* [BUG][babel] Tangling into directories does not add directories to org file @ 2014-10-08 13:21 Rainer M Krug 2014-10-09 12:37 ` Rainer M Krug 0 siblings, 1 reply; 11+ messages in thread From: Rainer M Krug @ 2014-10-08 13:21 UTC (permalink / raw) To: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 853 bytes --] When in the tangling taerget a directory is specified, this is not reflected in the comments in the tangled file when comments are set to include links: ,---- | * `link' The code block is wrapped in comments which contain | pointers back to the original Org file from which the code was | tangled. `---- In the org file =prodMixStands.org=: ,---- | :PROPERTIES: | :header-args+: :tangle ./R/update.cache.R | :END: | #+begin_src R | test | #+end_src `---- results in the file =update.cache.R= in a link to the file =prodMixStands.org= and not =./../prodMixstands.org=: ,---- | ## [[file:prodMixStands.org::*Begin][Begin:1]] `---- This is particularly bad when using ess and developer mode to develop a package. Cheers, Rainer -- Rainer M. Krug email: Rainer<at>krugs<dot>de PGP: 0x0F52F982 [-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --] ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-08 13:21 [BUG][babel] Tangling into directories does not add directories to org file Rainer M Krug @ 2014-10-09 12:37 ` Rainer M Krug 2014-10-10 2:13 ` Grant Rettke 2014-10-10 3:55 ` Aaron Ecay 0 siblings, 2 replies; 11+ messages in thread From: Rainer M Krug @ 2014-10-09 12:37 UTC (permalink / raw) To: emacs-orgmode I'd like to ping this as I think it is an important bug. It e.g. make debugging of R packages, whose source is in org, more difficult, (the .R files are tangled into ./R/) as ess does not find the source of the R code in R as it uses the links in the comments to find the org file. Temporary solution: I created a link to the org file in the ./R directory. Cheers, Rainer Rainer M Krug <Rainer@krugs.de> writes: > When in the tangling taerget a directory is specified, this is not > reflected in the comments in the tangled file when comments are set to > include links: > > ,---- > | * `link' The code block is wrapped in comments which contain > | pointers back to the original Org file from which the code was > | tangled. > `---- > > In the org file =prodMixStands.org=: > > ,---- > | :PROPERTIES: > | :header-args+: :tangle ./R/update.cache.R > | :END: > | #+begin_src R > | test > | #+end_src > `---- > > results in the file =update.cache.R= in a link to the file > =prodMixStands.org= and not =./../prodMixstands.org=: > > ,---- > | ## [[file:prodMixStands.org::*Begin][Begin:1]] > `---- > > This is particularly bad when using ess and developer mode to develop a > package. > > Cheers, > > Rainer -- Rainer M. Krug email: Rainer<at>krugs<dot>de PGP: 0x0F52F982 ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-09 12:37 ` Rainer M Krug @ 2014-10-10 2:13 ` Grant Rettke 2014-10-10 8:24 ` Rainer M Krug 2014-10-10 3:55 ` Aaron Ecay 1 sibling, 1 reply; 11+ messages in thread From: Grant Rettke @ 2014-10-10 2:13 UTC (permalink / raw) To: Rainer M Krug; +Cc: emacs-orgmode@gnu.org Sounds like a valuable use of R. Do you have a writeup on the approach or is it a standard feature of org and ess? On Thu, Oct 9, 2014 at 7:37 AM, Rainer M Krug <Rainer@krugs.de> wrote: > > I'd like to ping this as I think it > is an important bug. It e.g. make debugging of R packages, whose source > is in org, more difficult, (the .R files are tangled into ./R/) as ess > does not find the source of the R code in R as it uses the links in the > comments to find the org file. > > Temporary solution: I created a link to the org file in the ./R directory. > > Cheers, > > Rainer > > Rainer M Krug <Rainer@krugs.de> writes: > >> When in the tangling taerget a directory is specified, this is not >> reflected in the comments in the tangled file when comments are set to >> include links: >> >> ,---- >> | * `link' The code block is wrapped in comments which contain >> | pointers back to the original Org file from which the code was >> | tangled. >> `---- >> >> In the org file =prodMixStands.org=: >> >> ,---- >> | :PROPERTIES: >> | :header-args+: :tangle ./R/update.cache.R >> | :END: >> | #+begin_src R >> | test >> | #+end_src >> `---- >> >> results in the file =update.cache.R= in a link to the file >> =prodMixStands.org= and not =./../prodMixstands.org=: >> >> ,---- >> | ## [[file:prodMixStands.org::*Begin][Begin:1]] >> `---- >> >> This is particularly bad when using ess and developer mode to develop a >> package. >> >> Cheers, >> >> Rainer > > -- > Rainer M. Krug > email: Rainer<at>krugs<dot>de > PGP: 0x0F52F982 > -- Grant Rettke gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-10 2:13 ` Grant Rettke @ 2014-10-10 8:24 ` Rainer M Krug 2014-10-10 14:41 ` Grant Rettke 0 siblings, 1 reply; 11+ messages in thread From: Rainer M Krug @ 2014-10-10 8:24 UTC (permalink / raw) To: Grant Rettke; +Cc: emacs-orgmode@gnu.org [-- Attachment #1: Type: text/plain, Size: 7007 bytes --] Grant Rettke <gcr@wisdomandwonder.com> writes: > Sounds like a valuable use of R. It definitely is. > > Do you have a writeup on the approach or is it a standard feature of > org and ess? No - but please bug me - I can post in the intermediate future an example demonstrating the points. But the main points are: * Setup ** I added the following to my emacs.org *** Add local variable in tangled files if they match [.]R The variable =org-babel-tangled-file t= enables ess to trace back the source from the .R file to the .org file, using the comments which have to include the org links. See the thread "Automatically adding local variables to tangled file" for details #+begin_src emacs-lisp (defvar org-babel-tangled-file nil "If non-nill, current file was tangled with org-babel-tangle") (put 'org-babel-tangled-file 'safe-local-variable 'booleanp) (defun org-babel-mark-file-as-tangled () (when (buffer-file-name) (when (string-match "[.]R" (buffer-file-name)) (add-file-local-variable 'org-babel-tangled-file t) (add-file-local-variable 'buffer-read-only t) (add-file-local-variable 'eval: '(auto-revert-mode)) (basic-save-buffer)))) (add-hook 'org-babel-post-tangle-hook 'org-babel-mark-file-as-tangled) #+end_src ** Tangling - The files have to be tangled with the header argument =:comments link= (or both) for this to work. - =:padline no= is necessary (at least it was) as the empty lines in the tangled file caused ess to identify the wrong line in the source code ** This should now work. * Use code as "package" Effectively, I do the following: ** code tangle all .R files to ./R *without variables transfer*. These should contain definitions of functions and not executable code. ** data data files (i.e. the variables transferred from org) are transfered as tangled files in in the ./data directory. *** Species names and espre codes of species used by Vallet :PROPERTIES: :header-args+: :tangle ./data/SPECIESVALLET.R :header-args+: :rownames yes :header-args+: :colnames yes :END: #+NAME: SPECIESVALLET | | fullName | shortName | espre | IFNName | color | |---------+-----------------+-----------+---------+-----------------+-------| | fagus | Fagus sylvatica | fagus | 4 | fagus_sylvatica | red | | quercus | Quercus robur | quercus | 3 | quercus_robur | green | #+begin_src R :var SPECIESVALLET=SPECIESVALLET #+end_src which evaluates to ./data/SPECIESVALLET.R ,---- | ## Species names and espre codes of species used by Vallet | ## :PROPERTIES: | ## :header-args+: :tangle ./data/SPECIESVALLET.R | ## :header-args+: :rownames yes | ## :header-args+: :colnames yes | ## :END: | ## #+NAME: SPECIESVALLET | ## | | fullName | shortName | espre | IFNName | color | | ## |---------+-----------------+-----------+---------+-----------------+-------| | ## | fagus | Fagus sylvatica | fagus | 4 | fagus_sylvatica | red | | ## | quercus | Quercus robur | quercus | 3 | quercus_robur | green | | | ## [[file:prodMixStands.org::*Species%20names%20and%20espre%20codes%20of%20species%20used%20by%20Vallet][Species\ names\ and\ espre\ codes\ of\ species\ used\ by\ Vallet:1]] | SPECIESVALLET <- local({ | con <- textConnection( | "\"fullName\" \"shortName\" \"espre\" \"IFNName\" \"color\" | \"fagus\" \"Fagus sylvatica\" \"fagus\" \"4\" \"fagus_sylvatica\" \"red\" | \"quercus\" \"Quercus robur\" \"quercus\" \"3\" \"quercus_robur\" \"green\"" | ) | res <- utils::read.table( | con, | header = TRUE, | row.names = 1, | sep = "\t", | as.is = TRUE | ) | close(con) | res | }) | ## Species\ names\ and\ espre\ codes\ of\ species\ used\ by\ Vallet:1 ends here | | ## Local Variables: | ## org-babel-tangled-file: t | ## buffer-read-only: t | ## eval:: (auto-revert-mode) | ## End: `---- ** evaluation data and code is *never* evaluated, i.e. :PROPERTIES: :header-args+: :eval never :END: The code and data is loaded as follow: #+begin_src R library(devtools) load_all("./") #+end_src and there you go. To debug the code, I enable developer mode in ESS and add the package =the_name_of_the_directory_./= to be debugged. * Using the code I have a second subtree (except of the one containing the code and the data) which is evaluated (as some lengthy analysis are involved, not on export but before) and contains the actual analysis. * Advantages - All code and data is enclosed in a "package" environment and, - when the project is finished, it can be easily packed in a package and handed on to other users. - documentation to the functions can be added using roxygen which can easily be translated into .rd files * Final words I hope this clarifies my approach. For me, this is a very "natural" approach, as I like to use packages and capsulate everything in environments / packages, and it seems very "clean" to me to define the core of the analysis as functions in =./R/*.R= files, the variables in =./data/*= files and the actual analysis as mainly a few function calls. If you have any further questions, please go on and ask. Cheers, Rainer > > Online Thu, Oct 9, 2014 at 7:37 AM, Rainer M Krug <Rainer@krugs.de> wrote: >> >> I'd like to ping this as I think it >> is an important bug. It e.g. make debugging of R packages, whose source >> is in org, more difficult, (the .R files are tangled into ./R/) as ess >> does not find the source of the R code in R as it uses the links in the >> comments to find the org file. >> >> Temporary solution: I created a link to the org file in the ./R directory. >> >> Cheers, >> >> Rainer >> >> Rainer M Krug <Rainer@krugs.de> writes: >> >>> When in the tangling taerget a directory is specified, this is not >>> reflected in the comments in the tangled file when comments are set to >>> include links: >>> >>> ,---- >>> | * `link' The code block is wrapped in comments which contain >>> | pointers back to the original Org file from which the code was >>> | tangled. >>> `---- >>> >>> In the org file =prodMixStands.org=: >>> >>> ,---- >>> | :PROPERTIES: >>> | :header-args+: :tangle ./R/update.cache.R >>> | :END: >>> | #+begin_src R >>> | test >>> | #+end_src >>> `---- >>> >>> results in the file =update.cache.R= in a link to the file >>> =prodMixStands.org= and not =./../prodMixstands.org=: >>> >>> ,---- >>> | ## [[file:prodMixStands.org::*Begin][Begin:1]] >>> `---- >>> >>> This is particularly bad when using ess and developer mode to develop a >>> package. >>> >>> Cheers, >>> >>> Rainer >> >> -- >> Rainer M. Krug >> email: Rainer<at>krugs<dot>de >> PGP: 0x0F52F982 >> -- Rainer M. Krug email: Rainer<at>krugs<dot>de PGP: 0x0F52F982 [-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --] ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-10 8:24 ` Rainer M Krug @ 2014-10-10 14:41 ` Grant Rettke 0 siblings, 0 replies; 11+ messages in thread From: Grant Rettke @ 2014-10-10 14:41 UTC (permalink / raw) To: Rainer M Krug; +Cc: emacs-orgmode@gnu.org On Fri, Oct 10, 2014 at 3:24 AM, Rainer M Krug <Rainer@krugs.de> wrote: > Grant Rettke <gcr@wisdomandwonder.com> writes: > >> Sounds like a valuable use of R. > > It definitely is. > > >> >> Do you have a writeup on the approach or is it a standard feature of >> org and ess? > > No - but please bug me - I can post in the intermediate future an > example demonstrating the points. I will read and ask, thanks. ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-09 12:37 ` Rainer M Krug 2014-10-10 2:13 ` Grant Rettke @ 2014-10-10 3:55 ` Aaron Ecay 2014-10-10 8:45 ` Rainer M Krug 1 sibling, 1 reply; 11+ messages in thread From: Aaron Ecay @ 2014-10-10 3:55 UTC (permalink / raw) To: Rainer M Krug, emacs-orgmode Hi Rainer, 2014ko urriak 9an, Rainer M Krug-ek idatzi zuen: > > I'd like to ping this as I think it > is an important bug. It e.g. make debugging of R packages, whose source > is in org, more difficult, (the .R files are tangled into ./R/) as ess > does not find the source of the R code in R as it uses the links in the > comments to find the org file. FWIW, I agree with you, but personally it’s hard to see myself having time to address this in the near