Felipe
Felipe Parodi
commited on
Update ACP website (#3)
Browse files* Revamp website and add PrimateFace
* Fix GitHub Pages permissions in PR preview workflow
---------
Co-authored-by: Felipe Parodi <felipeparodi@hnt-0115.vpn.private.upenn.edu>
- .github/pull_request_template.md +38 -19
- .github/workflows/link-check.yml +69 -0
- .github/workflows/pr-preview.yml +85 -0
- .github/workflows/website.py +646 -32
- .gitignore +4 -1
- CONTRIBUTING.md +28 -2
- README.md +43 -6
- index.html +574 -83
- scripts/dev-preview.py +67 -0
- scripts/test-workflows.sh +71 -0
.github/pull_request_template.md
CHANGED
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## Paper/Project Addition
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- [ ] Added to correct section (Projects/Datasets/Reviews/Related)
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-
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<!-- Any other relevant information about this addition -->
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-
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<!-- Link any related issues here -->
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## π Paper/Project Addition
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<!--
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π Thanks for contributing! A preview of your changes will be automatically generated below.
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Need help? Check our [Contributing Guide](CONTRIBUTING.md)
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-->
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+
### π Paper Details
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- [ ] **Title:**
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- [ ] **Year:**
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- [ ] **Link:**
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- [ ] **Topics:** (use PD, BPE, FD, FLE, FR, FAC, BR, AM, SI, RL, O)
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- [ ] **Animal Species:**
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- [ ] **Model Available:** Yes/No/Code only/Upon request
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- [ ] **Data Available:** Yes/No/Upon request
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### β
Pre-submission Checklist
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- [ ] Added paper in correct chronological position (newest first)
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- [ ] Verified all links are accessible and working
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- [ ] Used correct topic abbreviations from the legend
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- [ ] Confirmed model/data availability status is accurate
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- [ ] Followed table formatting (7 columns with proper | separators)
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- [ ] Added to correct section (Projects/Datasets/Reviews/Related)
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- [ ] Tested locally with `python scripts/dev-preview.py` (optional but recommended)
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+
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+
### π·οΈ Type of Change
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- [ ] New paper addition
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- [ ] Correction/update to existing entry
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- [ ] Documentation improvement
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- [ ] Website enhancement
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- [ ] Other: ___________
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+
### π Summary
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+
<!-- Brief description of what you're adding/changing -->
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+
### π Additional Notes
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<!-- Any other relevant information, special considerations, or context -->
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+
---
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+
**Preview:** A preview link will be automatically posted below once the automation runs β‘
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.github/workflows/link-check.yml
ADDED
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@@ -0,0 +1,69 @@
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name: Check Links
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on:
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+
schedule:
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+
- cron: '0 0 * * 1' # Weekly on Monday
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workflow_dispatch:
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| 7 |
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pull_request:
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| 8 |
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paths: ['README.md']
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| 9 |
+
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| 10 |
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jobs:
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link-check:
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| 12 |
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runs-on: ubuntu-latest
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| 13 |
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permissions:
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| 14 |
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contents: read
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| 15 |
+
issues: write
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| 16 |
+
pull-requests: write
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| 17 |
+
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steps:
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| 19 |
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- name: Checkout
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| 20 |
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uses: actions/checkout@v4
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+
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+
- name: Link Checker
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| 23 |
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uses: lycheeverse/lychee-action@v1
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| 24 |
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with:
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args: --verbose --no-progress --exclude-mail README.md
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fail: false
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+
env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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+
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+
- name: Create Issue for Broken Links
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| 31 |
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if: failure() && github.event_name == 'schedule'
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uses: actions/github-script@v6
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with:
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script: |
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| 35 |
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const date = new Date().toISOString().split('T')[0];
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github.rest.issues.create({
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owner: context.repo.owner,
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repo: context.repo.repo,
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title: `π Broken Links Found - ${date}`,
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body: `Automated link checking found broken links in the repository.
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Please check the workflow logs for details: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
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| 43 |
+
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+
---
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| 45 |
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*This issue was automatically created by the link checker workflow.*`,
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| 46 |
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labels: ['maintenance', 'broken-links']
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});
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+
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| 49 |
+
- name: Comment on PR if links are broken
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if: failure() && github.event_name == 'pull_request'
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uses: actions/github-script@v6
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with:
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script: |
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| 54 |
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github.rest.issues.createComment({
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issue_number: context.issue.number,
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owner: context.repo.owner,
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repo: context.repo.repo,
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| 58 |
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body: `β οΈ **Link Check Failed**
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| 59 |
+
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| 60 |
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Some links in your changes appear to be broken or inaccessible. Please check the workflow logs and fix any broken links before merging.
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| 61 |
+
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| 62 |
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**How to check locally:**
|
| 63 |
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\`\`\`bash
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| 64 |
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pip install lychee
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| 65 |
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lychee README.md
|
| 66 |
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\`\`\`
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+
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| 68 |
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*This comment was automatically generated by the link checker.*`
|
| 69 |
+
});
|
.github/workflows/pr-preview.yml
ADDED
|
@@ -0,0 +1,85 @@
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| 1 |
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name: PR Preview
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| 2 |
+
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| 3 |
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on:
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| 4 |
+
pull_request:
|
| 5 |
+
branches: [ main ]
|
| 6 |
+
paths: [ 'README.md' ]
|
| 7 |
+
|
| 8 |
+
jobs:
|
| 9 |
+
preview:
|
| 10 |
+
runs-on: ubuntu-latest
|
| 11 |
+
permissions:
|
| 12 |
+
contents: read
|
| 13 |
+
pull-requests: write
|
| 14 |
+
|
| 15 |
+
steps:
|
| 16 |
+
- name: Checkout PR
|
| 17 |
+
uses: actions/checkout@v4
|
| 18 |
+
|
| 19 |
+
- name: Set up Python
|
| 20 |
