diff --git a/.envrc b/.envrc
new file mode 100644
index 0000000..e3fecb3
--- /dev/null
+++ b/.envrc
@@ -0,0 +1,2 @@
+use flake
+
diff --git a/.gitignore b/.gitignore
index 8b79034..f547a73 100644
--- a/.gitignore
+++ b/.gitignore
@@ -117,3 +117,8 @@ ENV/
 # MDSAPT-generated files
 timer.dat
 input.yaml
+*.out
+
+# Direnv files
+.direnv/
+
diff --git a/docs/install.rst b/docs/install.rst
index e7413d5..b26ec42 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -33,3 +33,22 @@ To ensure it's been installed correctly, run `mdsapt` or `python3 -m mdsapt`.
     Commands:
       generate  Generate a template input file at filename.
       run       Run a SAPT calculation using the configuration in in_file.
+
+
+Creating a Development Environment
+__________________________________
+
+Using Nix
+^^^^^^^^^
+
+Make sure you have the `nix package manager <https://nixos.wiki/wiki/Nix_package_manager>`_ installed and clone the repository.
+The development shell can be entered with the following commands, but note that the initial build it will take a long time to complete.
+
+.. code-block:: bash
+
+   git clone https://github.com/calpolyccg/MDSAPT.git
+   cd MDSAPT
+   nix develop
+
+Alternatively if you have `direnv <https://direnv.net/>`_ you will simply be promoted to approve the directory, then the environment will be built, this method has the advantage of being automatically applied when you enter the MDSAPT directory
+
diff --git a/flake.lock b/flake.lock
new file mode 100644
index 0000000..113f18c
--- /dev/null
+++ b/flake.lock
@@ -0,0 +1,224 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1710146030,
+        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1710146030,
+        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nix-github-actions": {
+      "inputs": {
+        "nixpkgs": [
+          "poetry2nix",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1703863825,
+        "narHash": "sha256-rXwqjtwiGKJheXB43ybM8NwWB8rO2dSRrEqes0S7F5Y=",
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "rev": "5163432afc817cf8bd1f031418d1869e4c9d5547",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1718160348,
+        "narHash": "sha256-9YrUjdztqi4Gz8n3mBuqvCkMo4ojrA6nASwyIKWMpus=",
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "57d6973abba7ea108bac64ae7629e7431e0199b6",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1717298511,
+        "narHash": "sha256-9sXuJn/nL+9ImeYtlspTvjt83z1wIgU+9AwfNbnq+tI=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "6634a0509e9e81e980b129435fbbec518ab246d0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable-small",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_3": {
+      "locked": {
+        "lastModified": 1718149104,
+        "narHash": "sha256-Ds1QpobBX2yoUDx9ZruqVGJ/uQPgcXoYuobBguyKEh8=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "e913ae340076bbb73d9f4d3d065c2bca7caafb16",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "poetry2nix": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nix-github-actions": "nix-github-actions",
+        "nixpkgs": "nixpkgs_2",
+        "systems": "systems_3",
+        "treefmt-nix": "treefmt-nix"
+      },
+      "locked": {
+        "lastModified": 1717965289,
+        "narHash": "sha256-62VsS1MvwcsyYWnxxOD9rX5yqDUvMXH7qE3Kj8HECYE=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "304f8235fb0729fd48567af34fcd1b58d18f9b95",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "type": "github"
+      }
+    },
+    "qchem": {
+      "inputs": {
+        "nixpkgs": "nixpkgs_3"
+      },
+      "locked": {
+        "lastModified": 1718194260,
+        "narHash": "sha256-dgsRQ2cnTJLs527VFmOVJOc8veSEPE5AXc+KOTzArlw=",
+        "owner": "Nix-QChem",
+        "repo": "NixOS-QChem",
+        "rev": "69adddbd0f17b383befa096d01f93764c8225c38",
+        "type": "github"
+      },
+      "original": {
+        "owner": "Nix-QChem",
+        "repo": "NixOS-QChem",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "poetry2nix": "poetry2nix",
