* bump example notebooks branch
* add ipykernel to env
* roll back to fixing septop branch
* i dont think we want ipykernel
* bump to tmp_fix_docs branch
* point to branch revert-237-v1.7_cookbooks
* point to latest example notebooks release
* 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
* fix nb link
* bump examplenotebooks version
* add dark mode option back in
* temporary pin to working ofe theme branch
* remove unused code
* bump ci
* bump ofe-sphinx-theme pin
* 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>
* SepTop docs improvements lambda schedule and restraint selection
* Remove set_openmm_threads_1 logic from test_septop_slow
* change femto acknowledgements
* update method docstring limitations
* Make sure we fail when we have virtual sites and reassign_velocities is False
* clean up usage of openmm imports
* clean up equil settings output indices so that it enforces all
* generate smc_off_B on the fly
* Update enforcement of all output indices
* Simulation overview unclear on if the same restraint is used between repeats
* Add test for output indices validation
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* 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
* updating pins
* remove min 8.2 pin
* pin example notebooks version
* update branch
* a comma
* min of 8.1.1
* add comment about pydantic min
* adding comment for openff-units pin
* updating openmm pin
* draft for Konnektor integration
* changing back to mappers iterable as parameter
* consistently using Konnektor also in loading fep or orion net
* adding handles for Konnektor functionality.
* used black for formatting.
* Update test_network_planning.py
fix for tests
* fixes for unittests:
- fix removing the central ligand from list.
* Update test_network_planning.py
remove test for testing if a central component is part of the other component list. This can not happen anymore with the current Konnektor implementation, therefore I propose removing the test.
* updating docstrings
* adjusting n_processes docstring language
* fixing central_ligand default
* rename mappers to mapper to avoid api break
* Revert "rename mappers to mapper to avoid api break"
This reverts commit bf82085d7a86be63d2eaca11e105261107229ecc.
* fixing mapper/s to avoid api break
* switching arg names from 'ligands' to new 'components' keyword to match konnektor
* reverting ordering change
* fixing docstring
* pull konnektor from main for development only
* mapper back to mappers to avoid api break
* clean up
* formatting
* mapper->mappers
* fixing call to network_from_indices
* update radial network test scorer to return between 0 and 1
* organizing tests into classes
* expect only one mapping per edge for maximal networks
* adding TODOs
* adding TODOs for later
* update index error string to match konnektor's clarity improvement
* updating pytest.raises to look for RuntimeError instead of ValueError
* adding TODO
* making unreachable test clearer
* fixing regex AGAIN
* some light formatting
* cleaning up diff
* central_ligand -> central component for msg regex
* regex
* updating regexes to match new konnektor behavior
* formatting :(
* formatting :(
* add connectedness check
* updating TODO
* fix comment
* update progress bar docstring
* fix ambiguous var name
* remove unused imports
* fix mypy checks
* remove unused testing code
* pin konnektor to 0.2
* remove completed TODOs
* add konnektor to docs env
* remove completed TODO
* updating news
* clarifying process and progress additions in news
---------
Co-authored-by: Alyssa Travitz <atravitz@umich.edu>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* updates to cli from_json
* replacing dump instances with to_json
* Remove unnecessary imports of JSON_HANDLER
* addressing review
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: David L. Dotson <dotsdl@gmail.com>
