[O] department logo/header image in koma/latex export?
Hi all i am looking into using koma and orgmode to export to recommendation letters. Does anyone have an example of adding a department logo/header image to the top of the page and/or bottom? i have zero latex knowledge so this maybe trivial :) best Z
Re: [O] jabref like orgmode based solution to bibliography management (not for latex)
Hi again Titus and list so the semester is finally nearing the end which means i finally have some time (and a life :)) to get back to what i partially started a few months ago. i have a question regarding Predefined searches. i have a search that works well for searching papers i authored. i am thinking of moving towards 2 bib files instead of 1 big one, that is one for my papers and one for the rest (any disadvantages of using 2 bib files?). i want to add in the Predefined search to only draw from my file (mypaper.bib), even though in the default helm-bibtex sources it will have 2 inputs. is such a thing possible? this is how a current search i have looks like #+BEGIN_SRC emacs-lisp :results none ;; Define helm-search with predefined search expression: (defun helm-bibtex-ikloog-publications () "Search BibTeX entries authored by me" (interactive) (helm :sources '(helm-source-bibtex) :full-frame t :input "kloog !unpublished !prep " :candidate-number-limit 500)) #+END_SRC how does one add the specific .bib file filter? best Z On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg wrote: > > On 2015-05-31 Sun 03:01, Xebar Saram wrote: > > Thanks so much everyone for these great replies. i will investigate this > > further today and let everyone know how im going with my transition :) > > > > thanks again > > > > PS: Titus, do you think that the helm-bibtex APA style reference list > > could be user customizable in the future? > > Depends on what you mean by customizable. If you mean a customization > option to allows you to replace the function for APA formatting with > another function, then yes that would definitely make sense. > > Titus > > > > > Z. > > > > On Sat, May 30, 2015 at 6:56 PM, John Kitchin > > wrote: > > > >> > >> > >> On Saturday, May 30, 2015, Titus von der Malsburg > >> wrote: > >> > >>> > >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote: > >>> > Hi all > >>> > > >>> > i have been using jabref for the past 2-4 years in my academia work > to > >>> > manage my reference library. i dont use latex (..its on my TODO > >>> list...when > >>> > (f ever) i have time..) so for now i just want something to manage my > >>> > references. the key things i need to move over from jabref are: > >>> > >>> Author of helm-bibtex here. > >>> > >>> > 1. easy add references > >>> > >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX > >>> file by hand. BibTeX retrieved from journals is almost always messy > and > >>> I need to edit it anyway. It’s not too hard, though: I click on BibTeX > >>> export on the journal page, the BibTeX file is opened in Emacs, I fix > >>> it, and use a command that appends it to my bibliography. > >>> > >>> However, I think org-ref has tools that do more to support importing > new > >>> entries and org-ref combines well with helm-bibtex. > >> > >> > >> Org-ref has doi-utils that let you add bibtex entries and download PDFs > >> from a doi or crossref query. > >> > >> > >>> > >>> > 2. a way to quick filter references (helm bibtex seems like a good > >>> solution) > >>> > >>> That’s what helm-bibtex was written to solve. > >>> > >>> > 3. filter lists based on tags/keywords (orgmode has that covered) > >>> > >>> In helm-bibtex you can also search for keywords and tags. > >>> > >>> > 4. this one is important: a way to quickly export selected > references in > >>> > word/odf/html based on a pre fixed style (ie Nature, Chicago etc) > >>> > >>> helm-bibtex can generate references in APA style but as far as I can > see > >>> Chicago style is very similar, so it shouldn’t be hard to add support > >>> for that. > >>> > >>> > anyone uses such a system in emacs/org and can recommend the way to > >>> > go? > >>> > >>> For more details, see: https://github.com/tmalsburg/helm-bibtex > >>> > >>> Titus > >>> > >>> > >> > >> -- > >> John > >> > >> --- > >> 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] Org mode export from a large file is slow since release 8.3
Hello, Viktor Rosenfeld writes: > I updated from 8.2.9 to 8.3.2 today and now the export has become very slow. > Creating an HTML page or a LaTeX buffer used to be instantaneous but now > takes up to 30 seconds. > > It seems that this is mostly related to file size. For example, > exporting a subtree from a large notes file (~8600 lines) is very slow > (11 seconds) but if I truncate the file significantly (to ~3000 lines) > the export is faster (<2 seconds), and if I move the subtree to > a fresh file (while still exporting the subtree only and not the file) > it is again instantaneous. > > It also seems that the maint branch has fixed this problem somewhat, although > I can’t really quantify it, but the problem persists. > > In the *Messages* buffer, I see a new message that hasn’t been there before: > > org-babel-exp process C at line 7982... > org-babel-exp process C at line 7998... > org-babel-exp process C at line 8024... > org-babel-exp process C at line 8064... > org-babel-exp process patch at line 8103... > org-babel-exp process patch at line 8119... > org-babel-exp process patch at line 8132... > org-babel-exp process patch at line 8148... > org-babel-exp process C at line 8179... > 30 unique files scanned for IDs [8 times] > > Curiously, after trying to debug this issue, the problem went away for > one file but persists for another. IIRC this was fixed in master a few weeks ago. The export process was scanning id:... links outside of the export scope. Regards, -- Nicolas Goaziou
Re: [O] footnote fontify causing massive slowdown
Hello, Derek Feichtinger writes: > While diagnosing a server condition, I was listing parts of a system log > via a babel expression. The 130 lines in the babel output are wrapped in > an example block. This block caused massive slowdown of scrolling and > other operations. > > Using the emacs profiler I see: > > - redisplay_internal (C function) 8232 88% > - jit-lock-function 8226 88% > - jit-lock-fontify-now 8226 88% >- funcall 8226 88% > - # 8226 88% > - run-hook-with-args 8226 88% > - font-lock-fontify-region 8226 88% >- font-lock-default-fontify-region 8226 88% > - font-lock-fontify-keywords-region 8226 88% > - org-activate-footnote-links 8158 87% > - org-footnote-next-reference-or-definition 8158 87% >- byte-code 8158 87% > - org-footnote-at-reference-p 4114 44% > - org-footnote-in-valid-context-p 4106 44% > + org-inside-LaTeX-fragment-p 2380 25% > + org-in-block-p 1563 16% > + org-in-verbatim-emphasis 159 1% > org-at-comment-p 4 0% > > Checking for footnote pattern matches (org-footnote-re) in the wrapped > block, I see that > every line matches based on the very simple and trivial pattern of > number enclosed in angular brackets, so all the process numbers > following the "sshd" in these lines like "sshd[1234]" do match and cause load. > > # > /var/log/secure-20151129:Nov 23 02:25:36 some-host sshd[20089]: Rhosts > authentication refused for userXYZ: bad ownership or modes for home directory. > /var/log/secure-20151129:Nov 23 02:25:36 some-host sshd[20089]: Rhosts > authentication refused for userXYZ: bad ownership or modes for home directory. > /var/log/secure-20151129:Nov 23 02:25:41 some-host sshd[20089]: > pam_ldap: error trying to bind as user "x" (Invalid credentials) > # > > Since this kind of pattern is so common in logs and 130 lines are really not > a large number, it makes it hard to use > org for this purpose. Can this be turned off selectively, or can it be > prevented in example blocks? This is a limitation of our current way to fontify a buffer. Changing it implies some serious work, which I'd rather spend on switching to syntax-based (instead of regexp-based) fontification. However, this report raises an interesting question about footnotes: should we still support plain (e.g., "[1]") footnotes in Org documents? The pattern is very common an regularly introduces false positives. Also, IIRC, it was introduced for non-Org buffers (e.g., in Message mode buffers), to provide some common features with "footnote.el" library. I think we could remove this kind of footnotes, and yet preserve `org-footnote-normalize' to change Org footnotes into these ones, for foreign documents. WDYT? Regards, -- Nicolas Goaziou
Re: [O] Issues w/ hacking Org font-lock for variable pitch prose
Hello, Göktuğ Kayaalp writes: > /I’ll first explain the situation and append the code to the message./ > Go to code: [ M-x re-search-forward RET ^CODE RET ] > > I read in Org mode a lot, and I dislike reading prose in monospace > fonts. So I have turned on ‘variable-pitch-mode’ for Org mode. But > because some stuff has to stay in stoichedon, so I set some faces to be > monospace: > > I have also add a keyword to font-lock keywords as part of the Org hook, > so that I can have a face attached to initial whitespace and lists (-, > and 1., 2. etc). I set this face to monospace too, so that I have nice > aligned left line, while the actual prose stays in variable pitch. > > I just updated today, from the default Org mode of Emacs 24.5 to the > latest release (8.3.2, from git). > > The problems are as follows: > > 1. My code is buggy, and I can’t understand why. With previous Org some > font-lock actions were happening only after I hit enter at the end of a > line, and if I have less than 3 newlines at the end of the file > sometimes font-locking of headings didn’t work. For example, if I’m > writing a paragraph, I write it in a single physical line, and I use > word wrapping. If that paragraph happended to contain an inline > footnote, which I use very often, that note is not highlighted until I > insert a line-feed. > > And with the new version, while the problem persists, when I hit enter, > thus inserting a newline at the end of a line, Emacs hangs up, and > sometimes I see this error: > > org-element--current-element: Wrong type argument: integer-or-marker-p, nil > ;; See end of message for the backtrace… > ;; [ M-x re-search-forward RET ^BACK RET ] Your code is probably not buggy. You are encountering a cache error. Does it happen on a fresh buffer (e.g., open a new buffer, and copy contents there, then let your code apply appropriate fontification)? Regards, -- Nicolas Goaziou
