discussion and development of Emacs Snakemake mode
 help / color / mirror / code / Atom feed
blob 5e4118b02051193076e789b14a9c873df36f4014 19299 bytes (raw)
name: snakemake-mode.el 	 # note: path name is non-authoritative(*)

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
 
;;; snakemake-mode.el --- Major mode for editing Snakemake files  -*- lexical-binding: t; -*-

;; Copyright all Snakemake mode contributors <snakemake-mode@inbox.kyleam.com>

;; Author: Kyle Meyer <kyle@kyleam.com>
;; URL: https://git.kyleam.com/snakemake-mode/about
;; Keywords: tools
;; Version: 1.8.0
;; Package-Requires: ((emacs "24.5") (cl-lib "0.5") (magit-popup "2.4.0"))

;; 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 <https://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.
;;
;; See also snakemake.el, which is packaged with snakemake-mode.el and
;; provides an interface for running Snakemake commands.
;;
;; 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.
;;
;; snakemake-mode.el also includes support for highlighting embedded R
;; code.  See the snakemake-mode-setup-mmm function documentation for how.
;;
;; [1] https://snakemake.github.io/

;;; Code:

(require 'cl-lib)
(require 'python)

\f
;;; Customization

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

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

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

(defcustom snakemake-indent-value-offset 4
  "Offset for field values that the line below the field key."
  :type 'integer)

\f
;;; Regexp

(eval-and-compile
  (defconst snakemake-rx-constituents
    `((named-rule . ,(rx (and (group symbol-start
                                     (or "checkpoint" "rule" "subworkflow"))
                              " "
                              (group (one-or-more
                                      (or (syntax word) (syntax symbol)))))))
      (anon-rule . ,(rx symbol-start "rule"))
      (field-key . ,(rx symbol-start
                        (or "benchmark"
                            "cache"
                            "conda"
                            "container"
                            "cwl"
                            "envmodules"
                            "group"
                            "input"
                            "log"
                            "message"
                            "name"
                            "output"
                            "params"
                            "priority"
                            "resources"
                            "run"
                            "script"
                            "shadow"
                            "shell"
                            "singularity"
                            "threads"
                            "version"
                            "wildcard_constraints"
                            "wrapper"
                            ;; Keys for subworkflow blocks
                            "configfile"
                            "snakefile"
                            "workdir")
                        symbol-end))
      (sm-command . ,(rx symbol-start
                         (or "configfile"
                             "container"
                             "envvars"
                             "include"
                             "localrules"
                             "onerror"
                             "onsuccess"
                             "report"
                             "ruleorder"
                             "singularity"
                             "wildcard_constraints"
                             "workdir")
                         symbol-end))
      (sm-builtin . ,(rx symbol-start
                         (or "ancient"
                             "checkpoints"
                             "directory"
                             "dynamic"
                             "expand"
                             "input"
                             "multiext"
                             "output"
                             "params"
                             "pipe"
                             "protected"
                             "report"
                             "shell"
                             "temp"
                             "touch"
                             "unpack"
                             "wildcards")
                         symbol-end))
      ;; Deprecated.  Use `sm-builtin' instead.
      (sm-func . sm-builtin))
    "Snakemake-specific sexps for `snakemake-rx'.")

  (defmacro snakemake-rx (&rest regexps)
    "Specialized `rx' for Snakemake mode."
    ;; Modified from `python-rx'.
    (let ((rx-constituents (append snakemake-rx-constituents rx-constituents)))
      (cond ((null regexps)
             (error "No regexp"))
            ((cdr regexps)
             (rx-to-string `(and ,@regexps) t))
            (t
             (rx-to-string (car regexps) t))))))

(defconst snakemake-rule-or-subworkflow-re
  (snakemake-rx line-start (zero-or-more space)
                (or named-rule (group anon-rule))
                (zero-or-more space) ":")
  "Regexp matching a rule or subworkflow.")

