Re: [Skim-app-users] Skimnotes app and Unicode

[Christiaan Hofman]

Note that Skim puts the data in a separate data structure, while other viewers 
embed the notes in the PDF data. So I guess other readers implicitly normalize 
the unicode when they write not to the Pdf. We don;’t do anything to the 
strings, so it will be the way it is entered.

Christiaan

> On 12 Apr 2024, at 14:16, Mark Roberts  wrote:
> 
> Hi,
> 
> Thanks for your message. Let me try to ask this question a little differently.
> 
> Regarding Unicode, it appears that Skim behaves unlike every other PDF reader 
> I've got, e.g., Acrobat, PDF Expert, Foxit Reader, and Preview.
> 
> If I copy some text from a PDF file that uses Unicode, all of these PDF 
> readers will perform Unicode normalization, while Skim does not.
> 
> For example, I copy the string "shū" from a PDF using any of the other reader 
> apps, and the clipboard contains 7368c5ab.
> 
> If I try this with Skim, though, the clipboard contains 736875cc84. You can 
> verify this using the command line, e.g., echo -n "shū" | xxd -p
> 
> Similarly, the output via skimnotes is not being normalized. So, it seems 
> that other PDF reader apps are doing normalization, but Skim does not.
> 
> When you say "any normalization should happen before the data was created" — 
> in fact this is not how all other PDF reader apps that I've got seem to work.
> 
> Would you consider adding an option for skimnotes to behave like other PDF 
> apps w.r.t. Unicode?
> 
> Thanks,
> 
> M.
> 
> On Fri, Apr 12, 2024 at 6:21 PM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> That would be useless. SkimNotes does not process the data, it just copies it 
> between different locations. Also passing the file through conversion does 
> not work, as none of the formats involved are unicode text files. The point 
> is that the strings included as part off the data may represent strings in 
> some encoding in some form. So any normalization should happen before the 
> data was created (which is not an option), or by parsing the plist, 
> normalizing all strings in it, and reassemble the plist.
> 
> Christiaan
> 
>> On 12 Apr 2024, at 04:48, Mark Roberts > <mailto:mroberts1...@gmail.com>> wrote:
>> 
>> Hi,
>> 
>> Thanks for clarifying.
>> 
>> I looked for a tool to do this, but I haven't found anything.
>> 
>> Some people suggest running a text file through oconv, but that seems to be 
>> just a brute force approach to patch specific characters.
>> 
>> What would you think about an option to skimnotes that invokes 
>> precomposedStringWithCanonicalMapping() or whatever the appropriate function 
>> is?
>> 
>> Thanks !
>> 
>> On Thu, Apr 11, 2024 at 11:18 PM Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> 
>> 
>>> On 11 Apr 2024, at 13:31, Mark Roberts >> <mailto:mroberts1...@gmail.com>> wrote:
>>> 
>>> I've been using the skimnotes command line app to "get" skim notes as a 
>>> plist, and to then convert them to XML with plutil.
>>> 
>>> One thing I've discovered is that notes in Unicode may not be normalized.
>>> 
>>> Some apps can handle this, but some cannot.
>>> 
>>> Question: is there a way to get skimnotes to normalize the Unicode, or 
>>> could you suggest an app I can use in a pipe with plutil... ?
>>> 
>>> Thanks !
>> 
>> I don’t think there exists a tool to normalize unicode strings in a binary 
>> plist. I am pretty sure that any tool that may exist to convert a binary 
>> plist to an XML plist goes through the same system code from Apple, so it 
>> will all do the same thing. Perhaps there is a tool to post-process the XML 
>> to normalize any strings as Unicode, but I could not help you there either.
>> 
>> Christiaan

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Re: [Skim-app-users] Skimnotes app and Unicode

[Christiaan Hofman]

That would be useless. SkimNotes does not process the data, it just copies it 
between different locations. Also passing the file through conversion does not 
work, as none of the formats involved are unicode text files. The point is that 
the strings included as part off the data may represent strings in some 
encoding in some form. So any normalization should happen before the data was 
created (which is not an option), or by parsing the plist, normalizing all 
strings in it, and reassemble the plist.

Christiaan

> On 12 Apr 2024, at 04:48, Mark Roberts  wrote:
> 
> Hi,
> 
> Thanks for clarifying.
> 
> I looked for a tool to do this, but I haven't found anything.
> 
> Some people suggest running a text file through oconv, but that seems to be 
> just a brute force approach to patch specific characters.
> 
> What would you think about an option to skimnotes that invokes 
> precomposedStringWithCanonicalMapping() or whatever the appropriate function 
> is?
> 
> Thanks !
> 
> On Thu, Apr 11, 2024 at 11:18 PM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> 
> 
>> On 11 Apr 2024, at 13:31, Mark Roberts > <mailto:mroberts1...@gmail.com>> wrote:
>> 
>> I've been using the skimnotes command line app to "get" skim notes as a 
>> plist, and to then convert them to XML with plutil.
>> 
>> One thing I've discovered is that notes in Unicode may not be normalized.
>> 
>> Some apps can handle this, but some cannot.
>> 
>> Question: is there a way to get skimnotes to normalize the Unicode, or could 
>> you suggest an app I can use in a pipe with plutil... ?
>> 
>> Thanks !
> 
> I don’t think there exists a tool to normalize unicode strings in a binary 
> plist. I am pretty sure that any tool that may exist to convert a binary 
> plist to an XML plist goes through the same system code from Apple, so it 
> will all do the same thing. Perhaps there is a tool to post-process the XML 
> to normalize any strings as Unicode, but I could not help you there either.
> 
> Christiaan

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Re: [Skim-app-users] note-tool-type randomly resets

[Christiaan Hofman]

Sorry, that should be ’n’.

See also the Wiki, and ‘?’.

Chrristiaan

> On 11 Apr 2024, at 23:01, Christiaan Hofman  wrote:
> 
> I think you typed ‘a’ without modifier.
> 
> Christiaan
> 
>> On 11 Apr 2024, at 20:32, Scott McLaughlin  wrote:
>> 
>> Hi,
>> 
>> I love this app, really wonderful, thank you.
>> 
>> I don't understand how, but at random moments it switches note type, always 
>> to 'anchored note' (I have it set to 'highlight'). This happens about once 
>> every hour or two, no idea why or what the trigger is (there's no obvious 
>> conditions under which this happens). I doubt that I'm hitting the shortcut 
>> key (ctrl+cmd+2 is not an easy thing to hit by accident), but could there be 
>> some other shortcut I'm hitting without knowing it, or some default I'm 
>> tripping? Any advice appreciated.
>> 
>> I'm on Mac M1 (Big Sur) and running up-to-date Skim (Version 1.7.2 (154))
>> 
>> best,
>> Scott



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Re: [Skim-app-users] note-tool-type randomly resets

[Christiaan Hofman]

I think you typed ‘a’ without modifier.

Christiaan

> On 11 Apr 2024, at 20:32, Scott McLaughlin  wrote:
> 
> Hi,
> 
> I love this app, really wonderful, thank you.
> 
> I don't understand how, but at random moments it switches note type, always 
> to 'anchored note' (I have it set to 'highlight'). This happens about once 
> every hour or two, no idea why or what the trigger is (there's no obvious 
> conditions under which this happens). I doubt that I'm hitting the shortcut 
> key (ctrl+cmd+2 is not an easy thing to hit by accident), but could there be 
> some other shortcut I'm hitting without knowing it, or some default I'm 
> tripping? Any advice appreciated.
> 
> I'm on Mac M1 (Big Sur) and running up-to-date Skim (Version 1.7.2 (154))
> 
> best,
> Scott



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Re: [Skim-app-users] Skimnotes app and Unicode

[Christiaan Hofman]

> On 11 Apr 2024, at 13:31, Mark Roberts  wrote:
> 
> I've been using the skimnotes command line app to "get" skim notes as a 
> plist, and to then convert them to XML with plutil.
> 
> One thing I've discovered is that notes in Unicode may not be normalized.
> 
> Some apps can handle this, but some cannot.
> 
> Question: is there a way to get skimnotes to normalize the Unicode, or could 
> you suggest an app I can use in a pipe with plutil... ?
> 
> Thanks !

I don’t think there exists a tool to normalize unicode strings in a binary 
plist. I am pretty sure that any tool that may exist to convert a binary plist 
to an XML plist goes through the same system code from Apple, so it will all do 
the same thing. Perhaps there is a tool to post-process the XML to normalize 
any strings as Unicode, but I could not help you there either.

Christiaan

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[Skim-app-users] Skim 1.7.2

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.7.2

New Features
  *  Allow highlighting all search results, through context menu.
  *  Allow displaying thumbnails or contents while searching.
  *  Add swipe actions  to show/hide or delete in snapshot table.

Bugs Fixed
  *  Fix repeated PDF-TeX syncing.
  *  Allow fractional duration in presentation tradition field.
  *  Allow warnings to be visible when editing transitions in presentation mode.
  *  Reorganize menus.
  *  Improve page navigation by swiping in single page mode.
  *  Fix text baseline in toolbar.
  *  Don't change Automatically Resize from fitting links.
  *  Fix page background in magnify tool.
  *  Fix crash when entering Presentation from a document that is full screen 
and tabbed.

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Re: [Skim-app-users] Zoom level resets when clicking on a bookmark (destination)

[Christiaan Hofman]

> On 27 Mar 2024, at 02:42, Chenji, Harsha  wrote:
> 
> On macos Sonoma 14.4.1 with skim.app v1.7.1. When reading a pdf with 
> bookmarks, suppose I choose Zoom to Fit when reading a page. When I click on 
> a bookmark in the left sidebar to navigate away to another page, the zoom 
> level changes such that the entire page is visible in the window. How do I 
> change this behavior and preserve the zoom level when I click a bookmark/go 
> to a "destination”?

This is really the outline item (i.e. bookmark) prescribing a zoom level or fit 
direction. So we are just doing what the PDF tells us to do. There is no way to 
prevent this.

Christiaan

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Re: [Skim-app-users] Printing Without or With Notes

[Christiaan Hofman]

> On 23 Mar 2024, at 21:24, Friedrich Vosberg  wrote:
> 
> Hi there.
> 
> Is there in Skim a switch for chosing to print a file either with the 
> personal annotations or without?
> 
> Thanks in advance and kind regards, Friedrich


Yes, you can use the Hide Notes item in the Notes menu.

Christiaan

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Re: [Skim-app-users] Micro-zoom ?

[Christiaan Hofman]

That is really a far too complex, it is not really a setting. As should be 
clear from your rather lengthy description, which isn’t even com plate (as I 
still don’t see exactly what you want). Anyway, you can do what you can do, not 
something else. Perhaps you can also try the Open file setting to Fit to PDF. 
Although that is more or less doing it the other way around (i.e. fit the 
window to the PDF). 

