Documenting Math in Python with Sphinx

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# 📐 Documenting Math in Python with Sphinx

### Adding Beautiful Equations to Python Docstrings

@luk036 👨‍💻 · 2026 📅

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### 📋 Agenda

**Part 1: Motivation** 🤔
- The Challenge of Math in Code Docs
- Comparing Solutions: MathJax vs KaTeX vs Unicode

**Part 2: Sphinx Setup** ⚙️
- `conf.py` Configuration
- MathJax Extension
- Writing Equations in Docstrings

]

**Part 3: Project Walkthroughs** 🏗️
- `rat-trig` — Rational Trigonometry
- `ellalgo` — Ellipsoid Method
- `lds-gen` — Low-Discrepancy Sequences
- `ginger` — Polynomial Root-finding
- `projgeom-py` — Projective Geometry

**Part 4: Summary** 💡
- Key Takeaways
- Q&A
]

---

### 🤔 The Challenge

Mathematical libraries need **mathematical documentation**:

```python
def spread(v1, v2):
    """Calculate the spread between two vectors."""
    ...
```

❌ Without equations: Users must guess the formula from code

✅ With Sphinx + MathJax:

```python
def spread(v1, v2):
    r"""Spread between two 2D vectors.

.. math::

s = \frac{(v_1 \times v_2)^2}{Q(v_1) Q(v_2)}

:param v1: First vector
    :param v2: Second vector
    :return: The spread
    """
```

Rendered: $$ s = \frac{(v_1 \times v_2)^2}{Q(v_1) Q(v_2)} $$

---

### ⚖️ Solution Comparison

| Approach | Pros | Cons |
|----------|------|------|
| **Unicode Math** 😊 | Zero setup, works everywhere | Limited to simple symbols |
| **MathJax** 🏆 | Full LaTeX, Sphinx-native | Heavier rendering |
| **KaTeX** ⚡ | Fastest rendering | Needs header injection |
| **Image-based** 🖼️ | No JS needed | Unscalable, unsearchable |

**Our choice: MathJax** ✅
- Built into Sphinx (`sphinx.ext.mathjax`)
- Seamless integration with autodoc
- Renders `.. math::` directives natively

]

**What MathJax gives you:**

$$ \int_{-\infty}^{\infty} e^{-x^2} dx = \sqrt{\pi} $$

$$ \sum_{k=0}^{n} \binom{n}{k} x^{n-k} y^k $$

$$ \det\begin{bmatrix} a & b \\ c & d \end{bmatrix} = ad - bc $$

]

---

### ⚙️ Sphinx Setup — `conf.py`

**One extension** enables math in all docstrings:

```python
# docs/conf.py
extensions = [
    "sphinx.ext.autodoc",    # Auto-document from docstrings
    "sphinx.ext.mathjax",    # Math rendering
    "sphinx.ext.napoleon",   # Google/NumPy docstrings
]
```

**For Markdown files, also add MyST with dollarmath:**

```python
extensions.append("myst_parser")

myst_enable_extensions = [
    "dollarmath",   # $$ display, $ inline
    "amsmath",      # \begin{align}...\end{align}
]
```

---

### 📐 Writing Equations

**Three contexts, three syntaxes:**

**In RST files (`*.rst`):**

```rst
.. math::

\alpha_k = \frac{r_k^T r_k}{p_k^T A p_k}

Inline: :math:`E = mc^2`
```

**In Markdown files (`*.md`):**

```markdown
$$ \alpha_k = \frac{r_k^T r_k}{p_k^T A p_k} $$

Inline: $E = mc^2$
```

**Python docstrings — RST style in raw strings:**

```python
r"""The conjugate gradient update:

.. math::

\alpha_k = \frac{r_k^T r_k}{p_k^T A p_k}
"""
```

---

### ⚡ Key Rules

**Rule 1: Raw strings `r"""`** preserve backslashes for LaTeX:

```python
# WRONG — \mathbf becomes mathbf
def f():
    """Uses \mathbf{x}"""

# CORRECT
def f():
    r"""Uses \mathbf{x}"""
```

**Rule 2: Use `\begin{aligned}` for multi-line formulas with `&`:**

```python
r"""
.. math::

\begin{aligned}
   x &= y + z \\\\
   a &= b + c
   \end{aligned}
"""
```

