Re: [O] Dr Wozniak’s tasklist implementation
Dear Michal, On Sun, 29-01-2017, at 15:10, Michal Rus <m...@michalrus.com> wrote: > Hello! > > I’d like to start using dr Wozniak’s tasklist idea [1] in Org. He’s > the original author of spaced repetition and SuperMemo. > [Being nit-picky here: :-) Wozniak is the author of SuperMemo and he has made many changes/adjustments to the algorithms for optimal spacing, and he is probably the one responsible for making this thing popular but, as he himself makes clear, the spaced repetition phenomenon is something documented in the psychological literature long before SuperMemo] > It’s about assigning values ($) and time (hrs) to each task. Then, > priorities ($ divided by hrs) can be calculated, and then you do the > tasks with the highest priority; effectively, spending your time in > the most valuable way. (That is if you assign the value and time > correctly, but it can be learned.) > > Is there anything like that implemented? I couldn’t find anything. > org-drill was designed specifically for this http://orgmode.org/worg/org-contrib/org-drill.html (you might also want to look at : http://stackoverflow.com/questions/34983106/how-to-install-org-drill) Best, R. > If not, how hard would it be? Where would it be best to start? > > Thank you! > > [1] https://www.supermemo.com/articles/tasklists.htm -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Android org app with sync?
Dear Alasdair, On Sun, 18-12-2016, at 01:59, Alasdair McAndrew <amc...@gmail.com> wrote: > I'm sure this has been asked and answered many times before, but > I've hunted about - both on the web and on Google Play - to find > some app which can sync with my org files. The closest I've come > is orgzly: > > https://play.google.com/store/apps/details?id=com.orgzly > > which however only syncs with Dropbox, which I don't use (I use a > self-hosted ownCloud instead). > > Are there any other apps which will allow me to update and edit > org files on my android device, and have them sync automatically? > > I guess I can probably use orgzly with a local file, and have a > third party app sync with my ownCloud files. Seems like extra > fuss, though! You can used orgzly with syncthing (syncing the directory where file reading from/writing to takes place) so Dropbox is not needed. I assume something similar could be done with ownCloud. That said, at least some of us are still waiting for Orgzly to become free software: https://plus.google.com/112212983680346701286/posts/hGnkkxDsUjT But http://www.orgzly.com/help#Source doesn't give many specifics. I use MobileOrg (the app and link Eric gave). Best, R. > > Thanks, > Alasdair -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
On Fri, 15-04-2016, at 23:49, Adam Porter <a...@alphapapa.net> wrote: > Ramon Diaz-Uriarte <rdia...@gmail.com> writes: > >> Faster? How did you do that? For me it is slower, noticeably (I estimate no >> less than 3 to 4 times; from less than one second to about two or more >> seconds in many simple tasks such as opening a link from a email under >> emacs; yes, I am reusing a running firefox with "--new-window"). I guess I >> might need to disable extensions, etc? > > Firefox has always seemed slow to open new windows for me too, at least > on Linux. Seems faster on Windows. Might have something to do with the > /usr/bin/firefox shell script, or how it calls the actual binary. OK, so not a lot of room to try and do much it seems. Thanks anyway. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
On Sat, 16-04-2016, at 03:44, Eric Abrahamsen <e...@ericabrahamsen.net> wrote: > Ramon Diaz-Uriarte <rdia...@gmail.com> writes: > >> On Thu, 14-04-2016, at 09:07, Eric Abrahamsen <e...@ericabrahamsen.net> >> wrote: >>>> (...) >>>> Eric, do you mean the dlbsnail and S3.dlbsnail? Or do you mean the >>>> "LinkDownloads"? The last one I've not been able to get to work (seems to >>>> do nothing). >>> >>> I only installed the dlbsnail, and I think it works okay. >> >> Understood, thanks. >> >> >>> (...) >>> Apart from that, though, this setup is fairly Conkeror like. Just >>> faster, and with fewer mysterious silent crashes! >> >> Faster? How did you do that? For me it is slower, noticeably (I estimate no >> less than 3 to 4 times; from less than one second to about two or more >> seconds in many simple tasks such as opening a link from a email under >> emacs; yes, I am reusing a running firefox with "--new-window"). I guess I >> might need to disable extensions, etc? > > I'm not the right one to ask, I'm afraid -- I have no idea! I try hard > not to use browsers at all, and don't really have any plugins installed. > Conkeror used to struggle mightily just to keep up with my typing (and > this is not a boast about my typing speed, sadly), and regularly > "stopped to think" for several seconds. I never really looked into it... Thanks for the clarification. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
On Thu, 14-04-2016, at 09:07, Eric Abrahamsen <e...@ericabrahamsen.net> wrote: >> (...) >> Eric, do you mean the dlbsnail and S3.dlbsnail? Or do you mean the >> "LinkDownloads"? The last one I've not been able to get to work (seems to >> do nothing). > > I only installed the dlbsnail, and I think it works okay. Understood, thanks. > (...) > Apart from that, though, this setup is fairly Conkeror like. Just > faster, and with fewer mysterious silent crashes! Faster? How did you do that? For me it is slower, noticeably (I estimate no less than 3 to 4 times; from less than one second to about two or more seconds in many simple tasks such as opening a link from a email under emacs; yes, I am reusing a running firefox with "--new-window"). I guess I might need to disable extensions, etc? -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
On Wed, 13-04-2016, at 21:44, Haider Rizvi <hari...@gmail.com> wrote:
> Ramon Diaz-Uriarte <rdia...@gmail.com> writes:
>
>> For me Conkeror works just great most of the time. But the main problem
>> (for me) is that some of the extensions of Firefox will not work with
>> Conkeror.
>
> Yes, well aware of the extensions issue. Since I had no solution, I
> started looking at it as a blessing in disguise ;-) It makes me use
:-)
> less extensions, only adblock and https-everywhere right now on
> Conkeror. But then I have a lot of stuff in javascript!
>
>
> I could never get into zotero, when I tried last. I use a combination
> of Pocket, Evernote, and org files for research / notes taking.
In a sense, I am conceptually/aesthetically unhappy with how I keep some
things under Zotero (mostly anything that could potentially have a PDF
attached, like papers) but all the rest of my notes and links under org and
some things to learn under Anki. In practice, I somehow have adopted a
scheme that works well for me (i.e., I seem to know where to search for
what).
>
>> (problem being that sometimes, while browsing, I decide "let's add
>> this to Zotero" and then I need to start firefox, copy the link,
>> etc).
>
> You probably know this, but you can write a function and assign a
> key for this to make life a bit easier.
>
> // open in Firefox
> function open_in_firefox (url, window) {
> var cmd_str = 'open -a firefox '+url;
> if (window != null) {
> window.minibuffer.message('Issuing ' + cmd_str);
> }
> shell_command_blind(cmd_str);
> }
>
> interactive("firefox", "Send url to Firefox",
> function (I) {
> open_in_firefox(I.buffer.display_uri_string, I.window);
> });
> define_key(content_buffer_normal_keymap, "f5", "firefox");
>
Actually, I am very embarrassed to say I did not know this at all. In fact,
what is worse, it never occurred to me to try something like that. Thanks a
lot
Best,
R.
>
>
>>> I have tried out Vimium with Chrome, and liked it. You may want to
>>> try it out if you haven't already.
>>
>> Thanks for the suggestion; I did not know it.
>>
>> I'll have to revisit it, because I just tried it and was unable to activate
>> it in any page (get the icon on the bar to be colored). I must be doing
>> something silly. However, I looked over the documentation quickly and I
>> could not see how to mark stuff for downloading. Do I need more coffee?
>>
>>
>> Best,
>>
>> R.