Christiaan

> On 19 Mar 2024, at 23:20, Thomas Schneider via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
> Thanks for all your efforts on this great program.
> 
>> "Zoom to fit" isnot a setting, it is an action.
>> I think you are confused with "Automatically Resize",which is a
>> setting that can also be set as a default.
> 
> Ok I sort of understand.
> 
> But it doesn't answer my question of how to automatically 'Zoom to fit'
> so that I don't have to keep doing this with every pdf.
> 
> I like to have my PDFs cover from top to bottom of my screen (for
> maximum visibility) and sideways standard page size.  Then I want the
> image to maximize into that space ("zoom to fit").  But I don't want
> to have to do this all the time.  So how do I set this up?
> 
> Tom



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Re: [Skim-app-users] Programmatically cropping PDF images

[Christiaan Hofman]

> On 18 Mar 2024, at 07:20, list_email--- via Skim-app-users 
>  wrote:
> 
> I am making PDF plots using Plotly which sometimes leaves more white space at 
> the margins than seems necessary, especially when considering cramming them 
> into a column in a paper. Skim does a nice job of cropping, but I’m wondering 
> if there is a way to do this programmatically, e.g,. from Python, Julia, or 
> Ada. I know that Skim is scriptable but I can’t find anything in Skim’s 
> Applescript dictionary about cropping.
> 
> I know that if there is an Applescript for doing this on a specified file or 
> all the PDFs in a folder that I can issue the command from any of the other 
> mentioned languages. I would gladly consider a non-Skim way also but I need a 
> method that detects the white-space margins rather than having me manually 
> determine the coordinates of a crop box since they will be different for 
> different images.
> 
> Jerry


There are various bounds properties for pages in the Skim AppleScript 
dictionary. there is a “bounds”, “media bounds” and “content bounds”. In 
particular, the latter one especially detects the white margins of the page. 
The other two are properties of the PDF that can also be changed (in particular 
the “bounds” for the crop box). 

Note that by default the page bounds are not saved by Skim, as they are part of 
the PDF data which we leave alone. So you need to export with embedded note to 
have it saved. That can also be done from AppleScript.

Christiaan

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Re: [Skim-app-users] scrolling by screen

[Christiaan Hofman]

Please note that version 1.9.2 should fix scrolling by page. So if you set the 
hidden preference I described, you could revert that.

Christiaan

> On 27 Feb 2024, at 16:24, Christiaan Hofman  wrote:
> 
> That is correct. The view does extend below the tool- and titlebar, that is 
> related to the blurred shine through effect in the titlebar. And the problem 
> does seem to get worse when the area it moves behind is bigger. Although it 
> does not seem be directly equal to it (i.e. the wrong offset you get in 
> scrolling is not equal the size of the title- and toolbar, it is luckily much 
> smaller, which I find a bit strange, Apple’s making a very weird calculation 
> error). So I guess without the toolbar, it would be even less. And if in 
> addition you add the find bar (Cmd-F), the problem is even worse.
> 
> If you think this problem is really intrusive for you, we have a hidden 
> preference to not extend the view below the title, tool, and find bar which 
> you could turn on. You can find the details about setting on the Wiki. The 
> preference is called SKDisableSearchBarBlurring. 
> 
> It looks like with that option it will scroll exactly by the view area. As I 
> said before, I still think that is wrong, as it should scroll by less than 
> that. For instance, if the line at the bottom is only partially visible, you 
> should see the full line after scrolling, not the lower half (you never read 
> upper and lower halfs separately). Hopefully Apple will fix this in a future 
> OS version, but unfortunately scrolling and navigation the PDF view has never 
> worked without problems (although the bugs vary by OS version).
> 
> Christiaan
> 
>> On 27 Feb 2024, at 13:52, Derek Van Ittersum > <mailto:derek.vanitter...@gmail.com>> wrote:
>> 
>> One follow up here--I notice when I set the toolbar to "text only" (instead 
>> of "icon only") there is nearly no problem--there doesn't appear to be any 
>> lines missing in the scroll. It almost seems as if the bigger toolbar 
>> obscures the view of the PDF. 
>> 
>> On Mon, Feb 26, 2024 at 10:03 AM Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> 
>> 
>>> On 26 Feb 2024, at 13:35, Derek Van Ittersum >> <mailto:derek.vanitter...@gmail.com>> wrote:
>>> 
>>> This question is in reference to another earlier thread: 
>>> https://sourceforge.net/p/skim-app/mailman/message/37882805/ 
>>> <https://sourceforge.net/p/skim-app/mailman/message/37882805/>
>>> 
>>> I'm not sure I understand the logic here or how to work around it. When I 
>>> am reading a PDF and scrolling via the space bar, I need to adjust the 
>>> viewable content with the up arrow key after each press of the space bar. 
>>> That is, I don't want to scroll to the top of the next page, I want to read 
>>> the next screenful of content. Yet, when I press the space bar, the next 
>>> screenful of content has skipped about a line and a half. Could there be an 
>>> option to designate how much overlap in content to show when scrolling via 
>>> the space bar (or page down key)?
>>> 
>>> Thanks,
>>> Derek
>> 
>> The scrolling in the PDF view is implemented by Apple, so for us (and you) 
>> it just works the way it does. There is no way we can change that, so we 
>> cannot provide an option to do it differently. 
>> 
>> I do think it should really scroll by a little /less/ than a full view 
>> height, which is what scroll views normally do .But for some reason, in the 
>> PDF view it does not do that. I consider that a bug, but one of Apple, which 
>> only they can fix. I already did report that to them, but never got a 
>> reaction. You may also file a bug report with Apple if you want.
>> 
>> Christiaan

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Re: [Skim-app-users] Micro-zoom ?

[Christiaan Hofman]

“Zoom to fit” isnot a setting, it is an action. I think you are confused with 
“Automatically Resize”,which is a setting that can also be set as a default.

Christiaan

> On 5 Mar 2024, at 02:34, Thomas Schneider via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> Here's what the AppleScript for zoom in could look like:
> 
> That's interesting, may be it could be used to solve a problem I've
> had with Skim for some years now?  When I open Skim it is not set to
> 'Zoom to fit' and I have to do that every time.  I've asked you about
> how to do this a number of times and never got a solution.
> 
> Maybe it could be done automatically with a script?
> 
> Tom
> 
>  Thomas D. Schneider, Ph.D.
>  Senior Investigator
>  National Institutes of Health
>  National Cancer Institute
>  Center for Cancer Research
>  RNA Biology Laboratory
>  Biological Information Theory Group
>  Frederick, Maryland  21702-1201
>  schne...@mail.nih.gov
>  https://ccr.cancer.gov/staff-directory/thomas-d-schneider
>  alum.mit.edu/www/toms
>  https://alum.mit.edu/www/toms
> 
> 
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Christiaan

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[Skim-app-users] Skim 1.7.1

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.7.1

New Features
  *  Change defaults when changing text note font while holding Shift.
  *  Change defaults when changing note line attributes while holding Shift.

Bugs Fixed
  *  Work around initial page navigation bug on newer OS systems.
  *  Fix string cleaning for highlights and search.
  *  Tweak scrolling by page amount.

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Re: [Skim-app-users] Micro-zoom ?

[Christiaan Hofman]

Here’s what the AppleScript for zoom in could look like:

property theZoom : 2 ^ 0.125
tell application "Skim"
tell front document
set theScale to scale factor of (get view settings)
set theScale to theZoom * theScale
if theScale > 20 then set theScale to 20
set view settings to {scale factor:theScale, auto scales:false}
end tell
end tell

And for zoom out:

property theZoom : 2 ^ -0.125
tell application "Skim"
tell front document
set theScale to scale factor of (get view settings)
set theScale to theZoom * theScale
if theScale < 0.1 then set theScale to 0.1
set view settings to {scale factor:theScale, auto scales:false}
end tell
end tell

I chose 2^0.125 because then calling it twice does the same as normal zoom in 
(which effectively uses 2^0.25).

Christiaan

> On 2 Mar 2024, at 00:00, Christiaan Hofman  wrote:
> 
> 
> 
>> On 1 Mar 2024, at 22:35, Toby Thurston > <mailto:thurs...@eml.cc>> wrote:
>> 
>> "Command +" and "Command -" are useful keybaord short cuts for zoom in and 
>> zoom out, but sometimes I want finer steps to set the zoom level precisely.
>> 
>> Is this an area that the app has control over?   
>> 
>> Would it be possible to add a modifier ("Option Command +" and "Option 
>> Command -") so that the zoom level was incremented or decremented in smaller 
>> steps?
>> 
>> If so, what's the right way to request a feature?
>> 
>> Thanks, Toby Thurston
> 
> 
> The right way is to add a feature request tacker.
> 
> But this one would not be feasible. For one thing, zooming/out is implemented 
> as it is by Apple, not by us. And moreover, there is a real problem with 
> available shortcuts, which should also work on all key board layouts.
> 
> What you could do though is write two AppleScripts that do such things, and 
> add them to the Script menu. There is more information about the Script menu 
> and how to install scripts there on the Wiki. You could then assign shortcuts 
> to them in your System Preferences.
> 
> Christiaan

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Re: [Skim-app-users] Micro-zoom ?

[Christiaan Hofman]

> On 1 Mar 2024, at 22:35, Toby Thurston  wrote:
> 
> "Command +" and "Command -" are useful keybaord short cuts for zoom in and 
> zoom out, but sometimes I want finer steps to set the zoom level precisely.
> 
> Is this an area that the app has control over?   
> 
> Would it be possible to add a modifier ("Option Command +" and "Option 
> Command -") so that the zoom level was incremented or decremented in smaller 
> steps?
> 
> If so, what's the right way to request a feature?
> 
> Thanks, Toby Thurston


The right way is to add a feature request tacker.

But this one would not be feasible. For one thing, zooming/out is implemented 
as it is by Apple, not by us. And moreover, there is a real problem with 
available shortcuts, which should also work on all key board layouts.

What you could do though is write two AppleScripts that do such things, and add 
them to the Script menu. There is more information about the Script menu and 
how to install scripts there on the Wiki. You could then assign shortcuts to 
them in your System Preferences.

Christiaan

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Re: [Skim-app-users] scrolling by screen

[Christiaan Hofman]

That is correct. The view does extend below the tool- and titlebar, that is 
related to the blurred shine through effect in the titlebar. And the problem 
does seem to get worse when the area it moves behind is bigger. Although it 
does not seem be directly equal to it (i.e. the wrong offset you get in 
scrolling is not equal the size of the title- and toolbar, it is luckily much 
smaller, which I find a bit strange, Apple’s making a very weird calculation 
error). So I guess without the toolbar, it would be even less. And if in 
addition you add the find bar (Cmd-F), the problem is even worse.

If you think this problem is really intrusive for you, we have a hidden 
preference to not extend the view below the title, tool, and find bar which you 
could turn on. You can find the details about setting on the Wiki. The 
preference is called SKDisableSearchBarBlurring. 

