Fixed the Nix Flake default package

I also upgraded the flake.nix file.
- `mkShell` now use `packages` instead of `buildInputs` (See https://discourse.nixos.org/t/difference-between-buildinputs-and-packages-in-mkshell/60598/2)
- Now using `venvShellHook` to create the Python virtual environment
- Remove useless variables
- Added `meta` attrset
- Now using `python3Packages` variables instead
- Explicitly use the `build-system` field
- Now using `substituteInPlace` within `postPatch`
- Using the `pyproject` field instead of `format`
- Removed bad pratices, etc..

flake.lock

@@ -20,17 +20,17 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1731676054,
-        "narHash": "sha256-OZiZ3m8SCMfh3B6bfGC/Bm4x3qc1m2SVEAlkV6iY7Yg=",
-        "owner": "NixOS",
+        "lastModified": 1753345091,
+        "narHash": "sha256-CdX2Rtvp5I8HGu9swBmYuq+ILwRxpXdJwlpg8jvN4tU=",
+        "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "5e4fbfb6b3de1aa2872b76d49fafc942626e2add",
+        "rev": "3ff0e34b1383648053bba8ed03f201d3466f90c9",
         "type": "github"
       },
       "original": {
-        "owner": "NixOS",
-        "ref": "nixos-unstable",
+        "owner": "nixos",
         "repo": "nixpkgs",
+        "rev": "3ff0e34b1383648053bba8ed03f201d3466f90c9",
         "type": "github"
       }
     },