\f
;;; Info and navigation

(defun snakemake-block-info ()
  "Return description of rule or subworkflow block at point."
  (save-excursion
    (save-restriction
      (widen)
      (let ((pos (point)))
        (end-of-line)
        (and (re-search-backward snakemake-rule-or-subworkflow-re nil t)
             (let ((type (or (match-string-no-properties 1)
                             "rule"))
                   (name (match-string-no-properties 2))
                   (start (or (match-beginning 1)
                              (match-beginning 3)))
                   (rule-indent (current-indentation))
                   end)
               (beginning-of-line)
               (forward-line)
               (while (and (or (< rule-indent (current-indentation))
                               (looking-at-p "^\\s-*$"))
                           (or (not (eobp))
                               (progn (setq end (point-max))
                                      nil)))
                 (setq end (line-end-position))
                 (forward-line))
               (when (<= start pos end)
                 (list type name start end))))))))

(defun snakemake-beginning-of-block (&optional arg)
  "Move to beginning of rule block.
With ARG, do it that many times.  Negative ARG signals to move
forward rather than backward."
  (when (or (null arg) (zerop arg))
    (setq arg 1))
  (funcall (if (> arg 0)
               #'re-search-backward
             (lambda (&rest args)
               (end-of-line)
               (prog1 (apply #'re-search-forward args)
                 (beginning-of-line))))
           snakemake-rule-or-subworkflow-re
           nil 'move (abs arg))
  (looking-at-p snakemake-rule-or-subworkflow-re))

(defun snakemake-end-of-block ()
  "Move to end of rule or subworkflow block."
  (let ((end (nth 3 (snakemake-block-info))))
    (when end (goto-char end))))

(defun snakemake-beginning-of-defun (&optional arg)
  "Move to beginning of current rule block or function.
With ARG, do it that many times.  Negative ARG signals to move
forward rather than backward."
  (when (or (null arg) (zerop arg))
    (setq arg 1))
  (let ((choose-fn (if (> arg 0) #'max #'min))
        (cands (delq nil
                     (mapcar
                      (lambda (f)
                        (save-excursion (and (funcall f arg) (point))))
                      (list #'snakemake-beginning-of-block
                            #'python-nav-beginning-of-defun)))))
    (cond (cands
           (goto-char (apply choose-fn cands)))
          ((> arg 0)
           (goto-char (point-min))
           nil)
          (t
           (goto-char (point-max))
           nil))))

(defun snakemake-end-of-defun ()
  "Move to end of current rule block or function."
  (or (snakemake-end-of-block)
      (python-nav-end-of-defun)))

(defun snakemake-block-or-defun-name ()
  "Return name of current rule or function.
This function is appropriate to use as the value of
`add-log-current-defun-function'."
  (or (nth 1 (snakemake-block-info))
      (python-info-current-defun)))

\f
;;; Indentation

(defun snakemake--calculate-indentation (&optional previous)
  "Return indentation offset for the current line.

A non-nil value for PREVIOUS indicates that the previous command
was an indentation command.

When Python mode should handle the indentation, a nil value is
returned."
  (when (memq (car (python-indent-context))
              (list :after-line
                    ;; If point is on a value line following a naked
                    ;; field value, `python-indent-context' returns
                    ;; :after-block-start.
                    :after-block-start))
    (let* ((initial-indent (current-indentation))
           (goto-first-p (or (not previous) (zerop initial-indent))))
      (save-excursion
        (save-restriction
          (widen)
          (beginning-of-line)
          (if (looking-at-p (snakemake-rx
                             line-start (zero-or-more space)
                             (or (and field-key (zero-or-more space) ":")
                                 (or "\"\"\"" "'''"))))
              (and goto-first-p
                   (let (rule-indent)
                     (while (not (or rule-indent (bobp)))
                       (forward-line -1)
                       (when (looking-at-p snakemake-rule-or-subworkflow-re)
                         (setq rule-indent (current-indentation))))
                     (and rule-indent
                          (+ rule-indent snakemake-indent-field-offset))))
            ;; We need to look back to determine indentation.
            (skip-chars-backward " \t\n")
            (beginning-of-line)
            (cond
             ((looking-at-p (snakemake-rx
                             line-start (zero-or-more space)
                             (or named-rule anon-rule
                                 field-key sm-command)
                             (zero-or-more space) ":" (zero-or-more space)
                             (zero-or-one (and "#" (zero-or-more not-newline)))
                             line-end))
              (let ((above-indent (current-indentation)))
                (cond (goto-first-p
                       (+ above-indent snakemake-indent-value-offset))
                      ((< above-indent initial-indent)
                       above-indent))))
             ((looking-at (snakemake-rx
                           line-start (zero-or-more space)
                           field-key
                           (zero-or-more space) ":" (zero-or-more space)))
              (let ((above-indent (current-indentation)))
                (cond (goto-first-p
                       (- (match-end 0) (line-beginning-position)))
                      ((< above-indent initial-indent)
                       above-indent))))
             ((save-excursion
                (let ((above-indent (current-indentation))
                      field-indent)
                  (when (> above-indent 0)
                    (while (and (not (bobp))
                                (or (= above-indent
                                       (setq field-indent (current-indentation)))
                                    (looking-at-p "^\\s-*$")))
                      (forward-line -1)))
                  (and (looking-at (snakemake-rx
                                    line-start (zero-or-more space)
                                    (group field-key)
                                    (zero-or-more space) ":"
                                    (zero-or-more space)
                                    (group (zero-or-more not-newline))))
                       (not (equal (match-string-no-properties 1)
                                   "run"))
                       (cond (goto-first-p
                              (let ((field-val (match-string-no-properties 2)))
                                (if (or (equal field-val "")
                                        (string-match-p "\\`#" field-val))
                                    above-indent
                                  (- (match-beginning 2) (line-beginning-position)))))
                             ((< field-indent initial-indent)
                              field-indent)))))))))))))