+
uses: actions/setup-python@v4
|
| 21 |
+
with:
|
| 22 |
+
python-version: '3.x'
|
| 23 |
+
|
| 24 |
+
- name: Install dependencies
|
| 25 |
+
run: pip install pandas
|
| 26 |
+
|
| 27 |
+
- name: Generate preview website
|
| 28 |
+
run: python .github/workflows/website.py
|
| 29 |
+
|
| 30 |
+
- name: Upload preview as artifact
|
| 31 |
+
uses: actions/upload-artifact@v4
|
| 32 |
+
with:
|
| 33 |
+
name: website-preview
|
| 34 |
+
path: index.html
|
| 35 |
+
retention-days: 7
|
| 36 |
+
|
| 37 |
+
- name: Deploy preview (if Pages enabled)
|
| 38 |
+
uses: peaceiris/actions-gh-pages@v4
|
| 39 |
+
continue-on-error: true
|
| 40 |
+
with:
|
| 41 |
+
github_token: ${{ secrets.GITHUB_TOKEN }}
|
| 42 |
+
publish_dir: .
|
| 43 |
+
destination_dir: pr-${{ github.event.number }}
|
| 44 |
+
keep_files: false
|
| 45 |
+
|
| 46 |
+
- name: Comment PR with preview link
|
| 47 |
+
uses: actions/github-script@v6
|
| 48 |
+
with:
|
| 49 |
+
script: |
|
| 50 |
+
const prNumber = context.payload.pull_request.number;
|
| 51 |
+
const repoOwner = context.repo.owner;
|
| 52 |
+
const repoName = context.repo.repo;
|
| 53 |
+
const previewUrl = `https://${repoOwner}.github.io/${repoName}/pr-${prNumber}/`;
|
| 54 |
+
|
| 55 |
+
const comment = `## π Website Preview
|
| 56 |
+
|
| 57 |
+
Your changes have been processed!
|
| 58 |
+
|
| 59 |
+
**π Preview Artifact:** Check the "website-preview" artifact above to download the generated HTML file.
|
| 60 |
+
|
| 61 |
+
${previewUrl ? `**π Live Preview:** ${previewUrl}` : '**βΉοΈ Live preview:** GitHub Pages not configured for this repository.'}
|
| 62 |
+
|
| 63 |
+
---
|
| 64 |
+
|
| 65 |
+
### π οΈ How to test locally:
|
| 66 |
+
\`\`\`bash
|
| 67 |
+
# Clone and test your changes
|
| 68 |
+
git checkout ${{ github.head_ref }}
|
| 69 |
+
python .github/workflows/website.py
|
| 70 |
+
python -m http.server 8000
|
| 71 |
+
# Visit: http://localhost:8000
|
| 72 |
+
\`\`\`
|
| 73 |
+
|
| 74 |
+
### β
Validation Status:
|
| 75 |
+
- β
Website generated successfully
|
| 76 |
+
- β
Table format validated
|
| 77 |
+
- β
Ready for review
|
| 78 |
+
`;
|
| 79 |
+
|
| 80 |
+
github.rest.issues.createComment({
|
| 81 |
+
issue_number: prNumber,
|
| 82 |
+
owner: repoOwner,
|
| 83 |
+
repo: repoName,
|
| 84 |
+
body: comment
|
| 85 |
+
});
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.github/workflows/website.py
CHANGED
|
@@ -1,44 +1,658 @@
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-
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-
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import pandas as pd
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import re
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def to_link_if_markdown(cell_text: str) -> str:
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| 7 |
-
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| 8 |
cell_text = re.sub(r'\[(.*?)\]\((.*?)\)', r'<a href="\2">\1</a>', cell_text)
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-
return cell_text
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| 10 |
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-
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-
table
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-
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-
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-
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-
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-
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-
# %%
|
| 25 |
-
with open("/home/runner/work/awesome-computational-primatology/awesome-computational-primatology/index.html", "w") as f:
|
| 26 |
-
f.write("""<html>
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| 27 |
<head>
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| 28 |
-
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-
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-
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-
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| 32 |
</head>
|
| 33 |
<body>
|
| 34 |
-
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| 35 |
-
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| 36 |
-
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| 37 |
-
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| 38 |
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| 39 |
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|
| 40 |
});
|
| 41 |
-
|
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|
| 42 |
</body>
|
| 43 |
-
|
| 44 |
-
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|
| 1 |
+
#!/usr/bin/env python3
|
| 2 |
+
"""
|
| 3 |
+
Generate enhanced HTML website from README.md table
|
| 4 |
+
"""
|
| 5 |
import pandas as pd
|
| 6 |
import re
|
| 7 |
+
import os
|
| 8 |
|
| 9 |
def to_link_if_markdown(cell_text: str) -> str:
|
| 10 |
+
"""Convert markdown links [text](url) to HTML <a> tags"""
|
| 11 |
+
if not isinstance(cell_text, str):
|
| 12 |
+
return str(cell_text)
|
| 13 |
cell_text = re.sub(r'\[(.*?)\]\((.*?)\)', r'<a href="\2">\1</a>', cell_text)
|
| 14 |
+
return cell_text.strip()
|
| 15 |
|
| 16 |
+
def extract_table_from_readme(readme_path: str) -> pd.DataFrame:
|
| 17 |
+
"""Extract the main projects table from README.md"""
|
| 18 |
+
with open(readme_path, "r", encoding='utf-8') as f:
|
| 19 |
+
text = f.readlines()
|
| 20 |
+
|
| 21 |
+
table = []
|
| 22 |
+
in_projects_section = False
|
| 23 |
+
|
| 24 |
+
for line in text:
|
| 25 |
+
# Check if we're in the Projects section
|
| 26 |
+
if line.strip() == "### Projects":
|
| 27 |
+
in_projects_section = True
|
| 28 |
+
continue
|
| 29 |
+
|
| 30 |
+
# Stop if we hit another section
|
| 31 |
+
if in_projects_section and line.startswith("### ") and "Projects" not in line:
|
| 32 |
+
break
|
| 33 |
+
|
| 34 |
+
# Extract table rows (has 8 | characters for 7 columns)
|
| 35 |
+
if in_projects_section and len(re.findall(r"\|", line)) == 8:
|
| 36 |
+
row = [cell.strip() for cell in line.split("|")[1:-1]]
|
| 37 |
+
table.append(row)
|
| 38 |
+
|
| 39 |
+
if len(table) < 2:
|
| 40 |
+
raise ValueError("Could not find valid table in README.md")
|
| 41 |
+
|
| 42 |
+
# First row is header, second row is separator, rest is data
|
| 43 |
+
header = table[0]
|
| 44 |
+
data = table[2:] if len(table) > 2 else []
|
| 45 |
+
|
| 46 |
+
df = pd.DataFrame(data, columns=header)
|
| 47 |
+
# Apply markdown to HTML conversion
|
| 48 |
+
df = df.applymap(to_link_if_markdown)
|
| 49 |
+
|
| 50 |
+
return df
|
| 51 |
|
| 52 |
+
def get_enhanced_html_template() -> str:
|
| 53 |
+
"""Return the enhanced HTML template"""
|
| 54 |
+
return '''<!DOCTYPE html>
|
| 55 |
+
<html>
|
|
|
|
|
|
|
|
|
|
| 56 |
<head>
|
| 57 |
+
<meta charset="UTF-8">
|
| 58 |
+
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
| 59 |
+
<title>Awesome Computational Primatology</title>
|
| 60 |
+
|
| 61 |
+
<!-- External Libraries -->
|
| 62 |
+
<script src="https://code.jquery.com/jquery-3.7.1.min.js"></script>
|
| 63 |
+
<link rel="stylesheet" href="https://cdn.datatables.net/2.0.2/css/dataTables.dataTables.css" />
|
| 64 |
+
<link rel="stylesheet" href="https://cdn.datatables.net/buttons/3.0.0/css/buttons.dataTables.css" />
|
| 65 |
+
<link rel="stylesheet" href="https://cdn.datatables.net/searchpanes/2.3.0/css/searchPanes.dataTables.css" />
|
| 66 |
+
<link rel="stylesheet" href="https://cdn.datatables.net/select/2.0.0/css/select.dataTables.css" />
|
| 67 |
+
|
| 68 |
+
<script src="https://cdn.datatables.net/2.0.2/js/dataTables.js"></script>
|
| 69 |
+
<script src="https://cdn.datatables.net/buttons/3.0.0/js/dataTables.buttons.js"></script>
|
| 70 |
+
<script src="https://cdn.datatables.net/buttons/3.0.0/js/buttons.html5.min.js"></script>
|
| 71 |
+
<script src="https://cdn.datatables.net/searchpanes/2.3.0/js/dataTables.searchPanes.js"></script>
|
| 72 |
+
<script src="https://cdn.datatables.net/select/2.0.0/js/dataTables.select.js"></script>
|
| 73 |
+
|
| 74 |
+
<!-- Icons -->
|
| 75 |
+
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/all.min.css">
|
| 76 |
+
|
| 77 |
+
<style>
|
| 78 |
+
:root {
|
| 79 |
+
--primary-color: #2c3e50;
|
| 80 |
+
--secondary-color: #3498db;
|
| 81 |
+
--accent-color: #e74c3c;
|
| 82 |
+
--success-color: #27ae60;
|
| 83 |
+
--warning-color: #f39c12;
|
| 84 |
+
--background-color: #f8f9fa;
|
| 85 |
+
--card-background: #ffffff;
|
| 86 |
+
--text-color: #2c3e50;
|
| 87 |
+
--border-color: #dee2e6;
|
| 88 |
+
--shadow: 0 2px 4px rgba(0,0,0,0.1);
|
| 89 |
+
}
|
| 90 |
+
|
| 91 |
+
* {
|
| 92 |
+
box-sizing: border-box;
|
| 93 |
+
}
|
| 94 |
+
|
| 95 |
+
body {
|
| 96 |
+
font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
|
| 97 |
+
background-color: var(--background-color);
|
| 98 |
+
margin: 0;
|
| 99 |
+
padding: 20px;
|
| 100 |
+
color: var(--text-color);
|
| 101 |
+
line-height: 1.6;
|
| 102 |
+
}
|
| 103 |
+
|
| 104 |
+
.container {
|
| 105 |
+
max-width: 1400px;
|
| 106 |
+
margin: 0 auto;
|
| 107 |
+
background: var(--card-background);
|
| 108 |
+
padding: 30px;
|
| 109 |
+
border-radius: 12px;
|
| 110 |
+
box-shadow: var(--shadow);
|
| 111 |
+
}
|
| 112 |
+
|
| 113 |
+
.header {
|
| 114 |
+
text-align: center;
|
| 115 |
+
margin-bottom: 40px;
|
| 116 |
+
padding-bottom: 20px;
|
| 117 |
+
border-bottom: 2px solid var(--border-color);
|
| 118 |
+
}
|
| 119 |
+
|
| 120 |
+
h1 {
|
| 121 |
+
color: var(--primary-color);
|
| 122 |
+
font-size: 2.5rem;
|
| 123 |
+
margin-bottom: 10px;
|
| 124 |
+
font-weight: 700;
|
| 125 |
+
}
|
| 126 |
+
|
| 127 |
+
.subtitle {
|
| 128 |
+
color: #666;
|
| 129 |
+
font-size: 1.1rem;
|
| 130 |
+
margin-bottom: 20px;
|
| 131 |
+
}
|
| 132 |
+
|
| 133 |
+
.stats {
|
| 134 |
+
display: flex;
|
| 135 |
+
justify-content: center;
|
| 136 |
+
gap: 30px;
|
| 137 |
+
margin-bottom: 20px;
|
| 138 |
+
flex-wrap: wrap;
|
| 139 |
+
}
|
| 140 |
+
|
| 141 |
+
.stat-item {
|
| 142 |
+
text-align: center;
|
| 143 |
+
padding: 15px;
|
| 144 |
+
background: linear-gradient(135deg, var(--secondary-color), #5dade2);
|
| 145 |
+
color: white;
|
| 146 |
+
border-radius: 8px;
|
| 147 |
+
min-width: 120px;
|
| 148 |
+
box-shadow: var(--shadow);
|
| 149 |
+
}
|
| 150 |
+
|
| 151 |
+
.stat-number {
|
| 152 |
+
font-size: 1.8rem;
|
| 153 |
+
font-weight: bold;
|
| 154 |
+
display: block;
|
| 155 |
+
}
|
| 156 |
+
|
| 157 |
+
.stat-label {
|
| 158 |
+
font-size: 0.9rem;
|
| 159 |
+
opacity: 0.9;
|
| 160 |
+
}
|
| 161 |
+
|
| 162 |
+
.legend {
|
| 163 |
+
background: #f8f9fa;
|
| 164 |
+
padding: 20px;
|
| 165 |
+
border-radius: 8px;
|
| 166 |
+
margin-bottom: 30px;
|
| 167 |
+
border-left: 4px solid var(--secondary-color);
|
| 168 |
+
}
|
| 169 |
+
|
| 170 |
+
.legend h3 {
|
| 171 |
+
margin-top: 0;
|
| 172 |
+
color: var(--primary-color);
|
| 173 |
+
}
|
| 174 |
+
|
| 175 |
+
.legend-grid {
|
| 176 |
+
display: grid;
|
| 177 |
+
grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
|
| 178 |
+
gap: 10px;
|
| 179 |
+
margin-top: 15px;
|
| 180 |
+
}
|
| 181 |
+
|
| 182 |
+
.legend-item {
|
| 183 |
+
display: flex;
|
| 184 |
+
align-items: center;
|
| 185 |
+
gap: 8px;
|
| 186 |
+
}
|
| 187 |
+
|
| 188 |
+
.legend-badge {
|
| 189 |
+
background: var(--secondary-color);
|
| 190 |
+
color: white;
|
| 191 |
+
padding: 2px 8px;
|
| 192 |
+
border-radius: 4px;
|
| 193 |
+
font-size: 0.8rem;
|
| 194 |
+
font-weight: bold;
|
| 195 |
+
min-width: 35px;
|
| 196 |
+
text-align: center;
|
| 197 |
+
}
|
| 198 |
+
|
| 199 |
+
.table-container {
|
| 200 |
+
background: white;
|
| 201 |
+
border-radius: 8px;
|
| 202 |
+
overflow: hidden;
|
| 203 |
+
box-shadow: var(--shadow);
|
| 204 |
+
}
|
| 205 |
+
|
| 206 |
+
table.dataTable {
|
| 207 |
+
border-collapse: separate;
|
| 208 |
+
border-spacing: 0;
|
| 209 |
+
width: 100% !important;
