository
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run: git fetch --no-tags --no-recurse-submodules https://github.com/CU-ESIIL/Working_group_OASIS.git +refs/heads/*:refs/remotes/template/*
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- name: Merge changes from template repository
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run: |
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git merge --no-commit --no-ff --allow-unrelated-histories template/main || true
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git checkout --ours .
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git add .
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- name: Commit changes
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run: git commit -am "Merge changes from template repository"
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- name: Push changes
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uses: ad-m/github-push-action@v0.6.0
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/gh-pages.yml‎

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name: Publish docs via GitHub
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on:
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push:
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branches:
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- main
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jobs:
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build:
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name: Deploy docs
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: run requirements file
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run: pip install -r requirements.txt
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- name: Deploy docs
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run: mkdocs gh-deploy --force
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env:
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GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}

‎.gitignore‎

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# History files
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.Rhistory
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.Rapp.history
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# Session Data files
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.RData
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.RDataTmp
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# User-specific files
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.Ruserdata
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# Example code in package build process
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*-Ex.R
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# Output files from R CMD build
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/*.tar.gz
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# Output files from R CMD check
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/*.Rcheck/
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# RStudio files
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.Rproj.user/
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# produced vignettes
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vignettes/*.html
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vignettes/*.pdf
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# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
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.httr-oauth
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# knitr and R markdown default cache directories
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*_cache/
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/cache/
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# Temporary files created by R markdown
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*.utf8.md
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*.knit.md
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# R Environment Variables
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.Renviron
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# translation temp files
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po/*~
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# RStudio Connect folder
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rsconnect/
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# macOS
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.DS_Store

‎LICENSE‎

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MIT License
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Copyright (c) 2023 Environmental Data Science Innovation and Inclusion Lab (ESIIL)
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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[![DOI](https://zenodo.org/badge/727888683.svg)](https://zenodo.org/doi/10.5281/zenodo.11166898)
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# [Your Working Group Name]
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Welcome to the **[Your Working Group Name]** repository, an integral part of the Environmental Data Science Innovation and Inclusion Lab (ESIIL). This repository is the central hub for our working group, encompassing our project overview, proposals, team member information, codebase, and more.
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## Our Project
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[Provide a brief overview of your project here. Describe what you aim to achieve, the importance of your project, and its expected impact.]
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## Documentation
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- Access detailed documentation on our [GitHub Pages site](https://your-gh-pages-url/).
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- Find comprehensive guides, tutorials, and additional resources.
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## Project Proposal
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[Link to the detailed project proposal document or include it directly in the repository. Outline the goals, methodologies, anticipated challenges, and projected timelines.]
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## Group Members
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- Member 1: Brief description or role within the group.
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- Member 2: Brief description or role within the group.
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- ...
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- [Link to more detailed bios or profiles if available.]
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## Repository Structure
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- **containers/**: Docker configurations for reproducible development environments.
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- **docs/**: Project documentation organized into:
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- **orientation/**: Onboarding materials and training resources.
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- **meeting-notes/**: Notes from group meetings.
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- **code/**: Documentation for data processing, analysis, and visualization.
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- **manuscript/**: Drafts and manuscript content.
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- **references/**: Citations and reading notes.
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## Meeting Notes and Agendas
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- Regular updates to keep all group members informed and engaged with the project's progress and direction.
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## Contributing to This Repository
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- Contributions from all group members are welcome.
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- Please adhere to these guidelines:
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- Ensure commits have clear and concise messages.
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- Document major changes in the meeting notes.
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- Review and merge changes through pull requests for oversight.
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## Getting Help
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- If you encounter any issues or have questions, please refer to the [ESIIL Support Page](https://esiil-support-page-url/) or contact the repository maintainers directly.
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## Customize Your Repository
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- **Edit This Readme**: Update with information specific to your project.
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- **Update Group Member Bios**: Add detailed information about each group member's expertise and role.
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- **Organize Your Code**: Use logical structure and clear naming conventions.
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- **Document Your Data**: Include a data directory with README files for datasets.
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- **Outline Your Methods**: Create a METHODS.md file for methodologies and tools.
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- **Set Up Project Management**: Use 'Issues' and 'Projects' for task tracking.
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- **Add a License**: Include an appropriate open-source license.
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- **Create Contribution Guidelines**: Establish a CONTRIBUTING.md file.
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- **Review and Merge Workflow**: Document your process for reviewing and merging changes.
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- **Establish Communication Channels**: Set up channels like Slack or Discord for discussions.
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Remember, the goal is to make your repository clear, accessible, and useful for all current and future members of your working group. Happy researching!