Re: [O] jabref like orgmode based solution to bibliography management (not for latex)
Try (untested) (defun helm-bibtex-ikloog-publications () "Search BibTeX entries authored by me" (interactive) (let ((helm-bibtex-bibliography "your special bibfile")) (helm :sources '(helm-source-bibtex) :full-frame t :input "kloog !unpublished !prep " :candidate-number-limit 500))) John --- 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 On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram wrote: > Hi again Titus and list > > so the semester is finally nearing the end which means i finally have some > time (and a life :)) to get back to what i partially started a few months > ago. > > i have a question regarding Predefined searches. i have a search that > works well for searching papers i authored. > i am thinking of moving towards 2 bib files instead of 1 big one, that is > one for my papers and one for the rest (any disadvantages of using 2 bib > files?). > i want to add in the Predefined search to only draw from my file > (mypaper.bib), > even though in the default helm-bibtex sources it will have 2 inputs. is > such a thing possible? > > this is how a current search i have looks like > > #+BEGIN_SRC emacs-lisp :results none > > ;; Define helm-search with predefined search expression: > (defun helm-bibtex-ikloog-publications () >"Search BibTeX entries authored by me" >(interactive) >(helm :sources '(helm-source-bibtex) > :full-frame t > :input "kloog !unpublished !prep " > :candidate-number-limit 500)) > #+END_SRC > > how does one add the specific .bib file filter? > > best > > Z > > On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg < > malsb...@posteo.de> wrote: > >> >> On 2015-05-31 Sun 03:01, Xebar Saram wrote: >> > Thanks so much everyone for these great replies. i will investigate this >> > further today and let everyone know how im going with my transition :) >> > >> > thanks again >> > >> > PS: Titus, do you think that the helm-bibtex APA style reference list >> > could be user customizable in the future? >> >> Depends on what you mean by customizable. If you mean a customization >> option to allows you to replace the function for APA formatting with >> another function, then yes that would definitely make sense. >> >> Titus >> >> > >> > Z. >> > >> > On Sat, May 30, 2015 at 6:56 PM, John Kitchin >> > wrote: >> > >> >> >> >> >> >> On Saturday, May 30, 2015, Titus von der Malsburg >> >> wrote: >> >> >> >>> >> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote: >> >>> > Hi all >> >>> > >> >>> > i have been using jabref for the past 2-4 years in my academia work >> to >> >>> > manage my reference library. i dont use latex (..its on my TODO >> >>> list...when >> >>> > (f ever) i have time..) so for now i just want something to manage >> my >> >>> > references. the key things i need to move over from jabref are: >> >>> >> >>> Author of helm-bibtex here. >> >>> >> >>> > 1. easy add references >> >>> >> >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX >> >>> file by hand. BibTeX retrieved from journals is almost always messy >> and >> >>> I need to edit it anyway. It’s not too hard, though: I click on >> BibTeX >> >>> export on the journal page, the BibTeX file is opened in Emacs, I fix >> >>> it, and use a command that appends it to my bibliography. >> >>> >> >>> However, I think org-ref has tools that do more to support importing >> new >> >>> entries and org-ref combines well with helm-bibtex. >> >> >> >> >> >> Org-ref has doi-utils that let you add bibtex entries and download PDFs >> >> from a doi or crossref query. >> >> >> >> >> >>> >> >>> > 2. a way to quick filter references (helm bibtex seems like a good >> >>> solution) >> >>> >> >>> That’s what helm-bibtex was written to solve. >> >>> >> >>> > 3. filter lists based on tags/keywords (orgmode has that covered) >> >>> >> >>> In helm-bibtex you can also search for keywords and tags. >> >>> >> >>> > 4. this one is important: a way to quickly export selected >> references in >> >>> > word/odf/html based on a pre fixed style (ie Nature, Chicago etc) >> >>> >> >>> helm-bibtex can generate references in APA style but as far as I can >> see >> >>> Chicago style is very similar, so it shouldn’t be hard to add support >> >>> for that. >> >>> >> >>> > anyone uses such a system in emacs/org and can recommend the way to >> >>> > go? >> >>> >> >>> For more details, see: https://github.com/tmalsburg/helm-bibtex >> >>> >> >>> Titus >> >>> >> >>> >> >> >> >> -- >> >> John >> >> >> >> --- >> >> 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] jabref like orgmode based solution to bibliography management (not for latex)
Hi John Thanks for the quick answer. this does seem to work but as a side effect seems to break the TAB key to select action the message window shows: helm-select-nth-action: Nothing is selected No Actions available [8 times] thx again Z On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin wrote: > Try (untested) > > (defun helm-bibtex-ikloog-publications () >"Search BibTeX entries authored by me" >(interactive) > (let ((helm-bibtex-bibliography "your special bibfile")) >(helm :sources '(helm-source-bibtex) > :full-frame t > :input "kloog !unpublished !prep " > :candidate-number-limit 500))) > > > > John > > --- > 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 > > > On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram wrote: > >> Hi again Titus and list >> >> so the semester is finally nearing the end which means i finally have >> some time (and a life :)) to get back to what i partially started a few >> months ago. >> >> i have a question regarding Predefined searches. i have a search that >> works well for searching papers i authored. >> i am thinking of moving towards 2 bib files instead of 1 big one, that is >> one for my papers and one for the rest (any disadvantages of using 2 bib >> files?). >> i want to add in the Predefined search to only draw from my file >> (mypaper.bib), >> even though in the default helm-bibtex sources it will have 2 inputs. is >> such a thing possible? >> >> this is how a current search i have looks like >> >> #+BEGIN_SRC emacs-lisp :results none >> >> ;; Define helm-search with predefined search expression: >> (defun helm-bibtex-ikloog-publications () >>"Search BibTeX entries authored by me" >>(interactive) >>(helm :sources '(helm-source-bibtex) >> :full-frame t >> :input "kloog !unpublished !prep " >> :candidate-number-limit 500)) >> #+END_SRC >> >> how does one add the specific .bib file filter? >> >> best >> >> Z >> >> On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg < >> malsb...@posteo.de> wrote: >> >>> >>> On 2015-05-31 Sun 03:01, Xebar Saram wrote: >>> > Thanks so much everyone for these great replies. i will investigate >>> this >>> > further today and let everyone know how im going with my transition :) >>> > >>> > thanks again >>> > >>> > PS: Titus, do you think that the helm-bibtex APA style reference list >>> > could be user customizable in the future? >>> >>> Depends on what you mean by customizable. If you mean a customization >>> option to allows you to replace the function for APA formatting with >>> another function, then yes that would definitely make sense. >>> >>> Titus >>> >>> > >>> > Z. >>> > >>> > On Sat, May 30, 2015 at 6:56 PM, John Kitchin >> > >>> > wrote: >>> > >>> >> >>> >> >>> >> On Saturday, May 30, 2015, Titus von der Malsburg >> > >>> >> wrote: >>> >> >>> >>> >>> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote: >>> >>> > Hi all >>> >>> > >>> >>> > i have been using jabref for the past 2-4 years in my academia >>> work to >>> >>> > manage my reference library. i dont use latex (..its on my TODO >>> >>> list...when >>> >>> > (f ever) i have time..) so for now i just want something to manage >>> my >>> >>> > references. the key things i need to move over from jabref are: >>> >>> >>> >>> Author of helm-bibtex here. >>> >>> >>> >>> > 1. easy add references >>> >>> >>> >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX >>> >>> file by hand. BibTeX retrieved from journals is almost always messy >>> and >>> >>> I need to edit it anyway. It’s not too hard, though: I click on >>> BibTeX >>> >>> export on the journal page, the BibTeX file is opened in Emacs, I fix >>> >>> it, and use a command that appends it to my bibliography. >>> >>> >>> >>> However, I think org-ref has tools that do more to support importing >>> new >>> >>> entries and org-ref combines well with helm-bibtex. >>> >> >>> >> >>> >> Org-ref has doi-utils that let you add bibtex entries and download >>> PDFs >>> >> from a doi or crossref query. >>> >> >>> >> >>> >>> >>> >>> > 2. a way to quick filter references (helm bibtex seems like a good >>> >>> solution) >>> >>> >>> >>> That’s what helm-bibtex was written to solve. >>> >>> >>> >>> > 3. filter lists based on tags/keywords (orgmode has that covered) >>> >>> >>> >>> In helm-bibtex you can also search for keywords and tags. >>> >>> >>> >>> > 4. this one is important: a way to quickly export selected >>> references in >>> >>> > word/odf/html based on a pre fixed style (ie Nature, Chicago etc) >>> >>> >>> >>> helm-bibtex can generate references in APA style but as far as I can >>> see >>> >>> Chicago style is very similar, so it shouldn’t be hard to add support >>> >>> for that. >>> >>> >>> >>> > anyone uses such a system in emacs/org and can recommen
