ndwarshuis
/
org-mode
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
org-mode/testing/lisp/test-ob-R.el

252 lines
8.1 KiB
EmacsLisp
Raw Normal View History

fix leftover cruft in test-ob-R.el
2011-09-21 15:31:38 -04:00
;;; test-ob-R.el --- tests for ob-R.el
adding a file for R tests * testing/lisp/test-ob-R.el (test-ob-R/simple-session): Simple session test.
2011-09-21 08:57:07 -04:00
Update copyright year
2019-01-01 05:50:56 -05:00
;; Copyright (c) 2011-2014, 2019 Eric Schulte
adding a file for R tests * testing/lisp/test-ob-R.el (test-ob-R/simple-session): Simple session test.
2011-09-21 08:57:07 -04:00
;; Authors: Eric Schulte
Fix copyright notices for test files.
2012-12-13 11:24:19 -05:00
;; This file is not part of GNU Emacs.
;; 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
Prefer HTTPS to HTTP for links to gnu.org
2021-03-20 03:27:57 -04:00
;; along with this program. If not, see <https://www.gnu.org/licenses/>.
adding a file for R tests * testing/lisp/test-ob-R.el (test-ob-R/simple-session): Simple session test.
2011-09-21 08:57:07 -04:00
Fix the master branch. I started from the 78ec8e commit then cherry-picked and squashed commits that have been done in master since then, except the bad commits that overwrote the tree (in master) with the tree in maint. This commit also bumps the version number to 7.8.06. The only "fix" that was made between 78ec8e and the previous commit is e0072f which has been reported to break stuff.
2012-03-19 16:38:12 -04:00
;;; Code:
only load those test files for which the required executables are present * testing/org-test.el (org-exe-not-found): An error type used to signal a missing executable (org-test-for-executable): A function used by test files to throw an error if a required executable is not present. (org-test-load): Simply skip files for which the required executables are not present. * testing/lisp/test-ob-R.el: Conditional loading. * testing/lisp/test-ob-awk.el: Conditional loading. * testing/lisp/test-ob-fortran.el: Conditional loading.
2011-09-21 18:34:43 -04:00
(org-test-for-executable "R")
(unless (featurep 'ess)
Indicate tests with missing dependencies by adding a expected failing test * testing/lisp/test-ob-R.el (featurep): Signal missing dependencies with an error rather than a throw. * testing/org-test.el (missing-test-dependency): Define the error signal for missing dependencies. (org-test-for-executable): Signal missing dependencies with an error rather than a throw. (org-test-load): Define an expected failing test for each file with missing dependencies.
2011-11-13 14:30:25 -05:00
(signal 'missing-test-dependency "ESS"))
Fix the master branch. I started from the 78ec8e commit then cherry-picked and squashed commits that have been done in master since then, except the bad commits that overwrote the tree (in master) with the tree in maint. This commit also bumps the version number to 7.8.06. The only "fix" that was made between 78ec8e and the previous commit is e0072f which has been reported to break stuff.
2012-03-19 16:38:12 -04:00
(unless (featurep 'ob-R)
(signal 'missing-test-dependency "Support for R code blocks"))
adding a file for R tests * testing/lisp/test-ob-R.el (test-ob-R/simple-session): Simple session test.
2011-09-21 08:57:07 -04:00
(ert-deftest test-ob-R/simple-session ()
testing/lisp/test-ob-R.el: Initialize ESS vars for :session tests * test-ob-R.el: (test-ob-R/simple-session, test-ob-R/results-file) tests start sessions. As a consequence `ess-ask-for-ess-directory' and `ess-history-file' are let bound to `nil' to avoid prompting for the startup directory and using a history file. Bug Reported by: Achim Gratz Subject: [Bug] Testing: ESS (*R*, R (newest)) starting data directory? Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/104424>
2016-01-24 13:04:43 -05:00
(let (ess-ask-for-ess-directory ess-history-file)
do not set variables belonging to ESS * lisp/ob-R.el (org-babel-R-initiate-session): Protect against use of unbound variable `ess-ask-for-ess-directory´. The default for this variable is true, so act accordingly if it is found unbound. * lisp/ob-R.el: Remove initialization with `nil´ from `ess-ask-for-ess-directory´ and `ess-local-process-name´. Remove second declaration for `ess-local-process-name´. * testing/lisp/test-ob-R.el (test-ob-R/simple-session): Bind `ess-ask-for-ess-directory´ to nil to facilitate batch testing.