(defun snakemake-indent-line (&optional previous)
  "Snakemake mode variant of `python-indent-line'."
  (let ((follow-indentation-p
         (and (<= (line-beginning-position) (point))
              (>= (+ (line-beginning-position)
                     (current-indentation))
                  (point)))))
    (save-excursion
      (indent-line-to
       (or (snakemake--calculate-indentation previous)
           (python-indent-calculate-indentation previous))))
    (when follow-indentation-p
      (back-to-indentation))))

(defun snakemake-indent-line-function ()
  "Snakemake mode variant of `python-indent-line-function'."
  (snakemake-indent-line
   (and (memq this-command python-indent-trigger-commands)
        (eq last-command this-command))))

\f
;;; Imenu

(defun snakemake-imenu-create-index ()
  "Create Imenu index for rule blocks.
If `python-imenu-create-index' returns a non-nil value, also
include these results and append a \"(rule)\" to the index
label."
  (let ((py-index (python-imenu-create-index))
        (sm-index (snakemake--imenu-build-rule-index)))
    (if py-index
        (append (mapcar (lambda (x)
                          (cons (concat (car x) " (rule)") (cdr x)))
                        sm-index)
                py-index)
      sm-index)))

(defun snakemake--imenu-build-rule-index ()
  (goto-char (point-min))
  (let (index)
    (while (re-search-forward snakemake-rule-or-subworkflow-re nil t)
      (push (cons (match-string-no-properties 2)
                  (save-excursion (beginning-of-line)
                                  (point-marker)))
            index))
    (nreverse index)))

\f
;;; Embedded language syntax-highlighting

(declare-function mmm-add-classes "mmm-vars")
(declare-function mmm-add-mode-ext-class "mmm-vars")

(defun snakemake-mode-setup-mmm ()
  "Set up MMM mode to highlight embedded R code.

You must have the R-strings either within a R(\"\"\" \"\"\") function
call or a code block delimited with \"\"\"#r and \"\"\".  (Triple
single-quotes also accepted.)

For automatic highlighting of embedded regions, you need to set
`mmm-global-mode' to `maybe'."
  (unless (require 'mmm-mode nil t)
    (user-error "You need to install mmm-mode"))

  (when (unless (bound-and-true-p mmm-global-mode))
    (display-warning 'snakemake-mode "To get automatic syntax highlighting of
embedded R, you need to set mmm-global-mode to a non-nil value such as 'maybe."))

