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Website Scripts

extract_metadata.py

Imports task classes from the installed pyhealth package and writes data/tasks.json. Run this whenever a task class is added or renamed.

Prerequisites: pyhealth installed in your active Python environment.

# From the pyhealth.github.io repo root:
python scripts/extract_metadata.py

# Custom output path:
python scripts/extract_metadata.py --output data/tasks.json

Output goes to data/tasks.json by default.

Workflow for adding a new task

  1. Add the task class to PyHealth/pyhealth/tasks/.
  2. Run the script to regenerate data/tasks.json.
  3. Add one entry to data/tasks_extra.json (see format below).
  4. Commit both JSON files — the site renders from them automatically.

data/tasks.json (auto-generated, do not hand-edit)

Each entry is one Python class found in pyhealth/tasks/:

{
  "class_name":    "MortalityPredictionMIMIC3",
  "task_name":     "MortalityPredictionMIMIC3",
  "description":   "Task for predicting mortality using MIMIC-III...",
  "input_schema":  {"conditions": "sequence", "procedures": "sequence"},
  "output_schema": {"mortality": "binary"},
  "output_type":   "binary",
  "source_file":   "pyhealth/tasks/mortality_prediction.py"
}

output_type is inferred from output_schema values. Classes that set their schema dynamically in __init__ will have null here — override via tasks_extra.json.

data/tasks_extra.json (hand-authored)

Controls which tasks appear on the site and in what order. Fields:

Field Required Description
class_name Yes Python class name — used to join with tasks.json
display_name Yes Human-readable title shown on the card
display_class No Short name shown in the code snippet (defaults to class_name)
datasets Yes Array of dataset pill labels, e.g. ["MIMIC-III"]
description Yes One-sentence description for the card
colab_url No Colab notebook URL
docs_url No ReadTheDocs URL (defaults to the tasks index page)
output_type No Override auto-detected type (needed when schema is set in __init__)

Minimal entry:

{
  "class_name":   "MyNewTask",
  "display_name": "My New Task",
  "datasets":     ["MIMIC-IV"],
  "description":  "One sentence for the website card.",
  "colab_url":    "https://colab.research.google.com/drive/..."
}

Testing locally

The site fetches JSON via fetch(), so it must be served over HTTP:

cd /path/to/pyhealth.github.io
python -m http.server 8080
# open http://localhost:8080/tasks.html

build_blog_index.py (blog index + metadata)

This script scans the blogs/ folder and writes the blog index used by the site.

  • Input: blogs/YYYY-MM-DD/*.md (uses the first .md file in each dated folder)
  • Output: data/blogs.json
  • What it computes: title/author (from frontmatter or # ...), preview text, word_count, and read_time_min (based on words-per-minute).

Run it whenever you:

  • add a new blog post folder,
  • rename the .md file inside a post folder,
  • or change post content and want preview / word_count / read_time_min updated.
# From the pyhealth.github.io repo root:
python scripts/build_blog_index.py

How blog pages render

  • blog_list.html loads data/blogs.json to render the list.
  • blog.html?post=YYYY-MM-DD loads data/blogs.json to find the markdown filename, then fetches blogs/YYYY-MM-DD/<file>.md and converts the Markdown to HTML in the browser.

Previewing the blog locally

Because the site uses fetch(), preview via an HTTP server:

cd /path/to/pyhealth.github.io
python -m http.server 8080
# open http://localhost:8080/blog_list.html

To open a specific post:

  • http://localhost:8080/blog.html?post=YYYY-MM-DD