| name | academic-pdf-to-gfm |
| description | Convert academic PDF papers to GitHub-renderable GFM markdown with math equations. TRIGGERS - PDF, GitHub markdown, math |
| allowed-tools | Read, Grep, Glob, Bash, Write, Edit |
Academic PDF → GitHub GFM Conversion
A battle-tested workflow for converting academic/research PDF papers into GitHub-renderable GFM markdown with inline figures, mathematically correct LaTeX, and validated output.
Battle-tested on: López de Prado (2026) "How to Use the Sharpe Ratio" — 51 pages, 82 equations, 8 figures.
Self-Evolving Skill: This skill improves through use. If instructions are wrong, parameters drifted, or a workaround was needed — fix this file immediately, don't defer. Only update for real, reproducible issues.
Quick Start — Per-Page Routing Workflow
Do NOT try to apply a single extraction method to the entire PDF. Modern academic papers mix text, tables, and figures; route each page individually.
Step 1: Render all pages at 300 DPI
uv run --python 3.14 --with pymupdf python3 << 'EOF'
import fitz, os
doc = fitz.open('paper.pdf')
os.makedirs("pages", exist_ok=True)
for i in range(len(doc)):
pix = doc[i].get_pixmap(matrix=fitz.Matrix(300/72, 300/72), alpha=False)
pix.save(f"pages/page{i:04d}.png")
print(f"Page {i}: {pix.width}×{pix.height}")
EOF
Step 2: Detect page type for each page
S=${S:-~/eon/cc-skills/plugins/unlimited-ocr/scripts/unlimited_ocr.py}
for img in pages/page*.png; do
echo "=== $(basename $img) ==="
uv run --no-project $S parse --input "$img" --collapse-math-spacing --quiet 2>&1 | \
grep "<|det|>" | cut -d'>' -f2 | cut -d' ' -f1 | sort | uniq -c
done
Step 3: Route each page
Based on the detected <|det|> markers:
| Detected | Route to | Command |
|---|
text only (no equation, image, chart) | pymupdf4llm or pdftotext | See Tool Comparison below |
equation or table present | Unlimited-OCR (with --table-format pipe) | uv run --no-project $S parse --input page.png |
image or chart present | Segment + describe | Use unlimited-ocr-segment-figure skill + vision model |
Mixed (table + image) | Unlimited-OCR for table + segment for images | Split the output, route images separately |
Step 4: Assemble and validate
cat pages/page*.md > paper-raw.md
uv run --python 3.14 --with pymupdf python3 references/extract-images.py paper.pdf
node references/validate-math.mjs paper-raw.md --fix
Tool Comparison (by page type)
A single academic PDF is routinely born-digital prose on most pages and equation-dense or figure-dense on a few. Routing the entire document as one type wastes capability and silently loses content.
The Per-Page Routing Strategy
For every page in the PDF:
- Render at 300 DPI to a PNG (required for Unlimited-OCR accuracy; 150 DPI hallucinates silently)
- Detect page type by running Unlimited-OCR locally (~2.4 s/page on Apple Silicon)
- Route based on what the model found:
- Text-only pages (no math, no charts): extract with
pymupdf4llm or pdftotext (cheaper, preserves structure)
- Equation-bearing pages: use Unlimited-OCR output (returns real LaTeX, e.g.
\left\{ \begin{array} ... \end{array} \right\})
- Chart-bearing pages: segment with Unlimited-OCR, hand each panel to a vision model for description (verified 2026-07-31: charts return empty text from Unlimited-OCR)
- Fallback: if a page's text-layer extraction is too thin, re-run through Unlimited-OCR
Why Per-Page Matters
The silent failure. Unlimited-OCR localizes charts with perfect bounding boxes and returns zero characters inside. A user who routes the entire document as "Type C, use Unlimited-OCR" on chart-heavy input loses all chart content AND GETS A WELL-FORMED RESULT, so nothing looks wrong until the output is reviewed.
