Merge branch 'develop' into patch-1

core/core-packages.el

@@ -96,9 +96,13 @@ missing) and shouldn't be deleted.")
       package-user-dir (expand-file-name "elpa" doom-packages-dir)
       package-enable-at-startup nil
       package-archives
-      '(("gnu"   . "https://elpa.gnu.org/packages/")
+      (if (getenv "INSECURE")
-        ("melpa" . "https://melpa.org/packages/")
+          '(("gnu"   . "http://elpa.gnu.org/packages/")
-        ("org"   . "https://orgmode.org/elpa/"))
+            ("melpa" . "http://melpa.org/packages/")
+            ("org"   . "http://orgmode.org/elpa/"))
+        '(("gnu"   . "https://elpa.gnu.org/packages/")
+          ("melpa" . "https://melpa.org/packages/")
+          ("org"   . "https://orgmode.org/elpa/")))
       ;; I omit Marmalade because its packages are manually submitted rather
       ;; than pulled, so packages are often out of date with upstream.
 

core/core-ui.el

@@ -597,7 +597,8 @@ windows, switch to `doom-fallback-buffer'. Otherwise, delegate to original
           ((doom-real-buffer-p buf)
            (if (and buffer-file-name
                     (buffer-modified-p buf)
-                    (not (y-or-n-p "Buffer %s is modified; kill anyway?")))
+                    (not (y-or-n-p
+                          (format "Buffer %s is modified; kill anyway?" buf))))
                (message "Aborted")
              (set-buffer-modified-p nil)
              (when (or ;; if there aren't more real buffers than visible buffers,

init.example.el

@@ -41,6 +41,7 @@
 
        :tools
        dired             ; making dired pretty [functional]
+       ein               ; tame Jupyter notebooks with emacs
        electric-indent   ; smarter, keyword-based electric-indent
        eshell            ; a consistent, cross-platform shell (WIP)
        gist              ; interacting with github gists

modules/feature/file-templates/templates/dockerfile-mode/__

@@ -1,4 +1,4 @@
 FROM ${1:phusion/baseimage:latest}
-MAINTAINER ${2:Henrik Lissner <henrik@lissner.net>}
+MAINTAINER ${2:`user-full-name` <`user-mail-address`>}
 
 $0

modules/feature/workspaces/autoload/workspaces.el

@@ -361,7 +361,7 @@ end of the workspace list."
                  (index (cl-position current-name persps)))
             (when (= perspc 1)
               (user-error "No other workspaces"))
-            (+workspace/switch-to (% (+ index n) perspc))
+            (+workspace/switch-to (% (+ index n perspc) perspc))
             (unless (called-interactively-p 'interactive)
               (+workspace/display)))
         ('user-error (+workspace-error (cadr ex) t))

modules/lang/latex/+fontification.el

@@ -8,6 +8,8 @@
         ("addbibresource" "[{")
         ;; Standard commands
         ("cite" "[{")
+        ("citep" "[{")
+        ("citet" "[{")
         ("Cite" "[{")
         ("parencite" "[{")
         ("Parencite" "[{")

modules/lang/latex/README.org

@@ -26,28 +26,54 @@ Set these variables in your private configuration with:
 #+END_SRC
 If the variables are not set, they are ignored.
 
+** Choose View Program
+You have four options to choose from for the viewer of your PDF rendered files.
+*** Okular
+Use Okular as default PDF viewer.
+
+Activate with the flag '+okular' of the latex module in your private init.el.
+#+BEGIN_SRC emacs_lisp
+(latex +okular)
+#+END_SRC
+
+*** Skim
+For Mac users. Use Skim to preview your PDFs.
+
+Activate with the flag '+skim' of the latex module in your private init.el.
+#+BEGIN_SRC emacs_lisp
+(latex +skim)
+#+END_SRC
+
+*** PDF Tools
+Use the PDF Tools package to preview your PDFs. Requires the tools module ~pdf~ enabled in your configuration.
+#+BEGIN_SRC emacs_lisp
+(:tools pdf)
+#+END_SRC
+
+Activate with the flag '+pdf-tools' of the latex module in your private init.el.
+#+BEGIN_SRC emacs_lisp
+(latex +pdf-tools=)
+#+END_SRC
+
+*** Preview Pane
+You may wish to use the old school package ~latex-preview-pane~ instead of the
+other alternatives. ~latex-preview-pane~ uses a ~DocView~ instead.
+
+Activate with the flag '+preview-pane' of the latex module in your private init.el.
+#+BEGIN_SRC emacs_lisp
+(latex +preview-pane)
+#+END_SRC
+
 ** LatexMk
-Use LatexMk instead of normal LaTeX to compile documents. LatexMk only needs to run once to get all references, bibliography and other things right.
+Use LatexMk instead of normal LaTeX to compile documents. LatexMk only needs to
+run once to get all references, bibliography and other things right.
 
