summaryrefslogtreecommitdiff
path: root/snakemake-test.el
diff options
context:
space:
mode:
authorKyle Meyer <kyle@kyleam.com>2016-02-28 11:44:27 -0500
committerKyle Meyer <kyle@kyleam.com>2016-02-28 11:56:52 -0500
commit4f253dac766e5d67c9cf0979d77e2e793b3ced34 (patch)
tree4dc325ab1adbee10d28ed22d7351c114794066db /snakemake-test.el
parentc47351925529d72164c78dce685a01b0004ebcd4 (diff)
downloadsnakemake-mode-4f253dac766e5d67c9cf0979d77e2e793b3ced34.tar.gz
Rename test file for MELPA filtering
MELPA excludes test.el, tests.el, *-test.el, and *-tests.el.
Diffstat (limited to 'snakemake-test.el')
-rw-r--r--snakemake-test.el759
1 files changed, 759 insertions, 0 deletions
diff --git a/snakemake-test.el b/snakemake-test.el
new file mode 100644
index 0000000..36ee489
--- /dev/null
+++ b/snakemake-test.el
@@ -0,0 +1,759 @@
+;;; snakemake-test.el --- Test snakemake{,-mode}.el
+
+;; Copyright (C) 2015-2016 Kyle Meyer <kyle@kyleam.com>
+
+;; Author: Kyle Meyer <kyle@kyleam.com>
+
+;; 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 of the License, 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 this program. If not, see <http://www.gnu.org/licenses/>.
+
+;;; Code:
+
+(require 'cl-lib)
+(require 'snakemake-mode)
+(require 'snakemake)
+(require 'ert)
+
+;; This is modified from `org-tests.el' (55c0708).
+(defmacro snakemake-with-temp-text (text &rest body)
+ "Run body in a temporary Snakemake mode buffer.
+
+Fill the buffer with TEXT. If the string \"<point>\" appears in
+TEXT then remove it and place the point there before running
+BODY, otherwise place the point at the beginning of the inserted
+text.
+
+Also, mute messages."
+ (declare (indent 1))
+ `(cl-letf (((symbol-function 'message) (lambda (&rest args) nil)))
+ (let ((inside-text (if (stringp ,text) ,text (eval ,text))))
+ (with-temp-buffer
+ (snakemake-mode)
+ (let ((point (string-match "<point>" inside-text)))
+ (if point
+ (progn
+ (insert (replace-match "" nil nil inside-text))
+ (goto-char (1+ (match-beginning 0))))
+ (insert inside-text)
+ (goto-char (point-min))))
+ ,@body))))
+(def-edebug-spec snakemake-with-temp-text (form body))
+
+(defmacro snakemake-with-temp-dir (&rest body)
+ "Run BODY in a temporary directory with Snakefile.
+`snakemake-test-dir' is bound to top-level directory."
+ (declare (indent 0) (debug t))
+ `(cl-letf (((symbol-function 'message) (lambda (&rest args) nil)))
+ (let* ((snakemake-test-dir (file-name-as-directory
+ (make-temp-file "sm-test-dir" t)))
+ (snakemake-root-dir-function `(lambda () ,snakemake-test-dir)))
+ (unwind-protect
+ (let ((default-directory snakemake-test-dir))
+ (mkdir "subdir")
+ (with-temp-file "Snakefile"
+ (insert "\
+
+rule aa:
+ output: \"aa.out\"
+ shell: \"echo aa.content > {output}\"
+
+rule bb:
+ input: \"aa.out\"
+ output: \"bb.out\"
+ shell: \"cat {input} > {output}\"
+
+rule cc_wildcards:
+ input: \"bb.out\"
+ output: \"{name}.outwc\"
+ shell: \"cat {input} > {output}\"
+
+rule dd_subdir:
+ input: \"aa.out\"
+ output: \"subdir/dd.out\"
+ shell: \"cat {input} > {output}\""))
+ ,@body)
+ (delete-directory snakemake-test-dir t)))))
+(def-edebug-spec snakemake-with-temp-dir (body))
+
+
+;;; snakemake-mode.el
+
+;;;; Indentation
+
+(ert-deftest test-snakemake-mode/indentation-at-rule-block ()
+ "Test `snakemake-indent-line' at top of rule block."
