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Merge pull request #30 from NFDI4Chem/development
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‎.github/workflows/dev-build.yml‎

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# This worklflow will perform following actions when the code is pushed to development branch:
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# - Build the latest docker image in development which needs test to pass first.
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# - Push the docker image to Docker Hub under namespace - caffeinejena with tag:dev-latest.
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#
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# Maintainers:
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# - name: Nisha Sharma
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# - email: nisha.sharma@uni-jena.de
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name : Dev Build, Test and Publish
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on:
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push:
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branches: [development]
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env:
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DOCKER_HUB_USERNAME : ${{ secrets.DOCKER_USERNAME }}
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DOCKER_HUB_PASSWORD : ${{ secrets.DOCKER_PASSWORD }}
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REPOSITORY_NAME: nmrkit
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REPOSITORY_NAMESPACE: caffeinejena
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8 pytest
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- name: Analysing the code with pylint
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run: |
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flake8 --ignore E402,E501,W503 $(git ls-files '*.py')
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# - name: Run test
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# run: |
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# pytest -p no:warnings
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push_to_registry:
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name: Push Docker image to Docker Hub
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runs-on: ubuntu-latest
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needs: test
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steps:
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- name: Check out the repo
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uses: actions/checkout@v3
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- name: Log in to Docker Hub
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uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
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with:
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username: ${{ env.DOCKER_HUB_USERNAME }}
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password: ${{ env.DOCKER_HUB_PASSWORD }}
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- name: Build and push Docker image
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uses: docker/build-push-action@v4
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with:
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context: .
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file: ./Dockerfile
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push: true
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build-args: |
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RELEASE_VERSION=dev-latest
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tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:dev-latest
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username: ${{ env.DOCKER_HUB_USERNAME }}
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password: ${{ env.DOCKER_HUB_PASSWORD }}

.github/workflows/deploy.yml renamed to .github/workflows/doc-deploy.yml

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‎.github/workflows/prod-build.yml‎

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# This worklflow will perform following actions when the code is pushed to main branch:
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# - Build the latest docker image in development which needs test to pass first.
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# - Push the docker image to Docker Hub under namespace - caffeinejena with tag:[release_version].
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#
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# Maintainers:
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# - name: Nisha Sharma
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# - email: nisha.sharma@uni-jena.de
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name : Prod Build, Test and Publish
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on:
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release:
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types: [published]
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env:
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DOCKER_HUB_USERNAME : ${{ secrets.DOCKER_USERNAME }}
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DOCKER_HUB_PASSWORD : ${{ secrets.DOCKER_PASSWORD }}
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REPOSITORY_NAME: nmrkit
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REPOSITORY_NAMESPACE: caffeinejena
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jobs:
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push_to_registry:
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name: Push Docker image to Docker Hub
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v3
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#Fetch Latest release
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- name: Fetch latest release
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id: fetch-latest-release
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uses: InsonusK/get-latest-release@v1.0.1
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with:
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myToken: ${{ github.token }}
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exclude_types: "draft"
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view_top: 10
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- name: "Print release name"
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run: |
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echo "tag_name: ${{ steps.fetch-latest-release.outputs.tag_name }}"
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#Login to Docker Hub
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- name: Log in to Docker Hub
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uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
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with:
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username: ${{ env.DOCKER_HUB_USERNAME }}
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password: ${{ env.DOCKER_HUB_PASSWORD }}
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#Build and push Docker image
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- name: Build and push Docker image
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uses: docker/build-push-action@v4
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with:
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context: .
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file: ./Dockerfile
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push: true
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build-args: |
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RELEASE_VERSION=${{ steps.fetch-latest-release.outputs.tag_name }}
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tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:${{ steps.fetch-latest-release.outputs.tag_name }}
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username: ${{ env.DOCKER_HUB_USERNAME }}
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password: ${{ env.DOCKER_HUB_PASSWORD }}

‎.github/workflows/release-please.yml‎

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# This worklflow will perform following actions when the code is pushed to main branch.
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# - Trigger release-please action to create release.
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# - Test linting with pylint.
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# - Test the code with pytest.
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# - Trigger release-please action to create release which needs test to pass first.
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#
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# Maintainers:
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# - name: Nisha Sharma
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# - email: nisha.sharma@uni-jena.de
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name: release-please
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name: release-please-action
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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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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Analysing the code with pylint
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run: |
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flake8 --ignore E402,E501,W503 $(git ls-files '*.py')
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- name: Run test
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run: |
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python3 -m pytest -p no:warnings
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release-please:
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runs-on: ubuntu-latest
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needs: test
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steps:
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- uses: google-github-actions/release-please-action@v3
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with:
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release-type: python
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package-name: release-please-action
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token: ${{ secrets.GITHUB_TOKEN }}
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token: ${{ secrets.PAT }}
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prerelease: true

‎Dockerfile‎

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COPY ./requirements.txt /code/requirements.txt
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COPY ./alembic.ini /code/alembic.ini
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RUN pip3 install --upgrade setuptools pip
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RUN pip3 install --upgrade setuptools pip && \
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apt-get update && apt-get install -y git
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RUN pip3 install --no-cache-dir -r /code/requirements.txt
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RUN python3 -m pip uninstall -y uvicorn

‎docs/.vitepress/config.ts‎

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base: '/nmrkit/',
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cleanUrls: false,
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srcDir: 'src',
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themeConfig: {
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logo: {
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light: '/logo.svg',
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dark: '/logo-dark.svg',
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},
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nav: [
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{ text: 'Home', link: '/introduction' },
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{ text: 'API', link: '' },
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{ text: 'Home', link: '/nmrkit/introduction' },
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{ text: 'API', link: 'https://api.nmrxiv.org/latest/docs' },
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{ text: 'GitHub', link: 'https://github.com/NFDI4Chem/nmrkit' }
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],
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sidebar: [
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{

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