Nix shell updates for `develop` (#18131)

* shell.nix: Update `tomlkit` to 0.11.4 using a Nixpkgs overlay

The used Nixpkgs snapshot contains `tomlkit` version 0.7.0, which is
affected by https://www.github.com/sdispater/tomlkit/issues/148; that
bug is triggered by `pyproject.toml` from `jsonschema` >= 4.11.0,
preventing the build of that module.

Just adding `tomlkit = "*"` to the `[tool.poetry.dev-dependencies]`
section of `nix/pyproject.toml` does not fix the `jsonschema` build,
because `makeRemoveSpecialDependenciesHook` inside `poetry2nix` is not
affected by `nix/pyproject.toml`.  Add a Nixpkgs overlay which updates
the `tomlkit` Python module globally, so that `poetry2nix` would also
use the updated version internally.

* shell.nix: Bump `poetry2nix` to the most recent version

The new `poetry2nix` version includes overrides which are required for
recent versions of some Python packages (in particular, `jsonschema` and
`dotty-dict`).

* shell.nix: Bump QMK CLI to 1.1.1; update other Python deps

Update `pyproject.toml` to match `requirements*.txt`:

- add `pyserial = "*"`
- replace `qmk-dotty-dict = "*"` with `dotty-dict = "*"` (#18117, also
  required for compatibility with `qmk` 1.1.1, where this replacement
  had already been performed)

Add build dependencies of various Python modules to `pyproject.toml`:

- `hatchling`, `hatch-vcs`, `hatch-fancy-pypi-readme` (required by
  `jsonschema` >= 4.11.0)
- `pytest` (a newer version is required to solve the dependency conflict
  with the `hatchling` module due to the upper bound on `pluggy`)
- `flit-core` (a more recent version is required to build `tomli`)
- `poetry-core` (required for `dotty-dict` >= 1.3.1, and the version
  from Nixpkgs does not build on Darwin due to NixOS/nix#4758)

Update `poetry.lock` to use the most recent versions of Python modules.

The complete list of Python module updates as listed in `poetry.lock`
(note that other modules might be present in the Python environment,
e.g., if they come from Nixpkgs):

- `atomicwrites`: none -> 1.4.1 (but this module is not actually used,
  because the corresponding dependency of `pytest` is win32-only)
- `attrs`: 21.4.0 -> 22.1.0
- `colorama`: 0.4.4 -> 0.4.5
- `coverage`: 6.4 -> none
- `dotty-dict`: none -> 1.3.1 (used instead of `qmk-dotty-dict`)
- `editables`: none -> 0.3
- `flake8`: 4.0.1 -> 5.0.4
- `flake8-polyfill`: 1.0.2 -> none
- `flit-core`: none -> 3.7.1
- `hatch-fancy-pypi-readme`: none -> 22.3.0
- `hatch-vcs`: none -> 0.2.0
- `hatchling`: none -> 1.8.0
- `hjson`: 3.0.2 -> 3.1.0
- `importlib-resources`: 5.7.1 -> 5.9.0
- `iniconfig`: none -> 1.1.1
- `jsonschema`: 4.5.1 -> 4.14.0
- `mccabe`: 0.6.1 -> 0.7.0
- `nose2`: 0.11.0 -> 0.12.0
- `packaging`: none -> 21.3
- `pathspec`: none -> 0.9.0
- `pep8-naming`: 0.12.1 -> 0.13.2
- `pillow`: 9.1.1 -> 9.2.0
- `pkgutil-resolve-name`: none -> 1.3.10
- `pluggy`: none -> 1.0.0
- `poetry-core`: none -> 1.0.8
- `py`: none -> 1.11.0
- `pycodestyle`: 2.8.0 -> 2.9.1
- `pyflakes`: 2.4.0 -> 2.5.0
- `pygments`: 2.12.0 -> 2.13.0
- `pyparsing`: none -> 3.0.9
- `pyserial`: none -> 3.5
- `pytest`: none -> 7.1.2
- `qmk`: 1.1.0 -> 1.1.1
- `qmk-dotty-dict`: 1.3.0.post1 -> none (replaced by `dotty-dict`)
- `setuptools-scm`: none -> 7.0.5
- `tomli`: none -> 2.0.1
- `typing-extensions`: none -> 4.3.0
- `zipp`: 3.8.0 -> 3.8.1

