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Diffstat (limited to 'test-snakemake.el')
| -rw-r--r-- | test-snakemake.el | 759 |
1 files changed, 0 insertions, 759 deletions
diff --git a/test-snakemake.el b/test-snakemake.el deleted file mode 100644 index 0f83821..0000000 --- a/test-snakemake.el +++ /dev/null @@ -1,759 +0,0 @@ -;;; test-snakemake.el --- Tests for 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 'test-snakemake) -;;; test-snakemake.el ends here |