future. Maybe you could try making a patch yourself. It sounds like the sort of thing that should be self-contained and easy to fix (famous last words, I know...) -- Aaron Ecay ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-10 3:55 ` Aaron Ecay @ 2014-10-10 8:45 ` Rainer M Krug 2014-10-10 16:34 ` Aaron Ecay 0 siblings, 1 reply; 11+ messages in thread From: Rainer M Krug @ 2014-10-10 8:45 UTC (permalink / raw) To: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 1840 bytes --] Aaron Ecay <aaronecay@gmail.com> writes: > Hi Rainer, > > 2014ko urriak 9an, Rainer M Krug-ek idatzi zuen: >> >> I'd like to ping this as I think it >> is an important bug. It e.g. make debugging of R packages, whose source >> is in org, more difficult, (the .R files are tangled into ./R/) as ess >> does not find the source of the R code in R as it uses the links in the >> comments to find the org file. > > FWIW, I agree with you, but personally it’s hard to see myself having > time to address this in the near future. Maybe you could try making a > patch yourself. It sounds like the sort of thing that should be > self-contained and easy to fix (famous last words, I know...) It looks like this - but I am always shocked by the number of brackets in lisp. The "problem" is in the function =defun org-babel-spec-to-string (spec)= in the file =lisp/ob-tangle.R= in the section #+begin_src emacs-lisp (file (if org-babel-tangle-use-relative-file-links (file-relative-name (nth 1 spec)) (nth 1 spec))) (link (let ((link (nth 2 spec))) (if org-babel-tangle-use-relative-file-links (when (string-match "^\\(file:\\|docview:\\)\\(.*\\)" link) (let* ((type (match-string 1 link)) (path (match-string 2 link)) (origpath path) (case-fold-search nil)) (setq path (file-relative-name path)) (concat type path))) link))) #+end_src the function file-relative-name (file-relative-name FILENAME &optional DIRECTORY). If I am not mistaken, the optional argument DIRECTORY needs to be set to the directory of the tangled file. I assume it is not set at the moment. But I have no idea how to get this path and how to pass it to the function. Rainer -- Rainer M. Krug email: Rainer<at>krugs<dot>de PGP: 0x0F52F982 [-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --] ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-10 8:45 ` Rainer M Krug @ 2014-10-10 16:34 ` Aaron Ecay 2014-10-10 16:50 ` Thorsten Jolitz 2014-10-10 16:55 ` Aaron Ecay 0 siblings, 2 replies; 11+ messages in thread From: Aaron Ecay @ 2014-10-10 16:34 UTC (permalink / raw) To: Rainer M Krug, emacs-orgmode Hi Rainer, 2014ko urriak 10an, Rainer M Krug-ek idatzi zuen: > It looks like this - but I am always shocked by the number of brackets > in lisp. It’s a bit of an adjustment. If you get into any serious lisp coding, check out paredit – it forces you to always have balanced brackets in the file, thus avoiding a whole class of silly but hard-to-spot mistakes on lines ending with and avalanche of ))))) <http://www.emacswiki.org/emacs/ParEdit> > > The "problem" is in the function =defun org-babel-spec-to-string (spec)= > in the file =lisp/ob-tangle.R= in the section > > #+begin_src emacs-lisp > (file (if org-babel-tangle-use-relative-file-links > (file-relative-name (nth 1 spec)) > (nth 1 spec))) > (link (let ((link (nth 2 spec))) > (if org-babel-tangle-use-relative-file-links > (when (string-match "^\\(file:\\|docview:\\)\\(.*\\)" link) > (let* ((type (match-string 1 link)) > (path (match-string 2 link)) > (origpath path) > (case-fold-search nil)) > (setq path (file-relative-name path)) > (concat type path))) > link))) > #+end_src > > the function file-relative-name (file-relative-name FILENAME &optional > DIRECTORY). If I am not mistaken, the optional argument DIRECTORY > needs to be set to the directory of the tangled file. I assume it is > not set at the moment. > > But I have no idea how to get this path and how to pass it to the > function. Something like (file-name-directory (buffer-file-name)) should do the trick, I think. It would be good if you could test tangling from a remote (i.e. via TRAMP) org file to a local output file and vice versa to make sure that this DTRT in those cases as well. Don’t hesitate to ask if you have more questions! -- Aaron Ecay ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-10 16:34 ` Aaron Ecay @ 2014-10-10 