Update CI

.github/workflows/CI.yaml

@@ -19,21 +19,22 @@ jobs:
       fail-fast: false
       matrix:
         cfg:
-          - { os: ubuntu-latest, python-version: 3.7, docs: true,  openmm: latest }
-          - { os: macos-latest,  python-version: 3.7, docs: true,  openmm: latest }
-          - { os: ubuntu-latest, python-version: 3.8, docs: false, openmm: latest }
-          - { os: ubuntu-latest, python-version: 3.7, docs: false, openmm: nightly }
-          - { os: ubuntu-latest, python-version: 3.8, docs: false, openmm: nightly }
-          - { os: ubuntu-latest, python-version: 3.7, docs: false, openmm: conda-forge }
-          - { os: ubuntu-latest, python-version: 3.8, docs: false, openmm: conda-forge }
+          - { os: ubuntu-latest, python-version: "3.8", docs: true,  openmm: latest }
+          - { os: macos-latest,  python-version: "3.8", docs: true,  openmm: latest }
+          - { os: ubuntu-latest, python-version: "3.9", docs: false, openmm: latest }
+          - { os: ubuntu-latest, python-version: "3.8", docs: false, openmm: nightly }
+          - { os: ubuntu-latest, python-version: "3.9", docs: false, openmm: nightly }
+          - { os: ubuntu-latest, python-version: "3.8", docs: false, openmm: conda-forge }
+          - { os: ubuntu-latest, python-version: "3.9", docs: false, openmm: conda-forge }
+          - { os: ubuntu-latest, python-version: "3.10", docs: false, openmm: conda-forge }
 
     env:
       OPENMM: ${{ matrix.cfg.openmm }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
       PACKAGENAME: yank
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Additional info about the build
         shell: bash
@@ -42,35 +43,32 @@ jobs:
           df -h
           ulimit -a
 
-      # More info on options: https://github.com/conda-incubator/setup-miniconda
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Set up conda environment
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          python-version: ${{ matrix.cfg.python-version }}
           environment-file: devtools/conda-envs/test_env.yaml
-          activate-environment: test
-          auto-update-conda: true
-          auto-activate-base: false
-          show-channel-urls: true
+          extra-specs: |
+            python=${{ matrix.cfg.python-version }}
 
       - name: Refine test environment
         shell: bash -l {0}
         run: |
           case ${{ matrix.cfg.openmm }} in
             latest)
               echo "Using latest release OpenMM."
-              conda install --quiet -c omnia openmm;;
+              micromamba install --quiet -c omnia openmm;;
             rc)
               echo "Using OpenMM rc"
-              conda install --quiet -c omnia/label/rc openmm;;
+              micromamba install --quiet -c omnia/label/rc openmm;;
             beta)
               echo "Using OpenMM beta"
-              conda install --quiet -c omnia/label/beta openmm;;
+              micromamba install --quiet -c omnia/label/beta openmm;;
             nightly)
               echo "Using OpenMM nightly dev build."
-              conda install --quiet -c omnia-dev openmm;;
+              micromamba install --quiet -c omnia-dev openmm;;
             conda-forge)
               echo "Using OpenMM conda-forge testing build."
-              conda install --quiet -c conda-forge/label/test openmm;;
+              micromamba install --quiet -c conda-forge/label/test openmm;;
           esac
 
       - name: Install package

.gitignore

@@ -3,6 +3,9 @@
 # C extensions
 *.so
 
+# macOS
+.DS_Store
+
 # Packages
 *.egg
 *.egg-info

Yank/analyze.py

@@ -30,7 +30,10 @@
 
 import mpiplus
 import numpy as np
-import simtk.unit as units
+try:
+    import openmm.unit as units
+except ImportError: # OpenMM < 7.6
+    import simtk.unit as units
 import openmmtools as mmtools
 from pymbar import timeseries
 

Yank/commands/analyze.py

@@ -151,7 +151,10 @@ def single_run():
 
 def extract_analyzer_kwargs(args, quantities_as_strings=False):
 
-    import simtk.unit as unit
+    try:
+        import openmm.unit as unit
+    except ImportError: # OpenMM < 7.6
+        import simtk.unit as unit
 
     """Return a dictionary with the keyword arguments to pass to the analyzer."""
     analyzer_kwargs = {}

Yank/commands/platforms.py

@@ -34,7 +34,10 @@
 
 
 def dispatch(args):
-    from simtk import openmm
+    try:
+        import openmm
+    except ImportError: # OpenMM < 7.6
+        from simtk import openmm
     print("Available OpenMM platforms:")
     for platform_index in range(openmm.Platform.getNumPlatforms()):
         print("{0:5d} {1:s}".format(platform_index, openmm.Platform.getPlatform(platform_index).getName()))