 Activate with the flag '+latexmk' of the latex module in init.el.
 #+BEGIN_SRC emacs_lisp
 (latex +latexmk)
 #+END_SRC
 
-** Okular
+You can enable both a custom view program and LatexMk with a call such as:
-Use Okular as default PDF viewer.
-
-Activate with the flag '+okular' of the latex module in init.el.
 #+BEGIN_SRC emacs_lisp
-(latex +okular)
+(latex +latexmk +okular)
-#+END_SRC
-
-** Preivew-Pane
-Instead of using an external program to display rendered .tex files, use an emacs window to display the rendered file. 
-
-This flag is incompatible with the ~+okular~ flag.
-
-Activate with the flag '+preview-pane' of the latex module in init.el.
-#+BEGIN_SRC emacs_lisp
-(latex +preview-pane)
 #+END_SRC

modules/lang/latex/config.el

@@ -103,21 +103,31 @@
                  LaTeX-indent-environment-list))))
 
 (after! latex
-  ;; Use Okular is the user says so.
+  ;; Use Okular if the user says so.
   (when (featurep! +okular)
     ;; Configure Okular as viewer. Including a bug fix
     ;; (https://bugs.kde.org/show_bug.cgi?id=373855)
     (add-to-list 'TeX-view-program-list
                  '("Okular" ("okular --unique file:%o" (mode-io-correlate "#src:%n%a"))))
     (add-to-list 'TeX-view-program-selection
-                 '(output-pdf "Okular"))))
+                 '(output-pdf "Okular")))
 
-(after! latex
+  ;; Or Skim
   (when (featurep! +skim)
     (add-to-list 'TeX-view-program-list
                  '("Skim" "/Applications/Skim.app/Contents/SharedSupport/displayline -b -g %n %o %b"))
     (add-to-list 'TeX-view-program-selection
-                 '(output-pdf "Skim"))))
+                 '(output-pdf "Skim")))
+
+  ;; Or PDF-tools, but only if the module is also loaded
+  (when (and (featurep! :tools pdf) (featurep! +pdf-tools))
+    (add-to-list 'TeX-view-program-list
+                 '("PDF Tools" ("TeX-pdf-tools-sync-view")))
+    (add-to-list 'TeX-view-program-selection
+                 '(output-pdf "PDF Tools"))
+    ;; Enable auto reverting the PDF document with PDF Tools
+    (add-hook 'TeX-after-compilation-finished-functions #'TeX-revert-document-buffer)))
+
 
 
 (def-package! preview
@@ -136,6 +146,8 @@
         reftex-toc-split-windows-fraction 0.3)
   (unless (string-empty-p +latex-bibtex-file)
     (setq reftex-default-bibliography (list (expand-file-name +latex-bibtex-file))))
+  (add-hook! (latex-mode LaTeX-mode) #'turn-on-reftex)
+  :config
   ;; Get ReTeX working with biblatex
   ;; http://tex.stackexchange.com/questions/31966/setting-up-reftex-with-biblatex-citation-commands/31992#31992
   (setq reftex-cite-format
@@ -146,8 +158,6 @@
           (?f . "\\footcite[]{%l}")
           (?n . "\\nocite{%l}")
           (?b . "\\blockcquote[]{%l}{}")))
-  (add-hook! (latex-mode LaTeX-mode) #'turn-on-reftex)
-  :config
   (map! :map reftex-mode-map
         :localleader :n ";" 'reftex-toc)
   (add-hook! 'reftex-toc-mode-hook