16:50 ` Thorsten Jolitz 2014-10-10 18:37 ` Grant Rettke 2014-10-10 16:55 ` Aaron Ecay 1 sibling, 1 reply; 11+ messages in thread From: Thorsten Jolitz @ 2014-10-10 16:50 UTC (permalink / raw) To: emacs-orgmode Aaron Ecay <aaronecay@gmail.com> writes: Hi Rainer, > 2014ko urriak 10an, Rainer M Krug-ek idatzi zuen: >> It looks like this - but I am always shocked by the number of brackets >> in lisp. > > It’s a bit of an adjustment. If you get into any serious lisp coding, > check out paredit – it forces you to always have balanced brackets in > the file, thus avoiding a whole class of silly but hard-to-spot mistakes > on lines ending with and avalanche of ))))) > > <http://www.emacswiki.org/emacs/ParEdit> if you are less into bondage&submission, smartparens.el is another option, it *helps* to have balanced brackets w/o breaking your will ;-) -- cheers, Thorsten ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-10 16:50 ` Thorsten Jolitz @ 2014-10-10 18:37 ` Grant Rettke 0 siblings, 0 replies; 11+ messages in thread From: Grant Rettke @ 2014-10-10 18:37 UTC (permalink / raw) To: Thorsten Jolitz; +Cc: emacs-orgmode@gnu.org On Fri, Oct 10, 2014 at 11:50 AM, Thorsten Jolitz <tjolitz@gmail.com> wrote: > Aaron Ecay <aaronecay@gmail.com> writes: > > Hi Rainer, > >> 2014ko urriak 10an, Rainer M Krug-ek idatzi zuen: >>> It looks like this - but I am always shocked by the number of brackets >>> in lisp. >> >> It’s a bit of an adjustment. If you get into any serious lisp coding, >> check out paredit – it forces you to always have balanced brackets in >> the file, thus avoiding a whole class of silly but hard-to-spot mistakes >> on lines ending with and avalanche of ))))) >> >> <http://www.emacswiki.org/emacs/ParEdit> > > if you are less into bondage&submission, smartparens.el is another option, > it *helps* to have balanced brackets w/o breaking your will ;-) It is more about ease-of-coding them B&D. =turn-on-smartparens-strict-mode= add years to ones life to allow for more hacking. Seriously. ^ permalink raw reply [flat|nested] 11+ messages in thread
* Re: [BUG][babel] Tangling into directories does not add directories to org file 2014-10-10 16:34 ` Aaron Ecay 2014-10-10 16:50 ` Thorsten Jolitz @ 2014-10-10 16:55 ` Aaron Ecay 1 sibling, 0 replies; 11+ messages in thread From: Aaron Ecay @ 2014-10-10 16:55 UTC (permalink / raw) To: Rainer M Krug, emacs-orgmode Hi Rainer, 2014ko urriak 10an, Aaron Ecay-ek idatzi zuen: [...] >> the function file-relative-name (file-relative-name FILENAME &optional >> DIRECTORY). If I am not mistaken, the optional argument DIRECTORY >> needs to be set to the directory of the tangled file. I assume it is >> not set at the moment. >> >> But I have no idea how to get this path and how to pass it to the >> function. > > Something like (file-name-directory (buffer-file-name)) should do the > trick, I think. I just (re)-read the “...and pass it to the function” part. The lisp convention is that function calls look like: (FUNCTION ARG1 ARG2 ... ARGN) So you’d want something like: (file (if org-babel-tangle-use-relative-file-links (file-relative-name (nth 1 spec) (file-name-directory (buffer-file-name))) ;;; <- addition here (nth 1 spec))) (link (let ((link (nth 2 spec))) (if org-babel-tangle-use-relative-file-links (when (string-match "^\\(file:\\|docview:\\)\\(.*\\)" link) (let* ((type (match-string 1 link)) (path (match-string 2 link)) (origpath path) (case-fold-search nil)) (setq path (file-relative-name path (file-name-directory (buffer-file-name)))) ;;; <- addition here (concat type path))) link))) Apologies if this is too basic an explanation, or otherwise unclear... -- Aaron Ecay ^ permalink raw reply [flat|nested] 11+ messages in thread
end of thread, other threads:[~2014-10-10 18:37 UTC | newest] Thread overview: 11+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2014-10-08 13:21 [BUG][babel] Tangling into directories does not add directories to org file Rainer M Krug 2014-10-09 12:37 ` Rainer M Krug 2014-10-10 2:13 ` Grant Rettke 2014-10-10 8:24 ` Rainer M Krug 2014-10-10 14:41 ` Grant Rettke 2014-10-10 3:55 ` Aaron Ecay 2014-10-10 8:45 ` Rainer M Krug 2014-10-10 16:34 ` Aaron Ecay 2014-10-10 16:50 ` Thorsten Jolitz 2014-10-10 18:37 ` Grant Rettke 2014-10-10 16:55 ` Aaron Ecay
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