It looks like with that option it will scroll exactly by the view area. As I 
said before, I still think that is wrong, as it should scroll by less than 
that. For instance, if the line at the bottom is only partially visible, you 
should see the full line after scrolling, not the lower half (you never read 
upper and lower halfs separately). Hopefully Apple will fix this in a future OS 
version, but unfortunately scrolling and navigation the PDF view has never 
worked without problems (although the bugs vary by OS version).

Christiaan

> On 27 Feb 2024, at 13:52, Derek Van Ittersum  
> wrote:
> 
> One follow up here--I notice when I set the toolbar to "text only" (instead 
> of "icon only") there is nearly no problem--there doesn't appear to be any 
> lines missing in the scroll. It almost seems as if the bigger toolbar 
> obscures the view of the PDF. 
> 
> On Mon, Feb 26, 2024 at 10:03 AM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> 
> 
>> On 26 Feb 2024, at 13:35, Derek Van Ittersum > <mailto:derek.vanitter...@gmail.com>> wrote:
>> 
>> This question is in reference to another earlier thread: 
>> https://sourceforge.net/p/skim-app/mailman/message/37882805/ 
>> <https://sourceforge.net/p/skim-app/mailman/message/37882805/>
>> 
>> I'm not sure I understand the logic here or how to work around it. When I am 
>> reading a PDF and scrolling via the space bar, I need to adjust the viewable 
>> content with the up arrow key after each press of the space bar. That is, I 
>> don't want to scroll to the top of the next page, I want to read the next 
>> screenful of content. Yet, when I press the space bar, the next screenful of 
>> content has skipped about a line and a half. Could there be an option to 
>> designate how much overlap in content to show when scrolling via the space 
>> bar (or page down key)?
>> 
>> Thanks,
>> Derek
> 
> The scrolling in the PDF view is implemented by Apple, so for us (and you) it 
> just works the way it does. There is no way we can change that, so we cannot 
> provide an option to do it differently. 
> 
> I do think it should really scroll by a little /less/ than a full view 
> height, which is what scroll views normally do .But for some reason, in the 
> PDF view it does not do that. I consider that a bug, but one of Apple, which 
> only they can fix. I already did report that to them, but never got a 
> reaction. You may also file a bug report with Apple if you want.
> 
> Christiaan

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Re: [Skim-app-users] scrolling by screen

[Christiaan Hofman]

> On 26 Feb 2024, at 13:35, Derek Van Ittersum  
> wrote:
> 
> This question is in reference to another earlier thread: 
> https://sourceforge.net/p/skim-app/mailman/message/37882805/ 
> 
> 
> I'm not sure I understand the logic here or how to work around it. When I am 
> reading a PDF and scrolling via the space bar, I need to adjust the viewable 
> content with the up arrow key after each press of the space bar. That is, I 
> don't want to scroll to the top of the next page, I want to read the next 
> screenful of content. Yet, when I press the space bar, the next screenful of 
> content has skipped about a line and a half. Could there be an option to 
> designate how much overlap in content to show when scrolling via the space 
> bar (or page down key)?
> 
> Thanks,
> Derek

The scrolling in the PDF view is implemented by Apple, so for us (and you) it 
just works the way it does. There is no way we can change that, so we cannot 
provide an option to do it differently. 

I do think it should really scroll by a little /less/ than a full view height, 
which is what scroll views normally do .But for some reason, in the PDF view it 
does not do that. I consider that a bug, but one of Apple, which only they can 
fix. I already did report that to them, but never got a reaction. You may also 
file a bug report with Apple if you want.

Christiaan

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Re: [Skim-app-users] App unstable during searches

[Christiaan Hofman]

> On 19 Feb 2024, at 14:24, David Scott via Skim-app-users 
>  wrote:
> 
> Hi, since the update to version Version 1.7 (152), my copy has become 
> unstable and has crashed five times in the last week during the use of the 
> top lefthand search box. It crashes after text is typed in, during the search 
> and just clicking into the box. I’ve sent reports via the usual crash log 
> system, is there any info I can send to help deal with this issue?
> 
> -
> David
> 
> David Scott. Technology Support.
> 59a Reading Road, Northolt. UB5 4PH
> 07956-589433


That is an open bug report.It is already fixedforthe next release.

Christiaan

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Re: [Skim-app-users] Auto font size?

[Christiaan Hofman]

> On 17 Feb 2024, at 11:24, Christiaan Hofman  wrote:
> 
> 
> 
>> On 17 Feb 2024, at 01:33, ajpearceUK <60406...@opayq.com 
>> <mailto:60406...@opayq.com>> wrote:
>> 
>> When I make a note, the font size is either too small to see on screen, or 
>> too big to fit in the available box. The problem is that this changes with 
>> every pdf. Some need massive fonts, some need tiny fonts, depending on the 
>> resolution of the pdf, I presume. 
>> 
>> I can see that font size has been discussed before on this list, but it's 
>> hard to find what I'm looking for in those 160 pages of search results.
>> 
>> How do you handle this? 
>> 
>> Thanks for watching this list! 
> 
> 
> I cannot say in general how you should handle this, it really depends on your 
> personal situation. You can change the font size for individual notes using 
> the font panel (Cmd-T). You could also write some AppleScrips to change the 
> font size of the selected note to some preferred sizes, which you could 
> install in the script menu. 
> 
> Christiaan
> 


And you can also use the font action from the Font menu Ctr-Cmd-+/- to change 
the font of the selected text note.

Christiaan

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Re: [Skim-app-users] Auto font size?

[Christiaan Hofman]

> On 17 Feb 2024, at 01:33, ajpearceUK <60406...@opayq.com> wrote:
> 
> When I make a note, the font size is either too small to see on screen, or 
> too big to fit in the available box. The problem is that this changes with 
> every pdf. Some need massive fonts, some need tiny fonts, depending on the 
> resolution of the pdf, I presume. 
> 
> I can see that font size has been discussed before on this list, but it's 
> hard to find what I'm looking for in those 160 pages of search results.
> 
> How do you handle this? 
> 
> Thanks for watching this list! 


I cannot say in general how you should handle this, it really depends on your 
personal situation. You can change the font size for individual notes using the 
font panel (Cmd-T). You could also write some AppleScrips to change the font 
size of the selected note to some preferred sizes, which you could install in 
the script menu. 

Christiaan

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[Skim-app-users] Skim 1.7

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.7

NOTE: macOS 10.12 (Sierra) and earlier are no longer supported as of 1.7

New Features
  *  Update Sparkle updater, enhanced security.
  *  Hidden shortcut ',' in Presentation mode to show the cursor settings.

Bugs Fixed
  *  Tweak links that implicitly fit the target.
  *  Improve initial print panel settings.
  *  Try to fix certain relative links.
  *  Fix snapshot thumbnails on newer OS systems.
  *  Fix presentation page transitions on newer OS systems.
  *  Improve full screen animation.
  *  Fix Windows menu layout.
  *  Remove deprecated Greeking Threshold and Anti-Alias preferences.
  *  Fix exiting Presentation after adding multiple temporary freehand notes.
  *  Allow dvi and ps conversion command from homebrew.
  *  Allow PostScript transparency commands for ps2pdf from regular 
installations.
  *  Fix restoring scroll location in PDF.
  *  Better feedback when dragging multiple pages from Overview.

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[Skim-app-users] SkimNotes 1.6

[Christiaan Hofman]

For those interested in the SkimNotes framework or tools, I'd like to say that 
there is a new version 1.6 released. It can be downloaded from the Skim web 
page.

Christiaan

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Re: [Skim-app-users] Save only .skim files

[Christiaan Hofman]

> On 29 Jan 2024, at 10:47, Carlos Pita  wrote:
> 
> Hi all,
> 
> it's me again, still wrapping my mind around some Skim idiosyncrasies.
> 
> I usually store the pdfs for my projects in Google Drive. One of my
> motivations to try Skim was to avoid the constant uploading of large
> files. I thought it would be nice to save frequent backups of the
> annotations and every once in a while to also store full PDF/A
> exports.
> 
> But now I realize that each time I save a file in Skim it writes
> extended attributes and even though these are not synchronized to
> Google Drive (since it doesn't support them at all) the modification
> date for the file changes and it's uploaded to Google Drive anyway.
> It's the worst possible scenario because the only thing that actually
> changed (xattrs) is the only thing that's not synchronized, so I'm
> still constantly uploading a large file with the only difference being
> that now it's always the same file...
> 
> Then I found out that Skim has a hidden setting to let it start from
> pdf+skim files, instead of reading the xattrs. So I can export skim
> files instead of saving the pdf, although this is a little
> inconvenient: a few extra steps and a confirmation to overwrite the
> existing skim file. I'm unable to find a way to get "save" to write
> skim files instead of xattrs. Is there any way?
> 
> Best regards,
> Carlos


No, that is not correct. You cannot have Skim use pdf with only .skim files. 
The .skim files can only be saved as a backup, in addition to the extended 
attributes, and read in when the extended attributes were lost.

Christiaan

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Re: [Skim-app-users] Highlights & notes when exporting

[Christiaan Hofman]

It is meant as a description of the note. Like in the table, and in a Skim 
notes file. Otherwise, it would just say that it is a highlight on a page, not 
which one. It is partially also historically, as we also did not have the 
highlighted text in the extension in the table. And Preview did not have the 
extra popup squares you mentioned.So in Skim, it is not meant to be seen as an 
extra note. Just the description of the note, that you can also edit if you 
want. It’s when you convert that it becomes an extra annotation attached to the 
note. But we don’t control the conversion, that is done by Apple’s PDFKit.