+
+ ;; Always shift first line of block to column 0.
+ (should
+ (string=
+ "rule abc:"
+ (snakemake-with-temp-text
+ "rule abc:"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "rule abc:"
+ (snakemake-with-temp-text
+ " rule abc:"
+ (snakemake-indent-line)
+ (buffer-string))))
+
+ ;; Don't move point if beyond column 0.
+ (should
+ (string=
+ "rule abc: "
+ (snakemake-with-temp-text
+ " rule abc: <point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "rule "
+ (snakemake-with-temp-text
+ " rule <point>abc: <point>"
+ (snakemake-indent-line)
+ (buffer-substring (point-min) (point))))))
+
+(ert-deftest test-snakemake-mode/indentation-outside-rule ()
+ "Test `snakemake-indent-line' outside rule block."
+ ;; Use standard Python mode indentation outside of rule blocks.
+ (should
+ (string=
+ "
+def ok():
+ "
+ (snakemake-with-temp-text
+ "
+def ok():
+<point>"
+ (snakemake-indent-line)
+ (buffer-string)))))
+
+(ert-deftest test-snakemake-mode/indentation-field-key ()
+ "Test `snakemake-indent-line' on field key line."
+
+ ;; Always indent first line to `snakemake-indent-field-offset'.
+ ;; Move point to `snakemake-indent-field-offset' if it is before any
+ ;; text on the line.
+ (should
+ (string=
+ "
+rule abc:
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+<point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+<point>"
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ text"
+ (snakemake-with-temp-text
+ "
+rule abc:
+text<point>"
+ (snakemake-indent-line)
+ (buffer-substring (point-min) (point)))))
+ (should
+ (string=
+ "
+rule abc:
+ te"
+ (snakemake-with-temp-text
+ "
+rule abc:
+te<point>xt"
+ (snakemake-indent-line)
+ (buffer-substring (point-min) (point)))))
+
+ ;; Always indent field key to `snakemake-indent-field-offset'.
+ ;; Move point to `snakemake-indent-field-offset' if it is before any
+ ;; text on the line.
+ (should
+ (string=
+ "
+rule abc:
+ input: 'infile'
+ output:"
+ (snakemake-with-temp-text
+ "
+rule abc:
+ input: 'infile'
+<point>output:"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ input: 'infile'
+ output:"
+ (snakemake-with-temp-text
+ "
+rule abc:
+ input: 'infile'
+<point>output:"
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ input: 'infile'
+ output: "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ input: 'infile'
+output: <point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ input: 'infile'
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ input: 'infile'
+<point> output:"
+ (snakemake-indent-line)
+ (buffer-substring (point-min) (point))))))
+
+(ert-deftest test-snakemake-mode/indentation-field-value ()
+ "Test `snakemake-indent-line' on field value line."
+
+ ;; Always indent line below naked field key to
+ ;; `snakemake-indent-field-offset' +
+ ;; `snakemake-indent-value-offset'. Move point to to this position
+ ;; as well if it is before any text on the line.
+ (should
+ (string=
+ "
+rule abc:
+ output:
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+<point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output:
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+<point>"
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output:
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+ <point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+
+ ;; Add step with Python indentation for non-blank lines under naked
+ ;; field keys. Field keys with values starting on the same line do
+ ;; not use Python indentation because this is invalid syntax in
+ ;; Snakemake.
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file{}{}'.format('one',
+ 'two'"
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file{}{}'.format('one',
+<point>'two'"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output:
+ 'file{}{}'.format('one',
+ 'two'"
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+ 'file{}{}'.format('one',
+<point>'two'"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output:
+ 'file{}{}'.format('one',
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+ 'file{}{}'.format('one',
+<point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+
+ ;; On non-naked field key cycle indentation between
+ ;; `snakemake-indent-field-offset' and column of previous field
+ ;; value. If point is before any text on the line, move it to the
+ ;; start of the text instead.