|
| 210 |
+
margin: 0 !important;
|
| 211 |
+
}
|
| 212 |
+
|
| 213 |
+
table.dataTable thead th {
|
| 214 |
+
background: linear-gradient(135deg, var(--primary-color), #34495e);
|
| 215 |
+
color: white;
|
| 216 |
+
padding: 15px 10px;
|
| 217 |
+
font-weight: 600;
|
| 218 |
+
text-align: left;
|
| 219 |
+
border: none;
|
| 220 |
+
position: sticky;
|
| 221 |
+
top: 0;
|
| 222 |
+
z-index: 10;
|
| 223 |
+
}
|
| 224 |
+
|
| 225 |
+
table.dataTable tbody td {
|
| 226 |
+
padding: 12px 10px;
|
| 227 |
+
border-bottom: 1px solid #eee;
|
| 228 |
+
vertical-align: middle;
|
| 229 |
+
}
|
| 230 |
+
|
| 231 |
+
table.dataTable tbody tr:hover {
|
| 232 |
+
background-color: #f8f9fa;
|
| 233 |
+
}
|
| 234 |
+
|
| 235 |
+
.status-badge {
|
| 236 |
+
padding: 4px 8px;
|
| 237 |
+
border-radius: 20px;
|
| 238 |
+
font-size: 0.8rem;
|
| 239 |
+
font-weight: 600;
|
| 240 |
+
text-decoration: none !important;
|
| 241 |
+
display: inline-block;
|
| 242 |
+
}
|
| 243 |
+
|
| 244 |
+
.status-yes {
|
| 245 |
+
background: #d4edda;
|
| 246 |
+
color: #155724;
|
| 247 |
+
border: 1px solid #c3e6cb;
|
| 248 |
+
}
|
| 249 |
+
|
| 250 |
+
.status-no {
|
| 251 |
+
background: #f8d7da;
|
| 252 |
+
color: #721c24;
|
| 253 |
+
border: 1px solid #f5c6cb;
|
| 254 |
+
}
|
| 255 |
+
|
| 256 |
+
.status-partial {
|
| 257 |
+
background: #fff3cd;
|
| 258 |
+
color: #856404;
|
| 259 |
+
border: 1px solid #ffeeba;
|
| 260 |
+
}
|
| 261 |
+
|
| 262 |
+
.status-request {
|
| 263 |
+
background: #d1ecf1;
|
| 264 |
+
color: #0c5460;
|
| 265 |
+
border: 1px solid #bee5eb;
|
| 266 |
+
}
|
| 267 |
+
|
| 268 |
+
.topic-tag {
|
| 269 |
+
background: var(--secondary-color);
|
| 270 |
+
color: white;
|
| 271 |
+
padding: 2px 6px;
|
| 272 |
+
border-radius: 3px;
|
| 273 |
+
font-size: 0.75rem;
|
| 274 |
+
margin-right: 4px;
|
| 275 |
+
display: inline-block;
|
| 276 |
+
margin-bottom: 2px;
|
| 277 |
+
}
|
| 278 |
+
|
| 279 |
+
.year-cell {
|
| 280 |
+
font-weight: 600;
|
| 281 |
+
color: var(--primary-color);
|
| 282 |
+
background: linear-gradient(135deg, #ecf0f1, #bdc3c7);
|
| 283 |
+
text-align: center;
|
| 284 |
+
}
|
| 285 |
+
|
| 286 |
+
.species-macaque { background-color: #e8f5e8; }
|
| 287 |
+
.species-chimp { background-color: #fff3e0; }
|
| 288 |
+
.species-gorilla { background-color: #f3e5f5; }
|
| 289 |
+
.species-marmoset { background-color: #e1f5fe; }
|
| 290 |
+
.species-cross { background-color: #f9f9f9; }
|
| 291 |
+
|
| 292 |
+
.dt-button {
|
| 293 |
+
background: var(--secondary-color) !important;
|
| 294 |
+
color: white !important;
|
| 295 |
+
border: none !important;
|
| 296 |
+
padding: 8px 15px !important;
|
| 297 |
+
border-radius: 6px !important;
|
| 298 |
+
margin-right: 8px !important;
|
| 299 |
+
font-size: 0.9rem !important;
|
| 300 |
+
transition: all 0.3s ease !important;
|
| 301 |
+
}
|
| 302 |
+
|
| 303 |
+
.dt-button:hover {
|
| 304 |
+
background: #2980b9 !important;
|
| 305 |
+
transform: translateY(-1px);
|
| 306 |
+
box-shadow: 0 4px 8px rgba(0,0,0,0.2) !important;
|
| 307 |
+
}
|
| 308 |
+
|
| 309 |
+
/* Footer */
|
| 310 |
+
.footer {
|
| 311 |
+
margin-top: 40px;
|
| 312 |
+
padding: 30px 20px;
|
| 313 |
+
background: linear-gradient(135deg, #f8f9fa, #e9ecef);
|
| 314 |
+
border-radius: 8px;
|
| 315 |
+
text-align: center;
|
| 316 |
+
border-top: 3px solid var(--secondary-color);
|
| 317 |
+
}
|
| 318 |
+
|
| 319 |
+
.footer p {
|
| 320 |
+
margin: 8px 0;
|
| 321 |
+
color: #666;
|
| 322 |
+
}
|
| 323 |
+
|
| 324 |
+
.footer a {
|
| 325 |
+
color: var(--secondary-color);
|
| 326 |
+
text-decoration: none;
|
| 327 |
+
font-weight: 500;
|
| 328 |
+
transition: color 0.3s ease;
|
| 329 |
+
}
|
| 330 |
+
|
| 331 |
+
.footer a:hover {
|
| 332 |
+
color: var(--primary-color);
|
| 333 |
+
text-decoration: underline;
|
| 334 |
+
}
|
| 335 |
+
|
| 336 |
+
.footer-note {
|
| 337 |
+
font-size: 0.9rem;
|
| 338 |
+
color: #888;
|
| 339 |
+
}
|
| 340 |
+
|
| 341 |
+
#last-updated {
|
| 342 |
+
font-weight: 600;
|
| 343 |
+
color: var(--secondary-color);
|
| 344 |
+
}
|
| 345 |
+
|
| 346 |
+
@media (max-width: 768px) {
|
| 347 |
+
.container { padding: 15px; }
|
| 348 |
+
h1 { font-size: 2rem; }
|
| 349 |
+
.stats { gap: 15px; }
|
| 350 |
+
.stat-item { min-width: 100px; padding: 10px; }
|
| 351 |
+
table.dataTable thead th,
|
| 352 |
+
table.dataTable tbody td { padding: 8px 6px; font-size: 0.9rem; }
|
| 353 |
+
.legend-grid { grid-template-columns: 1fr; }
|
| 354 |
+
.footer { margin-top: 20px; padding: 20px 15px; }
|
| 355 |
+
}
|
| 356 |
+
</style>
|
| 357 |
</head>
|
| 358 |
<body>
|
| 359 |
+
<div class="container">
|
| 360 |
+
<div class="header">
|
| 361 |
+
<h1>π Awesome Computational Primatology</h1>
|
| 362 |
+
<p class="subtitle">A curated list of machine learning research for non-human primatology</p>
|
| 363 |
+
|
| 364 |
+
<div class="stats">
|
| 365 |
+
<div class="stat-item">
|
| 366 |
+
<span class="stat-number" id="total-papers">{total_papers}</span>
|
| 367 |
+
<span class="stat-label">Papers</span>
|
| 368 |
+
</div>
|
| 369 |
+
<div class="stat-item">
|
| 370 |
+
<span class="stat-number" id="years-span">{years_span}</span>
|
| 371 |
+
<span class="stat-label">Years</span>
|
| 372 |
+
</div>
|
| 373 |
+
<div class="stat-item">
|
| 374 |
+
<span class="stat-number" id="with-code">{with_code}</span>
|
| 375 |
+
<span class="stat-label">With Code</span>
|
| 376 |
+
</div>
|
| 377 |
+
<div class="stat-item">
|
| 378 |
+
<span class="stat-number" id="with-data">{with_data}</span>
|
| 379 |
+
<span class="stat-label">With Data</span>
|
| 380 |
+
</div>
|
| 381 |
+
</div>
|
| 382 |
+
</div>
|
| 383 |
+
|
| 384 |
+
<div class="legend">
|
| 385 |
+
<h3>π·οΈ Topic Legend</h3>
|
| 386 |
+
<div class="legend-grid">
|
| 387 |
+
<div class="legend-item">
|
| 388 |
+
<span class="legend-badge">PD</span>
|
| 389 |
+
<span>Primate Detection</span>
|
| 390 |
+
</div>
|
| 391 |
+
<div class="legend-item">
|
| 392 |
+
<span class="legend-badge">BPE</span>
|
| 393 |
+
<span>Body Pose Estimation</span>
|
| 394 |
+
</div>
|
| 395 |
+
<div class="legend-item">
|
| 396 |
+
<span class="legend-badge">FD</span>
|
| 397 |
+
<span>Face Detection</span>
|
| 398 |
+
</div>
|
| 399 |
+
<div class="legend-item">
|
| 400 |
+
<span class="legend-badge">FLE</span>
|
| 401 |
+
<span>Facial Landmark Estimation</span>
|
| 402 |
+
</div>
|
| 403 |
+
<div class="legend-item">
|
| 404 |
+
<span class="legend-badge">FR</span>
|
| 405 |
+
<span>Face Recognition</span>
|
| 406 |
+
</div>
|
| 407 |
+
<div class="legend-item">
|
| 408 |
+
<span class="legend-badge">FAC</span>
|
| 409 |
+
<span>Facial Action Coding</span>
|
| 410 |
+
</div>
|
| 411 |
+
<div class="legend-item">
|
| 412 |
+
<span class="legend-badge">BR</span>
|
| 413 |
+
<span>Behavior Recognition</span>
|
| 414 |
+
</div>
|
| 415 |
+
<div class="legend-item">
|
| 416 |
+
<span class="legend-badge">AM</span>
|
| 417 |
+
<span>Avatar/Mesh</span>
|
| 418 |
+
</div>
|
| 419 |
+
<div class="legend-item">
|
| 420 |
+
<span class="legend-badge">SI</span>
|
| 421 |
+
<span>Species Identification</span>
|
| 422 |
+
</div>
|
| 423 |
+
<div class="legend-item">
|
| 424 |
+
<span class="legend-badge">RL</span>
|
| 425 |
+
<span>Reinforcement Learning</span>
|
| 426 |
+
</div>
|
| 427 |
+
</div>
|
| 428 |
+
</div>
|
| 429 |
+
|
| 430 |
+
<div class="table-container">
|
| 431 |
+
{table_html}
|
| 432 |
+
</div>
|
| 433 |
+
|
| 434 |
+
<div class="footer">
|
| 435 |
+
<p>
|
| 436 |
+
<strong>Maintained by:</strong>
|
| 437 |
+
<a href="http://kordinglab.com" target="_blank">π§ Kording Lab</a> β’
|
| 438 |
+
<a href="mailto:fparodi@upenn.edu">π§ Felipe Parodi</a> β’
|
| 439 |
+
<a href="https://github.com/KordingLab/awesome-computational-primatology" target="_blank">β Star on GitHub</a>
|
| 440 |
+
</p>
|
| 441 |
+
<p class="footer-note">
|
| 442 |
+
Found a paper we missed? <a href="https://github.com/KordingLab/awesome-computational-primatology/blob/main/CONTRIBUTING.md">Contribute here!</a>
|
| 443 |
+
β’ Last updated: <span id="last-updated"></span>
|
| 444 |
+
</p>
|
| 445 |
+
</div>
|
| 446 |
+
</div>
|
| 447 |
+
|
| 448 |
+
<script>
|
| 449 |
+
$(document).ready(function() {
|
| 450 |
+
var table = $('#table').DataTable({
|
| 451 |
+
paging: true,
|
| 452 |
+
pageLength: 25,
|
| 453 |
+
lengthMenu: [10, 25, 50, 100, -1],
|
| 454 |
+
searching: true,
|
| 455 |
+
ordering: true,
|
| 456 |
+
info: true,
|
| 457 |
+
responsive: true,
|
| 458 |
+
|
| 459 |
+
dom: 'Bfrtip',
|
| 460 |
+
buttons: [
|
| 461 |
+
{
|
| 462 |
+
extend: 'searchPanes',
|
| 463 |
+
config: {
|
| 464 |
+
cascadePanes: true,
|
| 465 |
+
viewTotal: true,
|
| 466 |
+
columns: [0, 2, 3, 4, 5]
|
| 467 |
+
}
|
| 468 |
+
},
|
| 469 |
+
'copy', 'csv', 'excel',
|
| 470 |
+
{
|
| 471 |
+
text: 'Clear Filters',
|
| 472 |
+
action: function(e, dt, node, config) {
|
| 473 |
+
dt.searchPanes.clearSelections();
|
| 474 |
+
}
|
| 475 |
+
}
|
| 476 |
+
],
|
| 477 |
+
|
| 478 |
+
searchPanes: {
|
| 479 |
+
cascadePanes: true,
|
| 480 |
+
viewTotal: true,
|
| 481 |
+
columns: [0, 2, 3, 4, 5],
|
| 482 |
+
initCollapsed: true
|
| 483 |
+
},
|
| 484 |
+
|
| 485 |
+
columnDefs: [
|
| 486 |
+
{
|
| 487 |
+
targets: 0,
|
| 488 |
+
type: 'num',
|
| 489 |
+
className: 'year-cell',
|
| 490 |
+
width: '80px'
|
| 491 |
+
},
|
| 492 |
+
{
|
| 493 |
+
targets: 2,
|
| 494 |
+
width: '150px',
|
| 495 |
+
render: function(data, type, row) {
|
| 496 |
+
if (type === 'display') {
|
| 497 |
+
const topics = data.split(', ');
|
| 498 |
+
return topics.map(topic =>
|
| 499 |
+
'<span class="topic-tag">' + topic.trim() + '</span>'
|
| 500 |
+
).join(' ');
|
| 501 |
+
}
|
| 502 |
+
return data;
|
| 503 |
+
}
|
| 504 |
+
},
|
| 505 |
+
{
|
| 506 |
+
targets: 3,
|
| 507 |
+
width: '120px',
|
| 508 |
+
render: function(data, type, row) {
|
| 509 |
+
if (type === 'display') {
|
| 510 |
+
let className = 'species-cross';
|
| 511 |
+
const lowerData = data.toLowerCase();
|
| 512 |
+
if (lowerData.includes('macaque')) className = 'species-macaque';
|
| 513 |
+
else if (lowerData.includes('chimp')) className = 'species-chimp';
|
| 514 |
+
else if (lowerData.includes('gorilla')) className = 'species-gorilla';
|
| 515 |
+
else if (lowerData.includes('marmoset')) className = 'species-marmoset';
|
| 516 |
+
|
| 517 |
+
return '<span class="' + className + '" style="padding: 4px 8px; border-radius: 4px; display: inline-block;">' + data + '</span>';
|
| 518 |
+
}
|
| 519 |
+
return data;
|
| 520 |
+
}
|
| 521 |
+
},
|
| 522 |
+
{
|
| 523 |
+
targets: [4, 5],
|
| 524 |
+
width: '100px',
|
| 525 |
+
render: function(data, type, row) {
|
| 526 |
+
if (type === 'display') {
|
| 527 |
+
let className = 'status-no';
|
| 528 |
+
let icon = '<i class="fas fa-times"></i> ';
|
| 529 |
+
|
| 530 |
+
if (data.includes('Yes')) {
|
| 531 |
+
className = 'status-yes';
|
| 532 |
+
icon = '<i class="fas fa-check"></i> ';
|
| 533 |
+
} else if (data.includes('Code only') || data.includes('Some')) {
|
| 534 |
+
className = 'status-partial';
|
| 535 |
+
icon = '<i class="fas fa-code"></i> ';
|
| 536 |
+
} else if (data.includes('Upon request')) {
|
| 537 |
+
className = 'status-request';
|
| 538 |
+
icon = '<i class="fas fa-envelope"></i> ';
|
| 539 |
+
}
|
| 540 |
+
|
| 541 |
+
return '<span class="status-badge ' + className + '">' + icon + data + '</span>';
|
| 542 |
+
}
|
| 543 |
+
return data;
|
| 544 |
+
}
|
| 545 |
+
}
|
| 546 |
+
],
|
| 547 |
+
|
| 548 |
+
order: [[0, 'desc']],
|
| 549 |
+
|
| 550 |
+
language: {
|
| 551 |
+
search: '<i class="fas fa-search"></i>',
|
| 552 |
+
searchPlaceholder: 'Search papers...',
|
| 553 |
+
lengthMenu: 'Show _MENU_ papers per page',
|
| 554 |
+
info: 'Showing _START_ to _END_ of _TOTAL_ papers',
|
| 555 |
+
processing: '<i class="fas fa-spinner fa-spin"></i> Loading...'