---

## 🏗️ Project Walkthroughs

---

### 📐 rat-trig — Rational Trigonometry

**Project**: Rational Trigonometry (Norman Wildberger)

**Key formulas added:**

| Function | KaTeX Formula |
|----------|---------------|
| `quad` | $$ Q(v) = x^2 + y^2 $$ |
| `dot` | $$ v_1 \cdot v_2 = x_1 x_2 + y_1 y_2 $$ |
| `cross` | $$ v_1 \times v_2 = x_1 y_2 - y_1 x_2 $$ |
| `archimedes` | $$ \mathcal{A} = 4 q_1 q_2 - (q_1 + q_2 - q_3)^2 $$ |
| `spread` | $$ s = \frac{(v_1 \times v_2)^2}{Q(v_1) Q(v_2)} $$ |
| `spread_law` | $$ S_3 = \frac{4 q_1 q_2 - (q_1 + q_2 - q_3)^2}{4 q_1 q_2} $$ |
| `triple_quad` | $$ T = (q_1 + q_2)^2 - 4 q_1 q_2 (1 - s_3) $$ |

**File**: `src/rat_trig/trigonom.py`

---

### 🎯 ellalgo — Ellipsoid Method

**Project**: Convex optimization via the Ellipsoid Method

**Ellipsoid update** (core algorithm):

$$ \begin{aligned}
\tilde{g} &= M\,g \\\\
\omega &= g^T \tilde{g} \\\\
\tau^2 &= \kappa\,\omega \\\\
x_c &\leftarrow x_c - \frac{\rho}{\omega}\,\tilde{g} \\\\
M &\leftarrow M - \frac{\sigma}{\omega}\,\tilde{g}\,\tilde{g}^T \\\\
\kappa &\leftarrow \delta\,\kappa
\end{aligned} $$

**LDL^T factorization update** (stable variant):

$$ w = L^{-1}g,\quad z = D^{-1}w,\quad \omega = w^T z,\quad q = L^{-T}z $$

---

### 🎯 ellalgo — Cut Formulas

**Deep cut** (biased cut):

$$ \eta = \tau + n \beta,\quad \rho = \frac{\eta}{n+1},\quad \sigma = \frac{2\eta}{(n+1)(\tau+\beta)},\quad \delta = \frac{n^2}{n^2-1} \cdot \frac{\tau^2 - \beta^2}{\tau^2} $$

**Parallel bias cut:**

$$ \eta = \tau^2 + n\,\beta_0\beta_1,\quad \bar\beta = \frac{\beta_0+\beta_1}{2} $$

$$ h = \tfrac12(\tau^2 + \beta_0\beta_1) + n\bar\beta^2,\quad k = h + \sqrt{h^2 - (n+1)\eta\bar\beta^2} $$

$$ \sigma = \frac{\eta}{k},\quad \rho = \bar\beta\,\sigma $$

**Conjugate Gradient:**

$$ \alpha_k = \frac{r_k^T r_k}{p_k^T A p_k},\quad x_{k+1} = x_k + \alpha_k p_k,\quad r_{k+1} = r_k - \alpha_k A p_k $$

---

### 📊 lds-gen — Low-Discrepancy Sequences

**Project**: Quasi-Monte Carlo sequence generators

**van der Corput** (fundamental operation):

$$ n = \sum_{k=0}^{m} d_k b^k \quad\longrightarrow\quad \phi_b(n) = \sum_{k=0}^{m} \frac{d_k}{b^{k+1}} $$

**Geometric mappings:**

| Generator | Formula |
|-----------|---------|
| **Circle** | $$ \theta = 2\pi v,\quad (\cos\theta,\; \sin\theta) $$ |
| **Disk** | $$ \theta = 2\pi v_\theta,\quad r = \sqrt{v_r},\quad (r\cos\theta,\; r\sin\theta) $$ |
| **Sphere** | $$ \phi = 2v-1,\quad (\sqrt{1-\phi^2}\cos\theta,\; \sqrt{1-\phi^2}\sin\theta,\; \phi) $$ |
| **3-Sphere** | $$ (\cos\eta\cdot e^{i\psi},\; \sin\eta\cdot e^{i(\phi+\psi)}) $$ (Hopf fibration) |

---

### 📊 lds-gen — N-Sphere Generation

**3-Sphere via covariance mapping:**

$$ \theta = \frac{\pi}{2} v,\quad \chi = F_2^{-1}(\theta),\quad (\sin\chi \cdot \mathbf{s},\; \cos\chi) $$