Re: [O] jabref like orgmode based solution to bibliography management (not for latex)
I cannot reproduce that, and it shouldn't have any effect. Maybe something else is going on. > > Thanks for the quick answer. this does seem to work but as a side effect > seems to break the TAB key to select action > the message window shows: > > helm-select-nth-action: Nothing is selected > No Actions available [8 times] > > thx again > > Z > > On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin > wrote: > >> Try (untested) >> >> >> >> >> >> John >> >> --- >> 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 >> >> >> On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram wrote: >> >>> Hi again Titus and list >>> >>> so the semester is finally nearing the end which means i finally have >>> some time (and a life :)) to get back to what i partially started a few >>> months ago. >>> >>> i have a question regarding Predefined searches. i have a search that >>> works well for searching papers i authored. >>> i am thinking of moving towards 2 bib files instead of 1 big one, that is >>> one for my papers and one for the rest (any disadvantages of using 2 bib >>> files?). >>> i want to add in the Predefined search to only draw from my file >>> (mypaper.bib), >>> even though in the default helm-bibtex sources it will have 2 inputs. is >>> such a thing possible? >>> >>> this is how a current search i have looks like >>> >>> #+BEGIN_SRC emacs-lisp :results none >>> >>> ;; Define helm-search with predefined search expression: >>> (defun helm-bibtex-ikloog-publications () >>>"Search BibTeX entries authored by me" >>>(interactive) >>>(helm :sources '(helm-source-bibtex) >>> :full-frame t >>> :input "kloog !unpublished !prep " >>> :candidate-number-limit 500)) >>> #+END_SRC >>> >>> how does one add the specific .bib file filter? >>> >>> best >>> >>> Z >>> >>> On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg < >>> malsb...@posteo.de> wrote: >>> On 2015-05-31 Sun 03:01, Xebar Saram wrote: > Thanks so much everyone for these great replies. i will investigate this > further today and let everyone know how im going with my transition :) > > thanks again > > PS: Titus, do you think that the helm-bibtex APA style reference list > could be user customizable in the future? Depends on what you mean by customizable. If you mean a customization option to allows you to replace the function for APA formatting with another function, then yes that would definitely make sense. Titus > > Z. > > On Sat, May 30, 2015 at 6:56 PM, John Kitchin >>> > > wrote: > >> >> >> On Saturday, May 30, 2015, Titus von der Malsburg >>> > >> wrote: >> >>> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote: >>> > Hi all >>> > >>> > i have been using jabref for the past 2-4 years in my academia work to >>> > manage my reference library. i dont use latex (..its on my TODO >>> list...when >>> > (f ever) i have time..) so for now i just want something to manage my >>> > references. the key things i need to move over from jabref are: >>> >>> Author of helm-bibtex here. >>> >>> > 1. easy add references >>> >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX >>> file by hand. BibTeX retrieved from journals is almost always messy and >>> I need to edit it anyway. It’s not too hard, though: I click on BibTeX >>> export on the journal page, the BibTeX file is opened in Emacs, I fix >>> it, and use a command that appends it to my bibliography. >>> >>> However, I think org-ref has tools that do more to support importing new >>> entries and org-ref combines well with helm-bibtex. >> >> >> Org-ref has doi-utils that let you add bibtex entries and download PDFs >> from a doi or crossref query. >> >> >>> >>> > 2. a way to quick filter references (helm bibtex seems like a good >>> solution) >>> >>> That’s what helm-bibtex was written to solve. >>> >>> > 3. filter lists based on tags/keywords (orgmode has that covered) >>> >>> In helm-bibtex you can also search for keywords and tags. >>> >>> > 4. this one is important: a way to quickly export selected references in >>> > word/odf/html based on a pre fixed style (ie Nature, Chicago etc) >>> >>> helm-bibtex can generate references in APA style but as far as I can see >>> Chicago style is very similar, so it shouldn’t be hard to add support >>> for that. >>> >>> > anyone uses such a system in emacs/org and can recommend the way to >>> > go? >>> >>> For more details, s
Re: [O] [PATCH] org-protocol: Allow key=val&key2=value2-style URLs
Hi Sacha, Thanks for the patch. It looks great! I assume eventually we will want to deprecate the old-style links, and make new-style the only style. Unfortunately, this would mean another API change to remove the ‘new-style’ arguments from these functions. I don’t have any clever ideas to solve this, and it’s not an objection to your patch – just something I thought I’d mention in case someone can think of a way to deal with the eventual deprecation without an API change. A few comments below: 2015ko abenudak 4an, Sacha Chua-ek idatzi zuen: > From aff151930a73c22bb3fdf3ae9b442cecc08aaa67 Mon Sep 17 00:00:00 2001 > From: Sacha Chua > Date: Wed, 2 Dec 2015 10:53:07 -0500 > Subject: [PATCH] org-protocol: Allow key=val&key2=val2-style URLs > > * lisp/org-protocol.el: Update documentation. > (org-protocol-parse-parameters): New function to simplify handling of > old- or new-style links. > (org-protocol-assign-parameters): New function to simplify handling of > old- or new-style links. You can combine these like: (org-protocol-parse-parameters, org-protocol-assign-parameters): New functions. I also think the convention in Changelogs is not to put in details, but just to say “New function” or “Accept new-style links”. A narrative explanation can be put in the git commit message below the changelog section (and will not be included in the Changelog file distributed with Emacs). But I’ll admit I don’t understand Changelog conventions and think they are a pointless relic, so YMMV. [...] > > +(defun org-protocol-parse-parameters (info new-style &optional default-order > unhexify separator) Is there ever a case where we would want unhexify to be something other than t? Hexification is imposed by the URL format, there is no optionality about it. Handler functions get access to the raw string if they need it for some reason, I don’t think our helper functions need to bother with the unhexify != t case. Similarly, I would not have a separator argument, but use the value of ‘org-protocol-data-separator’ directly. In the rare case that a caller needs to influence the separator, they can let-bind that variable. TLDR: can we get rid of unhexify and separator arguments? [...] > (defun org-protocol-check-filename-for-protocol (fname restoffiles client) >[...docstring omitted...] >(let ((sub-protocols (append org-protocol-protocol-alist > org-protocol-protocol-alist-default))) > (catch 'fname > @@ -532,19 +604,27 @@ as filename." > (when (string-match the-protocol fname) >(dolist (prolist sub-protocols) > (let ((proto (concat the-protocol > - (regexp-quote (plist-get (cdr prolist) > :protocol)) ":/+"))) > + (regexp-quote (plist-get (cdr prolist) > :protocol)) "\\(:/+\\|\\?\\)"))) >(when (string-match proto fname) > (let* ((func (plist-get (cdr prolist) :function)) > (greedy (plist-get (cdr prolist) :greedy)) > (split (split-string fname proto)) > - (result (if greedy restoffiles (cadr split > + (result (if greedy restoffiles (cadr split))) > +(new-style (string= (match-string 1 fname) "?"))) As a way to encourage users to move to new-style links, should we add a warning if new-style = nil? Thanks again for the patch, -- Aaron Ecay
Re: [O] footnote fontify causing massive slowdown
Hi Nicolas, 2015ko abenudak 5an, Nicolas Goaziou-ek idatzi zuen: > > This is a limitation of our current way to fontify a buffer. Changing it > implies some serious work, which I'd rather spend on switching to > syntax-based (instead of regexp-based) fontification. Indeed. However, this code was needlessly slow because it failed to take advantage of short-circuit evaluation. I pushed a fix in 046310d. > > However, this report raises an interesting question about footnotes: > should we still support plain (e.g., "[1]") footnotes in Org documents? > > The pattern is very common an regularly introduces false positives. > Also, IIRC, it was introduced for non-Org buffers (e.g., in Message mode > buffers), to provide some common features with "footnote.el" library. > > I think we could remove this kind of footnotes, and yet preserve > `org-footnote-normalize' to change Org footnotes into these ones, for > foreign documents. > > WDYT? Do [1]-type footnotes present other performance problems today? I’d rather see if simple solutions to those can be effective before going for a breaking change to syntax. Then there’s the fact that syntax fontification (incl. org-elements cache) is going to have such different performance characteristics I’m not sure we can predict where the bottlenecks will be. -- Aaron Ecay
Re: [O] department logo/header image in koma/latex export?