Verified (2026-07-31): Unlimited-OCR detects charts (via <|det|>chart markers) and returns perfect bounding boxes but zero text inside. Pages containing only charts (no text, equations, or tables) would indeed render empty; per-page routing catches this and routes those pages to text-layer extraction or manual inspection instead.
Page Type Detection (Measured at 300 DPI)
Run Unlimited-OCR on every page and inspect the <|det|> markers:
| If the output contains | Infer | Route to |
|---|
text regions, no equation or chart | Text-only page | pymupdf4llm or pdftotext (fallback: Unlimited-OCR) |
equation regions | Math-bearing page | Unlimited-OCR (returns real LaTeX) |
chart regions | Figure-bearing page | Segment + describe (use unlimited-ocr-segment-figure then a chart-reading model) |
| Empty output (zero characters, no regions) | Page likely unhandled by text layer | Retry with Unlimited-OCR or manual inspection |
Example: TimeMixer (ICLR 2024, 28 pages)
Verified 2026-07-31 on /Users/terryli/eon/quantml/data/papers/a599/b338e44af70d8e9c87be3c5417bde7864b2c92074e1346703f3e2b641e3d.pdf:
Page 0 — Title page with abstract (route to text extraction)
uv run --python 3.14 --with pymupdf python3 -c "
import fitz
doc = fitz.open('timemixer-iclr-2024.pdf')
pix = doc[0].get_pixmap(matrix=fitz.Matrix(300/72, 300/72), alpha=False)
pix.save('page0.png')
"
S=~/eon/cc-skills/plugins/unlimited-ocr/scripts/unlimited_ocr.py
uv run --no-project $S parse --input page0.png --collapse-math-spacing --quiet 2>&1 | head -15
Output (actual):
<|det|>header [173, 33, 482, 49]<|/det|>Published as a conference paper at ICLR 2024
<|det|>title [172, 99, 818, 149]<|/det|>TIMEMIXER: DECOMPOSABLE MULTISCALE MIXING FOR TIME SERIES FORECASTING
<|det|>text [181, 170, 777, 200]<|/det|>Shiyu Wang \( ^{1,*} \) , Haixu Wu \( ^{2,*} \) , Xiaoming Shi \( ^{1} \) , Tengge Hu \( ^{2} \) , Huakun Luo \( ^{2} \) , Lintao Ma \( ^{1✉} \) , James Y. Zhang \( ^{1} \) , Jun Zhou \( ^{1✉} \)
<|det|>text [182, 200, 781, 243]<|/det|>\( ^{1} \) Ant Group, Hangzhou, China \( ^{2} \) Tsinghua University, Beijing, China {weiming.wsy,lintao.mlt,peter.sxm,james.z,jun.zhoujun}@antgroup.com, {wuhx23,htg21,luhk19}@mails.tsinghua.edu.cn
<|det|>title [452, 279, 547, 293]<|/det|>ABSTRACT
<|det|>text [230, 311, 770, 575]<|/det|>Time series forecasting is widely used in extensive applications, such as traffic planning…
Routing decision: Only header, title, text regions detected. No equation, no chart → route to pymupdf4llm or pdftotext (faster, preserves structure).
Page 6 — Benchmark table (route to Unlimited-OCR)
uv run --no-project $S parse --input page6.png --collapse-math-spacing --quiet 2>&1 | head -20
Output (actual):
<|det|>text [187, 114, 812, 129]<|/det|>Table 1: Summary of benchmarks. Forecastability is one minus the entropy of Fourier domain.
<|det|>table [175, 131, 825, 287]<|/det|>| Tasks | Dataset | Variate | Predict Length | Frequency | Forecastability | Information |
| Long-term forecasting | ETT (4 subsets) | 7 | 96~720 | 15 mins | 0.46 | Temperature |
| Weather | 21 | 96~720 | 10 mins | 0.75 | Weather |
| Solar-Energy | 137 | 96~720 | 10min | 0.33 | Electricity |
…
Routing decision: table detected → keep Unlimited-OCR output (already in pipe-markdown format, --table-format pipe converts any HTML to markdown).