|
| 556 |
+
}
|
| 557 |
+
});
|
| 558 |
+
|
| 559 |
+
// Set last updated date
|
| 560 |
+
const lastUpdated = new Date().toLocaleDateString('en-US', {
|
| 561 |
+
year: 'numeric',
|
| 562 |
+
month: 'long',
|
| 563 |
+
day: 'numeric'
|
| 564 |
});
|
| 565 |
+
document.getElementById('last-updated').textContent = lastUpdated;
|
| 566 |
+
});
|
| 567 |
+
</script>
|
| 568 |
</body>
|
| 569 |
+
</html>'''
|
| 570 |
+
|
| 571 |
+
def calculate_stats(df: pd.DataFrame) -> dict:
|
| 572 |
+
"""Calculate statistics from the dataframe"""
|
| 573 |
+
total_papers = len(df)
|
| 574 |
+
|
| 575 |
+
# Count years
|
| 576 |
+
years = set()
|
| 577 |
+
for year in df.iloc[:, 0]: # First column is year
|
| 578 |
+
if str(year).isdigit():
|
| 579 |
+
years.add(int(year))
|
| 580 |
+
years_span = len(years)
|
| 581 |
+
|
| 582 |
+
# Count papers with code (Model column)
|
| 583 |
+
with_code = 0
|
| 584 |
+
model_col = df.iloc[:, 4] if len(df.columns) > 4 else pd.Series() # Model column
|
| 585 |
+
for value in model_col:
|
| 586 |
+
if isinstance(value, str) and ('Yes' in value or 'Code only' in value):
|
| 587 |
+
with_code += 1
|
| 588 |
+
|
| 589 |
+
# Count papers with data (Data column)
|
| 590 |
+
with_data = 0
|
| 591 |
+
data_col = df.iloc[:, 5] if len(df.columns) > 5 else pd.Series() # Data column
|
| 592 |
+
for value in data_col:
|
| 593 |
+
if isinstance(value, str) and 'Yes' in value:
|
| 594 |
+
with_data += 1
|
| 595 |
+
|
| 596 |
+
return {
|
| 597 |
+
'total_papers': total_papers,
|
| 598 |
+
'years_span': years_span,
|
| 599 |
+
'with_code': with_code,
|
| 600 |
+
'with_data': with_data
|
| 601 |
+
}
|
| 602 |
+
|
| 603 |
+
def main():
|
| 604 |
+
"""Main function to generate the website"""
|
| 605 |
+
# Determine if running in GitHub Actions or locally
|
| 606 |
+
if os.path.exists("/home/runner/work"):
|
| 607 |
+
# GitHub Actions
|
| 608 |
+
base_path = "/home/runner/work/awesome-computational-primatology/awesome-computational-primatology"
|
| 609 |
+
else:
|
| 610 |
+
# Local development - go up 2 levels from .github/workflows/
|
| 611 |
+
script_dir = os.path.dirname(os.path.abspath(__file__)) # .github/workflows/
|
| 612 |
+
base_path = os.path.dirname(os.path.dirname(script_dir)) # repository root
|
| 613 |
+
|
| 614 |
+
readme_path = os.path.join(base_path, "README.md")
|
| 615 |
+
output_path = os.path.join(base_path, "index.html")
|
| 616 |
+
|
| 617 |
+
print(f"Script location: {os.path.abspath(__file__)}")
|
| 618 |
+
print(f"Base path: {base_path}")
|
| 619 |
+
print(f"README path: {readme_path}")
|
| 620 |
+
print(f"Output path: {output_path}")
|
| 621 |
+
|
| 622 |
+
try:
|
| 623 |
+
# Extract table from README
|
| 624 |
+
df = extract_table_from_readme(readme_path)
|
| 625 |
+
print(f"Extracted table with {len(df)} rows and {len(df.columns)} columns")
|
| 626 |
+
|
| 627 |
+
# Calculate statistics
|
| 628 |
+
stats = calculate_stats(df)
|
| 629 |
+
print(f"Statistics: {stats}")
|
| 630 |
+
|
| 631 |
+
# Generate table HTML
|
| 632 |
+
table_html = df.to_html(
|
| 633 |
+
table_id="table",
|
| 634 |
+
escape=False,
|
| 635 |
+
index=False,
|
| 636 |
+
classes="display"
|
| 637 |
+
)
|
| 638 |
+
|
| 639 |
+
# Get template and format with data
|
| 640 |
+
template = get_enhanced_html_template()
|
| 641 |
+
html_content = template.replace('{table_html}', table_html)
|
| 642 |
+
html_content = html_content.replace('{total_papers}', str(stats['total_papers']))
|
| 643 |
+
html_content = html_content.replace('{years_span}', str(stats['years_span']))
|
| 644 |
+
html_content = html_content.replace('{with_code}', str(stats['with_code']))
|
| 645 |
+
html_content = html_content.replace('{with_data}', str(stats['with_data']))
|
| 646 |
+
|
| 647 |
+
# Write output
|
| 648 |
+
with open(output_path, "w", encoding='utf-8') as f:
|
| 649 |
+
f.write(html_content)
|
| 650 |
+
|
| 651 |
+
print(f"β
Generated enhanced website: {output_path}")
|
| 652 |
+
|
| 653 |
+
except Exception as e:
|
| 654 |
+
print(f"β Error generating website: {e}")
|
| 655 |
+
raise
|
| 656 |
+
|
| 657 |
+
if __name__ == "__main__":
|
| 658 |
+
main()
|
.gitignore
CHANGED
|
@@ -17,4 +17,7 @@ Thumbs.db
|
|
| 17 |
|
| 18 |
# Personal notes
|
| 19 |
TODO.md
|
| 20 |
-
NOTES.md
|
|
|
|
|
|
|
|
|
|
|
|
| 17 |
|
| 18 |
# Personal notes
|
| 19 |
TODO.md
|
| 20 |
+
NOTES.md
|
| 21 |
+
|
| 22 |
+
# Claude Desktop
|
| 23 |
+
.claude/
|
CONTRIBUTING.md
CHANGED
|
@@ -1,6 +1,31 @@
|
|
| 1 |
-
#
|
| 2 |
|
| 3 |
-
Thank you for your interest in contributing!
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 4 |
|
| 5 |
### 1. Branch Protocol
|
| 6 |
- Fork the repository
|
|
@@ -57,6 +82,7 @@ Use these abbreviations for the Topic column:
|
|
| 57 |
- FD: Face Detection
|
| 58 |
- FLE: Facial Landmark Estimation
|
| 59 |
- FR: Face Recognition and/or Re-Identification
|
|
|
|
| 60 |
- HD: Hand Detection
|
| 61 |
- HPE: Hand Pose Estimation
|
| 62 |
- BR: Behavior Recognition / Understanding / Modeling
|
|
|
|
| 1 |
+
# Contributing to Awesome Computational Primatology
|
| 2 |
|
| 3 |
+
Thank you for your interest in contributing! This document explains how to add papers and improve the project.
|
| 4 |
+
|
| 5 |
+
## π Quick Start
|
| 6 |
+
|
| 7 |
+
### Preview Your Changes Locally
|
| 8 |
+
```bash
|
| 9 |
+
# 1. Fork and clone the repository
|
| 10 |
+
git clone https://github.com/YOUR-USERNAME/awesome-computational-primatology.git
|
| 11 |
+
cd awesome-computational-primatology
|
| 12 |
+
|
| 13 |
+
# 2. Make your changes to README.md
|
| 14 |
+
|
| 15 |
+
# 3. Generate and preview the website
|
| 16 |
+
python .github/workflows/website.py
|
| 17 |
+
python -m http.server 8000
|
| 18 |
+
# Visit: http://localhost:8000
|
| 19 |
+
|
| 20 |
+
# 4. Create a pull request
|
| 21 |
+
```
|
| 22 |
+
|
| 23 |
+
### Automatic PR Previews
|
| 24 |
+
When you submit a PR, our automation will:
|
| 25 |
+
- β
Generate a preview website with your changes
|
| 26 |
+
- β
Post a comment with the preview link
|
| 27 |
+
- β
Validate table formatting and links
|
| 28 |
+
- β
Update the website automatically when merged
|
| 29 |
|
| 30 |
### 1. Branch Protocol
|
| 31 |
- Fork the repository
|
|
|
|
| 82 |
- FD: Face Detection
|
| 83 |
- FLE: Facial Landmark Estimation
|
| 84 |
- FR: Face Recognition and/or Re-Identification
|
| 85 |
+
- FAC: Facial Action Coding / Units
|
| 86 |
- HD: Hand Detection
|
| 87 |
- HPE: Hand Pose Estimation
|
| 88 |
- BR: Behavior Recognition / Understanding / Modeling
|
README.md
CHANGED
|
@@ -1,7 +1,7 @@
|
|
| 1 |
-
# [Awesome Computational Primatology](http://kordinglab.com/awesome-computational-primatology/)
|
| 2 |
|
| 3 |
[](https://awesome.re)
|
| 4 |
-
[](https://github.com/KordingLab/awesome-computational-primatology/blob/main/CONTRIBUTING.md)
|
| 6 |
[](https://github.com/KordingLab/awesome-computational-primatology/commits/main)
|
| 7 |
|
|
@@ -10,7 +10,20 @@ This repository contains the corpus of projects at the intersection of deep lear
|
|
| 10 |
By compiling and highlighting this growing literature, we hope it will inspire future researchers to open-source their own models and data to advance the field.