On Saturday, 5 Dec 2015 at 12:16, Xebar Saram wrote:
> Hi all
>
> i am looking into using koma and orgmode to export to recommendation
> letters.
> Does anyone have an example of adding a department logo/header image to the
> top of the page and/or bottom?
You can redefined \firsthead and/or \firstfoot to whatever you want them
to be in your own LCO file for koma letters. For instance, I have the
following in my firsthead:
#+begin_src latex
\firsthead{%
~
\vspace*{1cm}\hspace*{-2cm}\includegraphics[width=\paperwidth]{/home/ucecesf/synced/cartas/ucl-line-logo}
\vspace*{-4cm}
\usekomavar{fromaddress}
\usekomavar{fromname}
}
#+end_src
> i have zero latex knowledge so this maybe trivial :)
Nontrivial with or without LaTeX knowledge...
My magical incantation above, requiring moving backwards in the page, is
because the UCL logo for letterheads is the full width of the page.
I specify the LCO to use in the org file with
#+lco: fraga
The other alternative in LaTeX is to use the textpos package which
allows you to place arbitrary text boxes anywhere on the page.
HTH,
eric
--
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.2-363-g5c13a6
Re: [O] [ANN] Radio lists update
Hi Nicolas, 2015ko abenudak 3an, Nicolas Goaziou-ek idatzi zuen: > > Hello, > > I just pushed a patch which should make radio lists on par with radio > tables. In particular, it fixes a long standing issue with > `org-list-to-generic' which was not really usable, and thus side-stepped > in every back-end transformer (e.g. `org-list-to-latex'). > > Internally `org-list-parse-list' is obsoleted in favor of > `org-list-to-lisp' (much like `org-table-to-lisp'), which is a simpler > representation of lists. It is now easier to define programmatically > a plain list. See docstring for details. > > Feedback welcome. It looks good. Thanks for your work. -- Aaron Ecay
Re: [O] syncing my life (orgmode :)) to a mobile (android) device..cant find a holistic reliable way..how do you guys manage to do it?
On Saturday, 5 Dec 2015 at 09:10, Xebar Saram wrote: [...] > all this is great yet i travel alot to conferences and meeting and do rely > on a mobile device (in my case a android nexus 6) in many situations. I > check my emails on it as much as i do on my PC, look at upcoming and > schedule appointments, look at timed TODOS, add new contacts i meet and > collect info on the go (web links, food recipes etc). > > Out of all the things i do only email (via offlineimap and mu4e) seems to > be able to Sync correctly. Yes, this is probably a valid summary of the current state of the art re: org and Android devices. > So my question is (sorry for the long intro :)) what do orgmode users (who > also are heavy mobile users) do? do they give up on contacts and > calendaring on the mobile? maintain 2 separate databases? what tools do > people use to overcome this issue? > > I once had a nokia n900 which ran basically Debian linux, and thus emacs > could be run naively , these days it seems like all are android devices. I > still haven't found a gui friendly way to run emacs there. I have two different working environments, depending on which mobile device I use: Case 1: if I use an Android device (nexus 4 or 7), I rely on mobileorg heavily to synchronise my calendar. I have mobileorg suck in any events I create in Google calendar and export all org events to Google. This works quite well. However, creating notes etc. on the mobile device in this case is not ideal as mobileorg is not a full implementation of org (and, to be fair, it wasn't intended to be). Although there is an emacs distribution for Android, I've never really managed to get it working satisfactorily, with or without a bluetooth keyboard. Android is a crippled Linux unfortunately... (in my opinion). In the end, I primarily use my nexus devices as phones (really?) and for facebook (as one must). Case 2: this is my preferred mobile solution. I have an OpenPandora palmtop computer [1] running the full Debian testing distribution with Emacs and the org from git, not to mention gnus, LaTeX, Libreoffice, Octave, ... The Pandora has WiFi and bluetooth but not 3/4G connectivity. I use my phone to tether the Pandora to the 'net when I need to connect outside a WiFi zone. In this case, the Pandora and my other systems are fully synchronised using unison. Finally, the Pandora has 2 full SD slots which allow me to walk around with 128 GB of disk space. I bought my Pandora specifically because I wanted a full org mobile experience! I am awaiting the release of the Pyra, the upgrade of the Pandora, very eagerly indeed! Oh, and the Pandora has a fantastic audio system :-) Sorry if I have come across as an advert for the Pandora but I am obviously a satisfied customer. HTH, eric Footnotes: [1] https://boards.openpandora.org/pandora/pandoramain.html/ -- : Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.2-363-g5c13a6
Re: [O] syncing my life (orgmode :)) to a mobile (android) device..cant find a holistic reliable way..how do you guys manage to do it?
Thx Eric I am also really looking forward to the new Pyra, im seriously considering buying it when it comes out :D it seems that that would be the easiest solution to orgmode on the go. shame i will have to carry 2 devices though, brings me back to the days of a crappy cell and a PDA :) best Z On Sat, Dec 5, 2015 at 4:08 PM, Eric S Fraga wrote: > On Saturday, 5 Dec 2015 at 09:10, Xebar Saram wrote: > > [...] > > > all this is great yet i travel alot to conferences and meeting and do > rely > > on a mobile device (in my case a android nexus 6) in many situations. I > > check my emails on it as much as i do on my PC, look at upcoming and > > schedule appointments, look at timed TODOS, add new contacts i meet and > > collect info on the go (web links, food recipes etc). > > > > Out of all the things i do only email (via offlineimap and mu4e) seems to > > be able to Sync correctly. > > Yes, this is probably a valid summary of the current state of the art > re: org and Android devices. > > > So my question is (sorry for the long intro :)) what do orgmode users > (who > > also are heavy mobile users) do? do they give up on contacts and > > calendaring on the mobile? maintain 2 separate databases? what tools do > > people use to overcome this issue? > > > > I once had a nokia n900 which ran basically Debian linux, and thus emacs > > could be run naively , these days it seems like all are android devices. > I > > still haven't found a gui friendly way to run emacs there. > > I have two different working environments, depending on which mobile > device I use: > > Case 1: if I use an Android device (nexus 4 or 7), I rely on mobileorg > heavily to synchronise my calendar. I have mobileorg suck in any > events I create in Google calendar and export all org events to > Google. This works quite well. However, creating notes etc. on the > mobile device in this case is not ideal as mobileorg is not a full > implementation of org (and, to be fair, it wasn't intended to be). > > Although there is an emacs distribution for Android, I've never really > managed to get it working satisfactorily, with or without a bluetooth > keyboard. Android is a crippled Linux unfortunately... (in my opinion). > > In the end, I primarily use my nexus devices as phones (really?) and for > facebook (as one must). > > Case 2: this is my preferred mobile solution. I have an OpenPandora > palmtop computer [1] running the full Debian testing distribution with > Emacs and the org from git, not to mention gnus, LaTeX, Libreoffice, > Octave, ... The Pandora has WiFi and bluetooth but not 3/4G > connectivity. I use my phone to tether the Pandora to the 'net when I > need to connect outside a WiFi zone. In this case, the Pandora and my > other systems are fully synchronised using unison. Finally, the Pandora > has 2 full SD slots which allow me to walk around with 128 GB of disk > space. > > I bought my Pandora specifically because I wanted a full org mobile > experience! I am awaiting the release of the Pyra, the upgrade of the > Pandora, very eagerly indeed! > > Oh, and the Pandora has a fantastic audio system :-) > > Sorry if I have come across as an advert for the Pandora but I am > obviously a satisfied customer. > > HTH, > eric > > > Footnotes: > [1] https://boards.openpandora.org/pandora/pandoramain.html/ > > -- > : Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.2-363-g5c13a6 >
[O] problems with tex4ht and SVG images