4 files changed, 460 insertions, 185 deletions

diff --git a/shell.nix b/shell.nix
index 7e3704d010..63e5af0525 100644
--- a/shell.nix
+++ b/shell.nix
@@ -1,9 +1,29 @@
 let
   # We specify sources via Niv: use "niv update nixpkgs" to update nixpkgs, for example.
   sources = import ./util/nix/sources.nix { };
+
+  # `tomlkit` >= 0.8.0 is required to build `jsonschema` >= 4.11.0 (older
+  # version do not support some valid TOML syntax: sdispater/tomlkit#148).  The
+  # updated `tomlkit` must be used by `makeRemoveSpecialDependenciesHook`
+  # inside `poetry2nix`, therefore just providing the updated version through
+  # our `nix/pyproject.toml` does not work, and using an overlay is required.
+  pythonOverlay = final: prev: {
+    python3 = prev.python3.override {
+      packageOverrides = self: super: {
+        tomlkit = super.tomlkit.overridePythonAttrs(old: rec {
+          version = "0.11.4";
+          src = super.fetchPypi {
+            inherit (old) pname;
+            inherit version;
+            sha256 = "sha256-MjWpAQ+uVDI+cnw6wG+3IHUv5mNbNCbjedrsYPvUSoM=";
+          };
+        });
+      };
+    };
+  };
 in
 # However, if you want to override Niv's inputs, this will let you do that.
-{ pkgs ? import sources.nixpkgs { }
+{ pkgs ? import sources.nixpkgs { overlays = [ pythonOverlay ]; }
 , poetry2nix ? pkgs.callPackage (import sources.poetry2nix) { }
 , avr ? true
 , arm ? true
diff --git a/util/nix/poetry.lock b/util/nix/poetry.lock
index e87672f193..dc1b38be84 100644
--- a/util/nix/poetry.lock
+++ b/util/nix/poetry.lock
@@ -15,64 +15,74 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-test = ["coverage", "flake8", "pexpect", "wheel"]
+test = ["wheel", "pexpect", "flake8", "coverage"]
+
+[[package]]
+name = "atomicwrites"
+version = "1.4.1"
+description = "Atomic file writes."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.4.0"
+version = "22.1.0"
 description = "Classes Without Boilerplate"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.5"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
+tests_no_zope = ["cloudpickle", "pytest-mypy-plugins", "mypy (>=0.900,!=0.940)", "pytest (>=4.3.0)", "pympler", "hypothesis", "coverage[toml] (>=5.0.2)"]
+tests = ["cloudpickle", "zope.interface", "pytest-mypy-plugins", "mypy (>=0.900,!=0.940)", "pytest (>=4.3.0)", "pympler", "hypothesis", "coverage[toml] (>=5.0.2)"]
+docs = ["sphinx-notfound-page", "zope.interface", "sphinx", "furo"]
+dev = ["cloudpickle", "pre-commit", "sphinx-notfound-page", "sphinx", "furo", "zope.interface", "pytest-mypy-plugins", "mypy (>=0.900,!=0.940)", "pytest (>=4.3.0)", "pympler", "hypothesis", "coverage[toml] (>=5.0.2)"]
 
 [[package]]
 name = "colorama"
-version = "0.4.4"
+version = "0.4.5"
 description = "Cross-platform colored terminal text."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
-name = "coverage"
-version = "6.4"
-description = "Code coverage measurement for Python"
+name = "dotty-dict"
+version = "1.3.1"
+description = "Dictionary wrapper for quick access to deeply nested keys."
+category = "main"
+optional = false
+python-versions = ">=3.5,<4.0"
+
+[[package]]
+name = "editables"
+version = "0.3"
+description = "Editable installations"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
-[package.extras]
-toml = ["tomli"]
-
 [[package]]
 name = "flake8"
-version = "4.0.1"
+version = "5.0.4"
 description = "the modular source code checker: pep8 pyflakes and co"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.1"
 
 [package.dependencies]
-mccabe = ">=0.6.0,<0.7.0"
-pycodestyle = ">=2.8.0,<2.9.0"
-pyflakes = ">=2.4.0,<2.5.0"
+mccabe = ">=0.7.0,<0.8.0"
+pycodestyle = ">=2.9.0,<2.10.0"
+pyflakes = ">=2.5.0,<2.6.0"
 
