diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index fbc85aea..be78bbd3 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -19,13 +19,9 @@ 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 }}
@@ -33,7 +29,7 @@ jobs:
       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
diff --git a/.gitignore b/.gitignore
index 57e49b3e..513fb432 100644
--- a/.gitignore
+++ b/.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
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index df4a45f9..640ba618 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/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
diff --git a/docs/conf.py b/docs/conf.py
index 41320237..8b545f5a 100644
--- a/docs/conf.py
+++ b/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'),
 ]
 
diff --git a/docs/yank-yaml-cookbook/all-options.yaml b/docs/yank-yaml-cookbook/all-options.yaml
index 0ad9389d..45238e93 100644
--- a/docs/yank-yaml-cookbook/all-options.yaml
+++ b/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.
diff --git a/docs/yank-yaml-cookbook/combinatorial-experiment.yaml b/docs/yank-yaml-cookbook/combinatorial-experiment.yaml
index 97240428..8d1b1bf2 100644
--- a/docs/yank-yaml-cookbook/combinatorial-experiment.yaml
+++ b/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.
diff --git a/setup.py b/setup.py
index d8d055a3..51a1e751 100644
--- a/setup.py
+++ b/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",
diff --git a/Yank/__init__.py b/yank/__init__.py
similarity index 100%
rename from Yank/__init__.py
rename to yank/__init__.py
diff --git a/Yank/analyze.py b/yank/analyze.py
similarity index 99%
rename from Yank/analyze.py
rename to yank/analyze.py
index 4191b822..d85fef57 100644
--- a/Yank/analyze.py
+++ b/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
diff --git a/Yank/cli.py b/yank/cli.py
similarity index 100%
rename from Yank/cli.py
rename to yank/cli.py
diff --git a/Yank/commands/__init__.py b/yank/commands/__init__.py
similarity index 100%
rename from Yank/commands/__init__.py
rename to yank/commands/__init__.py
diff --git a/Yank/commands/analyze.py b/yank/commands/analyze.py
similarity index 100%
rename from Yank/commands/analyze.py
rename to yank/commands/analyze.py
diff --git a/Yank/commands/cite.py b/yank/commands/cite.py
similarity index 100%
rename from Yank/commands/cite.py
rename to yank/commands/cite.py
diff --git a/Yank/commands/cleanup.py b/yank/commands/cleanup.py
similarity index 100%
rename from Yank/commands/cleanup.py
rename to yank/commands/cleanup.py
diff --git a/Yank/commands/help.py b/yank/commands/help.py
similarity index 100%
rename from Yank/commands/help.py
rename to yank/commands/help.py
diff --git a/Yank/commands/platforms.py b/yank/commands/platforms.py
similarity index 100%
rename from Yank/commands/platforms.py
rename to yank/commands/platforms.py
diff --git a/Yank/commands/script.py b/yank/commands/script.py
similarity index 100%
rename from Yank/commands/script.py
rename to yank/commands/script.py
diff --git a/Yank/commands/selftest.py b/yank/commands/selftest.py
similarity index 99%
rename from Yank/commands/selftest.py
rename to yank/commands/selftest.py
index 1828311a..efaf7a89 100644
--- a/Yank/commands/selftest.py
+++ b/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
diff --git a/Yank/commands/status.py b/yank/commands/status.py
similarity index 100%
rename from Yank/commands/status.py
rename to yank/commands/status.py
diff --git a/Yank/experiment.py b/yank/experiment.py
similarity index 99%
rename from Yank/experiment.py
rename to yank/experiment.py
index 2b266403..c9076f1d 100644
--- a/Yank/experiment.py
+++ b/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]).
diff --git a/Yank/pipeline.py b/yank/pipeline.py
similarity index 99%
rename from Yank/pipeline.py
rename to yank/pipeline.py
index 41bbe935..f4fcf08c 100644
--- a/Yank/pipeline.py
+++ b/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
     ----------
diff --git a/Yank/reports/YANK_Health_Report_Example.ipynb b/yank/reports/YANK_Health_Report_Example.ipynb
similarity index 100%
rename from Yank/reports/YANK_Health_Report_Example.ipynb
rename to yank/reports/YANK_Health_Report_Example.ipynb
diff --git a/Yank/reports/YANK_Health_Report_Template.ipynb b/yank/reports/YANK_Health_Report_Template.ipynb
similarity index 100%
rename from Yank/reports/YANK_Health_Report_Template.ipynb
rename to yank/reports/YANK_Health_Report_Template.ipynb
diff --git a/Yank/reports/__init__.py b/yank/reports/__init__.py
similarity index 100%
rename from Yank/reports/__init__.py
rename to yank/reports/__init__.py
diff --git a/Yank/reports/notebook.py b/yank/reports/notebook.py
similarity index 100%
rename from Yank/reports/notebook.py
rename to yank/reports/notebook.py
diff --git a/Yank/restraints.py b/yank/restraints.py
similarity index 100%
rename from Yank/restraints.py
rename to yank/restraints.py
diff --git a/Yank/schema/__init__.py b/yank/schema/__init__.py
similarity index 100%
rename from Yank/schema/__init__.py
rename to yank/schema/__init__.py
diff --git a/Yank/schema/validator.py b/yank/schema/validator.py
similarity index 100%
rename from Yank/schema/validator.py
rename to yank/schema/validator.py
diff --git a/Yank/tests/__init__.py b/yank/tests/__init__.py
similarity index 100%
rename from Yank/tests/__init__.py
rename to yank/tests/__init__.py
diff --git a/Yank/tests/data/README.md b/yank/tests/data/README.md
similarity index 100%
rename from Yank/tests/data/README.md
rename to yank/tests/data/README.md
diff --git a/Yank/tests/data/abl-imatinib-explicit/2HYY-pdbfixer.pdb b/yank/tests/data/abl-imatinib-explicit/2HYY-pdbfixer.pdb
similarity index 100%
rename from Yank/tests/data/abl-imatinib-explicit/2HYY-pdbfixer.pdb
rename to yank/tests/data/abl-imatinib-explicit/2HYY-pdbfixer.pdb
diff --git a/Yank/tests/data/abl-imatinib-explicit/STI02.mol2 b/yank/tests/data/abl-imatinib-explicit/STI02.mol2
similarity index 100%
rename from Yank/tests/data/abl-imatinib-explicit/STI02.mol2
rename to yank/tests/data/abl-imatinib-explicit/STI02.mol2
diff --git a/Yank/tests/data/benzene-toluene-explicit/benzene.frcmod b/yank/tests/data/benzene-toluene-explicit/benzene.frcmod
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/benzene.frcmod
rename to yank/tests/data/benzene-toluene-explicit/benzene.frcmod