Hello, just a heads up for those that may run into the same problem I have. If you try to use babel with LaTeX to create an SVG file, and if you have texlive 2014 installed, you may run into errors like this: , | ! Undefined control sequence. | \pgfsys@svg@newline ->\Hnewline | | l.190 \pgfusepathqfill} ` This is due to a bug introduced in texlive 2014, as described here: http://tex.stackexchange.com/questions/185349/error-using-pgfsysdriver-with-tex4ht-only-shows-up-with-texlive-2014-ok-with-t The problem is not with org. -- : Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.2, Org release_8.3.2-363-g5c13a6
Re: [O] footnote fontify causing massive slowdown
Hello, Aaron Ecay writes: > Indeed. However, this code was needlessly slow because it failed to > take advantage of short-circuit evaluation. According to the profile report, I don't understand the logic of your patch. >>> - org-footnote-in-valid-context-p 4106 44% >>> + org-inside-LaTeX-fragment-p 2380 25% >>> + org-in-block-p 1563 16% >>> + org-in-verbatim-emphasis 159 1% ISTM that `org-in-block-p' is marginally slower (15%) than `org-inside-LaTeX-fragment-p' (9%). Of course, in OP's report, `org-in-block-p' is the test returning early, so pushing it earlier is faster since you don't call `org-inside-LaTeX-fragment-p', but this is only a very specific optimization made at the expense of other cases (and contradicts your commit message). Am I missing something? I don't understand either the benefit of adding `not' calls all over the place. I generally use de Morgan's law the other way and save a few primcalls. > Do [1]-type footnotes present other performance problems today? The main problem of plain footnotes isn't really their performance, but false positives'. Anytime something looks like a footnote in a buffer, you get a performance hit. This happens much more often with plain footnotes than with other footnote types. Moreover, false positives can introduce not-so-subtle problems during export (see for example 2c66e40c). Note that suggesting to not use them (the default value, actually, per `org-footnote-auto-label') doesn't help, since false positives are the problem, not real footnotes. Eventually, removing them doesn't remove any feature to Org. Of course, this is an incompatible change, and some users will need to update documents using plain footnotes. We can provide a function for that, and use `org-lint' to check for obsolete footnotes. The benefit is to avoid a whole class of problems. Regards, -- Nicolas Goaziou
Re: [O] footnote fontify causing massive slowdown
Hi Nicolas, 2015ko abenudak 5an, Nicolas Goaziou-ek idatzi zuen: > > Hello, > > Aaron Ecay writes: > >> Indeed. However, this code was needlessly slow because it failed to >> take advantage of short-circuit evaluation. > > According to the profile report, I don't understand the logic of your > patch. > - org-footnote-in-valid-context-p 4106 44% + org-inside-LaTeX-fragment-p 2380 25% + org-in-block-p 1563 16% + org-in-verbatim-emphasis 159 1% > > ISTM that `org-in-block-p' is marginally slower (15%) than > `org-inside-LaTeX-fragment-p' (9%). I’m not sure where 15 and 9 come from. The way I read the report, org-footnote-in-valid-context-p takes 44% of the cumulative time, which is composed of org-inside-LaTeX-fragment-p (25%) + org-in-block-p (16%) + other stuff (3%). So org-inside-LaTeX-fragment-p accounts for >50% of the time spent in org-footnote-in-valid-context-p. > > Of course, in OP's report, `org-in-block-p' is the test returning early, > so pushing it earlier is faster since you don't call > `org-inside-LaTeX-fragment-p', but this is only a very specific > optimization made at the expense of other cases (and contradicts your > commit message). Am I missing something? ...no, you’re not missing anything. I looked at my patch again, and it seems completely dumb. I should not write code before finishing my morning cup of tea. I reverted in a198d81. > > I don't understand either the benefit of adding `not' calls all over the > place. I generally use de Morgan's law the other way and save a few > primcalls. > >> Do [1]-type footnotes present other performance problems today? > > The main problem of plain footnotes isn't really their performance, but > false positives'. Anytime something looks like a footnote in a buffer, > you get a performance hit. This happens much more often with plain > footnotes than with other footnote types. > > Moreover, false positives can introduce not-so-subtle problems during > export (see for example 2c66e40c). > > Note that suggesting to not use them (the default value, actually, per > `org-footnote-auto-label') doesn't help, since false positives are the > problem, not real footnotes. > > Eventually, removing them doesn't remove any feature to Org. Of course, > this is an incompatible change, and some users will need to update > documents using plain footnotes. We can provide a function for that, and > use `org-lint' to check for obsolete footnotes. The benefit is to avoid > a whole class of problems. I see. Eventually it sounds like a good idea, indeed. Maybe we should use something a bit stronger than org-lint to warn of the deprecation. What if opening a document with plain footnotes generated a warning? Thanks, -- Aaron Ecay
[O] Proposal and RFC for improving ob-python
Hello,
I've been playing around with the Org-mode Babel framework and I am
grateful to all the contributors for making this wonderful library. After
some time I noticed that Python support seems a little hacky and
inconsistent and after reading through ob-python.el and consulting Python
documentation I came up with a proposal for improving it.
The ob-ipython project tries to solve this hackiness in a different way by
using the client-server infrastructure of IPython/Jupyter. That works quite
well too, but my hope is that improving ob-python.el would also make it
simpler to use IPython as the python REPL, relying only on the core of the
Python language.
It essentially boils down to implementing progn-like eval() function in
Python which would return the result of the last statement if it is an
expression. I have come up with a prototype of such a function by diving
into Python scope internals and its AST capabilities. It was written using
Org-mode and tangling so it is thoroughly documented and explained, a test
suite is included. This interesting exercise made me appreciate Lisp even
more. Here it is
https://github.com/smartass101/python_block_eval
I haven't licensed it yet, because I'm not sure what license would be
appropriate if it was used by org-mode. Any suggestions?
My proposal is to implement an equivalent of the following bash pseudo code
for non session mode
python -i << HEREDOC_END
ret = block_eval("""
""")
open().write(str(ret))
HEREDOC_END
For session mode it would be even simpler, lines containing HEREDOC above
would be dropped and the rest piped directly into the Python REPL.
This also means that the 'org_babel_python_eoe' string indicator may not be
necessary anymore because end of evaluation would be simply shown by a new
line with the primary prompt appearing.
The reason why `python -i` (force interactive mode) is used is the IMHO
poor design choice in the CPython implementation (and other implementations
have a similar issue AFAIK) to have fast but RO access to local variable
scope in non-top-level (i.e. functions calling functions) frames/scopes. I
tried to hack my way around it in the update_locals_after_eval branch of my
repo to no avail, perhaps some Pythonista among you may know a solution.
I also favor piping input into `python -i` because it means that a
temporary file does not have to be created.
As explained in the README.org in my repo, this inconsistency can be worked
around by explicitly first evaluating the side-effect-only part of the
block and than the last expression with a direct eval() call for each. This
makes it longer by 2 lines, but has the advantage of properly handling
variable scope and separating side-effects, which could be used to e.g.
suppress output. Nevertheless, I think that for Org-mode Babel usage the
`python -i` and block_eval() approach suffices, unless someone finds a way
to use the advantages of the alternative approach to improve ob-python.el
even further.
I'm not a skilled Elisp programmer, so I wanted to ask around as to the
feasibility of this endeavor or possibly availability of helping hands
before I devote more time to this.
Kind regards,
Ondřej Grover
Re: [O] syncing my life (orgmode :)) to a mobile (android) device..cant find a holistic reliable way..how do you guys manage to do it?