Page 7 — Figure and table mixed (route Unlimited-OCR for table only)
uv run --no-project $S parse --input page7.png --collapse-math-spacing --quiet 2>&1 | head -30
Output (actual):
<|det|>table [186, 174, 819, 384]<|/det|>| Case | Decompose | Past mixing | Future mixing | M4 | PEMS04 | ETTm1 |
…
Note: Page 7 contains 6 embedded image objects in the PDF (verified via PyMuPDF), but Unlimited-OCR's 300-DPI screenshot rendering does not detect image or image_caption regions. Extract images separately via references/extract-images.py and route them to a vision model for description.
Routing decision: table detected → keep Unlimited-OCR output; extract embedded images separately and hand to a vision model for description (see unlimited-ocr-segment-figure skill).
Type Classification (Historical, kept for reference)
Type A — Word-Generated PDF (Type A: most modern academic papers)
Signs: Embedded fonts, copyable text, Unicode math chars when you copy-paste (∑, π, α, β, γ, →)
Math encoding: Math is Unicode text in PDF stream — NOT images, NOT glyph maps
Consequence: OCR tools like marker-pdf cannot extract LaTeX — they see text like "γ₄" not \gamma_4. They may return empty output or crash silently.
Type B — LaTeX-Generated PDF
Signs: Computer Modern fonts, precise mathematical spacing, arxiv.org source available
Math encoding: Glyph-mapped — structure is partially extractable
Type C — Scanned/Image PDF
Signs: All pages are raster images, zero copyable text
Table Format Notice
Tables from Unlimited-OCR come back as HTML <table> markup (measured by Baidu at ~88% of real tables). The CLI converts them to pipe-markdown by default (--table-format pipe), which is suitable for markdown documents. If you are comparing outputs across readers, pipe-markdown is the canonical form.
Tool Comparison
| Tool | Page type | Install | Pros | Cons |
|---|
| pymupdf4llm | Text-only, native text layer | uv run --with pymupdf4llm | Best structure preservation, fast | Math comes as Unicode, not LaTeX |
| pdftotext | Text-only, plain extraction | brew install poppler | Very fast, minimal deps | Loses table structure entirely |
| Unlimited-OCR | Tables, math, mixed pages | uv run --no-project (no install) | Real LaTeX formulas, tables as pipe-markdown, layout boxes, 300 DPI accurate | Returns empty text for charts; use segment-figure for those |
| markitdown | Text-only alternative | uv run --with 'markitdown[pdf]' | Reasonable structure | Slight over-spacing; same math limit as pymupdf4llm |
| marker-pdf | Scanned PDFs (Type C only) | pip install marker-pdf | Works on scanned images | Never use on Type A/B — fails silently (Unicode text bug) |
Recommendation: For per-page routing:
- Text-only pages →
pymupdf4llm (preserves formatting) or pdftotext (speed)
- Tables/math pages → Unlimited-OCR (returns real LaTeX and pipe-markdown tables)
- Chart-bearing pages → Unlimited-OCR (detects charts but returns empty text; route to segment-figure skill + vision model for descriptions)
- Mixed pages → Unlimited-OCR (handles tables and layout detection in one pass; segment images separately)
Image Extraction
Save references/extract-images.py:
import fitz, os, sys
doc = fitz.open(sys.argv[1])
os.makedirs("references/media", exist_ok=True)
saved = []
for page_num in range(len(doc)):
for img_idx, img in enumerate(doc[page_num].get_images(full=True)):
xref = img[0]
base_image = doc.extract_image(xref)
img_bytes = base_image["image"]
if len(img_bytes) < 2048:
continue
ext = base_image["ext"]
fname = f"fig-p{page_num+1:02d}-{img_idx+1:02d}.{ext}"
with open(f"references/media/{fname}", "wb") as f:
f.write(img_bytes)
saved.append((page_num+1, fname, base_image.get("width"), base_image.get("height")))
print(f"Saved: {fname} ({len(img_bytes)//1024}KB, {base_image.get('width')}×{base_image.get('height')})")
doc.close()
print(f"\n{len(saved)} images saved to references/media/")
Naming: fig-p{page:02d}-{idx:02d}.{ext} — page number in name for easy location matching.
