Cleanup setting up eglot/flymake mode configs

Remove some packages not being used anymore

Switch python-flymake back-end to use flake8 instead of pyflakes

init.el

@@ -911,21 +911,16 @@ Try `magit-clone-default-directory' if available, fall back to
           ("C-c c e" . eglot)
           ("C-c c a" . eglot-code-actions)
           ("C-c c r" . eglot-rename))
-  :hook (((nix-mode
+  :hook (((nix-mode python-base-mode fortran-mode f90-mode) . eglot-ensure)
-           lua-mode
+         (eglot-managed-mode . (lambda () (add-hook 'flymake-diagnostic-functions
-           python-base-mode
+                                               'eglot-flymake-backend nil t))))
-           rust-ts-mode
-           fortran-mode
-           f90-mode
-           js-ts-mode)
-          . eglot-ensure)
-         (eglot-managed-mode . (lambda () (add-to-list 'flymake-diagnostic-functions #'eglot-flymake-backend t))))
   :custom
   (eglot-extend-to-xref t)
   (eglot-autoshutdown t)
   (eglot-autoreconnect nil)
-  :config
+  :init
   (setq eglot-stay-out-of '(flymake))
+  :config
   (setq-default eglot-workspace-configuration
                 '( :pylsp ( :plugins
                             ( :autopep8 (:enabled nil)
@@ -974,7 +969,7 @@ Try `magit-clone-default-directory' if available, fall back to
 (use-package flymake
   :bind (("C-c C-." . flymake-goto-next-error)
          ("C-c C-," . flymake-goto-prev-error))
-  :hook (prog-mode . flymake-mode)
+  :hook (prog-mode . (lambda () (flymake-mode +1)))
   :config (require 'flymake-collection))
 
 (use-package flymake-popon
@@ -983,7 +978,6 @@ Try `magit-clone-default-directory' if available, fall back to
   (global-flymake-popon-mode +1))
 
 (use-package flymake-collection
-  :defer
   :after flymake
   :custom
   ;; Extra mypy config
@@ -998,18 +992,6 @@ Try `magit-clone-default-directory' if available, fall back to
   :after flymake
   :hook (sh-mode . flymake-shellcheck-load))
 
-(use-package flymake-clippy
-  :after flymake
-  :hook ((rust-mode rust-ts-mode) . flymake-clippy-setup-backend))
-
-(use-package flymake-eslint
-  :after flymake
-  :hook (js-ts-mode . flymake-eslint-enable))
-
-(use-package flymake-ruff
-  :after flymake
-  :hook (python-base-mode . flymake-ruff-load))
-
 (setq project-switch-use-entire-map t
       project-switch-commands '((project-find-file "Find file")
                                 (project-find-regexp "Find regexp")
@@ -1056,31 +1038,27 @@ Try `magit-clone-default-directory' if available, fall back to
   (require 'nix-store)
   (nix-prettify-global-mode +1))
 
-(use-package nushell-ts-mode
-  :defer t
-  :mode "\\.nu\\'")
-
-(use-package lua-mode
-  :defer t)
-
 (defun my/enable-fill-column (col)
   "Set and enable fill column to `COL'."
   (set-fill-column col)
   (display-fill-column-indicator-mode +1))
 
 (use-package python
-  :defer t
+  :hook ((python-base-mode . (lambda () (my/enable-fill-column 88)))
+         (python-base-mode . (lambda () (add-hook 'flymake-diagnostic-functions
+                                             'flymake-collection-mypy nil t))))
   :custom
-  (python-check-command (cond ((executable-find "ruff") "ruff check --output-format=pylint")
+  (python-flymake-command
-                              ((executable-find "pyflakes") "pyflakes")
+   (cond ((executable-find "flake8") '("flake8" "-"))
-                              ((executable-find "epylint") "epylint")
+         (t ("pyflakes"))))
+  (python-check-command
+   (cond ((executable-find "flake8") "flake8")
          (t "pyflakes")))
   :config
-  (setq python-ts-mode-hook python-mode-hook)
+  (setq python-ts-mode-hook python-mode-hook))
-  (add-hook 'python-base-mode-hook (lambda () (my/enable-fill-column 88))))
 
-(use-package cargo
+(use-package python-docstring
-  :hook (rust-ts-mode . cargo-minor-mode))
+  :hook python-base-mode)
 
 (use-package tramp
   :defer t