updated development runtime envirnment

.editorconfig

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: CC-BY-SA-4.0
+
 root = true
 
 [*]
@@ -6,19 +8,6 @@ insert_final_newline = true
 trim_trailing_whitespace = true
 charset = utf-8
 
-[{Makefile,*.mk}]
-indent_style = tab
-indent_size = 4
-
-[*.md]
-indent_style = space
-indent_size = 2
-
-[*.{yml,yaml}]
-indent_style = space
-indent_size = 2
-
 [*.nix]
 indent_style = tab
 indent_size = 2
-

.envrc

@@ -1,5 +1,11 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+# https://github.com/direnv/direnv/wiki
+
 use flake
 
+layout python3
+
 watch_file ./nix/shell.nix
 
 eval "$shellHook"

.gitignore

@@ -1,14 +1,32 @@
-.vscode
+# SPDX-License-Identifier: CC-BY-SA-4.0
-flow_backup.json
+
-flows/.main.json.backup
+# General
+.reuse
+*.dll
 *.log
+*.so
+*.swp
 export
-tmp
 img
-docs/_*
+tmp
-*.jpg
+
-*.png
+# Nix
-*.pyc
-*__pycache__*
 .direnv
-.reuse
+.pre-commit-config.yaml
+result
+
+# Python
+/*.py[cod]
+/__pycache__
+/.benchmark
+/.coverage*
+/.pytest_cache
+
+# Node-Red
+/.main.json.backup
+/flow_backup.json
+
+# Mkdocs
+dist
+docs/_*
+site

.mdlrc

@@ -1 +0,0 @@
-rules "MD001","MD002","MD003","MD004","MD005","MD006","MD007","MD010","MD011","MD012","MD014","MD018","MD019","MD020","MD021","MD022","MD023","MD024","MD025","MD027","MD028","MD029","MD030","MD031","MD032","MD033","MD034","MD035","MD036","MD037","MD038","MD039","MD040","MD041","MD047"

.vscode/extensions.json

@@ -0,0 +1,20 @@
+{
+	"recommendations": [
+		"bungcip.better-toml",
+		"cab404.vscode-direnv",
+		"davidanson.vscode-markdownlint",
+		"editorconfig.editorconfig",
+		"esbenp.prettier-vscode",
+		"exiasr.hadolint",
+		"kamadorueda.alejandra",
+		"kamikillerto.vscode-colorize",
+		"mechatroner.rainbow-csv",
+		"ms-python.black-formatter",
+		"ms-python.python",
+		"oderwat.indent-rainbow",
+		"pinage404.nix-extension-pack",
+		"redhat.vscode-yaml",
+		"yatki.vscode-surround",
+		"yzhang.markdown-all-in-one",
+	],
+}

.vscode/settings.json

@@ -0,0 +1,22 @@
+{
+    "[nix]": {
+        "editor.defaultFormatter": "kamadorueda.alejandra",
+        "editor.formatOnSave": true,
+    },
+    "[toml]": {
+        "editor.formatOnSave": true,
+        "editor.insertSpaces": true,
+        "editor.codeLens": true
+    },
+    "python.formatting.provider": "black",
+    "python.globalModuleInstallation": false,
+    "python.languageServer": "Pylance",
+    "python.linting.enabled": true,
+    "python.linting.lintOnSave": true,
+    "python.linting.pycodestyleEnabled": true,
+    "python.linting.pydocstyleEnabled": true,
+    "python.linting.pylintEnabled": true,
+    "python.testing.autoTestDiscoverOnSaveEnabled": true,
+    "python.testing.pytestEnabled": true,
+    "python.defaultInterpreterPath": "${workspaceFolder}/.direnv/dev/bin/python3",
+}

