Re: [O] Best diagram, image software?
Hi, I'm using the following header, which lets me export to PDF and HTML, both (basically from here: http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html). #+header: :exports results :file fsa.png #+header: :imagemagick yes :iminoptions -density 600 :imoutoptions -geometry 1200 #+header: :fit yes :noweb yes :headers '("\\usepackage{tikz}") #+begin_src latex :exports results :results raw :file fsa.png (and no #+Results line, but I don't know if this matters) Also, regarding the babel I use the following to map source blocks to "supported" LaTeX listings languages: Add “text” and “conf” to =latex-listings-langs= with empty (space as a trick) language name to be used in the LaTeX listings package. #+begin_src emacs-lisp (add-to-list 'org-latex-listings-langs '(text " ")) (add-to-list 'org-latex-listings-langs '(conf " ")) (add-to-list 'org-latex-listings-langs '(nxml "XML")) (add-to-list 'org-latex-listings-langs '(org " ")) Best regards On Thu, 06 Oct 2016 12:48:52 -0400 Peter Davis wrote: > Since several people recommended TikZ, I decided to take a look at it. > It seems very powerful, but I'm unable to get any example to work. For > example, using the example here: > > http://doblogit.com/posts/2015-10-23-org-graphics.html > > #+begin_src latex :exports results :results output raw :file > images/fsa.png > % Define block styles > \usetikzlibrary{shapes,arrows} > \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, > fill=blue!25] > \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, > fill=red!25] > > \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node > distance=2.8cm, semithick] > \node [astate] (1) at (0,0) {1}; > \node [astate] (2) at (1,0) {2}; > \node [rstate] (3) at (2,0) {3}; > \path (1) edge [bend left] node {b} (2) > (2) edge node {b} (3) > (2) edge [bend left] node {a} (1) > (3) edge [loop above] node {(a, b)} (3); > \end{tikzpicture} > #+end_src > > > I get: > > org-babel-exp process latex at line 6... > executing Latex code block... > org-latex-compile: PDF file > c:/Users/pdavis/AppData/Local/Temp/orgtex5448hGP.pdf wasn’t produced > > I've got ImageMagick installed. I don't know how to debug this. > >
Re: [O] [RFC] Change visibility for bracket links
Hello, Clément Pit--Claudel writes: > What about having our cake and eating it too? :) We could do just the > same as what prettify-symbols-mode does with its > prettify-symbols-unprettify-at-point variable. Namely, we could show > the brackets when point is at the edge of a link, and hide them > otherwise. The same trick could be applied to subscripts (I have > working code for that for a different project, at > https://github.com/cpitclaudel/company-coq/blob/master/company-coq.el#L4287). > > Wouldn't this preserve the flow of reading, while allowing for easier > editing? I have the feeling that it would cause some visual "jumping" when the link is very different (e.g., wider) than its visible pars. Some links tend to be very long. So showing the full link is not an option. I don't know about showing only the brackets. Would you want to provide a mock-up ? Thank you. Regards, -- Nicolas Goaziou
Re: [O] Bug: org-mode interprets * as a headline in text between #+BEGIN_.. and #+END_...
Hello, Nick Dokos writes: > Is the "* on column 0 is a headline" convention a consequence of the > dependence on outline.el? Or is it just historical baggage? I cannot > remember the grammar rules, but I'm wondering if the parser could be > made to say "not a headline" in this situation, and if so, what the > consequences might be (particularly, the bad consequences). > > I'm not sure whether Nicolas has actually explained this situation in > the past, but, with gmane non compos mentis, I did not attempt to find > an earlier discussion. This is inherent on how the syntax is defined, and how the parser is implemented. As an outliner, the main syntactic element in an Org document is the headline. Everything else has a lower priority. Therefore, a block will not be parsed before a headline. The good side of headlines being top level elements is that parsing (without cache) only needs to start from the closest headline above. If blocks could be parsed before headlines, parsing should start from the beginning of the document every time. Regards, -- Nicolas Goaziou
[O] mass conversion?
