Improve sections on Org and Python

* Add patch for python-lsp-server.
* Swap order of sections on programming and editing.

README.org

@@ -956,6 +956,7 @@ The code in listing [[lst:customize-org-babel]], [[lst:customize-org]], and
      '(org-latex-listings 'minted)
      '(org-latex-minted-langs '((cc "c++")
                                 (cperl "perl")
+                                (diff "diff")
                                 (shell-script "bash")
                                 (caml "ocaml")
                                 (org "latex")))
@@ -1273,25 +1274,45 @@ blocks) do not work in [[info:org#Export Settings][#+SETUPFILE: <FILE>]], but on
 :CUSTOM_ID: sec:setupfile+include-usage
 :END:
 
-Listing [[lst:source-file-export-keyword-settings]] shows a copie of the first six
+Evaluation of the source block in listing
-lines of this [[file:README.org]] file.  The last two lines shows that the file
+[[lst:make-source-block-with-export-keyword-settings]] produces the source block
-[[file:setup-include]] serves as a [[info:org#Export Settings][#+SETUPFILE:FILE]] file and as a [[info:org#Export Settings][#+INCLUDE: FILE]].
+that exports to listing [[lst:source-file-export-keyword-settings]] which shows the
+first six lines of this [[file:README.org]] file.  The last two lines show that
+[[file:setup-include.org][setup-include.org]] is argument for [[info:org#Export Settings][#+SETUPFILE:]] *and* [[info:org#Export Settings][#+INCLUDE:]].
 
+#+caption[Make setup and include file export keyword settings source block]:
+#+caption: The shell script to make the source block containing the export
+#+caption: keyword settings.
+#+name: lst:make-source-block-with-export-keyword-settings
+#+begin_src shell :exports both :results drawer
+  echo "#+caption[Source file export keyword settings]:"
+  echo "#+caption: The first six lines of README.org containing the export"
+  echo "#+caption: keyword settings."
+  echo "#+name: lst:source-file-export-keyword-settings"
+  echo "#+begin_src org :tangle no"
+  head -n 6 README.org
+  echo -n "#+end_src"
+#+end_src
+
+#+RESULTS: lst:make-source-block-with-export-keyword-settings
+:results:
 #+caption[Source file export keyword settings]:
-#+caption: Source file export keyword settings.
+#+caption: The first six lines of README.org containing the export
+#+caption: keyword settings.
 #+name: lst:source-file-export-keyword-settings
 #+begin_src org :tangle no
-  ,#+title: Emacs setup for use with LaTeX, Org, and Python
+#+title: Emacs setup for use with LaTeX, Org, and Python
-  ,#+author: Gerard Vermeulen
+#+author: Gerard Vermeulen
-  ,#+latex_class: article
+#+latex_class: article
-  ,#+latex_class_options: [11pt,a4paper,english,svgnames,tables]
+#+latex_class_options: [11pt,a4paper,english,svgnames,tables]
-  ,#+setupfile: "setup-include.org"
+#+setupfile: "setup-include.org"
-  ,#+include: "setup-include.org"
+#+include: "setup-include.org"
 #+end_src
+:end:
 
 Listing [[lst:setup-include-export-keyword-settings]], [[lst:use-latex-header-1]],
 [[lst:use-latex-header-2]], [[lst:use-latex-header-3]], and [[lst:use-latex-header-4]]
-tangle into the [[file:setup-include]] file.
+tangle into the [[file:setup-include.org][setup-include.org]] file.
 
 #+caption[Setup and include file export keyword settings]:
 #+caption: Setup and include file export keyword settings.
@@ -1523,6 +1544,260 @@ Listing [[lst:emacs-lisp-setup-call]] initializes the buffer local variables
   \end{titlepage}
 #+end_src
 
+* Programming
+:PROPERTIES:
+:CUSTOM_ID: sec:programming
+:END:
+
+** Emacs-lisp programming
+:PROPERTIES:
+:CUSTOM_ID: sec:emacs-lisp-programming
+:END:
+
+** [[https://www.seas.upenn.edu/~chaoliu/2017/09/01/python-programming-in-emacs/][Python programming]]
+:PROPERTIES:
+:CUSTOM_ID: sec:python-coding
+:END:
+
+The [[https://www.emacswiki.org/emacs/PythonProgrammingInEmacs][Python Programming in Emacs]] wiki page lists options to enhance Emacs's
+built-in ~python-mode~. Here, the focus is on two packages:
+1. [[https://github.com/joaotavora/eglot][Eglot - Emacs polyGLOT: an Emacs LSP client that stays out of your way]].  The
+   maintainer also contributes to Emacs itself and has a deep understanding of
+   [[https://sheer.tj/the_way_of_emacs.html][the Way of Emacs]].  He refuses to add new features without seeing how they fit
+   into [[https://sheer.tj/the_way_of_emacs.html][the Way of Emacs]] as this discussion on [[https://github.com/joaotavora/eglot/issues/523][org-mode source code blocks]]
+   shows.
+2. [[https://github.com/pythonic-emacs/anaconda-mode][Anaconda - code navigation, documentation lookup, and completion for Python]].
+In my opinion, [[https://github.com/joaotavora/eglot][eglot]] has more potential than [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]], but [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]] is
+compatible with [[info:org#Editing Source Code][source code block editing]] while [[https://github.com/joaotavora/eglot][eglot]] is not.  Listing
+[[lst:configure-python]] configures [[https://www.python.org][Python]].
+
+*** [[https://git.savannah.gnu.org/cgit/emacs.git/tree/lisp/progmodes/python.el][Python-mode]]
+
+#+caption[Configure =python=]:
+#+caption: Configure =python=.
+#+name: lst:configure-python
+#+begin_src elisp
+  (with-eval-after-load 'python
+    (custom-set-variables
+     '(python-indent-guess-indent-offset nil)
+     '(python-shell-interpreter-args "-i -E")))
+#+end_src
+
+*** [[https://github.com/joaotavora/eglot][Eglot]]
+
+Listing [[lst:configure-eglot-for-python]] configures [[https://github.com/joaotavora/eglot][eglot]] with [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]]
+for [[https://www.python.org][Python]].  It defines a hook function to launch [[https://github.com/joaotavora/eglot][eglot]] when it sees a proper
+[[info:emacs#Directory
+ Variables][.dir-locals.el]] file in the root directory of any [[https://www.python.org][Python]] project.  Listing
+[[lst:eglot-directory-variables-for-python]] shows such a proper [[info:emacs#Directory Variables][.dir-locals.el]]
+file.
+
+#+caption[Configure =eglot= for Python]:
+#+caption: Configure =eglot= for Python.
+#+name: lst:configure-eglot-for-python
+#+begin_src emacs-lisp
+  (with-eval-after-load 'eglot
+    (add-to-list 'eglot-server-programs '(python-mode "pylsp"))
+
+    (setq-default
+     eglot-workspace-configuration
+     '((:pylsp . (:plugins (:jedi
+                            (:auto_import_modules ["numpy" "scipy"]))))
+       (:pylsp . (:plugins (:jedi_completion
+                            (:cache_for ["astropy"]))))
+       (:pylsp . (:plugins (:jedi_completion (:eager t)))))))
+
+  (when (fboundp 'eglot-ensure)
+    ;; The two hooks `after-change-major-mode-hook' and
+    ;; `hack-local-variables-hook' are OK, but `<ANY>-mode-hook' is not.
+    (add-hook 'hack-local-variables-hook
+              (defun on-hack-local-variables-hook-eglot-maybe ()
+                (when (and (derived-mode-p 'python-mode)
+                           (assoc 'eglot-workspace-configuration
+                                  dir-local-variables-alist))
+                  (eglot-ensure)))))
+#+end_src
+
+#+caption[Propose =directory-variables= to launch =eglot=]:
+#+caption: Propose =directory-variables= in the root of any Python project to
+#+caption: launch =eglot=.
+#+name: lst:eglot-directory-variables-for-python
+#+begin_src emacs-lisp :tangle no
+  ;; Proposal for a .dir-locals.el file in the root of any Python project.
+  ((python-mode
+    . ((eglot-workspace-configuration
+        . ((:pylsp . (:plugins (:jedi
+                                (:auto_import_modules ["numpy" "scipy"]))))
+           (:pylsp . (:plugins (:jedi_completion
+                                (:cache_for ["astropy"]))))
+           (:pylsp . (:plugins (:jedi_completion (:eager nil)))))))))
+#+end_src
+
+[[https://jedi.readthedocs.io/en/latest/][Jedi]] provides grammar checking and completion candidates to [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]].
+Only [[https://jedi.readthedocs.io/en/latest/docs/changelog.html][jedi-0.18.1]] works with for instance [[https://numpy.org/][numpy-1.21.5]] in the sense that it
+handles builtins and universal functions provided that [[https://jedi.readthedocs.io/en/latest/][jedi]] does not parse but
+imports [[https://numpy.org/][numpy-1.21.5]] (see [[https://github.com/davidhalter/jedi/issues/1744][jedi issue #1744]], [[https://github.com/davidhalter/jedi/issues/1745][#1745]], and [[https://github.com/davidhalter/jedi/issues/1746][#1746]]).
+
+#+header:  :wrap "src diff :exports code :tangle pylsp-auto-import-modules.patch"
+#+begin_src shell :exports both :results org
+  git -C $HOME/VCS/python-lsp-server diff
+#+end_src
+
+#+RESULTS:
+#+begin_src diff :exports code :tangle pylsp-auto-import-modules.patch
+diff --git a/pylsp/config/schema.json b/pylsp/config/schema.json
+index c29d78b..f54b67a 100644
+--- a/pylsp/config/schema.json
++++ b/pylsp/config/schema.json
+@@ -69,6 +69,14 @@
+       "default": null,
+       "description": "List of errors and warnings to enable."
+     },
++    "pylsp.plugins.jedi.auto_import_modules": {
++      "type": "array",
++        "default": ["numpy", "scipy", "gi"],
++      "items": {
++        "type": "string"
++      },
++      "description": "List of module names for jedi to import (jedi.settings.auto_import_modules)."
++    },
+     "pylsp.plugins.jedi.extra_paths": {
+       "type": "array",
+       "default": [],
+diff --git a/pylsp/workspace.py b/pylsp/workspace.py
+index bf312f6..49e967a 100644
+--- a/pylsp/workspace.py
++++ b/pylsp/workspace.py
+@@ -14,6 +14,8 @@ from . import lsp, uris, _utils
+
+ log = logging.getLogger(__name__)
+
++DEFAULT_AUTO_IMPORT_MODULES = ["numpy", "scipy", "gi"]
++
+ # TODO: this is not the best e.g. we capture numbers
+ RE_START_WORD = re.compile('[A-Za-z_0-9]*$')
+ RE_END_WORD = re.compile('^[A-Za-z_0-9]*')
+@@ -252,6 +254,8 @@ class Document:
+
+         if self._config:
+             jedi_settings = self._config.plugin_settings('jedi', document_path=self.path)
++            jedi.settings.auto_import_modules = jedi_settings.get('auto_import_modules',
++                                                                  DEFAULT_AUTO_IMPORT_MODULES)
+             environment_path = jedi_settings.get('environment')
+             extra_paths = jedi_settings.get('extra_paths') or []
+             env_vars = jedi_settings.get('env_vars')
+#+end_src
+
+*** [[https://github.com/pythonic-emacs/anaconda-mode][Anaconda]]
+
+Listing [[lst:configure-anaconda-for-python]] configures [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]]. See
+[[https://github.com/jorgenschaefer/elpy/blob/8d0de310d41ebf06b22321a8534546447456870c/elpy.el#L2775][elpy-module-company]] for how to handle ~company-backends~ as a local variable and
+the call to [[info:elisp#Advising Functions][advice-add]] opens Python org-mode edit-buffers in ~anaconda-mode~.
+
+#+caption[Configure =anaconda= for Python]:
+#+caption: Configure =anaconda= for Python.
+#+name: lst:configure-anaconda-for-python
+#+begin_src emacs-lisp
+  (with-eval-after-load 'python
+    (with-eval-after-load 'company
+      (when (and (fboundp 'anaconda-mode)
+                 (fboundp 'company-anaconda))
+        (defun my-disable-anaconda-mode ()
+          (when (derived-mode-p 'python-mode)
+            (anaconda-mode -1)
+            (make-variable-buffer-local 'company-backends)
+            (setq company-backends
+                  (delq 'company-anaconda
+                        (mapcar #'identity company-backends)))
+            (anaconda-eldoc-mode -1)))
+        (defun my-enable-anaconda-mode ()
+          (when (derived-mode-p 'python-mode)
+            (anaconda-mode +1)
+            (make-variable-buffer-local 'company-backends)
+            (setq company-backends
+                  (cons 'company-anaconda
+                        (delq 'company-semantic
+                              (delq 'company-capf
+                                    (mapcar #'identity company-backends)))))
+            (anaconda-eldoc-mode
+             (if (file-remote-p default-directory) -1 1))))))
+
+    (unless (and (fboundp 'my-disable-anaconda-mode)
+                 (fboundp 'my-enable-anaconda-mode))
+      (when (fboundp 'anaconda-mode)
+        (defun my-disable-anaconda-mode ()
+          (when (derived-mode-p 'python-mode)
+            (anaconda-mode -1)
+            (anaconda-eldoc-mode -1)))
+        (defun my-enable-anaconda-mode ()
+          (when (derived-mode-p 'python-mode)
+            (anaconda-mode +1)
+            (anaconda-eldoc-mode
+             (if (file-remote-p default-directory) -1 1))))))
+
+    (when (fboundp 'my-enable-anaconda-mode)
+      (advice-add 'org-edit-src-code :after #'my-enable-anaconda-mode))
+    (when (and (fboundp 'my-disable-anaconda-mode)
+               (fboundp 'my-enable-anaconda-mode))
+      (defun my-toggle-anaconda-mode ()
+        "Toggle anaconda-mode with bells and whistles."
+        (interactive)
+        (if (bound-and-true-p anaconda-mode)
+            (my-disable-anaconda-mode)
+          (my-enable-anaconda-mode)))))
+#+end_src
+
+*** [[https://jedi.readthedocs.io/en/latest/][Jedi]]
+
+Listing [[lst:example-py]] is a [[https://www.python.org][Python]] example to test whether [[https://jedi.readthedocs.io/en/latest/][jedi]] in combination
+with and either [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]] or [[https://github.com/joaotavora/eglot][eglot]] works when coding certain functions of for
+instance [[https://numpy.org/][numpy]] and [[https://scipy.org/][scipy]].
+
+#+caption[Tangle the =example.py= file]:
+#+caption: Tangle the =example.py= file.
+#+name: lst:example-py
+#+begin_src python :tangle example.py
+  import numpy
+  import astropy.units as apu
+
+  a = numpy.arange(0, 11)
+  a = numpy.linspace(0, 10, num=11)
+  a = numpy.arccos(a)
+  q = apu.Quantity(a, apu.meter)
+  print(q)
+#+end_src
+
+*** [[https://github.com/pyenv/pyenv][Pyenv]]
+
+Listing [[lst:enable-pyenv-mode]] configures and enables =pyenv-mode=.
+
+#+caption[Enable =pyenv-mode=]:
+#+caption: Enable =pyenv-mode=.
+#+name: lst:enable-pyenv-mode
+#+begin_src emacs-lisp
+  (when (and (executable-find "pyenv")
+             (require 'pyenv-mode nil 'noerror))
+    (pyenv-mode +1)
+    (pyenv-mode-set "3.9.9/envs/python-3.9.9"))
+#+end_src
+
+*** Info
+
+Listing [[lst:configure-info]] adds a path in my home directory to the places where
+=info= looks for files.
+
+#+caption[Configure =info=]:
+#+caption: Configure =info=.
+#+name: lst:configure-info
+#+begin_src emacs-lisp
+  (with-eval-after-load 'info
+    (add-to-list 'Info-directory-list
+                 (expand-file-name "~/.local/share/info")))
+#+end_src
+
+*** TODO Look into: editing facilities
+1. [[https://github.com/douglasdavis/numpydoc.el/blob/main/numpydoc.el][Emacs extension to insert numpy style docstrings in function definitions]]
+
 * Editing
 
 ** [[https://www.emacswiki.org/emacs/DisabledCommands][Enable disabled commands and inform]]
@@ -1624,7 +1899,7 @@ on tables by means of =org-narrow-to-table=.
       (add-hook 'text-mode-hook #'ws-butler-mode)))
 #+end_src
 
-** Structural editing
+** [[https://countvajhula.com/2021/09/25/the-animated-guide-to-symex/][Structural editing]]
 :PROPERTIES:
 :CUSTOM_ID: sec:structural-editing
 :END:
@@ -1737,189 +2012,6 @@ code formatter for Python]].
     (yas-global-mode +1))
 #+end_src
 
-* Coding
-:PROPERTIES:
-:CUSTOM_ID: sec:coding
-:END:
-
-** Emacs-lisp coding
-:PROPERTIES:
-:CUSTOM_ID: sec:emacs-lisp-coding
-:END:
-
-** Python coding
-:PROPERTIES:
-:CUSTOM_ID: sec:python-coding
-:END:
-
-The [[https://www.emacswiki.org/emacs/PythonProgrammingInEmacs][Python Programming in Emacs]] wiki page lists options to enhance Emacs's
-built-in ~python-mode~. Here, the focus is on two packages:
-1. [[https://github.com/joaotavora/eglot][Eglot - Emacs polyGLOT: an Emacs LSP client that stays out of your way]].  The
-   maintainer also contributes to Emacs itself and has a deep understanding of
-   [[https://sheer.tj/the_way_of_emacs.html][the Way of Emacs]].  He refuses to add new features without seeing how they fit
-   into [[https://sheer.tj/the_way_of_emacs.html][the Way of Emacs]] as this discussion on [[https://github.com/joaotavora/eglot/issues/523][org-mode source code blocks]]
-   shows.
-2. [[https://github.com/pythonic-emacs/anaconda-mode][Anaconda - code navigation, documentation lookup, and completion for Python]].
-In my opinion, [[https://github.com/joaotavora/eglot][eglot]] has more potential than [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]], but [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]] is
-compatible with [[info:org#Editing Source Code][source code block editing]] while [[https://github.com/joaotavora/eglot][eglot]] is not.  Listing
-[[lst:configure-python]] configures [[https://www.python.org][Python]].
-
-#+caption[Configure =python=]:
-#+caption: Configure =python=.
-#+name: lst:configure-python
-#+begin_src elisp
-  (with-eval-after-load 'python
-    (custom-set-variables
-     '(python-indent-guess-indent-offset nil)
-     '(python-shell-interpreter-args "-i -E")))
-#+end_src
-
-Listing [[lst:configure-eglot-for-python]] configures [[https://github.com/joaotavora/eglot][eglot]] for [[https://www.python.org][Python]].  It defines
-a hook function to launch [[https://github.com/joaotavora/eglot][eglot]] by means of a proper [[info:emacs#Directory Variables][directory variables]] file in
-the root directory of any [[https://www.python.org][Python]] project.  Listing
-[[lst:eglot-directory-variables-for-python]] does shows such a proper [[info:emacs#Directory Variables][directory
-variables]] file.
-
-#+caption[Configure =eglot= for Python]:
-#+caption: Configure =eglot= for Python.
-#+name: lst:configure-eglot-for-python
-#+begin_src emacs-lisp
-  (with-eval-after-load 'eglot
-    (add-to-list 'eglot-server-programs '(python-mode "pylsp"))
-    (setq-default
-     eglot-workspace-configuration
-     '((:pylsp . (:plugins (:jedi_completion
-                            (:cache_for ["astropy" "numpy" "scipy"]))))
-       (:pylsp . (:plugins (:jedi_completion (:eager nil)))))))
-
-  (when (fboundp 'eglot-ensure)
-    ;; The two hooks `after-change-major-mode-hook' and
-    ;; `hack-local-variables-hook' are OK, but `<ANY>-mode-hook' is not.
-    (add-hook 'hack-local-variables-hook
-              (defun on-hack-local-variables-hook-eglot-maybe ()
-                (when (and (derived-mode-p 'python-mode)
-                           (assoc 'eglot-workspace-configuration
-                                  dir-local-variables-alist))
-                  (eglot-ensure)))))
-#+end_src
-
-#+caption[Propose =directory-variables= to launch =eglot=]:
-#+caption: Propose =directory-variables= in the root of any Python project to
-#+caption: launch =eglot=.
-#+name: lst:eglot-directory-variables-for-python
-#+begin_src emacs-lisp :tangle no
-  ;; Proposal for a .dir-locals.el file in the root of any Python project.
-  ((python-mode
-    . ((eglot-workspace-configuration
-        . ((:pylsp . (:plugins (:jedi_completion
-                                (:cache_for ["astropy" "numpy" "scipy"]))))
-           (:pylsp . (:plugins (:jedi_completion (:eager nil)))))))))
-#+end_src
-
-Listing [[lst:configure-anaconda-for-python]] configures [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]]. See
-[[https://github.com/jorgenschaefer/elpy/blob/8d0de310d41ebf06b22321a8534546447456870c/elpy.el#L2775][elpy-module-company]] for how to handle ~company-backends~ as a local variable and
-the call to [[info:elisp#Advising Functions][advice-add]] opens Python org-mode edit-buffers in ~anaconda-mode~.
-
-#+caption[Configure =anaconda= for Python]:
-#+caption: Configure =anaconda= for Python.
-#+name: lst:configure-anaconda-for-python
-#+begin_src emacs-lisp
-  (with-eval-after-load 'python
-    (with-eval-after-load 'company
-      (when (and (fboundp 'anaconda-mode)
-                 (fboundp 'company-anaconda))
-        (defun my-disable-anaconda-mode ()
-          (when (derived-mode-p 'python-mode)
-            (anaconda-mode -1)
-            (make-variable-buffer-local 'company-backends)
-            (setq company-backends
-                  (delq 'company-anaconda
-                        (mapcar #'identity company-backends)))
-            (anaconda-eldoc-mode -1)))
-        (defun my-enable-anaconda-mode ()
-          (when (derived-mode-p 'python-mode)
-            (anaconda-mode +1)
-            (make-variable-buffer-local 'company-backends)
-            (setq company-backends
-                  (cons 'company-anaconda
-                        (delq 'company-semantic
-                              (delq 'company-capf
-                                    (mapcar #'identity company-backends)))))
-            (anaconda-eldoc-mode
-             (if (file-remote-p default-directory) -1 1))))))
-
-    (unless (and (fboundp 'my-disable-anaconda-mode)
-                 (fboundp 'my-enable-anaconda-mode))
-      (when (fboundp 'anaconda-mode)
-        (defun my-disable-anaconda-mode ()
-          (when (derived-mode-p 'python-mode)
-            (anaconda-mode -1)
-            (anaconda-eldoc-mode -1)))
-        (defun my-enable-anaconda-mode ()
-          (when (derived-mode-p 'python-mode)
-            (anaconda-mode +1)
-            (anaconda-eldoc-mode
-             (if (file-remote-p default-directory) -1 1))))))
-
-    (when (fboundp 'my-enable-anaconda-mode)
-      (advice-add 'org-edit-src-code :after #'my-enable-anaconda-mode))
-    (when (and (fboundp 'my-disable-anaconda-mode)
-               (fboundp 'my-enable-anaconda-mode))
-      (defun my-toggle-anaconda-mode ()
-        "Toggle anaconda-mode with bells and whistles."
-        (interactive)
-        (if (bound-and-true-p anaconda-mode)
-            (my-disable-anaconda-mode)
-          (my-enable-anaconda-mode)))))
-#+end_src
-
-Listing [[lst:example-py]] is a [[https://www.python.org][Python]] example showing differences in the handling
-of compiled foreign language modules and pure [[https://www.python.org][Python]] modules.  The underlying
-[[https://jedi.readthedocs.io/en/latest/][jedi]] library parses modules (instead of imports) in order to handle completion
-and documentation request.  Therefore, [[https://jedi.readthedocs.io/en/latest/][jedi]] and consequently [[https://github.com/joaotavora/eglot][eglot]] as well as
-[[https://github.com/pythonic-emacs/anaconda-mode][anaconda]] treat compiled foreign language modules as second zone citizens.  This
-is noticible when coding certain functions of for instance [[https://numpy.org/][numpy]] and [[https://scipy.org/][scipy]].
-
-#+caption[Tangle the =example.py= file]:
-#+caption: Tangle the =example.py= file.
-#+name: lst:example-py
-#+begin_src python :tangle example.py :comments link
-  import numpy
-  import astropy.units as apu
-
-  a = numpy.arange(0, 11)
-  a = numpy.linspace(0, 10, num=11)
-  q = apu.Quantity(a, apu.meter)
-  print(q)
-#+end_src
-
-Listing [[lst:enable-pyenv-mode]] configures and enables =pyenv-mode=.
-
-#+caption[Enable =pyenv-mode=]:
-#+caption: Enable =pyenv-mode=.
-#+name: lst:enable-pyenv-mode
-#+begin_src emacs-lisp
-  (when (and (executable-find "pyenv")
-             (require 'pyenv-mode nil 'noerror))
-    (pyenv-mode +1)
-    (pyenv-mode-set "3.9.9/envs/python-3.9.9"))
-#+end_src
-
-Listing [[lst:configure-info]] adds a path in my home directory to the places where
-=info= looks for files.
-
-#+caption[Configure =info=]:
-#+caption: Configure =info=.
-#+name: lst:configure-info
-#+begin_src emacs-lisp
-  (with-eval-after-load 'info
-    (add-to-list 'Info-directory-list
-                 (expand-file-name "~/.local/share/info")))
-#+end_src
-
-Look into:
-1. [[https://github.com/douglasdavis/numpydoc.el/blob/main/numpydoc.el][Emacs extension to insert numpy style docstrings in function definitions]]
-
 * [[https://lists.gnu.org/archive/html/emacs-devel/2020-04/msg00775.html][Appearance]]
 
 ** [[info:emacs#Faces][Text faces (or styles)]]

pylsp-auto-import-modules.patch

@@ -0,0 +1,41 @@
+diff --git a/pylsp/config/schema.json b/pylsp/config/schema.json
+index c29d78b..f54b67a 100644
+--- a/pylsp/config/schema.json
++++ b/pylsp/config/schema.json
+@@ -69,6 +69,14 @@
+       "default": null,
+       "description": "List of errors and warnings to enable."
+     },
++    "pylsp.plugins.jedi.auto_import_modules": {
++      "type": "array",
++        "default": ["numpy", "scipy", "gi"],
++      "items": {
++        "type": "string"
++      },
++      "description": "List of module names for jedi to import (jedi.settings.auto_import_modules)."
++    },
+     "pylsp.plugins.jedi.extra_paths": {
+       "type": "array",
+       "default": [],
+diff --git a/pylsp/workspace.py b/pylsp/workspace.py
+index bf312f6..49e967a 100644
+--- a/pylsp/workspace.py
++++ b/pylsp/workspace.py
+@@ -14,6 +14,8 @@ from . import lsp, uris, _utils
+
+ log = logging.getLogger(__name__)
+
++DEFAULT_AUTO_IMPORT_MODULES = ["numpy", "scipy", "gi"]
++
+ # TODO: this is not the best e.g. we capture numbers
+ RE_START_WORD = re.compile('[A-Za-z_0-9]*$')
+ RE_END_WORD = re.compile('^[A-Za-z_0-9]*')
+@@ -252,6 +254,8 @@ class Document:
+
+         if self._config:
+             jedi_settings = self._config.plugin_settings('jedi', document_path=self.path)
++            jedi.settings.auto_import_modules = jedi_settings.get('auto_import_modules',
++                                                                  DEFAULT_AUTO_IMPORT_MODULES)
+             environment_path = jedi_settings.get('environment')
+             extra_paths = jedi_settings.get('extra_paths') or []
+             env_vars = jedi_settings.get('env_vars')