>>
>>
>>>
>>> Regards,
>
> --
>
> Regards,
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
Dear Haider, On Tue, 12-04-2016, at 19:53, Haider Rizvi <hari...@gmail.com> wrote: > Eric Abrahamsen <e...@ericabrahamsen.net> writes: > >> I've been using Conkeror (based on Xulrunner/Firefox) for a while >> now, and like it enough to stick with it. It's completely keyboard >> driven, which I love. It's also not super stable, nor does it seem >> to be actively maintained, which I don't love. If anyone has >> recommendations for better keyboard-driven browsers, I'd love to >> hear them... > > Eric, I use Conkeror as well. And worried that one day it'll go away. > For me Conkeror works just great most of the time. But the main problem (for me) is that some of the extensions of Firefox will not work with Conkeror. In particular, the connector with Zotero standalone just cannot work with it. And this has forced me to "use Conkeror always, except if I need to do reference-related work" (problem being that sometimes, while browsing, I decide "let's add this to Zotero" and then I need to start firefox, copy the link, etc). KeySnail so far seems to be an alternative to avoid my schizoid behavior. > I have tried out Vimium with Chrome, and liked it. You may want to try > it out if you haven't already. Thanks for the suggestion; I did not know it. I'll have to revisit it, because I just tried it and was unable to activate it in any page (get the icon on the bar to be colored). I must be doing something silly. However, I looked over the documentation quickly and I could not see how to mark stuff for downloading. Do I need more coffee? Best, R. > > Regards, -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
On Mon, 11-04-2016, at 13:56, Eric Abrahamsen <e...@ericabrahamsen.net> wrote: > Ramon Diaz-Uriarte <rdia...@gmail.com> writes: > >> On Mon, 11-04-2016, at 10:12, Marcin Borkowski <mb...@mbork.pl> wrote: >>> On 2016-04-11, at 06:37, Adam Porter <a...@alphapapa.net> wrote: >>> >>>> Eric Abrahamsen ericabrahamsen.net> writes: >>>> >>>>> I had no idea Firefox did this... >>>> >>>> ...You're not the only one... >>> >>> Me too, thanks for that tip!!! >> >> Add another one. :-) >> >> That said, though, I am finding the behavior of KeySnail's hok's very >> flexible (follow the link, open multiple links in tabs, open link in a tab >> and switch to it, open in a tab but do not switch to it, open in a new >> window, copy the link, save [download] the link, etc). > > Hok, the history search plugin, and the download manager plugin are all Eric, do you mean the dlbsnail and S3.dlbsnail? Or do you mean the "LinkDownloads"? The last one I've not been able to get to work (seems to do nothing). In fact, after these couple of days of usage, I have tweaked the config so that most of my muscle memory with Conkeror does not need to be changed. But the download thing is still not great because when I try to save something I am eventually offered one of those dreaded pop-up file-explorer-like windows. In contrast, with Conkeror after typing a key (s) and the hint, in the bottom mini-buffer like I can use common Emacs keybindings to modify path, names, etc. Am I am missing something? Best, R. > very much inspired by Conkeror. Which I think is a great thing -- > Conkeror had a wonderful design, but it never quite got the sustained > development love it needed. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] Emacs on Android
Thanks! On Sun, 10-04-2016, at 17:15, Scott Randby <sran...@gmail.com> wrote: > Since there have been discussions on this list about using Org on an > Android phone, I thought some might be interested in this: > http://endlessparentheses.com/running-emacs-on-android.html > > Scott Randby > > sran...@gmail.com > > http://srandby.org/ > > PGP key ID: 0xF2D38A63 > > Key server: http://pool.sks-keyservers.net/ > > Key fingerprint: 5418 123E DCD3 7DA0 1770 0BDE 301E E657 F2D3 8A63 -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
On Mon, 11-04-2016, at 10:12, Marcin Borkowski <mb...@mbork.pl> wrote: > On 2016-04-11, at 06:37, Adam Porter <a...@alphapapa.net> wrote: > >> Eric Abrahamsen ericabrahamsen.net> writes: >> >>> I had no idea Firefox did this... >> >> ...You're not the only one... > > Me too, thanks for that tip!!! Add another one. :-) That said, though, I am finding the behavior of KeySnail's hok's very flexible (follow the link, open multiple links in tabs, open link in a tab and switch to it, open in a tab but do not switch to it, open in a new window, copy the link, save [download] the link, etc). > > Best, -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OT] A new web browser‽
Dear Eric, On Sun, 10-04-2016, at 15:17, Eric Abrahamsen <e...@ericabrahamsen.net> wrote: > Eric S Fraga <e.fr...@ucl.ac.uk> writes: > > > I installed the eww-lnum package right away, as that provides the main > functionality I liked from Conkeror: hit a key, and pick a link to do > something with. Rather strangely, the KeySnail plugin for Firefox seems > to do everything *but* this, which I thought was weird since, if you're > going to control your browser through the keyboard, following links is > generally the main thing you want to do. I've only had it for a few > hours, though, so maybe I'm missing something. > I think you might want to try the "HoK" (hit a hint for KeySnail) extension, available here https://github.com/mooz/keysnail/wiki/plugin In fact, it might already be available by default (I think it was in my installation) but you might not have key bindings set up for it (you can check if it is available by M-x: hok) There is a comment about this extension (and the also very neat Tanything extension) in http://blog.binchen.org/posts/use-firefox-in-emacs-way-3.html I have configured HoK in my .keysnail.js so that the behavior of HoK is now similar to what I had with conkeror (follow links in new buffers (or tabs) or new windows, etc). Caveat emptor: I only started playing with KeySnail a few hours ago, after seeing Rasmus' comment this morning. Best, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] MobileOrg does not sync with local Android calendar
On Sat, 06-02-2016, at 19:03, cschr <cs...@freenet.de> wrote: > Thanks Ramon and Eric > > Are you using custom agenda views ? Someone wrote on the web that this Not that I am aware of. Where would I have done that (so I can check)? > is required - is he right ? > > Chris > > -Original Message- > From: emacs-orgmode-bounces+cschr=freenet...@gnu.org > [mailto:emacs-orgmode-bounces+cschr=freenet...@gnu.org] On Behalf Of Ramon > Diaz-Uriarte > Sent: Sonntag, 31. Januar 2016 16:13 > To: Eric S Fraga > Cc: emacs-orgmode@gnu.org; cschr > Subject: Re: [O] MobileOrg does not sync with local Android calendar > > > > > On Sun, 31-01-2016, at 13:36, Eric S Fraga <e.fr...@ucl.ac.uk> wrote: >> On Sunday, 31 Jan 2016 at 08:42, cschr wrote: >>> Hi >>> >>> I set up MobileOrg and it now shows the appointments from my emacs >>> diary and my orgmode agenda. But nothing shows in my local android >>> calendar, although I configured MobileOrg to sync with the android >>> calendar. Is this functionality known to work, at all, and are there >>> any special preconditions ? I tried with two different smartphones >>> – a Sony Xperia Pro with Android 4.0.4, and a Mobistel Cygnus with >>> Android 4.4.2 >>> >> >> It syncs with my calendar on cyanogenmod latest nightly snapshot on a >> Nexus 4. I've had no issues in this regard in a very long time. >> > > It has also worked for me for a long time in several tablets/phones. Right > now it is working on two tablets (BQ edison 3 and Nexus 7) with stock android > 4.4 and a phone with stock android 5. It has worked in the past with Android > 4.1. > > > > >> I think what I am using is roughly equivalent to android 5.1? Not >> entirely sure however but definitely well past 4.x versions. Whether >> this is relevant or not is unclear! -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] "atomic knowledge" modeling tool
On Mon, 01-02-2016, at 22:25, luke call <luke...@onemodel.org> wrote: > On 01/31/16 08:37, Ramon Diaz-Uriarte wrote: > > Thanks for the link. Good-faith question here: does it support spaced > > repetition such as provided by org-drill > > (http://orgmode.org/worg/org-contrib/org-drill.html) or Anki > > (http://ankisrs.net/), for memorizing some of the stored knowledge? I > > skimmed through the docs and googled for it, but did not find anything > > relevant. > > It's interesting that you asked, as i like anki and have planned for > some time to add that feature to OM. OM is partly already set up for > it, just not fully implemented yet. This has a dependency on another > future feature which is to associate scripts with objects (entities) in > the system, so that the menu can also reflect any user-defined > operations on the entity in view. Thanks for the details. (As Eric Fraga mentioned, though, I really like that org is all text; and specifically for the spaced repetition part, even if I do use Anki, I actually feel slightly uneasy with Anki because I miss the sense of control and immediacy of just opening a simple text file and modifying it ---yes, I know I can import and export from/to text). Best, > > Patches/assistance welcome. :) I'm currently seeing how to get postgres > to do what OM wants, for windows installation. > > You might want to sign up for the announcements list at least. > > -Luke -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] MobileOrg does not sync with local Android calendar
On Mon, 01-02-2016, at 17:35, Karl Voit <devn...@karl-voit.at> wrote: > * Ramon Diaz-Uriarte <rdia...@gmail.com> wrote: >> >> On Mon, 01-02-2016, at 14:20, Karl Voit <devn...@karl-voit.at> wrote: >> >>>> The calendar name is set to "org-calendar" (I think that is the >>>> default, since I do not recall ever having changed/set it). >>> >>> Mine is "Org". But in my calendar app, there is no "Org" calendar, >>> just three others. >> >> No idea why that happens. >> >>> Whenever I choose an existing calendar within MobileOrg preferences, >>> it stays at the non-existing "Org" calendar. I guess this is the >>> reason why there is no data sync to my calendar. >> >> No idea what is happening there. > > Okay. A little bit confused now: > > When I checked MobileOrg a couple of minutes ago, I did see some > (not all!) Org-mode events for the first time. Only scheduled > things, no events with time-slots. I did not check any further. > > I recognized, that MobileOrg settings is showing me the previously > selected existing calendar. > > In calendar, I noticed that sync was activated. Gr. I hate it, > when something silently leaks my private data to the public cloud! > > After I disabled the sync-checkboxes for my three calendars, the > Org-mode events were gone again. > > Quite disappointing, the whole story. Karl, I am sorry I can provide no additional help here and that the whole thing is frustrating. I've been using mobile-org for several years without much tweaking and, yes, enabling (not happily) the syncing of calendar with Google's cloud. That said, sometimes (for reasons I don't understand) things do not work fully (the calendar is not updated completely, events are missing, events get duplicated, etc). So this is not always 100% reliable. As for Android's calendar syncing with Google's cloud, and after reading Brian van den Broek's and Bingo UV's comments about Offline Calendar, I think I'll be trying that so I can get rid of the cloud. Best, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] MobileOrg does not sync with local Android calendar
On Mon, 01-02-2016, at 12:11, Karl Voit <devn...@karl-voit.at> wrote: > * cschr <cs...@freenet.de> wrote: >> >> I set up MobileOrg and it now shows the appointments from my emacs diary and >> my orgmode agenda. But nothing shows in my local android calendar, although >> I configured MobileOrg to sync with the android calendar. Is this >> functionality known to work, at all, and are there any special preconditions >> ? I tried with two different smartphones - a Sony Xperia Pro with Android >> 4.0.4, and a Mobistel Cygnus with Android 4.4.2 > > Contrary to many mentions on the mailinglist, this feature never > worked at my side as well: Hummm... I am just looking at the config in my phone (with Android 5). I have checked "Synchronize with calendar". The calendar name is set to "org-calendar" (I think that is the default, since I do not recall ever having changed/set it). Under "Advanced" I set "Assimilate calendar entries" (this I find very useful for the odd case when i enter things in the android calendar directly). I have NOT checked "Delete on assimilation". > > Nexus 5 with CyanogenMod 12.1-20150808-NIGHTLY-hammerhead (Android > 5.1.1) > I do not understand why the following is leading to trouble, so I think I am seriously misunderstanding something. > Current situation: in MobileOrg settings, I want to choose a > calendar which gets populated by MobileOrg. I do not recall ever having to do anything especial here. > In the list of available calendars You mean the list that is available when you try to set the options under "Calendar name"? I see there six entries (one for my gmail user, one for "PC Sync" that I have no idea what it is, then "org-calendar", a fourth called "Cumpleaños" [birthdays] and then "Holidays in Spain" and a sixth one which seems to be the same but in Spanish). > I can choose whatever calendar I want but afterwards, MobileOrg shows > "Org" (the default one) as the selected calendar. If I understand correctly, this is used by MobileOrg to place its entries in a calendar that the Android calendar will use. When the entries are displayed in your Android calendar, you'll see these as coming from "Org" (or mobile-org). Why would you not want to set it to "Org"? > > Maybe it has something to do with my disabled sync settings: I don't > sync to the Google cloud. Aha, I think this is probably needed. I think I only get entries updated if I enable syncing of the calendar (but you can decide what you sync with google --- no need to sync everything, from email to contacts to ). > > I gave up and use MobileOrg mainly for capturing and (seldom) > browsing my Org files for information. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] MobileOrg does not sync with local Android calendar
