Fix/support python 310

.github/workflows/CI.yaml

@@ -19,21 +19,17 @@ 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: "3.9", docs: false, openmm: conda-forge }
+          - { os: ubuntu-latest, python-version: "3.10", docs: false, openmm: conda-forge }
+          - { os: ubuntu-latest, python-version: "3.11", 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
@@ -51,26 +47,18 @@ jobs:
           auto-update-conda: true
           auto-activate-base: false
           show-channel-urls: true
+          mamba-version: "*"
 
       - name: Refine test environment
         shell: bash -l {0}
         run: |
           case ${{ matrix.cfg.openmm }} in
-            latest)
+            7.7)
               echo "Using latest release OpenMM."
-              conda install --quiet -c omnia openmm;;
-            rc)
-              echo "Using OpenMM rc"
-              conda install --quiet -c omnia/label/rc openmm;;
-            beta)
-              echo "Using OpenMM beta"
-              conda install --quiet -c omnia/label/beta openmm;;
-            nightly)
-              echo "Using OpenMM nightly dev build."
-              conda install --quiet -c omnia-dev openmm;;
+              conda install --quiet -c conda-forge openmm=7.7;;
             conda-forge)
               echo "Using OpenMM conda-forge testing build."
-              conda install --quiet -c conda-forge/label/test openmm;;
+              conda install --quiet -c conda-forge openmm;;
           esac
 
       - name: Install package

.gitignore

@@ -36,10 +36,9 @@ nosetests.xml
 .pydevproject
 
 yank/version.py
-Yank/version.py
 
 # emacs
 *~
 
 # Cython files generated by setup.py
-Yank/mixing/_mix_replicas.c
+yank/mixing/_mix_replicas.c

devtools/conda-envs/test_env.yaml

@@ -2,7 +2,6 @@ name: test
 channels:
   - conda-forge
   - defaults
-  - omnia
   - openeye
   - salilab
 dependencies:
@@ -16,19 +15,19 @@ dependencies:
   - mdtraj >=1.7.2
   - openmmtools >=0.18.3
   - pymbar <4
-  - ambermini >=16.16.0
   - docopt
   - openmoltools >=0.7.5
   - mpiplus
   - pyyaml
   - clusterutils
   - sphinxcontrib-bibtex
-  - cerberus ==1.1 # yank uses buggy cerberus 1.1 behavior as a feature ¯\_(ツ)_/¯
+  - cerberus
   - matplotlib
   - jupyter
   - pdbfixer
   - openeye-toolkits
   - modeller
+  - parmed
   # test
   - nose
   - nose-timer

docs/conf.py

@@ -222,7 +222,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'Yank.tex', u'Yank Documentation',
+  ('index', 'yank.tex', u'yank Documentation',
    u'John Chodera', 'manual'),
 ]
 
@@ -252,7 +252,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'yank', u'Yank Documentation',
+    ('index', 'yank', u'yank Documentation',
      [u'John Chodera'], 1)
 ]
 
@@ -266,8 +266,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'Yank', u'Yank Documentation',
-   u'John Chodera', 'Yank', 'A flexible GPU-accelerated Python framework for alchemical free energy calculations.',
+  ('index', 'yank', u'yank Documentation',
+   u'John Chodera', 'yank', 'A flexible GPU-accelerated Python framework for alchemical free energy calculations.',
    'Miscellaneous'),
 ]
 

docs/yank-yaml-cookbook/all-options.yaml

@@ -1,14 +1,14 @@
 # Here are listed all the options that is possible to specify in a
-# Yank YAML script. There are no mandatory options. If not specified,
+# yank YAML script. There are no mandatory options. If not specified,
 # an option assumes the default value listed below.
 ---
 options:
   # GENERAL OPTIONS
   # ---------------
   verbose: no                       # Turn on/off verbose output.
-  resume_setup: no                  # By default, Yank will raise an error when it detects
+  resume_setup: no                  # By default, yank will raise an error when it detects
   resume_simulation: no             # that it will have to overwrite an existing file. Set
-                                    # resume_setup and/or resume_simulation if you want Yank
+                                    # resume_setup and/or resume_simulation if you want yank
                                     # to resume from an existing setup (molecules and system
                                     # files) and/or simulation (netcdf4 trajectory files)
                                     # respectively instead.