‎containers/jupyterlab/Dockerfile‎

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FROM jupyter/r-notebook:hub-4.0.1
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USER root
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# Set up package manager
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RUN apt-get install -y apt-transport-https && \
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apt-get clean && apt-get update && apt-get install -y software-properties-common && \
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add-apt-repository multiverse && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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# Install some base software
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RUN apt-get update --yes && \
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apt-get install --yes \
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fonts-dejavu \
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unixodbc \
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unixodbc-dev \
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r-base \
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r-cran-rodbc && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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# Add sudo to jovyan user
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RUN apt update && \
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apt install -y sudo && \
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apt clean && \
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rm -rf /var/lib/apt/lists/*
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# This is where we can control which root permissions the jovyan user will have
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ARG PRIV_CMDS='/bin/ch*,/bin/cat,/bin/gunzip,/bin/tar,/bin/mkdir,/bin/ps,/bin/mv,/bin/cp,/usr/bin/apt*,/usr/bin/pip*,/bin/yum,/opt,/opt/conda/bin/*,/usr/bin/*'
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RUN usermod -aG sudo jovyan && \
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echo "$LOCAL_USER ALL=NOPASSWD: $PRIV_CMDS" >> /etc/sudoers
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RUN addgroup jovyan
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RUN usermod -aG jovyan jovyan
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# Install RStudio
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RUN apt-get update && apt-get install --yes gdebi-core && \
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wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.09.1-494-amd64.deb && \
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gdebi -n rstudio-server-2023.09.1-494-amd64.deb && \
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rm rstudio-server-2023.09.1-494-amd64.deb && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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# Install Geospatial libraries
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RUN apt-get update && \
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apt install -y \
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gdal-bin \
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lbzip2 \
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libfftw3-dev \
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libgdal-dev \
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libgeos-dev \
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libgsl0-dev \
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libgl1-mesa-dev \
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libglu1-mesa-dev \
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libhdf4-alt-dev \
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libhdf5-dev \
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libjq-dev \
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libpq-dev \
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libproj-dev \
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libprotobuf-dev \
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libnetcdf-dev \
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libsqlite3-dev \
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libudunits2-dev \
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lsb-release \
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netcdf-bin \
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postgis \
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protobuf-compiler \
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sqlite3 \
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tk-dev \
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libfmt-dev \
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unixodbc-dev && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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# Fix RStudio / Conda openssl version mismatch
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RUN wget https://www.openssl.org/source/openssl-3.2.0.tar.gz && \
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tar xfz openssl-3.2.0.tar.gz && \
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mkdir openssl-build && cd openssl-build && \
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../openssl-3.2.0/Configure --libdir=/lib/x86_64-linux-gnu/ && \
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make && \
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make install
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# Update permissions for /opt/conda
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RUN mkdir /usr/local/bin/start-notebook.d && \
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chown -R jovyan:users /opt/conda/share /usr/local/share /usr/local/bin/start-notebook.d
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USER jovyan
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# Install jupyterlab and rstudio dependencies
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RUN conda install -c conda-forge \
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jupyter_client \
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jupyter_core \
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jupyterlab_server \
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jupyter_server \
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r-rgl \
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r-htmlwidgets \
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r-htmltools && \
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jupyter lab clean
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# reinstall R packages. Here is where you add any new R packages you would like to install
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RUN mamba install --quiet --yes \
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r-base \
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r-tidyverse \
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r-terra \
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r-future \
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r-future.apply \
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r-furrr \
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&& \
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mamba clean --all -f -y
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# Install Jupyter Lab Proxy extensions (cards in Launcher)
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RUN pip install jupyter-rsession-proxy jupyter-server-proxy jupyter-shiny-proxy jupyterlab-git
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# Install Mamba Gator package manager
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RUN rm -f ~/.jupyter/lab/workspaces/default* && \
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mamba install -y -c conda-forge mamba_gator
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# Install and configure jupyter lab
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COPY jupyter_notebook_config.json /opt/conda/etc/jupyter/jupyter_notebook_config.json
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# Rebuild the Jupyter Lab with new tools
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RUN jupyter lab build
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# Build Conda environment. Any packages you would like to install with conda need to be added to the environment.yml file in this Dockerfiles directory
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RUN conda update -y conda && \
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conda config --remove channels conda-forge && \
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conda config --add channels conda-forge
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WORKDIR /home/jovyan
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COPY environment.yml /home/jovyan/
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RUN mamba env create -f /home/jovyan/environment.yml
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RUN . /opt/conda/etc/profile.d/conda.sh && conda deactivate && conda activate custom && python -m ipykernel install --name custom && pip install jupyter_contrib_nbextensions
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# Install R packages from CRAN and GitHub
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RUN R -e "remotes::install_github('tomroh/ecoregions')"
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RUN R -e "install.packages('mblm', repos='http://cran.rstudio.com/')"
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# Set any required environment variables
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ENV PROJ_LIB=/opt/conda/envs/custom/share/proj
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RUN echo "PROJ_LIB=/opt/conda/envs/custom/share/proj" > /home/jovyan/.Renviron

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