In an org-mode document which is then converted I'm using the latex glossary package, which shows my glossary items as '\gls{foo}'. I'm now getting to the stage of having a paper copy of the latexed PDF but am finding that the glossary items in the main text do not show at all when using just black text on a white background in the PDF. So what I'm trying to do is to underline each one in the org-mode text which converts very easily to underlined in the black/white paper PDF. But how can I do it globally please, using just a couple of commands to work on all instances in the org-mode file please? Thanks Sharon. -- A taste of linux = http://www.sharons.org.uk TGmeds = http://www.tgmeds.org.uk Debian 8.4, fluxbox 1.3.7, emacs 25.1.1 signature.asc Description: PGP signature
Re: [O] Best diagram, image software?
That is probably because with minted you have to modify how the pdf is built to use pdflatex -shell-escape. The variable org-latex-pdf-process controls this. Peter Davis writes: > Ok, my problem was that the minted package was causing errors. Taking > that out lets me generate pdf. > > Now to figure out how to generate other formats, to work with HTML and > LaTeX/PDF output. > > Thanks, all!! > > -pd -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu
[O] MySQL params as global properties?
I guess I've been out of the loop for a while. I used to have this at the end of my org-mode SQL files: #+PROPERTY: engine mysql #+PROPERTY: dbhost xx.xx.xx.xx #+PROPERTY: dbuser xx #+PROPERTY: dbpassword x #+PROPERTY: database x But since I recently updated org-mode, these don't have any effect anymore. In ob-sql I can see they're not getting passed to org-babel-execute:sql. I tried a different form that I saw in the doc: #+PROPERTY: header-args:sql :engine mysql #+PROPERTY: header-args:sql :dbhost xxx #+PROPERTY: header-args:sql :dbuser xxx #+PROPERTY: header-args:sql :dbpassword xx #+PROPERTY: header-args:sql :database but that doesn't work either. Can anyone tell me the proper new-style form for passing header args to all sql code blocks? thanks! -- Gary
Re: [O] Best diagram, image software?
That implies you have not configured org-mode to include the tikz package. If you execute this block in a buffer does it work? #+BEGIN_SRC emacs-lisp (org-babel-do-load-languages 'org-babel-load-languages '((emacs-lisp . t) (python . t) (ditaa . t) (dot . t) (plantuml . t) (gnuplot . t) (sh . t) (org . t) (latex . t))) (setq org-latex-packages-alist (quote (("" "color" t) ("" "minted" t) ("" "parskip" t) ("" "tikz" t (setq org-latex-create-formula-image-program 'imagemagick) #+END_SRC Peter Davis writes: > On Thu, Oct 6, 2016, at 01:59 PM, John Kitchin wrote: >> I tried this, and it worked for me. Check *Messages* for things like: >> Failed to create dvi file from >> /var/folders/5q/lllv2yf95hg_n6h6kjttbmdwgn/T/orgtex93386BIQ.tex >> >> if you see that try manually building the tex file to see if there are >> LaTeX issues. >> > > Thanks, John. Just running pdflatex from the command line gives me: > > ! Undefined control sequence. > l.36 \tikz > [remember picture]\node[coordinate,yshift=0.5em] (n1) {}; > > So perhaps TikZ itself is not available to some part of this. > > Thanks, > -pd -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu
Re: [O] Bug: org-mode interprets * as a headline in text between #+BEGIN_.. and #+END_...
John Hendy writes: > On Thu, Oct 6, 2016 at 3:28 PM, David Talmage > wrote: >> I often paste verbatim text into the lab notebook I keep with org-mode. >> Org-mode always interprets any line that begins with an asterisk as a >> headline, even when the line is surrounded by #+BEGIN_... and #+END_... >> patterns. This breaks org-special-edit, making it complain, "No special >> environment to edit here", unless I manually insert another character at the >> beginning of every line in the block that begins with an asterisk. >> >> The behavior surprised me. I found two ways to work around it. First, I >> can edit the would-be verbatim text as described above. It will always look >> like the original text in org-special-edit. That's marginally acceptable >> because it alters my original text and makes me take one more step before I >> can copy and paste it elsewhere. Second, I can put such text in a drawer. >> I discovered that org-mode does not mis-interpret my text in a drawer. >> >> > > I don't have a good explanation of why, but I know you need a comma to > escape org syntax, even within src blocks: > - mention of it in the manual (footnote 4): > http://orgmode.org/manual/Literal-examples.html > - SO answer: > http://stackoverflow.com/questions/7431167/escaping-org-mode-example-block-inside-of-an-example-block > C-c ' to edit the block will rewrite it with a , in front - but only if the line does not start with a * - if it starts with a *, then C-c ' will complain as the OP posted. And if you have speed keys enabled, then comma or space will not self-insert, and you got to do something like C-q , to enter the comma or C-q SPC for a space, making the whole thing even more confusing. I don't know how it would interact with org-indent turned off: I didn't try that. Is the "* on column 0 is a headline" convention a consequence of the dependence on outline.el? Or is it just historical baggage? I cannot remember the grammar rules, but I'm wondering if the parser could be made to say "not a headline" in this situation, and if so, what the consequences might be (particularly, the bad consequences). I'm not sure whether Nicolas has actually explained this situation in the past, but, with gmane non compos mentis, I did not attempt to find an earlier discussion. -- Nick
Re: [O] Bug: org-mode interprets * as a headline in text between #+BEGIN_.. and #+END_...
