diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 6b76dae..7666224 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -21,16 +21,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: ["3.8", "3.9"]
+        os: [macOS-latest, ubuntu-latest, macOS-13]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     # Cache our conda packages.
     # More info: https://github.com/conda-incubator/setup-miniconda#caching-packages
     - name: Cache conda environment
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       env:
         # Increase this value to reset cache if environment.yml has not changed
         CACHE_NUMBER: 0
@@ -41,15 +41,15 @@ jobs:
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - name: Set up Anaconda environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: environment.yml
-        channels: psi4,conda-forge,defaults
+        channels: conda-forge,defaults
         activate-environment: mdsapt
         auto-update-conda: false
         auto-activate-base: false
-        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          #use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
     
     # TODO: make pyright happier someday in the future
     # - name: Type-check
@@ -83,8 +83,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9]
+        os: [macOS-13, ubuntu-latest]
+        python-version: [3.9, 3.10, 3.11, 3.12]
         include:
           - os: macOS-latest
             output-folder: osx-64
@@ -116,7 +116,7 @@ jobs:
         activate-environment: mdsapt-build
         auto-update-conda: false
         auto-activate-base: false
-        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          #use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
 
     - name: Build MDSAPT conda package
       # conda requires this special shell
@@ -139,8 +139,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9]
+        os: [macOS-latest, macOS-13, ubuntu-latest]
+        python-version: [3.9, 3.10, 3.11, 3.12]
 
     steps:
     - uses: actions/checkout@v2
diff --git a/README.md b/README.md
index 4892732..1403195 100644
--- a/README.md
+++ b/README.md
@@ -3,8 +3,8 @@ MD-SAPT
 SAPT Calculations for MDAnalysis
 
 [//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/alescoulie/MDSAPT/workflows/CI/badge.svg)](https://github.com/alescolie/MDSAPT/actions?query=workflow%3ACI)
-[![codecov](https://codecov.io/gh/alescoulie/MDSAPT/branch/master/graph/badge.svg)](https://codecov.io/gh/alescoulie/MDSAPT/branch/master)
+[![GitHub Actions Build Status](https://github.com/calpolyccg/MDSAPT/workflows/CI/badge.svg)](https://github.com/alescolie/MDSAPT/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/calpolyccg/MDSAPT/branch/master/graph/badge.svg)](https://codecov.io/gh/alescoulie/MDSAPT/branch/master)
 [![Documentation Status](https://readthedocs.org/projects/mdsapt/badge/?version=latest)](https://mdsapt.readthedocs.io/en/latest/?badge=latest)
 [![Launch binder demo](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/calpolyccg/MDSAPT_demo/master?labpath=MD-SAPT_demo.ipynb)
 
diff --git a/flake.nix b/flake.nix
index 0de6daa..7155bef 100644
--- a/flake.nix
+++ b/flake.nix
@@ -62,7 +62,7 @@
 
         devEnv = pkgs.mkShell {
           propagatedBuildInputs = [ poetryEnv];
-          buildInputs = with pkgs; [pkgs.qchem.psi4 pkgs.qchem.openmm pkgs.qchem.pdbfixer ];
+          buildInputs = with pkgs; [pkgs.qchem.psi4 pkgs.qchem.openmm pkgs.qchem.pdbfixer pkgs.act ];
         };
 
         # DON'T FORGET TO PUT YOUR PACKAGE NAME HERE, REMOVING `throw`
diff --git a/mdsapt/__init__.py b/mdsapt/__init__.py
index 8ccb27f..0c96db4 100644
--- a/mdsapt/__init__.py
+++ b/mdsapt/__init__.py
@@ -1,5 +1,6 @@
 # pylint: skip-file
 """An MDA-kit for calcuating quantum interactions in psi4."""
+from . import _version
 import logging
 
 from . import log
@@ -34,5 +35,4 @@ def log_banner() -> None:
 logger = create_logger()
 log_banner()
 
-from . import _version
 __version__ = _version.get_versions()['version']
diff --git a/mdsapt/_version.py b/mdsapt/_version.py
index 25e5815..74d9c69 100644
--- a/mdsapt/_version.py
+++ b/mdsapt/_version.py
@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -19,6 +18,9 @@
 from typing import Any, Callable, Dict, List, Optional, Tuple
 import functools
 