Christiaan

> On 29 Jan 2024, at 00:03, Carlos Pita  wrote:
> 
> Thank you very much, that worked!
> 
> Would you mind explaining the rationale behind storing notes that way?
> I feel like I'm not getting the gist of it. I see highlights as one
> thing that you may or may not associate with a note, and when you
> associate a note to them this is marked somehow near the highlight so
> as to hint you that there is an annotation there. I could achieve this
> in Skim with an anchored note next to the highlight, but since the
> highlight itself has its own field for the annotation it seems to me
> that I'm missing something. Anyway, supposing that I changed the
> default note of the highlight, then: 1. I could not tell from the
> highlight itself whether it is annotated or not, 2. Even from the
> sidebar it would be difficult to find actually annotated (I mean, by
> me) highlights, because all of them are annotated by default.
> 
> Is there a general structure behind this? Like if everything has to
> have a title and content or something like that?
> 
> Best regards,
> Carlos
> 
> On Sun, Jan 28, 2024 at 7:28 PM Christiaan Hofman  wrote:
>> 
>> 
>> 
>> On 28 Jan 2024, at 23:15, Christiaan Hofman  wrote:
>> 
>> 
>> 
>> On 28 Jan 2024, at 19:23, Carlos Pita  wrote:
>> 
>> Hi all,
>> 
>> when I save a pdf with notes embedded from Skim I get something like
>> the attached image in Preview and other readers. Skim has this
>> particular thing of creating an annotation with the same content than
>> the associated highlight that doesn't play very well with the way
>> other readers and editors work (usually you explicitly add a note to a
>> highlight with your own thoughts).
>> 
>> Moreover, if I save the file in Preview and open it again in Skim I
>> often see note icons added by Preview next to each highlight, even
>> though those notes were automatically created by Skim and not actually
>> annotations of my own.
>> 
>> Is there any way to disable this behavior?
>> 
>> Best regards,
>> Carlos
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>> 
>> 
>> No, there is no way to disable this.BTW, you can still clear it in Skim.
>> 
>> Christiaan
>> 
>> 
>> Apologies, it is possible to disable the default text for the notes. Set the 
>> hidden preference SKDisableUpdateContentsFromEnclosedText to 2. Please see 
>> the Wiki for details.
>> 
>> 
>> Christiaan



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Re: [Skim-app-users] Highlights & notes when exporting

[Christiaan Hofman]

> On 28 Jan 2024, at 23:15, Christiaan Hofman  wrote:
> 
> 
> 
>> On 28 Jan 2024, at 19:23, Carlos Pita > <mailto:carlosjosep...@gmail.com>> wrote:
>> 
>> Hi all,
>> 
>> when I save a pdf with notes embedded from Skim I get something like
>> the attached image in Preview and other readers. Skim has this
>> particular thing of creating an annotation with the same content than
>> the associated highlight that doesn't play very well with the way
>> other readers and editors work (usually you explicitly add a note to a
>> highlight with your own thoughts).
>> 
>> Moreover, if I save the file in Preview and open it again in Skim I
>> often see note icons added by Preview next to each highlight, even
>> though those notes were automatically created by Skim and not actually
>> annotations of my own.
>> 
>> Is there any way to disable this behavior?
>> 
>> Best regards,
>> Carlos
>> ___
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> 
> 
> No, there is no way to disable this.BTW, you can still clear it in Skim.
> 
> Christiaan
> 


Apologies, it is possible to disable the default text for the notes. Set the 
hidden preference SKDisableUpdateContentsFromEnclosedText to 2. Please see the 
Wiki for details.


Christiaan

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Re: [Skim-app-users] Highlights & notes when exporting

[Christiaan Hofman]

> On 28 Jan 2024, at 19:23, Carlos Pita  wrote:
> 
> Hi all,
> 
> when I save a pdf with notes embedded from Skim I get something like
> the attached image in Preview and other readers. Skim has this
> particular thing of creating an annotation with the same content than
> the associated highlight that doesn't play very well with the way
> other readers and editors work (usually you explicitly add a note to a
> highlight with your own thoughts).
> 
> Moreover, if I save the file in Preview and open it again in Skim I
> often see note icons added by Preview next to each highlight, even
> though those notes were automatically created by Skim and not actually
> annotations of my own.
> 
> Is there any way to disable this behavior?
> 
> Best regards,
> Carlos
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No, there is no way to disable this.BTW, you can still clear it in Skim.

Christiaan

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Re: [Skim-app-users] Edit highlights from other tools

[Christiaan Hofman]

> On 27 Jan 2024, at 19:57, Carlos Pita  wrote:
> 
> Hi all,
> 
> I know that highlights are not saved within the pdf except that you
> export it, but what about the other way around? I have many pdfs
> previously annotated with Preview, and although I can see the
> annotations in the document itself, they are not listed in the sidebar
> nor I am able to edit them.
> 
> Best regards,
> Carlos
> 


That is correct, these highlights can not be seen as (editable) Skim notes. You 
can convert them to Skim notes using File > Convert Notes though. Please read 
the FAQ on the Wiki.

Christiaan

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Re: [Skim-app-users] Trying to join Notes

[Christiaan Hofman]

It doesn’t work with text notes, as they cannot be joined.Text notes with 
multiple components do not exist.It works for markup and freehand notes.

Christiaan

> On 25 Jan 2024, at 19:16, Maurice Frankel  wrote:
> 
> I  can’t get this to work either  If I:
> 
> •  create two adjacent text notes on the same page of a pdf opened in Skim 
> 
> •  select one note
> 
> •  press and hold shift
> 
> • select the other note with shift still held down
> 
> all that happens is that the 2nd note is selected and the first de-selected!
> 
> This is with Skim 1.6.21 on a MacBook Pro running High Sierra 10.13.6
> 
> Maurice
> 
>> On 25 Jan 2024, at 18:08, Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> 
>> Also, it is about selecting in the PDF, not in the table.
>> 
>> Christiaan
>> 
>>> On 25 Jan 2024, at 19:01, Christiaan Hofman >> <mailto:cmhof...@gmail.com>> wrote:
>>> 
>>> Well, that should just work. So what *exactly* are you doing? Are you 
>>> holding the Shift key while you click on the second highlight, while the 
>>> first one was already selected? Then they should just be joined. Perhaps 
>>> you misunderstand what joined means here? It does not mean making a 
>>> continuous selection, it means creating a single note out of the two 
>>> selected ranges.
>>> 
>>> Christiaan
>>> 
>>>> On 25 Jan 2024, at 21:47, HARRY BIMS via Skim-app-users 
>>>> >>> <mailto:skim-app-users@lists.sourceforge.net>> wrote:
>>>> 
>>>> Unfortunately, I am trying to merge two highlights with the same color on 
>>>> the same page.  Selecting the two of them using the Shift key does nothing 
>>>> other than to simply highlight them in the Notes pane.  They do not 
>>>> automatically merge simply by selecting them.
>>>> 
>>>> Harry
>>>> 
>>>> 
>>>>> On Jan 25, 2024, at 9:08 AM, Christiaan Hofman >>>> <mailto:cmhof...@gmail.com>> wrote:
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 25 Jan 2024, at 20:36, HARRY BIMS via Skim-app-users 
>>>>>> >>>>> <mailto:skim-app-users@lists.sourceforge.net>> wrote:
>>>>>> 
>>>>>> Hello,
>>>>>> 
>>>>>> I have read the Skim Wiki which says to join Notes, simply press the 
>>>>>> Shift key and select the Notes.  However, this does not actually join 
>>>>>> anything.  What is the next step that actually joins Notes together?
>>>>>> 
>>>>>> Harry
>>>>> 
>>>>> 
>>>>> They have to be Skim notes, notes of the same type, and on the same page.
>>>>> 
>>>>> Christiaan

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Re: [Skim-app-users] Trying to join Notes

[Christiaan Hofman]

Also, it is about selecting in the PDF, not in the table.

Christiaan

> On 25 Jan 2024, at 19:01, Christiaan Hofman  wrote:
> 
> Well, that should just work. So what *exactly* are you doing? Are you holding 
> the Shift key while you click on the second highlight, while the first one 
> was already selected? Then they should just be joined. Perhaps you 
> misunderstand what joined means here? It does not mean making a continuous 
> selection, it means creating a single note out of the two selected ranges.
> 
> Christiaan
> 
>> On 25 Jan 2024, at 21:47, HARRY BIMS via Skim-app-users 
>> > <mailto:skim-app-users@lists.sourceforge.net>> wrote:
>> 
>> Unfortunately, I am trying to merge two highlights with the same color on 
>> the same page.  Selecting the two of them using the Shift key does nothing 
>> other than to simply highlight them in the Notes pane.  They do not 
>> automatically merge simply by selecting them.
>> 
>> Harry
>> 
>> 
>>> On Jan 25, 2024, at 9:08 AM, Christiaan Hofman >> <mailto:cmhof...@gmail.com>> wrote:
>>> 
>>> 
>>> 
>>>> On 25 Jan 2024, at 20:36, HARRY BIMS via Skim-app-users 
>>>> >>> <mailto:skim-app-users@lists.sourceforge.net>> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> I have read the Skim Wiki which says to join Notes, simply press the Shift 
>>>> key and select the Notes.  However, this does not actually join anything.  
>>>> What is the next step that actually joins Notes together?
>>>> 
>>>> Harry
>>> 
>>> 
>>> They have to be Skim notes, notes of the same type, and on the same page.
>>> 
>>> Christiaan

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Re: [Skim-app-users] Trying to join Notes

[Christiaan Hofman]

Well, that should just work. So what *exactly* are you doing? Are you holding 
the Shift key while you click on the second highlight, while the first one was 
already selected? Then they should just be joined. Perhaps you misunderstand 
what joined means here? It does not mean making a continuous selection, it 
means creating a single note out of the two selected ranges.

Christiaan

> On 25 Jan 2024, at 21:47, HARRY BIMS via Skim-app-users 
>  wrote:
> 
> Unfortunately, I am trying to merge two highlights with the same color on the 
> same page.  Selecting the two of them using the Shift key does nothing other 
> than to simply highlight them in the Notes pane.  They do not automatically 
> merge simply by selecting them.
> 
> Harry
> 
> 
>> On Jan 25, 2024, at 9:08 AM, Christiaan Hofman  wrote:
>> 
>> 
>> 
>>> On 25 Jan 2024, at 20:36, HARRY BIMS via Skim-app-users 
>>> >> <mailto:skim-app-users@lists.sourceforge.net>> wrote:
>>> 
>>> Hello,
>>> 
>>> I have read the Skim Wiki which says to join Notes, simply press the Shift 
>>> key and select the Notes.  However, this does not actually join anything.  
>>> What is the next step that actually joins Notes together?
>>> 
>>> Harry
>> 
>> 
>> They have to be Skim notes, notes of the same type, and on the same page.
>> 
>> Christiaan

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Re: [Skim-app-users] Trying to join Notes

[Christiaan Hofman]

> On 25 Jan 2024, at 20:36, HARRY BIMS via Skim-app-users 
>  wrote:
> 
> Hello,
> 
> I have read the Skim Wiki which says to join Notes, simply press the Shift 
> key and select the Notes.  However, this does not actually join anything.  
> What is the next step that actually joins Notes together?
> 
> Harry


They have to be Skim notes, notes of the same type, and on the same page.

