Dima
fff63051b4
Tests ( #600 )
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* Harden MMseqs species ID resolution fallback
* Reorganize tests for CPU coverage CI
* New
* Fix function coverage checker def-line false positives
* Expand unit coverage for helper and backend manager utilities
* New.
* New.
* Expand unit coverage for template and post-processing helpers
* Expand unit coverage for objects.py edge cases
* Publish HTML coverage reports via GitHub Pages
* Add CPU unit coverage for AlphaFold3 backend helpers
* Reorganize tests and expand backend coverage
* Reset shared test flags between cases
* Expand AF3 prepare_input unit coverage
* Cover AF3 and truemultimer feature creation
* Test AF3 multimer MSA translation paths
* Cover AF3 duplicate-residue multimer fallback
* Cover AF2 resume and postprocess edge paths
* Cover AF3 template mmCIF preparation
* Test small script entry points
* Expand workflow and ModelCIF test coverage
* Add backend extras and install guide
* Clarify AF3 backend installation path
* Stabilize cluster GPU test runners
* Document AF3 CMake SQLite hints
* Simplify backend installation guide
* Align AF3 install with working cluster env
* Backfill typing dataclass_transform for AF2
* Pin TensorFlow for cluster installs
* Fallback AF2 relax when CUDA OpenMM is unavailable
* Raise AF3 default minimum bucket size
* Simplify backend cluster installation guide
* Fix AF3 wrapper JSON output isolation
* Fix AF3 JSON wrapper outputs and MMseqs ID parsing
* Fix CI entrypoint stub and Python 3.8 typing
* Document release readiness test gates
2026-04-01 14:13:35 +02:00
Dima
a181956cf2
ignore SSL certificate validation
2026-03-19 15:28:28 +01:00
Dima
e58fa46c9d
setuptools<82 for pdbfixer at relaxation
2026-02-25 13:05:32 +01:00
Dima
4dfa6613cf
Resolve issue with hash mismatches
2026-02-10 11:47:03 +01:00
Dima
a0c731690e
Remove conda, build dev-requirements.txt on-the-fly
2026-01-08 12:18:37 +01:00
Dima
69af382af0
Force numpy<2 installation
2026-01-08 12:17:07 +01:00
Dima
7cd4a2e73f
Fix formatting of alphapulldown_input_parser installation
2025-11-13 15:34:21 +01:00
Dima
25c7ebcd07
Add alphapulldown_input_parser to AF3 Dockerfile
2025-11-13 15:01:36 +01:00
Dima
8336829041
Fix typing_extensions=4.14.0 and reduce image size by 5GB
2025-11-07 10:22:40 +01:00
Dima
94f0e4ac35
Fix and trim to 11.7 GB
2025-10-28 14:15:22 +01:00
Copilot
d0216854d8
Remove redundant CUDA toolchain from alphalink.dockerfile and consolidate environment settings ( #537 )
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* Initial plan
* Update alphalink.dockerfile to fix Uni-Core build and optimize image
Co-authored-by: DimaMolod <33123184+DimaMolod@users.noreply.github.com >
---------
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com >
Co-authored-by: DimaMolod <33123184+DimaMolod@users.noreply.github.com >
2025-10-27 14:39:08 +01:00
Dima
215dedac6c
Rename docker files; Make alphalink image smaller
2025-10-09 12:33:24 +02:00
Dima
ff2d7d736c
Rename pulldown to alphafold2
2025-10-08 14:42:15 +02:00
Dima
fc41c1a5eb
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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- Strip _entity_poly_seq from generated template mmCIF so AF3 reconstructs _pdbx_poly_seq_scheme from _atom_site, avoiding UNK/gap mismatches
- Build query_to_template_map using only residues with atoms to prevent OOB indexing in template features
- Add --debug_templates flag to optionally dump generated template mmCIFs into templates_debug/
- Keep templates enabled; test test__chopped_dimer now passes
2025-08-12 14:04:33 +02:00
Dima
712bb76b1c
simplify XLA flags, unified_memory=1
2025-06-26 13:03:51 +02:00
Dima
a9ff96e23e
Update env vars for GPU, activate conda env by default
2025-06-25 15:07:13 +02:00
Dima
751d794c35
--solver is no longer supported by mamba
...