On Thu, Oct 6, 2016 at 3:28 PM, David Talmage wrote: > I often paste verbatim text into the lab notebook I keep with org-mode. > Org-mode always interprets any line that begins with an asterisk as a > headline, even when the line is surrounded by #+BEGIN_... and #+END_... > patterns. This breaks org-special-edit, making it complain, "No special > environment to edit here", unless I manually insert another character at the > beginning of every line in the block that begins with an asterisk. > > The behavior surprised me. I found two ways to work around it. First, I > can edit the would-be verbatim text as described above. It will always look > like the original text in org-special-edit. That's marginally acceptable > because it alters my original text and makes me take one more step before I > can copy and paste it elsewhere. Second, I can put such text in a drawer. > I discovered that org-mode does not mis-interpret my text in a drawer. > > I don't have a good explanation of why, but I know you need a comma to escape org syntax, even within src blocks: - mention of it in the manual (footnote 4): http://orgmode.org/manual/Literal-examples.html - SO answer: http://stackoverflow.com/questions/7431167/escaping-org-mode-example-block-inside-of-an-example-block > Here is an example. It's markdown text. I use #+{BEGIN,END}_EXAMPLE but > this behavior occurs in all of the #+BEGIN_.. and #+END_... patterns. > > #+BEGIN_EXAMPLE > This is the README.md for rfc-tools, a collection of programs for > processing IETF RFCs. > > * fetch-rfcs-by-title.sh downloads into the current directory the RFCs >whose titles contain the string given on the command line. Uses an > rfc-index file in the current directory. Prefers the PDF version of > RFCs but will obtain the text version if the PDF is not available. > > * fetch-sip-rfcs.sh downloads RFCs that contain "Session Initiation" > in their titles into the current directory. > > * search-rfc-index.sh searches an rfc-index file in the current > directory for the string given on the command line. The string can > contain spaces. > > * join-titles.awk turns the contents of an rfc-index file into a > series of long lines. Each line begins with the RFC number, then a > space, then the rest of the entry from the rfc-index. > #+END_EXAMPLE >
[O] Bug: org-mode interprets * as a headline in text between #+BEGIN_.. and #+END_...
I often paste verbatim text into the lab notebook I keep with org-mode. Org-mode always interprets any line that begins with an asterisk as a headline, even when the line is surrounded by #+BEGIN_... and #+END_... patterns. This breaks org-special-edit, making it complain, "No special environment to edit here", unless I manually insert another character at the beginning of every line in the block that begins with an asterisk. The behavior surprised me. I found two ways to work around it. First, I can edit the would-be verbatim text as described above. It will always look like the original text in org-special-edit. That's marginally acceptable because it alters my original text and makes me take one more step before I can copy and paste it elsewhere. Second, I can put such text in a drawer. I discovered that org-mode does not mis-interpret my text in a drawer. Here is an example. It's markdown text. I use #+{BEGIN,END}_EXAMPLE but this behavior occurs in all of the #+BEGIN_.. and #+END_... patterns. #+BEGIN_EXAMPLE This is the README.md for rfc-tools, a collection of programs for processing IETF RFCs. * fetch-rfcs-by-title.sh downloads into the current directory the RFCs whose titles contain the string given on the command line. Uses an rfc-index file in the current directory. Prefers the PDF version of RFCs but will obtain the text version if the PDF is not available. * fetch-sip-rfcs.sh downloads RFCs that contain "Session Initiation" in their titles into the current directory. * search-rfc-index.sh searches an rfc-index file in the current directory for the string given on the command line. The string can contain spaces. * join-titles.awk turns the contents of an rfc-index file into a series of long lines. Each line begins with the RFC number, then a space, then the rest of the entry from the rfc-index. #+END_EXAMPLE
Re: [O] Best diagram, image software?