docs/yank-yaml-cookbook/combinatorial-experiment.yaml

@@ -37,10 +37,10 @@ molecules:
     strip_protons: yes
 
   imatinib:
-    filepath: clinical-kinase-inhibitors.csv        # Yank supports pdb, mol2, sdf and csv files. The last one
+    filepath: clinical-kinase-inhibitors.csv        # yank supports pdb, mol2, sdf and csv files. The last one
                                                     # must contain one row for each molecule. The second column
                                                     # must be the SMILES description of the molecule (the first
-                                                    # column if the csv file has only one). Yank can use the
+                                                    # column if the csv file has only one). yank can use the
                                                     # OpenEye toolkits to generate a molecule from its name or
                                                     # its SMILES description. Instead of using "filepath", you
                                                     # can directly use "smiles" or "name". For example, to
@@ -154,7 +154,7 @@ systems:                                                 # If you don't need com
     solvent: !Combinatorial [RF, vacuum]                 #   solvent: RF
     pack: yes                                            # If the ligand is far away from the receptor or if there
                                                          # are clashing atoms (defined as closer than 1.5 angstroms),
-                                                         # Yank will randomly translate and rotate the ligand until
+                                                         # yank will randomly translate and rotate the ligand until
                                                          # this is solved. Set this to "no" if you don't wan't to
                                                          # modify the initial position of the ligand as defined in
                                                          # your input file.

setup.py

@@ -61,7 +61,7 @@ def _minimal_ext_cmd(cmd):
     return GIT_REVISION
 
 
-def write_version_py(filename='Yank/version.py'):
+def write_version_py(filename='yank/version.py'):
     cnt = """
 # This file is automatically generated by setup.py
 short_version = '{base_version:s}'
@@ -126,12 +126,12 @@ def find_package_data(data_root, package_root):
     url='https://github.com/choderalab/yank',
     platforms=['Linux', 'Mac OS-X', 'Unix', 'Windows'],
     classifiers=CLASSIFIERS.splitlines(),
-    package_dir={'yank': 'Yank'},
+    package_dir={'yank': 'yank'},
     # Helper line which did not work reliably for the packages key
     # + ['yank.{}'.format(package) for package in find_packages('yank')],
     packages=['yank', "yank.tests", "yank.tests.data", "yank.commands", "yank.reports", "yank.schema"],
 
-    package_data={'yank': find_package_data('Yank/tests/data', 'yank') + ['reports/*.ipynb'],
+    package_data={'yank': find_package_data('yank/tests/data', 'yank') + ['reports/*.ipynb'],
                   },
     zip_safe=False,
     python_requires=">=3.6",

Yank/analyze.py → yank/analyze.py

@@ -525,7 +525,7 @@ def get_mixing_data(self):
     @_copyout
     def get_experiment_free_energy_data(self):
         """
-        Get the free Yank Experiment free energy, broken down by phase and total experiment
+        Get the free yank Experiment free energy, broken down by phase and total experiment
 
         Output is of the form:
 
@@ -746,7 +746,7 @@ def get_analyzer(file_base_path, **analyzer_kwargs):
 
     Returns
     -------
-    analyzer : instance of implemented :class:`Yank*Analyzer`
+    analyzer : instance of implemented :class:`yank*Analyzer`
         Analyzer for the specific phase.
     """
     # Eventually extend this to get more reporters, but for now simple placeholder

Yank/commands/selftest.py → yank/commands/selftest.py

@@ -67,8 +67,8 @@ def dispatch(args):
     print("YANK Selftest")
     print("-------------")
 
-    # Yank Version
-    print("Yank Version %s \n" % version.version)
+    # yank Version
+    print("yank Version %s \n" % version.version)
 
     # OpenMM Platforms
     if not (args['platforms'] > 0):  # Don't need to check for --skip since invalid without argument

Yank/experiment.py → yank/experiment.py

@@ -8,7 +8,7 @@
 Experiment
 ==========
 
-Tools to build Yank experiments from a YAML configuration file.
+Tools to build yank experiments from a YAML configuration file.
 