diff --git a/Yank/tests/data/benzene-toluene-explicit/benzene.gaff.mol2 b/yank/tests/data/benzene-toluene-explicit/benzene.gaff.mol2
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/benzene.gaff.mol2
rename to yank/tests/data/benzene-toluene-explicit/benzene.gaff.mol2
diff --git a/Yank/tests/data/benzene-toluene-explicit/benzene.tripos.mol2 b/yank/tests/data/benzene-toluene-explicit/benzene.tripos.mol2
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/benzene.tripos.mol2
rename to yank/tests/data/benzene-toluene-explicit/benzene.tripos.mol2
diff --git a/Yank/tests/data/benzene-toluene-explicit/complex.inpcrd b/yank/tests/data/benzene-toluene-explicit/complex.inpcrd
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/complex.inpcrd
rename to yank/tests/data/benzene-toluene-explicit/complex.inpcrd
diff --git a/Yank/tests/data/benzene-toluene-explicit/complex.prmtop b/yank/tests/data/benzene-toluene-explicit/complex.prmtop
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/complex.prmtop
rename to yank/tests/data/benzene-toluene-explicit/complex.prmtop
diff --git a/Yank/tests/data/benzene-toluene-explicit/solvent.inpcrd b/yank/tests/data/benzene-toluene-explicit/solvent.inpcrd
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/solvent.inpcrd
rename to yank/tests/data/benzene-toluene-explicit/solvent.inpcrd
diff --git a/Yank/tests/data/benzene-toluene-explicit/solvent.prmtop b/yank/tests/data/benzene-toluene-explicit/solvent.prmtop
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/solvent.prmtop
rename to yank/tests/data/benzene-toluene-explicit/solvent.prmtop
diff --git a/Yank/tests/data/benzene-toluene-explicit/toluene.frcmod b/yank/tests/data/benzene-toluene-explicit/toluene.frcmod
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/toluene.frcmod
rename to yank/tests/data/benzene-toluene-explicit/toluene.frcmod
diff --git a/Yank/tests/data/benzene-toluene-explicit/toluene.tripos.mol2 b/yank/tests/data/benzene-toluene-explicit/toluene.tripos.mol2
similarity index 100%
rename from Yank/tests/data/benzene-toluene-explicit/toluene.tripos.mol2
rename to yank/tests/data/benzene-toluene-explicit/toluene.tripos.mol2
diff --git a/Yank/tests/data/benzene-toluene-standard-state/README.md b/yank/tests/data/benzene-toluene-standard-state/README.md
similarity index 100%
rename from Yank/tests/data/benzene-toluene-standard-state/README.md
rename to yank/tests/data/benzene-toluene-standard-state/README.md
diff --git a/Yank/tests/data/benzene-toluene-standard-state/standard_state_complex.inpcrd b/yank/tests/data/benzene-toluene-standard-state/standard_state_complex.inpcrd
similarity index 100%
rename from Yank/tests/data/benzene-toluene-standard-state/standard_state_complex.inpcrd
rename to yank/tests/data/benzene-toluene-standard-state/standard_state_complex.inpcrd
diff --git a/Yank/tests/data/benzene-toluene-standard-state/standard_state_complex.prmtop b/yank/tests/data/benzene-toluene-standard-state/standard_state_complex.prmtop
similarity index 100%
rename from Yank/tests/data/benzene-toluene-standard-state/standard_state_complex.prmtop
rename to yank/tests/data/benzene-toluene-standard-state/standard_state_complex.prmtop
diff --git a/Yank/tests/data/benzene-toluene-standard-state/standard_state_complex_boxless.inpcrd b/yank/tests/data/benzene-toluene-standard-state/standard_state_complex_boxless.inpcrd
similarity index 100%
rename from Yank/tests/data/benzene-toluene-standard-state/standard_state_complex_boxless.inpcrd
rename to yank/tests/data/benzene-toluene-standard-state/standard_state_complex_boxless.inpcrd
diff --git a/Yank/tests/data/benzene-toluene-standard-state/standard_state_complex_nan.inpcrd b/yank/tests/data/benzene-toluene-standard-state/standard_state_complex_nan.inpcrd
similarity index 100%
rename from Yank/tests/data/benzene-toluene-standard-state/standard_state_complex_nan.inpcrd
rename to yank/tests/data/benzene-toluene-standard-state/standard_state_complex_nan.inpcrd
diff --git a/Yank/tests/data/p-xylene-gromacs-example/complex.gro b/yank/tests/data/p-xylene-gromacs-example/complex.gro
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/complex.gro
rename to yank/tests/data/p-xylene-gromacs-example/complex.gro
diff --git a/Yank/tests/data/p-xylene-gromacs-example/complex.top b/yank/tests/data/p-xylene-gromacs-example/complex.top
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/complex.top
rename to yank/tests/data/p-xylene-gromacs-example/complex.top
diff --git a/Yank/tests/data/p-xylene-gromacs-example/solvent.gro b/yank/tests/data/p-xylene-gromacs-example/solvent.gro
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/solvent.gro
rename to yank/tests/data/p-xylene-gromacs-example/solvent.gro
diff --git a/Yank/tests/data/p-xylene-gromacs-example/solvent.top b/yank/tests/data/p-xylene-gromacs-example/solvent.top
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/solvent.top
rename to yank/tests/data/p-xylene-gromacs-example/solvent.top
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/atomtypes.atp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/atomtypes.atp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/atomtypes.atp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/atomtypes.atp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/cmap.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/cmap.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/cmap.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/cmap.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffbonded.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffbonded.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffbonded.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffbonded.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffnonbonded.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffnonbonded.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffnonbonded.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ffnonbonded.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.doc b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.doc
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.doc
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.doc