Size filter: Skip < 2 KB (captures icons, watermarks, horizontal rules). Review everything ≥ 2 KB — some are decorative but most are figures.
Insert in markdown:
Place immediately after the nearest section heading or the paragraph that references the figure.
GitHub GFM Math Rendering Rules
The $$ vs ```math ``` Decision — Root Cause
GitHub's Markdown pre-processor runs BEFORE the math renderer. It treats \\ as an escaped backslash and collapses it to \. This breaks LaTeX line breaks in display math.
The rule is simple:
| Equation type | Use | Reason |
|---|
| Single-line display | $$...$$ | No \\ → pre-processor safe |
Multi-line (contains \\, \begin{aligned}, matrices) | ```math ``` | Pre-processor does NOT process code fences |
| Inline | $...$ | Standard |
# BROKEN on GitHub — \\ stripped by pre-processor:
$$
\begin{aligned}
a &= b + c \\
d &= e + f
\end{aligned}
$$
# CORRECT on GitHub:
```math
\begin{aligned}
a &= b + c \\
d &= e + f
\end{aligned}
```
### Display Block Formatting Rules
- `$$` must be on its **own line** — not `$$formula$$` on one line
- **Blank line required** before AND after every `$$` block
- **Blank line required between consecutive** `$$` blocks
- These rules do NOT apply to `` ```math ``` `` blocks
### Supported/Unsupported LaTeX
See [references/github-math-support-table.md](./references/github-math-support-table.md) for the full table.
**Key things to avoid**:
| Command | Problem | Fix |
|---------|---------|-----|
| `\begin{align}` | ❌ Not supported by GitHub | Use `\begin{aligned}` |
| `\boxed{}` | ⚠️ Can cause raw LaTeX passthrough | Remove or use bold text |
| `\operatorname{}` | ⚠️ Active GitHub bug, inconsistent | Use `\text{}` or `\mathrm{}` |
| `\newcommand` | ❌ Was briefly available, then pulled | Expand all macros inline |
| `x^_y` | Superscript immediately before subscript | Write `x^{*}_{i}` with braces |
### Common Gotchas
- `\\[8pt]` vertical spacing inside `$$` → eaten by pre-processor → move to `` ```math ``` ``
- `\frac{1}{T}:\left(` → spurious colon after fraction → remove colon
- Pearson vs excess kurtosis: most finance formulas need Pearson (γ₄ = 3 for Gaussian), not excess. **Always document the kurtosis convention in the formula comment.**
- `\begin{pmatrix}` with `\\` → must use `` ```math ``` ``
- `\begin{cases}` with multiple rows → must use `` ```math ``` ``
---
## GitLab: No Workarounds Needed
**Empirically verified 2026-03-15** on GitLab CE 18.9.2. Confirmed by Comrak source code analysis.
GitLab uses the **Comrak** Rust parser with `math_dollars: true`. When Comrak encounters `$$`, it calls `handle_dollars` which slices the raw input buffer directly and stores it as a `NodeMath` AST node — CommonMark's backslash handler is never invoked on math content. The raw LaTeX is passed to KaTeX via `<span data-math-style="display/inline">` unchanged.
**Every GitHub workaround is unnecessary on GitLab:**
| GitHub problem | GitHub fix required | GitLab |
|----------------|---------------------|--------|
| `\\` in `$$` stripped → broken multiline | Use ` ```math ``` ` | `$$` works with `\\` |
| `\left\{` → `\left{` (delimiter error) | Use `\left\lbrace` | `\left\{` works |
| `\{...\}` set notation → invisible braces | Use `\lbrace...\rbrace` | `\{...\}` works |
| `\,` in `$$` → literal comma | Remove `\,` | `\,` works |
| `\,` in inline `$` → literal comma | Remove `\,` | `\,` works |
On GitLab you can write standard LaTeX without any platform-specific workarounds. If you're targeting GitLab (or hosting your own GitLab CE), skip all the `\lbrace`/`\rbrace` substitutions and ` ```math ``` ` conversions — plain `$$` with standard LaTeX is correct.
