* 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>
* reorg for clarity
* moving try/except into function for clarity
* reorg data parsing for clarity
* remove unused function
* add try/except to pass through info about failed edges
* updating tests for new expected failed simulation checking behavior
* pass through for raw and ddg
* pass through failures for dgs
* remove unused import
* adding a missing check
* docstrings
* cleaning up logic
* cleaning up logic
* docstrings and formatting
* fixing conditionals bug
* more docstrings
* make 'name' a tuple for consistency
* make functions private
* updating output statement for clarity (hopefully)
* remove unused dg raw expected output
* adding comment description
* updating tests
* cleaning up test to not use tmp dir
* only use non-None legs for deciding whether to do rbfe/rhfe
* fix typo
* pass empty list instead of None through to ddg
* add cmet data
* add assert success tests - still need output validation
* light reordering for clarity
* adding pytest regressions
* don't include stderr in file regression
* making output more legible
* switch from runtime error to exit(1)
* add missing complex legs test
* adding regressoin tsvs to manifest
* reordering functions for clarity
* updating tests
* adding test for disconnected network
* updating warning message, not throwing error for now
* updating tests for missing runs
* add disconnected network check
* switch from NaN to Error
* removing unused regression files
* fixing typo
* adding test coverage
* fix typo
* adding news entry
* Alphabetize environment.yaml
Have been having some dependency issues. Noticed numpy in there twice.
* Complete alphabetization
---------
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* switch to assert_click_success to make debugging easier
* fixing tests to look for logger.INFO instead of warnings (due to gufe change)
* updating expected output due to gufe changes
* updating expected transformations
* remove easy prefix, passing 2fe7741b9448
* define _settings_cls, tests pass against g3c6d5f9
* update string match for partial charge logging
* be able to manually trigger package tests
* run package tests on each pr, no reason not to
* we should be installing from conda forge
* skip some openfecli tests if we don't have nagl installed
* plz lets use conda-forge
* Add perses back in for testing
* Update environment.yml
* bump up rtol for bootstrap tests
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update gpu-runner.yaml
* test on a g4dn.xlarge @ 53 cents an hour
* testing on a p2.xlarge @ 90 cents an hour
* Update gpu-runner.yaml
* Update gpu-runner.yaml
* update AMI to correct region (still the 'Deep Learning Base OSS Nvidia Driver GPU AMI' AMI)
* fix default shell, yolo that there is no syntax issues
* use the _REAL_ correct default shell
* Add a timeout of 12 hrs instead of the default 6
* Added oe toolkit + espaloma_charge to GPU env for testing
* fix channel name
* got a download error on the cudatoolkit shim which we don't want anyway
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* Test with main on Lomap dev branch
* Switch to packaging for version checks
* more version fixes
* enforce lomap regression tests to use the same kwargs
* Fix several tests for new lomap changes
* comment a few things
* Add news entry
* Actually let's test removing the conda-forge lomap install fully
* Update environment.yml
* see if this is enough to test the removal of gaff
* see if now we get the right error message
* rerun ci
* rerun ci
* see what happens if we the solver do its thing
* add omff version to matrix
* Added note about how to use gaff
* depending on the ommff version, we make sure the test does what we expect
* add an osx arm test since we should be able to do that now
* see if we can install missing stubs
* add missing stubs directly
* we return a sampler and not a system for the rfe
* Apply suggestions from code review
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* added link to give some context
* testing on python 3.12 now
* unpin numpy
* no openeye toolkits for 3.12
---------
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