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ 'text'"
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>'text'"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ 'text'"
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>'text'"
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ 'text' "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+'text' <point>"
+ (snakemake-indent-line)
+ (buffer-string))))
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point> 'text'"
+ (snakemake-indent-line)
+ (buffer-substring (point-min) (point)))))
+ (should
+ (string=
+ "
+rule abc:
+ output: 'file'
+ 'text'"
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point> 'text'"
+ (snakemake-indent-line)
+ (snakemake-indent-line)
+ (buffer-string))))
+
+ ;; Indent body of run field according to Python mode.
+ (should
+ (string=
+ "
+rule abc:
+ run:
+ with this:
+ "
+ (snakemake-with-temp-text
+ "
+rule abc:
+ run:
+ with this:
+<point>"
+ (snakemake-indent-line)
+ (buffer-string)))))
+
+;;;; Other
+
+(ert-deftest test-snakemake-mode/in-rule-block ()
+ "Test `snakemake-in-rule-or-subworkflow-block-p'"
+
+ ;; At top of block
+ (snakemake-with-temp-text
+ "
+<point>rule abc:
+ output: 'file'"
+ (should (snakemake-in-rule-or-subworkflow-block-p)))
+
+ ;; Body of block
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: <point>'file'"
+ (should (snakemake-in-rule-or-subworkflow-block-p)))
+
+ ;; First blank line after
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (should (snakemake-in-rule-or-subworkflow-block-p)))
+
+ ;; Second blank line after
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+
+<point>"
+ (should-not (snakemake-in-rule-or-subworkflow-block-p)))
+
+
+ ;; Blank line in docstring
+ (snakemake-with-temp-text
+ "
+rule abc:
+ \"\"\"docstring header
+
+ docstring line
+ \"\"\"
+ output: 'file'<point>"
+ (should (snakemake-in-rule-or-subworkflow-block-p)))
+
+ ;; Before
+ (snakemake-with-temp-text
+ "<point>
+rule abc:
+ output: 'file'"
+ (should-not (snakemake-in-rule-or-subworkflow-block-p)))
+
+ ;; Subworkflow
+ (snakemake-with-temp-text
+ "
+subworkflow otherworkflow:
+<point> workdir: '../path/to/otherworkflow'
+ snakefile: '../path/to/otherworkflow/Snakefile'"
+ (should (snakemake-in-rule-or-subworkflow-block-p))))
+
+(ert-deftest test-snakemake-mode/first-field-line-p ()
+ "Test `snakemake-first-field-line-p'."
+ (snakemake-with-temp-text
+ "
+rule abc:
+<point>"
+ (should (snakemake-first-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+<point> output: 'file'"
+ (should (snakemake-first-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+<point>"
+ (should-not (snakemake-first-field-line-p))))
+
+(ert-deftest test-snakemake-mode/below-naked-field-p ()
+ "Test `snakemake-below-naked-field-p'."
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+<point>"
+ (should (snakemake-below-naked-field-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (should-not (snakemake-below-naked-field-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: <point>"
+ (should-not (snakemake-below-naked-field-p))))
+
+(ert-deftest test-snakemake-mode/naked-field-line-p ()
+ "Test `snakemake-naked-field-line-p'."
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+<point>"
+ (should (snakemake-naked-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output:
+ 'file',
+ <point>"
+ (should (snakemake-naked-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: <point>"
+ (should (snakemake-naked-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (should-not (snakemake-naked-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ input:
+ 'infile'
+ output: 'file'
+<point>"
+ (should-not (snakemake-naked-field-line-p))))
+
+(ert-deftest test-snakemake-mode/run-field-line-p ()
+ "Test `snakemake-run-field-line-p'."
+ (snakemake-with-temp-text
+ "
+rule abc:
+ run:
+<point>"
+ (should (snakemake-run-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ run:
+ with file:
+<point>"
+ (should (snakemake-run-field-line-p)))
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (should-not (snakemake-run-field-line-p))))
+
+(ert-deftest test-snakemake-mode/previous-field-value-column ()
+ "Test `snakemake-previous-field-value-column'."