 [[package]]
-name = "flake8-polyfill"
-version = "1.0.2"
-description = "Polyfill package for Flake8 plugins"
+name = "flit-core"
+version = "3.7.1"
+description = "Distribution-building parts of Flit. See flit package for more information"
 category = "dev"
 optional = false
-python-versions = "*"
-
-[package.dependencies]
-flake8 = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "halo"
@@ -90,7 +100,50 @@ spinners = ">=0.0.24"
 termcolor = ">=1.1.0"
 
 [package.extras]
-ipython = ["IPython (==5.7.0)", "ipywidgets (==7.1.0)"]
+ipython = ["ipywidgets (==7.1.0)", "IPython (==5.7.0)"]
+
+[[package]]
+name = "hatch-fancy-pypi-readme"
+version = "22.3.0"
+description = "Fancy PyPI READMEs with Hatch"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+hatchling = "*"
+tomli = {version = "*", markers = "python_version < \"3.11\""}
+
+[package.extras]
+tests = ["wheel", "pytest-icdiff", "pytest", "coverage", "build"]
+dev = ["mypy", "hatch-fancy-pypi-readme"]
+
+[[package]]
+name = "hatch-vcs"
+version = "0.2.0"
+description = "Hatch plugin for versioning with your preferred VCS"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+hatchling = ">=0.21.0"
+setuptools-scm = {version = ">=6.4.0", markers = "python_version > \"3\""}
+
+[[package]]
+name = "hatchling"
+version = "1.8.0"
+description = "Modern, extensible Python build backend"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+editables = ">=0.3"
+packaging = ">=21.3"
+pathspec = ">=0.9"
+pluggy = ">=1.0.0"
+tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "hid"
@@ -102,7 +155,7 @@ python-versions = "*"
 
 [[package]]
 name = "hjson"
-version = "3.0.2"
+version = "3.1.0"
 description = "Hjson, a user interface for JSON."
 category = "main"
 optional = false
@@ -110,7 +163,7 @@ python-versions = "*"
 
 [[package]]
 name = "importlib-resources"
-version = "5.7.1"
+version = "5.9.0"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
@@ -120,12 +173,20 @@ python-versions = ">=3.7"
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+testing = ["pytest-mypy (>=0.9.1)", "pytest-black (>=0.3.7)", "pytest-enabler (>=1.3)", "pytest-cov", "pytest-flake8", "pytest-checkdocs (>=2.4)", "pytest (>=6)"]
+docs = ["jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "jaraco.packaging (>=9)", "sphinx"]
+
+[[package]]
+name = "iniconfig"
+version = "1.1.1"
+description = "iniconfig: brain-dead simple config-ini parsing"
+category = "dev"
+optional = false
+python-versions = "*"
 
 [[package]]
 name = "jsonschema"
-version = "4.5.1"
+version = "4.14.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
@@ -134,11 +195,12 @@ python-versions = ">=3.7"
 [package.dependencies]
 attrs = ">=17.4.0"
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
 pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
 
 [package.extras]
-format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
-format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["webcolors (>=1.11)", "uri-template", "rfc3986-validator (>0.1.0)", "rfc3339-validator", "jsonpointer (>1.13)", "isoduration", "idna", "fqdn"]
+format = ["webcolors (>=1.11)", "uri-template", "rfc3987", "rfc3339-validator", "jsonpointer (>1.13)", "isoduration", "idna", "fqdn"]
 
 [[package]]
 name = "log-symbols"
@@ -153,11 +215,11 @@ colorama = ">=0.3.9"
 
 [[package]]
 name = "mccabe"
-version = "0.6.1"
+version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "milc"
@@ -176,68 +238,132 @@ spinners = "*"
 
 [[package]]
 name = "nose2"
-version = "0.11.0"
-description = "unittest2 with plugins, the succesor to nose"
+version = "0.12.0"
+description = "unittest2 with plugins, the successor to nose"
 category = "dev"
 optional = false
 python-versions = "*"
 
+[package.extras]
+dev = ["sphinx-issues", "mock", "sphinx-rtd-theme", "sphinx"]
+coverage_plugin = ["coverage"]
+
+[[package]]
+name = "packaging"
+version = "21.3"
+description = "Core utilities for Python packages"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [package.dependencies]
-coverage = ">=4.4.1"
-six = ">=1.7"
+pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
-[package.extras]
-coverage_plugin = ["coverage (>=4.4.1)"]
-dev = ["Sphinx (>=1.6.5)", "sphinx-rtd-theme", "mock", "coverage", "sphinx-issues"]
+[[package]]
+name = "pathspec"
+version = "0.9.0"
+description = "Utility library for gitignore style pattern matching of file paths."
+category = "dev"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [[package]]
 name = "pep8-naming"
-version = "0.12.1"
+version = "0.13.2"
 description = "Check PEP-8 naming conventions, plugin for flake8"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 
 [package.dependencies]
 flake8 = ">=3.9.1"
-flake8-polyfill = ">=1.0.2,<2"
 
