remove to_rbfe_alchemical_network

[atravitz]

in v1.12, we announced this would be released in v1.13 - that's now!

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LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no
If yes, please provide details here:

Checklist

• Added a news entry
• Filled in the AI-generated code disclosure.

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• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.64%. Comparing base (46a3977) to head (8822582).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #819      +/-   ##
==========================================
- Coverage   98.65%   98.64%   -0.02%     
==========================================
  Files          43       43              
  Lines        2825     2797      -28     
==========================================
- Hits         2787     2759      -28     
  Misses         38       38              

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[github-actions]

🚨 API breaking changes detected! 🚨

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Griffe output

$ griffe check "gufe" -s src --no-inspection --no-color --verbose -a origin/main
src/gufe/ligandnetwork.py:0: LigandNetwork.to_rbfe_alchemical_network:
Public object was removed

src/gufe/tests/test_ligand_network.py:0: TestLigandNetwork.test_to_rbfe_alchemical_network:
Public object was removed

src/gufe/tests/test_ligand_network.py:0: TestLigandNetwork.test_to_rbfe_alchemical_network_autoname_false:
Public object was removed

src/gufe/tests/test_ligand_network.py:0: TestLigandNetwork.test_to_rbfe_alchemical_network_autoname_true:
Public object was removed

src/gufe/tests/test_ligand_network.py:0: TestLigandNetwork.test_to_rhfe_alchemical_network:
Public object was removed

[atravitz]

re: griffe failure - this is the api break we are doing intentionally.

[IAlibay]

This looks good - we'll need to remove / fix some of the cookbook docs too. For example, the create_alchemical_network cookbook uses this API point.

[atravitz]

This looks good - we'll need to remove / fix some of the cookbook docs too. For example, the create_alchemical_network cookbook uses this API point.

yes! tracked here OpenFreeEnergy/ExampleNotebooks#291