Merge branch 'main' into feat/improve_docker_building

.github/workflows/CI.yaml

@@ -1,6 +1,7 @@
 name: CI
 
 on:
+  merge_group:
   pull_request:
     branches:
       - "main"
@@ -23,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.9, "3.10"]
         openmm: ["8.0", "7.7"]
         include:
           - openmm: "dev"
@@ -49,12 +50,13 @@ jobs:
         with:
           environment-file: devtools/conda-envs/test_env.yaml
           environment-name: test
-          channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge/label/openmm_dev/linux-64,conda-forge,openeye
+          channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge/label/openmm_dev,conda-forge,openeye
           channel-priority: flexible
           cache-env: true
           cache-downloads: true
           extra-specs: |
             python==${{ matrix.python-version }}
+            openmmtools==0.23.0
             openmm==8.0.0dev3
 
       - name: Setup micromamba
@@ -68,6 +70,7 @@ jobs:
           extra-specs: |
             python==${{ matrix.python-version }}
             openmm==${{ matrix.openmm }}
+            openmmtools==0.23.0
 
       - name: Install package
         shell: bash -l {0}
@@ -103,4 +106,4 @@ jobs:
         uses: codecov/codecov-action@v1
         with:
           file: ./coverage.xml
-          fail_ci_if_error: true
+          fail_ci_if_error: true

devtools/conda-envs/test_env.yaml

@@ -3,12 +3,13 @@ channels:
   - conda-forge
   - openeye
 dependencies:
+  - ambertools <23
   - arsenic
   - autograd
   - click
   - cloudpathlib-s3 >=0.13.0
   - coverage
-  - dask
+  - dask <2023.5
   - dask-jobqueue
   - dicttoxml
   - distributed
@@ -27,7 +28,7 @@ dependencies:
   - openff-units >=0.1.8
   - openmm >=7.7
   - openmmforcefields >=0.9.0
-  - openmmtools >=0.21.5 # may need to sort out ambermini/ambertools/parmed dependencies
+  - openmmtools # may need to sort out ambermini/ambertools/parmed dependencies
   - openmoltools # may need to sort out ambermini/ambertools/parmed dependencies (we don't want ambertools)
   - parmed # may need to sort out ambermini/ambertools/parmed dependencies
   - pdbfixer

docs/changelog.rst

@@ -8,6 +8,69 @@ This section lists features and improvements of note in each release.
 
 The full release history can be viewed `at the GitHub perses releases page <https://github.com/choderalab/perses/releases>`_.
 
