forked from enviPath/enviPy
Liam Brydon
901de4640c
**This pull request will need a separate migration pull-request**
I have added an alert box in two places when the user tries to predict with stereo chemistry.
When a user predicts a pathway with stereo chemistry an alert box is shown in that node's hover.
To do this I added two new fields. Pathway now has a "predicted" BooleanField indicating whether it was predicted or not. It is set to True if the pathway mode for prediction is "predict" or "incremental" and False if it is "build". I think it is a flag that could be useful in the future, perhaps for analysing how many predicted pathways are in enviPath?
Node now has a `stereo_removed` BooleanField which is set to True if the Node's parent Pathways has "predicted" as true and the node SMILES has stereochemistry.
<img width="500" alt="{927AC9FF-DBC9-4A19-9E6E-0EDD3B08C7AC}.png" src="attachments/69ea29bc-c2d2-4cd2-8e98-aae5c5737f69">
When a user does a prediction on a model's page it shows at the top of the list. This did not require any new fields as the entered SMILES does not get saved anywhere.
<img width="500" alt="{BED66F12-5F07-419E-AAA6-FE1FE5B4F266}.png" src="attachments/5fcc3a9b-4d1a-4e48-acac-76b7571f6507">
I think the alert box is an alright solution but if you have a great idea for something that looks/fits better please change it or let me know.
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#250
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
135 lines
3.5 KiB
YAML
135 lines
3.5 KiB
YAML
name: CI
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on:
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pull_request:
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branches:
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- develop
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workflow_dispatch:
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jobs:
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test:
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if: ${{ !contains(gitea.event.pull_request.title, 'WIP') }}
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runs-on: ubuntu-latest
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services:
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postgres:
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image: postgres:16
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env:
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POSTGRES_USER: ${{ vars.POSTGRES_USER }}
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POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
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POSTGRES_DB: ${{ vars.POSTGRES_DB }}
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ports:
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- ${{ vars.POSTGRES_PORT}}:5432
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options: >-
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--health-cmd="pg_isready -U postgres"
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--health-interval=10s
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--health-timeout=5s
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--health-retries=5
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#redis:
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# image: redis:7
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# ports:
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# - 6379:6379
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# options: >-
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# --health-cmd "redis-cli ping"
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# --health-interval=10s
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# --health-timeout=5s
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# --health-retries=5
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env:
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RUNNER_TOOL_CACHE: /toolcache
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EP_DATA_DIR: /opt/enviPy/
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ALLOWED_HOSTS: 127.0.0.1,localhost
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DEBUG: True
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LOG_LEVEL: INFO
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MODEL_BUILDING_ENABLED: True
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APPLICABILITY_DOMAIN_ENABLED: True
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ENVIFORMER_PRESENT: True
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ENVIFORMER_DEVICE: cpu
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FLAG_CELERY_PRESENT: False
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PLUGINS_ENABLED: True
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SERVER_URL: http://localhost:8000
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ADMIN_APPROVAL_REQUIRED: True
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REGISTRATION_MANDATORY: True
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LOG_DIR: ''
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# DB
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POSTGRES_SERVICE_NAME: postgres
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POSTGRES_DB: ${{ vars.POSTGRES_DB }}
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POSTGRES_USER: ${{ vars.POSTGRES_USER }}
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POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
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POSTGRES_PORT: 5432
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# SENTRY
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SENTRY_ENABLED: False
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# MS ENTRA
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MS_ENTRA_ENABLED: False
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Install system tools via apt
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run: |
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sudo apt-get update
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sudo apt-get install -y postgresql-client redis-tools openjdk-11-jre-headless
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- name: Setup ssh
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run: |
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echo "${{ secrets.ENVIPY_CI_PRIVATE_KEY }}" > ~/.ssh/id_ed25519
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chmod 600 ~/.ssh/id_ed25519
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ssh-keyscan git.envipath.com >> ~/.ssh/known_hosts
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eval $(ssh-agent -s)
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ssh-add ~/.ssh/id_ed25519
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- name: Install pnpm
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uses: pnpm/action-setup@v4
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with:
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version: 10
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- name: Use Node.js
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uses: actions/setup-node@v4
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with:
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node-version: 20
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cache: "pnpm"
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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enable-cache: true
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- name: Setup venv
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run: |
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uv sync --locked --all-extras --dev
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source .venv/bin/activate
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playwright install --with-deps
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- name: Run PNPM Commands
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run: |
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uv run python scripts/pnpm_wrapper.py install
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cat << 'EOF' > pnpm-workspace.yaml
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onlyBuiltDependencies:
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- '@parcel/watcher'
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- '@tailwindcss/oxide'
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EOF
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uv run python scripts/pnpm_wrapper.py run build
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- name: Wait for services
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run: |
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until pg_isready -h postgres -U postgres; do sleep 2; done
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# until redis-cli -h redis ping; do sleep 2; done
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- name: Run Django Migrations
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run: |
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source .venv/bin/activate
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python manage.py migrate --noinput
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- name: Run frontend tests
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run: |
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source .venv/bin/activate
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python manage.py test --tag frontend
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- name: Run Django tests
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run: |
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source .venv/bin/activate
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python manage.py test tests --exclude-tag slow --exclude-tag frontend
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