path: root/snakemake-mode.el

;;; snakemake-mode.el --- Major mode for editing Snakemake files

;; Copyright (C) 2014 Kyle Meyer

;; Author: Kyle Meyer <kyle@kyleam.com>
;; URL: https://github.com/kyleam/snakemake-mode
;; Keywords: tools
;; Version: 0.1.0
;; Package-Requires: ((emacs "24"))

;; This program is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 3, or (at your option)
;; any later version.
;;
;; This program is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.
;;
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.

;;; Commentary:

;; Snakemake mode provides support for editing Snakemake [1] files.  It
;; builds on Python mode to provide fontification, indentation, and
;; imenu indexing for Snakemake's rule blocks.
;;
;; If Snakemake mode is installed from MELPA, no additional setup is
;; required.  It will be loaded the first time a file named 'Snakefile'
;; is opened.
;;
;; Otherwise, put snakemake-mode.el in your `load-path' and add
;;
;;     (require 'snakemake-mode)
;;
;; to your initialization file.
;;
;; [1] https://bitbucket.org/johanneskoester/snakemake/wiki/browse/

;;; Code:

(require 'python)


;;; Customization

;;;###autoload
(defgroup snakemake nil
  "Support for Snakemake files"
  :group 'tools
  :prefix "snakemake-")

(defcustom snakemake-mode-hook nil
  "Hook run when entering `snakemake-mode'."
  :group 'snakemake
  :type 'hook)

(defcustom snakemake-indent-field-offset 4
  "Offset for field indentation."
  :group 'snakemake
  :type 'integer)

(defcustom snakemake-indent-run-offset 2
  "Additional offset for 'run' field value."
  :group 'snakemake
  :type 'integer)

(defcustom snakemake-executable "snakemake"
  "Snakemake executable to use in compile command."
  :group 'snakemake
  :type 'string)

(defcustom snakemake-compile-command-options nil
  "Flags to add to default Snakemake compilation command."
  :group 'snakemake
  :type '(repeat string))


;;; Regexp

(defconst snakemake-rule-or-subworkflow-re
  "\\(rule\\|subworkflow\\) \\([a-zA-Z0-9_]+\\):"
  "Regexp matching a rule or subworkflow.")

(defconst snakemake-rule-or-subworkflow-line-re
  (concat "^" snakemake-rule-or-subworkflow-re)
  "Regexp matching a rule or subworkflow at start of line.")

(defconst snakemake-toplevel-command-re
  "^\\(include\\|workdir\\|ruleorder\\):"
  "Regexp matching other toplevel commands aside from 'rule'.")

(defconst snakemake-field-key-re
  (concat "\\(input\\|output\\|shell\\|run\\|workdir\\|priority"
          "\\|message\\|threads\\|versions\\|resources\\|params"
          "\\|snakefile\\):")
  "Regexp matching a rule or subworkflow field key.")

(defconst snakemake-field-key-indented-re
  (concat  "^[ \t]+" snakemake-field-key-re)
  "Regexp matching a field key, including indentation.")

(defconst snakemake-builtin-function-re
  "\\(expand\\|shell\\|protected\\|temp\\|dynamic\\)("
  "Regexp matching a builtin functions.")


;;; Indentation

(defun snakemake-indent-line ()
  "Indent the current line.
Outside of rule blocks, indentation is handled as it would be in
a Python mode buffer (using `python-indent-line-function').
Inside rule blocks (or on a blank line directly below),
`snakemake-indent-rule-line' is called."
  (interactive)
  (if (snakemake-in-rule-or-subworkflow-block-p)
      (snakemake-indent-rule-line)
    (python-indent-line-function)))

(defun snakemake-indent-rule-line ()
  "Indent rule line.

- At the top of rule block

  All indentation is removed.

- At a rule field key ('input', 'output',...)

  The line is indented to `snakemake-indent-field-offset'.

- Below a 'run' subkey

  The first line below 'run' will be indented to
  `snakemake-indent-field-offset' plus
  `snakemake-indent-run-offset'.  Other lines are indented with
  `python-indent-line-function'.

- Otherwise

  Alternate between no indentation,
  `snakemake-indent-field-offset', and the column of the previous
  field value."
  (save-excursion
    (let ((start-indent (current-indentation)))
      (beginning-of-line)
      (cond
       ((looking-at (concat "^[ \t]*" snakemake-rule-or-subworkflow-re))
        (delete-horizontal-space))
       ((looking-at (concat "^[ \t]*" snakemake-field-key-re))
        (delete-horizontal-space)
        (indent-to snakemake-indent-field-offset))
       ((snakemake-run-field-first-line-p)
        (delete-horizontal-space)
        (indent-to (+ snakemake-indent-field-offset
                      snakemake-indent-run-offset)))
       ((snakemake-run-field-line-p)
        (python-indent-line-function))
       ((< start-indent snakemake-indent-field-offset)
        (delete-horizontal-space)
        (indent-to snakemake-indent-field-offset))
       (t
        (let ((prev-col (snakemake-previous-field-value-column)))
          (when prev-col
            (delete-horizontal-space)
            (when (< start-indent prev-col)
              (indent-to prev-col))))))))
  (if (< (current-column) (current-indentation))
      (forward-to-indentation 0)))

