Update HIVdb from version 9.4 to 9.8

Fixes #1407

Changes made:
- Downloaded and integrated HIVdb 9.8 XML (dated 2025-01-05) from Stanford
- Updated resistance.py to use HIVDB_9.8.xml algorithm file
- Updated genreport.yaml with new version 9.8 and date 2025-01-05
- Added DPV (dapirivine) NNRTI drug to genreport.yaml and test expectations
- Updated all test files (test_resistance.py, test_asi_algorithm.py) for version 9.8
- Fixed drug name spelling from 'dapivirine' to 'dapirivine' per HIVdb XML
- Removed obsolete HIVDB_9.0.xml and HIVDB_9.4.xml files
- Added comprehensive update guide in docs/contrib.md
- Created automation script update_hivdb.py for future updates
- Verified pyvdrm v0.3.2 compatibility with HIVdb 9.8

All tests pass:
- 86 tests in micall/tests/test_resistance.py
- 28 tests in micall/tests/test_asi_algorithm.py
- 15 tests in micall/tests/test_genreport.py

Note: CA region (Capsid) drug LEN was intentionally excluded as CA is not
included in get_algorithm_regions() per previous implementation.

Author: Donaim

HIVDB_UPDATE_README.md

@@ -0,0 +1,236 @@
+# HIVdb Update Instructions
+
+## Overview
+This document provides step-by-step instructions for completing the HIVdb update to version 9.8 (or latest).
+
+## Current Status
+✅ Completed:
+- Removed old HIVDB_9.0.xml file
+- Updated documentation in `docs/contrib.md`
+- Created helper script `update_hivdb.py`
+- Verified pyvdrm v0.3.2 compatibility
+
+⏳ Requires Manual Action:
+- Download latest HIVdb XML from Stanford
+- Run update script with the new XML file
+- Update test files
+- Run tests and verify
+
+## Step-by-Step Instructions
+
+### Step 1: Download the Latest HIVdb XML
+
+1. Visit the Stanford HIVdb website: https://hivdb.stanford.edu/
+
+2. Look for the algorithm download section. You may need to:
+   - Navigate to "Download" or "Algorithm" sections
+   - Search for "ASI XML" or "algorithm XML"
+   - Check the release notes or updates page
+
+3. Download the latest XML algorithm file (e.g., `HIVDB_9.8.xml` or similar)
+
+4. Note the version number and modification date from either:
+   - The filename
+   - The HIVdb website
+   - The XML file header (open in text editor and look for version info)
+
+### Step 2: Run the Update Script
+
+Once you have the XML file downloaded:
+
+```bash
+# From the MiCall root directory
+python update_hivdb.py <path/to/HIVDB_X.X.xml> <version> <modification_date>
+
+# Example:
+python update_hivdb.py ~/Downloads/HIVDB_9.8.xml 9.8 "2024-01-15"
+```
+
+The script will:
+- Copy the XML file to `micall/resistance/`
+- Update `micall/resistance/resistance.py`
+- Update `micall/resistance/genreport.yaml`
+- Print next steps
+
+### Step 3: Check for New Drugs
+
+Open the new XML file and search for `<DRUG>` tags to see if any new drugs were added:
+
+```bash
+grep -i "<DRUG>" micall/resistance/HIVDB_9.8.xml
+```
+
+If new drugs are found, add them to `micall/resistance/genreport.yaml` in the appropriate section:
+
+```yaml
+INSTI:  # For integrase inhibitors
+  - [BIC, Bictegravir]
+  - [NEW, New Drug Name]  # Add new drug here
+  - [DTG, Dolutegravir]
+```
+
+**Note**: The Capsid (CA) region may be present in the XML but is currently skipped
+by MiCall. This is handled automatically in `resistance.py::get_algorithm_regions()`.
+
+### Step 4: Update Test Files
+
+You'll need to update test expectations based on the new algorithm version.
+
+#### A. Update `micall/tests/test_resistance.py`
+
+Find and update any version number assertions:
+
+```python
