Emacs - Python LSP setup.cfg not honored

Question

I'm using vanilla Emacs and I installed lsp-mode as follows:

(use-package lsp-mode
  :init
  (setq lsp-keymap-prefix "C-c l")
  :commands (lsp lsp-deferred)
  :config (defun lsp-go-install-save-hooks ()
            (add-hook 'before-save-hook #'lsp-format-buffer t t)
            (add-hook 'before-save-hook #'lsp-organize-imports t t))
  :hook (
         (lsp-mode . lsp-enable-which-key-integration)
         (go-mode . lsp-deferred)
         (go-mode . lsp-go-install-save-hooks)
         (typescript-mode . lsp-deferred)
         (python-mode . lsp-deferred)
         )
  )

For Python I installed this. Everything seems to be working fine, but the problem is that I'm not able to override the default pycodestyle settings. For example, it complains about long lines > 79 so I tried adding in the root of the project the following setup.cfg:

[pycodestyle]
max-line-length=99

But it's not taken into account, am I missing something? I saw that there's the possibility to change the setting globally, but I'd like to have it on a per-project basis.

UPDATE

If pycodestyle is ran from the terminal it works as expected: it complains with the default line-length limit and it doesn't if I increase it to a value that is greater to the longest line that I have in the code.

The *lsp-log* buffer doesn't seem to provide any meaningful information:

Command "pyls" is not present on the path.
Command "pylsp" is present on the path.
Command "pyls" is not present on the path.
Command "pylsp" is present on the path.
Found the following clients for /<some path>/sample-app/sample_app/__init__.py: (server-id pylsp, priority -1)
The following clients were selected based on priority: (server-id pylsp, priority -1)

If I exec the flycheck-describe-checker command this is the output:

lsp is a Flycheck syntax checker.

  This syntax checker checks syntax in the major mode(s)
  `python-mode', `lsp-placeholder-mode', and uses a custom predicate.

Documentation:
A syntax checker using the Language Server Protocol (LSP)
provided by lsp-mode.
See https://github.com/emacs-lsp/lsp-mode.

If I disable flycheck by executing the command flycheck-disable-checker indeed the warnings go away, but it stops all the checks. So it seems like flycheck is the responsible for not honoring the setup.cfg.

Answer 1

I was able to understand what it seems to be happening. It seems that under the hood flycheck is using flake8 instead of pycodestyle. Indeed after I change setup.cfg into this:

[flake8]
max-line-length=99

Everything started working as expected.

The problem is that according to the documentation of python-lsp-server by default it should use pycodestyle. Moreover, checking through flake8 seems to be requiring 3rd party plugins according to the doc that I didn't install.

Not everything works as expected yet, as for example I have some complaints related to D100 and D104 that if I put them as ignore in the configuration their not honored yet.