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| Original file line number | Diff line number | Diff line change |
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| name: build-docs | ||
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| on: | ||
| workflow_dispatch: | ||
| push: | ||
| branches: [main] | ||
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| # set GITHUB_TOKEN permissions to allow deployment to GitHub Pages | ||
| permissions: | ||
| contents: read | ||
| pages: write | ||
| id-token: write | ||
|
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| jobs: | ||
| build-docs: | ||
| if: github.repository_owner == 'materialsproject' && github.ref == 'refs/heads/main' | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ github.event.workflow_run.head_branch }} | ||
|
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| - name: Install pandoc | ||
| run: sudo apt-get install pandoc | ||
|
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| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.10" | ||
| cache: pip | ||
| cache-dependency-path: pyproject.toml | ||
|
|
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| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install .[strict,docs] | ||
| - name: Build | ||
| run: sphinx-build docs docs_build | ||
|
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| - name: Upload build artifact | ||
| uses: actions/upload-pages-artifact@v2 | ||
| with: | ||
| path: ./docs_build | ||
|
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| deploy: | ||
| environment: | ||
| name: github-pages | ||
| url: ${{ steps.deployment.outputs.page_url }} | ||
| needs: build-docs | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Deploy to GitHub Pages | ||
| id: deployment | ||
| uses: actions/deploy-pages@v2 |
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| @@ -0,0 +1,29 @@ | ||
| name: Check Links | ||
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| on: | ||
| push: | ||
| branches: [main] | ||
| pull_request: | ||
| branches: [main] | ||
| workflow_dispatch: | ||
|
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| jobs: | ||
| check_links: | ||
| runs-on: ubuntu-latest | ||
|
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| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v4 | ||
|
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| - name: Set up Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.11" | ||
|
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| - name: Install dependencies | ||
| run: | | ||
| pip install pytest-check-links nbconvert | ||
| - name: Run link check | ||
| run: | | ||
| pytest --check-links **/**/*.md **/**/*.ipynb --check-links-ignore "https://www.gauss-centre.eu" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,53 @@ | ||
| # Stores | ||
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| ## Overview | ||
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| Jobflow relies on the [maggma package](https://github.com/materialsproject/maggma) to provide a unified interface to a variety of data stores. By default, all calculations are run using a `MemoryStore`, which persists solely in the current process' memory. In production calculations, one will generally want to use a persistent data store, such as a MongoDB database. This also allows one to run calculations in a distributed manner with a common data store. | ||
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| For a list of all available data stores, refer to the [maggma documentation](https://materialsproject.github.io/maggma/getting_started/stores/#list-of-stores). Here, we will go over how to use Jobflow with MongoDB via a [`MongoStore`](https://materialsproject.github.io/maggma/reference/stores/#maggma.stores.mongolike.MemoryStore). | ||
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| ## Configuring a `MongoStore` | ||
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| ### Creating a `jobflow.yaml` File | ||
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| To modify basic Jobflow settings, you will first need to make a `jobflow.yaml` file if you haven't done so already. You will then need to define a `JOBFLOW_CONFIG_FILE` environment variable pointing to the file you made. For instance, in your `~/.bashrc` file, add the following line: | ||
|
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| ```bash | ||
| export JOBFLOW_CONFIG_FILE="/path/to/my/jobflow.yaml" | ||
| ``` | ||
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| If this environment variable is not specified, Jobflow will look for the file in `~/.jobflow.yaml`. | ||
|
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| ### Basic Configuration | ||
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| In your `jobflow.yaml` copy the example below and fill in the fields with the appropriate values for a MongoDB store. | ||
|
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| ```yaml title="jobflow.yaml" | ||
| JOB_STORE: | ||
| docs_store: | ||
| type: MongoStore | ||
| host: <host name> | ||
| port: 27017 | ||
| username: <username> | ||
| password: <password> | ||
| database: <database name> | ||
| collection_name: <collection name> | ||
| ``` | ||
| ### MongoDB Atlas | ||
| If you are using a URI (as is common with MongoDB Atlas), then you will instead have a `jobflow.yaml` file that looks like the example below. Here, you will put the full URI in the `host` field. The `username` and `password` are part of the URI and so should not be included elsewhere in the YAML file. | ||
|
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| ```yaml title="jobflow.yaml" | ||
| JOB_STORE: | ||
| docs_store: | ||
| type: MongoStore | ||
| host: <URI> | ||
| port: 27017 | ||
| database: <database name> | ||
| collection_name: <collection name> | ||
| ``` | ||
|
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| ## Additional Details | ||
|
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| For additional details on how to specify a data store as well as the various settings available to modify in Jobflow, refer to the [API documentation](https://materialsproject.github.io/jobflow/jobflow.settings.html) for `jobflow.settings`. |
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