# biometal Documentation Review & Recommendations

**Date**: November 5, 2025
**Status**: Post v1.0.0 Launch (PyPI ✅ + crates.io ✅)

---

## ✅ What's Working Well

### 1. **README.md** - Excellent
- ✅ Clear installation instructions for both Rust and Python
- ✅ FAQ section explains biometal vs biometal-rs naming
- ✅ crates.io badges present
- ✅ Comprehensive examples
- ✅ Evidence-based optimization details
- ✅ Cross-platform support documented

### 2. **Installation Verification**
- ✅ **PyPI**: `biometal-rs 1.0.0` live and installable
- ✅ **crates.io**: `biometal 1.0.0` live and installable
- ✅ Both tested and working

### 3. **Specialized Guides**
- ✅ `CRATES_IO_PUBLISHING.md` - Comprehensive guide
- ✅ `PYPI_RELEASE_INSTRUCTIONS.md` - Detailed workflow
- ✅ `CLAUDE.md` - Developer guidelines

---

## 📝 Recommended Updates

### Priority 1: Add PyPI Badge to README (HIGH)

**Current badges**:
```markdown
[![Crates.io](https://img.shields.io/crates/v/biometal.svg)](https://crates.io/crates/biometal)
[![Documentation](https://docs.rs/biometal/badge.svg)](https://docs.rs/biometal)
[![License](https://img.shields.io/crates/l/biometal.svg)](https://github.com/shandley/biometal#license)
```

**Recommended addition**:
```markdown
[![PyPI](https://img.shields.io/pypi/v/biometal-rs.svg)](https://pypi.org/project/biometal-rs/)
[![Python Versions](https://img.shields.io/pypi/pyversions/biometal-rs.svg)](https://pypi.org/project/biometal-rs/)
```

**Why**: Shows Python users the package is on PyPI and supported versions.

**Location**: After line 9 in README.md

---

### Priority 2: Update PYTHON.md Installation Section (MEDIUM)

**Current**: Only shows "From Source" installation

**Recommended**: Add PyPI installation first

```markdown
## Installation

### From PyPI (Recommended)

```bash
pip install biometal-rs
```

Verify installation:
```bash
python -c "import biometal; print(biometal.__version__)"
# Output: 1.0.0
```

**Supported platforms**:
- macOS ARM (M1/M2/M3/M4) - Pre-built wheels
- macOS x86_64 (Intel Macs) - Pre-built wheels
- Linux x86_64 - Pre-built wheels
- Other platforms - Build from source

**Requirements**: Python 3.9-3.14

> **Note**: The package is called `biometal-rs` on PyPI (install name), but you import it as `biometal` in Python code.

### From Source

[... existing content ...]
```

---

### Priority 3: Update QUICKSTART.md (MEDIUM)

**Line 14**: Change from
```bash
# Option 1: From PyPI (when published)
```

**To**:
```bash
# From PyPI (Recommended)
```

Remove "(when published)" - it's live!

---

### Priority 4: Update PYTHON.md Requirements (LOW)

**Line 31**: Update Python version
```markdown
- Python 3.8+
```

**To**:
```markdown
- Python 3.9-3.14 (tested and verified)
```

---

### Priority 5: Add "Getting Started" Links to README (LOW)

After the badges (line 13), add quick navigation:

```markdown
**Quick Links**:
[Installation](#quick-start) |
[Rust Docs](https://docs.rs/biometal) |
[Python Guide](PYTHON.md) |
[Examples](examples/) |
[FAQ](#faq)
```

---

### Priority 6: Update Release Links in Multiple Files (LOW)

Several files reference "(when published)" or future tense. Update to present tense:

**Files to check**:
- `CHANGELOG.md` - Ensure v1.0.0 is marked as released
- `NEXT_STEPS.md` - Mark PyPI/crates.io as complete
- Any TODO comments in code

---

## 🎨 Optional Enhancements

### 1. Add Installation GIF/Video (NICE TO HAVE)

Create a short animated GIF showing:
1. `pip install biometal-rs`
2. Quick Python example
3. Output

**Tools**: asciinema, terminalizer
**Location**: Top of QUICKSTART.md or PYTHON.md

---

### 2. Add Download Stats to README (NICE TO HAVE)

Once you have some downloads, add badges:

```markdown
[![PyPI Downloads](https://pepy.tech/badge/biometal-rs)](https://pepy.tech/project/biometal-rs)
[![Crates.io Downloads](https://img.shields.io/crates/d/biometal.svg)](https://crates.io/crates/biometal)
```

**When**: After first 100 downloads (shows traction)

---

### 3. Create CONTRIBUTING.md (NICE TO HAVE)

Currently mentioned in README but no dedicated file.