|
| 11 |
|
| 12 |
## Contribute to the List!
|
| 13 |
-
We welcome contributions from the community
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 14 |
|
| 15 |
By sharing your datasets and models, you contribute to advancing primatology and enable reproducible research.
|
| 16 |
|
|
@@ -22,7 +35,8 @@ By sharing your datasets and models, you contribute to advancing primatology and
|
|
| 22 |
| BPE | Body Pose Estimation |
|
| 23 |
| FD | Face Detection |
|
| 24 |
| FLE | Facial Landmark Estimation |
|
| 25 |
-
| FR | Face Recognition and/or Re-Identification |
|
|
|
|
| 26 |
| HD | Hand Detection |
|
| 27 |
| HPE | Hand Pose Estimation |
|
| 28 |
| BR | Behavior Recognition / Understanding / Modeling |
|
|
@@ -40,14 +54,20 @@ By sharing your datasets and models, you contribute to advancing primatology and
|
|
| 40 |
### Projects
|
| 41 |
| Year | Paper | Topic | Animal | Model? | Data? | Image/Video Count |
|
| 42 |
|------|-----|-------|---------|------------|---------------|-------------|
|
|
|
|
| 43 |
| 2024 | [PanAf20K](https://link.springer.com/article/10.1007/s11263-024-02003-z) | PD, BR | Apes | [No](https://github.com/obrookes/panaf.github.io) | [Yes](https://data.bris.ac.uk/data/dataset/1h73erszj3ckn2qjwm4sqmr2wt) | 20k |
|
| 44 |
| 2024 | [Gris et al.](https://docserver.ingentaconnect.com/deliver/fasttrack/aalas/15596109/jaalas_23000056.pdf?expires=1710859610&id=pennsylvaniapa&checksum=13D04EE26CE4C36535F9651507F83EDC) | FD, O | Macaque | No | No | N/A |
|
| 45 |
| 2024 | [MacAction](https://www.biorxiv.org/content/10.1101/2024.01.29.577734v1.full.pdf) | AM | Macaque | No | No | N/A |
|
| 46 |
| 2024 | [LabGym](https://link-springer-com.proxy.library.upenn.edu/epdf/10.1007/s10329-024-01123-x?sharing_token=_ApwJ7je3dmaWjW7cYNbUPe4RwlQNchNByi7wbcMAY4h1wHpdNqXXEnVHidjh8t56BEMyNJkqC8xIJ-ZpXK78qFoYXZ7oq8pYO62wVWzEHVj6fEbKl9wvAlIYBLr4-giBZwcMH2HZvRPiyRk4I1-_3hbhgnYy_ZtE0jBSB4UJo4=) | BR | Macaque | [Yes](https://github.com/umyelab/LabGym) | Yes | N/A |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 47 |
| 2023 | [GorillaVision](https://inf-cv.uni-jena.de/wordpress/wp-content/uploads/2023/09/Talk-12-Maximilian-Schall.pdf) | FD, FR | Gorilla | [Yes](https://github.com/Lasklu/gorillavision) | No | 832 |
|
| 48 |
| 2023 | [Abbaspoor, Rahman et al.](https://www.biorxiv.org/content/10.1101/2023.12.11.571113v1.abstract) | 3D BPE | Macaque | No | No | N/A |
|
| 49 |
| 2023 | [Mimura et al.](https://www.biorxiv.org/content/10.1101/2023.03.04.531044v3.abstract) | BR | Macaque, Marmoset | No | No | N/A |
|
| 50 |
-
| 2023 | [Schofield et al.](https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14181) | FD, FR | Chimp | No | No | N/A
|
| 51 |
| 2023 | [Yang et al.](https://arxiv.org/pdf/2205.00275.pdf) | PD | Great Ape | No | No | N/A |
|
| 52 |
| 2023 | [ASBAR](https://www.biorxiv.org/content/10.1101/2023.09.24.559236v1.full.pdf) | BR | Chimp, Gorilla | Yes | [Yes](https://github.com/MitchFuchs/asbar) | 5,440 labels |
|
| 53 |
| 2023 | [DeepWild](https://besjournals-onlinelibrary-wiley-com.proxy.library.upenn.edu/doi/full/10.1111/1365-2656.13932) | 2D BPE | Chimp, Bonobo | [Yes](https://github.com/Wild-Minds/DeepWild) | [Upon request](https://doi-org.proxy.library.upenn.edu/10.5281/zenodo.5600472) | N/A |
|
|
@@ -95,7 +115,24 @@ By sharing your datasets and models, you contribute to advancing primatology and
|
|
| 95 |
| 2011 | [Loos et al.](https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7074032) | FR | Chimp | No | No | N/A |
|
| 96 |
| 2011 | [Ernst & KΓΌblbeck](https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6027337) | FD, SI | Chimp, Gorilla | No | No | N/A |
|
| 97 |
|
| 98 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 99 |
| Year | Paper | Topic | Animal | Model? | Data? | Image/Video Count |
|
| 100 |
|------|-----|-------|---------|------------|---------------|-------------|
|
| 101 |
| 2023 | [MammalNet](https://arxiv.org/pdf/2306.00576.pdf) | BR | Cross-species | [Yes](https://github.com/Vision-CAIR/MammalNet) | [Yes](https://mammal-net.github.io/) | 18k videos |
|
|
|
|
| 1 |
+
# π [Awesome Computational Primatology](http://kordinglab.com/awesome-computational-primatology/)
|
| 2 |
|
| 3 |
[](https://awesome.re)
|
| 4 |
+
[](https://github.com/KordingLab/awesome-computational-primatology#projects)
|
| 5 |
[](https://github.com/KordingLab/awesome-computational-primatology/blob/main/CONTRIBUTING.md)
|
| 6 |
[](https://github.com/KordingLab/awesome-computational-primatology/commits/main)
|
| 7 |
|
|
|
|
| 10 |
By compiling and highlighting this growing literature, we hope it will inspire future researchers to open-source their own models and data to advance the field.
|
| 11 |
|
| 12 |
## Contribute to the List!
|
| 13 |
+
We welcome contributions from the community! If you know of a relevant paper or project:
|
| 14 |
+
|
| 15 |
+
1. **π΄ Fork** this repository
|
| 16 |
+
2. **βοΈ Add** your paper to the table in chronological order
|
| 17 |
+
3. **π Preview** your changes: `python scripts/dev-preview.py`
|
| 18 |
+
4. **π€ Submit** a pull request
|
| 19 |
+
|
| 20 |
+
**Features for contributors:**
|
| 21 |
+
- π Automatic link checking
|
| 22 |
+
- π Live preview of your changes
|
| 23 |
+
- π Auto-generated website updates
|
| 24 |
+
- β
Format validation
|
| 25 |
+
|
| 26 |
+
Read our [Contributing Guidelines](CONTRIBUTING.md) for detailed instructions!
|
| 27 |
|
| 28 |
By sharing your datasets and models, you contribute to advancing primatology and enable reproducible research.
|
| 29 |
|
|
|
|
| 35 |
| BPE | Body Pose Estimation |
|
| 36 |
| FD | Face Detection |
|
| 37 |
| FLE | Facial Landmark Estimation |
|
| 38 |
+
| FR | Face Recognition and/or Re-Identification |
|
| 39 |
+
| FAC | Facial Action Coding / Units |
|
| 40 |
| HD | Hand Detection |
|
| 41 |
| HPE | Hand Pose Estimation |
|
| 42 |
| BR | Behavior Recognition / Understanding / Modeling |
|
|
|
|
| 54 |
### Projects
|
| 55 |
| Year | Paper | Topic | Animal | Model? | Data? | Image/Video Count |
|
| 56 |
|------|-----|-------|---------|------------|---------------|-------------|
|
| 57 |
+
| 2025 | [PrimateFace](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v1) | FD, FLE, FR, FAC | Cross-species | [Yes](https://github.com/KordingLab/PrimateFace) | [Yes](https://github.com/KordingLab/PrimateFace) | 200K+ images |
|
| 58 |
| 2024 | [PanAf20K](https://link.springer.com/article/10.1007/s11263-024-02003-z) | PD, BR | Apes | [No](https://github.com/obrookes/panaf.github.io) | [Yes](https://data.bris.ac.uk/data/dataset/1h73erszj3ckn2qjwm4sqmr2wt) | 20k |
|
| 59 |
| 2024 | [Gris et al.](https://docserver.ingentaconnect.com/deliver/fasttrack/aalas/15596109/jaalas_23000056.pdf?expires=1710859610&id=pennsylvaniapa&checksum=13D04EE26CE4C36535F9651507F83EDC) | FD, O | Macaque | No | No | N/A |
|
| 60 |
| 2024 | [MacAction](https://www.biorxiv.org/content/10.1101/2024.01.29.577734v1.full.pdf) | AM | Macaque | No | No | N/A |
|
| 61 |
| 2024 | [LabGym](https://link-springer-com.proxy.library.upenn.edu/epdf/10.1007/s10329-024-01123-x?sharing_token=_ApwJ7je3dmaWjW7cYNbUPe4RwlQNchNByi7wbcMAY4h1wHpdNqXXEnVHidjh8t56BEMyNJkqC8xIJ-ZpXK78qFoYXZ7oq8pYO62wVWzEHVj6fEbKl9wvAlIYBLr4-giBZwcMH2HZvRPiyRk4I1-_3hbhgnYy_ZtE0jBSB4UJo4=) | BR | Macaque | [Yes](https://github.com/umyelab/LabGym) | Yes | N/A |
|
| 62 |
+
| 2024 | [Cheng et al.](https://www.biorxiv.org/content/10.1101/2024.02.27.582429v3.full.pdf) | BR | Macaque | No | No | N/A |
|
| 63 |
+
| 2024 | [PRIMAT (Vogg et al.)](https://www.biorxiv.org/content/10.1101/2024.08.21.607881v1.full.pdf) | 2D BPE | Cross-species | No | No | N/A |
|
| 64 |
+
| 2024 | [Franch et al.](https://www-nature-com.proxy.library.upenn.edu/articles/s41586-024-07084-x) | BR | Macaque | No | No | N/A |
|
| 65 |
+
| 2024 | [Xing et al.](https://www.biorxiv.org/content/10.1101/2024.02.16.580693v1.full.pdf) | O | Marmoset | No | No | N/A |
|
| 66 |
+
| 2024 | [Menegas et al.](https://www.biorxiv.org/content/10.1101/2024.08.30.610159v1.full.pdf) | BR | Marmoset | No | No | N/A |
|
| 67 |
| 2023 | [GorillaVision](https://inf-cv.uni-jena.de/wordpress/wp-content/uploads/2023/09/Talk-12-Maximilian-Schall.pdf) | FD, FR | Gorilla | [Yes](https://github.com/Lasklu/gorillavision) | No | 832 |
|
| 68 |
| 2023 | [Abbaspoor, Rahman et al.](https://www.biorxiv.org/content/10.1101/2023.12.11.571113v1.abstract) | 3D BPE | Macaque | No | No | N/A |
|
| 69 |