as it integrated directly into conda
2025-05-06 08:56:22 +02:00
Dima
df426c4c3b
Install from git rather than make a local copy
2025-04-22 12:35:47 +02:00
Dima
2a0cf896fd
update jax
2025-04-22 10:15:17 +02:00
Dima
ecdfe7e0d2
pass CMAKE_CXX_STANDAR=17
2025-01-27 20:00:08 +01:00
Dima
09421df38f
update alphafold.model.model
2025-01-27 18:12:42 +01:00
Dima
38fc03d770
External deps are solved, but alphafold3 structure has changed
2025-01-27 16:55:01 +01:00
Dima
d2966dbd5f
Added ml_collections
2025-01-24 15:59:37 +01:00
Dima
5e058eb7ae
Added appdirs for colabfold
2025-01-24 14:37:44 +01:00
Dima
f75a552821
Easier requerements to biopython
2025-01-24 13:55:46 +01:00
Dima
b7d9309580
install missing deps
2025-01-24 13:45:36 +01:00
Dima Molodenskiy
95a907f331
debug: where is alphafold3?
2025-01-22 16:34:17 +01:00
Dima
5976bfbfa5
build af3 dependencies on top of AP
2025-01-22 15:11:07 +01:00
Dima Molodenskiy
1cf7c81987
Build alphafold3 container
2025-01-22 10:04:54 +01:00
Dima Molodenskiy
af8d7a2879
New
2024-11-21 12:56:22 +01:00
Dima
385e72bb20
don't use editable installations for ci/cd. revert to setup.py
2024-11-05 16:29:21 +01:00
Dima Molodenskiy
a282ff8fbb
revert for now
2024-10-30 17:38:15 +01:00
Dima Molodenskiy
c1e1ade3ea
install submodules automatically
2024-10-30 15:12:43 +01:00
Dima Molodenskiy
f8b8e64e6d
simplify
2024-10-30 14:44:56 +01:00
Dima
f52ba4ca61
Update pulldown.dockerfile
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multiple updates
2024-10-30 13:50:29 +01:00
Dima
f5c2295dd4
add github to knownhosts and pass ssh key
2024-10-11 15:56:27 +02:00
Dima
f7abf52100
Update github_actions.yml ( #416 )
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* use advanced syntax for pip install with ssh
2024-10-11 15:35:03 +02:00
Dima
21f6d0d8a2
Update pulldown.dockerfile
2024-10-11 11:58:22 +02:00
Dima Molodenskiy
56cda1430c
Rm ccp4
2024-10-11 10:39:00 +02:00
Dima Molodenskiy
5a88e1ebb2
Remove cctbx from dependencies
2024-10-02 14:38:40 +02:00
Dima Molodenskiy
2b7c334bc2
Create hard-coded temp dir for pi_score
2024-09-25 09:57:05 +02:00
Dima
a7f6506a21
Fix: use relative path. Use image from kosinskilab
2024-08-05 13:24:27 +02:00
Dima
4dcef6c52e
Fix syntax error
2024-08-05 10:40:40 +02:00
Dima Molodenskiy
e4ab9ccfd2
Install hmmer from conda. Use miniforge instead of miniconda
2024-08-05 10:15:23 +02:00
Dima
f0e12dc659
Install modelcif for pulldown.dockerfile
2024-07-23 11:08:13 +02:00
Dingquan Yu
baed41fa26
Update pulldown.dockerfile
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switched the installation order
2024-07-02 14:35:21 +02:00
maurerv
4c9ef32876
Moved to classic solver
2024-06-14 13:40:12 +02:00
maurerv
f78da683ab
Moved to classic solver
2024-06-14 11:30:53 +02:00
Dingquan Yu
30bfc6d283
Update pulldown.dockerfile
2024-06-12 13:50:34 +02:00
Dingquan Yu
2c42567b2f
Update pulldown.dockerfile
2024-06-12 13:43:38 +02:00
