* add more checks
* make precommit manual
* apply formatting to pyproject.toml
* add TODO
* remove unneeded, add a few more
* add ruff, but turn everything off
* add openfe known first party
* format highest-level files
* first half of openfe protocols
* second half of openfe protocols
* openfe protocols formatting, with alyssa's fmt skips
* add ruff formatter to precommit
* fmt: off all vendored _rfe_utils code
* addressing review comments
* Disable user supplied host & guest atoms in restraint settings
* disable validator
* Fix some tests
* Store selection indices
* Add partial test
* Update serialized results
* try to make mypy happy
* Update equil_septop_method.py
* update partial charge tests now that a production NAGL model is available (#1506)
* update tests now that a production NAGL model is available
* fix mock
* clean up mocking
* add nagl test news item
* debug slow python 3.13 tests (#1468)
* Turn off minimization when we do a dry run
---------
Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>
* update quickrun execution docs and add MPS link (#1483)
* add jq cookbook (#1488)
* add jq code blocks
* use tutorial data
* news
* debug docs build (#1489)
* don't build openmm
* mambaforge->miniconda for rtd
* artifically small build for debugging
* dont build env
* just build python
* add channels
* add sphinx packages to env
* add all non-openfe-ecosystem deps
* remove shim channel
* add openfe package
* add everything except openmm and toolkit
* add openmm
* add openff-toolkit
* only openff-toolkit
* try openff-toolkit-base
* try latest openff
* everybody back in
* build without openmm
* build with openff-toolkit-base
* bump rtd
* add pip build
* remove any openff-toolkit
* build w/o openmm
* add pip install
* build everything without pip install
* try no deps
* try custom build
* only python and pip
* try openfe-toolkit-base
* add temp deps for build with openff-toolkit-base
* add temp deps for build with openff-toolkit-base
* mock imports
* dont mock with toolkit base
* bump toolkit version
* Revert "bump toolkit version"
This reverts commit 6e3108a836.
* add mocks
* try pinnint to toolkit-base 0.13.0, no mocks
* back to >= 0.13.0 toolkit to make sure it wasn't a fluke
* mock imports
* add pipe example for jq (#1505)
* add pipe example for jq
* pin to docutil 0.20
* try to avoid memory error
* debug rtd build memory error (#1510)
* try mambaforge build
* Revert "try mambaforge build"
This reverts commit 683e07f1ea.
* try explicit build
* try removing ambertools
* use the right env
* just add gufe pip install back
* add back openfe eco packages
* mock py3dmol
* add note for pip installs
* fix quote
* temporarily resort to SettingsBaseModel to get build
* specific imports
* dont use base settings placeholder
* temp pin numpy (#1542)
* Removing unnecessary limit on resids (#1539)
* Removing unnecessary limit on resids indices gathering
* Updated CHANGELOG for 1.6.1
* add summary
* update docs theme (#1545)
* adding new branding assets
* remove images
* update theme branch
* CantinaPurple accent
* lowercase convention
* updating text
* remove dark mode for now
* fix sidebars
* fix formatting
* capitalization
* don't break spaces
* bump ci
* favicon!
* whitespace :(
* pin to sphinx release
* pin to gufe 1.6.1
* move env info before test imports
* bump single file installer to 3.12.11 to match colab
---------
Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
* Install numpy 2, openmm 8.2
* import openff-models from gufe
* update installer to use our dev build
* match google colab
* match what we are doing on main
* add news blurb
* debug script for people to test openmm
* Added news entry
* added checking which platforms can do mixed p
* fix typo in debug script
* added how to run script
* point to new showcase
* give full path to assests to avoid copying notebooking into build env
* rerun ci
* fix mypy env
* looks like we still need to pin mypy but can relax python
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* update rbfe_results.tar.gz for new settings schema
* re-enable test_gather tests
* devscript for updating rbfe_results.tar.gz
* cli: gather: rework raw gather to work off protocol_result dict
this allows us to later deduplicate and remove the unit_results key from results dicts
* cli: gather: update expected gather results
current raw results are only one replicate, should probably have multiple repeats to test raw output
* cli: gather: use \t escape code in gather raw test
could instead normalise the whitespace to be more permissive...
* Apply suggestions from code review
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* rerun ci
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* see if this can push to ghcr
* fix URI
* don't push docker image
* don't push docker image
* see if this lets us login to ghcr
* we can push to github's container registry directly
* now when we trigger a build, we build the latest version we can discover from the tags
* forgot to remove bit where we install package from source
* use docker ignore to make sure we keep the context as small as we can
* make it explicit we don't push before we test, and make sure we have the same build args for when we do push
* add juypterlab and notebook to docker image
* Apply suggestions from code review