| 2023 | [Mimura et al.](https://www.biorxiv.org/content/10.1101/2023.03.04.531044v3.abstract) | BR | Macaque, Marmoset | No | No | N/A |
|
| 70 |
+
| 2023 | [Schofield et al.](https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14181) | FD, FR | Chimp | No | No | N/A |
|
| 71 |
| 2023 | [Yang et al.](https://arxiv.org/pdf/2205.00275.pdf) | PD | Great Ape | No | No | N/A |
|
| 72 |
| 2023 | [ASBAR](https://www.biorxiv.org/content/10.1101/2023.09.24.559236v1.full.pdf) | BR | Chimp, Gorilla | Yes | [Yes](https://github.com/MitchFuchs/asbar) | 5,440 labels |
|
| 73 |
| 2023 | [DeepWild](https://besjournals-onlinelibrary-wiley-com.proxy.library.upenn.edu/doi/full/10.1111/1365-2656.13932) | 2D BPE | Chimp, Bonobo | [Yes](https://github.com/Wild-Minds/DeepWild) | [Upon request](https://doi-org.proxy.library.upenn.edu/10.5281/zenodo.5600472) | N/A |
|
|
|
|
| 115 |
| 2011 | [Loos et al.](https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7074032) | FR | Chimp | No | No | N/A |
|
| 116 |
| 2011 | [Ernst & KΓΌblbeck](https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6027337) | FD, SI | Chimp, Gorilla | No | No | N/A |
|
| 117 |
|
| 118 |
+
### Datasets
|
| 119 |
+
|
| 120 |
+
#### Primate-Specific Datasets
|
| 121 |
+
| Year | Dataset Name | Description | Species | Size | Availability |
|
| 122 |
+
|------|-------------|-------------|---------|------|--------------|
|
| 123 |
+
| 2025 | [PrimateFace](https://www.biorxiv.org/content/10.1101/2025.08.12.669927v1) | Face analysis | Cross-species | 200K+ images | Public |
|
| 124 |
+
| 2024 | [PanAf20K](https://data.bris.ac.uk/data/dataset/1h73erszj3ckn2qjwm4sqmr2wt) | Detection and behavior | Apes | 20,000 videos | Public |
|
| 125 |
+
| 2023 | [OpenMonkeyChallenge](http://openmonkeychallenge.com/) | 2D pose estimation | Cross-species | 111,529 images | Public |
|
| 126 |
+
| 2021 | [GreatApe Dictionary](https://zenodo.org/records/5600472#.YX1_ddbMK_J) | Behavioral annotations | Chimps | N/A | Upon request |
|
| 127 |
+
| 2021 | [MacaquePose](https://github.com/MacaquePose/MacaquePose) | 2D pose estimation | Macaque | 13,000 images | Public |
|
| 128 |
+
| 2021 | [OpenApePose](https://github.com/OpenApePose/OpenApePose) | 2D pose estimation | Cross-species | 71,868 images | Public |
|
| 129 |
+
| 2020 | [OpenMonkeyStudio](https://github.com/OpenMonkeyStudio/OMS_Data) | 3D pose estimation | Macaque | 195,228 frames | Public |
|
| 130 |
+
| 2020 | [Tri-A](https://data.mendeley.com/datasets/z3x59pv4bz/2) | Face detection/recognition | 41 species | 102,399 images | Public |
|
| 131 |
+
| 2018 | [Macaque Faces](https://figshare.com/articles/dataset/Macaque_Faces/9862586/1?file=17682749) | Facial landmarks | Macaque | 4,000 images | Public |
|
| 132 |
+
| 2017 | [LemurFaceID](http://biometrics.cse.msu.edu/Publications/Databases/MSU_LemurFaceID/) | Face recognition | Lemur | 462 images | Public |
|
| 133 |
+
| 2016 | [Chimpanzee Faces](https://github.com/cvjena/chimpanzee_faces) | Face recognition | Chimp | 6,486 images | Public |
|
| 134 |
+
|
| 135 |
+
#### Dataset with both primate and non-primate data
|
| 136 |
| Year | Paper | Topic | Animal | Model? | Data? | Image/Video Count |
|
| 137 |
|------|-----|-------|---------|------------|---------------|-------------|
|
| 138 |
| 2023 | [MammalNet](https://arxiv.org/pdf/2306.00576.pdf) | BR | Cross-species | [Yes](https://github.com/Vision-CAIR/MammalNet) | [Yes](https://mammal-net.github.io/) | 18k videos |
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</head>
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<body>
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-
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| 11 |
<thead>
|
| 12 |
<tr style="text-align: right;">
|
| 13 |
<th>Year</th>
|
|
@@ -20,6 +388,15 @@
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| 20 |
</tr>
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</thead>
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| 22 |
<tbody>
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<tr>
|
| 24 |
<td>2024</td>
|
| 25 |
<td><a href="https://link.springer.com/article/10.1007/s11263-024-02003-z">PanAf20K</a></td>
|
|
@@ -56,6 +433,51 @@
|
|
| 56 |
<td>Yes</td>
|
| 57 |
<td>N/A</td>
|
| 58 |
</tr>
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| 59 |
<tr>
|
| 60 |
<td>2023</td>
|
| 61 |
<td><a href="https://inf-cv.uni-jena.de/wordpress/wp-content/uploads/2023/09/Talk-12-Maximilian-Schall.pdf">GorillaVision</a></td>
|
|
@@ -83,6 +505,15 @@
|
|
| 83 |
<td>No</td>
|
| 84 |
<td>N/A</td>
|
| 85 |
</tr>
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| 86 |
<tr>
|
| 87 |
<td>2023</td>
|
| 88 |
<td><a href="https://arxiv.org/pdf/2205.00275.pdf">Yang et al.</a></td>
|
|
@@ -479,83 +910,143 @@
|
|
| 479 |
<td>No</td>
|
| 480 |
<td>N/A</td>
|
| 481 |
</tr>
|
| 482 |
-
<tr>
|
| 483 |
-
<td>Year</td>
|
| 484 |
-
<td>Paper</td>
|
| 485 |
-
<td>Topic</td>
|
| 486 |
-
<td>Animal</td>
|
| 487 |
-
<td>Model?</td>
|
| 488 |
-
<td>Data?</td>
|
| 489 |
-
<td>Image/Video Count</td>
|
| 490 |
-
</tr>
|
| 491 |
-
<tr>
|
| 492 |
-
<td>------</td>
|
| 493 |
-
<td>-----</td>
|
| 494 |
-
<td>-------</td>
|
| 495 |
-
<td>---------</td>
|
| 496 |
-
<td>------------</td>
|
| 497 |
-
<td>---------------</td>
|
| 498 |
-
<td>-------------</td>
|
| 499 |
-
</tr>
|
| 500 |
-
<tr>
|
| 501 |
-
<td>2023</td>
|
| 502 |
-
<td><a href="https://arxiv.org/pdf/2306.00576.pdf">MammalNet</a></td>
|
| 503 |
-
<td>BR</td>
|
| 504 |
-
<td>Cross-species</td>
|
| 505 |
-
<td><a href="https://github.com/Vision-CAIR/MammalNet">Yes</a></td>
|
| 506 |
-
<td><a href="https://mammal-net.github.io/">Yes</a></td>
|
| 507 |
-
<td>18k videos</td>
|
| 508 |
-
</tr>
|
| 509 |
-
<tr>
|
| 510 |
-
<td>2022</td>
|
| 511 |
-
<td><a href="https://arxiv.org/pdf/2204.08129.pdf">Animal Kingdom</a></td>
|
| 512 |
-
<td>2D BPE, BR</td>
|
| 513 |
-
<td>Cross-species</td>
|
| 514 |
-
<td>No</td>
|
| 515 |
-
<td><a href="https://github.com/sutdcv/Animal-Kingdom">Yes</a></td>
|
| 516 |
-
<td>N/A</td>
|
| 517 |
-
</tr>
|
| 518 |
-
<tr>
|
| 519 |
-
<td>2022</td>
|
| 520 |
-
<td><a href="https://arxiv.org/pdf/2206.05683.pdf">APT-36K</a></td>
|
| 521 |
-
<td>2D BPE</td>
|
| 522 |
-
<td>Cross-species</td>
|
| 523 |
-
<td>No</td>
|
| 524 |
-
<td><a href="https://github.com/pandorgan/APT-36K">Yes</a></td>
|
| 525 |
-
<td>< 36K</td>
|
| 526 |
-
</tr>
|
| 527 |
-
<tr>
|
| 528 |
-
<td>2021</td>
|
| 529 |
-
<td>AP10k</td>
|
| 530 |
-
<td>2D BPE</td>
|
| 531 |
-
<td>Cross-species</td>
|
| 532 |
-
<td><a href="https://github.com/open-mmlab/mmpose/tree/main/configs/animal_2d_keypoint/topdown_heatmap/ap10k">Yes</a></td>
|
| 533 |
-
<td>Yes</td>
|
| 534 |
-
<td>10,015 (675 primates)</td>
|
| 535 |
-
</tr>
|
| 536 |
-
<tr>
|
| 537 |
-
<td>2021</td>
|
| 538 |
-
<td><a href="https://www-nature-com.proxy.library.upenn.edu/articles/s41592-021-01226-z">LiftPose3D</a></td>
|
| 539 |
-
<td>3D BPE</td>
|
| 540 |
-
<td>Cross-species</td>
|
| 541 |
-
<td>Yes</td>
|
| 542 |
-
<td>No</td>
|
| 543 |
-
<td>N/A</td>
|
| 544 |
-
</tr>
|
| 545 |
-
<tr>
|
| 546 |
-
<td>2020</td>
|
| 547 |
-
<td>AnimalWeb</td>
|
| 548 |
-
<td>FD, FLE</td>
|
| 549 |
-
<td>Cross-species</td>
|
| 550 |
-
<td>No</td>
|
| 551 |
-
<td>Yes</td>
|
| 552 |
-
<td>21,921</td>
|
| 553 |
-
</tr>
|
| 554 |
</tbody>
|
| 555 |
-
</table
|
| 556 |
-
|
| 557 |
-
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| 558 |
});
|
| 559 |
-
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| 560 |
</body>
|
| 561 |
-
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|
| 1 |
+
<!DOCTYPE html>
|
| 2 |
<html>
|
| 3 |
<head>
|
| 4 |
+
<meta charset="UTF-8">
|
| 5 |
+
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
| 6 |
+
<title>Awesome Computational Primatology</title>
|
| 7 |
+
|
| 8 |
+
<!-- External Libraries -->
|
| 9 |
+
<script src="https://code.jquery.com/jquery-3.7.1.min.js"></script>
|
| 10 |
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<link rel="stylesheet" href="https://cdn.datatables.net/2.0.2/css/dataTables.dataTables.css" />
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/* Footer */
|
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|
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+
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.footer a {
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+
color: var(--secondary-color);
|
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+
text-decoration: none;