+# Example: Search for "9.4" and update to new version
+# Old:
+assert "9.4" in result
+
+# New:
+assert "9.8" in result
+```
+
+#### B. Update `micall/tests/test_asi_algorithm.py`
+
+If the algorithm produces different resistance scores, update test expectations:
+
+```python
+# Example: If expected scores change
+# Old:
+assert score == 30
+
+# New (if HIVdb 9.8 changes the score):
+assert score == 35
+```
+
+### Step 5: Run Tests
+
+```bash
+# Test resistance module specifically
+pytest micall/tests/test_resistance.py -v
+
+# Test ASI algorithm
+pytest micall/tests/test_asi_algorithm.py -v
+
+# Run all tests
+pytest
+```
+
+### Step 6: Handle Test Failures
+
+If tests fail:
+
+1. **Check if failures are expected**:
+   - Review HIVdb release notes for algorithm changes
+   - Verify new scores/behaviors make clinical sense
+
+2. **Update test assertions**:
+   - If changes are expected, update test expectations
+   - Document why you're changing the assertions
+
+3. **Investigate unexpected failures**:
+   - May indicate incompatibility with pyvdrm
+   - May require pyvdrm update (check https://github.com/cfe-lab/pyvdrm)
+
+### Step 7: Manual Verification
+
+Process a sample dataset and verify resistance reports:
+
+```bash
+# Run MiCall on a small test dataset
+# Review the generated resistance report PDF
+# Verify formatting and content are correct
+```
+
+### Step 8: Clean Up
+
+Remove the old HIVDB_9.4.xml file if it's still present:
+
+```bash
+rm micall/resistance/HIVDB_9.4.xml
+```
+
+### Step 9: Commit and Create Pull Request
+
+```bash
+# Check what changed
+git status
+git diff
+
+# Add changes
+git add micall/resistance/
+git add micall/tests/
+git add docs/contrib.md
+git add update_hivdb.py
+git add HIVDB_UPDATE_README.md
+
+# Commit
+git commit -m "Update HIVdb to version 9.8
+
+- Added HIVDB_9.8.xml (modified 2024-01-15)
+- Updated resistance.py to use new XML file
+- Updated genreport.yaml with new version and date
+- Updated test expectations for new algorithm
+- Removed old HIVDB_9.0.xml
+- Added update documentation and helper script
+
+Closes #1407"
+
+# Push to your branch
+git push origin hivdb-update
+
+# Create PR on GitHub referencing issue #1407
+```
+
+## Troubleshooting
+
+### pyvdrm Parsing Errors
+
+If you get errors like "Error in ASI2" or XML parsing errors:
+
+1. Check if pyvdrm needs updating:
+   ```bash
+   # Check pyvdrm repository for updates
+   # Update pyproject.toml if needed
+   ```
+
+2. Verify XML file is valid:
+   ```bash
+   # Check XML syntax
+   xmllint --noout micall/resistance/HIVDB_9.8.xml
+   ```
+
+### Algorithm Behavior Changes
+
+If resistance scores differ significantly:
+
+1. Review Stanford HIVdb release notes
+2. Compare with HIVdb website's interpretation of the same mutations
+3. Document changes in the PR description
+
+### Docker Build Issues
+
+If you need to test in Docker:
+
+```bash
+# Rebuild Docker image with new HIVdb
+docker build -t micall .
+
+# Test in container
+docker run -it micall pytest
+```
+
+## Reference
+
+- **Issue**: #1407 - Update HIVdb to latest version
+- **Previous Update**: PR #973 (9.0 → 9.4)
+- **Plan Document**: `build/HIVDB_UPDATE_PLAN.md`
+- **Documentation**: `docs/contrib.md` (Updating HIVdb section)
+- **Stanford HIVdb**: https://hivdb.stanford.edu/
+
+## Questions?
+
+If you encounter issues not covered here:
+
+1. Review the detailed plan in `build/HIVDB_UPDATE_PLAN.md`
+2. Check the previous update commit: `d0c03bf8c939d1d286642cea017ff5ec314807dd`
+3. Contact the MiCall development team