* Add CLI septop gather tests for current SepTop AnalysisUnit behaviour
* Add a bit of docs
* [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>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* 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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* store protocol dag using transformation key
* use assert_click_success
* Update the CLI quickrun help info
* Add userguide documentation on how to use quickrun
* this reference instead?
* fix things a little bit
* update the title
* Update environment.yml
* Update docs/guide/cli/quickrun.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* update for new name for now
* Update docs/guide/cli/quickrun.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* update for new changes
* Add to the execution guide instead
* some fixes
* Add `>` where it's a CLI command
* formatting fixes
---------
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>
* split off cron test into its own test
* add feedstock build test for release prep
* add yq
* temp run on PR to main for testing
* update syntax for using with yq github action
* fix straggling '
* fix the path
* fix gufe version
* update dispatch triggers
* 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>
* tmpdir -> tmp_path
* cleaning up conventions in md protocol test
* more tmpdir -> tmp_path
* migrate abfe tmpdir to tmp_path
* update tmp factory for lomap test data
* tmpdir -> tmp_path in septop tests
* tidy things up for consistency
* filepath formatting
* 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>
