Feature/bulk prefetch decomposition

.env.example

@@ -0,0 +1,19 @@
+# Neo4j Database Connection
+# Connection URL for the Reactome Neo4j database
+NEO4J_URL=bolt://localhost:7687
+NEO4J_USER=neo4j
+NEO4J_PASSWORD=your_password_here
+
+# Pathway Processing
+# Path to file containing list of pathway IDs to process
+PATHWAY_LIST_FILE=pathways.tsv
+
+# Output Configuration
+# Directory where generated files will be saved
+OUTPUT_DIR=output
+
+# Logging Configuration
+# Log level: DEBUG, INFO, WARNING, ERROR, CRITICAL
+LOG_LEVEL=INFO
+# Log file path (optional, logs to console if not set)
+# LOG_FILE=pathway_generation.log

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,50 @@
+---
+name: Bug Report
+about: Report a bug to help us improve
+title: '[BUG] '
+labels: bug
+assignees: ''
+---
+
+## Bug Description
+
+A clear and concise description of what the bug is.
+
+## Steps to Reproduce
+
+1. Run command '...'
+2. With pathway ID '...'
+3. See error
+
+## Expected Behavior
+
+A clear description of what you expected to happen.
+
+## Actual Behavior
+
+What actually happened instead.
+
+## Error Message
+
+```
+Paste error message here if applicable
+```
+
+## Environment
+
+- OS: [e.g., Ubuntu 22.04, macOS 14]
+- Python Version: [e.g., 3.10.5]
+- Poetry Version: [e.g., 1.7.1]
+- Neo4j Version: [e.g., Release94]
+
+## Pathway Information
+
+- Pathway ID: [e.g., 69620]
+- Pathway Name: [if known]
+
+## Additional Context
+
+Add any other context about the problem here, such as:
+- Does it happen with all pathways or just specific ones?
+- Is this a regression (did it work before)?
+- Any relevant log files or output

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Reactome Community
+    url: https://reactome.org/community
+    about: Ask questions and discuss with the Reactome community

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,38 @@
+---
+name: Feature Request
+about: Suggest an idea for this project
+title: '[FEATURE] '
+labels: enhancement
+assignees: ''
+---
+
+## Feature Description
+
+A clear and concise description of the feature you'd like to see.
+
+## Problem Statement
+
+What problem does this feature solve? Is your feature request related to a problem?
+Example: "I'm always frustrated when..."
+
+## Proposed Solution
+
+Describe the solution you'd like to see implemented.
+
+## Alternatives Considered
+
+Describe any alternative solutions or features you've considered.
+
+## Use Case
+
+How would you use this feature? Provide specific examples if possible.
+
+## Additional Context
+
+Add any other context, screenshots, or examples about the feature request here.
+
+## Would you like to implement this?
+
+- [ ] Yes, I'd like to work on this
+- [ ] No, just suggesting
+- [ ] Need guidance on how to implement

.github/pull_request_template.md

@@ -0,0 +1,65 @@
+## Description
+
+Brief description of what this PR does.
+
+## Type of Change
+
+- [ ] Bug fix (non-breaking change that fixes an issue)
+- [ ] New feature (non-breaking change that adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+- [ ] Code quality improvement (refactoring, performance, etc.)
+
+## Related Issue
+
+Fixes #(issue number)
+
+## Changes Made
+
+- Change 1
+- Change 2
+- Change 3
+
+## Testing
+
+### Unit Tests
+- [ ] All existing unit tests pass locally (`poetry run pytest tests/ -v -m "not database"`)
+- [ ] Added new unit tests for changes (if applicable)
+
+### Integration Tests (Optional - requires Neo4j)
+- [ ] All integration tests pass locally (`poetry run pytest tests/ -v`)
+
+### Manual Testing
+Describe any manual testing performed:
+- Tested with pathway ID(s):
+- Verified output files:
+
+## Code Quality
+
+- [ ] Code follows project style guidelines (ruff)
+- [ ] Ran `poetry run ruff check src/` with no errors
+- [ ] Ran `poetry run ruff format src/`
+- [ ] Type hints added/updated where applicable
+- [ ] Ran `poetry run mypy --ignore-missing-imports src/` (optional)
+
+## Documentation
+
+- [ ] Updated README.md (if needed)
+- [ ] Added/updated docstrings
+- [ ] Updated relevant documentation in `docs/`
+
+## Checklist
+
+- [ ] Self-review completed
+- [ ] Code is well-commented, particularly in complex areas
+- [ ] No debugging code left in (print statements, breakpoints, etc.)
+- [ ] No credentials or sensitive information in code
+- [ ] Git commit messages are clear and descriptive
+
+## Screenshots (if applicable)
+
+Add screenshots or terminal output if it helps explain the changes.
+
+## Additional Notes
+
+Any additional information that reviewers should know.

.github/workflows/ruff.yml

@@ -8,12 +8,12 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: '3.12'
 
     - name: Install dependencies
       run: |

.github/workflows/test.yml

@@ -0,0 +1,39 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Poetry
+      run: pip install poetry
+
+    - name: Install dependencies
+      run: poetry install
+
+    - name: Type check (mypy on src/)
+      run: poetry run mypy src/
+
+    - name: Run unit tests with coverage (no Neo4j, no generated artifacts)
+      # 40% floor reflects unit-tier scope only: pathway_generator and
+      # neo4j_connector are exercised in the integration/database tiers and
+      # naturally lower the unit number. Raise the floor as those tiers
+      # become CI-runnable.
+      run: poetry run pytest tests/ -v -m "not database and not integration" --cov=src --cov-report=term --cov-fail-under=40

.gitignore

@@ -1,14 +1,49 @@
+# Log files
+*.log
 debug_log.txt
+debug_run.log
+pathway_generation.log
+test_generation.log
 
-# Ignore Python bytecode files
+# Python bytecode files
 __pycache__/
 *.pyc
 *.pyo
 *.pyd
+.Python
+*.egg-info/
 
+# Test artifacts
+.pytest_cache/
+.coverage
+htmlcov/
+*.coverage
 
-#output folder of results
+# IDE
+.vscode/
+.idea/
+*.swp
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Temporary files
+*.tmp
+*.bak
+
+# Environment variables
+.env
+.env.*
+!.env.example
+
+# Output folder of results
 output
 
-#vim files
-*.swp
+# Generated data files
+db_id_to_name_mapping.tsv
+pathway_logic_network_*.csv
+uuid_mapping_*.csv
+reaction_connections_*.csv
+decomposed_uid_mapping_*.csv
+best_matches_*.csv

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: mixed-line-ending
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.0
+    hooks:
+      - id: mypy
+        files: ^src/
+        # Match CI: no --ignore-missing-imports, real stubs for our deps.
+        # types-all was archived; replaced with the specific stubs we need.
+        additional_dependencies:
+          - pandas-stubs