 [[package]]
 name = "pillow"
-version = "9.1.1"
+version = "9.2.0"
 description = "Python Imaging Library (Fork)"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinx-rtd-theme (>=1.0)", "sphinxext-opengraph"]
-tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+tests = ["pytest-timeout", "pytest-cov", "pytest", "pyroma", "packaging", "olefile", "markdown2", "defusedxml", "coverage", "check-manifest"]
+docs = ["sphinxext-opengraph", "sphinx-removed-in", "sphinx-issues (>=3.0.1)", "sphinx-copybutton", "sphinx (>=2.4)", "olefile", "furo"]
+
+[[package]]
+name = "pkgutil-resolve-name"
+version = "1.3.10"
+description = "Resolve a name to an object."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "pluggy"
+version = "1.0.0"
+description = "plugin and hook calling mechanisms for python"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+testing = ["pytest-benchmark", "pytest"]
+dev = ["tox", "pre-commit"]
+
+[[package]]
+name = "poetry-core"
+version = "1.0.8"
+description = "Poetry PEP 517 Build Backend"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[[package]]
+name = "py"
+version = "1.11.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "pycodestyle"
-version = "2.8.0"
+version = "2.9.1"
 description = "Python style guide checker"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "pyflakes"
-version = "2.4.0"
+version = "2.5.0"
 description = "passive checker of Python programs"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "pygments"
-version = "2.12.0"
+version = "2.13.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[package.extras]
+plugins = ["importlib-metadata"]
+
+[[package]]
+name = "pyparsing"
+version = "3.0.9"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+category = "dev"
+optional = false
+python-versions = ">=3.6.8"
+
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
+
 [[package]]
 name = "pyrsistent"
 version = "0.18.1"
@@ -247,6 +373,38 @@ optional = false
 python-versions = ">=3.7"
 
 [[package]]
+name = "pyserial"
+version = "3.5"
+description = "Python Serial Port Extension"
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.extras]
+cp2110 = ["hidapi"]
+
+[[package]]
+name = "pytest"
+version = "7.1.2"
+description = "pytest: simple powerful testing with Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
+attrs = ">=19.2.0"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=0.12,<2.0"
+py = ">=1.8.2"
+tomli = ">=1.0.0"
+
+[package.extras]
+testing = ["xmlschema", "requests", "pygments (>=2.7.2)", "nose", "mock", "hypothesis (>=3.56)", "argcomplete"]
+
+[[package]]
 name = "pyusb"
 version = "1.2.1"
 description = "Python USB access module"
@@ -256,29 +414,39 @@ python-versions = ">=3.6.0"
 
 [[package]]
 name = "qmk"
-version = "1.1.0"
+version = "1.1.1"
 description = "A program to help users work with QMK Firmware."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
+dotty-dict = "*"
 hid = "*"
 hjson = "*"
 jsonschema = ">=4"
 milc = ">=1.4.2"
 pillow = "*"
 pygments = "*"
+pyserial = "*"
 pyusb = "*"
-qmk-dotty-dict = "*"
 
 [[package]]
-name = "qmk-dotty-dict"
-version = "1.3.0.post1"
-description = "Dictionary wrapper for quick access to deeply nested keys."
-category = "main"
+name = "setuptools-scm"
+version = "7.0.5"
+description = "the blessed package to manage your versions by scm tags"
+category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
+
+[package.dependencies]
+packaging = ">=20.0"
+tomli = ">=1.0.0"
+typing-extensions = "*"
+
+[package.extras]
+toml = ["setuptools (>=42)"]
+test = ["virtualenv (>20)", "pytest (>=6.2)"]
 
 [[package]]
 name = "six"
@@ -305,6 +473,22 @@ optional = false
 python-versions = "*"
 
 [[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "typing-extensions"
+version = "4.3.0"
+description = "Backported and Experimental Type Hints for Python 3.7+"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
 name = "yapf"
 version = "0.32.0"
 description = "A formatter for Python code."
@@ -314,20 +498,20 @@ python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.8.0"
+version = "3.8.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
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