+# pylint: disable=consider-using-f-string
+# pylint: disable=invalid-name
+
 
 def get_keywords() -> Dict[str, str]:
     """Get the keywords needed to look up the version information."""
@@ -162,7 +164,7 @@ def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
     # _version.py.
     keywords: Dict[str, str] = {}
     try:
-        with open(versionfile_abs, "r") as fobj:
+        with open(versionfile_abs, "r") as fobj:  # pylint: disable=unspecified-encoding
             for line in fobj:
                 if line.strip().startswith("git_refnames ="):
                     mo = re.search(r'=\s*"(.*)"', line)
diff --git a/mdsapt/cli.py b/mdsapt/cli.py
index b58564c..1403be8 100644
--- a/mdsapt/cli.py
+++ b/mdsapt/cli.py
@@ -1,9 +1,9 @@
+# pylint: disable=missing-module-docstring
 import logging
 import os
 import sys
 
 import click
-from mdsapt.config import RangeFrameSelection
 
 # Note that we do not import MDSAPT. This is a speed optimization; it is imported later.
 
@@ -16,11 +16,13 @@
 
 @click.group()
 def cli():
+    # pylint: disable=line-too-long
     """
     MDSAPT - Molecular Dynamics Symmetry-Adapted Perturbation Theory, by Alia Lescoulie, Astrid Yu, and Ashley Ringer McDonald.
 
     This command-line interface lets you easily do common MDSAPT-related tasks.
     """
+    # pylint: disable=line-too-long
 
 
 @cli.command()
@@ -43,17 +45,19 @@ def generate(filename: str, template: str, force: bool):
     """
     Generate a template input file at filename.
     """
+    # pylint: disable=fixme
     ensure_safe_to_overwrite(filename, force)
 
     # TODO: make a wizard for these templates
     template_path = os.path.join(_dir_path, 'data', f'{template}_template.yaml')
 
-    with open(template_path, 'r') as template:
+    with open(template_path, 'r', encoding='utf-8') as template:
         template_data = template.read()
-    with open(filename, 'w') as new_file:
+    with open(filename, 'w', encoding='utf-8') as new_file:
         new_file.write(template_data)
 
-    logger.info(f'Generated template input file {filename}')
+    logger.info('Generated template input file %s', filename)
+    # pylint: enable=fixme
 
 
 @cli.command()
@@ -75,7 +79,7 @@ def run(in_file: str, out_file: str, force: bool):
     Run a SAPT calculation using the configuration in in_file. Outputs will be written to
     out_file.
     """
-    import mdsapt
+    import mdsapt  # pylint: disable=import-outside-toplevel
 
     ensure_safe_to_overwrite(out_file, force)
 
diff --git a/mdsapt/config.py b/mdsapt/config.py
index ea6acfa..4c53137 100644
--- a/mdsapt/config.py
+++ b/mdsapt/config.py
@@ -43,7 +43,8 @@ class Psi4Config(BaseModel):
     Attributes:
         method:
             The SAPT method to use.
-            NOTE: You can use any valid Psi4 method, but it might fail if you don't use a SAPT method.
+            NOTE: You can use any valid Psi4 method, but it might fail
+            if you don't use a SAPT method.
         basis:
             The basis to use.
             NOTE: We do not verify if this is a valid basis set or not.
@@ -51,7 +52,8 @@ class Psi4Config(BaseModel):
             Whether to save the raw output of Psi4. May be useful for debugging.
         settings:
             Other Psi4 settings you would like to provide. These will be passed into
-            `psi4.set_options <https://psicode.org/psi4manual/master/api/psi4.driver.set_options.html>`_.
+            `psi4.set_options 
+            <https://psicode.org/psi4manual/master/api/psi4.driver.set_options.html>`_.
     """
 
     method: str
@@ -97,10 +99,12 @@ class TopologySelection(BaseModel):
     Attributes:
         path: Where the topology file is located.
         topology_format: If specified, overrides the format to import with.
-        charge_overrides: An optional dictionary, where keys are atom numbers and values are their charges.
+        charge_overrides: An optional dictionary, where keys are atom numbers and 
+        values are their charges.
 