Christiaan

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Re: [Skim-app-users] Search/ Highlight Kindle Clippings in Skim

[Christiaan Hofman]

You probably want to first collect all the texts to highlight and then 
highlight all at once:

-- Prompt the user to select a text file
set filePath to choose file with prompt "Please select a text file:" of type 
{"txt"}

-- Read the content of the selected text file
set inputText to read file filePath as «class utf8»


-- Function to extract the first 7 words from each text block using a regular 
expression
on extractFirst7WordsFromBlocks(inputText)
set wordsLists to {}

-- Set text item delimiters to find the text blocks
set oldDelimiters to AppleScript's text item delimiters
set AppleScript's text item delimiters to "***"

-- Split the text into items, each item corresponds to a text block
set textItems to text items of inputText

-- Regular expression to match 7 consecutive words
set regex to "(?i)\\b\\w+\\b(\\W+\\w+){0,6}"

-- Iterate through each text block and extract the first 7 words using 
a regular expression
repeat with i from 2 to count of textItems by 2
set textBlock to item i of textItems
set wordsList to extractWordsWithRegex(textBlock, regex)

-- Search for the text in the open PDF file in Skim
if wordsList is not equal to "" then
set wordsLists to wordsLists & {wordsList}
end if
end repeat

set AppleScript's text item delimiters to oldDelimiters

return wordsLists
end extractFirst7WordsFromBlocks

-- Helper function to extract words using a regular expression
on extractWordsWithRegex(textBlock, regex)
try
set wordMatches to do shell script "echo " & quoted form of 
textBlock & " | grep -oE " & quoted form of regex
set wordsList to paragraphs of wordMatches
set resultText to item 1 of wordsList
on error
set resultText to ""
end try

return resultText
end extractWordsWithRegex

-- Helper function to set the search term in Skim and highlight the found text
on setSearchAndHighlightInSkim(searchTexts)
tell application "Skim"
activate

if (count of documents) is 0 then
beep
display dialog "No documents found." buttons {"•"} 
default button 1 giving up after 3
return
end if

set noteType to my chooseNoteType({"Highlight"})
if noteType is 0 then return

set numberOfMatches to 0

tell document 1
repeat with searchText in searchTexts
set theSel to find text searchText
repeat while theSel is not {}
set numberOfMatches to numberOfMatches 
+ 1
set theNote to make note with data 
theSel with properties {type:noteType}
set text of theNote to searchText
set theSel to find text searchText from 
theSel
end repeat
end repeat
end tell

beep
display dialog "Done selecting " & numberOfMatches & " 
occurrences of \"" & searchText & "\"." buttons {"•"} default button 1 giving 
up after 3
end tell
end setSearchAndHighlightInSkim

-- Helper function to choose the note type in Skim
on chooseNoteType(typeList)
tell application "Skim"

set noteTypeString to "Highlight"
return highlight note

end tell
end chooseNoteType

-- Call the function
set searchTexts to extractFirst7WordsFromBlocks(inputText)
if (count of searchTexts) is not 0 then
setSearchAndHighlightInSkim(searchTexts)
end if


Christiaan

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Re: [Skim-app-users] Search/ Highlight Kindle Clippings in Skim

[Christiaan Hofman]

> On 31 Dec 2023, at 05:23, haphaes haphaes  wrote:
> 
> On a remotely related issue, previously we could navigate among annotations 
> on Skim by selecting one on the page and pressing "alt+down arrow/." That 
> doesn't seem to work anymore?


That is Alt-Tab.

Christiaan

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Re: [Skim-app-users] Search/ Highlight Kindle Clippings in Skim

[Christiaan Hofman]

> On 30 Dec 2023, at 10:10, haphaes haphaes  wrote:
> 
> 
> Hi, 
> Apparently, what I would like to seek help about is quite similar to the 
> issue raised here: 
> https://sourceforge.net/p/skim-app/mailman/message/37743641/ 
> 
> 
> Specifically, what I need to do is the following: 
> If I have a lot of pdf files to read, here is what I usually do; 
> I convert them both to text-based pdfs and epubs, the same OCR app and then 
> send the epub file to Kindle using amazon's dedicated app. 
> 
> ... Then comes reading / highlighting on the Kindle and transferring the "My 
> Clippings" file in the kindle to the computer. Using a website I can get 
> transfer the highlights for only one book to, say, a text file.
> 
> Now, what would be incredibly useful is if after opening the pdf file on 
> Skim, I could have an applescript search for each highlight on the text file 
> in the pdf on skim and highlight it... 
> 
> Further, if for one single highlight the script cannot find it (probably 
> because, it's too long) the script can reduce the number of the words to look 
> for and then add the highlight once it finds a match. 
> 
> (e.g. a single highlight on Kindle: 
> "All men are mortal, Socrates is a man, therefore Socrates is mortal. "
> 
> When the script doesn't find a match for the whole sentence, it will search 
> for a phrase with a reduced number of words, say: 
> 
> "All men are mortal, Socrates is a man," 
> 
> if still no match, reduce 4 words again: 
> Hi, 
> Apparently, what I would like to seek help about is quite similar to the 
> issue raised here: 
> https://sourceforge.net/p/skim-app/mailman/message/37743641/ 
> 
> 
> Specifically, what I need to do is the following: 
> If I have a lot of pdf files to read, here is what I usually do; 
> I convert them both to text-based pdfs and epubs, the same OCR app and then 
> send the epub file to Kindle using amazon's dedicated app. 
> 
> ... Then comes reading / highlighting on the Kindle and transferring the "My 
> Clippings" file in the kindle to the computer. Using a website I can get the 
> highlights for only one book... 
> 
> Now, what would be incredibly useful is if I after opening the pdf files on 
> Skim, I could then get the highlights for the single book on a text file and 
> have an applescript search for each highlight on the text file in the pdf on 
> skim and highlight it... 
> 
> Further, if for one single highlight the script cannot find it (probably 
> because, it's too long) the script can reduce the number of the words to look 
> for and then add the highlight once it finds a match. 
> 
> (e.g. a single highlight on Kindle: 
> "All men are mortal, Socrates is a man, therefore Socrates is mortal. "
> 
> When the script doesn't find a match for the whole sentence, it will search 
> for a phrase with a reduced number of words, say: 
> 
> "All men are mortal, Socrates is a man," 
> 
> if still no match, delete the last 4 words from the search phrase again etc
> 
> "All men are mortal,"
> But stop there, don't search for less than, say, e.g 4  words
> 
> 
> Once it finds the phrase, the script will have skim highlight it.
> 
> And then will do the same for the second highlight from the Kindle/ ereader/ 
> any textfile separated by "paragraphs" etc. 
> 
> 
> What do you think? Any chance for that? I was hoping that would be possible 
> nowadays and asked, of course, what else, ChatGPT
>  Below is its reply: --well, it doesn't work..
> 
> Many thanks everyone!
> -- Specify the paths to your text file and PDF file
> set textFilePath to "/path/to/your/textfile.txt"
> set pdfFilePath to "/path/to/your/pdfdocument.pdf"
> 
> -- Read lines from the text file
> set linesToSearch to paragraphs of (read file textFilePath)
> 
> -- Iterate through each line and search for it in the PDF using Skim Reader
> repeat with currentLine in linesToSearch
> set searchString to currentLine
> 
> -- Use a shell command to search for the text in the PDF
> set searchCommand to "grep -n " & quoted form of searchString & " " & 
> quoted form of pdfFilePath
> set searchResult to do shell script searchCommand
> 
> -- Extract the line number from the search result
> set lineNumber to first word of searchResult
> 
> -- Use SkimNotes command-line tool to add annotation to the PDF
> set skimCommand to "skimnotes add -page " & lineNumber & " " & quoted 
> form of pdfFilePath
> do shell script skimCommand
> end repeat
> 
> ——

Interesting script, it shows AI picks up stuff, and does not understand what it 
means. It certainly isn’t ready for programming.

Although perhaps some ideas could be helpful. If I understand you correctly, 
you have a text file containing strings to highlight (is there no more 
information, like the location where they are?), and a PDF where you want to 
highlight those texts. 

Re: [Skim-app-users] Template help

[Christiaan Hofman]

My sample was just a fragment, as a replacement of the <$string> part. You 
should also add the <$textString> section as in your original.

Chrostiaan

> On 29 Nov 2023, at 19:51, Derek Van Ittersum  
> wrote:
> 
> Thanks for the suggestion. Unfortunately, when I use that template I don't 
> get the highlights, only the text note. (in the example above, only the "test 
> note" and not the "Hence" nor any other highlights).
> 
> I think I have resolved the problem. As long as I only add notes as separate 
> notes (rather than as notes attached to highlights), then I can use the 
> following template to get all of that information--separate text notes and 
> highlighted text.
> 
> <$notes.@arraySortedByPageIndexAndBounds>
> <$contents?>
> <$contents/> (p. 
> <$page.label?><$page.label/><$pageIndex.numberByAddingOne/>)
> 
> 
> 
> 
> On Wed, Nov 29, 2023 at 12:18 PM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> I just realized that perhaps you still could do what you want. It is possible 
> to use an evaluated value in a condition. So you could write a condition tag 
> like this (replacement of the second part of the template):
> 
> <$string=?>
> 
> 
> <$string/>
> 
> 
> 
> Christiaan
> 
>> On 29 Nov 2023, at 17:54, Derek Van Ittersum > <mailto:derek.vanitter...@gmail.com>> wrote:
>> 
>> Ok, I understand. Thanks for explaining.
>> 
>> On Wed, Nov 29, 2023 at 11:49 AM Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> I think, in terms of the data that exists, what you want is really a 
>> contradiction. On the one hand you want to both the content (string) of the 
>> notes and highlights, and the highlighted text. in your template. That is 
>> also what you achieve with your sample template. On the other hand, you say 
>> you *don’t* want both the content and the highlighted text of a highlight 
>> (because they just happen to be the same). You cannot have both, because 
>> they are contradictory requirements. 
>> 
>> As I understand you, case 1 and case 3 are really the same: they are 
>> highlights that have a content set. The only difference is really what the 
>> content is set to, and how you have done that. And as a result that in one 
>> case the two texts happen to be the same, and in the other case they are 
>> different. So as there is no essential difference in the data, there is 
>> simply no way a template can make a difference. 
>> 
>> You should realize that when you create a highlight in Skim, we just *set* 
>> the content to the highlighted text. You can always change out to some other 
>> value, just like you did in the other app before conversion (it’s just that 
>> the other app sets the content to nothing by default). So you could have 
>> created the situation for the highlighted “Hence” exactly the same way in 
>> Skim: highlight “Hence” and set the content to “Test note”.
>> 
>> Christiaan
>> 
>>> On 29 Nov 2023, at 16:40, Derek Van Ittersum >> <mailto:derek.vanitter...@gmail.com>> wrote:
>>> 
>>> Yes, I have done the "convert notes" function prior to exporting with the 
>>> template. Here's a screenshot of the three types of notes I have:
>>> 
>>> https://www.dropbox.com/scl/fi/h79t3tzikwzl7eb4wo6tz/Screenshot-2023-11-29-at-7.43.36-AM.png?rlkey=eyodn8094jr8yfd9qg4k9i37r=0
>>>  
>>> <https://www.dropbox.com/scl/fi/h79t3tzikwzl7eb4wo6tz/Screenshot-2023-11-29-at-7.43.36-AM.png?rlkey=eyodn8094jr8yfd9qg4k9i37r=0>
>>> 
>>> I am having a hard time understanding the templating process. I would love 
>>> to use conditional tags to achieve the result I'm looking for, but I would 
>>> need a bit of guidance. I've tried to use the suggestions made in this 
>>> previous conversation, but I never got all the data I was looking for--it 
>>> either skipped the highlighted text in the first note, or the note itself 
>>> (e.g., the note text "test note" and the highlighted text "Hence"): 
>>> https://sourceforge.net/p/skim-app/mailman/skim-app-users/thread/CAHwchkffF%2BZyPjg0ayYyNaWv-vf64-A-Yipo7UBqW8U9GbwR_A%40mail.gmail.com/#msg36703931
>>>  
>>> <https://sourceforge.net/p/skim-app/mailman/skim-app-users/thread/CAHwchkffF%2BZyPjg0ayYyNaWv-vf64-A-Yipo7UBqW8U9GbwR_A%40mail.gmail.com/#msg36703931>
>>> 
>>> On Wed, Nov 29, 2023 at 5:39 AM Christiaan Hofman >> <mailto:cmhof...@gmail.com>> wrote:
>>> I am not sure I completely understand your q