(defun snakemake-in-rule-or-subworkflow-block-p ()
  "Point is in block or on first blank line following one."
  (save-excursion
    (beginning-of-line)
    (when (looking-at "^ *$")
      (forward-line -1))
    (end-of-line)
    (let ((start (point)))
      (and (re-search-backward snakemake-rule-or-subworkflow-re nil t)
           (not (re-search-forward "^ *$" start t))))))

(defun snakemake-run-field-first-line-p ()
  "Point is on the first line below a run field key."
  (save-excursion
    (forward-line -1)
    (beginning-of-line)
    (and (re-search-forward "^[ \t]+run:" (point-at-eol) t)
         t)))

(defun snakemake-run-field-line-p ()
  "Point is on any line below a run field key.
This function assumes that
`snakemake-in-rule-or-subworkflow-block-p' is true.  If it's not,
it will give the wrong answer if below a rule block whose last
field is 'run'."
  (save-excursion
    (let ((rule-start (save-excursion
                        (end-of-line)
                        (re-search-backward snakemake-rule-or-subworkflow-re
                                            nil t))))
      (forward-line -1)
      (end-of-line)
      (re-search-backward snakemake-field-key-indented-re rule-start t)
      (string= (match-string 1) "run"))))

(defun snakemake-previous-field-value-column ()
  "Get column for previous field value.
If directly below a field key, this corresponds to the column for
the first non-blank character after 'key:'.  Otherwise, it is the
column of the first non-blank character."
  (save-excursion
    (forward-line -1)
    (beginning-of-line)
    ;; Because of multiline fields, the previous line may not have a
    ;; key.
    (let ((rule-re (concat "\\(?:" snakemake-field-key-indented-re
                           "\\)* *[^ ]")))
      (if (re-search-forward rule-re (point-at-eol) t)
          (1- (current-column))))))


;;; Compilation

(defun snakemake-compile-command ()
  "Return Snakemake compile command.
Flags are taken from `snakemake-compile-command-options'."
  (mapconcat 'identity
             (cons snakemake-executable snakemake-compile-command-options)
             " "))

(defun snakemake-compile-rule (jobs)
  "Run Snakemake with the rule at point as the target.

The numeric prefix JOBS controls the number of jobs that
Snakemake runs (defaults to 1).  If JOBS is zero, perform a dry
run.

Customize `snakemake-executable' and
`snakemake-compile-command-options' to control the compilation
command."
  (interactive "p")
  (unless (snakemake-in-rule-or-subworkflow-block-p)
    (user-error "Not in rule block"))
  (save-excursion
    (end-of-line)
    (re-search-backward snakemake-rule-or-subworkflow-re)
    (let ((block-type (match-string-no-properties 1))
          (rule-name (match-string-no-properties 2)))
      (pcase block-type
        ("rule"
         (let* ((job-flag (if (zerop jobs)
                              " -n "
                            (format " -j%s " jobs)))
                (compile-command (concat (snakemake-compile-command) job-flag
                                         rule-name)))
           (call-interactively #'compile)))
        ("subworkflow" (user-error "Cannot compile a subworkflow"))))))


;;; Mode

(defvar snakemake-mode-map
  (let ((map (make-sparse-keymap)))
    (set-keymap-parent map python-mode-map)
    (define-key map (kbd "C-c C-b") 'snakemake-compile-rule)
    map)
  "Keymap for `snakemake-mode'.")

(defvar snakemake-font-lock-keywords
  `((,snakemake-rule-or-subworkflow-line-re (1 font-lock-keyword-face)
                                            (2 font-lock-function-name-face))
    (,snakemake-toplevel-command-re 1 font-lock-keyword-face)
    (,snakemake-builtin-function-re 1 font-lock-builtin-face)
    (,snakemake-field-key-indented-re 1 font-lock-type-face)))

(defun snakemake-set-imenu-generic-expression ()
  "Extract rule names for `imenu' index."
  ;; Disable `python-info-current-defun'
  (setq imenu-extract-index-name-function nil)
  (setq imenu-create-index-function 'imenu-default-create-index-function)
  (setq imenu-generic-expression
        `((nil ,snakemake-rule-or-subworkflow-line-re 2))))

(add-hook 'snakemake-mode-hook 'snakemake-set-imenu-generic-expression)

;;;###autoload
(define-derived-mode snakemake-mode python-mode "Snakemake"
  "Mode for editing Snakemake files.

\\<snakemake-mode-map>\
Type \\[snakemake-compile-rule] to run Snakemake with the rule of
the block at point as the target.
\n\\{snakemake-mode-map}"
  (set (make-local-variable 'indent-line-function) 'snakemake-indent-line)
  (font-lock-add-keywords nil snakemake-font-lock-keywords)
  (set (make-local-variable 'compile-command) (snakemake-compile-command)))

;;;###autoload
(add-to-list 'auto-mode-alist '("Snakefile\\'" . snakemake-mode))
;;;###autoload
(add-to-list 'auto-mode-alist '("\\.smrules\\'" . snakemake-mode))

(provide 'snakemake-mode)

;; Local variables:
;; sentence-end-double-space: t
;; End:

;;; snakemake-mode.el ends here