Dima Molodenskiy
1d940d0b6a
docs: point Snakemake install docs at 2.5.0
...
Update AlphaPulldown README snippets to deploy AlphaPulldownSnakemake 2.5.0
and align the shared input-parser dependency with the public 0.5.0 parser API.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com >
2026-05-26 16:22:27 +02:00
Dima Molodenskiy
4577f56b2f
docs: point Snakemake deploy tag and env file to release 2.4.0
...
Update the snakedeploy --tag and the alphapulldown.yaml env URL from 2.1.8 to
the new 2.4.0 release.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com >
2026-05-21 10:32:36 +02:00
Dima Molodenskiy
4c3e83ce78
docs: sync structure-inference SLURM options with AlphaPulldownSnakemake
...
Mirror the expanded "SLURM defaults for structure inference" section from
AlphaPulldownSnakemake: add slurm_exclude_nodes and structure_inference_max_runtime
to the config example, and document GPU node exclusion / runtime cap and the
unified-memory options (structure_inference_unified_memory +
structure_inference_xla_mem_fraction, now defaulting to "auto" = host RAM / GPU VRAM).
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com >
2026-05-21 10:32:36 +02:00
Dima Molodenskiy
716c061230
Fix mocked precomputed MMseq A3M in integration test
2026-04-23 10:28:45 +02:00
Dima Molodenskiy
cdd5fb57bf
Align AF2 cluster tests with safer GPU defaults
2026-04-23 10:28:45 +02:00
Dima Molodenskiy
fb09717cf3
Harden precomputed MSA identifier enrichment
2026-04-23 10:28:45 +02:00
Dima Molodenskiy
ce4be4866b
Handle tuple-shaped AF2 prediction results
2026-04-23 10:28:45 +02:00
Dima Molodenskiy
ba2f6f09f5
Bump 2.4.0
2026-04-15 12:24:30 +02:00
Dima Molodenskiy
3e74e3551c
Make sure random seed is integer
2026-04-13 16:17:01 +02:00
Dima Molodenskiy
3d51beb2ec
Default threshold, better colors, flag to show best n complexesk
2026-04-13 13:43:49 +02:00
Dima
99a806fd31
Trim release-only AF3 trimer test scaffolding
2026-04-10 20:10:15 +02:00
Dima
7d18ea8ab2
Compare AF2 trimer translation with native AF3 pairing
2026-04-10 20:10:15 +02:00
Dima
7a8afc7c7a
Handle grouped identical chains in AF3 trimer test
2026-04-10 20:10:15 +02:00
Dima
f7176e87af
Force cluster AF3 tests to use checkout code
2026-04-10 20:10:15 +02:00
Dima
609fecb3cd
Add AF3 trimer cluster smoke test
2026-04-10 20:10:15 +02:00
Dima
0f081a4b02
Tighten AF3 trimer pairing summary
2026-04-10 20:10:15 +02:00
Dima
2c715001a9
fix( #42 ): add RF annotation to skip-MSA stockholm
2026-04-10 15:57:14 +02:00
Dima
392d3f7ec2
fix( #42 ): avoid AF2 bulk-db checks in skip-MSA mode
2026-04-10 15:57:14 +02:00
Dima
0f1f0c2cab
fix: address skip-MSA review edge cases
2026-04-10 15:57:14 +02:00
Dima
49db627f23
docs( #42 ): document the skip-MSA flag
2026-04-10 15:57:14 +02:00
Dima
3dfd6d8aad
fix( #42 ): add skip-MSA feature generation mode
2026-04-10 15:57:14 +02:00
Dima
098792fa21
[codex] Reuse existing monomer features in default TrueMultimer mode ( #609 )
...
* fix(#465 ): reuse existing monomer features in truemultimer
* fix(#465 ): validate reused truemultimer source sequences
2026-04-09 16:48:15 +02:00
Dima
0b09aa1cca
fix( #332 ): support custom templates with mmseqs2
2026-04-09 16:28:23 +02:00
Dima
39409d9387
fix: add distogram fallback for older af2plots
2026-04-09 15:55:50 +02:00
Dima
d668a3342b
fix: handle compressed diagnostics inputs and AP-style homo jobs
2026-04-09 15:55:50 +02:00
Dima
4e91d4e7bc
feat( #141 ): add interaction network plotting
2026-04-09 15:55:50 +02:00
Dima
0bd4d4771e
feat(#256,#258): add diagnostics plotting script
2026-04-09 15:55:50 +02:00
Dima
40c68b5738
feat( #336 ): add AlphaFold Server JSON exporter
2026-04-09 15:55:50 +02:00
Dima
fc9c93860f
fix( #463 ): match quick templates to chopped objects
2026-04-09 15:55:50 +02:00
Dima
1aaa473d67
fix( #471 ): preserve duplicate quick-template entries
2026-04-09 15:55:50 +02:00
Dima
12476a55c2
fix( #456 ): gate best-model relaxation by score
2026-04-09 15:55:50 +02:00
Dima
4f173d9aec
fix( #464 ): support template filters in quick multimer mode
2026-04-09 15:55:50 +02:00
Dima
34c04d1ade
fix( #293 ): skip full-db paths for reduced_dbs
2026-04-09 15:55:50 +02:00
Dima
894c4aa355
fix( #459 ): explain TrueMultimer template code logs
2026-04-09 15:55:50 +02:00
Dima
39309b2c67
i)AF3 rejects --use_mmseqs2 ii)more deterministic identification of a molecule type from FASTA iii)AF3 failures raises RuntimeError instead of Exception
2026-04-09 13:45:39 +02:00
Dima
6120be9500
Fix #602
2026-04-09 13:29:32 +02:00
Dima
74f2df62a7
cache species ids when using mmseqs2 features with precomputed MSAs
2026-04-08 18:09:16 +02:00
Dima Molodenskiy
0de121ea5e
Bump 2.3.0
2026-04-08 10:05:42 +02:00
Dima
fff63051b4
Tests ( #600 )
...
* 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
9bd18ce9b2
Keep testing instructions only in wiki
2026-03-27 16:24:08 +01:00
Dima
00aec3456f
Add CPU unit coverage for AlphaFold3 backend helpers
2026-03-27 15:57:10 +01:00
Dima
a941becec3
Publish HTML coverage reports via GitHub Pages
2026-03-27 15:57:10 +01:00
Dima
db61670129
Expand unit coverage for objects.py edge cases
2026-03-27 15:57:10 +01:00
Dima
090fb0b026
Expand unit coverage for template and post-processing helpers
2026-03-27 15:57:10 +01:00
Dima
3e6fc368cd
New.
2026-03-27 15:57:10 +01:00
Dima
cbfaf51b0e
New.
2026-03-27 15:57:10 +01:00
Dima
74d0e1cfaf
Expand unit coverage for helper and backend manager utilities
2026-03-27 15:57:10 +01:00
Dima
d78a93ff37
Fix function coverage checker def-line false positives
2026-03-27 15:57:10 +01:00
Dima
407764479b
New
2026-03-27 15:57:10 +01:00
Dima
7fd121f842
Reorganize tests for CPU coverage CI
2026-03-27 15:57:10 +01:00