     .. seealso::
-        `List of topology formats that MDAnalysis supports <https://docs.mdanalysis.org/1.1.1/documentation_pages/topology/init.html>`_
+        `List of topology formats that MDAnalysis supports 
+        <https://docs.mdanalysis.org/1.1.1/documentation_pages/topology/init.html>`_
     """
 
     path: Path
@@ -164,8 +168,14 @@ class TrajectoryAnalysisConfig(BaseModel):
     type: Literal['trajectory']
     topology: TopologySelection
     trajectories: List[FilePath]
-    pairs: List[Tuple[Annotated[int, Field(strict=True, ge=0)], Annotated[int, Field(strict=True, ge=0)]
-                      ]]
+    pairs: List[
+        Tuple[
+            Annotated[
+                int,
+                Field(strict=True, ge=0)],
+            Annotated[int, Field(strict=True, ge=0)]
+        ]
+    ]
     frames: RangeFrameSelection
     output: str
 
@@ -173,7 +183,10 @@ def create_universe(self, **universe_kwargs) -> mda.Universe:
         """
         Loads a universe from the given topology and trajectory
         """
-        return self.topology.create_universe([str(p) for p in self.trajectories], **universe_kwargs)
+        return self.topology.create_universe(
+            [str(p) for p in self.trajectories],
+            **universe_kwargs
+        )
 
     def get_selections(self) -> Set[int]:
         """
@@ -209,6 +222,10 @@ def get_invalid_residue_selections(residues: Iterable[int], unv: mda.Universe) -
 
 
 def get_individual_topologies(sel: TopologyGroupSelection) -> List[TopologySelection]:
+    """
+    Gets a list of :class:`mdsapt.config.TopolgoySelections` from a 
+    :class:`mdsapt.config.TopologyGroupSelection`
+    """
     if isinstance(sel, list):
         return sel
 
@@ -257,12 +274,27 @@ class DockingAnalysisConfig(BaseModel):
 
     @model_validator(mode='after')
     def ensure_presence_of_args(self) -> 'DockingAnalysisConfig':
-        provided_args = (self.combined_topologies is not None, self.protein is not None, self.ligands is not None)
+        """
+        Checks that arguments are correct
+        """
+        provided_args = (
+            self.combined_topologies is not None,
+            self.protein is not None,
+            self.ligands is not None
+        )
+
         if provided_args not in [(True, False, False), (False, True, True)]:
-            raise ValueError('Must provide `protein` and `ligands` keys, or only `combined_topologies`')
+            raise ValueError(
+                'Must provide `protein` and `ligands` keys, or only `combined_topologies`'
+            )
+
         return self
 
     def build_ensemble(self) -> Ensemble:
+        """
+        Creates an Ensemble containing the set of topologies used to analyze docking.
+
+        """
         return self._build_ensemble(combined_topologies=self.combined_topologies,
                                     protein=self.protein,
                                     ligands=self.ligands)
@@ -275,7 +307,9 @@ def _build_ensemble(
             protein: Optional[TopologySelection],
             ligands: Optional[TopologyGroupSelection],
     ) -> Ensemble:
-        """Fails if the wrong types of arguments are provided."""
+        """
+        Fails if the wrong types of arguments are provided.
+        """
         if combined_topologies is not None and (protein, ligands) == (None, None):
             return Ensemble.build_from_files(
                 [top.path for top in get_individual_topologies(combined_topologies)]
@@ -289,7 +323,9 @@ def _build_ensemble(
             ens = ens.merge(protein_mol)
             return ens
 