+        "qchem": "qchem"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_3": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "id": "systems",
+        "type": "indirect"
+      }
+    },
+    "treefmt-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "poetry2nix",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1717278143,
+        "narHash": "sha256-u10aDdYrpiGOLoxzY/mJ9llST9yO8Q7K/UlROoNxzDw=",
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "rev": "3eb96ca1ae9edf792a8e0963cc92fddfa5a87706",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/flake.nix b/flake.nix
new file mode 100644
index 0000000..0de6daa
--- /dev/null
+++ b/flake.nix
@@ -0,0 +1,75 @@
+{
+  description = "SAPT energy calculator built using MDAnalysis and Psi4 ";
+
+  inputs = {
+    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
+    flake-utils.url = "github:numtide/flake-utils";
+    poetry2nix.url = "github:nix-community/poetry2nix";
+    qchem.url = "github:Nix-QChem/NixOS-QChem";
+  };
+
+  outputs = { self, nixpkgs, flake-utils, poetry2nix, qchem }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        lib = nixpkgs.lib;
+
+        pkgs = import nixpkgs {
+          system = system;
+          overlays = [ 
+            qchem.overlays.qchem 
+            poetry2nix.overlays.default
+          ];
+        };
+
+
+        # Build dependencies for pacakges
+        pypkgs-build-reqs = {
+          mdanalysis = [ "setuptools" ];
+          mda-xdrlib = [ "setuptools" ];
+          mmtf-python = [ "setuptools" ];
+          mrcfile = [ "setuptools" ];
+          griddataformats = [ "setuptools" ];
+          pyright = [ "setuptools" ];
+          #matplotlib = [ "pybind11" ];
+          #scipy = [ "setuptools" "wheel" "pybind11" "pythran" ];
+        };
+
+        p2n-overrides = pkgs.poetry2nix.defaultPoetryOverrides.extend (final: prev:
+          builtins.mapAttrs (package: build-reqs:
+            (builtins.getAttr package prev).overridePythonAttrs (old: {
+              buildInputs = (old.buildInputs or [ ]) ++ (builtins.map (pkg: if builtins.isString pkg then builtins.getAttr pkg prev else pkg) build-reqs);
+            })
+          ) pypkgs-build-reqs
+        );
+
+        unfuckScipy = final: prev: {
+          scipy = pkgs.python311Packages.scipy;
+        };
+
+        unfuckNumpy = final: prev: {
+          numpy = pkgs.python311Packages.numpy;
+        };
+
+        python = pkgs.python311.override {
+          packageOverrides = unfuckScipy;
+        };
+        
+        poetryEnv = pkgs.poetry2nix.mkPoetryEnv {
+          projectDir = ./.;
+          python = python;
+          overrides = [ p2n-overrides unfuckScipy unfuckNumpy ]; #unfuckScipy ];
+        };
+
+        devEnv = pkgs.mkShell {
+          propagatedBuildInputs = [ poetryEnv];
+          buildInputs = with pkgs; [pkgs.qchem.psi4 pkgs.qchem.openmm pkgs.qchem.pdbfixer ];
+        };
+
+        # DON'T FORGET TO PUT YOUR PACKAGE NAME HERE, REMOVING `throw`
+        packageName = "MD-SAPT";
+
+      in {
+        devShells.default = devEnv;
+      });
+}
+
diff --git a/mdsapt/tests/test_sapt.py b/mdsapt/tests/test_sapt.py
index 71c39cf..bf993a5 100644
--- a/mdsapt/tests/test_sapt.py
+++ b/mdsapt/tests/test_sapt.py
@@ -9,32 +9,26 @@
 from ..config import Config, 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'))
+
+unv = traj_settings.analysis.create_universe()
+elements = guess_types(unv.atoms.names)
+unv.add_TopologyAttr('elements', elements)
 
 class TestSAPT:
     """
     Test object for SAPT analysis
     """
-    traj_settings: Config
-    dock_settings: Config
-    unv: MDAnalysis.Universe
-
-    def setup(self) -> None:
-        """
-        Sets up system and config for other tests
-        """
-        self.traj_settings = load_from_yaml_file(
-            os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'test_input.yaml'))
-        self.dock_settings = load_from_yaml_file(
-            os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'docking_in.yaml'))
