* initial cli ideas
* clean up names
* add test
* update docstrings and fix imports
* fix tests
* use gufe gzip branch
* clean up fixtures
* update fixtures
* adding membrane component to tests
* add membrane barostat check
* make output more consistent and add membrane args test
* error messages
* revert some out of scope typing things
* tidying fixtures
* update protein arg parsing
* clearer var naming
* add protein validate
* add validation
* fix handling for membrane solvents
* update docstring
* point to membrane tutorial branch
* linking
* remove redundant validation
* remove unneeded type hints
* Update src/openfecli/commands/plan_rbfe_network.py
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* Update src/openfecli/parameters/protein.py
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* clean up suggestions
* use click BadParameter
* testing arg errors
* update examplenotebook branch
* add news item
* use BadParameter
* fix test comments
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* split md protocol to setup and simulate, add restart support
* allow for resume in any stage
* add a single run dynamics function
* update restart to only look for checkpoints, split out remaining step logic, update tests
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Membrane support prototype start
* Point to corresponding branch in gufe
* Make plain md protocol membrane ready
* Dry run for membrane system for debugging
* Add box vectors to modeller
* Adapt htf to allow for membrane barostat
* Fix test
* Add test files membrane
* Change test to cpu
* Prints for debugging
* Some more debugginh stuff, remove later
* Small fix
* Temporarily use branches for openmmtools and openmmforcefield
* Small fixes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* support membrane in gather
* First pass membrane support for SepTop protocol
* Change validation solvent
* Move changes in solvent validation to validate_solvent
* Some small fixes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add membrane test septop
* Change box vector units for handling membrane barostat
* Test box vectors SepTop more
* First pass at ABFE membrane prototype
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Remove some prints
* Revert box changes
* Some fixes in SepTop to fix tests
* Apply suggestion from @hannahbaumann
* Add tests for system creation
* FIx test
* Add ABFE membrane tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* More tests membrane septop and more dry outputs in septop
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add validation for box vector in ProteinMembraneComponent
* Adapt gather for membranes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* small changes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Modify box vectors plain md
* Address review comments
* Remove unnecessary prints
* Subclass membrane test
* Small fix
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* remove unnecessary import
* Remove prints
* Small fix
* Small fix
* Larger change to checks for BaseSolventComponent, SolvatedPDBComponent, and adding barostat settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Some more changes
* Small fix
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* ABFE enforce timestep complex solvent the same
* Update test files
* Update environment.yaml with new openmmtools and openmmforcefield versions
* Remove unnecessary checks for box_vectors which are handled in gufe
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update openfe/protocols/openmm_afe/equil_binding_afe_method.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Attempt at rewriting validate_solvent
* Move get barostat to self
* Simplify mapping in test
* Add validator for surface_tension and membrane barostat
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add membrane barostat to adaptive settings rfe protocol
* Add validation/warning for barostat component mismatch
* Fix tests (except CLI)
* More merge fixes
* Remove unnecessary imports
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add test files
* Update tests
* Add lipid ff in adaptive settings
* remove commented out lines
* Update test abfe
* Update ABFE results with new settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix solvent validation
* change env to gufe main
* Apply suggestion from @hannahbaumann
* Remove files from before src layout change
* Update tests
* Small fix
* mark slow tests
* Update env file
* Small fix
* Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update src/openfe/protocols/openmm_utils/system_validation.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Address review comments 1
* update doc string
* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Address review comments 2
* Address review comments 3
* fix mypy
* Fix system creation tests
* Roundtrip box vectors to remove vec3 issues
* Roundtrip box vectors to remove vec3 issues
* Remove unnecessary imports
* Apply suggestion from @hannahbaumann
* Test mypy failure
* Test mypy failure 2
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* some fixes
* small fixes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update test files
* Update SepTop results settings
* add more tests for adaptive settings and others
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add news entry
* Fix for box vectors hybtop
* Make test slow again
* Make mypy happy
