* Modify quickrun to allow resuming
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* store protocol dag using transformation key
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* this reference instead?
* fix things a little bit
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* update for new name for now
* Update docs/guide/cli/quickrun.rst
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* update for new changes
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* split off cron test into its own test
* add feedstock build test for release prep
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* add check for protocol_dag.json
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* clearer language, hopefully
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* tmpdir -> tmp_path
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* Add comment
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* add news item
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* Safely close reporter and clear GPU contexts to avoid UnboundLocalErrors
Added try/except block to safely close things in case there's an unbound variable.
* small fix
small fix
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---------
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* add boilerplate
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updates:
- [github.com/tox-dev/pyproject-fmt: v2.8.0 → v2.11.1](https://github.com/tox-dev/pyproject-fmt/compare/v2.8.0...v2.11.1)
- [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.3...v0.14.10)
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* Disable NAGL as a partial charge backend when OEToolkit is installed but not chosen as the registry backend. (#1762)
* NAGL can no longer be used with oechem installed if you are using the rdkit backend.
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* rename openfecli fixture to avoid duplication with openfe fixture (#1755)
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* Fix issue 1795 (#1796)
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* remove mypy rdkit pin (#1753)
* remove mypy rdkit pin
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This reverts commit 00cc2a3729.
* disallow attr-defined error code
* try globally disabling attr-defined
* try specific override
* per-line ignores
* Make the multistate hybrid topology samplers not require the HybridTopologyFactory (#1768)
* make hybrid samplers not rely on htf but instead on the system & positions.
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* Move rfe protocol (#1769)
Move RFE protocol files around
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---------
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* Have two separate system generators for state A & B in hybrid protocol (#1772)
Make it so that the states A and B are generated using two different SystemGenerator objects, allowing for partial charge transformations.
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* :
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---------
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* update docs for multiple protocol units (#1793)
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* Small improvement in RelativeHybridTopologyProtocol docstring (#1797)
Updated class docstring to clarify the use of Hybrid Topology scheme.
* turn off zenodo retry (#1802)
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* remove retry_if_failed arg
* only run CI on macos python 3.12 (#1803)
* Turn AFE protocols into multiple units (#1776)
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* move to src layout (#1805)
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* Temporarily build pooch from main w/ hotfix (#1806)
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---------
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* make CLI starting guide easier to find from the landing page
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* change a word
* clarifying language