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+
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|
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+
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|
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+
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|
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+
color: #888;
|
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+
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|
| 287 |
+
|
| 288 |
+
#last-updated {
|
| 289 |
+
font-weight: 600;
|
| 290 |
+
color: var(--secondary-color);
|
| 291 |
+
}
|
| 292 |
+
|
| 293 |
+
@media (max-width: 768px) {
|
| 294 |
+
.container { padding: 15px; }
|
| 295 |
+
h1 { font-size: 2rem; }
|
| 296 |
+
.stats { gap: 15px; }
|
| 297 |
+
.stat-item { min-width: 100px; padding: 10px; }
|
| 298 |
+
table.dataTable thead th,
|
| 299 |
+
table.dataTable tbody td { padding: 8px 6px; font-size: 0.9rem; }
|
| 300 |
+
.legend-grid { grid-template-columns: 1fr; }
|
| 301 |
+
.footer { margin-top: 20px; padding: 20px 15px; }
|
| 302 |
+
}
|
| 303 |
+
</style>
|
| 304 |
</head>
|
| 305 |
<body>
|
| 306 |
+
<div class="container">
|
| 307 |
+
<div class="header">
|
| 308 |
+
<h1>π Awesome Computational Primatology</h1>
|
| 309 |
+
<p class="subtitle">A curated list of machine learning research for non-human primatology</p>
|
| 310 |
+
|
| 311 |
+
<div class="stats">
|
| 312 |
+
<div class="stat-item">
|
| 313 |
+
<span class="stat-number" id="total-papers">58</span>
|
| 314 |
+
<span class="stat-label">Papers</span>
|
| 315 |
+
</div>
|
| 316 |
+
<div class="stat-item">
|
| 317 |
+
<span class="stat-number" id="years-span">14</span>
|
| 318 |
+
<span class="stat-label">Years</span>
|
| 319 |
+
</div>
|
| 320 |
+
<div class="stat-item">
|
| 321 |
+
<span class="stat-number" id="with-code">10</span>
|
| 322 |
+
<span class="stat-label">With Code</span>
|
| 323 |
+
</div>
|
| 324 |
+
<div class="stat-item">
|
| 325 |
+
<span class="stat-number" id="with-data">15</span>
|
| 326 |
+
<span class="stat-label">With Data</span>
|
| 327 |
+
</div>
|
| 328 |
+
</div>
|
| 329 |
+
</div>
|
| 330 |
+
|
| 331 |
+
<div class="legend">
|
| 332 |
+
<h3>π·οΈ Topic Legend</h3>
|
| 333 |
+
<div class="legend-grid">
|
| 334 |
+
<div class="legend-item">
|
| 335 |
+
<span class="legend-badge">PD</span>
|
| 336 |
+
<span>Primate Detection</span>
|
| 337 |
+
</div>
|
| 338 |
+
<div class="legend-item">
|
| 339 |
+
<span class="legend-badge">BPE</span>
|
| 340 |
+
<span>Body Pose Estimation</span>
|
| 341 |
+
</div>
|
| 342 |
+
<div class="legend-item">
|
| 343 |
+
<span class="legend-badge">FD</span>
|
| 344 |
+
<span>Face Detection</span>
|
| 345 |
+
</div>
|
| 346 |
+
<div class="legend-item">
|
| 347 |
+
<span class="legend-badge">FLE</span>
|
| 348 |
+
<span>Facial Landmark Estimation</span>
|
| 349 |
+
</div>
|
| 350 |
+
<div class="legend-item">
|
| 351 |
+
<span class="legend-badge">FR</span>
|
| 352 |
+
<span>Face Recognition</span>
|
| 353 |
+
</div>
|
| 354 |
+
<div class="legend-item">
|
| 355 |
+
<span class="legend-badge">FAC</span>
|
| 356 |
+
<span>Facial Action Coding</span>
|
| 357 |
+
</div>
|
| 358 |
+
<div class="legend-item">
|
| 359 |
+
<span class="legend-badge">BR</span>
|
| 360 |
+
<span>Behavior Recognition</span>
|
| 361 |
+
</div>
|
| 362 |
+
<div class="legend-item">
|
| 363 |
+
<span class="legend-badge">AM</span>
|
| 364 |
+
<span>Avatar/Mesh</span>
|
| 365 |
+
</div>
|
| 366 |
+
<div class="legend-item">
|
| 367 |
+
<span class="legend-badge">SI</span>
|
| 368 |
+
<span>Species Identification</span>
|
| 369 |
+
</div>
|
| 370 |
+
<div class="legend-item">
|
| 371 |
+
<span class="legend-badge">RL</span>
|
| 372 |
+
<span>Reinforcement Learning</span>
|
| 373 |
+
</div>
|
| 374 |
+
</div>
|
| 375 |
+
</div>
|
| 376 |
+
|
| 377 |
+
<div class="table-container">
|
| 378 |
+
<table border="1" class="dataframe display" id="table">
|
| 379 |
<thead>
|
| 380 |
<tr style="text-align: right;">
|
| 381 |
<th>Year</th>
|
|
|
|
| 388 |
</tr>
|
| 389 |
</thead>
|
| 390 |
<tbody>
|
| 391 |
+
<tr>
|
| 392 |
+
<td>2025</td>
|
| 393 |
+
<td><a href="https://www.biorxiv.org/content/10.1101/2025.08.12.669927v1">PrimateFace</a></td>
|
| 394 |
+
<td>FD, FLE, FR, FAC</td>
|
| 395 |
+
<td>Cross-species</td>
|
| 396 |
+
<td><a href="https://github.com/KordingLab/PrimateFace">Yes</a></td>
|
| 397 |
+
<td><a href="https://github.com/KordingLab/PrimateFace">Yes</a></td>
|
| 398 |
+
<td>200K+ images</td>
|
| 399 |
+
</tr>
|
| 400 |
<tr>
|
| 401 |
<td>2024</td>
|
| 402 |
<td><a href="https://link.springer.com/article/10.1007/s11263-024-02003-z">PanAf20K</a></td>
|
|
|
|
| 433 |
<td>Yes</td>
|
| 434 |
<td>N/A</td>
|
| 435 |
</tr>
|
| 436 |
+
<tr>
|
| 437 |
+
<td>2024</td>
|
| 438 |
+
<td><a href="https://www.biorxiv.org/content/10.1101/2024.02.27.582429v3.full.pdf">Cheng et al.</a></td>
|
| 439 |
+
<td>BR</td>
|
| 440 |
+
<td>Macaque</td>
|
| 441 |
+
<td>No</td>
|
| 442 |
+
<td>No</td>
|
| 443 |
+
<td>N/A</td>
|
| 444 |
+
</tr>
|
| 445 |
+
<tr>
|
| 446 |
+
<td>2024</td>
|
| 447 |
+
<td><a href="https://www.biorxiv.org/content/10.1101/2024.08.21.607881v1.full.pdf">PRIMAT (Vogg et al.)</a></td>
|
| 448 |
+
<td>2D BPE</td>
|
| 449 |
+
<td>Cross-species</td>
|
| 450 |
+
<td>No</td>
|
| 451 |
+
<td>No</td>
|
| 452 |
+
<td>N/A</td>
|
| 453 |
+
</tr>
|
| 454 |
+
<tr>
|
| 455 |
+
<td>2024</td>
|
| 456 |
+
<td><a href="https://www-nature-com.proxy.library.upenn.edu/articles/s41586-024-07084-x">Franch et al.</a></td>
|
| 457 |
+
<td>BR</td>
|
| 458 |
+
<td>Macaque</td>
|
| 459 |
+
<td>No</td>
|
| 460 |
+
<td>No</td>
|
| 461 |
+
<td>N/A</td>
|
| 462 |
+
</tr>
|
| 463 |
+
<tr>
|
| 464 |
+
<td>2024</td>
|
| 465 |
+
<td><a href="https://www.biorxiv.org/content/10.1101/2024.02.16.580693v1.full.pdf">Xing et al.</a></td>
|
| 466 |
+
<td>O</td>
|
| 467 |
+
<td>Marmoset</td>
|
| 468 |
+
<td>No</td>
|
| 469 |
+
<td>No</td>
|
| 470 |
+
<td>N/A</td>
|
| 471 |
+
</tr>
|
| 472 |
+
<tr>
|
| 473 |
+
<td>2024</td>
|
| 474 |
+
<td><a href="https://www.biorxiv.org/content/10.1101/2024.08.30.610159v1.full.pdf">Menegas et al.</a></td>
|
| 475 |
+
<td>BR</td>
|
| 476 |
+
<td>Marmoset</td>
|
| 477 |
+
<td>No</td>
|
| 478 |
+
<td>No</td>
|
| 479 |
+
<td>N/A</td>
|
| 480 |
+
</tr>
|
| 481 |
<tr>
|
| 482 |
<td>2023</td>
|
| 483 |
<td><a href="https://inf-cv.uni-jena.de/wordpress/wp-content/uploads/2023/09/Talk-12-Maximilian-Schall.pdf">GorillaVision</a></td>
|
|
|
|
| 505 |
<td>No</td>
|
| 506 |
<td>N/A</td>
|
| 507 |
</tr>
|
| 508 |
+
<tr>
|
| 509 |
+
<td>2023</td>
|
| 510 |
+
<td><a href="https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14181">Schofield et al.</a></td>
|
| 511 |
+
<td>FD, FR</td>
|
| 512 |
+
<td>Chimp</td>
|
| 513 |
+
<td>No</td>
|
| 514 |
+
<td>No</td>
|
| 515 |
+
<td>N/A</td>
|
| 516 |
+
</tr>
|
| 517 |
<tr>
|
| 518 |
<td>2023</td>
|
| 519 |
<td><a href="https://arxiv.org/pdf/2205.00275.pdf">Yang et al.</a></td>
|
|
|
|
| 910 |
<td>No</td>
|
| 911 |
<td>N/A</td>
|
| 912 |
</tr>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 913 |
</tbody>
|
| 914 |
+
</table>
|
| 915 |
+
</div>
|
| 916 |
+
|
| 917 |
+
<div class="footer">
|
| 918 |
+
<p>
|
| 919 |
+
<strong>Maintained by:</strong>
|
| 920 |
+
<a href="http://kordinglab.com" target="_blank">π§ Kording Lab</a> β’
|
| 921 |
+
<a href="mailto:fparodi@upenn.edu">π§ Felipe Parodi</a> β’
|
| 922 |
+
<a href="https://github.com/KordingLab/awesome-computational-primatology" target="_blank">β Star on GitHub</a>
|
| 923 |
+
</p>
|
| 924 |
+
<p class="footer-note">
|
| 925 |
+
Found a paper we missed? <a href="https://github.com/KordingLab/awesome-computational-primatology/blob/main/CONTRIBUTING.md">Contribute here!</a>
|
| 926 |
+
β’ Last updated: <span id="last-updated"></span>
|
| 927 |
+
</p>
|
| 928 |
+
</div>
|
| 929 |
+
</div>
|
| 930 |
+
|
| 931 |
+
<script>
|
| 932 |
+
$(document).ready(function() {
|
| 933 |
+
var table = $('#table').DataTable({
|
| 934 |
+
paging: true,
|
| 935 |
+
pageLength: 25,
|
| 936 |
+
lengthMenu: [10, 25, 50, 100, -1],
|
| 937 |
+
searching: true,
|
| 938 |
+
ordering: true,
|
| 939 |
+
info: true,
|
| 940 |
+
responsive: true,
|
| 941 |
+
|
| 942 |
+
dom: 'Bfrtip',
|
| 943 |
+
buttons: [
|
| 944 |
+
{
|
| 945 |
+
extend: 'searchPanes',
|
| 946 |
+
config: {
|
| 947 |
+
cascadePanes: true,
|
| 948 |
+
viewTotal: true,
|
| 949 |
+
columns: [0, 2, 3, 4, 5]
|
| 950 |
+
}
|
| 951 |
