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Merge branch 'master' into 000971
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‎.github/scripts/collect_and_render.py

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import os
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from typing import List, Dict, Any, Optional
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from jinja2 import Environment, FileSystemLoader
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from dandi.dandiapi import DandiAPIClient
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def get_dandiset_metadata(dandiset_id: str) -> Optional[Dict[str, Any]]:
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"""
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Fetch metadata for a given dandiset ID.
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Parameters
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----------
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dandiset_id : str
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The ID of the dandiset to fetch metadata for.
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Returns
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-------
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Optional[Dict[str, Any]]
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A dictionary containing the dandiset metadata if successful, None otherwise.
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"""
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with DandiAPIClient() as client:
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try:
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dandiset = client.get_dandiset(dandiset_id)
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metadata = dandiset.get_raw_metadata()
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return metadata
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except Exception as e:
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print(f"Error fetching metadata for dandiset {dandiset_id}: {str(e)}")
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return None
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def find_notebooks(folder: str) -> List[str]:
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"""
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Recursively find all Jupyter notebooks in a given folder.
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Parameters
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----------
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folder : str
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The path to the folder to search in.
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Returns
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-------
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List[str]
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A list of relative paths to the found notebooks.
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"""
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notebooks = []
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for root, _, files in os.walk(folder):
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for file in files:
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if file.endswith('.ipynb'):
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rel_path = os.path.relpath(os.path.join(root, file), folder)
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notebooks.append(rel_path)
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return notebooks
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def collect_metadata() -> List[Dict[str, Any]]:
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"""
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Collect metadata and notebook information for all dandisets in the current directory.
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Returns
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-------
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List[Dict[str, Any]]
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A list of dictionaries, each containing information about a dandiset,
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sorted by dandiset ID.
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"""
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dandisets = []
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for folder in os.listdir('.'):
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if os.path.isdir(folder) and folder.isdigit():
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metadata = get_dandiset_metadata(folder)
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if metadata:
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notebooks = find_notebooks(folder)
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dandisets.append({
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'id': folder,
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'metadata': metadata,
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'notebooks': notebooks
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})
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dandisets.sort(key=lambda x: x['id'])
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return dandisets
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def render_webpage(dandisets: List[Dict[str, Any]]) -> None:
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"""
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Render the webpage using the collected dandiset information.
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Parameters
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----------
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dandisets : List[Dict[str, Any]]
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A list of dictionaries containing information about each dandiset.
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Returns
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-------
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None
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"""
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current_dir = os.path.dirname(os.path.abspath(__file__))
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template_dir = os.path.join(current_dir, '..', 'templates')
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env = Environment(loader=FileSystemLoader(template_dir))
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template = env.get_template('index.html')
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output = template.render(dandisets=dandisets)
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output_dir = os.path.join(current_dir, '..', '..', 'output')
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os.makedirs(output_dir, exist_ok=True)
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with open(os.path.join(output_dir, 'index.html'), 'w') as f:
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f.write(output)
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if __name__ == "__main__":
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dandisets = collect_metadata()
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render_webpage(dandisets)

‎.github/templates/index.html

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>DANDI Datasets</title>
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<style>
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body {
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font-family: 'Arial', sans-serif;
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line-height: 1.6;
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margin: 0;
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padding: 20px;
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}
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.container {
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max-width: 1200px;
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margin: 0 auto;
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}
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h1 {
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text-align: center;
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margin-bottom: 30px;
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}
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.dandiset {
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border-radius: 8px;
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box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1);
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margin-bottom: 30px;
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padding: 20px;
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transition: box-shadow 0.3s ease;
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}
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.dandiset:hover {
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box-shadow: 0 4px 8px rgba(0, 0, 0, 0.15);
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}
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.dandiset h2 {
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margin-top: 0;
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margin-bottom: 15px;
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}
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.dandiset p {
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margin-bottom: 10px;
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}
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.dandiset a {
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text-decoration: none;
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font-weight: bold;
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}
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.dandiset a:hover {
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text-decoration: underline;
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}
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.notebooks {
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margin-top: 15px;
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}
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.notebooks h3 {
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font-size: 1.1em;
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margin-bottom: 10px;
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}
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.notebooks ul {
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list-style-type: disc;
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padding-left: 20px;
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}
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.notebooks li {
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margin-bottom: 5px;
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}
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@media (max-width: 768px) {
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body {
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padding: 10px;
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}
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.dandiset {
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padding: 15px;
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}
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}
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</style>
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</head>
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<body>
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<div class="container">
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<h1>DANDI Datasets</h1>
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<div class="toc">
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<h2>Table of Contents</h2>
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<ul>
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{% for dandiset in dandisets %}
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<li><a href="#dandiset-{{ dandiset.id }}">{{ dandiset.id }} - {{ dandiset.metadata.name }}</a></li>
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{% endfor %}
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</ul>
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</div>
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{% for dandiset in dandisets %}
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<div id="dandiset-{{ dandiset.id }}" class="dandiset">
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<h2>{{ dandiset.metadata.name }}</h2>
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<p><strong>ID:</strong> {{ dandiset.id }}</p>
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<p><strong>Description:</strong> {{ dandiset.metadata.description }}</p>
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<p><a href="https://dandiarchive.org/dandiset/{{ dandiset.id }}" target="_blank">View on DANDI Archive</a></p>
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{% if dandiset.notebooks %}
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<div class="notebooks">
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<h3>Notebooks:</h3>
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<ul>
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{% for notebook in dandiset.notebooks %}
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<li><a href="https://github.com/dandi/example-notebooks/blob/master/{{ dandiset.id }}/{{ notebook }}" target="_blank">{{ notebook }}</a></li>
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{% endfor %}
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</ul>
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</div>
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{% endif %}
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</div>
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{% endfor %}
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</div>
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</body>
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</html>

‎.github/workflows/index_workflow.yml

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name: DANDI Metadata Collector
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on:
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push:
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branches: [ master ]
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jobs:
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collect-and-render:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.9'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install requests jinja2 dandi
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- name: Run metadata collector and renderer
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run: python .github/scripts/collect_and_render.py
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./output

‎.gitignore

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.ipynb_checkpoints
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*.DS_Store
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*__pycache__/
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*.ipynb_checkpoints/
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output/
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‎000010/DataJoint/DJ-NWB-Li-Daie-2015-2016/notebooks/Li-2015-examples.ipynb

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"metadata": {},
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"source": [
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"For each group of **contra** vs. **ipsi** selective units, the units are further sorted in to three categories:\n",
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"+ unit exibited selectivity during **sample** or **delay** and not **response** period\n",
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"+ unit exibited selectivity during **sample** or **delay** and **response** period\n",
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"+ unit exibited selectivity only during **response** period"
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"+ unit exhibited selectivity during **sample** or **delay** and not **response** period\n",
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"+ unit exhibited selectivity during **sample** or **delay** and **response** period\n",
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"+ unit exhibited selectivity only during **response** period"
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]
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},
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{

‎000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb

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