-        self.unv = self.traj_settings.analysis.create_universe()
-        elements = guess_types(self.unv.atoms.names)
-        self.unv.add_TopologyAttr('elements', elements)
 
     def test_run_traj_sapt(self) -> None:
         """
         Test running trajectory SAPT
         """
-        sapt12 = TrajectorySAPT(self.traj_settings)
+        sapt12 = TrajectorySAPT(traj_settings)
         sapt12.run(1, 2)
         cols_act = sapt12.results.columns
         cols_exp = ['residues', 'time', 'total', 'electrostatic',
@@ -47,7 +41,7 @@ def test_run_dock_sapt(self) -> None:
         """
         Test running docking SAPT
         """
-        docking = DockingSAPT(self.dock_settings)
+        docking = DockingSAPT(dock_settings)
         docking.run()
         cols_act = docking.results.columns
         cols_exp = ['structure', 'pair', 'total', 'electrostatic',
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..f65c5bd
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,1987 @@
+# This file is automatically @generated by Poetry 1.4.2 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 = [
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+]
+
+[[package]]
+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 = [
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
+[[package]]
+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 = [
+    {file = "astroid-3.2.2-py3-none-any.whl", hash = "sha256:e8a0083b4bb28fcffb6207a3bfc9e5d0a68be951dd7e336d5dcf639c682388c0"},
+    {file = "astroid-3.2.2.tar.gz", hash = "sha256:8ead48e31b92b2e217b6c9733a21afafe479d52d6e164dd25fb1a770c7c3cf94"},
+]
+
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
+
+[[package]]
+name = "autopep8"
+version = "2.2.0"
+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"},
+]
+
+[package.dependencies]
+pycodestyle = ">=2.11.0"
+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 = [
+    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
+    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+]
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.6.2"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
+    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
+]
+
+[[package]]
+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 = [
+    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9063e24fdb1e498ab71cb7419e24622516c4a04476b17a2dab57e8baa30d6e03"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6897af51655e3691ff853668779c7bad41579facacf5fd7253b0133308cf000d"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1d3193f4a680c64b4b6a9115943538edb896edc190f0b222e73761716519268e"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cd70574b12bb8a4d2aaa0094515df2463cb429d8536cfb6c7ce983246983e5a6"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8465322196c8b4d7ab6d1e049e4c5cb460d0394da4a27d23cc242fbf0034b6b5"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a9a8e9031d613fd2009c182b69c7b2c1ef8239a0efb1df3f7c8da66d5dd3d537"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:beb58fe5cdb101e3a055192ac291b7a21e3b7ef4f67fa1d74e331a7f2124341c"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:e06ed3eb3218bc64786f7db41917d4e686cc4856944f53d5bdf83a6884432e12"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:2e81c7b9c8979ce92ed306c249d46894776a909505d8f5a4ba55b14206e3222f"},
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diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..a6b1dde
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,29 @@
+[tool.poetry]
+name = "mdsapt"
+version = "2.0.3"
+description = "SAPT energy calculator built using MDAnalysis and Psi4"
+authors = ["Alia Lescoulie <alia.lescoulie@gmail.com>"]
+license = "GPL-3.0"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">3.9 <=3.12"
+#numpy = "1.26.1"
+mdanalysis = "^2.7"
+click = "^8.1.7"
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+autopep8 = "^2.2.0"
+pydantic = "^2.7.4"
+
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"