Re: [Skim-app-users] Template help

[Christiaan Hofman]

I just realized that perhaps you still could do what you want. It is possible 
to use an evaluated value in a condition. So you could write a condition tag 
like this (replacement of the second part of the template):

<$string=?>


<$string/>



Christiaan

> On 29 Nov 2023, at 17:54, Derek Van Ittersum  
> wrote:
> 
> Ok, I understand. Thanks for explaining.
> 
> On Wed, Nov 29, 2023 at 11:49 AM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> I think, in terms of the data that exists, what you want is really a 
> contradiction. On the one hand you want to both the content (string) of the 
> notes and highlights, and the highlighted text. in your template. That is 
> also what you achieve with your sample template. On the other hand, you say 
> you *don’t* want both the content and the highlighted text of a highlight 
> (because they just happen to be the same). You cannot have both, because they 
> are contradictory requirements. 
> 
> As I understand you, case 1 and case 3 are really the same: they are 
> highlights that have a content set. The only difference is really what the 
> content is set to, and how you have done that. And as a result that in one 
> case the two texts happen to be the same, and in the other case they are 
> different. So as there is no essential difference in the data, there is 
> simply no way a template can make a difference. 
> 
> You should realize that when you create a highlight in Skim, we just *set* 
> the content to the highlighted text. You can always change out to some other 
> value, just like you did in the other app before conversion (it’s just that 
> the other app sets the content to nothing by default). So you could have 
> created the situation for the highlighted “Hence” exactly the same way in 
> Skim: highlight “Hence” and set the content to “Test note”.
> 
> Christiaan
> 
>> On 29 Nov 2023, at 16:40, Derek Van Ittersum > <mailto:derek.vanitter...@gmail.com>> wrote:
>> 
>> Yes, I have done the "convert notes" function prior to exporting with the 
>> template. Here's a screenshot of the three types of notes I have:
>> 
>> https://www.dropbox.com/scl/fi/h79t3tzikwzl7eb4wo6tz/Screenshot-2023-11-29-at-7.43.36-AM.png?rlkey=eyodn8094jr8yfd9qg4k9i37r=0
>>  
>> <https://www.dropbox.com/scl/fi/h79t3tzikwzl7eb4wo6tz/Screenshot-2023-11-29-at-7.43.36-AM.png?rlkey=eyodn8094jr8yfd9qg4k9i37r=0>
>> 
>> I am having a hard time understanding the templating process. I would love 
>> to use conditional tags to achieve the result I'm looking for, but I would 
>> need a bit of guidance. I've tried to use the suggestions made in this 
>> previous conversation, but I never got all the data I was looking for--it 
>> either skipped the highlighted text in the first note, or the note itself 
>> (e.g., the note text "test note" and the highlighted text "Hence"): 
>> https://sourceforge.net/p/skim-app/mailman/skim-app-users/thread/CAHwchkffF%2BZyPjg0ayYyNaWv-vf64-A-Yipo7UBqW8U9GbwR_A%40mail.gmail.com/#msg36703931
>>  
>> <https://sourceforge.net/p/skim-app/mailman/skim-app-users/thread/CAHwchkffF%2BZyPjg0ayYyNaWv-vf64-A-Yipo7UBqW8U9GbwR_A%40mail.gmail.com/#msg36703931>
>> 
>> On Wed, Nov 29, 2023 at 5:39 AM Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> I am not sure I completely understand your question. 
>> 
>> You get the doubling because you include both the string and the textString. 
>> The former is the contents value of the note or highight, while the latter 
>> is the text behind the highlight. In Skim we set the string to the 
>> textString. That’s why you se the doubling.
>> 
>> As for 3, highlights added by other apps will not be part of the template, 
>> as Skim doesn’t see them. So I don’t understand why you would ever get them. 
>> Or did you convert them?
>> 
>> As I don’t understand what you mean by 3, I am not sure what to do. But 
>> perhaps you can add some condition tags for the type of the note around a 
>> part of your template.
>> 
>> Christiaan
>> 
>> > On 29 Nov 2023, at 01:32, Derek Van Ittersum > > <mailto:derek.vanitter...@gmail.com>> wrote:
>> > 
>> > Hello,
>> > 
>> > I am trying to create a template that will output:
>> > 
>> > 1. highlighted text
>> > 2. text notes
>> > 3. notes made on highlights (e.g., in other PDF apps, like the one on my 
>> > Boox device, I select the highlight then click "add note" to it)
>> > 
>> > I am getting all three of these bits of information with the following 
>> > tem

Re: [Skim-app-users] Template help

[Christiaan Hofman]

I think, in terms of the data that exists, what you want is really a 
contradiction. On the one hand you want to both the content (string) of the 
notes and highlights, and the highlighted text. in your template. That is also 
what you achieve with your sample template. On the other hand, you say you 
*don’t* want both the content and the highlighted text of a highlight (because 
they just happen to be the same). You cannot have both, because they are 
contradictory requirements. 

As I understand you, case 1 and case 3 are really the same: they are highlights 
that have a content set. The only difference is really what the content is set 
to, and how you have done that. And as a result that in one case the two texts 
happen to be the same, and in the other case they are different. So as there is 
no essential difference in the data, there is simply no way a template can make 
a difference. 

You should realize that when you create a highlight in Skim, we just *set* the 
content to the highlighted text. You can always change out to some other value, 
just like you did in the other app before conversion (it’s just that the other 
app sets the content to nothing by default). So you could have created the 
situation for the highlighted “Hence” exactly the same way in Skim: highlight 
“Hence” and set the content to “Test note”.

Christiaan

> On 29 Nov 2023, at 16:40, Derek Van Ittersum  
> wrote:
> 
> Yes, I have done the "convert notes" function prior to exporting with the 
> template. Here's a screenshot of the three types of notes I have:
> 
> https://www.dropbox.com/scl/fi/h79t3tzikwzl7eb4wo6tz/Screenshot-2023-11-29-at-7.43.36-AM.png?rlkey=eyodn8094jr8yfd9qg4k9i37r=0
>  
> <https://www.dropbox.com/scl/fi/h79t3tzikwzl7eb4wo6tz/Screenshot-2023-11-29-at-7.43.36-AM.png?rlkey=eyodn8094jr8yfd9qg4k9i37r=0>
> 
> I am having a hard time understanding the templating process. I would love to 
> use conditional tags to achieve the result I'm looking for, but I would need 
> a bit of guidance. I've tried to use the suggestions made in this previous 
> conversation, but I never got all the data I was looking for--it either 
> skipped the highlighted text in the first note, or the note itself (e.g., the 
> note text "test note" and the highlighted text "Hence"): 
> https://sourceforge.net/p/skim-app/mailman/skim-app-users/thread/CAHwchkffF%2BZyPjg0ayYyNaWv-vf64-A-Yipo7UBqW8U9GbwR_A%40mail.gmail.com/#msg36703931
>  
> <https://sourceforge.net/p/skim-app/mailman/skim-app-users/thread/CAHwchkffF%2BZyPjg0ayYyNaWv-vf64-A-Yipo7UBqW8U9GbwR_A%40mail.gmail.com/#msg36703931>
> 
> On Wed, Nov 29, 2023 at 5:39 AM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> I am not sure I completely understand your question. 
> 
> You get the doubling because you include both the string and the textString. 
> The former is the contents value of the note or highight, while the latter is 
> the text behind the highlight. In Skim we set the string to the textString. 
> That’s why you se the doubling.
> 
> As for 3, highlights added by other apps will not be part of the template, as 
> Skim doesn’t see them. So I don’t understand why you would ever get them. Or 
> did you convert them?
> 
> As I don’t understand what you mean by 3, I am not sure what to do. But 
> perhaps you can add some condition tags for the type of the note around a 
> part of your template.
> 
> Christiaan
> 
> > On 29 Nov 2023, at 01:32, Derek Van Ittersum  > <mailto:derek.vanitter...@gmail.com>> wrote:
> > 
> > Hello,
> > 
> > I am trying to create a template that will output:
> > 
> > 1. highlighted text
> > 2. text notes
> > 3. notes made on highlights (e.g., in other PDF apps, like the one on my 
> > Boox device, I select the highlight then click "add note" to it)
> > 
> > I am getting all three of these bits of information with the following 
> > template:
> > 
> > <$notes.@arraySortedByPageIndexAndBounds>
> > <$textString?>
> > <$textString/> (p. 
> > <$page.label?><$page.label/><$pageIndex.numberByAddingOne/>)
> > 
> > 
> > <$string?>
> > <$string/>
> > 
> >  
> > 
> > 
> > However--I am getting any highlight without a note on it twice. Is there 
> > any way to amend my template so that I get the 3 bits of information 
> > without repetition? I have tried many different template value keys (e.g., 
> > text, string, contents, textString) but any alteration I have tried to the 
> > above ends up leaving out one of the 3 bits of information. 
> > 
> > Thanks for any help or explanation,
> > 
> > Derek
> 

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Re: [Skim-app-users] Template help

[Christiaan Hofman]

I am not sure I completely understand your question. 

You get the doubling because you include both the string and the textString. 
The former is the contents value of the note or highight, while the latter is 
the text behind the highlight. In Skim we set the string to the textString. 
That’s why you se the doubling.

As for 3, highlights added by other apps will not be part of the template, as 
Skim doesn’t see them. So I don’t understand why you would ever get them. Or 
did you convert them?

As I don’t understand what you mean by 3, I am not sure what to do. But perhaps 
you can add some condition tags for the type of the note around a part of your 
template.