2012-09-23 05:07:18 -04:00
(org-test-with-temp-text
"#+begin_src R :session R\n paste(\"Yep!\")\n#+end_src\n"
(should (string= "Yep!" (org-babel-execute-src-block))))))
adding a file for R tests * testing/lisp/test-ob-R.el (test-ob-R/simple-session): Simple session test.
2011-09-21 08:57:07 -04:00
tests for the colnames header argument
2011-11-28 03:55:28 -05:00
(ert-deftest test-ob-R/colnames-yes-header-argument ()
(org-test-with-temp-text "#+name: eg
| col |
|-----|
| a |
| b |
#+header: :colnames yes
#+header: :var x = eg
#+begin_src R
x
#+end_src"
(org-babel-next-src-block)
(should (equal '(("col") hline ("a") ("b"))
(org-babel-execute-src-block)))))
(ert-deftest test-ob-R/colnames-nil-header-argument ()
(org-test-with-temp-text "#+name: eg
| col |
|-----|
| a |
| b |
#+header: :colnames nil
#+header: :var x = eg
#+begin_src R
x
#+end_src"
(org-babel-next-src-block)
(should (equal '(("col") hline ("a") ("b"))
(org-babel-execute-src-block)))))
(ert-deftest test-ob-R/colnames-no-header-argument ()
(org-test-with-temp-text "#+name: eg
| col |
|-----|
| a |
| b |
#+header: :colnames no
#+header: :var x = eg
#+begin_src R
x
#+end_src"
(org-babel-next-src-block)
(should (equal '(("col") ("a") ("b"))
(org-babel-execute-src-block)))))
ob-R.el: Trim extraneous newline from results * lisp/ob-R.el: org-babel-R-evaluate-external-process and org-babel-R-evaluate-session trim the extraneous newlines from the end of R output. * testing/lisp/test-ob-R.el: test-ob-R/results-file tests that `:results file' yields one line enclosed in square brackets for a result like "abc/def.ghi". Fixes issue noted by Andreas Leha Subject: [babel] return file from R Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/103658>
2016-01-19 22:32:11 -05:00
(ert-deftest test-ob-R/results-file ()
testing/lisp/test-ob-R.el: Initialize ESS vars for :session tests * test-ob-R.el: (test-ob-R/simple-session, test-ob-R/results-file) tests start sessions. As a consequence `ess-ask-for-ess-directory' and `ess-history-file' are let bound to `nil' to avoid prompting for the startup directory and using a history file. Bug Reported by: Achim Gratz Subject: [Bug] Testing: ESS (*R*, R (newest)) starting data directory? Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/104424>
2016-01-24 13:04:43 -05:00
(let (ess-ask-for-ess-directory ess-history-file)
(org-test-with-temp-text
"#+NAME: TESTSRC
ob-R.el: Trim extraneous newline from results * lisp/ob-R.el: org-babel-R-evaluate-external-process and org-babel-R-evaluate-session trim the extraneous newlines from the end of R output. * testing/lisp/test-ob-R.el: test-ob-R/results-file tests that `:results file' yields one line enclosed in square brackets for a result like "abc/def.ghi". Fixes issue noted by Andreas Leha Subject: [babel] return file from R Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/103658>
2016-01-19 22:32:11 -05:00
#+BEGIN_SRC R :results file
a <- file.path(\"junk\", \"test.org\")
a
#+END_SRC"
testing/lisp/test-ob-R.el: Initialize ESS vars for :session tests * test-ob-R.el: (test-ob-R/simple-session, test-ob-R/results-file) tests start sessions. As a consequence `ess-ask-for-ess-directory' and `ess-history-file' are let bound to `nil' to avoid prompting for the startup directory and using a history file. Bug Reported by: Achim Gratz Subject: [Bug] Testing: ESS (*R*, R (newest)) starting data directory? Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/104424>
2016-01-24 13:04:43 -05:00
(goto-char (point-min)) (org-babel-execute-maybe)
(org-babel-goto-named-result "TESTSRC") (forward-line 1)
(should (string= "[[file:junk/test.org]]"
(buffer-substring-no-properties (point-at-bol) (point-at-eol))))
(goto-char (point-min)) (forward-line 1)
(insert "#+header: :session\n")
(goto-char (point-min)) (org-babel-execute-maybe)
(org-babel-goto-named-result "TESTSRC") (forward-line 1)
(should (string= "[[file:junk/test.org]]"
(buffer-substring-no-properties (point-at-bol) (point-at-eol)))))))
test-ob-R.el: add tests for output with substrings matching prompt * testing/lisp/test-ob-R.el (test-ob-r/output-with-<>): new test for output angle brackets (test-ob-R/output-nonprinted): New test for output results that aren't explicitly printed. (Here all the lines are expected to be printed not just the last one) Patch suggested by Jack Kamm: https://orgmode.org/list/87h7slgbi5.fsf@gmail.com/
2021-05-02 18:18:33 -04:00
(ert-deftest test-ob-r/output-with-<> ()
"make sure angle brackets are well formatted"