+ (should (= 12
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file'
+<point>"
+ (snakemake-previous-field-value-column))))
+ (should (= 12
+ (snakemake-with-temp-text
+ "
+rule abc:
+ output: 'file',
+ 'another'
+<point>"
+ (snakemake-previous-field-value-column)))))
+
+
+;;; snakemake.el
+
+(ert-deftest test-snakemake/snakefile-directory ()
+ "Test `snakemake-snakefile-directory'."
+ (snakemake-with-temp-dir
+ (should (equal default-directory (snakemake-snakefile-directory)))
+ (let ((topdir default-directory))
+ (should (equal topdir
+ (let ((default-directory "subdir"))
+ (snakemake-snakefile-directory)))))))
+
+(ert-deftest test-snakemake/rule-targets ()
+ "Test `snakemake-rule-targets'."
+ (should
+ (equal '("aa" "bb" "dd_subdir")
+ (snakemake-with-temp-dir
+ (snakemake-rule-targets)))))
+
+(ert-deftest test-snakemake/all-rules ()
+ "Test `snakemake-all-rules'."
+ (should
+ (equal '("aa" "bb" "cc_wildcards" "dd_subdir")
+ (snakemake-with-temp-dir
+ (snakemake-all-rules)))))
+
+(ert-deftest test-snakemake/file-targets ()
+ "Test `snakemake-file-targets'."
+ (should
+ (equal
+ (and snakemake-file-target-program
+ '("aa.out" "bb.out" "subdir/dd.out"))
+ (snakemake-with-temp-dir
+ (snakemake-file-targets)))))
+
+(ert-deftest test-snakemake/check-target ()
+ "Test `snakemake-check-target'."
+ (should
+ (snakemake-with-temp-dir
+ (snakemake-check-target "aa.out")))
+ (should-not
+ (snakemake-with-temp-dir
+ (snakemake-check-target "aa.out.not-target"))))
+
+(ert-deftest test-snakemake/org-link-file-targets ()
+ "Test `snakemake-org-link-file-targets'."
+ (should (equal '("/path/to/fname")
+ (with-temp-buffer
+ (org-mode)
+ (insert "\n[[file:/path/to/fname][descr]]\n")
+ (forward-line -1)
+ (snakemake-org-link-file-targets)))))
+
+(ert-deftest test-snakemake/file-targets-at-point ()
+ "Test `snakemake-file-targets-at-point'."
+ (should
+ (equal '("aa.out")
+ (snakemake-with-temp-dir
+ (with-temp-buffer
+ (insert "aa.out")
+ (beginning-of-line)
+ (snakemake-file-targets-at-point 'check)))))
+ (should-not
+ (snakemake-with-temp-dir
+ (with-temp-buffer
+ (insert "aa.out.not-target")
+ (beginning-of-line)
+ (snakemake-file-targets-at-point 'check))))
+ (should
+ (equal '("aa.out.not-target")
+ (snakemake-with-temp-dir
+ (with-temp-buffer
+ (insert "aa.out.not-target")
+ (beginning-of-line)
+ (snakemake-file-targets-at-point))))))
+
+(ert-deftest test-snakemake/rule-at-point ()
+ "Test `snakemake-rule-targets-at-point'."
+ (should
+ (equal '("aa")
+ (snakemake-with-temp-dir
+ (with-temp-buffer
+ (snakemake-mode)
+ (insert-file-contents "Snakefile")
+ (re-search-forward "rule aa:")
+ (snakemake-rule-at-point 'target)))))
+ (should
+ (equal '("cc_wildcards")
+ (snakemake-with-temp-dir
+ (with-temp-buffer
+ (snakemake-mode)
+ (insert-file-contents "Snakefile")
+ (re-search-forward "rule cc_wildcards:")
+ (snakemake-rule-at-point)))))
+ (should-not
+ (snakemake-with-temp-dir
+ (with-temp-buffer
+ (snakemake-mode)
+ (insert-file-contents "Snakefile")
+ (re-search-forward "rule cc_wildcards:")
+ (snakemake-rule-at-point 'target)))))
+
+(provide 'snakemake-test)
+;;; snakemake-test.el ends here