Feat/lint ci

.github/workflows/api-tests.yml

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+name: API tests
+
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+    api-tests:
+        runs-on: ubuntu-latest
+        environment: testing
+        env:
+            ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+            OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+            LANGFUSE_SECRET_KEY: ${{ secrets.LANGFUSE_SECRET_KEY }}
+            LANGFUSE_PUBLIC_KEY: ${{ secrets.LANGFUSE_PUBLIC_KEY }}
+            LANGFUSE_HOST: ${{ secrets.LANGFUSE_HOST }}
+            RXN_CLASSIFICATION_MODEL_PATH: ${{ secrets.RXN_CLASSIFICATION_MODEL_PATH }}
+            AZ_MODEL_CONFIG_PATH: ${{ secrets.AZ_MODEL_CONFIG_PATH }}
+            AZ_MODELS_PATH: ${{ secrets.AZ_MODELS_PATH }}
+            AZURE_AI_API_KEY: ${{ secrets.AZURE_AI_API_KEY }}
+            AZURE_AI_API_BASE: ${{ secrets.AZURE_AI_API_BASE }}
+            DEEPINFRA_API_KEY: ${{ secrets.DEEPINFRA_API_KEY }}
+            AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+            AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+            TOGETHER_API_KEY: ${{ secrets.TOGETHER_API_KEY }}
+            FIREWORKS_AI_API_KEY: ${{ secrets.FIREWORKS_AI_API_KEY }}
+            ENABLE_LOGGING: False
+        defaults:
+            run:
+                working-directory: ./tests/
+        strategy:
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.9]
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v5
+              with:
+                python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies
+              run: |
+                python -m pip install --upgrade pip
+                pip install -r requirements_tests.txt
+
+            - name: Run all API tests
+              run: |
+                pytest ./api-tests/ -v --ignore=./api-tests/test_api_deepseek.py -v

.github/workflows/deepseek-tests.yml

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+name: Deepseek API tests
+
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+    deepseek-api-tests:
+        runs-on: ubuntu-latest
+        environment: testing
+        env:
+            ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+            OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+            LANGFUSE_SECRET_KEY: ${{ secrets.LANGFUSE_SECRET_KEY }}
+            LANGFUSE_PUBLIC_KEY: ${{ secrets.LANGFUSE_PUBLIC_KEY }}
+            LANGFUSE_HOST: ${{ secrets.LANGFUSE_HOST }}
+            RXN_CLASSIFICATION_MODEL_PATH: ${{ secrets.RXN_CLASSIFICATION_MODEL_PATH }}
+            AZ_MODEL_CONFIG_PATH: ${{ secrets.AZ_MODEL_CONFIG_PATH }}
+            AZ_MODELS_PATH: ${{ secrets.AZ_MODELS_PATH }}
+            AZURE_AI_API_KEY: ${{ secrets.AZURE_AI_API_KEY }}
+            AZURE_AI_API_BASE: ${{ secrets.AZURE_AI_API_BASE }}
+            DEEPINFRA_API_KEY: ${{ secrets.DEEPINFRA_API_KEY }}
+            AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+            AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+            TOGETHER_API_KEY: ${{ secrets.TOGETHER_API_KEY }}
+            FIREWORKS_AI_API_KEY: ${{ secrets.FIREWORKS_AI_API_KEY }}
+            ENABLE_LOGGING: False
+        defaults:
+            run:
+                working-directory: ./tests/
+        strategy:
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.9]
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v5
+              with:
+                python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies
+              run: |
+                python -m pip install --upgrade pip
+                pip install -r requirements_tests.txt
+
+            - name: Run deepseek tests
+              if: github.event_name != 'workflow_dispatch'
+              run: |
+                pytest ./api-tests/test_api_deepseek.py -v 

.github/workflows/frontend_tests.yml

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+name: frontend tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  viewer-tests:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./viewer/
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        node-version: [16.x]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node-version }}
+
+      - name: Create npmrc
+        run: |
+          echo "//registry.npmjs.org/:_authToken=" > .npmrc
+          echo "registry=https://registry.npmjs.org/" >> .npmrc
+          echo "always-auth=false" >> .npmrc
+
+      - name: Install Jest directly
+        run: |
+          npm install --no-package-lock [email protected] [email protected]
+
+      - name: Run tests
+        env:
+          NODE_AUTH_TOKEN: ""
+        run: npx jest --config jest.config.js --no-watchman

.github/workflows/lint_checks.yml

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+name: Python Code Formatting 
+
+on:
+  push: # ci work when pushing master branch
+    branches:
+      - main
+    paths:
+      - '**.py'
+  pull_request: # ci work when creating a PR to master branch
+    branches:
+      - main
+    paths:
+      - '**.py'
+
+jobs:
+  yapf:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set commit range (push to the main branch, e.g. merge)
+        if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+        run: |
+          echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV
+          echo $GITHUB_ENV
+
+      - name: Set commit range (pull request)
+        if: github.event_name == 'pull_request'
+        run: |
+          git fetch origin main
+          echo "COMMIT_RANGE=origin/main..." >> $GITHUB_ENV
+          echo $GITHUB_ENV
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: pip install yapf toml
+
+      - name: Check yapf formatting
+        continue-on-error: false 
+        run: |
+          yapf --version
+          CHANGED_FILES=`git diff --name-only $COMMIT_RANGE ':(exclude)src/variables.py' ':(exclude)tests/variables_test.py' | grep .py$ | grep -v contrib/ || true`
+          if [ -n "$CHANGED_FILES" ]; then
+            yapf -d $CHANGED_FILES
+          fi
+
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: pip install flake8 
+
+      - name: Check flake8 
+        continue-on-error: false 
+        run: |
+          flake8 --count . \
+          --ignore=E402 \
+          --exclude variables_test.py \
+          --exclude variables.py    

.github/workflows/llm-tests.yml

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+name: LLM tests
+
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+    llm-tests:
+        runs-on: ubuntu-latest
+        environment: testing
+        env:
+            ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+            OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+            LANGFUSE_SECRET_KEY: ${{ secrets.LANGFUSE_SECRET_KEY }}
+            LANGFUSE_PUBLIC_KEY: ${{ secrets.LANGFUSE_PUBLIC_KEY }}
+            LANGFUSE_HOST: ${{ secrets.LANGFUSE_HOST }}
+            RXN_CLASSIFICATION_MODEL_PATH: ${{ secrets.RXN_CLASSIFICATION_MODEL_PATH }}
+            AZ_MODEL_CONFIG_PATH: ${{ secrets.AZ_MODEL_CONFIG_PATH }}
+            AZ_MODELS_PATH: ${{ secrets.AZ_MODELS_PATH }}
+            AZURE_AI_API_KEY: ${{ secrets.AZURE_AI_API_KEY }}
+            AZURE_AI_API_BASE: ${{ secrets.AZURE_AI_API_BASE }}
+            DEEPINFRA_API_KEY: ${{ secrets.DEEPINFRA_API_KEY }}
+            AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+            AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+            TOGETHER_API_KEY: ${{ secrets.TOGETHER_API_KEY }}
+            FIREWORKS_AI_API_KEY: ${{ secrets.FIREWORKS_AI_API_KEY }}
+            ENABLE_LOGGING: False
+        defaults:
+            run:
+                working-directory: ./tests/
+        strategy:
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.9]
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v5
+              with:
+                python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies
+              run: |
+                python -m pip install --upgrade pip
+                pip install -r requirements_tests.txt
+
+            - name: Run LLM tests
+              run: |
+                pytest ./llm-tests/ -v