(let (ess-ask-for-ess-directory ess-history-file)
(should (string="[1] \"<X> <Y> <!>\"
[1] \"one <two> three\"
[1] \"end35\"
"
(org-test-with-temp-text "#+begin_src R :results output
print(\"<X> <Y> <!>\")
print(\"one <two> three\")
print(\"end35\")
#+end_src
"
(org-babel-execute-src-block))
))))
lisp/ob-R: Async evaluation in R * lisp/ob-R.el (ob-session-async-R-indicator): Add constant representing a prefix R to identity session. (ob-session-async-org-babel-R-evaluate-session): New function to evaluate R src block asynchrously. (ob-session-async-R-value-callback): New function that calls back the result of the asynchronous evaluation. (org-babel-R-evaluate): Add `async' parameter and call `ob-session-async-org-babel-R-evaluate-session' if `async' parameter is present. (org-babel-execute:R): Call `org-babel-comint-use-async' to check if async is among `params' and add async parameter to `org-babel-R-evaluate'. * testing/lisp/test-ob-R.el: Add 7 more tests for async evaluations, also taken from the `ob-session-async' package. This is almost a carbon copy of Jack Kamm's `ob-session-async'. The original source code can be found https://github.com/jackkamm/ob-session-async. Please refer to the following thread to trace back the discussion on async evaluation in R: https://list.orgmode.org/87eed9g9p6.fsf@gmail.com/
2021-09-26 12:25:23 -04:00
test-ob-R.el: add tests for output with substrings matching prompt * testing/lisp/test-ob-R.el (test-ob-r/output-with-<>): new test for output angle brackets (test-ob-R/output-nonprinted): New test for output results that aren't explicitly printed. (Here all the lines are expected to be printed not just the last one) Patch suggested by Jack Kamm: https://orgmode.org/list/87h7slgbi5.fsf@gmail.com/
2021-05-02 18:18:33 -04:00
;; (ert-deftest test-ob-r/output-with-error ()
;; "make sure angle brackets are well formatted"
;; (let (ess-ask-for-ess-directory ess-history-file)
;; (should (string="Error in print(1/a) : object 'a' not found"
;; (org-test-with-temp-text "#+begin_src R :results output
;; print(1/a)
;; #+end_src
;; "
;; (org-babel-execute-src-block))
;; ))))
(ert-deftest test-ob-R/output-nonprinted ()
(let (ess-ask-for-ess-directory ess-history-file)
(org-test-with-temp-text
"#+begin_src R :results output
4.0 * 3.5
log(10)
log10(10)
(3 + 1) * 5
3^-1
1/0
#+end_src"
(should (string= "[1] 14\n[1] 2.302585\n[1] 1\n[1] 20\n[1] 0.3333333\n[1] Inf\n" (org-babel-execute-src-block))))))
test-ob-R.el: add tests for how NA values are printed * testing/lisp/test-ob-R.el (ert-deftest test-ob-r/NA-blank): new test for :results value. Make sure that NA values in R data.frames are empty string instead of nil previously see https://orgmode.org/list/87pn1dufm2.fsf@gmail.com/
2021-05-02 18:23:36 -04:00
(ert-deftest test-ob-r/NA-blank ()
"For :results value, NAs should be empty"
(let (ess-ask-for-ess-directory ess-history-file)
(should (equal '(("A" "B") hline ("" 1) (1 2) (1 "") (1 4) (1 4))
(org-test-with-temp-text "#+BEGIN_SRC R :results value :colnames yes
data.frame(A=c(NA,1,1,1,1),B=c(1,2,NA,4,4))
#+end_src"
(org-babel-execute-src-block))))))
lisp/ob-R: Async evaluation in R * lisp/ob-R.el (ob-session-async-R-indicator): Add constant representing a prefix R to identity session. (ob-session-async-org-babel-R-evaluate-session): New function to evaluate R src block asynchrously. (ob-session-async-R-value-callback): New function that calls back the result of the asynchronous evaluation. (org-babel-R-evaluate): Add `async' parameter and call `ob-session-async-org-babel-R-evaluate-session' if `async' parameter is present. (org-babel-execute:R): Call `org-babel-comint-use-async' to check if async is among `params' and add async parameter to `org-babel-R-evaluate'. * testing/lisp/test-ob-R.el: Add 7 more tests for async evaluations, also taken from the `ob-session-async' package. This is almost a carbon copy of Jack Kamm's `ob-session-async'. The original source code can be found https://github.com/jackkamm/ob-session-async. Please refer to the following thread to trace back the discussion on async evaluation in R: https://list.orgmode.org/87eed9g9p6.fsf@gmail.com/
2021-09-26 12:25:23 -04:00
(ert-deftest ob-session-async-R-simple-session-async-value ()
(let (ess-ask-for-ess-directory
ess-history-file
(org-babel-temporary-directory "/tmp")
(org-confirm-babel-evaluate nil))
(org-test-with-temp-text
"#+begin_src R :session R :async yes\n Sys.sleep(.1)\n paste(\"Yep!\")\n#+end_src\n"
(should (let ((expected "Yep!"))
