* top directory level
* top level utils
* format tests/utils
* format tests/storage
* format tests/setup
* format top-level tests/protocols
* format tests/protocols/restraints
* format tests/protocols/openmm_septop
* format tests/protocols/openmm_rfe
* format tests/protocols/openmm_abfe
* format tests/protocols/openmm_ahfe
* format tests/protocols/openmm_md
* precommit
* remove openfe/tests/dev from exclude
* remove openfe/tests/data from exclude
* 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
* format openfe/utils
* format openfe/setup
* first batch of cli formatting
* second batch of cli formatting
* formatting the rest of openfecli commands
* format openfecli/parameters
* format openfe/storage
* run precommit
* Update openfecli/commands/gather.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* update example notebooks branch for v1.7.0 docs changes (#1615)
* 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
* remove colab button, point to updated example notebooks, reorg landing page (#1618)
* remove colab button from example notebooks in docs
* point to example notebooks 2025.10.2
* replace 'try' with CLI
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* 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
* Let's use python 3.12 on the docker image
* try installing the rdkit version I want to test
* free up diskspace
* include source
* Apply suggestion from @atravitz
* fix indent
---------
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* 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
* min python 3.10
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* 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
* escape string correctly
* Fix test to check if string is printed
This test used to use pytest.warns to check if we printed a string to
the terminal. This isn't the right way to test if things get printed to
terminal since it only checks warnings raised in python-land. The test
passed since the regex used to match warnings ended up matching warnings
raised since it was a negated character class which matches a single
character that is not any of the characters listed inside.
* 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
* install espaloma on long tests
* espaloma != espaloma_charge
* rename HAS_ESPALOMA to HAS_ESPALOMA_CHARGE
To disambiguate between esaplaoma and espaloma charge, we need to track
HAS_ESPALOMA separately from HAS_ESPALOMA_CHARGE
* skip test if espaloma is not installed
* fix HAS_ESPALOMA import
* see if installing espaloma gives us any issue
* import HAS_ESPALOMA
* only install espaloma when python != 3.13
* fix syntax
* Update openfe/tests/protocols/openmm_md/test_plain_md_protocol.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* 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>