 This is not something that should be normally invoked by the user, and instead
 created by going through the Command Line Interface with the ``yank script`` command.
@@ -79,7 +79,7 @@ def _is_phase_completed(status, number_of_iterations):
 # ==============================================================================
 
 class YamlParseError(Exception):
-    """Represent errors occurring during parsing of Yank YAML file."""
+    """Represent errors occurring during parsing of yank YAML file."""
     def __init__(self, message):
         super(YamlParseError, self).__init__(message)
         logger.error(message)
@@ -683,7 +683,7 @@ def parse(self, script):
         # Setup general logging
         utils.config_root_logger(self._options['verbose'], log_file_path=None)
 
-        # Configure ContextCache, platform and precision. A Yank simulation
+        # Configure ContextCache, platform and precision. A yank simulation
         # currently needs 3 contexts: 1 for the alchemical states and 2 for
         # the states with expanded cutoff.
         platform = self._configure_platform(self._options['platform'],
@@ -715,7 +715,7 @@ def parse(self, script):
 
     def run_experiments(self, write_status=False):
         """
-        Set up and run all the Yank experiments.
+        Set up and run all the yank experiments.
 
         Parameters
         ----------
@@ -784,7 +784,7 @@ def build_experiments(self):
 
     def setup_experiments(self):
         """
-        Set up all systems required for the Yank experiments without running them.
+        Set up all systems required for the yank experiments without running them.
         """
         # All paths must be relative to the script directory
         with moltools.utils.temporary_cd(self._script_dir):
@@ -2076,7 +2076,7 @@ def _get_trailblaze_checkpoint_dir_path(self, experiment_path, phase_name):
     # --------------------------------------------------------------------------
 
     def _check_resume_experiment(self, experiment_path, experiment):
-        """Check if Yank output files already exist.
+        """Check if yank output files already exist.
 
         Parameters
         ----------
@@ -3091,7 +3091,7 @@ def _build_experiment(self, experiment_path, experiment, use_dummy_protocol=Fals
         gromacs_include_dir = self._db.systems[system_id].get('gromacs_include_dir', None)
         charmm_parameter_files = self._db.systems[system_id].get('charmm_parameter_files', None)
 
-        # Prepare Yank arguments
+        # Prepare yank arguments
         phases = [None, None]
         # protocol is an OrderedDict so phases are in the correct
         # order (e.g. [complex, solvent] or [solvent1, solvent2]).

Yank/pipeline.py → yank/pipeline.py

@@ -8,7 +8,7 @@
 Pipeline
 ========
 
-Utility functions to help setting up Yank configurations.
+Utility functions to help setting up yank configurations.
 
 """
 
@@ -412,7 +412,7 @@ def create_system(parameters_file, box_vectors, create_system_args, system_optio
 
 def read_system_files(positions_file_path, parameters_file_path, system_options,
                       gromacs_include_dir=None, charmm_parameter_files=None):
-    """Create a Yank arguments for a phase from system files.
+    """Create a yank arguments for a phase from system files.
 