(and (not (string= expected (org-babel-execute-src-block)))
(string= expected
(progn
(sleep-for 0 200)
(goto-char (org-babel-where-is-src-block-result))
(org-babel-read-result)))))))))
(ert-deftest ob-session-async-R-simple-session-async-output ()
(let (ess-ask-for-ess-directory
ess-history-file
(org-babel-temporary-directory "/tmp")
(org-confirm-babel-evaluate nil))
(org-test-with-temp-text
"#+begin_src R :session R :results output :async yes\n Sys.sleep(.1)\n 1:5\n#+end_src\n"
(should (let ((expected "[1] 1 2 3 4 5"))
(and (not (string= expected (org-babel-execute-src-block)))
(string= expected
(progn
(sleep-for 0 200)
(goto-char (org-babel-where-is-src-block-result))
(org-babel-read-result)))))))))
(ert-deftest ob-session-async-R-named-output ()
(let (ess-ask-for-ess-directory
ess-history-file
(org-babel-temporary-directory "/tmp")
org-confirm-babel-evaluate
(src-block "#+begin_src R :async :session R :results output\n 1:5\n#+end_src")
(results-before "\n\n#+NAME: foobar\n#+RESULTS:\n: [1] 1")
(results-after "\n\n#+NAME: foobar\n#+RESULTS:\n: [1] 1 2 3 4 5\n"))
(org-test-with-temp-text
(concat src-block results-before)
(should (progn (org-babel-execute-src-block)
(sleep-for 0 200)
(string= (concat src-block results-after)
(buffer-string)))))))
(ert-deftest ob-session-async-R-named-value ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(src-block "#+begin_src R :async :session R :results value\n paste(\"Yep!\")\n#+end_src")
(results-before "\n\n#+NAME: foobar\n#+RESULTS:\n: [1] 1")
(results-after "\n\n#+NAME: foobar\n#+RESULTS:\n: Yep!\n"))
(org-test-with-temp-text
(concat src-block results-before)
(should (progn (org-babel-execute-src-block)
(sleep-for 0 200)
(string= (concat src-block results-after)
(buffer-string)))))))
(ert-deftest ob-session-async-R-output-drawer ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(src-block "#+begin_src R :async :session R :results output drawer\n 1:5\n#+end_src")
(result "\n\n#+RESULTS:\n:results:\n[1] 1 2 3 4 5\n:end:\n"))
(org-test-with-temp-text
src-block
(should (progn (org-babel-execute-src-block)
(sleep-for 0 200)
(string= (concat src-block result)
(buffer-string)))))))
(ert-deftest ob-session-async-R-value-drawer ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(src-block "#+begin_src R :async :session R :results value drawer\n 1:3\n#+end_src")
(result "\n\n#+RESULTS:\n:results:\n1\n2\n3\n:end:\n"))
(org-test-with-temp-text
src-block
(should (progn (org-babel-execute-src-block)
(sleep-for 0 200)
(string= (concat src-block result)
(buffer-string)))))))
fix leftover cruft in test-ob-R.el
2011-09-21 15:31:38 -04:00
(provide 'test-ob-R)
adding a file for R tests * testing/lisp/test-ob-R.el (test-ob-R/simple-session): Simple session test.
2011-09-21 08:57:07 -04:00
fix leftover cruft in test-ob-R.el
2011-09-21 15:31:38 -04:00
;;; test-ob-R.el ends here
test-ob-R.el: add tests for output with substrings matching prompt * testing/lisp/test-ob-R.el (test-ob-r/output-with-<>): new test for output angle brackets (test-ob-R/output-nonprinted): New test for output results that aren't explicitly printed. (Here all the lines are expected to be printed not just the last one) Patch suggested by Jack Kamm: https://orgmode.org/list/87h7slgbi5.fsf@gmail.com/
2021-05-02 18:18:33 -04:00