**Should include**:
- How to set up development environment
- Running tests
- Code style guidelines
- PR process
- Reference to CLAUDE.md for detailed guidelines

---

### 4. Add Jupyter Notebook Example (NICE TO HAVE)

Create `examples/biometal_tutorial.ipynb` showing:
- Installation verification
- Basic FASTQ streaming
- GC content analysis
- Performance comparison
- Visualization with matplotlib

**Why**: Many bioinformaticians use Jupyter

---

## 📊 Documentation Completeness Matrix

| Document | Status | PyPI Mentioned | crates.io Mentioned | Up-to-date |
|----------|--------|----------------|---------------------|------------|
| README.md | ✅ Good | ✅ Yes | ✅ Yes | ✅ Yes |
| PYTHON.md | ⚠️ Needs Update | ❌ No | N/A | ⚠️ Partial |
| QUICKSTART.md | ⚠️ Needs Update | ⚠️ Says "when published" | ✅ Yes | ⚠️ Partial |
| CHANGELOG.md | ✅ Good | ✅ Yes | ✅ Yes | ✅ Yes |
| CLAUDE.md | ✅ Good | ✅ Yes | ✅ Yes | ✅ Yes |
| FAQ.md | ❓ Not reviewed | ❓ Unknown | ❓ Unknown | ❓ Unknown |

---

## 🔍 Verification Commands

Test these commands work as documented:

### Python Installation
```bash
# Clean environment
python3 -m venv test_env
source test_env/bin/activate

# Install
pip install biometal-rs

# Verify
python -c "import biometal; print(biometal.__version__)"

# Test
python -c "import biometal; s = biometal.FastqStream.from_path('test.fq.gz'); print('Works!')"

# Cleanup
deactivate
rm -rf test_env
```

### Rust Installation
```bash
# New project
cargo new test_biometal
cd test_biometal

# Add dependency
cargo add biometal

# Build
cargo build

# Cleanup
cd ..
rm -rf test_biometal
```

---

## 🎯 Implementation Priority

### Do Now (15 minutes):
1. ✅ Add PyPI badge to README
2. ✅ Update PYTHON.md installation section
3. ✅ Fix QUICKSTART.md "(when published)" text

### Do Soon (1 hour):
4. Update version requirements across docs
5. Add quick links to README
6. Review and update FAQ.md

### Do Later (Nice to have):
7. Create CONTRIBUTING.md
8. Add Jupyter notebook example
9. Create installation GIF
10. Add download badges (after getting downloads)

---

## 📋 Specific File Changes

### 1. README.md (Line 9-12)

**Current**:
```markdown
[![Crates.io](https://img.shields.io/crates/v/biometal.svg)](https://crates.io/crates/biometal)
[![Documentation](https://docs.rs/biometal/badge.svg)](https://docs.rs/biometal)
[![License](https://img.shields.io/crates/l/biometal.svg)](https://github.com/shandley/biometal#license)
```

**Add**:
```markdown
[![Crates.io](https://img.shields.io/crates/v/biometal.svg)](https://crates.io/crates/biometal)
[![Documentation](https://docs.rs/biometal/badge.svg)](https://docs.rs/biometal)
[![PyPI](https://img.shields.io/pypi/v/biometal-rs.svg)](https://pypi.org/project/biometal-rs/)
[![Python](https://img.shields.io/pypi/pyversions/biometal-rs.svg)](https://pypi.org/project/biometal-rs/)
[![License](https://img.shields.io/crates/l/biometal.svg)](https://github.com/shandley/biometal#license)
```

---

### 2. PYTHON.md (Line 13-33)

**Replace entire "Installation" section** with updated version including PyPI.

---

### 3. QUICKSTART.md (Line 14)

**Current**:
```bash
# Option 1: From PyPI (when published)
pip install biometal-rs
```

**Change to**:
```bash
# From PyPI (Recommended)
pip install biometal-rs
```

---

## ✅ Summary

### What's Great:
- Both packages successfully published ✅
- Core documentation is solid ✅
- Installation instructions exist ✅
- FAQ explains naming ✅

### What Needs Updates:
- 🔧 Add PyPI badges (2 min)
- 🔧 Update PYTHON.md installation (5 min)
- 🔧 Fix "when published" references (3 min)
- 📋 Review FAQ.md
- 📋 Add quick links

### Total Time for Priority Items: ~15 minutes

---

**Recommendation**: Implement Priority 1-3 now (badges + installation docs), then tackle Priority 4-6 at your leisure. The documentation is already quite good - these are just polish items now that publishing is complete!

**Want me to implement these changes?** I can update all the files in one go.