  (mmm-add-classes
   '((snakemake-R-call-double
      :submode R-mode
      :front ".*R\(\"\"\""
      :back ".*\"\"\"\)")))

  (mmm-add-classes
   '((snakemake-R-call-regular
      :submode R-mode
      :front ".*R\('''"
      :back ".*'''\)")))

  (mmm-add-classes
   '((snakemake-R-string-double
      :submode R-mode
      :front ".*\"\"\" *# *[rR]"
      :back ".*\"\"\"")))

  (mmm-add-classes
   '((snakemake-R-string-regular
      :submode R-mode
      :front ".*''' *# *[rR]"
      :back ".*'''")))

  (mmm-add-mode-ext-class 'snakemake-mode nil 'snakemake-R-call-double)
  (mmm-add-mode-ext-class 'snakemake-mode nil 'snakemake-R-call-regular)
  (mmm-add-mode-ext-class 'snakemake-mode nil 'snakemake-R-string-double)
  (mmm-add-mode-ext-class 'snakemake-mode nil 'snakemake-R-string-regular))

\f
;;; Mode

(defvar snakemake--font-lock-keywords
    `((,snakemake-rule-or-subworkflow-re
       (1 font-lock-keyword-face nil 'lax)
       (2 font-lock-function-name-face nil 'lax)
       (3 font-lock-keyword-face nil 'lax))
      (,(snakemake-rx line-start (one-or-more space)
                      (group field-key)
                      (zero-or-more space) ":")
       1 font-lock-type-face)
      (,(snakemake-rx line-start (zero-or-more space)
                      (group sm-command)
                      (zero-or-more space) ":")
       1 font-lock-keyword-face)
      (,(snakemake-rx (group sm-builtin)) 1 font-lock-builtin-face)))

(if (bound-and-true-p python-font-lock-keywords-level-1)
    (with-no-warnings
      ;; In Emacs 27 `python-font-lock-keywords' was split up into
      ;; different decoration levels.
      (defvar snakemake-font-lock-keywords-level-1
        (append snakemake--font-lock-keywords
                python-font-lock-keywords-level-1))
      (defvar snakemake-font-lock-keywords-level-2
        (append snakemake--font-lock-keywords
                python-font-lock-keywords-level-2))
      (defvar snakemake-font-lock-keywords-maximum-decoration
        (append snakemake--font-lock-keywords
                python-font-lock-keywords-maximum-decoration))
      (defvar snakemake-font-lock-keywords
        ;; Mirrors `python-font-lock-keywords'.
        '(snakemake-font-lock-keywords-level-1
          snakemake-font-lock-keywords-level-1
          snakemake-font-lock-keywords-level-2
          snakemake-font-lock-keywords-maximum-decoration)))
  (defvar snakemake-font-lock-keywords
    (append snakemake--font-lock-keywords python-font-lock-keywords)))

;;;###autoload
(define-derived-mode snakemake-mode python-mode "Snakemake"
  "Mode for editing Snakemake files."
  (set (make-local-variable 'imenu-create-index-function)
       #'snakemake-imenu-create-index)
  (set (make-local-variable 'indent-line-function) 'snakemake-indent-line-function)
  (set (make-local-variable 'indent-region-function) nil)

  (set (make-local-variable 'beginning-of-defun-function)
       #'snakemake-beginning-of-defun)
  (set (make-local-variable 'end-of-defun-function)
       #'snakemake-end-of-defun)
  (set (make-local-variable 'add-log-current-defun-function)
       #'snakemake-block-or-defun-name)

  (set (make-local-variable 'font-lock-defaults)
       (cons snakemake-font-lock-keywords (cdr font-lock-defaults))))

;;;###autoload
(add-to-list 'auto-mode-alist '("Snakefile\\'" . snakemake-mode))
;;;###autoload
(add-to-list 'auto-mode-alist '("\\.\\(?:sm\\)?rules\\'" . snakemake-mode))
;;;###autoload
(add-to-list 'auto-mode-alist '("\\.smk\\'" . snakemake-mode))
;;;###autoload
(add-to-list 'auto-mode-alist '("\\.snakefile\\'" . snakemake-mode))

(provide 'snakemake-mode)
;;; snakemake-mode.el ends here

debug log:

solving 5e4118b ...
found 5e4118b in https://git.kyleam.com/snakemake-mode/

(*) Git path names are given by the tree(s) the blob belongs to.
    Blobs themselves have no identifier aside from the hash of its contents.^

Code repositories for project(s) associated with this public inbox

	https://git.kyleam.com/snakemake-mode/

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).