On Sat, 5 Dec 2015 14:08:19 + Eric S Fraga wrote: > Case 2: this is my preferred mobile solution. I have an OpenPandora > palmtop computer [1] running the full Debian testing distribution with > Oh, and the Pandora has a fantastic audio system :-) > > Sorry if I have come across as an advert for the Pandora but I am > obviously a satisfied customer. > > HTH, > eric > > > Footnotes: > [1] https://boards.openpandora.org/pandora/pandoramain.html/ > Hi Eric, Do you not find pandora too slow to run Emacs? My Asus EEEPC with celeron 900 MHz takes over a minute to generate agenda with 100-150 kB of org files, not too complicated. Exporting to HTML too takes minutes for 30 kB org file. My guess is that 1GHz ARM of pandora should be much slower than this. Do you have some trick up your sleeve to speed it up, or do you make do with slow pandora? Have you hacked it to increase memory? thanks
Re: [O] jabref like orgmode based solution to bibliography management (not for latex)
John’s code should do the trick. I don’t see how this could possibly cause your problems with the action menu. The change should be completely transparent for Helm. Regarding your other question: I don’t see any disadvantages of using several BibTeX files but I also don’t see an advantage because helm-bibtex gives you all you need to select your own publications with just a few key strokes. If helm-bibtex’ search does not work well in your case (perhaps another author has the same name as you), I would suggest using tags to mark your own publications: https://github.com/tmalsburg/helm-bibtex#tagging-publications Titus On 2015-12-05 Sat 05:31, John Kitchin wrote: > I cannot reproduce that, and it shouldn't have any effect. Maybe > something else is going on. > >> >> Thanks for the quick answer. this does seem to work but as a side effect >> seems to break the TAB key to select action >> the message window shows: >> >> helm-select-nth-action: Nothing is selected >> No Actions available [8 times] >> >> thx again >> >> Z >> >> On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin >> wrote: >> >>> Try (untested) >>> >>> >>> >>> >>> >>> John >>> >>> --- >>> 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 >>> >>> >>> On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram wrote: >>> Hi again Titus and list so the semester is finally nearing the end which means i finally have some time (and a life :)) to get back to what i partially started a few months ago. i have a question regarding Predefined searches. i have a search that works well for searching papers i authored. i am thinking of moving towards 2 bib files instead of 1 big one, that is one for my papers and one for the rest (any disadvantages of using 2 bib files?). i want to add in the Predefined search to only draw from my file (mypaper.bib), even though in the default helm-bibtex sources it will have 2 inputs. is such a thing possible? this is how a current search i have looks like #+BEGIN_SRC emacs-lisp :results none ;; Define helm-search with predefined search expression: (defun helm-bibtex-ikloog-publications () "Search BibTeX entries authored by me" (interactive) (helm :sources '(helm-source-bibtex) :full-frame t :input "kloog !unpublished !prep " :candidate-number-limit 500)) #+END_SRC how does one add the specific .bib file filter? best Z On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg < malsb...@posteo.de> wrote: > > On 2015-05-31 Sun 03:01, Xebar Saram wrote: > > Thanks so much everyone for these great replies. i will investigate > this > > further today and let everyone know how im going with my transition :) > > > > thanks again > > > > PS: Titus, do you think that the helm-bibtex APA style reference list > > could be user customizable in the future? > > Depends on what you mean by customizable. If you mean a customization > option to allows you to replace the function for APA formatting with > another function, then yes that would definitely make sense. > > Titus > > > > > Z. > > > > On Sat, May 30, 2015 at 6:56 PM, John Kitchin > > > wrote: > > > >> > >> > >> On Saturday, May 30, 2015, Titus von der Malsburg > > >> wrote: > >> > >>> > >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote: > >>> > Hi all > >>> > > >>> > i have been using jabref for the past 2-4 years in my academia > work to > >>> > manage my reference library. i dont use latex (..its on my TODO > >>> list...when > >>> > (f ever) i have time..) so for now i just want something to manage > my > >>> > references. the key things i need to move over from jabref are: > >>> > >>> Author of helm-bibtex here. > >>> > >>> > 1. easy add references > >>> > >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX > >>> file by hand. BibTeX retrieved from journals is almost always messy > and > >>> I need to edit it anyway. It’s not too hard, though: I click on > BibTeX > >>> export on the journal page, the BibTeX file is opened in Emacs, I fix > >>> it, and use a command that appends it to my bibliography. > >>> > >>> However, I think org-ref has tools that do more to support importing > new > >>> entries and org-ref combines well with helm-bibtex. > >> > >> > >> Org-ref has doi-utils that let you add bibtex entries and download > PDFs > >> from a doi or crossref query. > >> > >> > >>> > >
Re: [O] jabref like orgmode based solution to bibliography management (not for latex)
Hi Guys I have no clue why i had the issue before but after an emacs restart Johns code snippet does work :D thanks again guys, really appreciate your help as always kind regards Z On Sat, Dec 5, 2015 at 8:04 PM, Titus von der Malsburg wrote: > > John’s code should do the trick. I don’t see how this could possibly > cause your problems with the action menu. The change should be > completely transparent for Helm. > > Regarding your other question: I don’t see any disadvantages of using > several BibTeX files but I also don’t see an advantage because > helm-bibtex gives you all you need to select your own publications with > just a few key strokes. If helm-bibtex’ search does not work well in > your case (perhaps another author has the same name as you), I would > suggest using tags to mark your own publications: > > https://github.com/tmalsburg/helm-bibtex#tagging-publications > > Titus > > > On 2015-12-05 Sat 05:31, John Kitchin wrote: > > I cannot reproduce that, and it shouldn't have any effect. Maybe > > something else is going on. > > > >> > >> Thanks for the quick answer. this does seem to work but as a side effect > >> seems to break the TAB key to select action > >> the message window shows: > >> > >> helm-select-nth-action: Nothing is selected > >> No Actions available [8 times] > >> > >> thx again > >> > >> Z > >> > >> On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin > >> wrote: > >> > >>> Try (untested) > >>> > >>> > >>> > >>> > >>> > >>> John > >>> > >>> --- > >>> 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 > >>> > >>> > >>> On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram wrote: > >>> > Hi again Titus and list > > so the semester is finally nearing the end which means i finally have > some time (and a life :)) to get back to what i partially started a > few > months ago. > > i have a question regarding Predefined searches. i have a search that > works well for searching papers i authored. > i am thinking of moving towards 2 bib files instead of 1 big one, > that is > one for my papers and one for the rest (any disadvantages of using 2 > bib > files?). > i want to add in the Predefined search to only draw from my file > (mypaper.bib), > even though in the default helm-bibtex sources it will have 2 inputs. > is > such a thing possible? > > this is how a current search i have looks like > > #+BEGIN_SRC emacs-lisp :results none > > ;; Define helm-search with predefined search expression: > (defun helm-bibtex-ikloog-publications () > "Search BibTeX entries authored by me" > (interactive) > (helm :sources '(helm-source-bibtex) > :full-frame t > :input "kloog !unpublished !prep " > :candidate-number-limit 500)) > #+END_SRC > > how does one add the specific .bib file filter? > > best > > Z > > On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg < > malsb...@posteo.de> wrote: > > > > > On 2015-05-31 Sun 03:01, Xebar Saram wrote: > > > Thanks so much everyone for these great replies. i will investigate > > this > > > further today and let everyone know how im going with my > transition :) > > > > > > thanks again > > > > > > PS: Titus, do you think that the helm-bibtex APA style reference > list > > > could be user customizable in the future? > > > > Depends on what you mean by customizable. If you mean a > customization > > option to allows you to replace the function for APA formatting with > > another function, then yes that would definitely make sense. > > > > Titus > > > > > > > > Z. > > > > > > On Sat, May 30, 2015 at 6:56 PM, John Kitchin < > jkitc...@andrew.cmu.edu > > > > > > wrote: > > > > > >> > > >> > > >> On Saturday, May 30, 2015, Titus von der Malsburg < > malsb...@posteo.de > > > > > >> wrote: > > >> > > >>> > > >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote: > > >>> > Hi all > > >>> > > > >>> > i have been using jabref for the past 2-4 years in my academia > > work to > > >>> > manage my reference library. i dont use latex (..its on my TODO > > >>> list...when > > >>> > (f ever) i have time..) so for now i just want something to > manage > > my > > >>> > references. the key things i need to move over from jabref are: > > >>> > > >>> Author of helm-bibtex here. > > >>> > > >>> > 1. easy add references > > >>> > > >>> Helm-bibtex doesn’t deal with this because I prefer to edit my > BibTeX > > >>> file by hand. BibTeX retrieved from journals is almost al
Re: [O] syncing my life (orgmode :)) to a mobile (android) device..cant find a holistic reliable way..how do you guys manage to do it?