Ok, my problem was that the minted package was causing errors. Taking that out lets me generate pdf. Now to figure out how to generate other formats, to work with HTML and LaTeX/PDF output. Thanks, all!! -pd -- Peter Davis www.techcurmudgeon.com
Re: [O] Best diagram, image software?
On Thu, Oct 6, 2016 at 2:49 PM, Peter Davis wrote: > > On Thu, Oct 6, 2016, at 03:25 PM, Clément Pit--Claudel wrote: >> On 2016-10-06 15:10, Peter Davis wrote: >> >> > (add-to-list 'org-latex-packages-alist >> >> > '(("AUTO" "inputenc" t) >> >> >("" "color" t) >> >> >("" "minted" t) >> >> >("" "parskip" t) >> >> >("" "tikz" t))) >> Maybe I'm dense, but why is everyone recommending changing the alist? Granted, for future proofing and convenience this is nice... but I do a fair amount with TikZ and have never done this. ~/org/aux/setupfile.org contains: #+latex_header: \usepackage{tikz} #+latex_header: \usepackage[siunitx]{circuitikz} #+latex_header: \usetikzlibrary{shapes, positioning} any given .org file contains: #+setupfile: "~/org/aux/setupfile.org" I modified your original aim like so, ditching the .png output which looks like requires imagemagick. Maybe that's in org somehow, but when you're just starting out I'd suggest eliminating as many other mechanisms as possible. TikZ is in LaTeX, so just stick to pdf at the start. This works for me. #+latex_header: \usepackage{tikz} #+latex_header: \usetikzlibrary{shapes, positioning} * test #+begin_src latex :results raw % Define block styles \usetikzlibrary{shapes,arrows} \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, fill=blue!25] \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, fill=red!25] \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node distance=2.8cm, semithick] \node [astate] (1) at (0,0) {1}; \node [astate] (2) at (1,0) {2}; \node [rstate] (3) at (2,0) {3}; \path (1) edge [bend left] node {b} (2) (2) edge node {b} (3) (2) edge [bend left] node {a} (1) (3) edge [loop above] node {(a, b)} (3); \end{tikzpicture} #+end_src John >> This looks wrong. You're adding a single list to >> org-latex-package-alist, instead of adding multiple elements one-by-one. >> > > Ok, I tried changing it to: > > (add-to-list 'org-latex-packages-alist '("AUTO" "inputenc" t)) > (add-to-list 'org-latex-packages-alist '("" "color" t)) > (add-to-list 'org-latex-packages-alist '("" "minted" t)) > (add-to-list 'org-latex-packages-alist '("" "parskip" t)) > (add-to-list 'org-latex-packages-alist '("" "tikz")) > (add-to-list 'org-latex-packages-alist '("" "listingsutf8")) > > so now org-latex-packages-alist has the value > > (("" "listingsutf8") > ("" "tikz") > ("" "parskip" t) > ("" "minted" t) > ("" "color" t) > ("AUTO" "inputenc" t)) > > Still getting the failure on tikz output. > > Thanks! > -pd > > -- > Peter Davis > www.techcurmudgeon.com >
Re: [O] Best diagram, image software?
On Thu, Oct 6, 2016, at 03:25 PM, Clément Pit--Claudel wrote: > On 2016-10-06 15:10, Peter Davis wrote: > >> > (add-to-list 'org-latex-packages-alist > >> > '(("AUTO" "inputenc" t) > >> >("" "color" t) > >> >("" "minted" t) > >> >("" "parskip" t) > >> >("" "tikz" t))) > > This looks wrong. You're adding a single list to > org-latex-package-alist, instead of adding multiple elements one-by-one. > Ok, I tried changing it to: (add-to-list 'org-latex-packages-alist '("AUTO" "inputenc" t)) (add-to-list 'org-latex-packages-alist '("" "color" t)) (add-to-list 'org-latex-packages-alist '("" "minted" t)) (add-to-list 'org-latex-packages-alist '("" "parskip" t)) (add-to-list 'org-latex-packages-alist '("" "tikz")) (add-to-list 'org-latex-packages-alist '("" "listingsutf8")) so now org-latex-packages-alist has the value (("" "listingsutf8") ("" "tikz") ("" "parskip" t) ("" "minted" t) ("" "color" t) ("AUTO" "inputenc" t)) Still getting the failure on tikz output. Thanks! -pd -- Peter Davis www.techcurmudgeon.com
Re: [O] Best diagram, image software?