On Mon, 01-02-2016, at 14:20, Karl Voit <devn...@karl-voit.at> wrote: (I remove lots of stuff from previous thread) > >> The calendar name is set to "org-calendar" (I think that is the >> default, since I do not recall ever having changed/set it). > > Mine is "Org". But in my calendar app, there is no "Org" calendar, > just three others. No idea why that happens. > > >> I see there six entries (one for my gmail user, one for "PC Sync" that I >> have no idea what it is, then "org-calendar", a fourth called "Cumpleaños" >> [birthdays] and then "Holidays in Spain" and a sixth one which seems to be >> the same but in Spanish). > > I do have three entries, non of them named "Org". > > Whenever I choose an existing calendar within MobileOrg preferences, > it stays at the non-existing "Org" calendar. I guess this is the > reason why there is no data sync to my calendar. No idea what is happening there. > >>> Maybe it has something to do with my disabled sync settings: I don't >>> sync to the Google cloud. >> >> Aha, I think this is probably needed. I think I only get entries updated if >> I enable syncing of the calendar (but you can decide what you sync with >> google --- no need to sync everything, from email to contacts to ). > > OK, then MobileOrg -> Calendar feature is of no use to me since I > avoid the Google cloud. > > That's really weird since this feature is especially useful to > people not having Google Cloud sync activated. > >>> I gave up and use MobileOrg mainly for capturing and (seldom) >>> browsing my Org files for information. > > OK, at least I got a confirmation that MobileOrg needs this cloud > sync stuff. How unfortunate. I am not 100% sure if syncing the calendar with google is _required_. I'll try playing with it ASAP and report back. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] status of mobile (Android)
On Fri, 29-01-2016, at 20:11, Saša Janiška <g...@atmarama.com> wrote: > Hello, > > I'm returning to Emacs-land and wonder whether mobile-org is still > working with org-mode? > Yes, I use it daily in a tablet and a phone. > Do you have any other recommendation to sync tasks with Android phones? > I don't know of any other alternatives. > For contacts/calendars I was using org-vcard/org-caldav and they worked > pretty well via ownCloud, but now, when i use GNOME, I can't tell > whether calendars are visible on GNOME's status bar? > > There is Orgly, which is not open-source, but not sure whether it's > better than mobileorg? > Orgzly's author has said that probably around Q2 2016 Orgzly will be opensourced (https://plus.google.com/112212983680346701286/posts/hGnkkxDsUjT). However, as far as I can tell, Orgzly will not (as of now at least?) sync tasks/update your android calendar. > Is there something which would work with ownCloud? > No idea about ownCloud. I do all the syncing of my org files via Syncthing (https://syncthing.net/) but of course there is nothing org-specific here. This is just syncing files. Best, R. > > Sincerely, > Gour -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] "atomic knowledge" modeling tool
On Fri, 29-01-2016, at 19:21, luke call <luke...@onemodel.org> wrote: > There's a program that org-mode users (as I have been) specifically > might be interested in, a personal "knowledge manager"/list > manager/organizer/etc called OneModel (Free/AGPL). Instead of storing > data as text, it puts *everything* in a single object model backed by > postgresql, but text import/export are available. Everything one needs > to know at any given time is always on the screen, and it is *highly* > efficient to navigate (so far keyboard-only). Current strengths, > limitations, and future plans are at: >http://onemodel.org > > Pls forgive & spare the flames, I'll probably go quiet unless to answer > good-faith questions. Details & discussion at http://onemodel.org > site/lists if desired. Thanks for the link. Good-faith question here: does it support spaced repetition such as provided by org-drill (http://orgmode.org/worg/org-contrib/org-drill.html) or Anki (http://ankisrs.net/), for memorizing some of the stored knowledge? I skimmed through the docs and googled for it, but did not find anything relevant. Best, R. > > -Luke -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] MobileOrg does not sync with local Android calendar
On Sun, 31-01-2016, at 13:36, Eric S Fraga <e.fr...@ucl.ac.uk> wrote: > On Sunday, 31 Jan 2016 at 08:42, cschr wrote: >> Hi >> >> I set up MobileOrg and it now shows the appointments from my emacs >> diary and my orgmode agenda. But nothing shows in my local android >> calendar, although I configured MobileOrg to sync with the android >> calendar. Is this functionality known to work, at all, and are there >> any special preconditions ? I tried with two different smartphones >> – a Sony Xperia Pro with Android 4.0.4, and a Mobistel Cygnus with >> Android 4.4.2 >> > > It syncs with my calendar on cyanogenmod latest nightly snapshot on a > Nexus 4. I've had no issues in this regard in a very long time. > It has also worked for me for a long time in several tablets/phones. Right now it is working on two tablets (BQ edison 3 and Nexus 7) with stock android 4.4 and a phone with stock android 5. It has worked in the past with Android 4.1. > I think what I am using is roughly equivalent to android 5.1? Not > entirely sure however but definitely well past 4.x versions. Whether > this is relevant or not is unclear! -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
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, 05-12-2015, at 08:10, Xebar Saram <zelt...@gmail.com> wrote: > > 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 make a fairly standard, non-sophisticated, usage of MobileOrg. I set it to update the entries in the built-in Google Calendar: I find Google Calendar easier to read than what is provided by MobileOrg. I sync the Mobile org directory between computer(s) and tablet(s)/phone using syncthing (https://syncthing.net/), which requires that at least two devices be up (but I have a server that is supposed to be up all the time, so no problem here ---having a tablet and a phone, a tablet and a laptop, etc, would also do). So the computer -> tablet way works just fine. The other way around is slightly more cumbersome (I capture in the tablet and then, in the computer, process the flagged.org file created by MobileOrg --- this has been discussed in this list before, and other people have much more sophisticated procedures here). Contacts I do not worry about (I rarely do email on a tablet/phone). > > 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. > A few years ago I tried using emacs for android, etc, in the tablet, but I eventually gave up using it since it was too cumbersome for me. MobileOrg covers my needs pretty well. Note, however, that you can install Debian (or several other Linuxes) relatively easily in rooted Android devices and maybe even in non-rooted devices. There are two or three apps available; I use "Complete Linux Installer", and you should be able to get X in there, etc (I use it without X), so you might do Emacs and even start it from a shortcut in a desktop linux environment running inside your Android. But I haven't tried it (and it seems to me it'd probably not be the smoothest and most efficient experience). Best, R. > thanks so much > > best > > Z -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Citation processing via Zotero + zotxt
On Tue, 01-12-2015, at 01:32, John Kitchin <jkitc...@andrew.cmu.edu> wrote: > Martin Yrjölä writes: > >> Maybe two way sync between BibTeX and Zotero would be sufficient for >> power users? I know there is already automatic exporters to BibTex for >> Zotero, but some work needs to be done to make it a two-way sync. > > I am personally skeptical of this, having "translated" Endnote libraries > to Bibtex and back. The simple stuff mostly works, but accented names, > chemical formulas, and many other things tend to not translate very well. In addition, Zotero users often organize their references using collections, tags, and "related" (and the first two I find essential, both with Zotero itself and when using Zotero in a tablet). Some of these (e.g., collections, tags) might be synced/translated from BibTeX into Zotero though not always reliably. And trying to get these to work reliably is probably too much work. Best, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Citation processing via Zotero + zotxt
Dear Eric, On Mon, 30-11-2015, at 12:35, Eric S Fraga <e.fr...@ucl.ac.uk> wrote: > On Saturday, 28 Nov 2015 at 12:16, Richard Lawrence wrote: >> Hi everyone, >> >> For the past few days, I've been looking more closely at using the >> combination of Zotero [1] with Erik Hetzner's zotxt plugin [2] as a >> means of processing citations when exporting to non-LaTeX backends. I >> am now thinking that this is probably our best option, but I'd like to >> know what other people think before I sink a lot of work into it. > > Richard, > > thanks for the long and descriptive email. What you propose does seem > like a potentially attractive way forward especially in the context of > minimal impact for installation. > > I have two questions: > > 1. Is Zotero open source? I believe not so I wonder about the >implications of this for org. > Yes, it is open source (GNU GPL Affero, v.3): https://www.zotero.org/support/licensing And code is available from github: https://github.com/zotero Best, R. > 2. How would I use this starting from an org-bibtex database (which I >typically export to bibtex)? > > Regardless, my export requirements are usually satisfied by export to > LaTeX so my main concern will not be org to odt or HTML but on the user > interface aspects within org for inserting citations etc. > > Thanks again, > eric -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Org Mode and PDF Notes!
On Thu, 12-11-2015, at 15:28, Matt Lundin <m...@imapmail.org> wrote: > Ramon Diaz-Uriarte <rdia...@gmail.com> writes: > >> >> so we get the location of the highlight (and its properties), but not the >> textual contents. And this is the case whether I make the annotation with >> EzPDF or Okular or, for that matter, with pdf-tools itself. >> >> So it seems RepliGO is actually giving you a lot more by default :-) >> >>> >>> Politza and I are discussing this here: >>> https://github.com/politza/pdf-tools/issues/137 >>> >>> that might be a good place to ocntinue the conversation. >>> >> >> I'll do. In the meantime, I think this is a limitation coming from >> poppler. Other people have mentioned similar things (e.g., >> http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using other >> tools that depend on poppler (such as Leela: >> https://github.com/TrilbyWhite/Leela) also will not give us the text >> itself. > > I don't think this is a limitation of poppler so much as the way that > pdf annotations work. Typically, the subject/text field is not populated > by the text of the highlighted region. Rather, a highlight annotation > specifies bounds, color, style, etc. Basically what Repligo does (I > wouldn't recommend using it, as it is closed source and severely out of > date) is to grab the text *at the time of highlighting* and add it to > the notes field. I don't know of any other annotation tool that does the > same thing. Applications built on poppler could do it, though they > currently do not. I stand corrected. You are right; sorry for the sloppiness in the wording and ideas. > > For extracting the text of highlighted regions *after the fact*, I've > had good luck with this script that relies on the pdf-reader gem for > ruby: > > https://gist.github.com/danlucraft/5277732 That is also what I use for extracting the text from the highlighted regions. R. > > Matt -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Org Mode and PDF Notes!
