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Move partial charge CLI to how-to guides - #2347

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hannahbaumann wants to merge 5 commits into
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hannahbaumann wants to merge 5 commits into
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docs/howto-cli-charge

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@hannahbaumann

@hannahbaumann hannahbaumann commented Nov 10, 2026 •

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This PR is related to this PR in ExampleNotebooks: OpenFreeEnergy/ExampleNotebooks#361.
As discussed, here we're moving the CLI charge molecules to the how-to guides.

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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:

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  • Yes: [If yes, please provide details here]

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  • Read the AI Policy and filled in the AI-generated code disclosure.
  • Adhered to the contribution guidelines
  • All new code is appropriately documented (user-facing code must have complete docstrings).
  • Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.
  • Added a news entry, or the changes are not user-facing.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

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@hannahbaumann
hannahbaumann marked this pull request as ready for review November 10, 2026 12:18
Comment thread docs/conf.py
repo = git.Repo.clone_from(
"https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
branch="main",
branch="move_cli_charge_howto",

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Suggested change
branch="move_cli_charge_howto",
branch="main",

(just a reminder to update this before merging)

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Move the generating partial charges with the CLI from tutorials to How-to

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