Christiaan

> On 29 Nov 2023, at 01:32, Derek Van Ittersum  
> wrote:
> 
> Hello,
> 
> I am trying to create a template that will output:
> 
> 1. highlighted text
> 2. text notes
> 3. notes made on highlights (e.g., in other PDF apps, like the one on my Boox 
> device, I select the highlight then click "add note" to it)
> 
> I am getting all three of these bits of information with the following 
> template:
> 
> <$notes.@arraySortedByPageIndexAndBounds>
> <$textString?>
> <$textString/> (p. 
> <$page.label?><$page.label/><$pageIndex.numberByAddingOne/>)
> 
> 
> <$string?>
> <$string/>
> 
>  
> 
> 
> However--I am getting any highlight without a note on it twice. Is there any 
> way to amend my template so that I get the 3 bits of information without 
> repetition? I have tried many different template value keys (e.g., text, 
> string, contents, textString) but any alteration I have tried to the above 
> ends up leaving out one of the 3 bits of information. 
> 
> Thanks for any help or explanation,
> 
> Derek



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[Skim-app-users] Skim 1.6.21

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.21

Bugs Fixed
  *  Allow clicking links in note tool mode.
  *  Improve undo in presentation mode.
  *  Make sure committing text note edits is undone separately from adding 
notes.
  *  More efficient loading of documents with many notes.
  *  Prevent note edits when interaction settings don't allow it.
  *  Make sure forward search updates the correct document.
  *  Support transparency in PostScript conversion on Sonoma.

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Re: [Skim-app-users] no embedded notes option?

[Christiaan Hofman]

> On 28 Sep 2023, at 21:50, Glenn Hollingsworth  wrote:
> 
> This was brought up on the listserv on 1/2/23 but I didn't see any follow-up. 
> 
> I no longer see an option to export a PDF with embedded notes. I'm using 
> Version 1.6.20 (150) on Ventura 13.6. 
> 
> Did this function get renamed? Was it removed? Might something be wonky with 
> my setup? 
> 
> Not sure if this helps, but here are my export options - PDF, PDF Bundle, 
> Archive, Skim Notes, Notes as Text/RTF/RTFD/FDF. If the function was in "save 
> as", the only options I see there are PDF and PDF Bundle. 
> 
> Thank you.

It is still there. Did you use the Export action, and did you choose PDF? The 
option should then appear below the popup.

It can be that the PDF you are trying to export does not allow printing (see 
the Info window), which also means it does not allow writing (with embedded 
noes). 

Christiaan

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Re: [Skim-app-users] copy/paste note

[Christiaan Hofman]

BTW, if you transfer the file through iCloud, the notes should be preserved.

Christiaan

> On 24 Sep 2023, at 10:32, Christiaan Hofman  wrote:
> 
> No, you can transfer the file with the notes in another format. For instance, 
> as an archive, or a PDF bundle. That’s why we offer the archive feature. You 
> can also transfer a separate Skim notes file to keep the notes.
> 
> Christiaan
> 
>> On 24 Sep 2023, at 10:21, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>>  wrote:
>> 
>> Christiaan:
>> 
>>> Skim does not handle notes embedded in the PDF, it sees them just as
>>> part of the PDF background.If you want to manage them, you should
>>> convert the embedded notes to Skim notes.
>> 
>> Thanks for the quick response.
>> 
>> Hmm.  But then the notes would have been lost when I transferred the
>> PDF from one computer to the other because Skim embedded notes are
>> kept in the computer file operating system and not the PDF, right?  So
>> is this an impossible catch-22?  Or is there another way?
>> 
>> Tom



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Re: [Skim-app-users] copy/paste note

[Christiaan Hofman]

No, you can transfer the file with the notes in another format. For instance, 
as an archive, or a PDF bundle. That’s why we offer the archive feature. You 
can also transfer a separate Skim notes file to keep the notes.

Christiaan

> On 24 Sep 2023, at 10:21, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> Skim does not handle notes embedded in the PDF, it sees them just as
>> part of the PDF background.If you want to manage them, you should
>> convert the embedded notes to Skim notes.
> 
> Thanks for the quick response.
> 
> Hmm.  But then the notes would have been lost when I transferred the
> PDF from one computer to the other because Skim embedded notes are
> kept in the computer file operating system and not the PDF, right?  So
> is this an impossible catch-22?  Or is there another way?
> 
> Tom



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Re: [Skim-app-users] copy/paste note

[Christiaan Hofman]

Skim does not handle notes embedded in the PDF, it sees them just as part of 
the PDF background.If you want to manage them, you should convert the embedded 
notes to Skim notes.

Christiaan

> On 24 Sep 2023, at 03:55, Thomas Schneider via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
> Thanks much for all your efforts on the wonderful Skim program!
> 
> Using Skim 1.6.20 I wrote a note on a PDF containing the url that I
> got the PDF from.  I then embedded the note into the pdf
> (https://alum.mit.edu/www/toms/ftp/skimembed).  This allowed me to
> transfer the note along with the PDF to another computer.  Indeed, the
> note was on the other computer also under Skim 1.6.20.
> 
> Then I wanted to copy the URL for use on the second computer and was
> unable to copy/paste the note.  The text above and below the note
> showed up fine in my cut/paste buffer but the note did not.
> 
> The first computer is on Ventura macOS 13.6 22G120, up to date.  The
> second computer is on Ventura macOS 13.5.2 22G91, almost up to date.
> 
> What am I missing?  Why can't I copy the contents of a note?
> Maybe Skim could be changed so that one can copy the notes?
> 
> When I convert the entire PDF to text using pdftotext I get the URL
> from the note.  So it's in the PDF but not recognized by the macOS.
> 
> Tom



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Re: [Skim-app-users] Skims Speech Feature

[Christiaan Hofman]

> On 3 Sep 2023, at 05:31, Yomi Malibiran  wrote:
> 
> Is there a way we can speed up the text-to-speech feature in Skims? Thanks!

No.The speech feature is implemented by Apple, so you should petition them if 
you want that to change.

Christiaan

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Re: [Skim-app-users] Skim 1.6.20

[Christiaan Hofman]

I don’t see the boxes, and the links are working fine for me. Did you add 
(text) notes to the links? Perhaps you have the text note tool turned on, and 
added two text notes by accident?

Christiaan

> On 23 Aug 2023, at 22:32, Murray Eisenberg  wrote:
> 
> With skim 1.6.20 under macOS Ventura 13.5, if I click a hyperlink -- to 
> another page, section, theorem, etc. of a pdf document, or of a URL there, I 
> just get a little box pop up .
> 
> This happens with _all_ pdfs, including the file textLinks.pdf attached. Also 
> attached is the LaTeX source file I used to create it and a screenshot 
> showing what happens when I click a hyperlink: a little box appearing but no 
> jump to the link target happening.
> 
>  
> 
> 
> 
> 
>> On Aug 23, 2023, at 2:43 PM, Schneider, Thomas (NIH/NCI) [E] via 
>> Skim-app-users  wrote:
>> 
>> Murray:
>> 
>>> Does Skim _not_ support clicking on hyperlinks (say in a pdf
>>> produced from a LaTeX source that used the hyperref package) to jump
>>> to corresponding targets?
>>> 
>>> It is now working in at least two LaTeX-sourced pdf's that use
>>> hyperref to create links. Those links do work in the macOS Preview
>>> app, in Adobe Acrobat Reader, and in the TeXShop's internal pdf
>>> viewer.
>> 
>> I am using the latest Skim 1.6.20 and hyperlinks are working.  I have
>> reference links to my bibliography and they work to jump within the
>> paper to the references.  Within my bibliography I have \url{} inside
>> a 'note' and those work.
>> 
>> Example:
>> 
>> @article{Brenner1999,
>> author = "S. Brenner",
>> title = "{Theoretical biology in the third millennium}",
>> journal = "Philos Trans R Soc Lond B Biol Sci",
>> volume = "354",
>> pages = "1963--1965",
>> pmid = "10670016",
>> pmcid = "PMC1692708",
>> note = "\url
>> {https://doi.org/10.1098/rstb.1999.0535};,
>> comment = "2015/02/10 08:35:40 from Schuster2011, Keller2005 cited
>> this: '... it is clear that the prime intellectual task of the future
>> lies in constructing an appropriate theoretical framework for
>> biology.' ",
>> year = "1999"}
>> 
>> Tom
>> 
>>  Thomas D. Schneider, Ph.D.
>>  Senior Investigator
>>  National Institutes of Health
>>  National Cancer Institute
>>  Center for Cancer Research
>>  RNA Biology Laboratory
>>  Biological Information Theory Group
>>  Frederick, Maryland  21702-1201
>>  schne...@mail.nih.gov
>>  alum.mit.edu/www/toms
>>  https://alum.mit.edu/www/toms
>> 
> 
> ---
> Murray Eisenberg  murrayeisenb...@gmail.com
> Mobile (413)-427-5334
> 503 King Farm Blvd #101   
> Rockville, MD 20850-6667  
> 



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Re: [Skim-app-users] hyperlinks

[Christiaan Hofman]

> On 23 Aug 2023, at 22:07, Murray Eisenberg  wrote:
> 
> Does Skim _not_ support clicking on hyperlinks (say in a pdf produced from a 
> LaTeX source that used the hyperref package) to jump to corresponding targets?
> 
> It is not working in at least two LaTeX-sourced pdf's that use hyperref to 
> create links. Those links do work in the macOS Preview app, in Adobe Acrobat 
> Reader, and in the TeXShop's internal pdf viewer.
> ---
> Murray Eisenberg  murrayeisenb...@gmail.com
> Mobile (413)-427-5334
> 503 King Farm Blvd #101   
> Rockville, MD 20850-6667  

Skim does support internal and external links. This is part of Apple’s PDSFKit, 
on which Skim is based. I cannot say in your particular case what may be going 
wrong, as I don’t know what particular type of link you are talking about.

Christiaan

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[Skim-app-users] Skim 1.6.20

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

This version fixes an annoying bug in this morning’s release, so you are 
encouraged to update to this release when you downloaded that version.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.20

Bugs Fixed
  *  Fix removing notes.

Release notes for Skim version 1.6.19

New Features
  *  Switch to 2-up mode when changing book mode or RTL.
  *  Add UI to change the cursor in presentation; move the cursor to the bottom.
  *  Allow drawing temporary freehand notes in presentation mode, removed when 
closing.

Bugs Fixed
  *  Show preview tooltips only when the main window is key.
  *  Option to remove shadow in laser pointer cursor added by Night Shift.
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[Skim-app-users] Skim 1.6.19

[Christiaan Hofman]

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.19

New Features
  *  Switch to 2-up mode when changing book mode or RTL.
  *  Add UI to change the cursor in presentation; move the cursor to the bottom.
  *  Allow drawing temporary freehand notes in presentation mode, removed when 
closing.

Bugs Fixed
  *  Show preview tooltips only when the main window is key.
  *  Option to remove shadow in laser pointer cursor added by Night Shift.
  *  Fix retrieving saved passwords.

