Update the nix-shell environment (qmk#13316)

* Nix: Allow calls to `bin/qmk` even when the build was started by `qmk`

The `$PATH` modifications performed by the Nix wrapper for the `qmk`
executable prevent `bin/qmk` from working properly (the changed `$PATH`
contains a wrong `python3` executable which does not have the needed
Python modules in its module path).  As a workaround, disable the
generation of that wrapper for the `qmk` Python package (there is yet
another wrapper generated while building the Python environment, which
would still set the Python module path properly when running `qmk`).

Although `bin/qmk` is officially deprecated, QMK CLI still invokes it in
some cases (at least `qmk doctor` and `qmk pytest`), therefore keeping
these invocations working is useful.

* Nix: Update `util/nix/pyproject.toml` to match `requirements*.txt`

Update the Python dependency information used by Poetry to match the
current state of the qmk_firmware code.

* Nix: Bump QMK CLI dependency to 1.0.0; bump other Python deps

Update Python dependencies for nix-shell to the most recent releases:

 - dotty-dict: 1.3.0 -> no longer used
 - milc: 1.4.2 -> 1.6.2
 - pep8-naming: 0.11.1 -> 0.12.1
 - pygments: 2.9.0 -> 2.10.0
 - pyrsistent: 0.17.3 -> 0.18.0
 - pyusb: 1.1.1 -> 1.2.1
 - setuptools-scm: 6.0.1 -> no longer used
 - qmk: 0.1.0 -> 1.0.0
 - qmk-dotty-dict: not used -> 1.3.0.post1
 - yapf: 0.30.0 -> 0.31.0

Note to self: The command to update Python dependencies changed to:

    ( cd util/nix && nix run 'nixpkgs#poetry' -- update --lock )

shell.nix

@@ -12,6 +12,13 @@ let
   # files if the requirements*.txt files change
   pythonEnv = poetry2nix.mkPoetryEnv {
     projectDir = ./util/nix;
+    overrides = poetry2nix.overrides.withDefaults (self: super: {
+      qmk = super.qmk.overridePythonAttrs(old: {
+        # Allow QMK CLI to run "bin/qmk" as a subprocess (the wrapper changes
+        # $PATH and breaks these invocations).
+        dontWrapPythonPrograms = true;
+      });
+    });
   };
 in
 

util/nix/pyproject.toml

@@ -9,23 +9,27 @@ authors = []
 
 [tool.poetry.dependencies]
 python = "^3.8"
-appdirs = "^1.4.4"
-argcomplete = "^1.12.2"
-colorama = "^0.4.4"
-dotty-dict = "^1.3.0"
-hjson = "^3.0.2"
-jsonschema = "^3.2.0"
-milc = "^1.3.0"
-Pygments = "^2.8.0"
+appdirs = "*"
+argcomplete = "*"
+colorama = "*"
+hid = "*"
+hjson = "*"
+jsonschema = ">=3"
+milc = ">=1.4.2"
+Pygments = "*"
+pyusb = "*"
+qmk-dotty-dict = "*"
+
+# This dependency is not mentioned in requirements.txt (QMK CLI is not a
+# library package that is required by the Python code in qmk_firmware), but is
+# required to build a proper nix-shell environment.
 qmk = "*"
 
 [tool.poetry.dev-dependencies]
-nose2 = "^0.10.0"
-flake8 = "^3.8.4"
-hid = "^1.0.4"
-pep8-naming = "^0.11.1"
-pyusb = "^1.1.1"
-yapf = "^0.30.0"
+nose2 = "*"
+flake8 = "*"
+pep8-naming = "*"
+yapf = "*"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]