* try to make mypy happy again
* Adapt gather RFE membrane component types
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* use reference platform for the membrane energy test
* Add ChemicalSystem Component validation to Protocols
* Add test for chemicalsystem validation
* Apply suggestions from code review
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
* Update with slight variation to @jthorton 's suggestion
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* point gufe back at main
* Drop lipid17 from adaptive settings
* just a tiny nit change
* fix typo
* Add extra class to openfecli check
* Add total particle checks to abfe protocol tests
* remove lipid17 check from adaptive settings
* remove lipid17 check from adaptive settings
* Add some checks for number of particles & residues
* Fix up some tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Minimized protein
* Update protein
* Revert back to old protein
* Apply suggestion from @hannahbaumann
* Remove box roundtrip and fix solvent from get_components
* Merge conflicts
* Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix merge conflict
* Forgot another one
* Move box roundtrip to _pre_equilibrate
* First go at modifying the user guide for membranes and ABFE and SepTop
* some small fixes
* Add adaptive_settings to user guide
* Add example code loading protein membrane
* Add box vector explanation
* Some smaller changes
* Make adaptive settings subheading
* Some more changes
* Add warning adaptive settings
* Update docs/guide/setup/defining_protocols.rst
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Addressing review comments
* some more updates
* Test out subheadings
* Restructure user guide
* merge conflicts
* Small fix
* some small updates
* addressing review comments
* Small fix
* address review comments
* small fix
* Add news entry
* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* Update docs/guide/setup/defining_protocols.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* Addres review comment
* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
* Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
* Address review comment
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@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>
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
* Add an Analysis unit to SepTopProtocol.
* Update PDB writing via MDTraj in AFE and SepTop Protocols to account for box dimensions with mdtraj_from_openmm utility.
* Split up some SepTop tests into different files.
* Updated the CLI gathering to account for post openfe v1.11 Analysis units
---------
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* Modify quickrun to allow resuming
* fix the gather tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* add check for protocol_dag.json
* add basic test
* clearer language, hopefully
* store protocol dag using transformation key
* another tmpdir -> tmp_path fix
* add error handling check
* fix naming in test
* add news item
* use assert_click_success
* add test for interrupted job
* remove checkpoint when a job has completed successfully
* add handling for checkpoint error handling without --resume
* clean up logic
* check for warning
* add docs
* make a cache dir
* use clickexception
* update error message
* update kwarg
* keep everything in the quickrun cache
* clearer message
* it's ProtocolDAG not protocolDAG
* bump CI
* bump CI
* include output json in caching hash (#1890)
* first pass at adding caching with output json
* add (hopefully) helpful execution information
* add resume command
* fix testing path
* check that output file isn't created early
* clean up tests
* line break
* fix some comments to say cache instead of checkpoint
* fix typo in news item
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* update abfe test data
* fixing regression test data
* add tests for prior behavior
* Minor fix to support ABFE gathering with openfe v1.9+ (#1876)
* Minor fix to try to unblock v1.10
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add comment
* More exposition
* update expected results
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>
* add news item
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* 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
* Also improve deletion for the hybridtop protocol
Added error handling for reporter closure and context clearing.
* Add news item
* Update news/issue-1845.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
---------
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* add boilerplate
* define pooch cache at top level
* try downloading one file
* put pooch cache in utils
* use dict
* add all cli data
* keep registry data all in one place
* move downloader to openfe from openfecli
* add both registries to test
* rename for clarity
* better docstring
* update install instructions (#1744)
* update manifest to include all .gz files (#1746)
* update manifest to include all .gz files
* add min openmmforcefields pin
* bump cuda version to 11.8 (#1749)
* fix deprecation warning on view_components_3d (#1750)
* expose KartografAtomMapper alongside other AtomMappers (#1751)
* fix psutils import (#1779)
* fix psutils import
* swap import order
* [pre-commit.ci] pre-commit autoupdate (#1778)
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)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* 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.