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/forcefield.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/gb.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/gb.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/gb.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/gb.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ions.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ions.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ions.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/ions.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.arn b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.arn
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.arn
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.arn
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.c.tdb b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.c.tdb
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.c.tdb
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.c.tdb
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.hdb b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.hdb
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.hdb
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.hdb
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.n.tdb b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.n.tdb
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.n.tdb
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.n.tdb
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.r2b b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.r2b
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.r2b
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.r2b
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.rtp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.rtp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.rtp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.rtp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.vsd b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.vsd
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.vsd
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/merged.vsd
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/nbfix.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/nbfix.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/nbfix.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/nbfix.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spc.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spc.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spc.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spc.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spce.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spce.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spce.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/spce.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip3p.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip3p.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip3p.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip3p.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip4p.itp b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip4p.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip4p.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/tip4p.itp
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/watermodels.dat b/yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/watermodels.dat
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/watermodels.dat
rename to yank/tests/data/p-xylene-gromacs-example/top/charmm36.ff/watermodels.dat
diff --git a/Yank/tests/data/p-xylene-gromacs-example/top/p-xyle.itp b/yank/tests/data/p-xylene-gromacs-example/top/p-xyle.itp
similarity index 100%
rename from Yank/tests/data/p-xylene-gromacs-example/top/p-xyle.itp
rename to yank/tests/data/p-xylene-gromacs-example/top/p-xyle.itp
diff --git a/Yank/tests/data/p-xylene-implicit/181L-pdbfixer.pdb b/yank/tests/data/p-xylene-implicit/181L-pdbfixer.pdb
similarity index 100%
rename from Yank/tests/data/p-xylene-implicit/181L-pdbfixer.pdb
rename to yank/tests/data/p-xylene-implicit/181L-pdbfixer.pdb
diff --git a/Yank/tests/data/p-xylene-implicit/p-xylene.mol2 b/yank/tests/data/p-xylene-implicit/p-xylene.mol2
similarity index 100%
rename from Yank/tests/data/p-xylene-implicit/p-xylene.mol2
rename to yank/tests/data/p-xylene-implicit/p-xylene.mol2
diff --git a/Yank/tests/data/toluene-explicit/solvent.pdb b/yank/tests/data/toluene-explicit/solvent.pdb
similarity index 100%
rename from Yank/tests/data/toluene-explicit/solvent.pdb
rename to yank/tests/data/toluene-explicit/solvent.pdb
diff --git a/Yank/tests/data/toluene-explicit/solvent.xml b/yank/tests/data/toluene-explicit/solvent.xml
similarity index 100%
rename from Yank/tests/data/toluene-explicit/solvent.xml
rename to yank/tests/data/toluene-explicit/solvent.xml
diff --git a/Yank/tests/data/toluene-explicit/vacuum.pdb b/yank/tests/data/toluene-explicit/vacuum.pdb
similarity index 100%
rename from Yank/tests/data/toluene-explicit/vacuum.pdb
rename to yank/tests/data/toluene-explicit/vacuum.pdb
diff --git a/Yank/tests/data/toluene-explicit/vacuum.xml b/yank/tests/data/toluene-explicit/vacuum.xml
similarity index 100%
rename from Yank/tests/data/toluene-explicit/vacuum.xml
rename to yank/tests/data/toluene-explicit/vacuum.xml
diff --git a/Yank/tests/test_analyze.py b/yank/tests/test_analyze.py
similarity index 100%
rename from Yank/tests/test_analyze.py
rename to yank/tests/test_analyze.py
diff --git a/Yank/tests/test_cli.py b/yank/tests/test_cli.py
similarity index 100%
rename from Yank/tests/test_cli.py
rename to yank/tests/test_cli.py
diff --git a/Yank/tests/test_examples.py b/yank/tests/test_examples.py
similarity index 100%
rename from Yank/tests/test_examples.py
rename to yank/tests/test_examples.py
diff --git a/Yank/tests/test_experiment.py b/yank/tests/test_experiment.py
similarity index 99%
rename from Yank/tests/test_experiment.py
rename to yank/tests/test_experiment.py
index 840737ae..b2cd4941 100644
--- a/Yank/tests/test_experiment.py
+++ b/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')
diff --git a/Yank/tests/test_pipeline.py b/yank/tests/test_pipeline.py
similarity index 96%
rename from Yank/tests/test_pipeline.py
rename to yank/tests/test_pipeline.py
index 780b93ed..e5e779bd 100644
--- a/Yank/tests/test_pipeline.py
+++ b/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)
 