-        raise ValueError('Must provide `protein` and `ligands` keys, or only `combined_topologies`')
+        raise ValueError(
+            'Must provide `protein` and `ligands` keys, or only `combined_topologies`'
+        )
 
     def get_selections(self) -> Set[int]:
         """
diff --git a/mdsapt/repair.py b/mdsapt/repair.py
index be7fa7e..4d5ce18 100644
--- a/mdsapt/repair.py
+++ b/mdsapt/repair.py
@@ -57,6 +57,9 @@ def get_spin_multiplicity(molecule: Chem.Mol) -> int:
 
 
 def is_amino(unv: mda.Universe, resid: int) -> bool:
+    """
+    Checks resnames aganst list of anmino acids, returns boolean if its in the list.
+    """
     std_resids: Set[str] = {
         'ALA',
         'ARG',
@@ -80,7 +83,7 @@ def is_amino(unv: mda.Universe, resid: int) -> bool:
         'VAL'
     }
 
-    resname_atr = unv._topology.resnames
+    resname_atr = unv._topology.resnames  # pylint: disable=protected-access
     return resname_atr.values[resid - 1] in std_resids
 
 
diff --git a/mdsapt/sapt.py b/mdsapt/sapt.py
index 39b220e..ccd0142 100644
--- a/mdsapt/sapt.py
+++ b/mdsapt/sapt.py
@@ -206,6 +206,10 @@ class DockingSAPT:
         'SAPT DISP ENERGY'
     ]
 
+    _res_dict: Dict[str, List[float]]
+    _key_names: Dict[str, str]
+    results: pd.DataFrame
+
     def __init__(self, config: Config) -> None:
         """
         Sets up ligand topology systems.
@@ -247,7 +251,7 @@ def _single_system(self) -> None:
 
             coords = xyz_dict[pair[0]] + '\n--\n' + xyz_dict[pair[1]] + '\nunits angstrom'
 
-            logger.info(f'Starting SAPT for {pair}')
+            logger.info(f'Starting SAPT for {pair}')  # pylint: disable=logging-fstring-interpolation
 
             if self._cfg.psi4.save_output:
                 outfile = f'sapt_{self._key_names[self._key]}_{self._pair_names[pair]}.out'
diff --git a/mdsapt/tests/test_config.py b/mdsapt/tests/test_config.py
index 80b0084..ecd1191 100644
--- a/mdsapt/tests/test_config.py
+++ b/mdsapt/tests/test_config.py
@@ -5,7 +5,6 @@
 from tempfile import mktemp
 from typing import Dict, Any
 
-import pydantic
 import pytest
 
 from pydantic import ValidationError
diff --git a/mdsapt/tests/test_sapt.py b/mdsapt/tests/test_sapt.py
index bf993a5..2ce44a5 100644
--- a/mdsapt/tests/test_sapt.py
+++ b/mdsapt/tests/test_sapt.py
@@ -3,22 +3,22 @@
 """
 import os
 
-import MDAnalysis
 from MDAnalysis.topology.guessers import guess_types
 
-from ..config import Config, load_from_yaml_file
+from ..config import load_from_yaml_file
 from ..sapt import TrajectorySAPT, DockingSAPT
 
 traj_settings = load_from_yaml_file(
     os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'test_input.yaml'))
 
 dock_settings = load_from_yaml_file(
-            os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'docking_in.yaml'))
+    os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'docking_in.yaml'))
 
 unv = traj_settings.analysis.create_universe()
 elements = guess_types(unv.atoms.names)
 unv.add_TopologyAttr('elements', elements)
 
+
 class TestSAPT:
     """
     Test object for SAPT analysis
diff --git a/poetry.lock b/poetry.lock
index f65c5bd..0d0a325 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
 version = "0.7.16"
 description = "A light, configurable Sphinx theme"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -16,7 +15,6 @@ files = [
 name = "annotated-types"
 version = "0.7.0"
 description = "Reusable constraint types to use with typing.Annotated"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -28,7 +26,6 @@ files = [
 name = "astroid"
 version = "3.2.2"
 description = "An abstract syntax tree for Python with inference support."
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -41,25 +38,23 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "autopep8"
-version = "2.2.0"
+version = "2.3.0"
 description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "autopep8-2.2.0-py2.py3-none-any.whl", hash = "sha256:05418a981f038969d8bdcd5636bf15948db7555ae944b9f79b5a34b35f1370d4"},
-    {file = "autopep8-2.2.0.tar.gz", hash = "sha256:d306a0581163ac29908280ad557773a95a9bede072c0fafed6f141f5311f43c1"},
+    {file = "autopep8-2.3.0-py2.py3-none-any.whl", hash = "sha256:b716efa70cbafbf4a2c9c5ec1cabfa037a68f9e30b04c74ffa5864dd49b8f7d2"},
+    {file = "autopep8-2.3.0.tar.gz", hash = "sha256:5cfe45eb3bef8662f6a3c7e28b7c0310c7310d340074b7f0f28f9810b44b7ef4"},
 ]
 