+0.10.2 - Release
+----------------
+
+Bugfix release.
+
+Enhancements
+^^^^^^^^^^^^
+
+* Added support for reading input files (ex yaml, sdf, pdbs) from AWS, GCP, and Azure. See the documentation for [cloudpathlib](https://cloudpathlib.drivendata.org/stable/authentication/) for how to setup authentication. Currently only reading the yaml from S3 is unit tested (ie `perses-cli --yaml s3://perses-testing/template_s3.yaml`), but other cloud providers and input files should work. `AzureBlobPath`, `S3Path` and `GSPath` are supported URI endpoints. Please report any issues on our issue tracker!  by @mikemhenry in https://github.com/choderalab/perses/pull/1073
+* ``CUDA`` platform was hardcoded in geometry engine, generating performance issues by not clearing openmm contexts correctly. Fixed by defaulting to using the faster ``CPU`` platform (for the geometry engine) and explicitly deleting context variables after they are used. by @ijpulidos in https://github.com/choderalab/perses/pull/1091
+* Set aromatic draw style to `OEAromaticStyle_Circle` in atom mapper rendering by @mikemhenry in https://github.com/choderalab/perses/pull/1103
+* Ligands with atoms changing constrained status were not being handled by mapping proposal. Atoms in bonds that change constrained/unconstrained to unconstrained/constrained during the transformation are now _demapped_. by @ijpulidos in https://github.com/choderalab/perses/pull/1125
+* Now that upstream ``openmmtools`` is storing velocities on checkpoint, the small molecule transformation pipeline does not reassign velocities on resume by default. Instead, the velocities are read from the checkpoint file. by @ijpulidos in https://github.com/choderalab/perses/pull/1133
+* CLI workflow for replica exchange now uses the faster ``LangevinMiddleIntegrator`` via the ``LangevinDynamicsMove``. Tests were updated to reflect the changes.  by @ijpulidos in https://github.com/choderalab/perses/pull/1138
+* Add opencontainers image-spec to `Dockerfile` by @SauravMaheshkar in https://github.com/choderalab/perses/pull/1139
+* Updated to support openff-toolkit 0.11, which included API-breaking changes. by @jchodera in https://github.com/choderalab/perses/pull/1128
+* Make solute-only trajectory writing optional. This option is controlled by the `atom_selection` option in the yaml file. The syntax uses the MDTraj selection syntax, e.g. `not water` @mikemhenry in https://github.com/choderalab/perses/pull/1185
+* Users can now specify solvent model for simulations using the ``solvent_model`` field in the input YAML file. Supported values are 'tip3p', 'spce', 'tip4pew', 'tip5p', and 'swm4ndp' (polarizable) by @ijpulidos in https://github.com/choderalab/perses/pull/1202
+
+Documentation
+^^^^^^^^^^^^^
+* Document setting `ionic_strength` in `examples/new-cli/template.yaml` by @mikemhenry in https://github.com/choderalab/perses/pull/1104
+* Add reproducible version of COVID Moonshot example anyone can run as an example by @jchodera in https://github.com/choderalab/perses/pull/1145
+* Speed up RTD env generation by @mikemhenry in https://github.com/choderalab/perses/pull/1105
+* Fix documentation string for `ProteinMutationExecutor`, using `False` for `reassign_velocities` parameter. by @ijpulidos in https://github.com/choderalab/perses/pull/1169
+* Document how to control the log level in the CLI by @mikemhenry in https://github.com/choderalab/perses/pull/1198
+
+Bug Fixes
+^^^^^^^^^
+
+* Fixes bug where if a `:` was in a key, we could not override the argument in our perses-cli.  @mikemhenry in https://github.com/choderalab/perses/pull/1062
+* Resolves #1157 objects serialized with `utils.data.serialize` now will be compressed with `bzip2` or `gzip` depending on file name (`.gz` and `.bz2`, respectively) by @mikemhenry in https://github.com/choderalab/perses/pull/1163
+* Fixes for new openmmtools 0.23.0 by @mikemhenry in https://github.com/choderalab/perses/pull/1203
+
+Testing/CI/Packaging 
+^^^^^^^^^^^^^^^^^^^^
+* add python 3.10 to CI by @mikemhenry in https://github.com/choderalab/perses/pull/1080
+* skip broken tests by @mikemhenry in https://github.com/choderalab/perses/pull/1074
+* Feat/fix ssl gpu error by @mikemhenry in https://github.com/choderalab/perses/pull/1095
+* Previously the keyword argument `save_freq` in `validate_endstate_energies_md` was not functional and the value of `250` steps was hard coded. Now, `save_freq` works and has a default value of `250` steps. by @mikemhenry in https://github.com/choderalab/perses/pull/1101
+* fix issue with test asset name by @mikemhenry in https://github.com/choderalab/perses/pull/1102
+* Examples and benchmarks template input files now run vacuum, solvent and complex phases in order. by @ijpulidos in https://github.com/choderalab/perses/pull/1122
+* Add openmm 8  to testing matrix by @mikemhenry in https://github.com/choderalab/perses/pull/1124
+* Fix resume tests  to use new CLI (resolves issue #1150) by @mikemhenry in https://github.com/choderalab/perses/pull/1151
+* Avoid testing non-examples in CI by @ijpulidos in https://github.com/choderalab/perses/pull/1164
+* only run dev with newest python version by @mikemhenry in https://github.com/choderalab/perses/pull/1165
+* remove outdated recipe by @mikemhenry in https://github.com/choderalab/perses/pull/1159
+* update release process by @mikemhenry in https://github.com/choderalab/perses/pull/1162
+* add env caching to CI by @mikemhenry in https://github.com/choderalab/perses/pull/1178
+* Skip failing openmm 8 tests by @mikemhenry in https://github.com/choderalab/perses/pull/1186
+* Add small molecule repex consistency tests by @zhang-ivy in https://github.com/choderalab/perses/pull/1065
+* Fix RESTTopologyFactory test by @zhang-ivy in https://github.com/choderalab/perses/pull/1188
+* enable merge queue by @mikemhenry in https://github.com/choderalab/perses/pull/1206
+* Using default online analysis interval in GPU repex tests by @ijpulidos in https://github.com/choderalab/perses/pull/1207
+
+New Contributors
+^^^^^^^^^^^^^^^^
+
+* @SauravMaheshkar made their first contribution in https://github.com/choderalab/perses/pull/1139
+
+**Full Changelog**: https://github.com/choderalab/perses/compare/0.10.1...0.10.2
+
+
 0.10.1 - Release
 ----------------
 