Makefile

@@ -1,23 +0,0 @@
-##@ General
-
-help: ## Display this help.
-	@awk 'BEGIN {FS = ":.*##"; printf "\nUsage:\n  make \033[36m<target>\033[0m\n"} /^[a-zA-Z_0-9-]+:.*?##/ { printf "  \033[36m%-15s\033[0m %s\n", $$1, $$2 } /^##@/ { printf "\n\033[1m%s\033[0m\n", substr($$0, 5) } ' $(MAKEFILE_LIST)
-
-##@ Documentation
-
-docs-build: ## Build the MkDocs documentation
-	@mkdocs build
-
-docs-serve: ## Run mkdocs builtin development server
-	@mkdocs serve
-
-##@ Lint
-
-lint-markdown: ## Run markdown linter on all files
-	@mdl .
-
-lint-reuse: ## Run reuse linter on all files
-	@reuse lint
-
-%:
-	@true

flake.lock

@@ -31,57 +31,7 @@
         "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=",
@@ -120,28 +70,11 @@
         "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",
-        "nixpkgs": "nixpkgs_2",
         "pre-commit-hooks": "pre-commit-hooks"
       }
     }

flake.nix

@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
 {
   description = "Nix PlanktoScope";
   inputs = {
@@ -15,33 +16,20 @@
       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
+    flake-utils.lib.eachSystem ["x86_64-linux" "aarch64-linux"] (system: {
+      devShells.default = import ./nix/shell.nix inputs system;
+      checks = import ./nix/checks.nix inputs system;
       pkgs = import nixpkgs {
         inherit system;
+        config.allowUnfree = true;
+        config.allowAliases = true;
       };
-      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/checks.nix

@@ -0,0 +1,43 @@
+{
+  self,
+  pre-commit-hooks,
+  ...
+}: system:
+with self.pkgs.${system}; {
+  pre-commit-check =
+    pre-commit-hooks.lib.${system}.run
+    {
+      src = lib.cleanSource ../.;
+      hooks = {
+        alejandra.enable = true;
+        nix-linter.enable = true;
+        yamllint.enable = true;
+        # isort.enable = true;
+        # black.enable = true;
+        # shellcheck.enable = true;
+        # markdownlint.enable = true;
+      };
+      settings.nix-linter.checks = [
+        "DIYInherit"
+        "EmptyInherit"
+        "EmptyLet"
+        "EtaReduce"
+        "LetInInheritRecset"
+        "ListLiteralConcat"
+        "NegateAtom"
+        "SequentialLet"
+        "SetLiteralUpdate"
+        "UnfortunateArgName"
+        "UnneededRec"
+        "UnusedArg"
+        "UnusedLetBind"
+        "UpdateEmptySet"
+        "BetaReduction"
+        "EmptyVariadicParamSet"
+        "UnneededAntiquote"
+        "no-FreeLetInFunc"
+        "no-AlphabeticalArgs"
+        "no-AlphabeticalBindings"
+      ];
+    };
+}

nix/shell.nix

@@ -1,22 +1,43 @@
-{pkgs ? import <nixpkgs> {}}:
+{self, ...}: system:
-with pkgs;
+with self.pkgs.${system};
   mkShell {
-    name = "planctoscope";
+    name = "planktoscope";
-    nativeBuildInputs = with pkgs; [
+    nativeBuildInputs =
-      alejandra
+      [
-      docker
+        # Development
-      editorconfig-checker
+        editorconfig-checker
-      git
+        pre-commit
-      gnumake
+        python-language-server
-      hadolint
+        python37
-      mdl
+        python38
-      nixpkgs-fmt
+        python39
-      pre-commit
+        python310Full
-      python310Packages.mkdocs
+        python311
-      reuse
+        yaml-language-server
-      rnix-lsp
+      ]
-      vscodium-fhs
+      ++ lib.optionals (pkgs.hostPlatform.system == "x86_64-linux") [
-      yaml-language-server
+        vscodium-fhs
-      yamllint
+      ]
-    ];
+      ++ [
+        # Linter
+        git
+        yamllint
+
+        # Nix
+        alejandra
+        nix
+        nix-linter
+        rnix-lsp
+
+        # Service
+        mosquitto
+
+        # Misc
+        reuse
+      ];
+    shellHook = ''
+      ${self.checks.${system}.pre-commit-check.shellHook}
+      pip install --upgrade pip hatch
+      hatch env create dev
+    '';
   }