Maybe a distraction from the discussion on graphing alternatives that can be embedded into the org/LaTeX code but I am pretty happy with the results I get from using Veusz. http://home.gna.org/veusz/ Adding to the confusion by adding a recommendation for a program I use to create numerical data from graphs: http://markummitchell.github.io/engauge-digitizer/ -- Martin Schöön
Re: [O] Best diagram, image software?
On 2016-10-06 15:10, Peter Davis wrote: >> > (add-to-list 'org-latex-packages-alist >> > '(("AUTO" "inputenc" t) >> >("" "color" t) >> >("" "minted" t) >> >("" "parskip" t) >> >("" "tikz" t))) This looks wrong. You're adding a single list to org-latex-package-alist, instead of adding multiple elements one-by-one. signature.asc Description: OpenPGP digital signature
Re: [O] Best diagram, image software?
On Thu, Oct 6, 2016, at 02:59 PM, Nick Dokos wrote: > Peter Davis writes: > > > On Thu, Oct 6, 2016, at 02:15 PM, Nick Dokos wrote: > >> Peter Davis writes: > >> > >> > Since several people recommended TikZ, I decided to take a look at it. > >> > It seems very powerful, but I'm unable to get any example to work. For > >> > example, using the example here: > >> > > >> > http://doblogit.com/posts/2015-10-23-org-graphics.html > >> > > >> > >> Did you add tikz to org-latex-packages-alist? > >> > > > > I do have: > > > > (add-to-list 'org-latex-packages-alist > > '(("AUTO" "inputenc" t) > >("" "color" t) > >("" "minted" t) > >("" "parskip" t) > >("" "tikz" t))) > > > > Any other setup work I need? > > > > Yes, but have you executed that? What does C-h v org-latex-pacakges-alist > RET say? org-latex-packages-alist is a variable defined in ‘org.el’. Its value is (("" "tikz") ("" "listingsutf8") (("AUTO" "inputenc" t) ("" "color" t) ("" "minted" t) ("" "parskip" t) ("" "tikz" t))) -- Peter Davis www.techcurmudgeon.com
Re: [O] Best diagram, image software?
Peter Davis writes: > On Thu, Oct 6, 2016, at 02:15 PM, Nick Dokos wrote: >> Peter Davis writes: >> >> > Since several people recommended TikZ, I decided to take a look at it. >> > It seems very powerful, but I'm unable to get any example to work. For >> > example, using the example here: >> > >> > http://doblogit.com/posts/2015-10-23-org-graphics.html >> > >> >> Did you add tikz to org-latex-packages-alist? >> > > I do have: > > (add-to-list 'org-latex-packages-alist > '(("AUTO" "inputenc" t) >("" "color" t) >("" "minted" t) >("" "parskip" t) >("" "tikz" t))) > > Any other setup work I need? > Yes, but have you executed that? What does C-h v org-latex-pacakges-alist RET say? -- Nick
Re: [O] Best diagram, image software?
On Thu, Oct 6, 2016, at 02:15 PM, Nick Dokos wrote: > Peter Davis writes: > > > Since several people recommended TikZ, I decided to take a look at it. > > It seems very powerful, but I'm unable to get any example to work. For > > example, using the example here: > > > > http://doblogit.com/posts/2015-10-23-org-graphics.html > > > > Did you add tikz to org-latex-packages-alist? > I do have: (add-to-list 'org-latex-packages-alist '(("AUTO" "inputenc" t) ("" "color" t) ("" "minted" t) ("" "parskip" t) ("" "tikz" t))) Any other setup work I need? Thanks! -pd -- Peter Davis www.techcurmudgeon.com
Re: [O] Best diagram, image software?