     Parameters
     ----------

Yank/tests/test_experiment.py → yank/tests/test_experiment.py

@@ -54,7 +54,7 @@ def indent(input_string):
 
 
 def examples_paths():
-    """Return the absolute path to the Yank examples relevant to tests."""
+    """Return the absolute path to the yank examples relevant to tests."""
     data_dir = utils.get_data_filename(os.path.join('tests', 'data'))
     p_xylene_dir = os.path.join(data_dir, 'p-xylene-implicit')
     p_xylene_gro_dir = os.path.join(data_dir, 'p-xylene-gromacs-example')

Yank/tests/test_pipeline.py → yank/tests/test_pipeline.py

@@ -25,9 +25,9 @@
 
 def test_compute_min_dist():
     """Test computation of minimum distance between two molecules"""
-    mol1_pos = np.array([[-1, -1, -1], [1, 1, 1]], np.float)
-    mol2_pos = np.array([[3, 3, 3], [3, 4, 5]], np.float)
-    mol3_pos = np.array([[2, 2, 2], [2, 4, 5]], np.float)
+    mol1_pos = np.array([[-1, -1, -1], [1, 1, 1]], float)
+    mol2_pos = np.array([[3, 3, 3], [3, 4, 5]], float)
+    mol3_pos = np.array([[2, 2, 2], [2, 4, 5]], float)
     assert compute_min_dist(mol1_pos, mol2_pos, mol3_pos) == np.sqrt(3)
 
 
@@ -47,19 +47,19 @@ def test_compute_min_max_dist():
 
 def test_remove_overlap():
     """Test function remove_overlap()."""
-    mol1_pos = np.array([[-1, -1, -1], [1, 1, 1]], np.float)
-    mol2_pos = np.array([[1, 1, 1], [3, 4, 5]], np.float)
-    mol3_pos = np.array([[2, 2, 2], [2, 4, 5]], np.float)
+    mol1_pos = np.array([[-1, -1, -1], [1, 1, 1]], float)
+    mol2_pos = np.array([[1, 1, 1], [3, 4, 5]], float)
+    mol3_pos = np.array([[2, 2, 2], [2, 4, 5]], float)
     assert compute_min_dist(mol1_pos, mol2_pos, mol3_pos) < 0.1
     mol1_pos = remove_overlap(mol1_pos, mol2_pos, mol3_pos, min_distance=0.1, sigma=2.0)
     assert compute_min_dist(mol1_pos, mol2_pos, mol3_pos) >= 0.1
 
 
 def test_pull_close():
     """Test function pull_close()."""
-    mol1_pos = np.array([[-1, -1, -1], [1, 1, 1]], np.float)
-    mol2_pos = np.array([[-1, -1, -1], [1, 1, 1]], np.float)
-    mol3_pos = np.array([[10, 10, 10], [13, 14, 15]], np.float)
+    mol1_pos = np.array([[-1, -1, -1], [1, 1, 1]], float)
+    mol2_pos = np.array([[-1, -1, -1], [1, 1, 1]], float)
+    mol3_pos = np.array([[10, 10, 10], [13, 14, 15]], float)
     translation2 = pull_close(mol1_pos, mol2_pos, 1.5, 5)
     translation3 = pull_close(mol1_pos, mol3_pos, 1.5, 5)
     assert isinstance(translation2, np.ndarray)
@@ -72,7 +72,7 @@ def test_pack_transformation():
     BOX_SIZE = 5
     CLASH_DIST = 1
 
-    mol1 = np.array([[-1, -1, -1], [1, 1, 1]], np.float)
+    mol1 = np.array([[-1, -1, -1], [1, 1, 1]], float)
     mols = [np.copy(mol1),  # distance = 0
             mol1 + 2 * BOX_SIZE]  # distance > box
     mols_affine = [np.append(mol, np.ones((2, 1)), axis=1) for mol in mols]

Yank/tests/test_yank.py → yank/tests/test_yank.py

@@ -5,7 +5,7 @@
 
 DESCRIPTION
 
-This test suite generates a number of simple models to test the 'Yank' facility.
+This test suite generates a number of simple models to test the 'yank' facility.
 
 COPYRIGHT
 
@@ -644,7 +644,7 @@ def notest_LennardJonesPair(**kwargs):
 #                                        alchemical_states)
 #
 #     # Create new simulation.
-#     yank = Yank(store_dir, **options)
+#     yank = yank(store_dir, **options)
 #     yank.create(thermodynamic_state, alchemical_phase)
 #
 #     # Run the simulation.