Xebar Saram writes: > > So my question is (sorry for the long intro :)) what do orgmode users > (who also are heavy mobile users) do? do they give up on contacts and > calendaring on the mobile? maintain 2 separate databases? what tools > do people use to overcome this issue? There are lots of way to sync calendars. See http://orgmode.org/worg/org-tutorials/org-google-sync.html I've found the easiest method is a "poor man's sync" involving a read-only ics file (exported from org using the org-icalendar-* functions) and a writable calendar for new entries. (Trying to map org entries to ics entries gets messy.) The flow looks something like this: writable calendar (remote calendar for adding new items from android) > org files (with new entries pull from remote calendar) > read-only calendar (remote ics exported from org) I use a radicale server[fn:1] for this. Radicale has the advantage of using ics files as a backend (rather than a database), so I can pull new entries into org with Eric's ical2org.awk. If you use google calendar you could accomplish something similar with the following workflow: a) Export your org data to an ics file and put it in dropbox. In dropbox, grab a secret link to share that file. b) Point google calendar to the secret link. This will create a read-only calendar in google calendar. c) Script a tool like gcalcli[fn:2] to pull and delete new items from a writable google calendar. Convert the data to org markup and add them to an org file. (This is the part that will involve just a bit of basic shell scripting.) For syncing contacts from BBDB to google or carddav, asynk works well.[fn:3] > I once had a nokia n900 which ran basically Debian linux, and thus > emacs could be run naively , these days it seems like all are android > devices. I still haven't found a gui friendly way to run emacs there. For fun (but not much profit) you can set up a chroot linux environment on a rooted android device and install all your favorite software (emacs, org, etc.). See https://github.com/guardianproject/lildebi for instance. By far the easiest way to access org mode is to set up some sort of ssh access to a computer running emacs. There are several good ssh clients for android. The hacker's keyboard app offers all the familiar modifier keys (Ctrl, Alt, etc.) Footnotes: [fn:1] http://radicale.org/ [fn:2] https://github.com/insanum/gcalcli [fn:3] http://asynk.io/
Re: [O] Citation processing via Zotero + zotxt
Hi John, John Kitchin writes: > If a reference type is not listed in the CSL, it also will not be > supported by CSL I suppose. How is this different than biblatex or bibtex? A user could just modify the style or put in a request with a maintainer. > I also suppose the CSL must be backend specific to output formats > appropriate to org, html, LaTeX, markdown, etc... for any particular > style. AFAIU, CSL styles are backend agnostic (otherwise they wouldn't be of much use). It is the processor (citeproc-js, pandoc, etc.) that takes the instructions (e.g., font-style="italic" in a CSL file) and adds the appropriate markup for a defined backend. So once you add a new output format to a processor, it works with all styles. > We should not try to support all of these things. We could support a > small number of things that could be improved or increased in the > future. I would suggest that tapping into a CSL tool like zotero of citeproc-js is in fact *a small thing* we can do right now that would have a big payoff for lots of users, even if it does not support 100% of use cases. > The only time-tested, publication quality solutions for citations in > my opinion right now are bib(la)tex, MS Word/reference manager, and > "by hand". Even these get "edited" in their final print versions by > journals. Is this assessment based on your particular disciplinary experience? I ask because many of us in the humanities have not enjoyed the benefits of automated, text-based citation processing until quite recently, so *both* biblatex and CSL seem awesome. The citation style in my field (the Chicago Manual of Style) is more quirky and complex than any scientific citation style. Thus, it is likely more feasible to implement basic bibtex functionality in lisp than it is to re-implement biblatex-chicago.[fn:1] CSL offers the advantage of allowing export to backends that can easily be converted to Word (the format that humanities publishers require). > It might start making more sense to think of a lisp based citation > processor. It might even address some limitations of bib(la)tex. That would be very cool, especially if we could import/convert CSL files (I don't want to rewrite all 1200+ lines of the chicago-fullnote-bibliography CSL style). :) Matt Footnotes: [fn:1] I cloned the CSL repository and did a quick sort by word count. Not surprisingly, the longest files were all in the humanities: 1296 270044202 chicago-fullnote-bibliography-fr.csl 1273 259040935 chicago-fullnote-bibliography.csl 1264 257640674 chicago-fullnote-bibliography-no-ibid.csl 1241 253139515 chicago-library-list.csl 1241 253039535 chicago-annotated-bibliography.csl 1240 252439445 chicago-note-bibliography.csl 1235 250640168 zeitschrift-fur-religionswissenschaft-note.csl 1227 250839077 chicago-note-biblio-no-ibid.csl 1132 262041990 mcgill-fr.csl 1060 214934008 moorlands-college.csl 998 217534470 lluelles.csl 927 206631551 lluelles-no-ibid.csl 911 186229828 proinflow.csl 906 196128990 irish-historical-studies.csl 878 182829238 universite-laval-faculte-de-theologie-et-de-sciences-religieuses.csl 862 183029437 chicago-author-date-fr.csl 856 178228244 oxford-studies-in-ancient-philosophy.csl 809 194127717 university-college-dublin-school-of-history-and-archives.csl 809 179626790 turabian-fullnote-bibliography.csl 806 185727140 wheaton-college-phd-in-biblical-and-theological-studies.csl 796 179126472 modern-language-association-6th-edition-note.csl 793 167126453 sheffield-hallam-university-history.csl 792 191030773 pour-reussir-note.csl 788 179226377 svensk-exegetisk-arsbok.csl 781 178226316 early-christianity.csl 779 177226038 society-of-biblical-literature-fullnote-bibliography.csl 775 180826461 new-testament-studies.csl 768 235029928 clio-medica.csl 714 153322993 iso690-author-date-cs.csl 708 157825548 chicago-author-date-basque.csl 708 152022731 iso690-author-date-sk.csl 707 160524582 melbourne-school-of-theology.csl 701 153322280 moore-theological-college.csl 696 175625783 associacao-brasileira-de-normas-tecnicas-ufjf.csl 694 14749 podzemna-voda.csl 692 231529639 foerster-geisteswissenschaft.csl 692 159124881 oscola.csl
Re: [O] footnote fontify causing massive slowdown
On 05/12/15 23:58, Nicolas Goaziou wrote: Hello, Derek Feichtinger writes: While diagnosing a server condition, I was listing parts of a system log via a babel expression. The 130 lines in the babel output are wrapped in an example block. This block caused massive slowdown of scrolling and other operations. Using the emacs profiler I see: - redisplay_internal (C function) 8232 88% - jit-lock-function 8226 88% - jit-lock-fontify-now 8226 88% - funcall 8226 88% - # 8226 88% - run-hook-with-args 8226 88% - font-lock-fontify-region 8226 88% - font-lock-default-fontify-region 8226 88% - font-lock-fontify-keywords-region 8226 88% - org-activate-footnote-links 8158 87% - org-footnote-next-reference-or-definition 8158 87% - byte-code 8158 87% - org-footnote-at-reference-p 4114 44% - org-footnote-in-valid-context-p 4106 44% + org-inside-LaTeX-fragment-p 2380 25% + org-in-block-p 1563 16% + org-in-verbatim-emphasis 159 1% org-at-comment-p 4 0% Checking for footnote pattern matches (org-footnote-re) in the wrapped block, I see that every line matches based on the very simple and trivial pattern of number enclosed in angular brackets, so all the process numbers following the "sshd" in these lines like "sshd[1234]" do match and cause load. # /var/log/secure-20151129:Nov 23 02:25:36 some-host sshd[20089]: Rhosts authentication refused for userXYZ: bad ownership or modes for home directory. /var/log/secure-20151129:Nov 23 02:25:36 some-host sshd[20089]: Rhosts authentication refused for userXYZ: bad ownership or modes for home directory. /var/log/secure-20151129:Nov 23 02:25:41 some-host sshd[20089]: pam_ldap: error trying to bind as user "x" (Invalid credentials) # Since this kind of pattern is so common in logs and 130 lines are really not a large number, it makes it hard to use org for this purpose. Can this be turned off selectively, or can it be prevented in example blocks? This is a limitation of our current way to fontify a buffer. Changing it implies some serious work, which I'd rather spend on switching to syntax-based (instead of regexp-based) fontification. However, this report raises an interesting question about footnotes: should we still support plain (e.g., "[1]") footnotes in Org documents? The pattern is very common an regularly introduces false positives. Also, IIRC, it was introduced for non-Org buffers (e.g., in Message mode buffers), to provide some common features with "footnote.el" library. I think we could remove this kind of footnotes, and yet preserve `org-footnote-normalize' to change Org footnotes into these ones, for foreign documents. WDYT? Regards, I would be delighted to see the 'plain' footnote format abolished. I use org for writing legal text which often has things like Bank of New South Wales v Laing [1954] AC 135. Rasmus helped me with a patch to ignore these kinds of references, but they remain a nuisance. Special case, I know, but +1 for getting rid of the things. Cheers, Alan -- Alan L Tyreehttp://www2.austlii.edu.au/~alan Tel: 04 2748 6206 sip:typh...@iptel.org
Re: [O] footnote fontify causing massive slowdown
Alan L Tyree writes: > I would be delighted to see the 'plain' footnote format abolished. I > use org for writing legal text which often has things like Bank of New > South Wales v Laing [1954] AC 135. Rasmus helped me with a patch to > ignore these kinds of references, but they remain a nuisance. > > Special case, I know, but +1 for getting rid of the things. +1 here as well. A lot of text I clip from the web has numbers in brackets. Matt
Re: [O] Citation processing via Zotero + zotxt
Matt Lundin writes:
> Hi John,
>
> John Kitchin writes:
>
>> If a reference type is not listed in the CSL, it also will not be
>> supported by CSL I suppose.
>
> How is this different than biblatex or bibtex? A user could just modify
> the style or put in a request with a maintainer.
Its not different. Just to point out CSL has limitations too.
>> I also suppose the CSL must be backend specific to output formats
>> appropriate to org, html, LaTeX, markdown, etc... for any particular
>> style.
>
> AFAIU, CSL styles are backend agnostic (otherwise they wouldn't be of
> much use). It is the processor (citeproc-js, pandoc, etc.) that takes
> the instructions (e.g., font-style="italic" in a CSL file) and adds the
> appropriate markup for a defined backend. So once you add a new output
> format to a processor, it works with all styles.