modules/tools/ein/README.org

@@ -0,0 +1,39 @@
+#+TITLE: :tools ein
+
+* EIN -- Emacs IPython Notebook
+
+Tool to work with Jupyter notebooks within emacs.
+
+* Table of Contents :TOC:
+- [[EIN -- Emacs IPython Notebook][EIN -- Emacs IPython Notebook]]
+- [[Install][Install]]
+- [[Usage][Usage]]
+- [[Configuration][Configuration]]
+
+* Install
+Add =:tool ein= to your ~doom!~ call in your private ~init.el~.
+
+* Usage
+Three functions are available to start EIN:
+ 1. ~ein:jupyter-server-start~ --- Start a jupyter server within emacs
+ 2. ~ein:notebooklist-login~ --- Login to an existing jupyter server
+ 3. ~ein:notebooklist-open~ --- Open the list of jupyter notebooks
+
+These functions do not have default key bindings.
+
+When ~ein:jupyter-server-start~ is called, after successfully finishing,
+~ein:notebooklist-login~ and ~ein:notebooklist-open~ will be automatically
+called.
+
+When in the ~Notebook List~ buffer, the key ~o~ calls ~ace-link~ to speed up the
+process of selecting links in the buffer.
+
+If ~company-mode~ is enabled as a module, ~company-ein~ will be used for
+completion purposes.
+
+* Configuration
+Specify the default directory where EIN searches for notebooks using:
+
+~(set! :ein-notebook-dir "~/my-notebooks")~
+
+

modules/tools/ein/autoload.el

@@ -0,0 +1,26 @@
+;;; tools/ein/autoload.el -*- lexical-binding: t; -*-
+
+;;;###autoload
+(defun +ein/ace-link-ein ()
+  "Ace jump to links in ein notebooklist."
+  (interactive)
+  (let ((res (avy-with +ein/ace-link-ein
+               (avy--process
+                (+ein--collect-ein-buffer-links)
+                #'avy--overlay-pre))))
+                ;(avy--style-fn avy-style)))))
+    (when (numberp res)
+      (goto-char (1+ res))
+      (widget-button-press (point)))))
+
+;;;###autoload
+(defun +ein--collect-ein-buffer-links ()
+  (interactive)
+  (let ((end (window-end))
+        points)
+    (save-excursion
+      (goto-char (window-start))
+      (while (re-search-forward "~?/.+\\|\s\\[" end t)
+        (push (+ (match-beginning 0) 1) points))
+      (nreverse points))))
+

modules/tools/ein/config.el

@@ -0,0 +1,38 @@
+;;; tools/ein/config.el -*- lexical-binding: t; -*-
+
+(defvar +ein-notebook-dir "~/"
+  "Default directory from where Jupyter notebooks are to be opened.")
+
+(def-setting! :ein-notebook-dir (dir)
+  "Set the default directory from where to open Jupyter notebooks."
+  `(setq +ein-notebook-dir ,dir))
+
+
+(def-package! ein
+  :commands (ein:notebooklist-open ein:notebooklist-login ein:jupyter-server-start)
+  :init
+  (set! :popup "\\*ein:*" :ignore)
+  (set! :popup "\\*ein:notebooklist *" '((side . left)) '((size . 40) (select)))
+  ;; Ace-link on notebook list buffers
+  (add-hook! 'ein:notebooklist-mode-hook
+    (map! :map ein:notebooklist-mode-map
+          "o" #'+ein/ace-link-ein))
+  ;; Ein uses request to store http cookies. Store them in the cache dir.
+  (setq request-storage-directory (concat doom-cache-dir "/request"))
+  ;; Auto complete with company
+  (set! :company-backend '(ein:notebook-multilang-mode ein:notebook-python-mode ein:notebook-plain-mode)
+    'ein:company-backend)
+  :config
+  ;; Manually load the autoloads of EIN. This takes time...
+  (load "ein-loaddefs.el" nil t t)
+  (setq
+   ;; Slide images into rows so that we can navigate buffers with images more easily
+   ein:slice-image t
+   ein:jupyter-default-notebook-directory +ein-notebook-dir
+   ein:jupyter-default-server-command "/usr/bin/jupyter"
+   ein:jupyter-server-args '("--no-browser")
+   ein:notebook-modes
+   '(ein:notebook-multilang-mode ein:notebook-python-mode ein:notebook-plain-mode))
+  ;; Avy is required for showing links in the notebook list with ace-link.
+  (require 'avy))
+