Yank/commands/selftest.py

@@ -52,7 +52,10 @@ def dispatch(args):
     import doctest
     import pkgutil
     import subprocess
-    import simtk.openmm as mm
+    try:
+        import openmm as mm
+    except ImportError: # OpenMM < 7.6
+        import simtk.openmm as mm
     from .. import version
     from . import platforms
 

Yank/experiment.py

@@ -32,8 +32,13 @@
 import openmmtools as mmtools
 import openmoltools as moltools
 import yaml
-from simtk import unit, openmm
-from simtk.openmm.app import PDBFile, AmberPrmtopFile
+try:
+    import openmm
+    from openmm import unit
+    from openmm.app import PDBFile, AmberPrmtopFile
+except ImportError: # OpenMM < 7.6
+    from simtk import unit, openmm
+    from simtk.openmm.app import PDBFile, AmberPrmtopFile
 
 from . import utils, pipeline, restraints, schema
 from .yank import AlchemicalPhase, Topography
@@ -2243,7 +2248,7 @@ def _configure_platform(cls, platform_name, platform_precision):
 
         Returns
         -------
-        platform : simtk.openmm.Platform
+        platform : openmm.Platform
            The configured platform.
 
         Raises

Yank/pipeline.py

@@ -33,8 +33,13 @@
 import openmoltools as moltools
 import yaml
 from pdbfixer import PDBFixer
-from simtk import openmm, unit
-from simtk.openmm.app import PDBFile
+try:
+    import openmm
+    from openmm import unit
+    from openmm.app import PDBFile
+except ImportError: # OpenMM < 7.6
+    from simtk import openmm, unit
+    from simtk.openmm.app import PDBFile
 
 
 from . import utils
@@ -175,12 +180,12 @@ def compute_radius_of_gyration(positions):
 
     Parameters
     ----------
-    positions : simtk.unit.Quantity with units compatible with angstrom
+    positions : openmm.unit.Quantity with units compatible with angstrom
        The coordinate set (natoms x 3) for which the radius of gyration is to be computed.
 
     Returns
     -------
-    radius_of_gyration : simtk.unit.Quantity with units compatible with angstrom
+    radius_of_gyration : openmm.unit.Quantity with units compatible with angstrom
        The radius of gyration
 
     """
@@ -209,7 +214,7 @@ def compute_net_charge(system, atom_indices):
 
     Parameters
     ----------
-    system : simtk.openmm.System
+    system : openmm.System
         The system object containing the atoms of interest.
     atom_indices : list of int
         Indices of the atoms of interest.
@@ -245,7 +250,7 @@ def find_alchemical_counterions(system, topography, region_name):
 
     Parameters
     ----------
-    system : simtk.openmm.System
+    system : openmm.System
         The system object containing the atoms of interest.
     topography : yank.Topography
         The topography object holding the indices of the ions and the
@@ -328,7 +333,7 @@ def get_leap_recommended_pbradii(implicit_solvent):
     --------
     >>> get_leap_recommended_pbradii('OBC2')
     'mbondi2'
-    >>> from simtk.openmm.app import HCT
+    >>> from openmm.app import HCT
     >>> get_leap_recommended_pbradii(HCT)
     'mbondi'
 
@@ -347,7 +352,7 @@ def create_system(parameters_file, box_vectors, create_system_args, system_optio
 
     Parameters
     ----------
-    parameters_file : simtk.openmm.app.AmberPrmtopFile or GromacsTopFile
+    parameters_file : openmm.app.AmberPrmtopFile or GromacsTopFile
         The file used to create they system.
     box_vectors : list of Vec3
         The default box vectors of the system will be set to this value.
@@ -358,7 +363,7 @@ def create_system(parameters_file, box_vectors, create_system_args, system_optio
 
     Returns
     -------
-    system : simtk.openmm.System
+    system : openmm.System
         The system created.
 
     """
@@ -432,7 +437,7 @@ def read_system_files(positions_file_path, parameters_file_path, system_options,
 
     Returns
     -------
-    system : simtk.openmm.System
+    system : openmm.System
         The OpenMM System built from the given files.
     topology : openmm.app.Topology
         The OpenMM Topology built from the given files.
@@ -512,7 +517,7 @@ def read_system_files(positions_file_path, parameters_file_path, system_options,
         create_system_args = set(inspect.getargspec(openmm.app.CharmmPsfFile.createSystem).args)
         system_options['params'] = params
         system = create_system(parameters_file, box_vectors, create_system_args, system_options)
-            
+
     # Unsupported file format.
     else:
         raise ValueError('Unsupported format for parameter file {}'.format(parameters_file_extension))

Yank/reports/notebook.py

@@ -16,7 +16,10 @@
 from matplotlib import gridspec
 from pymbar import MBAR
 import seaborn as sns
-from simtk import unit as units
+try:
+    from openmm import unit as units
+except ImportError: # OpenMM < 7.6
+    from simtk import unit as units
 from openmmtools import multistate
 
 from .. import analyze