Merge pull request #48 from calpolyccg/nix-poetry

Add a Nix development enviornment to MD-SAPT

.envrc

@@ -0,0 +1,2 @@
+use flake
+

.gitignore

@@ -117,3 +117,8 @@ ENV/
 # MDSAPT-generated files
 timer.dat
 input.yaml
+*.out
+
+# Direnv files
+.direnv/
+

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
+

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;
+      });
+}
+

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',