Protein function prediction with GO - Part 3 #43
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| name: Verify Constants | |
| # Define the file paths under `paths` to trigger this check only when specific files are modified. | |
| # This script will then execute checks only on files that have changed, rather than all files listed in `paths`. | |
| # **Note** : To add a new file for checks, include its path in: | |
| # - `on` -> `push` and `pull_request` sections | |
| # - `jobs` -> `verify-constants` -> `steps` -> Verify constants -> Add a new if else for your file, with check logic inside it. | |
| on: | |
| push: | |
| paths: | |
| - "chebai/preprocessing/reader.py" | |
| pull_request: | |
| paths: | |
| - "chebai/preprocessing/reader.py" | |
| jobs: | |
| verify-constants: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [ | |
| # Only use 3.10 as of now | |
| # "3.9", | |
| "3.10", | |
| # "3.11" | |
| ] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set PYTHONPATH | |
| run: echo "PYTHONPATH=$PWD" >> $GITHUB_ENV | |
| - name: Get list of changed files | |
| id: changed_files | |
| run: | | |
| git fetch origin dev | |
| # Get the list of changed files compared to origin/dev and save them to a file | |
| git diff --name-only origin/dev > changed_files.txt | |
| # Print the names of changed files on separate lines | |
| echo "Changed files:" | |
| while read -r line; do | |
| echo "Changed File name : $line" | |
| done < changed_files.txt | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| # Setting a fix version for torch due to an error with latest version (2.5.1) | |
| # ImportError: cannot import name 'T_co' from 'torch.utils.data.dataset' | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install torch==2.4.1 --index-url https://download.pytorch.org/whl/cpu | |
| python -m pip install -e . | |
| - name: Export constants | |
| run: python .github/workflows/export_constants.py | |
| - name: Load constants into environment variables | |
| id: load_constants | |
| # "E_" is appended as suffix to every constant, to protect overwriting other sys env variables with same name | |
| run: | | |
| constants=$(cat constants.json) | |
| echo "$constants" | jq -r 'to_entries|map("E_\(.key)=\(.value|tostring)")|.[]' >> $GITHUB_ENV | |
| - name: Print all environment variables | |
| run: printenv | |
| - name: Verify constants | |
| run: | | |
| file_name="chebai/preprocessing/reader.py" | |
| if grep -q "$file_name" changed_files.txt; then | |
| echo "----------------------- Checking file : $file_name ----------------------- " | |
| # Define expected values for constants | |
| exp_embedding_offset="10" | |
| exp_cls_token="2" | |
| exp_padding_token_index="0" | |
| exp_mask_token_index="1" | |
| # Debugging output to check environment variables | |
| echo "Current Environment Variables:" | |
| echo "E_EMBEDDING_OFFSET = $E_EMBEDDING_OFFSET" | |
| echo "Expected: $exp_embedding_offset" | |
| # Verify constants match expected values | |
| if [ "$E_EMBEDDING_OFFSET" != "$exp_embedding_offset" ]; then | |
| echo "EMBEDDING_OFFSET ($E_EMBEDDING_OFFSET) does not match expected value ($exp_embedding_offset)!" | |
| exit 1 | |
| fi | |
| if [ "$E_CLS_TOKEN" != "$exp_cls_token" ]; then | |
| echo "CLS_TOKEN ($E_CLS_TOKEN) does not match expected value ($exp_cls_token)!" | |
| exit 1 | |
| fi | |
| if [ "$E_PADDING_TOKEN_INDEX" != "$exp_padding_token_index" ]; then | |
| echo "PADDING_TOKEN_INDEX ($E_PADDING_TOKEN_INDEX) does not match expected value ($exp_padding_token_index)!" | |
| exit 1 | |
| fi | |
| if [ "$E_MASK_TOKEN_INDEX" != "$exp_mask_token_index" ]; then | |
| echo "MASK_TOKEN_INDEX ($E_MASK_TOKEN_INDEX) does not match expected value ($exp_mask_token_index)!" | |
| exit 1 | |
| fi | |
| else | |
| echo "$file_name not found in changed_files.txt; skipping check." | |
| fi |