| |
| """Code-preserving parse of copernicus-marine-notebook-gallery notebooks. |
| Reuses the extract_code.py pattern: verbatim markdown + verbatim ```python |
| code cells + trimmed ```text outputs; classify recipe_kinds via regex. |
| Writes parsed/<name>/<notebook_id>.md and prints a JSON manifest to stdout. |
| """ |
| import json, re, sys |
| from pathlib import Path |
|
|
| REPO = Path("/Users/dmpantiu/copernicus_mcp/notebook_harvest/repos/copernicus-marine-notebook-gallery") |
| OUT = Path("/Users/dmpantiu/copernicus_mcp/notebook_harvest/parsed/copernicus-marine-notebook-gallery") |
| ROOT = Path("/Users/dmpantiu/copernicus_mcp") |
|
|
| DOWNLOAD_RE = re.compile( |
| r"cdsapi|\.retrieve\(|copernicusmarine|\bcm\.(subset|get|open_dataset)|" |
| r"motuclient|--service-id|--product-id|!?\bwget\b|urlretrieve|requests\.get|\.hda\b|EO:", |
| re.I) |
| ANALYZE_RE = re.compile( |
| r"\bimport xarray|\bxr\.|\.open_dataset|\.open_mfdataset|\bimport pandas|\bpd\.|" |
| r"\bimport numpy|\bnp\.|\bscipy|nc\.Dataset|netCDF4|\.groupby\(|\.resample\(|" |
| r"\.mean\(|\.sel\(|\.isel\(", re.I) |
| PLOT_RE = re.compile( |
| r"\bmatplotlib|\bplt\.|\bcartopy|\bccrs\b|\bcmocean|\.plot\(|\.plot\.|seaborn|\bsns\.|pcolor|contourf", |
| re.I) |
|
|
|
|
| def _src(cell): |
| s = cell.get("source", "") |
| return "".join(s) if isinstance(s, list) else s |
|
|
|
|
| def code_line_count(code): |
| n = 0 |
| for ln in code.splitlines(): |
| st = ln.strip() |
| if st and not st.startswith("#"): |
| n += 1 |
| return n |
|
|
|
|
| def text_outputs(cell): |
| out = [] |
| for o in cell.get("outputs", []): |
| ot = o.get("output_type"); s = None |
| if ot == "stream": |
| t = o.get("text", ""); s = "".join(t) if isinstance(t, list) else t |
| elif ot in ("execute_result", "display_data"): |
| tp = (o.get("data") or {}).get("text/plain") |
| if tp is not None: |
| s = "".join(tp) if isinstance(tp, list) else tp |
| if not s: |
| continue |
| s = s.strip() |
| if not s or re.fullmatch(r"<[^>]+>", s) or s.startswith("<Figure"): |
| continue |
| lines = [ln for ln in s.splitlines() |
| if "%|" not in ln and "it/s]" not in ln and "B/s]" not in ln] |
| s = "\n".join(lines).strip() |
| if len(s) >= 8: |
| out.append(s[:1500]) |
| return out |
|
|
|
|
| def classify(code): |
| kinds = [] |
| if DOWNLOAD_RE.search(code): kinds.append("download") |
| if ANALYZE_RE.search(code): kinds.append("analyze") |
| if PLOT_RE.search(code): kinds.append("plot") |
| return kinds or ["other"] |
|
|
|
|
| def slug(path): |
| return re.sub(r"[^A-Za-z0-9._-]+", "-", path.stem).strip("-") |
|
|
|
|
| def extract(path): |
| nb = json.loads(path.read_text(encoding="utf-8", errors="replace")) |
| parts = []; n_cells = 0; n_lines = 0; kinds = set(); title = "" |
| for cell in nb.get("cells", []): |
| ct = cell.get("cell_type") |
| if ct == "markdown": |
| txt = _src(cell).strip() |
| if txt: |
| parts.append(txt) |
| if not title: |
| for ln in txt.splitlines(): |
| if ln.startswith("# "): |
| title = ln[2:].strip(); break |
| elif ct == "code": |
| src = _src(cell).rstrip() |
| if not src.strip(): |
| continue |
| n_cells += 1; n_lines += code_line_count(src) |
| kinds.update(classify(src)) |
| parts.append("```python\n" + src + "\n```") |
| for to in text_outputs(cell): |
| parts.append("```text\n" + to + "\n```") |
| return {"md": "\n\n".join(parts).strip(), "title": title or path.stem, |
| "n_code_cells": n_cells, "n_code_lines": n_lines, |
| "recipe_kinds": sorted(kinds)} |
|
|
|
|
| def main(): |
| OUT.mkdir(parents=True, exist_ok=True) |
| recs = [] |
| for nb in sorted(REPO.rglob("*.ipynb")): |
| if ".ipynb_checkpoints" in nb.parts: |
| continue |
| nid = slug(nb) |
| ex = extract(nb) |
| if ex["n_code_cells"] == 0: |
| print(f"SKIP prose-only: {nid}", file=sys.stderr); continue |
| md = OUT / f"{nid}.md" |
| md.write_text(ex["md"], encoding="utf-8") |
| recs.append({ |
| "notebook_id": nid, "title": ex["title"], |
| "src_path": str(nb.relative_to(REPO)), |
| "md_path": str(md.relative_to(ROOT)), |
| "n_code_cells": ex["n_code_cells"], "n_code_lines": ex["n_code_lines"], |
| "recipe_kinds": ex["recipe_kinds"], |
| }) |
| print(json.dumps(recs, indent=2)) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