On Thu, 12-11-2015, at 23:52, Matt Price <mopto...@gmail.com> wrote: > On Thu, Nov 12, 2015 at 9:28 AM, Matt Lundin <m...@imapmail.org> wrote: > >> Ramon Diaz-Uriarte <rdia...@gmail.com> writes: >> > >> > I'll do. In the meantime, I think this is a limitation coming from >> > poppler. Other people have mentioned similar things (e.g., >> > http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using >> other >> > tools that depend on poppler (such as Leela: >> > https://github.com/TrilbyWhite/Leela) also will not give us the text >> > itself. >> >> I don't think this is a limitation of poppler so much as the way that >> pdf annotations work. Typically, the subject/text field is not populated >> by the text of the highlighted region. Rather, a highlight annotation >> specifies bounds, color, style, etc. Basically what Repligo does (I >> wouldn't recommend using it, as it is closed source and severely out of >> date) is to grab the text *at the time of highlighting* and add it to >> the notes field. I don't know of any other annotation tool that does the >> same thing. Applications built on poppler could do it, though they >> currently do not. >> >> For extracting the text of highlighted regions *after the fact*, I've >> had good luck with this script that relies on the pdf-reader gem for >> ruby: >> >> https://gist.github.com/danlucraft/5277732 >> >> This looks interesting. It searches for file "./markup_receiver", but > doesn't provide that file, which does not appear to be a gem. Any hints? I think I got it from https://www.omniref.com/github/danlucraft/pyranine/HEAD/files/lib/pyranine/markup_receiver.rb > > With politza's help am getting close to being able to extract annotation > text from within pdf-tools, but am not quite there yet. Neat! R. > > >> Matt >> -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Org Mode and PDF Notes!
On Wed, 11-11-2015, at 21:33, Matt Price <mopto...@gmail.com> wrote: >> >> >> instead of the text. Bummer! I wonder if RepliGO gives you a lot more >> than the rest, or if I am doing something silly. >> >> I think that there is no standard way of storing the highlight contents. I > chose Repligo over EZPDF because it gives you access to the text of the > highlights! I'll try to see if I can get repligo (I had it a few years ago) > > Okular, I think, stores your annotations in its own database, rather than > in the pdf. You can (I think!) attach the annotations to the pdf from > inside Okular. At leasts, that's what I remember from when I was looking > around. Actually, Okular stores the annotations in the PDF itself if you do "Save As". (It still keeps an internal db, but I never use it anymore). It is easy to check by doing that and then opening the file with another reader in another machine (e.g., in an android). > > Repligo stores the highlighted text in the "subject" field of the > annotation. It's possible that the content of the annotation is stored in > some other field, like "content". Maybe you can try: > > M-: (pdf-annot-get-annots) and look at the output in the *Messages* > buffer. Can you see any evidence of the the text? Can you share what you > learned? Nope, no evidence of the text. I get things such as (((buffer . #) (page . 13) (edges 0.113553 0.31717 0.868657 0.361746) (type . highlight) (id . annot-13-0) (flags . 4) (color . "#00") (contents . "") (modified 22081 45188) (label . "TF201") (subject . "Highlight") (opacity . 1.0) ...) so we get the location of the highlight (and its properties), but not the textual contents. And this is the case whether I make the annotation with EzPDF or Okular or, for that matter, with pdf-tools itself. So it seems RepliGO is actually giving you a lot more by default :-) > > Politza and I are discussing this here: > https://github.com/politza/pdf-tools/issues/137 > > that might be a good place to ocntinue the conversation. > I'll do. In the meantime, I think this is a limitation coming from poppler. Other people have mentioned similar things (e.g., http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using other tools that depend on poppler (such as Leela: https://github.com/TrilbyWhite/Leela) also will not give us the text itself. >> >> Until I found pdf-tools, I had planned to write a node wrapper for pdf.js > and grab the annotations that way. But I don't really know how to do that, > so this turned out to be easier :-) > > Anyway, I've judated the post, and it's now possible to create links to > individualt annotations, though you will have to use my updated version of > org-pdfview, until/unless Markus accepts my patch. I just updated packages, and things are working perfectly: I am jumping to the page and location. Thanks, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Org Mode and PDF Notes!
On Thu, 12-11-2015, at 14:11, Matt Price <mopto...@gmail.com> wrote: >> > >> > M-: (pdf-annot-get-annots) and look at the output in the *Messages* >> > buffer. Can you see any evidence of the the text? Can you share what you >> > learned? >> >> Nope, no evidence of the text. I get things such as >> >> (((buffer . #) (page . 13) (edges >> 0.113553 0.31717 0.868657 0.361746) (type . highlight) (id . annot-13-0) >> (flags . 4) (color . "#00") (contents . "") (modified 22081 45188) >> (label . "TF201") (subject . "Highlight") (opacity . 1.0) ...) >> >> >> so we get the location of the highlight (and its properties), but not the >> textual contents. And this is the case whether I make the annotation with >> EzPDF or Okular or, for that matter, with pdf-tools itself. >> >> So it seems RepliGO is actually giving you a lot more by default :-) >> >> > Try replacing > > (text (assoc-default 'subject annot)) > > with > > (text (pdf-info-gettext page (assoc-default 'edges annot))) > > > in the lambda function in pdf-annot-markups-as-org-text. This will fail on > cropped pdfs if you have added highlights using the most recent pdf-tools, > which stores negative values in the 'edges field, but I've found it works > otherwise. I'd love to hear if it works for you too. (I know you're > following the relevant bug report on the pdf-tools github repo). It works! I get the highlighted text (I have just tried with a pdf I highlighted with EzPDF, the one that, above, was giving just the location and properties). And it still does the correct thing in your pdf (the one from repligo). Awesome! Thanks. R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Org Mode and PDF Notes!
Dear Matt, On Wed, 11-11-2015, at 15:42, Matt Price <mopto...@gmail.com> wrote: > I've just written up a post on my workflow for PDF's Since my blog has, I > think, a readership of 0 (surely there's a way to get emacsers to follow > me? ah well), I will post a link here in the hopes that someone will be Add another 1 :-) > interested: > > http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/ > Really neat! A few comments/questions/ramblings: - The type of highlights you get from RepliGo contain the text itself. I mean, when in your pdf I use C-c C-a l, the buffer showing the contents of each highlight contain the highlighted text. This is not what I get from, say, EzPDF (which is what I use on Android), or from highlighting from pdf-tools itself using C-c C-a h, or from highlighting from Okular. The contents just gives the rectangle). Hu... Because of this, when I use your code on my pdfs, I only get things such as Highlight ([[pdfview:/home/ramon/Zotero-data/storage/ESHHD4KW/Frank_2015_Commentary.pdf::5][Frank_2015_Commentary]], 5) instead of the text. Bummer! I wonder if RepliGO gives you a lot more than the rest, or if I am doing something silly. - You have to call mwp/pdf-multi-extract on each file/set of files. I guess if I knew elisp, I'd find it trivial to iterate over a set of directories and subdirectories (and do this using a cron job at night), and also place everything in one single org file. Would this be something reasonable to do? (This might be related to your second Todo) - I know nothing about how it works, and it does not use pdf-tools, but in your first Todo you mention: "extend the pdfview link type (in org-pdfview) to permit me to specify the precise location of an annotation,". PDF.js (https://mozilla.github.io/pdf.js/), which is used for instance by zotfile (http://zotfile.com/) does that and it works out of the box with Okular (but I've not been able to get it to work with pdftools). - In case it matters, I have somewhat similar modus operandi. I do a lot of PDF reading, including note-taking and highlighting, in android tablets ---I use EzPDF, which also embeds the notes in the PDF. I have a cron job that extracts all the highlights and annotations of all the PDFs and places them in a single org file. The kludge is explained here: https://github.com/rdiaz02/Adios_Mendeley#extracting-all-pdf-annotations-and-placing-them-in-an-org-mode-file The truth is I use two mechanisms for PDF annotation and highlighting extraction, since none is fully satisfactory to me, but the one that uses Ruby (i.e., that does not depend on poppler) is able to actually extract the text of the highlights. Best, and thanks again for sharing, R. > All best! > Matt -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Favorite way of syncing?
On Sun, 13-09-2015, at 09:07, Paul Rudin <p...@rudin.co.uk> wrote: > Eric S Fraga <e.fr...@ucl.ac.uk> writes: > >> On Friday, 11 Sep 2015 at 18:42, Ramon Diaz-Uriarte wrote: >> >> [...] >> >>> I use syncthing (https://syncthing.net/) which, admittedly, does not >>> require a server nor uses SSH :-). I keep four computers in sync this way, >>> and also use it to send/receive the org files (with MobileOrg) to/from >> >> Thanks for the heads up on this. The only thing I use Dropbox for is >> MobileOrg and I would love to avoid using a proprietary *and* closed >> system, especially as some of the content is sensitive. > > If the content is sensitive you can either encrypt the data yourself > before it goes to Dropbox (see e.g. ecryptfs) or use a service that does > this as part of its process (see e.g. spideroak). > > Not that I have anything against doing thing other ways - I'm just > pointing out that privacy concerns don't, of themselves, mean you can't > use Dropbox (or similar). Sure, you are correct. However, if there are Android devices in the mix, encrypting locally before sending to Dropbox becomes inconvenient (or at least too inconvenient for me). I am not sure about spideroak's support for android, and I recall having experienced problems (I no longer remember the details) with Wuala. Best, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Favorite way of syncing?
