add flake config to manage dependencies via nix

.envrc

@@ -0,0 +1,3 @@
+use flake
+
+eval "$shellHook"

.gitignore

@@ -9,4 +9,5 @@ docs/_*
 *.jpg
 *.png
 *.pyc
-*__pycache__*
+*__pycache__*
+.direnv

flake.lock

@@ -0,0 +1,151 @@
+{
+  "nodes": {
+    "flake-compat": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1650374568,
+        "narHash": "sha256-Z+s0J8/r907g149rllvwhb4pKi8Wam5ij0st8PwAh+E=",
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "rev": "b4a34015c698c7793d592d66adbab377907a2be8",
+        "type": "github"
+      },
+      "original": {
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "type": "github"
+      }
+    },
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1659877975,
+        "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "locked": {
+        "lastModified": 1642700792,
+        "narHash": "sha256-XqHrk7hFb+zBvRg6Ghl+AZDq03ov6OshJLiSWOoX5es=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "846b2ae0fc4cc943637d3d1def4454213e203cba",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "mach-nix": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nixpkgs": "nixpkgs",
+        "pypi-deps-db": "pypi-deps-db"
+      },
+      "locked": {
+        "lastModified": 1654084003,
+        "narHash": "sha256-j/XrVVistvM+Ua+0tNFvO5z83isL+LBgmBi9XppxuKA=",
+        "owner": "DavHau",
+        "repo": "mach-nix",
+        "rev": "7e14360bde07dcae32e5e24f366c83272f52923f",
+        "type": "github"
+      },
+      "original": {
+        "id": "mach-nix",
+        "ref": "3.5.0",
+        "type": "indirect"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1643805626,
+        "narHash": "sha256-AXLDVMG+UaAGsGSpOtQHPIKB+IZ0KSd9WS77aanGzgc=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "554d2d8aa25b6e583575459c297ec23750adb6cb",
+        "type": "github"
+      },
+      "original": {
+        "id": "nixpkgs",
+        "ref": "nixos-unstable",
+        "type": "indirect"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1664281702,
+        "narHash": "sha256-haixZ4TJLu1Dciow54wrHrHvlGDVr5sW6MTeAV/ZLuI=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "7e52b35fe98481a279d89f9c145f8076d049d2b9",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "pre-commit-hooks": {
+      "inputs": {
+        "flake-utils": [
+          "flake-utils"
+        ],
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1663082609,
+        "narHash": "sha256-lmCCIu4dj59qbzkGKHQtolhpIEQMeAd2XUbXVPqgPYo=",
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "rev": "60cad1a326df17a8c6cf2bb23436609fdd83024e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "type": "github"
+      }
+    },
+    "pypi-deps-db": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1643877077,
+        "narHash": "sha256-jv8pIvRFTP919GybOxXE5TfOkrjTbdo9QiCO1TD3ZaY=",
+        "owner": "DavHau",
+        "repo": "pypi-deps-db",
+        "rev": "da53397f0b782b0b18deb72ef8e0fb5aa7c98aa3",
+        "type": "github"
+      },
+      "original": {
+        "owner": "DavHau",
+        "repo": "pypi-deps-db",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-compat": "flake-compat",
+        "flake-utils": "flake-utils",
+        "mach-nix": "mach-nix",
+        "nixpkgs": "nixpkgs_2",
+        "pre-commit-hooks": "pre-commit-hooks"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

flake.nix

@@ -0,0 +1,47 @@
+{
+  description = "Nix PlanktoScope";
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+
+    flake-compat = {
+      url = "github:edolstra/flake-compat";
+      flake = false;
+    };
+
+    flake-utils.url = "github:numtide/flake-utils";
+
+    pre-commit-hooks = {
+      url = "github:cachix/pre-commit-hooks.nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+      inputs.flake-utils.follows = "flake-utils";
+    };
+
+    mach-nix.url = "mach-nix/3.5.0";
+  };
+
+  outputs = {
+    self,
+    nixpkgs,
+    flake-utils,
+    mach-nix,
+    ...
+  } @ inputs:
+    flake-utils.lib.eachSystem ["x86_64-linux" "aarch64-linux"] (system: let
+      pkgs = import nixpkgs {
+        inherit system;
+      };
+      machNix = mach-nix.lib."${system}";
+    in rec {
+      packages = {
+        planktoscope = machNix.buildPythonPackage {
+          src = builtins.fetchGit {
+            url = "https://github.com/PlanktoScope/PlanktoScope";
+            ref = "master";
+            rev = "d52e194de0604e6fdd41ba2e13de9ab91e7789da";
+          };
+          extras = [];
+        };
+      };
+      devShell = import ./nix/shell.nix {inherit pkgs;};
+    });
+}

nix/shell.nix

@@ -0,0 +1,22 @@
+{pkgs ? import <nixpkgs> {}}:
+with pkgs;
+  mkShell {
+    name = "planctoscope";
+    nativeBuildInputs = with pkgs; [
+      alejandra
+      docker
+      editorconfig-checker
+      git
+      gnumake
+      hadolint
+      mdl
+      nixpkgs-fmt
+      pre-commit
+      python310Packages.mkdocs
+      reuse
+      rnix-lsp
+      vscodium-fhs
+      yaml-language-server
+      yamllint
+    ];
+  }