 
@@ -47,9 +47,9 @@ 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
@@ -57,9 +57,9 @@ def test_remove_overlap():
 
 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]
diff --git a/Yank/tests/test_restraints.py b/yank/tests/test_restraints.py
similarity index 100%
rename from Yank/tests/test_restraints.py
rename to yank/tests/test_restraints.py
diff --git a/Yank/tests/test_schema.py b/yank/tests/test_schema.py
similarity index 100%
rename from Yank/tests/test_schema.py
rename to yank/tests/test_schema.py
diff --git a/Yank/tests/test_utils.py b/yank/tests/test_utils.py
similarity index 100%
rename from Yank/tests/test_utils.py
rename to yank/tests/test_utils.py
diff --git a/Yank/tests/test_yank.py b/yank/tests/test_yank.py
similarity index 99%
rename from Yank/tests/test_yank.py
rename to yank/tests/test_yank.py
index 7ae42e85..e4e884c3 100644
--- a/Yank/tests/test_yank.py
+++ b/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.
diff --git a/Yank/utils.py b/yank/utils.py
similarity index 99%
rename from Yank/utils.py
rename to yank/utils.py
index a431d2c8..bba7c6f7 100644
--- a/Yank/utils.py
+++ b/yank/utils.py
@@ -31,7 +31,12 @@
 import itertools
 import contextlib
 import subprocess
-import collections
+
+try:
+    from collections import MutableMapping, Mapping
+except ImportError:
+    # Support python 3.10
+    from collections.abc import MutableMapping, Mapping
 