On Thu, Oct 6, 2016, at 01:59 PM, John Kitchin wrote: > I tried this, and it worked for me. Check *Messages* for things like: > Failed to create dvi file from > /var/folders/5q/lllv2yf95hg_n6h6kjttbmdwgn/T/orgtex93386BIQ.tex > > if you see that try manually building the tex file to see if there are > LaTeX issues. > Thanks, John. Just running pdflatex from the command line gives me: ! Undefined control sequence. l.36 \tikz [remember picture]\node[coordinate,yshift=0.5em] (n1) {}; So perhaps TikZ itself is not available to some part of this. Thanks, -pd -- Peter Davis www.techcurmudgeon.com
Re: [O] Best diagram, image software?
Peter Davis writes: > Since several people recommended TikZ, I decided to take a look at it. > It seems very powerful, but I'm unable to get any example to work. For > example, using the example here: > > http://doblogit.com/posts/2015-10-23-org-graphics.html > Did you add tikz to org-latex-packages-alist? > #+begin_src latex :exports results :results output raw :file > images/fsa.png > % Define block styles > \usetikzlibrary{shapes,arrows} > \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, > fill=blue!25] > \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, > fill=red!25] > > \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node > distance=2.8cm, semithick] > \node [astate] (1) at (0,0) {1}; > \node [astate] (2) at (1,0) {2}; > \node [rstate] (3) at (2,0) {3}; > \path (1) edge [bend left] node {b} (2) > (2) edge node {b} (3) > (2) edge [bend left] node {a} (1) > (3) edge [loop above] node {(a, b)} (3); > \end{tikzpicture} > #+end_src > > > I get: > > org-babel-exp process latex at line 6... > executing Latex code block... > org-latex-compile: PDF file > c:/Users/pdavis/AppData/Local/Temp/orgtex5448hGP.pdf wasn’t produced > > I've got ImageMagick installed. I don't know how to debug this. I always go back to straight LaTeX to debug such problems: --8<---cut here---start->8--- \documentclass{article} \usepackage{tikz} \usetikzlibrary{shapes,arrows} \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, fill=blue!25] \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, fill=red!25] \begin{document} \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node distance=2.8cm, semithick] \node [astate] (1) at (0,0) {1}; \node [astate] (2) at (1,0) {2}; \node [rstate] (3) at (2,0) {3}; \path (1) edge [bend left] node {b} (2) (2) edge node {b} (3) (2) edge [bend left] node {a} (1) (3) edge [loop above] node {(a, b)} (3); \end{tikzpicture} \end{document} %%% Local Variables: %%% mode: latex %%% TeX-master: t %%% End: --8<---cut here---end--->8--- -- Nick
Re: [O] Best diagram, image software?
I tried this, and it worked for me. Check *Messages* for things like: Failed to create dvi file from /var/folders/5q/lllv2yf95hg_n6h6kjttbmdwgn/T/orgtex93386BIQ.tex if you see that try manually building the tex file to see if there are LaTeX issues. #+BEGIN_SRC emacs-lisp (org-babel-do-load-languages 'org-babel-load-languages '((emacs-lisp . t) (python . t) (ditaa . t) (dot . t) (plantuml . t) (gnuplot . t) (sh . t) (org . t) (latex . t))) (setq org-latex-packages-alist (quote (("" "color" t) ("" "minted" t) ("" "parskip" t) ("" "tikz" t (setq org-latex-create-formula-image-program 'imagemagick) #+END_SRC #+RESULTS: : imagemagick #+begin_src latex :exports results :results output raw :file fsa.png % Define block styles \usetikzlibrary{shapes,arrows} \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, fill=blue!25] \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, fill=red!25] \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node distance=2.8cm, semithick] \node [astate] (1) at (0,0) {1}; \node [astate] (2) at (1,0) {2}; \node [rstate] (3) at (2,0) {3}; \path (1) edge [bend left] node {b} (2) (2) edge node {b} (3) (2) edge [bend left] node {a} (1) (3) edge [loop above] node {(a, b)} (3); \end{tikzpicture} #+end_src #+RESULTS: [[file:fsa.png]] Peter Davis writes: > Since several people recommended TikZ, I decided to take a look at it. > It seems very powerful, but I'm unable to get any example to work. For > example, using the example here: > > http://doblogit.com/posts/2015-10-23-org-graphics.html > > #+begin_src latex :exports results :results output raw :file > images/fsa.png > % Define block styles > \usetikzlibrary{shapes,arrows} > \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, > fill=blue!25] > \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, > fill=red!25] > > \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node > distance=2.8cm, semithick] > \node [astate] (1) at (0,0) {1}; > \node [astate] (2) at (1,0) {2}; > \node [rstate] (3) at (2,0) {3}; > \path (1) edge [bend left] node {b} (2) > (2) edge node {b} (3) > (2) edge [bend left] node {a} (1) > (3) edge [loop above] node {(a, b)} (3); > \end{tikzpicture} > #+end_src > > > I get: > > org-babel-exp process latex at line 6... > executing Latex code block... > org-latex-compile: PDF file > c:/Users/pdavis/AppData/Local/Temp/orgtex5448hGP.pdf wasn’t produced > > I've got ImageMagick installed. I don't know how to debug this. -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu
Re: [O] Problem with python session
Hi Florian I can reproduce your problem. This is (arguably) a bug in ob-python when using the vanilla python interpreter together with the :session argument. You can work around it by putting a blank line after the for-loop in your second code block. I say that it is arguable that this is a bug or not since you would have exactly the same error if you were to literally type your code block in at the python interactive prompt. That is, you have to give a second newline in order to close the loop and return to the top-level prompt. However, it is admittedly confusing to have different behavior with and without the ":session" argument. I had never come across this bug myself, since I use ob-ipython for interactive python sessions (https://github.com/gregsexton/ob-ipython) Here is a minimal example that shows the problem. Cheers Will * Test of ob-python in session mode with vanilla python interpreter ** FAILS: Without blank line after indented loop #+BEGIN_SRC python :session *ob-python session* for x in 1, 2: pass x #+END_SRC #+RESULTS: An error message appears in the =*ob-python session*= buffer, which can be visited via =C-c C-v C-z= with point inside the code block. #+BEGIN_EXAMPLE >>> 'org_babel_python_eoe' >>> 'org_babel_python_eoe' >>> for x in 1, 2: ... pass ... x File "", line 3 x ^ SyntaxError: invalid syntax #+END_EXAMPLE ** SUCCEEDS: With blank line after indented loop #+BEGIN_SRC python :session *ob-python session* for x in 1, 2: pass x #+END_SRC #+RESULTS: : 2 ** SUCCEEDS: Without using a session #+BEGIN_SRC python :return x for x in 1, 2: pass x #+END_SRC #+RESULTS: : 2 ** SUCCEEDS: Using ob-ipython instead of ob-python #+BEGIN_SRC ipython :session for x in 1, 2: pass x #+END_SRC #+RESULTS: : 2 On Thu, Oct 6, 2016 at 7:41 AM, Florian Lindner wrote: > Hello, > > I have an org file: > > * Overview of available basis functions > #+BEGIN_SRC python :session generateBFpics :exports results :results file > import matplotlib.pyplot as plt > import numpy as np > > def set_plotoptions(): > plt.xlabel("x") > plt.ylabel("$\phi(x)$") > plt.grid() > > > np.seterr(invalid='ignore') > > x = np.linspace(-3, 3, 1000) > > plt.plot(x, np.log(abs(x))*np.power(x, 2)) > plt.suptitle("Thin Plate Splines") > plt.title("$\phi(|x|) = \log(x) \cdot x^2$") > set_plotoptions() > plt.savefig("bf-tps.pdf") > plt.close() > "bf-tps.pdf" > #+END_SRC > > #+RESULTS: > [[file:bf-tps.pdf]] > > #+BEGIN_SRC python :session generateBFpics :exports results :results file > for shape in [1, 2, 3, 4]: > plt.plot(x, np.power(shape, 2) + np.power(x,2), label = "s = %i" % > shape) > plt.suptitle("Multi Quadrics") > plt.title("$\phi(|x|) = s^2 + x^2$") > plt.legend() > set_plotoptions() > plt.savefig("bf-multiquadrics.pdf") > plt.close() > "bf-multiquadrics.pdf" > #+END_SRC > > #+RESULTS: > [[file:bf-multiquadrics.pdf]] > > > > Both PDFs are generated. But only the first one has the content I expect, > the othe one is an empty plot (it's a plot, > yes, but empty axes. > > When I copy these pieces of code into on .py file it works just great. To > my understanding that just how session mode works. > > What could be the problem here? > > Thanks, > Florian > > > -- Dr William Henney, Instituto de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, Campus Morelia
Re: [O] Best diagram, image software?