 [package.dependencies]
-pycodestyle = ">=2.11.0"
+pycodestyle = ">=2.12.0"
 tomli = {version = "*", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "babel"
 version = "2.15.0"
 description = "Internationalization utilities"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -74,7 +69,6 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 name = "certifi"
 version = "2024.6.2"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -86,7 +80,6 @@ files = [
 name = "charset-normalizer"
 version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -186,7 +179,6 @@ files = [
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -201,7 +193,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -213,7 +204,6 @@ files = [
 name = "contourpy"
 version = "1.2.1"
 description = "Python library for calculating contours of 2D quadrilateral grids"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -277,7 +267,6 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 name = "coverage"
 version = "7.5.3"
 description = "Code coverage measurement for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -345,7 +334,6 @@ toml = ["tomli"]
 name = "cycler"
 version = "0.12.1"
 description = "Composable style cycles"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -361,7 +349,6 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 name = "dill"
 version = "0.3.8"
 description = "serialize all of Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -377,7 +364,6 @@ profile = ["gprof2dot (>=2022.7.29)"]
 name = "docutils"
 version = "0.20.1"
 description = "Docutils -- Python Documentation Utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -389,7 +375,6 @@ files = [
 name = "exceptiongroup"
 version = "1.2.1"
 description = "Backport of PEP 654 (exception groups)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -404,7 +389,6 @@ test = ["pytest (>=6)"]
 name = "fasteners"
 version = "0.19"
 description = "A python package that provides useful locks"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -416,7 +400,6 @@ files = [
 name = "fonttools"
 version = "4.53.0"
 description = "Tools to manipulate font files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -482,7 +465,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 name = "griddataformats"
 version = "1.0.2"
 description = "Reading and writing of data on regular grids in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -499,7 +481,6 @@ scipy = "*"
 name = "idna"
 version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -511,7 +492,6 @@ files = [
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -521,29 +501,27 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.1.0"
+version = "7.2.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-7.1.0-py3-none-any.whl", hash = "sha256:30962b96c0c223483ed6cc7280e7f0199feb01a0e40cfae4d4450fc6fab1f570"},
-    {file = "importlib_metadata-7.1.0.tar.gz", hash = "sha256:b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2"},
+    {file = "importlib_metadata-7.2.0-py3-none-any.whl", hash = "sha256:04e4aad329b8b948a5711d394fa8759cb80f009225441b4f2a02bd4d8e5f426c"},
+    {file = "importlib_metadata-7.2.0.tar.gz", hash = "sha256:3ff4519071ed42740522d494d04819b666541b9752c43012f85afb2cc220fcc6"},
 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "importlib-resources"
 version = "6.4.0"
 description = "Read resources from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -562,7 +540,6 @@ testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "p
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -574,7 +551,6 @@ files = [
 name = "isort"
 version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -589,7 +565,6 @@ colors = ["colorama (>=0.4.6)"]
 name = "jinja2"
 version = "3.1.4"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -607,7 +582,6 @@ i18n = ["Babel (>=2.7)"]
 name = "joblib"
 version = "1.4.2"
 description = "Lightweight pipelining with Python functions"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -619,7 +593,6 @@ files = [
 name = "kiwisolver"
 version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -733,7 +706,6 @@ files = [
 name = "markupsafe"
 version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -803,7 +775,6 @@ files = [
 name = "matplotlib"
 version = "3.9.0"
 description = "Python plotting package"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -857,7 +828,6 @@ dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6)", "setupto
 name = "mccabe"
 version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -869,7 +839,6 @@ files = [
 name = "mda-xdrlib"
 version = "0.2.0"
 description = "Stand-alone XDRLIB module (from cpython 3.10.8)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -884,7 +853,6 @@ testing = ["pytest"]
 name = "mdanalysis"
 version = "2.7.0"
 description = "An object-oriented toolkit to analyze molecular dynamics trajectories."
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -933,7 +901,6 @@ extra-formats = ["chemfiles (>=0.10)", "gsd (>3.0.0)", "h5py (>=2.10)", "netCDF4
 name = "mmtf-python"
 version = "1.1.3"
 description = "A decoding libary for the PDB mmtf format"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -952,7 +919,6 @@ test = ["coverage"]
 name = "mrcfile"
 version = "1.5.0"
 description = "MRC file I/O library"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -967,7 +933,6 @@ numpy = ">=1.16.0"
 name = "msgpack"
 version = "1.0.8"
 description = "MessagePack serializer"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1033,7 +998,6 @@ files = [
 name = "nodeenv"
 version = "1.9.1"
 description = "Node.js virtual environment builder"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -1045,7 +1009,6 @@ files = [
 name = "numpy"
 version = "1.26.4"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1091,7 +1054,6 @@ files = [
 name = "packaging"
 version = "24.1"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1103,7 +1065,6 @@ files = [
 name = "pandas"
 version = "2.2.2"
 description = "Powerful data structures for data analysis, time series, and statistics"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1141,8 +1102,8 @@ files = [
 [package.dependencies]
 numpy = [
     {version = ">=1.22.4", markers = "python_version < \"3.11\""},
-    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
     {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
+    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1177,7 +1138,6 @@ xml = ["lxml (>=4.9.2)"]
 name = "pillow"
 version = "10.3.0"
 description = "Python Imaging Library (Fork)"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1264,7 +1224,6 @@ xmp = ["defusedxml"]
 name = "platformdirs"
 version = "4.2.2"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1281,7 +1240,6 @@ type = ["mypy (>=1.8)"]
 name = "pluggy"
 version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1295,21 +1253,19 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pycodestyle"
-version = "2.11.1"
+version = "2.12.0"
 description = "Python style guide checker"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pycodestyle-2.11.1-py2.py3-none-any.whl", hash = "sha256:44fe31000b2d866f2e41841b18528a505fbd7fef9017b04eff4e2648a0fadc67"},
-    {file = "pycodestyle-2.11.1.tar.gz", hash = "sha256:41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f"},
+    {file = "pycodestyle-2.12.0-py2.py3-none-any.whl", hash = "sha256:949a39f6b86c3e1515ba1787c2022131d165a8ad271b11370a8819aa070269e4"},
+    {file = "pycodestyle-2.12.0.tar.gz", hash = "sha256:442f950141b4f43df752dd303511ffded3a04c2b6fb7f65980574f0c31e6e79c"},
 ]
 