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* rename openfecli fixture to avoid duplication with openfe fixture (#1755)
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* openfe gather: add progress bar for loading JSONs (#1786)
* all the profiling
* make progress bar pretty
* revert typing thing
* news
* all the profiling
* make progress bar pretty
* revert typing thing
* news
* update expected outputs
* update expected outputs
* add dill mock to fix openfe docs build (#1792)
* Fix issue 1795 (#1796)
* Update method name in CLI YAML documentation
* Fix command option case in CLI YAML guide
* manually add absolute settings news item to changelog (#1821)
* manually add absolute settings news item to changelog
* add link
* Fixes docstring to clarify argument does not have a default (#1819)
* Fixes docstring to clarify argument does not have a default
* Modernize typing
* fix ligand network cropping bug (#1822)
* fix ligand network cropping bug
* move to upstream func
* whitespace
* fix pydantic deprecation of copy method
* fix pydantic deprecation of dict method - septop (#1831)
* Updated CHANGELOG for 1.8.1
* fix changelog links
* add openeye w/ python 3.13 test to CI (#1745)
* add openeye w/ python 3.13 test to CI
* only run openeye on unbuntu w/ python 3.13
* add explicit openeye no
* bump python version for conda cron (#1748)
* remove mypy rdkit pin (#1753)
* remove mypy rdkit pin
* try more explicit import
* Revert "try more explicit import"
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.
* Migrate validation to Protocol._validate in HybridTopologyProtocol (#1740)
* Migrate & add validation to Protocol._validate for hybrid topology Protocol
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
* Move rfe protocol (#1769)
Move RFE protocol files around
* HybridTop Unit methods (#1770)
* Break down the Hybrid Top protocol unit into various methods.
---------
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* 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.
* HybridTop structural analysis via API rather than CLI (#1771)
* change structural analysis from using CLI to using API
* making some language clearer on github-facing things (#1758)
* making some language clearer on github-facing things
* :
* add pre-commit link
* clean up
* Moving AFE Protocols around a bit (#1775)
* move the protocols results to a single file and deduplicate
* rename base units file
* move units out of method files
* move a few things in init
* Create setup, run, and analysis units for HybridTop Protocol (#1773)
* Turn Hybrid Topology protocol into 3 units.
---------
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* update docs for multiple protocol units (#1793)
* Update docstring for hybridtop classes (#1794)
* Update docstring for classes
* [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>
* Small improvement in RelativeHybridTopologyProtocol docstring (#1797)
Updated class docstring to clarify the use of Hybrid Topology scheme.
* turn off zenodo retry (#1802)
* turn off zenodo retry
* remove retry_if_failed arg
* only run CI on macos python 3.12 (#1803)
* Turn AFE protocols into multiple units (#1776)
* Split the AFE protocol units into setup, simulation, and analysis.
* move to src layout (#1805)
* Move openfe project layout to `src`.
* Temporarily build pooch from main w/ hotfix (#1806)
* build with pooch@main to see if hotfix works
* add link
* make CLI starting guide easier to find from the landing page (#1787)
* make CLI starting guide easier to find from the landing page
* Python API -> API Docs
* bump ci
* bump example notebooks pin to 2026.01.26
* change a word
* clarifying language
* Update pyproject.toml (#1813)
* Update pyproject.toml
* update classifiers
* refactor: clean up test data handling (#1815)
* import pooch_cache from conftest
* remove unused files from pooch cache
* move zenodo cache to conftest
* remove duplicate code
* min pin pooch to fix data fetching (#1820)
* fix ligand network cropping bug (#1822)
* fix ligand network cropping bug
* move to upstream func
* whitespace
* fix api break check path (#1825)
* fix pydantic deprecation of copy method (#1829)
* fix scope mismatch with zenodo data (#1828)
* fix scope mismatch with zenodo data
* fix session scope
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
* all the profiling
* make progress bar pretty
* revert typing thing
* news
* all the profiling
* make progress bar pretty
* revert typing thing
* news
* update expected outputs
* update expected outputs
* NAGL can no longer be used with oechem installed if you are using the rdkit backend.