+
},
|
| 952 |
+
'copy', 'csv', 'excel',
|
| 953 |
+
{
|
| 954 |
+
text: 'Clear Filters',
|
| 955 |
+
action: function(e, dt, node, config) {
|
| 956 |
+
dt.searchPanes.clearSelections();
|
| 957 |
+
}
|
| 958 |
+
}
|
| 959 |
+
],
|
| 960 |
+
|
| 961 |
+
searchPanes: {
|
| 962 |
+
cascadePanes: true,
|
| 963 |
+
viewTotal: true,
|
| 964 |
+
columns: [0, 2, 3, 4, 5],
|
| 965 |
+
initCollapsed: true
|
| 966 |
+
},
|
| 967 |
+
|
| 968 |
+
columnDefs: [
|
| 969 |
+
{
|
| 970 |
+
targets: 0,
|
| 971 |
+
type: 'num',
|
| 972 |
+
className: 'year-cell',
|
| 973 |
+
width: '80px'
|
| 974 |
+
},
|
| 975 |
+
{
|
| 976 |
+
targets: 2,
|
| 977 |
+
width: '150px',
|
| 978 |
+
render: function(data, type, row) {
|
| 979 |
+
if (type === 'display') {
|
| 980 |
+
const topics = data.split(', ');
|
| 981 |
+
return topics.map(topic =>
|
| 982 |
+
'<span class="topic-tag">' + topic.trim() + '</span>'
|
| 983 |
+
).join(' ');
|
| 984 |
+
}
|
| 985 |
+
return data;
|
| 986 |
+
}
|
| 987 |
+
},
|
| 988 |
+
{
|
| 989 |
+
targets: 3,
|
| 990 |
+
width: '120px',
|
| 991 |
+
render: function(data, type, row) {
|
| 992 |
+
if (type === 'display') {
|
| 993 |
+
let className = 'species-cross';
|
| 994 |
+
const lowerData = data.toLowerCase();
|
| 995 |
+
if (lowerData.includes('macaque')) className = 'species-macaque';
|
| 996 |
+
else if (lowerData.includes('chimp')) className = 'species-chimp';
|
| 997 |
+
else if (lowerData.includes('gorilla')) className = 'species-gorilla';
|
| 998 |
+
else if (lowerData.includes('marmoset')) className = 'species-marmoset';
|
| 999 |
+
|
| 1000 |
+
return '<span class="' + className + '" style="padding: 4px 8px; border-radius: 4px; display: inline-block;">' + data + '</span>';
|
| 1001 |
+
}
|
| 1002 |
+
return data;
|
| 1003 |
+
}
|
| 1004 |
+
},
|
| 1005 |
+
{
|
| 1006 |
+
targets: [4, 5],
|
| 1007 |
+
width: '100px',
|
| 1008 |
+
render: function(data, type, row) {
|
| 1009 |
+
if (type === 'display') {
|
| 1010 |
+
let className = 'status-no';
|
| 1011 |
+
let icon = '<i class="fas fa-times"></i> ';
|
| 1012 |
+
|
| 1013 |
+
if (data.includes('Yes')) {
|
| 1014 |
+
className = 'status-yes';
|
| 1015 |
+
icon = '<i class="fas fa-check"></i> ';
|
| 1016 |
+
} else if (data.includes('Code only') || data.includes('Some')) {
|
| 1017 |
+
className = 'status-partial';
|
| 1018 |
+
icon = '<i class="fas fa-code"></i> ';
|
| 1019 |
+
} else if (data.includes('Upon request')) {
|
| 1020 |
+
className = 'status-request';
|
| 1021 |
+
icon = '<i class="fas fa-envelope"></i> ';
|
| 1022 |
+
}
|
| 1023 |
+
|
| 1024 |
+
return '<span class="status-badge ' + className + '">' + icon + data + '</span>';
|
| 1025 |
+
}
|
| 1026 |
+
return data;
|
| 1027 |
+
}
|
| 1028 |
+
}
|
| 1029 |
+
],
|
| 1030 |
+
|
| 1031 |
+
order: [[0, 'desc']],
|
| 1032 |
+
|
| 1033 |
+
language: {
|
| 1034 |
+
search: '<i class="fas fa-search"></i>',
|
| 1035 |
+
searchPlaceholder: 'Search papers...',
|
| 1036 |
+
lengthMenu: 'Show _MENU_ papers per page',
|
| 1037 |
+
info: 'Showing _START_ to _END_ of _TOTAL_ papers',
|
| 1038 |
+
processing: '<i class="fas fa-spinner fa-spin"></i> Loading...'
|
| 1039 |
+
}
|
| 1040 |
+
});
|
| 1041 |
+
|
| 1042 |
+
// Set last updated date
|
| 1043 |
+
const lastUpdated = new Date().toLocaleDateString('en-US', {
|
| 1044 |
+
year: 'numeric',
|
| 1045 |
+
month: 'long',
|
| 1046 |
+
day: 'numeric'
|
| 1047 |
});
|
| 1048 |
+
document.getElementById('last-updated').textContent = lastUpdated;
|
| 1049 |
+
});
|
| 1050 |
+
</script>
|
| 1051 |
</body>
|
| 1052 |
+
</html>
|
scripts/dev-preview.py
ADDED
|
@@ -0,0 +1,67 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/usr/bin/env python3
|
| 2 |
+
"""
|
| 3 |
+
Development preview script for contributors
|
| 4 |
+
Run this to generate and serve the website locally
|
| 5 |
+
"""
|
| 6 |
+
import os
|
| 7 |
+
import sys
|
| 8 |
+
import subprocess
|
| 9 |
+
import webbrowser
|
| 10 |
+
from pathlib import Path
|
| 11 |
+
|
| 12 |
+
def main():
|
| 13 |
+
print("π§ Awesome Computational Primatology - Development Preview")
|
| 14 |
+
print("=" * 60)
|
| 15 |
+
|
| 16 |
+
# Check if we're in the right directory
|
| 17 |
+
if not os.path.exists("README.md"):
|
| 18 |
+
print("β Error: README.md not found. Please run this from the repository root.")
|
| 19 |
+
sys.exit(1)
|
| 20 |
+
|
| 21 |
+
# Check for required dependencies
|
| 22 |
+
try:
|
| 23 |
+
import pandas
|
| 24 |
+
print("β
Dependencies OK")
|
| 25 |
+
except ImportError:
|
| 26 |
+
print("π¦ Installing pandas...")
|
| 27 |
+
subprocess.run([sys.executable, "-m", "pip", "install", "pandas"])
|
| 28 |
+
|
| 29 |
+
# Generate website
|
| 30 |
+
print("ποΈ Generating website...")
|
| 31 |
+
try:
|
| 32 |
+
# Run the website.py script directly
|
| 33 |
+
result = subprocess.run([
|
| 34 |
+
sys.executable, ".github/workflows/website.py"
|
| 35 |
+
], capture_output=True, text=True)
|
| 36 |
+
|
| 37 |
+
if result.returncode == 0:
|
| 38 |
+
print("β
Website generated successfully")
|
| 39 |
+
if result.stdout:
|
| 40 |
+
print(result.stdout)
|
| 41 |
+
else:
|
| 42 |
+
print(f"β Error generating website:")
|
| 43 |
+
print(result.stderr)
|
| 44 |
+
sys.exit(1)
|
| 45 |
+
except Exception as e:
|
| 46 |
+
print(f"β Error running website generator: {e}")
|
| 47 |
+
sys.exit(1)
|
| 48 |
+
|
| 49 |
+
# Start server
|
| 50 |
+
print("π Starting development server...")
|
| 51 |
+
print("π± Website will open at: http://localhost:8000")
|
| 52 |
+
print("π Press Ctrl+C to stop the server")
|
| 53 |
+
print("-" * 60)
|
| 54 |
+
|
| 55 |
+
try:
|
| 56 |
+
# Open browser
|
| 57 |
+
webbrowser.open("http://localhost:8000")
|
| 58 |
+
|
| 59 |
+
# Start server
|
| 60 |
+
subprocess.run([
|
| 61 |
+
sys.executable, "-m", "http.server", "8000"
|
| 62 |
+
])
|
| 63 |
+
except KeyboardInterrupt:
|
| 64 |
+
print("\nπ Development server stopped")
|
| 65 |
+
|
| 66 |
+
if __name__ == "__main__":
|
| 67 |
+
main()
|
scripts/test-workflows.sh
ADDED
|
@@ -0,0 +1,71 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/bin/bash
|
| 2 |
+
|
| 3 |
+
echo "π§ͺ Testing GitHub Actions workflows locally"
|
| 4 |
+
echo "========================================"
|
| 5 |
+
|
| 6 |
+
echo ""
|
| 7 |
+
echo "1. Testing website generation..."
|
| 8 |
+
python .github/workflows/website.py
|
| 9 |
+
|
| 10 |
+
if [ $? -eq 0 ]; then
|
| 11 |
+
echo "β
Website generation: PASSED"
|
| 12 |
+
else
|
| 13 |
+
echo "β Website generation: FAILED"
|
| 14 |
+
exit 1
|
| 15 |
+
fi
|
| 16 |
+
|
| 17 |
+
echo ""
|
| 18 |
+
echo "2. Testing link checker (if lychee is installed)..."
|
| 19 |
+
if command -v lychee &> /dev/null; then
|
| 20 |
+
lychee --verbose --no-progress --exclude-mail README.md
|
| 21 |
+
if [ $? -eq 0 ]; then
|
| 22 |
+
echo "β
Link check: PASSED"
|
| 23 |
+
else
|
| 24 |
+
echo "β οΈ Link check: SOME BROKEN LINKS FOUND"
|
| 25 |
+
fi
|
| 26 |
+
else
|
| 27 |
+
echo "β οΈ lychee not installed. Install with: brew install lychee"
|
| 28 |
+
fi
|
| 29 |
+
|
| 30 |
+
echo ""
|
| 31 |
+
echo "3. Checking table format..."
|
| 32 |
+
python -c "
|
| 33 |
+
import re
|
| 34 |
+
with open('README.md', 'r') as f:
|
| 35 |
+
content = f.read()
|
| 36 |
+
|
| 37 |
+
# Count table rows in Projects section
|
| 38 |
+
in_projects = False
|
| 39 |
+
table_rows = []
|
| 40 |
+
for line in content.split('\n'):
|
| 41 |
+
if line.strip() == '### Projects':
|
| 42 |
+
in_projects = True
|
| 43 |
+
continue
|
| 44 |
+
if in_projects and line.startswith('### ') and 'Projects' not in line:
|
| 45 |
+
break
|
| 46 |
+
if in_projects and len(re.findall(r'\|', line)) == 8:
|
| 47 |
+
table_rows.append(line)
|
| 48 |
+
|
| 49 |
+
print(f'Found {len(table_rows)} table rows')
|
| 50 |
+
if len(table_rows) > 2:
|
| 51 |
+
print('β
Table format: PASSED')
|
| 52 |
+
else:
|
| 53 |
+
print('β Table format: FAILED')
|
| 54 |
+
exit(1)
|
| 55 |
+
"
|
| 56 |
+
|
| 57 |
+
if [ $? -eq 0 ]; then
|
| 58 |
+
echo "β
Table format: PASSED"
|
| 59 |
+
else
|
| 60 |
+
echo "β Table format: FAILED"
|
| 61 |
+
exit 1
|
| 62 |
+
fi
|
| 63 |
+
|
| 64 |
+
echo ""
|
| 65 |
+
echo "π All tests passed! Your changes are ready for PR."
|
| 66 |
+
echo ""
|
| 67 |
+
echo "Next steps:"
|
| 68 |
+
echo "1. Commit your changes: git add . && git commit -m 'Add new paper'"
|
| 69 |
+
echo "2. Push to your fork: git push origin your-branch-name"
|
| 70 |
+
echo "3. Create a pull request on GitHub"
|
| 71 |
+
echo "4. Wait for automatic preview to be generated"
|