 [[package]]
 name = "pydantic"
 version = "2.7.4"
 description = "Data validation using Python type hints"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1329,7 +1285,6 @@ email = ["email-validator (>=2.0.0)"]
 name = "pydantic-core"
 version = "2.18.4"
 description = "Core functionality for Pydantic validation and serialization"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1421,7 +1376,6 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 name = "pygments"
 version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1436,7 +1390,6 @@ windows-terminal = ["colorama (>=0.4.6)"]
 name = "pylint"
 version = "3.2.3"
 description = "python code static checker"
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -1449,8 +1402,8 @@ astroid = ">=3.2.2,<=3.3.0-dev0"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
 dill = [
     {version = ">=0.2", markers = "python_version < \"3.11\""},
-    {version = ">=0.3.6", markers = "python_version >= \"3.11\""},
     {version = ">=0.3.7", markers = "python_version >= \"3.12\""},
+    {version = ">=0.3.6", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
 ]
 isort = ">=4.2.5,<5.13.0 || >5.13.0,<6"
 mccabe = ">=0.6,<0.8"
@@ -1467,7 +1420,6 @@ testutils = ["gitpython (>3)"]
 name = "pyparsing"
 version = "3.1.2"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.6.8"
 files = [
@@ -1480,14 +1432,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pyright"
-version = "1.1.367"
+version = "1.1.368"
 description = "Command line wrapper for pyright"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pyright-1.1.367-py3-none-any.whl", hash = "sha256:89de6502ae02f1552d0c4df4b46867887a419849f379db617695ef9308cf01eb"},
-    {file = "pyright-1.1.367.tar.gz", hash = "sha256:b1e5522ceb246ee6bc293a43d6d0162719d6467c1f1e9b81cee741aa11cdacbd"},
+    {file = "pyright-1.1.368-py3-none-any.whl", hash = "sha256:4a86e34b61c755b43b367af7fbf927fc6466fff6b81a9dcea07d42416c640af3"},
+    {file = "pyright-1.1.368.tar.gz", hash = "sha256:9b2aa48142d9d9fc9a6aedff743c76873cc4e615f3297cdbf893d5793f75b306"},
 ]
 
