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‎.dockerignore‎

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renv/library/
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renv/local/
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renv/lock/
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renv/python/
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renv/staging/
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test
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tests
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workflow_tests

‎.github/workflows/ci.yaml‎

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name: CI Workflow
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on:
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push:
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branches: ['main']
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# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: ${{ github.repository }}
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# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
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jobs:
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build-and-push-image:
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runs-on: ubuntu-latest
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# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
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permissions:
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contents: read
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packages: write
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attestations: write
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id-token: write
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#
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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# Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
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- name: Log in to the Container registry
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uses: docker/login-action@v3.3.0
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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# This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5.5.1
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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# This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
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# It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
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# It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
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- name: Build and push Docker image
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id: push
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uses: docker/build-push-action@v6.7.0
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with:
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context: .
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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# A PAT is needed for this action, GITHUB_TOKEN cannot get relevant permission
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# secrets: |
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# github_pat=${{ secrets.GH_PAT }}

‎.github/workflows/release.yaml‎

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name: Release Workflow
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on:
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push:
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tags:
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- '[0-9]+.[0-9]+.[0-9]+' # Push events to any matching semantic tag. For example, 1.10.1 or 2.0.0.
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# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: ${{ github.repository }}
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# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
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jobs:
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build-and-push-image:
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runs-on: ubuntu-latest
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# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
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permissions:
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contents: write
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packages: write
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attestations: write
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id-token: write
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#
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Update container in operator JSON
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run: |
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jq --arg variable "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${GITHUB_REF##*/}" '.container = $variable' operator.json
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# Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
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- name: Log in to the Container registry
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uses: docker/login-action@v3.3.0
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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# This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5.5.1
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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tags: |
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# minimal
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type=pep440,pattern={{version}}
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# This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
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# It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
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# It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
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- name: Build and push Docker image
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id: push
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uses: docker/build-push-action@v6.7.0
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with:
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context: .
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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# A PAT is needed for this action, GITHUB_TOKEN cannot get relevant permission
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# secrets: |
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# github_pat=${{ secrets.GH_PAT }}
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- name: Create required package.json
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run: echo '{}' > package.json
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- name: Build changelog
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id: Changelog
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uses: tercen/generate-changelog-action@master
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- name: Create release
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id: create_release
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uses: actions/create-release@latest
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
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with:
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tag_name: ${{ github.ref }}
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release_name: Release ${{ github.ref }}
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body: ${{steps.Changelog.outputs.changelog}}
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draft: false
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prerelease: false

‎.gitignore‎

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.idea
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venv/*

‎.vscode/extensions.json‎

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{
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"recommendations": ["ms-python.python", "ms-toolsai.jupyter"]
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}

‎.vscode/launch.json‎

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{
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"version": "0.2.0",
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"configurations": [
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{
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"name": "Python: Current File",
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"type": "python",
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"python": "/config/.pyenv/versions/3.9.0/bin/python",
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"request": "launch",
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"program": "${file}",
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"console": "integratedTerminal",
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"justMyCode": true,
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"env": { "PYTHONPATH": "${workspaceRoot}"}
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}
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]
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}

‎Dockerfile‎

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FROM tercen/runtime-python39:0.1.0
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COPY . /operator
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WORKDIR /operator
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ENV PYTHONPATH "${PYTHONPATH}:~/.pyenv/versions/3.9.0/bin/python3"
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RUN python3 -m pip install -r ./requirements.txt
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ENV TERCEN_SERVICE_URI https://tercen.com
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ENTRYPOINT ["python3", "main.py"]
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CMD ["--taskId", "someid", "--serviceUri", "https://tercen.com", "--token", "sometoken"]

‎README.md‎

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# Template Python Operator
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Cell-wise mean calculated implemented in Python.
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## Python operator - Development workflow
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* Set up [the Tercen Studio development environment](https://github.com/tercen/tercen_studio)
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* Create a new git repository based on the [template Python operator](https://github.com/tercen/template-python-operator)
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* Open VS Code Server by going to: http://127.0.0.1:8443
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* Clone this repository into VS Code (using the 'Clone from GitHub' command from the Command Palette for example)
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* Load the environment and install core requirements by running the following commands in the terminal:
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```bash
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source /config/.pyenv/versions/3.9.0/bin/activate
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pip install -r requirements.txt
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```
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* Develop your operator. Note that you can interact with an existing data step by specifying arguments to the `TercenContext` function:
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```python
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tercenCtx = ctx.TercenContext()
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```
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```python
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tercenCtx = ctx.TercenContext(
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workflowId="YOUR_WORKFLOW_ID",
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stepId="YOUR_STEP_ID",
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username="admin", # if using the local Tercen instance
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password="admin", # if using the local Tercen instance
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serviceUri = "http://tercen:5400/" # if using the local Tercen instance
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)
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```
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* Generate requirements
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```bash
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python3 -m tercen.util.requirements . > requirements.txt
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```
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* Push your changes to GitHub: triggers CI GH workflow
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* Tag the repository: triggers Release GH workflow
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* Go to tercen and install your operator
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## Helpful Commands
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### Install Tercen Python Client
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```bash
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python3 -m pip install --force git+https://github.com/tercen/tercen_python_client@0.7.1
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```
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### Wheel
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Though not strictly mandatory, many packages require it.
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```bash
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python3 -m pip install wheel
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```
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‎main.py‎

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from tercen.client import context as ctx
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import numpy as np
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tercenCtx = ctx.TercenContext()
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df = (
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tercenCtx
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.select(['.y', '.ci', '.ri'], df_lib="pandas")
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.groupby(['.ci','.ri'], as_index=False)
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.mean()
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.rename(columns={".y":"mean"})
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.astype({".ci": np.int32, ".ri": np.int32})
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)
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df = tercenCtx.add_namespace(df)
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tercenCtx.save(df)

‎operator.json‎

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{
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"name": "Template Python operator",
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"description": "Mean operator implemented in Python",
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"tags": ["template"],
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"authors": ["tercen"],
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"urls": ["https://github.com/tercen/template-python-operator"],
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"container":"ghcr.io/tercen/template-python-operator:latest",
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"properties": [
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{
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"kind": "DoubleProperty",
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"name": "Property1",
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"defaultValue": 42.0,
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"description": "Example Double Property"
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},
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{
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"kind": "StringProperty",
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"name": "Property2",
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"defaultValue": "42",
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"description": "Example String Property"
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},
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{
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"kind": "BooleanProperty",
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"name": "Property3",
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"defaultValue": true,
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"description": "Example Boolean Property"
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},
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{
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"kind": "EnumeratedProperty",
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"isSingleSelection":true,
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"name": "Property4",
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"defaultValue": "element2",
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"values": ["element1", "element2", "element3"],
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"description": "Example Enumerated Property"
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}
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]
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}

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