**N-Sphere via recursion:**

$$ \theta = v \in [0,1],\quad \chi = T_n^{-1}(\theta),\quad (\sin\chi \cdot \mathbf{s}_{n-2},\; \cos\chi) $$

**Precomputed tables** for the marginal CDF inversion:

$$ T_1(\theta) = -\cos\theta,\qquad T_n(\theta) = \frac{n-1}{n}\,T_{n-2}(\theta) + \frac{\cos\theta\,\sin^{\,n-1}\theta}{n} $$

---

### 🫚 ginger — Polynomial Root-Finding

**Project**: Parallel Bairstow + Aberth root-finding

**Aberth-Ehrlich correction** (cubic convergence):

$$ z_i' = z_i - \frac{P(z_i)}{P'(z_i)},\qquad P'(z_i) = P_1(z_i) - \sum_{j\neq i} \frac{P(z_i)}{z_i - z_j} $$

**Synthetic division** by a quadratic factor:

$$ P(x) = Q(x)\cdot(x^2 - r x - q) + A x + B $$

$$ b_0 = a_0,\quad b_1 = a_1 + r b_0,\quad b_k = a_k + r b_{k-1} + q b_{k-2} $$

**Initial guess (Bairstow):**

$$ c = -\frac{a_1}{n a_0},\quad R = \sqrt[n]{|P(c)|} $$

---

### 🫚 ginger — Bairstow Details

**Delta correction** (2x2 system):

$$ \begin{bmatrix} rp + s & p \\ qp & s \end{bmatrix}
   \begin{bmatrix} \Delta r \\ \Delta q \end{bmatrix}
   = \begin{bmatrix} A \\ B \end{bmatrix} $$

**Zero suppression** (adjoint matrix):

$$ \text{adj}\!\begin{bmatrix} r & q \\ p & s \end{bmatrix}
   = \begin{bmatrix} s & -p \\ -pq & pr+s \end{bmatrix} $$

**Quadratic formula:**

$$ x = \frac{r \pm \sqrt{r^2 + 4q}}{2} $$

---

### 🔯 projgeom-py — Projective Geometry

**Project**: Projective, elliptic, hyperbolic geometry

**Core operations:**

| Operation | Formula |
|-----------|---------|
| **Dot product** | $$ \mathbf{a} \cdot \mathbf{b} = a_1 b_1 + a_2 b_2 + a_3 b_3 $$ |
| **Cross product** | $$ \mathbf{a} \times \mathbf{b} = (a_2 b_3 - a_3 b_2,\; a_3 b_1 - a_1 b_3,\; a_1 b_2 - a_2 b_1) $$ |
| **Harmonic conj.** | $$ (A,B;C,D) = -1 $$ |
| **Linear comb.** | $$ \lambda\mathbf{a} + \mu\mathbf{b} $$ |

**Polar/pole per geometry:**

| Geometry | Absolute conic | Polar |
|----------|---------------|-------|
| **Elliptic** | $$ x_1^2 + x_2^2 + x_3^2 = 0 $$ | $$ \mathbf{p} = \mathbf{x} $$ |
| **Hyperbolic** | $$ x_1^2 + x_2^2 - x_3^2 = 0 $$ | $$ \mathbf{p} = (x_1, x_2, -x_3) $$ |

---

### 🔧 Pitfall 1: Raw Strings

Python interprets `\b`, `\n`, `\t` in regular strings:

```python
# WRONG — \mathbf becomes mathbf
def f():
    """Formula: \mathbf{x} = \tau \cdot \mathbf{g}"""

# CORRECT — raw string preserves backslashes
def f():
    r"""Formula: \mathbf{x} = \tau \cdot \mathbf{g}"""
```

If MathJax shows `mathbf{x}` instead of $\mathbf{x}$, you forgot the `r` prefix!