 from pkg_resources import resource_filename
 
@@ -276,7 +281,7 @@ def __repr__(self):
         return "Combinatorial({})".format(super(CombinatorialLeaf, self).__repr__())
 
 
-class CombinatorialTree(collections.MutableMapping):
+class CombinatorialTree(MutableMapping):
     """A tree that can be expanded in a combinatorial fashion.
 
     Each tree node with its subnodes is represented as a nested dictionary. Nodes can be
@@ -618,7 +623,7 @@ def recursive_find_leaves(node):
             leaf_paths = []
             leaf_vals = []
             for child_key, child_val in node.items():
-                if isinstance(child_val, collections.Mapping):
+                if isinstance(child_val, Mapping):
                     subleaf_paths, subleaf_vals = recursive_find_leaves(child_val)
                     # prepend child key to path
                     leaf_paths.extend([(child_key,) + subleaf for subleaf in subleaf_paths])
@@ -760,7 +765,7 @@ def update_nested_dict(original, updated):
     """
     new = original.copy()
     for key, value in updated.items():
-        if isinstance(value, collections.Mapping):
+        if isinstance(value, Mapping):
             replacement = update_nested_dict(new.get(key, {}), value)
             new[key] = replacement
         else:
@@ -1791,7 +1796,7 @@ def generate_development_feature(feature_dict):
         require instantiation. Function names are all given the `dev_` prefix to avoid clashes with other names its
         a part of its psudo-mixin properties
     """
-    base_err = ('This feature cannot be used because it has been marked as "Developmental" and ' 
+    base_err = ('This feature cannot be used because it has been marked as "Developmental" and '
                 'the following conditions have not been met:\n')
     valid = True  # Assume valid until proven otherwise
     check_dict = {}
diff --git a/Yank/yank.py b/yank/yank.py
similarity index 99%
rename from Yank/yank.py
rename to yank/yank.py
index b117365a..3eab9bab 100644
--- a/Yank/yank.py
+++ b/yank/yank.py
@@ -5,7 +5,7 @@
 # ==============================================================================
 
 """
-Yank
+yank
 ====
 
 Interface for automated free energy calculations.