On Fri, 11-09-2015, at 15:59, Tobias Frischholz <tob...@friolz.com> wrote: > Hey there! > > I was wondering what is your favorite way of syncing your org files and > everything. I’ve checked out unison, but I want more of an automated > system that synchronizes my two clients via an SSH server. > I use syncthing (https://syncthing.net/) which, admittedly, does not require a server nor uses SSH :-). I keep four computers in sync this way, and also use it to send/receive the org files (with MobileOrg) to/from android devices. It is as automatic as I can think of. Once set up, I have to do nothing and it just works. If you are familiar with BTsync you can think of syncthing as somewhat similar (but much better, and free software). It is possible to enable a rudimentary form of version control with syncthing itself, but I don't (the files change too often). Instead, one of the computers (which should always be on) is also running Seafile (https://www.seafile.com/en/home/), which actually I think uses git as a backend, so I can recover disasters. Syncthing provides conflict detection. It is not git, but it is enough for me with org files (I rarely edit in two or machines at the same time, and the last machine where I make a change is often connected before I work on another so I do not often have a chance for conflict). [In the past, I used dropbox ---instead of syncthing, though syncthing is not exactly a one-to-one replacement---, and nightly cron jobs that committed the org directory in one of the machines to a bzr repo ---instead of the seafile part--- for disaster recovery.] > So far, I’ve also read that people use TRAMP in conjunction with an SSH > Server (and work exclusively on this SSH server). > I’ve also read about org-sync and magit (git is an option for me). > And now I’m starting the get confused. > I use magit and git for version control but I do not find formal version control very useful with my org files. I like to be able to finish something, stop the timer on the laptop, and a second later put it to hibernate and leave my house/office, without the need for a commit and push, and knowing that all of that has been synced to all the other machines that are on and connected. I know, though, that other people feel differently. Best, R. > Any helpful thoughts would be greatly appreciated! > > Best regards, > Tobias Frischholz > > PGP PUBLIC KEY: http://pgp.mit.edu/pks/lookup?search=0xCD463AC1=index -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] What is the most practical workflow for capturing things in Mobileorg and later integrating them into the main files?
On Fri, 11-09-2015, at 16:00, Jorge <jorge13...@gmail.com> wrote: > Hi. When I capture something in MobileOrg, it by default is classified as > "Captures" and, when I do org-mobile-pull, those captures /silently/ go into > ~/org/from-mobile.org. This is bad. > > So one workflow would be to write some code that warns me if > ~/org/from-mobile.org is non-empty, and find a way of hooking it into > org-mobile-pull. Then: > 1) Capture something in MobileOrg > 2) Do org-mobile-pull > 3) If the code I wrote as above warns me that ~/org/from-mobile.org is >non-empty, then visit it, go through the entries, fix them (adding more >information now that I have a real keyboard) and use org-refile. > > Is there a more practical and easier option? > That is more or less what I do/what happens in my case: I get a notification that flagged.org has changed (though I don't recall ever having configured myself anything explicitly; I guess it is just that the buffer is open). And when I feel like it, I visit it, add the info wherever I need to, delete everything from it, and save flagged.org empty. Best, R. > Regards -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [OFF TOPIC] almost giving up on emacs email..looking for advice?
You have received several great answers already, but my 2 cents here. I've used mu4e with offlineimap[1] for about three years now, and I am reasonably happy with it. I particularly like the search capabilities (which I now often complement with helm-mu). Setting it up was not particularly hard (and how to configure for gmail was just a matter of following the documentation), and I do not recall experiencing any of the issues you mention (I had a few others, but they have disappeared over versions). Before that, I used wanderlust with offlineimap, and I also liked it a lot (I think I got this to work from emacs-fu, the blog of mu4e's author). Initial configuration wasn't really harder than mu4e (I think I quickly found how to configure gmail by googling around). In fact, if you are used to the gmail way of doing things, wanderlust might be more familiar; for example, placing the same email in several folders, or however you want to call them, or being shown the folder structure with options to collapse/expand easily. Now, I actually prefer mu4e's approach most of the time and don't care much about the folder structure (I search and find; no need to try to recall where I filed a message). Actually, to me, overall, wanderlust just seemed easier to use[2], and many of the defaults made a lot more sense to me (i.e., with wanderlust I had to google around less to find how to do what I wanted and I added less code to my .emacs). That said, I haven't made any serious change to my mu4e configuration in over two years, I think, so it is well amortized. I switched to mu4e because I was using wanderlust but searching for/within emails with mu so I figured I might just do the full switch; as well, development and activity around mu4e seemed, well, much more active. In terms of checking email with gmail from other devices (tablet, phone): I very rarely do so, but when I've needed to I've never had an issue while using wanderlust + offlineimap or mu4e + offlineimap. Things work the way I expect (changes in gmail if checked from my tablet show up in my computer and viceversa). Of course, checking email from multiple computers has no problems whatsoever. Finally, even if setting email with emacs was not a half hour thing, I am really glad I did so [3]. Best, R. [1] Offlineimap is slow, and has other issues. I searched for alternatives two or three years ago, and did not find anything convincing (e.g., see this resignated summary http://blog.ezyang.com/2012/08/offlineimap-sucks/ from a few years ago). After Titus' answer, I might give mbsync a try, since now encrypted passwords are supported, etc. [2] This is, of course, just my experience (or my incompetence). For example, with mu4e I had to search around to find how to get a reasonable way to add the date of the original message to the reply or forward but it worked just fine for me with wanderlust. I still struggle with address completion and blacklist in mu4e whereas address completion in wanderlust with BBDB always did exactly what I wanted. Or when I started using mu4e I missed a lot from wanderlust the C-c C-j that allows you to choose account to send from. In all fairness this is also available for mu4e (http://www.djcbsoftware.nl/code/mu/mu4e/Multiple-accounts.html) but requires you to add some extra code. [3] Why? I find the web interface of gmail slow to navigate, cumbersome, and bloated. I also used kmail which was, well, OK, but it was not the editor/environment I use for everything else (for a while, I used kmail but used emacsclient for email writing) and searching was not what it is with mu4e or helm-mu. On Thu, 06-08-2015, at 14:43, Xebar Saram zelt...@gmail.com wrote: Hi list I know this is a bit off topic but im desperately looking for some advice regarding email through emacs. i have tried a bunch of them over the last month (gnus, mu4e, wanderlust, rmail,mew and maybe other i forget). I had various levels of success with each one to setup (it was never easy) but i ended up sorta settling on mu4e. the problem is that mu4e never managed to work properly for me (headers were not updating when new mail arrived, reply was broken etc) so i had to give up What i want is basically pretty simple. an easy to setup email for emacs, but one that would work tightly with gmail since i do a lot of mail checking on the road via my cellphone. any advise. recommendations or setups that maybe people are willing to share? thx so much in advance Z -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] more helm-bibtex/org-ref questions
Dear John, On Fri, 26-06-2015, at 22:58, John Kitchin jkitc...@andrew.cmu.edu wrote: You could have multiple file fields I suppose, and adapt [1] to give you a choice of which one to open. That is an intriguing suggestion. I'll try to play with it. Personally, I have one pdf per bibtex entry, named by the key of the entry, in a directory called bibtex-pdfs somewhere defined by org-ref-pdf-directory. There are ~1300 pdfs in there now. I always access them through helm bibtex. admittedly, I don't have the SI or other stuff around usually. I don't use bibtex to keep track of the directories where I write manuscripts either. I don't use bibtex to keep track of the dirs where I write manuscripts either, but SI et al I often do want to store. The SI more and more as time goes by, given the current policy of many journals of moving the methods details to SI ---I could merge PDFs into a single one, but that is another step. You could always make links to these other things in the associated notes entry. or put org-links in a bibtex field, and then you can open them with C-c o (if you setup links to work everywhere). That way, opening the pdf is easy, and opening the other things is just opening the entry and running the link open command. That is a great suggestion. However, I just realized that I would not be able to then open any of the links in an Android device (where I do part of my reading) or in, say, JabRef (I'd need to have a script run to reformat them, but then propagating changes both ways starts getting very cumbersome). I need to think some more about this. Thanks for your suggestions. Best, R. Ramon Diaz-Uriarte writes: Dear All, (I am not sure this is the appropriate place, but this is neither a bug report nor an feature request about helm-bibtex or org-ref, but a question from ignorance and I am learning quite a bit from the other helm-bibtex questions). How do people deal with multiple files that are logically associated to an entry? I've been used to keeping the main file, supplementary materials, associated code, etc, in a directory per entry. This kind of modus operandi is something I adopted (fell into?) easily with Zotero and Mendeley. But I am not sure that this is the best way to proceed. If I end up with multiple files per directory, helm-bibtex-find-pdf[1] cannot know which one I want to open. I could keep the main file in the general directory, so it is found directly by helm-bibtex-find-pdf and specify other files (of secondary usage) in the file field (and maybe open them via ebib when/if needed)? But this does not seem elegant. Another is to have an entry per file, with unique key, but this does not seem right. Thanks, R. [1] Thanks to Titus' help (https://github.com/tmalsburg/helm-bibtex/issues/53), opening a PDF that is given in the file field with the directory name is now within my reach. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
[O] more helm-bibtex/org-ref questions
Dear All, (I am not sure this is the appropriate place, but this is neither a bug report nor an feature request about helm-bibtex or org-ref, but a question from ignorance and I am learning quite a bit from the other helm-bibtex questions). How do people deal with multiple files that are logically associated to an entry? I've been used to keeping the main file, supplementary materials, associated code, etc, in a directory per entry. This kind of modus operandi is something I adopted (fell into?) easily with Zotero and Mendeley. But I am not sure that this is the best way to proceed. If I end up with multiple files per directory, helm-bibtex-find-pdf[1] cannot know which one I want to open. I could keep the main file in the general directory, so it is found directly by helm-bibtex-find-pdf and specify other files (of secondary usage) in the file field (and maybe open them via ebib when/if needed)? But this does not seem elegant. Another is to have an entry per file, with unique key, but this does not seem right. Thanks, R. [1] Thanks to Titus' help (https://github.com/tmalsburg/helm-bibtex/issues/53), opening a PDF that is given in the file field with the directory name is now within my reach. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Cooperating with oneself using the cloud?
