flake.nix

{
  description = "Code driving the UWMISL CAS-9 implementation of DNA similarity-search.";

  inputs = {
    nixpkgs = {
      url = "github:NixOS/nixpkgs";
    };

    flake-utils = {
      url = "github:numtide/flake-utils";
    };

    pypi-deps-db = {
      url = github:DavHau/pypi-deps-db;
      flake = false;
    };

    mach-nix = {
      url = github:DavHau/mach-nix;
      inputs.nixpkgs.follows = "nixpkgs";
      inputs.flake-utils.follows = "flake-utils";
      inputs.pypi-deps-db.follows = "pypi-deps-db";
    };
  };

  outputs = { self, nixpkgs, flake-utils, pypi-deps-db, mach-nix }:
    flake-utils.lib.eachDefaultSystem (system:
      let
        pname = "kinda";
        version = "0.5";

        python_version = "python38";
        pkgs = nixpkgs.legacyPackages.${system};

        mach-nix-utils = import mach-nix {
          inherit pkgs;
          pypiDataRev = "90885674ac9a4005ec88b05904dc25b653363ab4";
          pypiDataSha256 = "08q5ii3k1p1azix6mwc3dkqc0l4p4md5zbjrdf9f6p3fyxwqk36g";
        };

        peppercorn = mach-nix-utils.buildPythonPackage rec {
          name = "peppercornenumerator";
          version = "v0.6.2";
          python = python_version;

          src = pkgs.fetchFromGitHub {
            owner  = "DNA-and-Natural-Algorithms-Group";
            repo   = "peppercornenumerator";
            rev    = "v0.6.2";
            sha256 = "0nmf1hyvn51cf9vkxlar15hpvl0yf9rd1cvg83r51w64kvszmr7r";
          };
        };

        python = mach-nix-utils.mkPython {
          python = python_version;
          requirements = builtins.readFile ./requirements.txt;
          packagesExtra = [
            #peppercorn
          ];
        };

        customOverrides = self: super: {
          # Overrides go here
        };

        app = mach-nix-utils.buildPythonApplication {
          inherit pname version;

          # add missing dependencies whenever necessary.
          packagesExtra = [
            python
          ];
          src = ./.;
        };

        packageName = "cas9-similarity-search";
      in {
          packages.${packageName} = app;

          defaultPackage = self.packages.${system}.${packageName};

          devShell = import ./shell.nix { inherit python; nixpkgs=pkgs; };
      });
}