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

.coveragerc

@@ -4,7 +4,8 @@ source =
     alphapulldown
 omit =
     alphapulldown/__init__.py
-    alphapulldown/analysis_pipeline/af2plots/*
+    alphapulldown/analysis_pipeline/*
+    alphapulldown/folding_backend/alphalink_backend.py
 
 [report]
 skip_empty = True