Along the lines of what Bruno suggested, at least these two services also claim to be encrypted locally (so during transit through the net and while on their servers things are always encrypted): https://mega.co.nz/ http://www.wuala.com/ In fact, for files that you really want to be kept private a paranoid setup could involve encrypting the org file with pgp[1] AND then sharing it via one of the cloud services that say things are encrypted there. Note, though, that many people report that those two (and spideroak) are not as fast as dropbox and/or not as easy to setup. Best, R. [1] Either a mechanism somewhat like Thierry suggested or a mechanism like the one, now incorporate into org (I think) and that was started with this thread from Jorge Alfaro: http://lists.gnu.org/archive/html/emacs-orgmode/2014-05/msg00422.html On Mon, 15-09-2014, at 16:51, Bruno Bigras bigras.br...@gmail.com wrote: - Maybe http://git-annex.branchable.com/assistant/ (it seems the xmpp feature is not activated on Windows right now but it could be the best tool soon) - Maybe https://github.com/joeyh/git-remote-gcrypt with a free bitbucket private repo. (this is a fork maintained by joeyh, the git-annex assistant creator) - Spideroak (non-free) has a dropbox like folder but the data is supposed to be encrypted. 2014-09-15 6:59 GMT-04:00 Martin Schöön martin.sch...@gmail.com: One of the things I use org-mode for is making and maintaining TODO-lists. I do this at home and at work and I want the org-files of interest to be available and up-to-date at home and at work. The work-related org-file can not be publicly available for obvious reasons. I have emailed these files back and forth. This works but it isn't fool-proof (sometimes I forget) and I think there should be a less clumsy way to do this. I have tried a free and secure web-dav service. They are closing down and it also was a bit on the clumsy side since I never got their windows client to work at work. (Linux at home using cadaver.) I have seen Git being mentioned in this context in these nooks of the woods. That should work if I can find a free Git repository allowing me to keep files secret. I have looked at a few but have not seen (key word!) clear information on this. Options like BitTorrent Sync work really well but only if both computers run simultaneous which is not the case. Other options? Dropboxish services that keep prying eyes at bay? -- Martin Schöön http://hem.bredband.net/b262106/index.html -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] MobileOrg documentation?
On Thu, 07-08-2014, at 15:41, Jorge A. Alfaro-Murillo jorge.alfaro-muri...@yale.edu wrote: David Masterson dsmaster...@gmail.com writes: Anyone using MobileOrg? I use it all the time, but the Android version. I do not think that it is a dead project, at the end of last year there were quite a few updates. I generally use it to read my org agenda and TODO list in my phone, to automatically transfer the org agenda to the Google calendar and to make captures in my phone that I later organize into the proper file and heading in my computer. For those three tasks it is a five star application. I still think that it is far from being org-mode in your phone, but you should not see it that way. If you want to something that allows complete org functionality in your phone you are better off using something like JuiceSSH and connecting to one of your computers. Best, My experience is the same as Jorge's. I use it often, and in particular I make captures in my tablet that are synced back (in my case via Dropbox) to my computer, and there I organize those notes. So, as he says, for those three tasks it is a five star application. Best, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] problem of accents with pdflatex export
Dear Joseph, One minor suggestion: before exporting/texing you can play around with the encoding used to save the file by doing C-x RET f and then specify the one you want (with tab completion as usual). You can see which one (among utf-8, or the several iso, etc) works for you before fixing them in the head line as suggested by Andrea. In my case (which I guess could be similar to yours in terms of types of accents, ñ, etc), I use iso-8859-15. Best, R. On Sun, 29-12-2013, at 07:05, joseph.vidal.ros...@gmail.com wrote: Many thanks Andrea, you are indeed very kind to try to help me when everything works fine in your configuration by default. My OS is Debian (testing) GNU Linux and I'm working with emacs-snapshot. In fact I have realized that this problem of accents appears only with Gnome pdf viewer immediately open after C-e l-o . There is no problem when I compile after directly to pdflatex the latex file produced with the org file. Therefore it is a minor bug or a minor problem. But I meet several difficulties with my tentative of transition from writing .tex files to .org files instead. Therefore I am going to write an email to this list of very kind and helpful people. Best wishes , Jo. 2013/12/29 Andrea Rossetti andrea.rosse...@gmail.com Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes: ... Is it a way to automatically save the .org file in utf8 ? In my emacs the encoding is utf8 by default. Sorry, I never customized file-coding-system-alist and related variables, defaults worked well for me, so unfortunately I don't have good hints... but please note that in my simple environment (Win7 + Emacs 24.3 + Org 8.2.2-elpa + nearly zero customizations) I can export org to PDF with àèìòù (Italian) without any need to specify encodings, it just worked out-of-the-box. I would suggest to investigate in these directions: 1) try to see what happens without customizations (maybe by running emacs -Q) 2) try to force utf8 on that specific org file, by saying in the head line: # -*- mode:org; your settings...; coding:utf-8 -*- 3) or alternatively: # -*- mode:org; your settings...; coding:iso-8859-1 -*- Kindest regards, Andrea -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Org Tutorials need more structure
carsten.domi...@gmail.com writes: Hi everyone, today I looked at our tutorial page at http://orgmode.org/worg/org-tutorials/index.html and came away with the feeling that that this page has become somewhat useless for people who are really new to Org. I think the page should start with a section of true recommendations for beginners, a path we tell every new users to take in order to learn about Org mode. Can we have a discussion here on how this path should look like? When you came to Org-mode as a newby, what were the three resources that really made an impression on by being accessible and providing feel and promise for digging deeper? Dear Carsten, For me it was one resource: the compact guide. I found it well written, with links to additional info if I needed it, and structured in such a way that I could really start using immediately what I was most interested in at the moment (initially outlines and scheduling). [Some context: I came to org looking for the outlines and scheduling, and a vague desire for literate programming, because I wanted these features fully within Emacs, after having played with Leo ---http://leoeditor.com/--- for around a year]. To see what I might feel today, I just went to the first hit I get in google for org mode (which is, of course, http://orgmode.org/) and still find the compact guide. But maybe it would be good to emphasize it a bit more (there are ten lines of text, and the compact guide is the fifth). As well, a link to the compact guide might be added from the org-tutorial page. Finally, regarding the org-tutorial page, as it has already been mentioned in this thread, videos might not be the best vehicle for everyone (certainly not for me ---I'd rather read text where I can adjust the pace to that of my brain). Sacha's Outlining your notes with org made a lasting impression, though (but Sacha's blog entry was written after I read the compact guide, IIRC). Best (and thanks for org), R. - Carsten -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] [SYNC] How do you sync your org-mode files between ndevices (n 2))
function. The ~CURRENT1~, ~CURRENT2~, and ~CURRENTARCH~ strings are replaced with the file from the first root, the file from the second root, and the last synchronized version. The ~NEW~ file is where Unison expects the file to be saved (which will be done by the ediff session). Thus, when an org file has been modified on both hosts, an ediff session will be launched in a new frame. Closing the frame will make Unison commit the merge (it waits until the command has finished). If one does not want to use backups, it's possible to use the simpler ediff (without ancestor) command as follows. #+BEGIN_EXAMPLE root = /Users/schmitta/dir1 root = ssh://user@remote/relative/path/to/dir2 servercmd = /usr/bin/unison merge = Name *.org - emacsclient -c --eval '(ediff-merge-files CURRENT1 CURRENT2 nil NEW)' #+END_EXAMPLE -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] advice needed: how do you guys sync org files between devices?
Hi Itai, zelt...@gmail.com writes: Hi all I have been using dropbox since i started using orgmode a few weeks ago (yeah im a neewb :)), which kinda works but i find it very annoying as it keeps creating conflicted copies, isnt reliable on my Linux main machine etc etc.. I was wondering what you guys do for syncing org files between PC's, Os's, devices (android etc).. Best Itai I use a combination of dropbox (between the computers ---all running Linux) and version control, and for syncing with Android I use mobile org. With Dropbox I've had a some conflicted copy issues; this is annoying (and is the sort of thing that would have been solved much more easily with version control) but happens very rarely. What I like about this is that my frequent changes in org files get propagated without the need for an explicit version control command. However, for safety and for tracking, I run a nightly job with bazaar where I commit all changes (this is done in only one of the machines, of course). This has actually proven extremely useful when, by mistake, I have deleted a complete subtree and only realized maybe a month later. HTH, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] OT: Annotating PDF Org
To set the (new) record straight: On Tue, 7 May 2013 00:44 Ramon Diaz-Uriarte rdiaz02 at gmail.com writes: (...) [Talking about Okular] Note, though, that incorporating annotations in the PDF itself, which means you use the Save As, is somewhat of a pain, because by default the file name and directory are not reasonable, in my opinion; see this feature request: https://bugs.kde.org/show_bug.cgi?id=319042. (This is why I now do most of my paper reading/PDF annotation in the tablet, even if I have no keyboard there). As of 45 minutes ago that is no longer the case, because the bug has been fixed/the request has been honored. https://projects.kde.org/projects/kde/kdegraphics/okular/repository/revisions/460502d1240ae5eaa865b3e2873a23322b836ebf https://bugs.kde.org/show_bug.cgi?id=319042 R. (...) On Tue, 7 May 2013 16:39:42 -0500,Russell Adams rlad...@adamsinfoserv.com wrote: On Tue, May 07, 2013 at 11:36:31PM +0200, Ramon Diaz-Uriarte wrote: - Annotate/highlight the PDF, keeping the annotations in the PDF itself (when on the computer I use Okular, and Save As; if in the tablet, I use ezPDF or similar). I emphasize this: the annotations are in the PDF itself (i.e., if you open the PDF with evince, acrobat reader, whatever, you'll see them there). My understanding was that Okular didn't update the PDF, it had a mini-database. You're saying if you save the PDF again it'll combine the annotations? -- Russell Adamsrlad...@adamsinfoserv.com PGP Key ID: 0x1160DCB3 http://www.adamsinfoserv.com/ Fingerprint:1723 D8CA 4280 1EC9 557F 66E8 1154 E018 1160 DCB3 -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] OT: Annotating PDF Org