---

### 🔧 Pitfall 2: Aligned Environments

`&` for alignment must be inside `\begin{aligned}`:

```python
# WRONG — Misplaced & error
r"""
.. math::

x &= y + z
"""
```

```python
# CORRECT
r"""
.. math::

\begin{aligned}
   x &= y + z \\\\
   a &= b + c
   \end{aligned}
"""
```

---

### 🔄 Python vs Rust: Equation Patterns

Same mathematical content — only syntax differs:

**Python (Sphinx + MathJax)** 🐍

```python
r"""The spread:

.. math::

s = 1 - \frac{(v_1 \cdot v_2)^2}
                 {|v_1|^2 |v_2|^2}

where :math:`v_1, v_2` are vectors.
"""
```

]

**Rust (rustdoc + KaTeX)** 🦀

```rust
/// The spread:
///
/// $$ s = 1 - \frac{(v_1 \cdot v_2)^2}{|v_1|^2 |v_2|^2} $$
///
/// where $v_1, v_2$ are vectors.
pub fn spread(...)
```

]

**Key differences:**
- Python: `r"""..."""` + `.. math::` + `:math:` infix
- Rust: `///` + `$$...$$` + `$...$` inline
- Same LaTeX content, different containers

---

### 🏗️ Full Architecture

subgraph "Math Rendering"
        B -->|html output| E[HTML with\n.. math:: directives]
        E -->|page load| F[MathJax renders\nSVG/HTML output]
    end

subgraph "5 Python Projects"
        G[rat-trig 🐍]
        H[ellalgo 🐍]
        I[lds-gen 🐍]
        J[ginger 🐍]
        K[projgeom-py 🐍]
    end

F --> G
    F --> H
    F --> I
    F --> J
    F --> K
    style A fill:#e3f2fd,stroke:#1565c0,stroke-width:3px
    style B fill:#fff9c4,stroke:#f57f17,stroke-width:3px
    style C fill:#e3f2fd,stroke:#1565c0,stroke-width:3px
    style D fill:#e3f2fd,stroke:#1565c0,stroke-width:3px
    style E fill:#c8e6c9,stroke:#2e7d32,stroke-width:3px
    style F fill:#fff9c4,stroke:#f57f17,stroke-width:3px
    style G fill:#ffccbc,stroke:#bf360c,stroke-width:3px
    style H fill:#ffccbc,stroke:#bf360c,stroke-width:3px
    style I fill:#ffccbc,stroke:#bf360c,stroke-width:3px
    style J fill:#ffccbc,stroke:#bf360c,stroke-width:3px
    style K fill:#ffccbc,stroke:#bf360c,stroke-width:3px
</pre>
]

---

### 📊 Results: By the Numbers

| Metric | Count |
|--------|-------|
| **Projects updated** | 5 |
| **Source files modified** | 16 |
| **Math formulas added** | 80+ |
| **Warnings introduced** | 0 |

**Coverage by domain:**

| Domain | Project | Key Formulas |
|--------|---------|--------------|
| 🔢 Rational Trigonometry | `rat-trig` | Quadrance, spread, cross |
| 🎯 Convex Optimization | `ellalgo` | Cut parameters, CG, LDL^T |
| 🔢 Low-Discrepancy | `lds-gen` | van der Corput, sphere maps |
| 🧮 Polynomial Roots | `ginger` | Aberth, Bairstow, Horner |
| 📐 Projective Geometry | `projgeom-py` | Cross ratio, polar/pole |

---

### 💡 Key Takeaways

**For Python Library Authors:**

1. **MathJax + Sphinx** is the gold standard
   - Built-in `sphinx.ext.mathjax`
   - Zero extra setup beyond `conf.py`

2. **Pattern for each function:**
   - Raw docstring `r"""..."""`
   - `.. math::` for display formulas
   - `:math:` for inline references

]

**Watch out for:**

3. **Raw strings** — `r"""`, not `"""`
4. **Aligned env** — wrap `&=` in `\begin{aligned}`
5. **Windows encoding** — set `PYTHONIOENCODING=utf-8`

**Format to follow:**

```python
r"""Description.

.. math::

formula

:param x: ...
:return: ...
"""
```

]

---

## ❓ Questions?

---

# 🙏 Thank You

### Happy Documenting!

**Slides**: [`luk036.github.io/idea/doc-eqn-py-remark`](https://luk036.github.io/idea/doc-eqn-py-remark.html)

**Repositories**:
- [`github.com/luk036/rat-trig`](https://github.com/luk036/rat-trig)
- [`github.com/luk036/ellalgo`](https://github.com/luk036/ellalgo)
- [`github.com/luk036/lds-gen`](https://github.com/luk036/lds-gen)
- [`github.com/luk036/ginger`](https://github.com/luk036/ginger)
- [`github.com/luk036/projgeom-py`](https://github.com/luk036/projgeom-py)

@luk036 👨‍💻 · 2026 📅