### GitLab.com Has a Hard 50-Span Per-Page Limit
**GitLab.com (SaaS) enforces a limit of 50 total math spans per page** (display + inline combined). After the 50th span, all subsequent equations silently fall back to raw LaTeX text. This limit exists to prevent DoS attacks and cannot be overridden on GitLab.com.
| Document math density | gitlab.com | Self-hosted CE |
|---|---|---|
| ≤ 50 total spans | ✅ Renders fully | ✅ |
| 51–100 spans | ⚠️ Partial render | ✅ |
| 100+ spans (academic papers) | ❌ Most equations raw text | ✅ Disable with `math_rendering_limits_enabled: false` |
**Validated on**: Sharpe ratio paper (341 spans) — breaks at span 51 on gitlab.com, renders fully on local CE.
**The W6 check in `validate-math.mjs`** warns when a file exceeds the limit.
**Summary: which platform to use**:
- **GitHub.com**: No math span limit. Use `\lbrace`/`\rbrace` workarounds (handled by `--fix`).
- **Self-hosted GitLab CE**: No limit (disable math_rendering_limits_enabled). No workarounds needed.
- **GitLab.com**: Only suitable for documents with ≤ 50 math spans.
### Self-hosting GitLab CE for Math-Heavy Documents
GitLab CE is free and runs on a single machine. On a 61 GB workstation with slim config:
- Memory footprint: ~3 GB (`puma['worker_processes'] = 2`, `sidekiq['concurrency'] = 5`, monitoring disabled)
- Push mirroring to GitHub: free on CE (syncs within 5 min)
- `glab` CLI: first-party, comparable to `gh`
```yaml
# docker-compose.yml — slim GitLab CE
services:
gitlab:
image: gitlab/gitlab-ce:latest
restart: unless-stopped
environment:
GITLAB_OMNIBUS_CONFIG: |
external_url 'http://YOUR_IP:8929'
puma['worker_processes'] = 2
sidekiq['concurrency'] = 5
prometheus_monitoring['enable'] = false
alertmanager['enable'] = false
node_exporter['enable'] = false
redis_exporter['enable'] = false
postgres_exporter['enable'] = false
gitlab_exporter['enable'] = false
ports: ["8929:8929", "8922:22"]
volumes:
- /srv/gitlab/config:/etc/gitlab
- /srv/gitlab/logs:/var/log/gitlab
- /srv/gitlab/data:/var/opt/gitlab
```
---
## Validation Pipeline
### Step 1: Install KaTeX Validator
```bash
bun add -g katex # Bun-first per project policy
# or: npm install -g katex
Step 2: Run Before Every Push
node references/validate-math.mjs your-file.md
node references/validate-math.mjs your-file.md --fix
The script is at references/validate-math.mjs. It runs two layers:
Layer 1 — KaTeX syntax: parse errors in $, $$, ```math ``` blocks
Layer 2 — GFM structural (issues KaTeX passes but GitHub breaks):
| Code | Severity | Issue | Auto-fix |
|---|
| E0 | Error | \! \, \; \{ \} in $$ block — pre-processor strips backslash → parse error cascade | ✅ spacing removed; \{→\lbrace |
| E0b | Warning | \{ \} \, in inline $...$ — invisible braces or literal commas in prose | ✅ → \lbrace/\rbrace; \, removed |
| E1 | Error | $$ block with \\ — GitHub pre-processor strips backslashes | ✅ → ```math ``` |
| E2 | Error | Consecutive $$ blocks without blank line — orphaned delimiter cascade | ✅ add blank line |
| W1 | Warning | Bare ^* in $$ or $ block — markdown italic pairing eats the * | ✅ → ^{\ast} |
| W2 | Warning | \begin{align} — not supported on GitHub | ✗ manual |
| W3 | Warning | \boxed{} — can cause raw LaTeX passthrough | ✗ manual |
| W4 | Warning | \operatorname{} — inconsistent GitHub support | ✗ manual |
E0 is the most dangerous: a single failing $$ block exposes its $$ delimiters as literal text, creating an orphaned $ that shifts ALL subsequent inline $...$ pairings. One broken equation takes down the entire document.