On Mon, 6 May 2013 08:39:07 -0500,Russell Adams rlad...@adamsinfoserv.com wrote: Given the emacs and Org oriented nature of this group, I'd like to know if anyone has found a good Orgish (ie: portable, text, etc) to annotate PDFs? Features would be items like highlighting blocks, adding notes (margins or sticky notes), and saving to either a sidecar file in a text format (ala Org) or directly appending the PDF. I am not sure this will be of much help since the annotations, etc, are not originally saved in a sidecar file but this is basically what I do: - Annotate/highlight the PDF, keeping the annotations in the PDF itself (when on the computer I use Okular, and Save As; if in the tablet, I use ezPDF or similar). I emphasize this: the annotations are in the PDF itself (i.e., if you open the PDF with evince, acrobat reader, whatever, you'll see them there). - Extract the annotations from my complete collection of PDFs (nightly cron job), storing all of them in an org file, with a link to the PDF. (I do the extraction with Leela ---https://github.com/TrilbyWhite/Leela---, which I find is more reliable than poppler-based approaches, such as that in recoll). So the orgish part is just the second one, but it works for me: I can search all of my annotations and jump directly to the PDF, from a single org file from within Emacs. Highlights? Nope, it does not work as Leela does not extract them and I could not find another tool to do it automagically. Recoll will extract all text from PDFs (not the annotations, though), so I can search for specific text on my complete PDF collection using recoll. But that ain't orgish at all ;-) and it is decoupled from the previous approach. A few more details, and some ugly R code that I use to do this are available here: http://ligarto.org/rdiaz/Zotero-Mendeley-Tablet.html#sec-9 Best, R. Thanks. -- Russell Adamsrlad...@adamsinfoserv.com PGP Key ID: 0x1160DCB3 http://www.adamsinfoserv.com/ Fingerprint:1723 D8CA 4280 1EC9 557F 66E8 1154 E018 1160 DCB3 -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] OT: Annotating PDF Org
On Tue, 7 May 2013 16:39:42 -0500,Russell Adams rlad...@adamsinfoserv.com wrote: On Tue, May 07, 2013 at 11:36:31PM +0200, Ramon Diaz-Uriarte wrote: - Annotate/highlight the PDF, keeping the annotations in the PDF itself (when on the computer I use Okular, and Save As; if in the tablet, I use ezPDF or similar). I emphasize this: the annotations are in the PDF itself (i.e., if you open the PDF with evince, acrobat reader, whatever, you'll see them there). My understanding was that Okular didn't update the PDF, it had a mini-database. You're saying if you save the PDF again it'll combine the annotations? It used to be that Okular saved the annotations in an external file (located at ~/.kde/share/apps/okular/docdata or similar), I think as an XML file (if memory serves me well). You can still do that, but as of some recent version of Okular (0.15? which you might need to compile yourself, depending on your Linux distro), you can also save the annotations and highlights in the PDF itself (the PDF, not the okular document). From the okular docs: http://docs.kde.org/stable/en/kdegraphics/okular/annotations.html The long thread, extending back in time five years, about this feature request, etc https://bugs.kde.org/show_bug.cgi?id=151614 I am not sure what you mean by combine the annotations. But if you do Save As, you can save the annotations in the PDF itself. You can, I guess, do both things (save in the external file, and save in the PDF), but I've never done that. Note, though, that incorporating annotations in the PDF itself, which means you use the Save As, is somewhat of a pain, because by default the file name and directory are not reasonable, in my opinion; see this feature request: https://bugs.kde.org/show_bug.cgi?id=319042. (This is why I now do most of my paper reading/PDF annotation in the tablet, even if I have no keyboard there). By the way, as of now (or a month or so back, at most), evince can save annotations in the PDF itself, but will not highlight. Best, R. -- Russell Adamsrlad...@adamsinfoserv.com PGP Key ID: 0x1160DCB3 http://www.adamsinfoserv.com/ Fingerprint:1723 D8CA 4280 1EC9 557F 66E8 1154 E018 1160 DCB3 -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] Offer for taking over maintainership
I offer to take over maintainership of Org. -1 too (or -infinity, if allowed, as previously suggested). -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
[O] Encrypting org Files tutorial: two changes?
Dear All, Two comments about the the Encrupting org Files tutorial (http://orgmode.org/worg/org-tutorials/encrypting-files.html), which might be specific to Debian. 1. In section Encrypting the Whole File Using EasyPG it says If you want to encrypt the whole file using gnupg, but still have the decrypted file recognized as an org file, you should make: (...) however, as far as I can tell, with both Emacs 23 and Emacs 24 anything with a name whatever.org.gpg will be automatically recognized as an org file even if one does not use that first line. Without that first line, however, it does prompt for a key whenever the file is saved. Maybe this section could be rewritten as: Any file saved with the .org.gpg extension will be recognized as an org file when decrypted. If you do not want to be prompted for a password every time you save a file, add to the first line of the file. 2. At least in Debian (require 'epa-file) (epa-file-enable) are not needed. Best, R. P.D. Versions of Emacs where I just verified it: Emacs 23: 23.4.1, from emacs23 23.4+1-4 in Debian. Emacs 24, 24.3.50.1, from emacs-snapshot 2:20121217-1 in Debian Nevertheless, these features have worked this way for quite some time (at least one or two years). -- Ramon Diaz-Uriarte Department of Biochemistry Universidad Autónoma de Madrid Instituto de Investigaciones Biomédicas “Alberto Sols” (UAM-CSIC) Madrid Spain Dirección - Address: Laboratorio B-25 Departamento de Bioquímica Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: ramon.d...@iib.uam.es rdia...@gmail.com http://ligarto.org/rdiaz
[O] org-mobile-push and SUMO buffer
Dear All, I think that the behavior of org-mobile-push has changed in some recent update. Since a few days ago (when I upgraded to v. 7.9.1-2, from Debian), whenever org-mobile-push runs, a new agenda buffer called *SUMO* is created, and the display redrawn. I can see (in file org-mobile.el) where this code lives. Now, I am not sure to understand this new behavior, nor if I should try to override it, nor what is the recommended approach. This is my problem: - I often have a bunch of org files opened in a single Emacs frame (split horizontally and vertically, etc). - One of the windows in that Emacs frame is always the org-mode agenda, called *Org Agenda*, and generated with M-x org-agenda (this command I call as soon as I start up that Emacs). - Then, when org-mobile-push runs (either because it tell it do so, or because the timer says so), the display gets redrawn, and I get only two windows, one with *Org Agenda* and the other with the *SUMO* buffer. This is very annoying to me because: a) as far as I can tell, the info in both buffers is the same; b) I get all my previous window setup messed up; yes, I do get back to it with winner mode. But I'd rather not have to do that every 30'. I guess I could hack the org-mobile.el file so that org-mobile-push does not redraw the display, or rename the org-agenda-buffer (either globally or just for org-mobile), etc, but I think there is something much simpler that I am missing. How can I fix this problem? Best, R. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
[O] Off-topic: *.gpg files and EasyPG
Dear All, Apologies if this is totally off-topic, but I think many people use org-mode + EasyPG to encrypt *.org.gpg files, and I could not think of a more knowledgeable list than this one ;-). * Summary: If an encrypted buffer is killed right when it is being opened (when you just typed the password), the contents of the encrypted buffer are left, as plain text, in other buffer(s). * Details: I routinely use org mode with EasyPG. Yesterday, after realizing that sometimes I leave a gpg buffer open for longer than I should, I figured I'd set a timer so that any buffers that end with *.gpg are killed periodically. This seems to work OK, except if the buffer is killed right at the moment when it is being visited; i.e., right after you have entered the password. If that happens, the contents of the encrypted file are left, as plain text, in one of the other buffers (often *Scratch* or *Messages*, if those exist, or some other buffer, and oftentimes one which is not currently visible). ** Reproducible example 1.I have the following code in my .emacs: --- ;; from ;; http://stackoverflow.com/questions/5097561/killing-buffers-whose-names-start-with-a-particular-string (require 'cl) (defun is-killable-buffer (buffer) (let ((name (buffer-name buffer))) (string-match .*\\.gpg$ name))) (defun kill-killable-buffers () (loop for buffer being the buffers do (and (is-killable-buffer buffer) (kill-buffer buffer (run-at-time t 120 'kill-killable-buffers) - 2. Now, create a *.gpg file, put something in there, and save it so symmetric encryption is used. 3. Change the interval when kill-killable-buffers runs. Set it at 1: (run-at-time t 1 'kill-killable-buffers) and evaluate the expression. 4. Try to visit the gpg file. As soon as you enter the password, the buffer is killed. So you never see it being opened. You do see the message Wrong type argument: stringp, nil But the contents, as decrypted, plain text, will be left in one of your other buffers; might be *Messages* or *Scratch* or *ESS* if you have it, but it could also be any other buffer you are visiting. If the contents end in another buffer you are visiting (say, buffer abc.txt), and you do not notice what happened, when you save abc.txt all the contents of the encrypted file end up in a plain text file. ** Questions. 1. Is this the way it should be? In particular, dumping the unencrypted content on another, normal buffer, seems worrisome. 2. Suppose the contents end up in *Scratch* or *Messages*. How serious a problem is this? Of course, if anybody has physical access to the machine while you are not there that is a problem. But I understand that the content of those buffers is never saved? And it cannot be accessed remotely? The reason for question 2. is that if those are not worrisome, then it might make sense to use the approach of having a timer to kill the gpg buffers periodically, and have it run in an emacs process that is dedicated, exclusively, to opening the gpg file(s). Best, -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25. Facultad de Medicina (UAM) Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
[O] agenda view: showing rows of a table with dates
Dear All, Suppose I have an entry with a table for a class schedule such as *** BM-1 2011-2012 schedule | Class | Group | Date | |-+---+--| | Presentation| All | 2011-09-26 Mon 09:30-11:00 | | Presentation Moodle | All | 2011-09-26 Mon 11:00-12:30 | | BLAST | A | 2011-09-28 Wed 11:00-12:30 | |-+---+--| Now, when I go to the agenda, what I see displayed is the BM-1 2011-2012 schedule. But I'd like to see the corresponding row in the table (so I know what I'm supposed to be talking about ;-). I think I recall reading something about this sometime in the past, but I do not seem to be able to find it in tutorials, the manual, or the mailing list. I guess an immediate solution is not to use a table to begin with. But I like the table because it lets me organize material nicely (group, lecturer, etc) and it is s easy to export and hand it to students. Am I missing something obvious? Thanks, R. -- Ramon Diaz-Uriarte Department of Biochemistry Universidad Autónoma de Madrid Spain http://ligarto.org/rdiaz Temporarily at: Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) Phone: +34-91-732-8000 ext. 3019 Fax: +-34-91-224-6972
Re: [O] zotero (or mendeley) integration with org
