feat: getting abfe working

[sg-s]

No description provided.

[Copilot]

Pull request overview

This pull request enables ABFE (Absolute Binding Free Energy) functionality by simplifying tests, updating mock server settings, adding fixture files, and adjusting default padding parameters.

Key changes:

• Simplified the test_sysprep_lv2 test to use the Complex.prepare() method directly
• Reduced default ABFE mock server duration from 300s to 30s for faster testing
• Changed default padding parameter from 1.5/2.0 to 1.0 across functions
• Added new ABFE tutorial notebook and multiple ligand fixture files

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_functions.py	Simplified sysprep test to use Complex.prepare() instead of direct function calls
tests/run_mock_server.py	Reduced default ABFE execution duration from 300s to 30s
tests/fixtures/tool-runs/ABFE/.../results.csv	Removed ABFE results CSV fixture file
tests/fixtures/function-runs/deeporigin.system-prep/...json	Updated system-prep fixture with reorganized JSON structure
tests/fixtures/files/entities/ligands/*.sdf	Added 7 new ligand SDF fixture files
tests/fixtures/executions/abfe9819-4204-474e-af9f-c92a7f20a9cc.json	Updated ABFE execution fixture with reorganized JSON
tests/fixtures/deeporigin.abfe-end-to-end/quotation-result.json	Updated quotation result fixture with reorganized JSON
tests/fixtures/deeporigin.abfe-end-to-end/billing-transaction.json	Updated billing transaction fixture with reorganized JSON
src/functions/sysprep.py	Changed default padding parameter from 1.5 to 1.0
src/drug_discovery/complex.py	Changed default padding parameter from 2.0 to 1.0
scripts/build_docs.sh	Added --abfe-duration 5 flag to mock server startup
docs/notebooks/clean/docking-many-ligands.ipynb	Removed unnecessary version check code
docs/notebooks/clean/abfe.ipynb	Added new ABFE workflow tutorial notebook
docs/dev/job-widget.md	Removed redundant example from documentation

Comments suppressed due to low confidence (2)

tests/fixtures/function-runs/deeporigin.system-prep/d18cb57f070ce5eab0d0adc52c3b68fddc48def2b3bd29767e416b260ed94fc7.json:146

• The padding value in userInputs.inputs is 1.5, but the padding value in functionOutputs.parameters is 2. These should be consistent, as the function output parameters should reflect the actual inputs used for the function run.
  tests/fixtures/function-runs/deeporigin.system-prep/d18cb57f070ce5eab0d0adc52c3b68fddc48def2b3bd29767e416b260ed94fc7.json:149
• The add_H_atoms value in userInputs.inputs is true, but the add_H_atoms value in functionOutputs.parameters is false. Similarly, protonate_protein differs (true vs false). These inconsistencies suggest that the function output doesn't accurately reflect the input parameters used.

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