v2.1.9

AlphaPulldown v2.1.9

🧬 Major fixes

• Fix: normalized asym_id handling

  • always return normalized asym_id feature copy
  • fixes incorrect chain IDs in AF2 multimer outputs
  • ensures consistent chain/entity mapping in PDB and ModelCIF outputs

---

🧪 AlphaFold3 / multimer support

• Added proper support for copy numbers in AF3 homooligomers

  • correct handling of copy notation (protein:N)
  • correct mapping between input copies and internal chain indices

---

⚙️ Backend / architecture

• backend is now always initialized explicitly

• introduced lazy backend manager

  • avoids importing AF2/AF3 dependencies at import time

• enforced rule: no direct backend imports outside backend manager

👉 result: lighter CLI startup, fewer import-time crashes, cleaner backend isolation

---

📦 Dependencies & packaging

• pinned setuptools < 82
• additional pin for pdbfixer compatibility during relaxation
• updated setuptools constraints in pyproject.toml
• switched to ap-parser 0.3.0

---

🧱 CI / containers

• removed heavy JAX installation on CPU-only environments

  • avoids installing unusable GPU builds
  • reduces environment size and install failures

• disabled AlphaLink container build job

• excluded backend-specific tests from AF2/AF3/AL2/CF builds

---

📚 Documentation

• updated README:

  • version numbers
  • SLURM setup instructions
  • general cleanup and fixes

---

⚠️ user-visible changes

• multimer chain IDs may differ vs 2.1.8 due to corrected asym_id normalization
• AF3 homooligomer jobs now correctly respect copy number
• lighter installation and fewer dependency conflicts
• fewer backend-related import errors

---

🧠 Summary

v2.1.9 is a correctness + stability release with two functional improvements:

• fixes chain identity (asym_id)
• adds proper AF3 homooligomer copy support