Dear Stephen, [My ---long--- comments refer only to Mendeley, not org, so maybe this should be off-list]. On Sat, Mar 26, 2011 at 4:47 PM, Stephen Eglen s.j.eg...@damtp.cam.ac.uk wrote: There was a mail-thread lastyear about zotero and integration with org. Now that there is an alpha release of 'org-standalone' http://www.zotero.org/blog/2011/02/ has anyone looked at whether this helps integrate org and zotero? I've not yet switched to a pdf manager (they're all stuffed into a folder, with a few subfolders, and the only meta-data is in the filename!), so I'd appreciate hearing what others to do to look after their pdfs. Mendeley is a possibility too (although syncing between machines is a must, and Mendeley doesn't offer that yet.) I've been using Mendeley for about 9 months now, after spending a few weeks examining how Mendeley, Zotero, and some other options, fitted into my habits. Here are some comments about your questions: 1. Syncing: the orthodox Mendeley way allows for two options: a) you sync the database of the refs (not pdfs) via their servers; b) you also sync the pdfs, which will most likely require you to pay for storage in their servers if you have a decent number of pdfs. However, I do the syncing myself. I've used rsync, then Dropbox, and for the last four months Wuala. I sync the directory where the dbs are (~/.local/share/data/Mendeley Ltd./Mendeley Desktop) and the directory where I store my pdfs. I have had this set up for the 9 months, shared between four machines, and it works fine (I try not to have Mendeley open in more than one machine at the same time, to prevent problems, but have never run into any). 2. All pdfs into a folder with a few subfolders. In Mendeley you can have each reference under its own subdirectory with some limited flexibility for the naming of the subdirectories (author, date, title, etc). Its not ideal (e.g., I dislike spaces in directory names), but I like it better than Zotero's (names of subdirectories are a random string). Keeping each ref in its own directory allows me to store other stuff (e.g., code, suppl. mat, etc) in the same place as the pdf. Now, that said, I am not all that happy with Mendeley. To begin with, Mendeley is not free software. Zotero is, but the naming of directories and the lack of a built-in pdf editor were a no-go for me. Mendeley's pdf editor allows me to underline and add notes to pdfs. At least in Linux, adding comments and underlining pdfs is not yet well solved: evince currently allows comments in the devel. version, but no underlining. Okular allows comments and underlining, but stores them in ~/.kde/share/apps/okular, which I dislike (it seems very fragile), and in okular you cannot underline a single column in papers with multi-column setup (another no-go for me). However, with Mendeley's pdf editor/viewer you can only display one pdf at a time, which is a pain if you want to compare two or more papers side by side. In fact, Mendely's pdf viewer is rather under-powered compared to, say, okular (e.g., lack of keyboard shortcuts for viewing to page or width size, difference between scrolling and moving to next page, fast searching, etc). If I only need read-only access to the pdf, even from within Mendeley, I use another pdf viewer. I thought about going back to JabRef, and using recoll for searching over all of my pdf collection (I like recoll's search much more than Mendeley's one). But that leaves unsolved the pdf commenting issue. Also, I like the ease of adding papers with Mendeley (e.g., when searching in the web, or its generally successful extraction of metadata from a paper's pdf); in fact, I find adding papers is even easier with Zotero (and friendlier also if you add things like web pages, etc). I also looked into paperpile, but I find it to be much more beta than Mendeley, and so far less flexible in almost everything. So I'd also like to know how others are dealing with pdfs. Anyway, and in spite of my complaints, since about 9 months ago I have not printed a single paper. It is great to have all those pdfs synced among my machines, be able to search them quickly, and not carry around kilograms of dead trees. Best, R. Stephen -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-732-8000 ext. 3019 Fax: +-34-91-224-6972
Re: [Orgmode] not showing DONE items in weekly/daily agenda
On 11/27/06, Carsten Dominik [EMAIL PROTECTED] wrote: Items that are DONE still show up on the day when they were scheduled. But they are not being carried over to the next day as being overdue. Yes, they are not carried to the next day, but they are shown (with a different color) in the agenda. Does that need to be an option? Maybe its just me, but it is easier for me to glance at the agenda and have listed only things that I need to do, not those done. If things that are done are shown, its like I need to do kind of a mental grep to filter those out. R. - Carsten On Nov 26, 2006, at 23:42, Ramon Diaz-Uriarte wrote: Apologies in advance, because I am sure this info is available, but I've been searching the manual, the FAQ, the customizations, and the email list, and I can't find it: when I do C-a a (for the weekly/daily agenda), how can I prevent the DONE (but scheduled or with deadline) items from being shown? In fact, from a previous posting in the emai list http://article.gmane.org/gmane.emacs.orgmode/105/match=done+agenda I get the impression that scheduled, but done, should not show by default in the agenda view. Thanks, R. -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz ___ Emacs-orgmode mailing list Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode -- Carsten Dominik Sterrenkundig Instituut Anton Pannekoek Universiteit van Amsterdam Kruislaan 403 NL-1098SJ Amsterdam phone: +31 20 525 7477 -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz ___ Emacs-orgmode mailing list Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] org - Palm
On 11/7/06, Carsten Dominik [EMAIL PROTECTED] wrote: Also I would be interested in a good way to use information maintained under org-mode on portable devices, and I would support such a development by writing the lisp code for the correct exporters and importers. However, I don't want to write five different That would be neat (of course, it is always easy to say this when someone else does the coding :-). exporters/importers, so agreeing to some format would be mandatory. Currently in this area, there are the following Ansätze. They mostly work one-way, to get information from Org-mode to a portable device, not the other way round. But there are exceptions, see below. - Bonsai Outliner === This is a two-way interface for basic outlines. I don't know what the status is and I have not not used it myself so far. Thomas, would you like to comment? I've never used Bonsai (I think it does not have a desktop counterpart for Linux). I've used Shadow (www.codejedi.com), which has a desktop counterpart for Linux, Win, and Mac (I think) which allows editing, etc, on the computer. From the web page of Bonsai, it seems that the features of Bonsai and Shadow are very similar. - iCalendar export Org-mode can export items with datestamps and deadlines as well as TODO items into a standard iCalendar file. These files can be read by most calendar programs both on PC/Mac/Linux machines, and as far as I know also on portable devices. I am using this mechanism to get information from org-mode into iCal on the Mac. Unfortunately, there is no good way to get the changed info back into org-mode. But it is useful to see what your TODO items and schedule are. iCalendar does not seem to be well supported by Palm (from surfing the net, it seems that the Palm vCalendar format does not support as many features as iCalendar). For Windows, its easy to find ways of going from iCalendar to your Palm. For Linux, I've not found those many. The following might be of use: http://jp-icalendar.sourceforge.net/ and I think that both KDE (Korganizer + Kpilot) and the equivalent Gnome apps. allow importing iCalendar and producing vCalendar (I use neither kde nor gnome, so I don't really know). - Fast external updates = Some time ago I worked with Tim O'Callaghan on the idea of delayed updates of Org-mode files, a feature he called fast updates. His idea was to copy an org-mode file to a mobile device, and to use some basic editor to mark lines that should be changed later the file gets back into an Emacs environment. Tim's idea was to mark headline with a single character *before* the stars. For example, if I have a todo item *** TODO Do this it could be marked d*** TODO Do this and next time Org-mode opens this file in Emacs, it would find this line and switch the TODO to DONE. The idea behind this is that input on mobile devices is never fun, on phones it is really terrible, so you want to be done with a single keystroke. And you could trigger more complex operations like archiving in this way. Some time ago I implemented this basic functionality. I still have the code if someone is interested. But unfortunately the project somehow got stuck. There were technical reasons, but I believe the underlying reason may be that by just putting the org-mode file into an editor on a mobile device with a small screen and no show/hide capabilities makes it much harder to read and handle than in Emacs. But I am not sure, and may be this project could be revived. - Editor on the Palm-side === Putting whole Org-mode files into a Palm editor has the advantage that you can keep them up-to-date on both machines using synchronization or, for example, cvs merging. Having an editor that actually implements a subset of Org-modes functionality using some scripting language (Rexx was mentioned) sounds attractive to me. So far, the suggestion of Tim O Callaghan (PalmED) and a few similar linked from there seem fine for me. - Print/export only the current TODO list === You can create TODO lists and then print them or export them to your Palm. Then you tick items off while on the go, and when you get back to a real computer you create the same TODO list again and update the done items (idea from Pete Phillips). While this sounds like double work, you can make it part of the review process to check where your projects stand. This is a really neat idea! Thanks. R. Carsten On Nov 5, 2006, at 22:39, Ramon Diaz-Uriarte wrote: Dear All, I am wondering if anybody has found out how to export from org, and get the stuff in a usable way into a Palm, and (ideally) edit it there and bring it back to org later. I saw in a fomer post From: Carsten Dominik
[Orgmode] org - Palm
Dear All, I am wondering if anybody has found out how to export from org, and get the stuff in a usable way into a Palm, and (ideally) edit it there and bring it back to org later. I saw in a fomer post From: Carsten Dominik dominik at science.uva.nl Subject: Other software development for Org-mode Newsgroups: gmane.emacs.orgmode Date: 2006-03-14 10:39:25 GMT (33 weeks, 5 days and 49 minutes ago) (...) Bonsai Outliner for Windows/PalmOS, export/import options for Org-mode files Thomas Baumann has been working on these, but not finished the org-to-bonsai branch if I remember correctly because of problems with the data format on the Palm. But my googling didn't find anything else. I actually have lowered my expectations to just (?) two things: a) outlines; b) calendar/deadlines info. a) For outlines, I used to use Shadow Plan (http://www.codejedi.com/) on my Palm. Getting the outlines into org is a piece of cake (at least under Linux); from the Shadow Desktop one exports as ASCII, and using sed (or whatever) one replaces \t by *. So now all that info is an org outline. I assume similar things can be done with other Palm outliners. But: a.1. How do I go back to the Palm? a.1.1. Via Plucker; export from org as html, use plucker for html - pdb. That works, but that is not editable in the Palm a.1.2. Convert the org file to a pdb using pyrite publisher (http://www.pyrite.org/publisher/index.html). That is a regular file that can be seen and edited inside the Palm, but one looses the structure, and if one edits the file in the Palm, how will the new stuff be incoporated in any reasonable way into org? b) calendar/dates, etc. The options are somewhat like a). One can see the info, but that stuff does not show up in the Palm calendar. I am wondering if anybody has any suggestiongs/ideas or things to try. My googling is not really finding much. Thanks, -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz ___ Emacs-orgmode mailing list Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