I believe that. I still don't totally see where font-style="italic" gets
converted to /text/ or text or \it{text} etc... I trust it
happens, I just don't see it. Where does one do something fancier like:
text
It sounds trivial, but imagine a day when we all have an orcid, and our
names are linked to our orcid pages in bibliographies, e.g. my name
would be http://orcid.org/-0003-2625-9232";>J. R.
Kitchin or some other format.
See this highly linked bibliography:
http://kitchingroup.cheme.cmu.edu/dept-publications-2014.html
Where almost every part of each entry is linked to something (true to
some stuff that is behind a paywall, but lets not get distracted by
that). Is that something a CSL/citation processor could do? These aren't
reasons not to do CSL, and they aren't mission critical to citations.
They just make them richer and more useful. And to be fair, the
information these pieces are linked to came from a bibliographic record
from Scopus, not a bibtex file I maintain, which only has a doi in it to
access that information.
Clearly I still don't see how a cite-processor actually works. I gather
that
1. you extract citation data from a document.
2. send citation data, style and bibliography data to the citation
processor
3. It returns replacement text, and the bibliography string
4. you substitute the replacements in the text and insert the
bibliography string somewhere.
If the CSL doesn't have the backend information, and the citation
processor doesn't know about org/html/etc... then somewhere between step
3 and 4 you add the formatting right? Does the processor get another
piece of information to tell it how to format the output? For example,
if your CSL says a citation should be superscripted, how does the
citation processor know to output 4 vs. $^4$? or ^{4}.
>> We should not try to support all of these things. We could support a
>> small number of things that could be improved or increased in the
>> future.
>
> I would suggest that tapping into a CSL tool like zotero of citeproc-js
> is in fact *a small thing* we can do right now that would have a big
> payoff for lots of users, even if it does not support 100% of use
> cases.
I have no objection to it. Getting high quality references into Word
documents from org-mode is one barrier to convincing more people
org-mode is a competitive writing tool for publications in my mind.
Clearly we need an external program for this. I looked at pandoc before
http://kitchingroup.cheme.cmu.edu/blog/2015/01/29/Export-org-mode-to-docx-with-citations-via-pandoc/
and it was ok, but had some issues getting to Word with citations.
Would zotero or citeproc-js be any better?
>> The only time-tested, publication quality solutions for citations in
>> my opinion right now are bib(la)tex, MS Word/reference manager, and
>> "by hand". Even these get "edited" in their final print versions by
>> journals.
>
> Is this assessment based on your particular disciplinary experience?
Certainly ;) Those have met 100% of my needs, and about 10% of my
desires in scientific publishing for the past 15 years. org-ref now
meets 99.9% of my desires ;)
Also, by time-tested, I mean I have published papers by those methods
specifically, so I know they work (including using org-mode to make
bibtex/latex files). I have not published any papers using org mode with
export to Word, so I don't know if it is possible to do it. The final
details of formatting may prove too difficult in some cases for direct
export.
> I
> ask because many of us in the humanities have not enjoyed the benefits
> of automated, text-based citation processing until quite recently, so
> *both* biblatex and CSL seem awesome.
So even Word/Endnote\|Papers\|Zotero has not been a
citation/bibliography solution?
>The citation style in my field
> (the Chicago Manual of Style) is more quirky and complex than any
> scientific citation style. Thus, it is likely more feasible to implement
> basic bibtex functionality in lisp than it is to re-implement
> biblatex-chicago.[fn:1] CSL offers the advantage of allowing export to
> backends that can easily be converted to Word (the format that
> hu
Re: [O] Issues w/ hacking Org font-lock for variable pitch prose
Hello, On Sat, Dec 05 2015 at 03:05:38 PM, Nicolas Goaziou wrote: > Hello, > > Göktuğ Kayaalp writes: > >> […] > > Your code is probably not buggy. You are encountering a cache error. > Does it happen on a fresh buffer (e.g., open a new buffer, and copy > contents there, then let your code apply appropriate fontification)? > When I copied the contents of a file to a fresh buffer, then run M-x org-mode in it, the last heading and its contents didn’t get fontified, and I got this error (the last entry was a level-1 entry): Error during redisplay: (jit-lock-function 9029) signaled (end-of-buffer) Another time with the last entry a level-3, immediate child of a level-2, last two did not render: Error during redisplay: (jit-lock-function 9490) signaled (end-of-buffer) Error during redisplay: (jit-lock-function 9418) signaled (end-of-buffer) font-lock-default-fontify-region: End of buffer I had ‘debug-on-error’ as ‘t’ during these tests. In both, the file ended with a single final newline. If there are more, I do not have an error. Best, -- İ. Göktuğ Kayaalp. http://gkayaalp.com/
Re: [O] footnote fontify causing massive slowdown
Nicolas Goaziou writes: > However, this report raises an interesting question about footnotes: > should we still support plain (e.g., "[1]") footnotes in Org documents? > > The pattern is very common an regularly introduces false positives. > Also, IIRC, it was introduced for non-Org buffers (e.g., in Message mode > buffers), to provide some common features with "footnote.el" library. > > I think we could remove this kind of footnotes, and yet preserve > `org-footnote-normalize' to change Org footnotes into these ones, for > foreign documents. > > WDYT? I'd be happy to kill [n] style footnotes. I've had issues with them in the past. Rasmus -- Not everything that goes around comes back around, you know
Re: [O] footnote fontify causing massive slowdown
as with others, i am ok with nixing those [1] footnotes if nobody objects. on the other hand, i strongly want inline footnotes to work again with multiple paragraphs, including in fontifying. i know export is incompatible with post-8.0 paragraphs and will accept a filter or something if needed as long as it isn't too kludgy.
Re: [O] fixmee / syntax-ppss
Aaron Ecay writes: > Org mode provides built-in functionality to create “TODO” annotations > (called inline tasks). These might server your purpose better than what > you are trying to do with fixmee. You need to put the following line in > your emacs init file: Hmm, I may be able to make this work. It's pretty important for my purposes that notes like this not show up in the published version. I'm still learning my way around org-mode, but my sense is that will be fairly straightforward to achieve. Thanks! -- Jeremy Hankins
Re: [O] footnote fontify causing massive slowdown
On 5 December 2015, Nicolas Goaziou wrote: However, this report raises an interesting question about footnotes: should we still support plain (e.g., "[1]") footnotes in Org documents? The pattern is very common an regularly introduces false positives. Also, IIRC, it was introduced for non-Org buffers (e.g., in Message mode buffers), to provide some common features with "footnote.el" library. I think we could remove this kind of footnotes, and yet preserve `org-footnote-normalize' to change Org footnotes into these ones, for foreign documents. +1. The false positives are a common problem for me, and [fn:1] works cleanly and clearly. Bill -- William Denton ↔ Toronto, Canada ↔ https://www.miskatonic.org/
Re: [O] footnote fontify causing massive slowdown
William Denton writes: > On 5 December 2015, Nicolas Goaziou wrote: > >> However, this report raises an interesting question about footnotes: >> should we still support plain (e.g., "[1]") footnotes in Org documents? >> >> The pattern is very common an regularly introduces false positives. >> Also, IIRC, it was introduced for non-Org buffers (e.g., in Message mode >> buffers), to provide some common features with "footnote.el" library. >> >> I think we could remove this kind of footnotes, and yet preserve >> `org-footnote-normalize' to change Org footnotes into these ones, for >> foreign documents. > > +1. The false positives are a common problem for me, and [fn:1] works > cleanly > and clearly. Same here. +1. All the best, Tom -- Thomas S. Dye http://www.tsdye.com
[O] Two column layout from org source?
Dear org users, I need to produce a two-column text, where each of these columns has the same content but in a different language. I would like to derive this from org documents. Any ideas on how to set this up are much appreciated! All the best, Christian -- Christian Wittern, Kyoto
Re: [O] Straight recursive fact prints in floating-point in org-babel but not in REPL
Brian Beckman writes: > Org-babel seems to print SLIME / SBCL bignums as floating point, at least in > this gist (please see > https://gist.github.com/rebcabin/f73cecd3c9b7da6218e9). I'd like to be able > to control whether bignums are printed out in full. Any advice for me? > I think this happens because babel turns result strings into elisp objects, using (read ...). This has two consequences: the string has to be legal emacs-lisp (that causes problems with e.g. scheme evaluators which return things like #t and #f on which the elisp reader chokes; note also the conversion of lisp-vector-to-list in ob-lisp.el which is done to avoid similar problems); it also does violence to some strings as you have observed - e.g. try (read "123456789123456789123456789") 1.2345678912345679e+26 I'm not sure whether the (read ...) is required in order for babel to work correctly, or whether it is a bug. I've wanted to look into this for a while now (ever since Lawrence Bottorff reported the #t problem with scheme), but I have not been able to find any time to do so. -- Nick