 [package.dependencies]
@@ -1501,7 +1452,6 @@ dev = ["twine (>=3.4.1)"]
 name = "pytest"
 version = "8.2.2"
 description = "pytest: simple powerful testing with Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1524,7 +1474,6 @@ dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments
 name = "pytest-cov"
 version = "5.0.0"
 description = "Pytest plugin for measuring coverage."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1543,7 +1492,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 name = "python-dateutil"
 version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1558,7 +1506,6 @@ six = ">=1.5"
 name = "pytz"
 version = "2024.1"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1570,7 +1517,6 @@ files = [
 name = "rdkit"
 version = "2023.9.6"
 description = "A collection of chemoinformatics and machine-learning software written in C++ and Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1609,7 +1555,6 @@ Pillow = "*"
 name = "requests"
 version = "2.32.3"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1631,7 +1576,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "scipy"
 version = "1.13.1"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1674,7 +1618,6 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1686,7 +1629,6 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1698,7 +1640,6 @@ files = [
 name = "sphinx"
 version = "7.3.7"
 description = "Python documentation generator"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1735,7 +1676,6 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=6.0)", "setuptools
 name = "sphinx-rtd-theme"
 version = "2.0.0"
 description = "Read the Docs theme for Sphinx"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1755,7 +1695,6 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 name = "sphinxcontrib-applehelp"
 version = "1.0.8"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1772,7 +1711,6 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "1.0.6"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1789,7 +1727,6 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.0.5"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1806,7 +1743,6 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jquery"
 version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
-category = "main"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -1821,7 +1757,6 @@ Sphinx = ">=1.8"
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1836,7 +1771,6 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "1.0.7"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1853,7 +1787,6 @@ test = ["pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "1.1.10"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1870,7 +1803,6 @@ test = ["pytest"]
 name = "threadpoolctl"
 version = "3.5.0"
 description = "threadpoolctl"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1882,7 +1814,6 @@ files = [
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1894,7 +1825,6 @@ files = [
 name = "tomlkit"
 version = "0.12.5"
 description = "Style preserving TOML library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1906,7 +1836,6 @@ files = [
 name = "tqdm"
 version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1927,7 +1856,6 @@ telegram = ["requests"]
 name = "typing-extensions"
 version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1939,7 +1867,6 @@ files = [
 name = "tzdata"
 version = "2024.1"
 description = "Provider of IANA time zone data"
-category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -1949,14 +1876,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.2.2"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+    {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"},
+    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
 ]
 
 [package.extras]
@@ -1969,7 +1895,6 @@ zstd = ["zstandard (>=0.18.0)"]
 name = "zipp"
 version = "3.19.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1983,5 +1908,5 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">3.9 <=3.12"
-content-hash = "de4abc3590ee6ed5010ba427f60d81657133ea3e48275e48370cc40f47d8bc64"
+python-versions = "^3.9"
+content-hash = "d5c6b0f166570820a27ebe0b2aa6690a12f291f5d7602522751e4f911bacbc7e"
diff --git a/pyproject.toml b/pyproject.toml
index a6b1dde..d4a1b93 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ license = "GPL-3.0"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">3.9 <=3.12"
+python = "^3.9"
 #numpy = "1.26.1"
 mdanalysis = "^2.7"
 click = "^8.1.7"