modules/tools/ein/packages.el

@@ -0,0 +1,4 @@
+;; -*- no-byte-compile: t; -*-
+;;; tools/ein/packages.el
+
+(package! ein)

modules/tools/pdf/+modeline.el

@@ -0,0 +1,10 @@
+;;; tools/pdf/+modeline.el -*- lexical-binding: t; -*-
+
+
+(def-modeline-segment! +pdf-tools-pages
+  "Current and total page indicator for PDF documents."
+  (format " P %d/%d" (pdf-view-current-page) (pdf-cache-number-of-pages)))
+
+(def-modeline! pdf-tools-modeline
+  (bar matches " " buffer-info  +pdf-tools-pages)
+  (major-mode vcs))

modules/tools/pdf/config.el

@@ -7,27 +7,21 @@
   (unless noninteractive
     (pdf-tools-install))
 
-(map! :map pdf-view-mode-map
+  (map! :map pdf-view-mode-map
-      "q" #'kill-this-buffer
+        "q" #'kill-this-buffer
-      doom-leader-key nil)
+        doom-leader-key nil)
 
   (setq-default pdf-view-display-size 'fit-page)
-  ;; turn off cua so copy works
+  ;; Turn off cua so copy works
-  (add-hook! 'pdf-view-mode-hook (cua-mode 0)))
+  (add-hook! 'pdf-view-mode-hook (cua-mode 0))
-
+  ;; Custom modeline that removes useless info and adds page numbers
-
+  (when (featurep! :ui doom-modeline)
-(when (featurep! :lang latex)
+    (load! +modeline)
-  (after! latex
+    (add-hook! pdf-tools-enabled (doom-set-modeline 'pdf-tools-modeline)))
-    ;; add to the program list
+  ;; Handle PDF-tools related popups better
-    (add-to-list 'TeX-view-program-selection
+  (set! :popup "^\\*Outline*" '((side . right) (size . 40)) '((select)))
-                 '(output-pdf "PDF Tools"))
+  ;; TODO: Add additional important windows that should be handled differently
-    (add-to-list 'TeX-view-program-list
+  ;; TODO: These two next rules don't work (they should), investigate
-                 '("PDF Tools" ("TeX-pdf-tools-sync-view")))
+  ;; (set! :popup "\\*Contents\\*" '((side . right) (size . 40)) nil)
-
+  ;; (set! :popup "* annots\\*$" '((side . left) (size . 40)) '((select)))
-    ;; enable document revert
+  )
-    (add-hook 'TeX-after-compilation-finished-functions
-              #'TeX-revert-document-buffer)
-
-    ;; correlated mode
-    (setq TeX-source-correlate-start-server t
-          TeX-source-correlate-mode t)))

modules/ui/doom-modeline/README.org

@@ -37,8 +37,8 @@ Some might want my modeline without the DOOM config altogether. I've tried to ma
 + Replace ~def-package!~ calls with ~use-package~.
 + Replace ~doom-project-root~ calls with ~projectile-project-root~.
 + The ~+doom-modeline--make-xpm~ function is memoized with the ~def-memoized!~ macro. Change ~def-memoized!~ to ~defun~.
-+ Copy the ~add-hook!~ macro definition from [[/master/core/core-lib.el][core/core-lib.el]].
++ Copy the ~add-hook!~ macro definition from [[/core/core-lib.el][core/core-lib.el]].
-+ Copy the following macros and functions from [[/master/core/core-ui.el][core/core-ui.el]]:
++ Copy the following macros and functions from [[/core/core-ui.el][core/core-ui.el]]:
   + ~def-modeline-segment!~
   + ~def-modeline!~
   + ~doom--prepare-modeline-segments~