examples/new-cli/README.md

@@ -45,6 +45,19 @@ Currently only `key:value` parts of the yaml can be overridden i.e. not sequence
 
 To view all options ultimately used in the simulation, a file named `perses-$date-$yaml_name.yaml` is created under the simulation/experiment directory.
 
+The `LOGLEVEL` environment variable is used to control the logging messages printed to the terminal.
+Two common methods to set this environmental variable are:
+1. Setting the environmental variable for all applications ran in the terminal session
+```bash
+$ export LOGLEVEL=DEBUG # This will set the log level to DEBUG for all programs ran after this export 
+$ perses-cli --yaml template.yaml
+```
+2. Setting the environmental variable for only one command
+```bash
+$ LOGLEVEL=DEBUG  perses-cli --yaml template.yaml
+```
+
+
 ## Example Use Case
 
 In this example folder we have a protein: [2ZFF](https://www.rcsb.org/structure/2zff) and some ligands which we will use for a series of free energy calculations.

examples/new-cli/template.yaml

@@ -67,7 +67,7 @@ trajectory_directory: lig0to1
 trajectory_prefix: out
 
 # Atoms to store in NetCDF files (MDTraj selection syntax)
-atom_selection: not water
+atom_selection: null
 
 # Calculation phases to run
 # Permitted phases: ['complex', 'solvent', 'vacuum']
@@ -78,3 +78,6 @@ phases:
 # Use geometry-derived mapping
 use_given_geometries: true
 given_geometries_tolerance: 0.4 # angstroms
+
+# Solvent model
+solvent_model: "tip3p"

perses/app/relative_point_mutation_setup.py

@@ -89,7 +89,7 @@ class PointMutationExecutor(object):
             hss = HybridRepexSampler(mcmc_moves=mcmc.LangevinSplittingDynamicsMove(timestep= 4.0 * unit.femtoseconds,
                                                                                   collision_rate=5.0 / unit.picosecond,
                                                                                   n_steps=250,
-                                                                                  reassign_velocities=True,
+                                                                                  reassign_velocities=False,
                                                                                   n_restart_attempts=20,
                                                                                   splitting="V R R R O R R R V",
                                                                                   constraint_tolerance=1e-06),

perses/app/relative_setup.py

@@ -21,8 +21,6 @@
 from openmmtools.constants import kB
 import logging
 import os
-import dask.distributed as distributed
-from collections import namedtuple
 from collections import namedtuple
 import random
 from scipy.special import logsumexp
@@ -72,6 +70,7 @@ def __init__(self,
                  use_given_geometries = False,
                  given_geometries_tolerance=0.2*unit.angstroms,
                  transform_waters_into_ions_for_charge_changes=True,
+                 solvent_model="tip3p"
                  ):
         """
         Initialize a NonequilibriumFEPSetup object
@@ -160,6 +159,7 @@ def __init__(self,
         self._use_given_geometries = use_given_geometries
         self._given_geometries_tolerance = given_geometries_tolerance
         self.small_molecule_forcefield = small_molecule_forcefield
+        self._solvent_model = solvent_model
         if isinstance(ligand_input, str):
             self._ligand_input = AnyPath(ligand_input)
         else:
@@ -408,7 +408,9 @@ def __init__(self,
             _logger.info(f"setting up complex phase...")
             self._setup_complex_phase()
             self._complex_topology_old_solvated, self._complex_positions_old_solvated, self._complex_system_old_solvated = self._solvate_system(
-            self._complex_topology_old, self._complex_positions_old,phase='complex',box_dimensions=self._complex_box_dimensions, ionic_strength=self._ionic_strength)
+                self._complex_topology_old, self._complex_positions_old, phase='complex',
+                box_dimensions=self._complex_box_dimensions, ionic_strength=self._ionic_strength,
+                model=self._solvent_model)
             _logger.info(f"successfully generated complex topology, positions, system")
 
