01-create-dirs.sh

@@ -5,4 +5,5 @@ mefs_indent_message "Directory tree creation..."
 mkdir -p $mefs_EMACSDIR/sources
 mkdir -p $mefs_EMACSDIR/flavors/
 ln -sf $mefs_THISREPODIR/configs $mefs_EMACSDIR/
+ln -sf $mefs_THISREPODIR/layers $mefs_EMACSDIR/
 

configs/spacemacs-default/dot-layers.el

@@ -21,7 +21,7 @@
      ;; csv
 
      ;; -------- Applications
-     ;; org
+     org
      ;; gnus
      ;; fasd
      lsp

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

 (defun dotspacemacs/user-config-specific ()
-  (defun ulys/config/org/babel ()
-
-    ;; FIXME julia bug - hack I 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)))
+  (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"))

configs/spacemacs-minimal/init.el

@@ -2,7 +2,7 @@
 ;; This file is loaded by Spacemacs at startup.
 ;; It must be stored in your home directory.
 
-;; Determine config directory
+;; Determine specific config directory
 (setq config-emacs-directory (replace-regexp-in-string "flavors" "configs" user-emacs-directory))
 
 (defun load-config-file (filename)
@@ -41,6 +41,7 @@ This function should only modify configuration layer settings."
    ;; List of additional paths where to look for configuration layers.
    ;; Paths must have a trailing slash (i.e. `~/.mycontribs/')
    dotspacemacs-configuration-layer-path '()
+
    ;; List of additional packages that will be installed without being
    ;; wrapped in a layer. If you need some configuration for these
    ;; packages, then consider creating a layer. You can also put the
@@ -48,7 +49,8 @@ This function should only modify configuration layer settings."
    ;; To use a local version of a package, use the `:location' property:
    ;; '(your-package :location "~/path/to/your-package/")
    ;; Also include the dependencies as they will not be resolved automatically.
-   dotspacemacs-additional-packages '()
+   dotspacemacs-additional-packages '(
+                                      )
 
    ;; A list of packages that cannot be updated.
    dotspacemacs-frozen-packages '()
@@ -75,6 +77,8 @@ This function should only modify configuration layer settings."
            helm-no-header t)
      emacs-lisp
      git
+     org
+     smartparens
      )
    )
 
@@ -274,11 +278,11 @@ It should only modify the values of Spacemacs settings."
 
    ;; If non-nil then the last auto saved layouts are resumed automatically upon
    ;; start. (default nil)
-   dotspacemacs-auto-resume-layouts nil
+   dotspacemacs-auto-resume-layouts t
 
    ;; If non-nil, auto-generate layout name when creating new layouts. Only has
    ;; effect when using the "jump to layout by number" commands. (default nil)
-   dotspacemacs-auto-generate-layout-names nil
+   dotspacemacs-auto-generate-layout-names t
 
    ;; Size (in MB) above which spacemacs will prompt to open the large file
    ;; literally to avoid performance issues. Opening a file literally means that
@@ -505,6 +509,8 @@ If you are unsure, try setting them in `dotspacemacs/user-config' first."
   ;; --------------------------------------------------
   ;; ------ Configuration common to all versions ------
   ;; --------------------------------------------------
+  (message (concat user-emacs-directory "../../layers/"))
+  ;; (setq-default dotspacemacs-configuration-layer-path '(concat user-emacs-directory "../../layers/"))
 
 
   ;; --------------------------------------------------
@@ -541,8 +547,10 @@ before packages are loaded."
   ;; --------------------------------------------------
   ;; ------ Configuration common to all versions ------
   ;; --------------------------------------------------
-  (setq undo-tree-auto-save-history t)
-  (setq hybrid-style-enable-hjkl-bindings t)
+
+  (ulys/conf/general)
+  (ulys/conf/dired)
+  (ulys/conf/kbd)
 
   ;; --------------------------------------------------
   ;; ----- Configuration specific to this version -----
@@ -551,5 +559,54 @@ before packages are loaded."
   (dotspacemacs/user-config-specific)
   )
 
+ ; general config
+(defun ulys/conf/general ()
+  (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)
+  (spacemacs/toggle-centered-point-globally-on)
+
+  ;; add time in powerline
+  (display-time-mode 1)
+
+  ;; New frame will open fullscreen
+  (add-to-list 'default-frame-alist '(fullscreen . fullboth))
+  )
+ ; dired config
+(defun ulys/conf/dired ()
+
+  ;; helpers
+  (defun ulys/dired-open-current-dir ()
+    (interactive)
+    (spacemacs/dired "."))
+  (defun ulys/conf/dired/kbd/C-hjkl ()
+    (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))
+
+  ;; Auto-refresh dired on file change
+  (add-hook 'dired-mode-hook 'auto-revert-mode)
+
+  (spacemacs/set-leader-keys "ad" 'ulys/dired-open-current-dir)
+
+  ;; (hide .~undo-tree~ files)
+  (setq dired-omit-verbose nil)
+  (add-hook 'dired-mode-hook (lambda () (dired-omit-mode)))
+  (ulys/conf/dired/kbd/C-hjkl))
+ ; 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.

configs/spacemacs-test/dot-layers.el

@@ -21,7 +21,7 @@
      ;; csv
 
      ;; -------- Applications
-     ;; org
+     org
      ;; gnus
      ;; fasd
      lsp
@@ -50,5 +50,11 @@
      ;; -------
      ;; theming
              ))
-   )
+
+dotspacemacs-additional-packages
+(append dotspacemacs-additional-packages
+        '(
+         )
+        )
+    )
   )

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

 (defun dotspacemacs/user-config-specific ()
   (defun ulys/config/org/babel ()
 
-    ;; FIXME julia bug - hack I have opened issue #13597 
-    (setq inferior-julia-program-name "julia") 
+
+    ;; FIXME julia bug - hack I have opened issue #13597
+    (setq inferior-julia-program-name "julia")
 
     (custom-set-variables
      '(org-babel-load-languages (quote ((emacs-lisp . t)
@@ -15,5 +16,9 @@
                                         (sql        . t)
                                         )))
      '(org-confirm-babel-evaluate nil)))
+
+
   (ulys/config/org/babel)
+
+  (require 'org-tempo)
   )