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* Add absolute alchemical settings
* Expose settings in AFE protocols
* expose settings in septop
* Fix up settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* add some tests
* Add septop tests for sterics force settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add news item
* add an extra parameterize option
* [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>
* feat: support `openfe gather` for septop (#1638)
* copy septop analysis notebook over
* add todos
* add plan and test
* format
* add failing tests
* comment out secondary tests
* add cli tmp
* clean up imports
* fix type hints in gather.py
* test passes for gather raw
* test passes for ddg
* tests pass for dg
* pull more error handling into septop
* condense code a bit
* MBAR uncertainty
* remove planning stub
* Revert "MBAR uncertainty"
This reverts commit bf32aa3c6e.
* format
* test with tolerances
* precommit format
* remove accidentally committed file
* Apply suggestions from code review
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
---------
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* feat: add abfe gathering support first draft (#1686)
* add abfe MVP with tests
* Apply suggestions from code review
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* fix incorrect var name
* fix abfe legs extraction
* fix merge bug
* remove unused import
---------
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* gather: fix septop rounding (#1696)
* only apply precision rounding at the end
* clean up code
* gather: update names parsing (septop and abfe) (#1698)
* update abfe names parsing
* update septop names parsing
* add todo
* get names from alchemical_components
* remove todo
* gather: refactor/unify rounding behavior (#1697)
* format septop outputs with format_df_with_precision
* only apply precision rounding at the end
* update gather abfe formatting to use format_df_with_precision
* remove unused import
* switch back to checking final outputs for abfes
* clean up code
* add rounding for dg mle
* simplify code
* gather: unify code structure between rbfe, septop, & abfe (#1700)
* format septop outputs with format_df_with_precision
* only apply precision rounding at the end
* update gather abfe formatting to use format_df_with_precision
* remove unused import
* switch back to checking final outputs for abfes
* clean up code
* add rounding for dg mle
* simplify code
* make gather_septop.py code more similar to gather.py
* make gather_abfe.py code more similar to gather.py
* remove unused function
* add stdout message for experimental gathering support (#1703)
* add warnings for experimental gathering
* use click to make output look nicer, not a true warning
* add warning text
* make yellow
* add tests
* remove unused code
* add news item
* speed up names gathering
* names should always return str
* add single repeat tests for abfe and septop
* remove unused imports
* make `gather septop/abfe` output headers accurately reflect error type (#1712)
* gather septop/abfe output headers accurately reflect error type
* split into func
* label all uncertainty columns more specifically
* add docstring
* update test data
* update error calculation
---------
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* Disable JAX acceleration by default
* ruff fmt
* add logging info
* fix url
* fix list
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* add example of error message
* added note about disabling jax acel by default
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* updating install recommendations to prioritize miniconda and conda-lock
* fix formatting
* Update docs/installation.rst
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* recommend openfe test
* remove miniforge
* update language and clean up install instructions
* add link
* adding news item
* add back miniforge instructions at the end
* make testing its own section
* clearer language and formatting
* why is rst like this
* why is rst like this??
* one sentence per line!
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* do we test this at all?
* start of logging improvements
* first pass at logging, worried about performance
* setup a base class + add type hints
* add placeholder url ref
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* update to new logging control
* Fix imports
* remove bit left over from being able to delete these log controlers
* looks like ... is used more than pass
* formatting fix
* Grab new format rule from main
* run ruff check --fix on conflicting files
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Added tests
* see if this fixes the doc build
* add back debugging code
* update openmm doc url
* add note about jax warning
* bump
* Remove debugging code to see if that fixes doc build
* ruff format
* Add url
* switch to using module instead of class w/ static methods
* Update docs/guide/troubleshooting.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* ruff fixes
* Ruff fix
* Added news entry
* Refactor to move things to private namespace
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>