Since several people recommended TikZ, I decided to take a look at it. It seems very powerful, but I'm unable to get any example to work. For example, using the example here: http://doblogit.com/posts/2015-10-23-org-graphics.html #+begin_src latex :exports results :results output raw :file images/fsa.png % Define block styles \usetikzlibrary{shapes,arrows} \tikzstyle{astate} = [circle, draw, text centered, font=\footnotesize, fill=blue!25] \tikzstyle{rstate} = [circle, draw, text centered, font=\footnotesize, fill=red!25] \begin{tikzpicture}[->,>=stealth', shorten >=1pt, auto, node distance=2.8cm, semithick] \node [astate] (1) at (0,0) {1}; \node [astate] (2) at (1,0) {2}; \node [rstate] (3) at (2,0) {3}; \path (1) edge [bend left] node {b} (2) (2) edge node {b} (3) (2) edge [bend left] node {a} (1) (3) edge [loop above] node {(a, b)} (3); \end{tikzpicture} #+end_src I get: org-babel-exp process latex at line 6... executing Latex code block... org-latex-compile: PDF file c:/Users/pdavis/AppData/Local/Temp/orgtex5448hGP.pdf wasn’t produced I've got ImageMagick installed. I don't know how to debug this. -- Peter Davis www.techcurmudgeon.com
Re: [O] [RFC] Change visibility for bracket links
On 6 October 2016, Eric S Fraga wrote: In any case, Nicolas, I am fully in favour of your proposed change. Editing links has always been very frustrating for me and your suggestion would make it much easier. +1 from me too. Bil -- William Denton :: Toronto, Canada :: https://www.miskatonic.org/ Caveat lector.
[O] Problem with python session
Hello, I have an org file: * Overview of available basis functions #+BEGIN_SRC python :session generateBFpics :exports results :results file import matplotlib.pyplot as plt import numpy as np def set_plotoptions(): plt.xlabel("x") plt.ylabel("$\phi(x)$") plt.grid() np.seterr(invalid='ignore') x = np.linspace(-3, 3, 1000) plt.plot(x, np.log(abs(x))*np.power(x, 2)) plt.suptitle("Thin Plate Splines") plt.title("$\phi(|x|) = \log(x) \cdot x^2$") set_plotoptions() plt.savefig("bf-tps.pdf") plt.close() "bf-tps.pdf" #+END_SRC #+RESULTS: [[file:bf-tps.pdf]] #+BEGIN_SRC python :session generateBFpics :exports results :results file for shape in [1, 2, 3, 4]: plt.plot(x, np.power(shape, 2) + np.power(x,2), label = "s = %i" % shape) plt.suptitle("Multi Quadrics") plt.title("$\phi(|x|) = s^2 + x^2$") plt.legend() set_plotoptions() plt.savefig("bf-multiquadrics.pdf") plt.close() "bf-multiquadrics.pdf" #+END_SRC #+RESULTS: [[file:bf-multiquadrics.pdf]] Both PDFs are generated. But only the first one has the content I expect, the othe one is an empty plot (it's a plot, yes, but empty axes. When I copy these pieces of code into on .py file it works just great. To my understanding that just how session mode works. What could be the problem here? Thanks, Florian
[O] [BUG] TRAMP error in PDF export
Not 100% sure this is a bug rather than misconfiguration, but it looks like it at first sight: Open an Org file via ssh: C-x C-f /ssh:me@host:/org/anOrgFile.org Export it to PDF: C-c C-e l p I get: (lots of pdfTex error text about not being able to find the file /ssh:me@host:/org/anOrgFile.tex) ending with: byte-code: Forbidden reentrant call of Tramp -- Phil Hudson http://hudson-it.ddns.net @UWascalWabbit PGP/GnuPG ID: 0x887DCA63
Re: [O] [RFC] Change visibility for bracket links
On Thursday, 6 Oct 2016 at 00:27, Clément Pit--Claudel wrote: > What about having our cake and eating it too? :) We could do just the > same as what prettify-symbols-mode does with its > prettify-symbols-unprettify-at-point variable. This would be nice. In any case, Nicolas, I am fully in favour of your proposed change. Editing links has always been very frustrating for me and your suggestion would make it much easier. Thanks, eric -- : Eric S Fraga (0xFFFCF67D), Emacs 25.1.1, Org release_8.3.6-1131-gd68497