             self._complex_md_topology_old_solvated = md.Topology.from_openmm(self._complex_topology_old_solvated)
@@ -466,7 +468,9 @@ def __init__(self,
                 _logger.info(f"no complex detected in phases...generating unique topology/geometry proposals...")
                 _logger.info(f"solvating ligand...")
                 self._ligand_topology_old_solvated, self._ligand_positions_old_solvated, self._ligand_system_old_solvated = self._solvate_system(
-                self._ligand_topology_old, self._ligand_positions_old,phase='solvent',box_dimensions=self._solvent_box_dimensions,ionic_strength=self._ionic_strength)
+                    self._ligand_topology_old, self._ligand_positions_old, phase='solvent',
+                    box_dimensions=self._solvent_box_dimensions, ionic_strength=self._ionic_strength,
+                    model=self._solvent_model)
                 self._ligand_md_topology_old_solvated = md.Topology.from_openmm(self._ligand_topology_old_solvated)
 
                 _logger.info(f"creating TopologyProposal")
@@ -532,8 +536,10 @@ def __init__(self,
 
             if self._proposal_phase is None:
                 _logger.info('No complex or solvent leg, so performing topology proposal for vacuum leg')
-                self._vacuum_topology_old, self._vacuum_positions_old, self._vacuum_system_old = self._solvate_system(self._ligand_topology_old,
-                                                                                                         self._ligand_positions_old,phase='vacuum')
+                # FIXME: We shouldn't use a "solvate" system method for the vacuum phase. Separate functionalities.
+                self._vacuum_topology_old, self._vacuum_positions_old, self._vacuum_system_old = self._solvate_system(
+                    self._ligand_topology_old,
+                    self._ligand_positions_old, phase='vacuum', model=self._solvent_model)
                 self._vacuum_topology_proposal = self._proposal_engine.propose(self._vacuum_system_old,
                                                                                self._vacuum_topology_old,
                                                                                current_mol_id=0, proposed_mol_id=1)
@@ -666,7 +672,8 @@ def _generate_solvent_topologies(self, topology_proposal, old_positions):
 
         # solvate the old ligand topology:
         old_solvated_topology, old_solvated_positions, old_solvated_system = self._solvate_system(
-            old_ligand_topology.to_openmm(), old_ligand_positions,phase='solvent', box_dimensions=self._solvent_box_dimensions)
+            old_ligand_topology.to_openmm(), old_ligand_positions, phase='solvent',
+            box_dimensions=self._solvent_box_dimensions, model=self._solvent_model)
 
         old_solvated_md_topology = md.Topology.from_openmm(old_solvated_topology)
 
@@ -826,7 +833,7 @@ def _solvate_system(self, topology, positions, model='tip3p',phase='complex', bo
         forcefield : SystemGenerator.forcefield
             forcefield file of solvent to add
         model : str, default 'tip3p'
-            solvent model to use for solvation
+            solvent model to use for solvation. Supported values are 'tip3p', 'spce', 'tip4pew', 'tip5p', and 'swm4ndp' (polarizable)
         box_dimensions : tuple of Vec3, default None
             if not None, padding distance will be omitted in favor of a pre-specified set of box dimensions
 
@@ -971,6 +978,7 @@ def activate_client(self,
                         LSF = True,
                         num_processes = 2,
                         adapt = False):
+        import dask.distributed as distributed
 
         if LSF:
             from dask_jobqueue import LSFCluster
@@ -1056,6 +1064,7 @@ def wait(self, futures):
         """
         wrapper to wait until futures are complete.
         """
+        import dask.distributed as distributed
         if self.client is None:
             pass
         else: