New strategy: with private layers

configs/spacemacs-default/dot-user-config.el

-(defun dotspacemacs/user-config-specific ()
-  (ulys/config/org)
-  (ulys/config/ess)
-  )
-
-; ESS config
-(defun ulys/config/ess ()
-  (ulys/conf/ess-devtools-save-silentely)
-  (add-hook 'ess-mode-hook
-            (lambda ()
-              (define-key ess-mode-map (kbd ";") 'ess-insert-assign)
-              (define-key ess-mode-map (kbd "C-;") 'ulys/conf/ess-insert-magrittr-pipe)
-              (define-key ess-mode-map (kbd "C-:")
-                'ulys/conf/ess-insert-right-assign-operator)
-              (define-key ess-mode-map (kbd "C-x C-j")
-                'ess-eval-line-invisibly-and-step)
-              (define-key ess-mode-map (kbd "C-`") 'ulys/conf/ess-backquote-from-dollar)
-              (define-key ess-mode-map (kbd "C-~") 'ulys/conf/ess-backquote-delete-df$)
-              )))
-(defun ulys/conf/ess-insert-magrittr-pipe ()
-  "Insert magrittr pipe at i.e. \"%>%\"."
-  (interactive)
-  (insert "\n  %>% "))
-(defun ulys/conf/ess-insert-right-assign-operator ()
-  "Insert  \"->\"."
-  (interactive)
-  (insert " -> "))
-(defun ulys/conf/ess-devtools-save-silentely ()
-  (setq ess-save-silently t))
-(defun ulys/conf/ess-backquote-from-dollar ()
-  "Surround with backquotes form last $ till point."
-  (interactive)
-  (insert "`")
-  (setq initial-position (point))
-  (evil-find-char-to-backward 1 (string-to-char "$"))
-  (insert "`")
-  (goto-char (+ 1 initial-position)))
-(defun ulys/conf/ess-backquote-delete-df$ ()
-  (interactive)
-  (ulys/conf/ess-backquote-from-dollar)
-  (evil-find-char-to-backward 1 (string-to-char "$"))
-  (setq dollar-position (point))
-  (evil-backward-WORD-begin)
-  (evil-sp-delete (point) dollar-position)
-  (evil-find-char 1 (string-to-char "`"))
-  (evil-forward-char)
-  )
-
-;; Org config
-(defun ulys/config/org ()
-  (ulys/config/org/misc)
-  (ulys/config/org/babel)
-  (ulys/config/org-calendar)
-;;  (ulys/config/org-minted)
-;;  (ulys/config/org-odt-export-latexml)
-;;  (ulys/config/org-capture)
-;;  (ulys/config/org-file-apps)
-  )
-(defun ulys/config/org/misc ()
-  (setq org-list-allow-alphabetical t)
-  (setq org-hide-emphasis-markers t)
-  ;; <sTAB => src block
-  (require 'org-tempo)
-  )
-(defun ulys/config/org/babel ()
-
-  (setq org-src-window-setup 'current-window)
-
-  ;; FIXME julia bug - hack - have opened issue #13597
-  (setq inferior-julia-program-name "julia")
-
-  (custom-set-variables
-   '(org-babel-load-languages (quote ((emacs-lisp . t)
-                                      (R          . t)
-                                      (latex      . t)
-                                      (shell      . t)
-                                      (ditaa      . t)
-                                      (julia      . t)
-                                      (python     . t)
-                                      (sql        . t)
-                                      )))
-   '(org-confirm-babel-evaluate nil)))
-(defun ulys/org-insert-csv-as-table (filename)
-  "Insert a csv file into the current buffer at point, and convert it to an org table."
-  (interactive (list (ido-read-file-name "csv file: ")))
-  (let* ((start (point))
-         (end (+ start (nth 1 (insert-file-contents filename)))))
-    (org-table-convert-region start end)))
-(defun ulys/config/org-capture ()
-  (setq org-default-notes-file "~/Nextcloud/org/tasks.org" )
-  (setq org-capture-templates
-        '(("t" "Thesis-related Task" entry
-            (file "~/Nextcloud/org/thesis.org")
-            "** TODO %?" :empty-lines 1)
-          ("u" "Teaching-related Task" entry
-           (file "~/Nextcloud/org/teaching.org")
-           "** TODO %?" :empty-lines 1)
-          ("h" "Hospital-related Task" entry
-           (file "~/Nextcloud/org/hospital.org")
-           "** TODO %?" :empty-lines 1))))
-(defun ulys/config/org-file-apps ()
-  (defun ulys/org-pdf-app (file-path link-without-schema)
-    "Open pdf file using pdf-tools and go to the specified page."
-    (let* ((page (if (not (string-match "\\.pdf::\\([0-9]+\\)\\'"
-                                        link-without-schema))
-                     1
-                   (string-to-number (match-string 1 link-without-schema)))))
-      (find-file-other-window file-path)
-      (pdf-view-goto-page page)))
-  (setq org-file-apps
-        '((auto-mode . emacs)
-          ("\\.x?html?\\'" . "firefox %s")
-          ("\\.pdf\\(::[0-9]+\\)?\\'" . whatacold/org-pdf-app)
-          ("\\.gif\\'" . "eog \"%s\"")
-          ("\\.mp4\\'" . "vlc \"%s\"")
-          ("\\.mkv" . "vlc \"%s\""))))
-(defun ulys/config/org-calendar ()
-  (setq calendar-week-start-day 1))
-(defun ulys/org//capture-helper-capture-with-yank-method (method arg)
-
-  ;; helper 1/2
-  (defun wrap-into-results-example (capture)
-    (concat
-     "#+RESULTS:\n"
-     "#+ATTR_LATEX: :options frame=lines\n"
-     "#+BEGIN_SRC R :eval no :tangle no\n"
-     capture
-     "\n#+END_SRC\n"))
-
-  ;; helper 2/2
-  (defun choose-process (arg)
-    (if (or arg ;; user asks for selection
-            (not (boundp 'R-process-target)) ;; target not set
-            ;; or target is not set to an active process:
-            (not (process-live-p (get-buffer-process
-                                  R-process-target))))
-        (setq R-process-target
-              (completing-read
-               "Choose R process: "
-               (seq-map (lambda (el) (buffer-name (process-buffer el)))
-                        (process-list))))))
-
-  ;; main
-  (choose-process arg)
-  (insert (wrap-into-results-example
-           (funcall method R-process-target))))
-(defun ulys/org/tibble-capture (arg)
-  "Let the user choose a R process, then kill last tibble output
-in the process and insert it in current buffer in a org
-#+RESULTS: format."
-  (interactive "P")
-
-  ;; helper 1/3
-  (defun extract-nrows-from-tibble-first-line (line)
-    "Extract the number N in the pattern: # A tibble N x M"
-    (let* (( line-without-commas (replace-regexp-in-string "," "" line))
-           ( x-position    (string-match " x" line-without-commas))
-           ( nrow-start-at (length "# A tibble ")))
-      (string-to-number
-       (substring line-without-commas nrow-start-at x-position))))
-
-
-  ;; helper 3/3
-  (defun yank-last-tibble-from-buffer (buffer)
-    (interactive)
-
-    (save-current-buffer
-      (set-buffer buffer)
-      (search-backward "tibble")
-      (beginning-of-line)
-      (let* ((tibble-beg (point))
-             (nrow (extract-nrows-from-tibble-first-line (thing-at-point 'line t)))
-             (tibble-end (progn
-                           (message "nrow: %d" nrow)
-                           (re-search-forward (concat "^" (number-to-string (min 10 nrow))))
-                           (while (search-forward "#"  nil t))   ;; t means no error
-                           (end-of-line)
-                           (point))))
-        (buffer-substring tibble-beg tibble-end))))
-
-  ;; main
-  (ulys/org//capture-helper-capture-with-yank-method 'yank-last-tibble-from-buffer arg))
-(defun ulys/org/glimpse-capture (arg)
-  "Let the user choose a R process, then kill last glimpse output
-in the process and insert it in current buffer in a org
-#+RESULTS: format."
-  (interactive "P")
-
-  ;; helper 1
-  (defun extract-nb-vars-from-glimpse-second-line (line)
-    "Extract the number N in the pattern: Variables: N"
-    (let (( nb-vars-start-at (length "Varialbes: "))
-          ( nb-vars-end-at   (length line)))
-      (string-to-number
-       (substring line nb-vars-start-at nb-vars-end-at))))
-
-  ;; helper 2
-  (defun suppress_$_in_front_of_lines (lines)
-    (replace-regexp-in-string "^\$ "  "" lines))
-
-  ;; helper 3
-  (defun yank-last-glimpse-from-buffer (buffer)
-    (interactive)
-
-    (save-current-buffer
-      (set-buffer buffer)
-      (search-backward "Observations: ")
-      (beginning-of-line)
-      (let* ((glimpse-beg (point))
-             (nrow (progn
-                     (forward-line)
-                     (extract-nb-vars-from-glimpse-second-line
-                      (thing-at-point 'line t))))
-             (glimpse-end (progn
-                           (forward-line nrow)
-                           (end-of-line)
-                           (point))))
-        (suppress_$_in_front_of_lines
-         (buffer-substring glimpse-beg glimpse-end) ))))
-
-  ;; main
-  (ulys/org//capture-helper-capture-with-yank-method 'yank-last-glimpse-from-buffer arg))
-(defun ulys/config/org-minted ()
-  (setq org-latex-listings 'minted
-        org-latex-packages-alist '(("" "minted"))
-        org-latex-pdf-process
-        '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
-          "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
-          "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f")))
-(defun ulys/config/org-odt-export-latexml ()
-  (setq org-latex-to-mathml-convert-command"latexmlmath \"%i\" --presentationmathml=%o"))
+(defun dotspacemacs/user-config-specific ())

configs/spacemacs-test/init.el

-../spacemacs-minimal/init.el
\ No newline at end of file

configs/spacemacs-test/init.el

+;; -*- mode: emacs-lisp; lexical-binding: t -*-
+;; This file is loaded by Spacemacs at startup.
+;; It must be stored in your home directory.
+
+;; Determine specific config directory
+(setq config-emacs-directory (replace-regexp-in-string "flavors" "configs" user-emacs-directory))
+
+(defun load-config-file (filename)
+  (load (concat config-emacs-directory filename)))
+
+(defun dotspacemacs/layers ()
+  "Layer configuration:
+This function should only modify configuration layer settings."
+
+  ;; --------------------------------------------------
+  ;; ------ Configuration common to all versions ------
+  ;; --------------------------------------------------
+
+  ;; Settings
+  (setq-default
+   dotspacemacs-distribution 'spacemacs
+   dotspacemacs-enable-lazy-installation nil
+   dotspacemacs-ask-for-lazy-installation t
+   dotspacemacs-configuration-layer-path (list
+                                          (concat user-emacs-directory
+                                                  "../../layers/"))
+   dotspacemacs-additional-packages '()
+   dotspacemacs-frozen-packages '()
+   dotspacemacs-excluded-packages '()
+   dotspacemacs-install-packages 'used-but-keep-unused)
+
+  ;; Layers
+  (setq-default
+   ;; List of configuration layers to load.
+   dotspacemacs-configuration-layers
+   '(
+     (general     :location local)
+     (smartparens :location local)
+     (dired       :location local)
+     (pdfs        :location local)
+     )
+   )
+
+  ;; --------------------------------------------------
+  ;; ----- Configuration specific to this version -----
+  ;; --------------------------------------------------
+
+  (load-config-file  "dot-layers.el")
+  (dotspacemacs/layers-specific)
+  )
+
+(defun dotspacemacs/init ()
+  "Instantiate Spacemacs core settings.
+All `dotspacemacs-' variables with values set different than their defaults.
+They are all defined in `~/.emacs.d/core/core-dotspacemacs.el'.
+Check `dotspacemacs/get-variable-string-list' for all vars you can configure."
+
+  ;; --------------------------------------------------
+  ;; ------ Configuration common to all versions ------
+  ;; --------------------------------------------------
+
+  (setq-default
+   dotspacemacs-editing-style 'hybrid
+   dotspacemacs-startup-banner 100
+   dotspacemacs-startup-lists '(
+                                (agenda . 10)
+                                (todos . 20)
+                                (projects . 5)
+                                (recents . 10)
+                                )
+   dotspacemacs-themes '(spacemacs-dark
+                         spacemacs-light)
+   dotspacemacs-default-font '("Source Code Pro"
+                               :size 13.0
+                               :weight normal
+                               :width normal)
+
+   dotspacemacs-leader-key "SPC"
+   dotspacemacs-emacs-command-key "SPC"
+   dotspacemacs-emacs-leader-key "M-m"
+   dotspacemacs-major-mode-emacs-leader-key (if window-system "<M-return>" "C-M-m")
+   dotspacemacs-default-layout-name "TODO"
+   dotspacemacs-display-default-layout t
+   dotspacemacs-auto-resume-layouts t
+   dotspacemacs-auto-generate-layout-names t
+   dotspacemacs-auto-save-file-location 'original
+   dotspacemacs-enable-paste-transient-state t
+   dotspacemacs-fullscreen-at-startup t
+   dotspacemacs-mode-line-unicode-symbols nil
+   dotspacemacs-line-numbers 'visual
+   dotspacemacs-search-tools '("ag" "rg" "pt" "ack" "grep")
+   dotspacemacs-whitespace-cleanup 'all
+   dotspacemacs-pretty-docs t)
+
+  ;; --------------------------------------------------
+  ;; ----- Configuration specific to this version -----
+  ;; --------------------------------------------------
+
+  (load-config-file  "dot-init.el")
+  (dotspacemacs/init-specific)
+  )
+
+(defun dotspacemacs/user-env ()
+  "Environment variables setup.
+This function defines the environment variables for your Emacs session. By
+default it calls `spacemacs/load-spacemacs-env' which loads the environment
+variables declared in `~/.spacemacs.env' or `~/.spacemacs.d/.spacemacs.env'.
+See the header of this file for more information."
+
+  ;; --------------------------------------------------
+  ;; ------ Configuration common to all versions ------
+  ;; --------------------------------------------------
+
+
+  ;; --------------------------------------------------
+  ;; ----- Configuration specific to this version -----
+  ;; --------------------------------------------------
+  (load-config-file  "dot-user-env.el")
+  (dotspacemacs/user-env-specific)
+  )
+
+(defun dotspacemacs/user-init ()
+  "Initialization for user code:
+This function is called immediately after `dotspacemacs/init', before layer
+configuration.
+It is mostly for variables that should be set before packages are loaded.
+If you are unsure, try setting them in `dotspacemacs/user-config' first."
+
+  ;; --------------------------------------------------
+  ;; ------ Configuration common to all versions ------
+  ;; --------------------------------------------------
+
+  ;; --------------------------------------------------
+  ;; ----- Configuration specific to this version -----
+  ;; --------------------------------------------------
+  (load-config-file  "dot-user-init.el")
+  (dotspacemacs/user-init-specific)
+  )
+
+(defun dotspacemacs/user-load ()
+  "Library to load while dumping.
+This function is called only while dumping Spacemacs configuration. You can
+`require' or `load' the libraries of your choice that will be included in the
+dump."
+  ;; --------------------------------------------------
+  ;; ------ Configuration common to all versions ------
+  ;; --------------------------------------------------
+
+
+  ;; --------------------------------------------------
+  ;; ----- Configuration specific to this version -----
+  ;; --------------------------------------------------
+  (load-config-file  "dot-user-load.el")
+  (dotspacemacs/user-load-specific)
+  )
+
+(defun dotspacemacs/user-config ()
+  "Configuration for user code:
+This function is called at the very end of Spacemacs startup, after layer
+configuration.
+Put your configuration code here, except for variables that should be set
+before packages are loaded."
+
+  ;; --------------------------------------------------
+  ;; ------ Configuration common to all versions ------
+  ;; --------------------------------------------------
+  (spacemacs/toggle-centered-point-globally-on)
+
+  (ulys/conf/dired)
+  (ulys/conf/kbd)
+
+  ;; --------------------------------------------------
+  ;; ----- Configuration specific to this version -----
+  ;; --------------------------------------------------
+  (load-config-file  "dot-user-config.el")
+  (dotspacemacs/user-config-specific)
+  )
+
+ ; dired config
+(defun ulys/conf/dired ()
+)
+ ; kbd config
+(defun ulys/conf/kbd ()
+
+  ;; --- others
+  ;; C-h to delete buffer and C-S-h for help
+  (global-set-key (kbd "C-h") 'spacemacs/kill-this-buffer)
+
+  ;; Simulates vim increment and decrement number
+  (define-key evil-normal-state-map  (kbd "C-a C-a") 'evil-numbers/inc-at-pt)
+  (define-key evil-normal-state-map  (kbd "C-x C-x") 'evil-numbers/dec-at-pt)
+
+  )
+
+
+;; Do not write anything past this comment. This is where Emacs will
+;; auto-generate custom variable definitions.

layers/dired/config.el

+;; helpers
+(defun ulys/dired-open-current-dir ()
+  (interactive)
+  (spacemacs/dired "."))
+
+(spacemacs/set-leader-keys "ad" 'ulys/dired-open-current-dir)
+
+(with-eval-after-load 'evil-core
+  )
+
+;; Auto-refresh dired on file change
+(add-hook 'dired-mode-hook 'auto-revert-mode)
+
+
+;; (hide .~undo-tree~ files)
+(setq dired-omit-verbose nil)
+(add-hook 'dired-mode-hook (lambda () (dired-omit-mode)))

layers/dired/keybindings.el

+(spacemacs/set-leader-keys "ad" 'ulys/dired-open-current-dir)
+
+;; I prefer C-h to kill buffer
+;; (evil-define-key '(normal) dired-mode-map  (kbd "C-h") 'dired-up-directory)
+(evil-define-key '(normal) dired-mode-map  (kbd "C-j") 'evil-next-line)
+(evil-define-key '(normal) dired-mode-map  (kbd "C-k") 'evil-previous-line)
+(evil-define-key '(normal) dired-mode-map  (kbd "C-l") 'dired-find-alternate-file)

layers/general/config.el

+(setq undo-tree-auto-save-history t)
+(setq vc-follow-symlinks t) ;; To edit .spacemacs without to be prompted each time
+
+(setq hybrid-style-enable-hjkl-bindings t)
+
+;; add time in powerline
+(display-time-mode 1)
+
+
+;; New frame will open fullscreen
+(add-to-list 'default-frame-alist '(fullscreen . fullboth))
+
+;; Org config
+(setq org-src-window-setup 'current-window)
+(setq org-list-allow-alphabetical t)
+(setq org-hide-emphasis-markers t)
+(require 'org-tempo)
+;; (ulys/config/org-babel)
+;; (ulys/config/org-calendar)
+;; (ulys/config/org-minted)
+;; (ulys/config/org-odt-export-latexml)
+;; (ulys/config/org-capture)
+;; (ulys/config/org-file-apps)
+
+(defun ulys/org-insert-csv-as-table (filename)
+  "Insert a csv file into the current buffer at point, and convert it to an org table."
+  (interactive (list (ido-read-file-name "csv file: ")))
+  (let* ((start (point))
+         (end (+ start (nth 1 (insert-file-contents filename)))))
+    (org-table-convert-region start end)))
+(defun ulys/config/org-capture ()
+  (setq org-default-notes-file "~/Nextcloud/org/tasks.org" )
+  (setq org-capture-templates
+        '(("t" "Thesis-related Task" entry
+            (file "~/Nextcloud/org/thesis.org")
+            "** TODO %?" :empty-lines 1)
+          ("u" "Teaching-related Task" entry
+           (file "~/Nextcloud/org/teaching.org")
+           "** TODO %?" :empty-lines 1)
+          ("h" "Hospital-related Task" entry
+           (file "~/Nextcloud/org/hospital.org")
+           "** TODO %?" :empty-lines 1))))
+(defun ulys/config/org-file-apps ()
+  (defun ulys/org-pdf-app (file-path link-without-schema)
+    "Open pdf file using pdf-tools and go to the specified page."
+    (let* ((page (if (not (string-match "\\.pdf::\\([0-9]+\\)\\'"
+                                        link-without-schema))
+                     1
+                   (string-to-number (match-string 1 link-without-schema)))))
+      (find-file-other-window file-path)
+      (pdf-view-goto-page page)))
+  (setq org-file-apps
+        '((auto-mode . emacs)
+          ("\\.x?html?\\'" . "firefox %s")
+          ("\\.pdf\\(::[0-9]+\\)?\\'" . whatacold/org-pdf-app)
+          ("\\.gif\\'" . "eog \"%s\"")
+          ("\\.mp4\\'" . "vlc \"%s\"")
+          ("\\.mkv" . "vlc \"%s\""))))
+(defun ulys/config/org-calendar ()
+  (setq calendar-week-start-day 1))
+(defun ulys/config/org-babel ()
+  (custom-set-variables
+   '(org-babel-load-languages (quote ((emacs-lisp . t)
+                                      (R          . t)
+                                      (latex      . t)
+                                      (shell      . t)
+                                      (ditaa      . t)
+                                      (julia      . t)
+                                      (python     . t)
+                                      (sql        . t))))
+   '(org-confirm-babel-evaluate nil)))
+(defun ulys/org//capture-helper-capture-with-yank-method (method arg)
+
+  ;; helper 1/2
+  (defun wrap-into-results-example (capture)
+    (concat
+     "#+RESULTS:\n"
+     "#+ATTR_LATEX: :options frame=lines\n"
+     "#+BEGIN_SRC R :eval no :tangle no\n"
+     capture
+     "\n#+END_SRC\n"))
+
+  ;; helper 2/2
+  (defun choose-process (arg)
+    (if (or arg ;; user asks for selection
+            (not (boundp 'R-process-target)) ;; target not set
+            ;; or target is not set to an active process:
+            (not (process-live-p (get-buffer-process
+                                  R-process-target))))
+        (setq R-process-target
+              (completing-read
+               "Choose R process: "
+               (seq-map (lambda (el) (buffer-name (process-buffer el)))
+                        (process-list))))))
+
+  ;; main
+  (choose-process arg)
+  (insert (wrap-into-results-example
+           (funcall method R-process-target))))
+(defun ulys/org/tibble-capture (arg)
+  "Let the user choose a R process, then kill last tibble output
+in the process and insert it in current buffer in a org
+#+RESULTS: format."
+  (interactive "P")
+
+  ;; helper 1/3
+  (defun extract-nrows-from-tibble-first-line (line)
+    "Extract the number N in the pattern: # A tibble N x M"
+    (let* (( line-without-commas (replace-regexp-in-string "," "" line))
+           ( x-position    (string-match " x" line-without-commas))
+           ( nrow-start-at (length "# A tibble ")))
+      (string-to-number
+       (substring line-without-commas nrow-start-at x-position))))
+
+
+  ;; helper 3/3
+  (defun yank-last-tibble-from-buffer (buffer)
+    (interactive)
+
+    (save-current-buffer
+      (set-buffer buffer)
+      (search-backward "tibble")
+      (beginning-of-line)
+      (let* ((tibble-beg (point))
+             (nrow (extract-nrows-from-tibble-first-line (thing-at-point 'line t)))
+             (tibble-end (progn
+                           (message "nrow: %d" nrow)
+                           (re-search-forward (concat "^" (number-to-string (min 10 nrow))))
+                           (while (search-forward "#"  nil t))   ;; t means no error
+                           (end-of-line)
+                           (point))))
+        (buffer-substring tibble-beg tibble-end))))
+
+  ;; main
+  (ulys/org//capture-helper-capture-with-yank-method 'yank-last-tibble-from-buffer arg))
+(defun ulys/org/glimpse-capture (arg)
+  "Let the user choose a R process, then kill last glimpse output
+in the process and insert it in current buffer in a org
+#+RESULTS: format."
+  (interactive "P")
+
+  ;; helper 1
+  (defun extract-nb-vars-from-glimpse-second-line (line)
+    "Extract the number N in the pattern: Variables: N"
+    (let (( nb-vars-start-at (length "Varialbes: "))
+          ( nb-vars-end-at   (length line)))