\{/\} trap: In $$ blocks, \left\{ becomes \left{ (invalid KaTeX delimiter → "Missing or unrecognized delimiter") and \{...\} set notation becomes invisible grouping. Fix: use \lbrace/\rbrace (letter-based, CommonMark-immune). This affects every equation using set notation like \{\hat{SR}_k\} or \min_T\left\{...\right\}.
Exits code 1 on errors (CI-friendly). Warnings do not block CI but should be reviewed.
Local Preview Tools
bun add -g @hyrious/gfm
gfm your-file.md --serve
gh extension install thiagokokada/gh-gfm-preview
gh gfm-preview your-file.md
VS Code extensions:
shd101wyy.markdown-preview-enhanced — closest to GitHub renderingbierner.markdown-preview-github-styles — GitHub CSS styling
Multi-Agent Adversarial Equation Validation
For papers with 10+ equations, use this multi-agent pattern:
Phase 1 — Parallel Extraction
- Agent A: Extract prose with pymupdf4llm, transcribe math from PDF screenshots
- Agent B: Extract and categorize all images
Phase 2 — Parallel Validation
- Agent C: Validate equations against reference implementation (if code/repo exists)
- Agent D: Numerical spot-checks — compute paper's exhibit values, compare
Phase 3 — Discrepancy Handling
- For each discrepancy: write
/tmp/paper-discrepancy/eq-{N}.md
- Spawn resolver agents to search online for authoritative third-party sources
- Authority rule: Paper is tentatively more authoritative than code implementation; a third independent source breaks ties
Phase 4 — Guarded Application
- Apply only HIGH-confidence fixes to the markdown
- For MEDIUM-confidence: spawn an independent audit agent before touching the file
- Document all discrepancies even if not fixed — future readers need to know
Anti-Patterns
| Anti-pattern | Why it fails | Fix |
|---|
\!\left( or \, in $$ blocks | GH pre-processor strips \!→! before KaTeX — !\left( crashes KaTeX, cascades all | Remove \! \, \; (spacing only) — or use ```math ``` |
\left\{ or \{...\} in $$/$ blocks | \{→{ (CommonMark escape), so \left\{→\left{ = "Missing delimiter" error, and \{x\} renders without visible braces | Replace with \left\lbrace, \right\rbrace, \lbrace, \rbrace |
$$\begin{aligned}...\\...\end{aligned}$$ | \\ stripped by GH pre-processor | Use ```math ``` |
Trusting marker-pdf on Word PDFs | Returns no output or zero math (Unicode bug) | Read as screenshots, transcribe manually |
\begin{align} in display math | Not supported by GitHub | Replace with \begin{aligned} |
\operatorname{Cov} | Active GH bug — sometimes renders raw | Use \text{Cov} or \mathrm{Cov} |
KaTeX validation only, no ```math ``` conversion | KaTeX passes but GH pre-processor still breaks \\ | Also convert ALL multi-line blocks |
\boxed{} for highlighting | Can cause raw LaTeX passthrough on GitHub | Use bold text or a blockquote callout |
| Excess kurtosis in formulas expecting Pearson | Silent ~50% underestimate in variance formulas | Always document convention; use scipy.stats.kurtosis(fisher=False) |
| Consecutive blocks without blank lines |
References
Related Skills
Post-Execution Reflection
After this skill completes, reflect before closing the task:
- Locate yourself. — Find this SKILL.md's canonical path before editing.
- What failed? — Fix the instruction that caused it.
- What worked better than expected? — Promote to recommended practice.
- What drifted? — Fix any script, reference, or dependency that no longer matches reality.
- Log it. — Evolution-log entry with trigger, fix, and evidence.
Do NOT defer. The next invocation inherits whatever you leave behind.