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Re: [Skim-app-users] page up/down misses some lines

[Christiaan Hofman]

> On 11 Aug 2023, at 19:07, contact_gmail  
> wrote:
> 
> Hello,
> 
> I use Skim V1.6.18 on Ventura 13.5 and just realized that page up or down 
> (paging through the document via space bar for example) does not fit 
> precisely the current pdf page. Two lines are scrolled over and are missed on 
> the current page. Is there a way to fix this or adjust the width/height in 
> some preferences somewhere? 
> 
> Any help would be appreciated! 
> 
> Thank you.
> Bernd-Jochen

That is correct. It scrolls roughly by the height of the displayed area (in 
scfolling mode), not by page.So it also depends on your zoom level. If you want 
to scroll by page, you should use the Next/Previous page actions, e.g. through 
Come-Arrow.

Christiaan

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[Skim-app-users] Skim 1.6.18

[Christiaan Hofman]

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.18

Bugs Fixed
  *  Fix page selection in overview in presentation mode.
  *  Change shortcut for Show/Hide Toolbar to standard one.
  *  Allow linking on older systems.
  *  Reduce animation target frame for fullscreen with main menu showing.

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[Skim-app-users] Skim 1.6.17

[Christiaan Hofman]

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.17

New Features
  *  New hidden preference to adjust the white point, to modify the white page 
background.
  *  AppleScript support for adjusted white point preference.
  *  Make spelling and grammar check options sticky in note text areas.
  *  Hidden preference on Sonoma for PostScript conversion tool to use.

Bugs Fixed
  *  Make Spelling menu consistent with current standard.
  *  Try to scroll back to page after large layout change immediately.
  *  Fix page preview in presentation.
  *  Improve efficiency of overview for large documents.
  *  Fix text note alignment on Apple Silicon.
  *  Use command line tools on Sonoma to convert PostScript documents.
  *  Correct relative links in PDF bundles.
  *  Fix displayed pages in magnify tool.

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Re: [Skim-app-users] Way to Disable Red Dot While Forward Searching?

[Christiaan Hofman]

It is not possible in an y version, and there is also no intention to change 
that.(And good reasons not to).

Christiaan

> On 23 Jun 2023, at 20:44, Russell Helder  wrote:
> 
> Thanks for your quick response! I should have clarified in my initial 
> question: do you mean it’s impossible in the current version of Skim, or that 
> it’s completely impossible? If it’s not completely impossible, I might submit 
> a feature request. Thanks again!
> 
> Russ
> 
>> On Jun 23, 2023, at 11:32 AM, Christiaan Hofman  wrote:
>> 
>> 
>> 
>>> On 23 Jun 2023, at 20:01, Russell Helder >> <mailto:russell.w.hel...@gmail.com>> wrote:
>>> 
>>> Hello,
>>> 
>>> I use Skim with Neovim and VimTeX. When forward searching, is it possible 
>>> for the line to be indicated just by the reading bar and not the red dot? I 
>>> cannot find a way to disable the red dot either in the Skim settings or in 
>>> the displayline script.
>>> 
>>> For me, the reading bar is sufficient to see where my cursor is in the tex 
>>> doc, and the red dot is unnecessary and annoyingly covers some of the text 
>>> (obviously, just a very small part of the text - but if I want to e.g. see 
>>> that a comma has been inserted properly, and the red dot is covering the 
>>> relevant area, the red dot can be truly inconvenient).
>>> 
>>> Thank you!
>>> Russ
>> 
>> 
>> No, this is mat possible.
>> 
>> Christiaan

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Re: [Skim-app-users] Way to Disable Red Dot While Forward Searching?

[Christiaan Hofman]

> On 23 Jun 2023, at 20:01, Russell Helder  wrote:
> 
> Hello,
> 
> I use Skim with Neovim and VimTeX. When forward searching, is it possible for 
> the line to be indicated just by the reading bar and not the red dot? I 
> cannot find a way to disable the red dot either in the Skim settings or in 
> the displayline script.
> 
> For me, the reading bar is sufficient to see where my cursor is in the tex 
> doc, and the red dot is unnecessary and annoyingly covers some of the text 
> (obviously, just a very small part of the text - but if I want to e.g. see 
> that a comma has been inserted properly, and the red dot is covering the 
> relevant area, the red dot can be truly inconvenient).
> 
> Thank you!
> Russ


No, this is mat possible.

Christiaan

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[Skim-app-users] SkimNotes 1.5.6

[Christiaan Hofman]

For those interested in the SkimNotes framework or tools, I'd like to say that 
there is a new version 1.5.6 released. It can be downloaded from the Skim web 
page.

Christiaan

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Re: [Skim-app-users] help

[Christiaan Hofman]

> On 7 Jun 2023, at 16:16, Frank C  wrote:
> 
> How to keep "Check Spelling While Typing" on. 
> 
> Hello,
> 
> I've been using Skim to take notes during school. I'll print a professor's 
> powerpoint to PDF. This allows me to markup and take notes anywhere on the 
> powerpoint presentation using "text note" and "freehand". 
> 
> However, it does not automatically spell check. I know there's a "Check 
> spelling while typing" option, but it turns off when I create a new text box. 
> Is there a way to have this automatically turn on whenever I create a new 
> text box?
> 
> Bonus question: Is it also possible to incorporate Mac's autocorrect?
> 
> Thanks! 

About that last: there is the Correct Spelling Automatically option. This 
default value for this can be set in the Keyboard system preferences.

Christiaan

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Re: [Skim-app-users] help

[Christiaan Hofman]

> On 7 Jun 2023, at 16:25, Christiaan Hofman  wrote:
> 
> 
> 
>> On 7 Jun 2023, at 16:16, Frank C > <mailto:fecorallu...@gmail.com>> wrote:
>> 
>> How to keep "Check Spelling While Typing" on. 
>> 
>> Hello,
>> 
>> I've been using Skim to take notes during school. I'll print a professor's 
>> powerpoint to PDF. This allows me to markup and take notes anywhere on the 
>> powerpoint presentation using "text note" and "freehand". 
>> 
>> However, it does not automatically spell check. I know there's a "Check 
>> spelling while typing" option, but it turns off when I create a new text 
>> box. Is there a way to have this automatically turn on whenever I create a 
>> new text box?
>> 
>> Bonus question: Is it also possible to incorporate Mac's autocorrect?
>> 
>> Thanks! 
> 
> No, there is no way to do this. It is not an ap[p wide setting, but a 
> function of each text input control by itself.
> 
> Christiaan

I think it would actually be worthwhile to remember your choice. So this (and 
related) settings will be sticky across (at least some) inputs and launches in 
the next release.

Christiaan

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Re: [Skim-app-users] help

[Christiaan Hofman]

> On 7 Jun 2023, at 16:16, Frank C  wrote:
> 
> How to keep "Check Spelling While Typing" on. 
> 
> Hello,
> 
> I've been using Skim to take notes during school. I'll print a professor's 
> powerpoint to PDF. This allows me to markup and take notes anywhere on the 
> powerpoint presentation using "text note" and "freehand". 
> 
> However, it does not automatically spell check. I know there's a "Check 
> spelling while typing" option, but it turns off when I create a new text box. 
> Is there a way to have this automatically turn on whenever I create a new 
> text box?
> 
> Bonus question: Is it also possible to incorporate Mac's autocorrect?
> 
> Thanks! 

No, there is no way to do this. It is not an ap[p wide setting, but a function 
of each text input control by itself.

Christiaan

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Re: [Skim-app-users] Skim app doesn't launch editor anymore

[Christiaan Hofman]

Perhaps there is a permission problem for Skim?

Christiaan

> On 18 May 2023, at 10:19, Pedro Andres Aranda Gutierrez  
> wrote:
> 
> Hi,
> 
> Thanks for the answer… I had it running before the last Skim update and I 
> haven’t updated my MacTeX for some time now. The same project generates 
> exactly the same file on my Linux system and there forward and backward 
> searching works. I’m pretty sure the script is not called on Linux, because I 
> generate a debug log on my /tmp/ and I can’t find any logs since the last 
> update.
> 
> /PA
> 
>> El 18 may 2023, a las 10:14, Christiaan Hofman > <mailto:cmhof...@gmail.com>> escribió:
>> 
>> 
>> 
>>> On 18 May 2023, at 08:14, Pedro Andres Aranda Gutierrez >> <mailto:paag...@gmail.com>> wrote:
>>> 
>>> Hi
>>> 
>>> My system is
>>> 
>>> Darwin Kernel Version 21.6.0: Thu Mar  9 20:08:59 PST 2023; 
>>> root:xnu-8020.240.18.700.8~1/RELEASE_X86_64 x86_64
>>> 
>>> And I have a script in /usr/local/bin to launch emacsclient. I’m using 
>>> Skim.app 1.6.16 and since the last upgrade there is neither direct nor 
>>> reverse lookup.
>>> 
>>> I have enabled logging and can’t see any activity, ie. my scripts are not 
>>> called by Skim.
>>> 
>>> Thx, /PA
>> 
>> The last release did not change anything related to syncing, and for quite a 
>> while for that matter. And for me both forward and backward sync work 
>> properly. So it must be something else locally for you, perhaps in the 
>> generation of the syntax file.
>> 
>> Christiaan

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Re: [Skim-app-users] Skim app doesn't launch editor anymore

[Christiaan Hofman]

> On 18 May 2023, at 08:14, Pedro Andres Aranda Gutierrez  
> wrote:
> 
> Hi
> 
> My system is
> 
> Darwin Kernel Version 21.6.0: Thu Mar  9 20:08:59 PST 2023; 
> root:xnu-8020.240.18.700.8~1/RELEASE_X86_64 x86_64
> 
> And I have a script in /usr/local/bin to launch emacsclient. I’m using 
> Skim.app 1.6.16 and since the last upgrade there is neither direct nor 
> reverse lookup.
> 
> I have enabled logging and can’t see any activity, ie. my scripts are not 
> called by Skim.
> 
> Thx, /PA

The last release did not change anything related to syncing, and for quite a 
while for that matter. And for me both forward and backward sync work properly. 
So it must be something else locally for you, perhaps in the generation of the 
syntax file.

Christiaan

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[Skim-app-users] Skim 1.6.16

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.16

New Features
  *  Allow selecting multiple pages in Overview for copying.

Bugs Fixed
  *  Support reduced motion accessibility option.
  *  Show search match in status bar.
  *  Support links that zoom or fit the PDF.
  *  Fix some localized terms.
  *  Fix touch bars for some sheets.
  *  Fix page navigation on 10.12.
  *  Allow choosing new file for bookmarks through contextual menu.

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Re: [Skim-app-users] Extracting pages from thumbnails

[Christiaan Hofman]

> On 28 Apr 2023, at 10:56, Christiaan Hofman  wrote:
> 
> 
> 
>> On 28 Apr 2023, at 01:50, Arthur Pinheiro via Skim-app-users 
>> > <mailto:skim-app-users@lists.sourceforge.net>> wrote:
>> 
>> Hello! 
>> 
>> Searching this mailing list, I've found a thread claiming that extracting 
>> multiple pages from the thumbnail view was not possible. I'm new to Skim, 
>> yet I recognize that it has some powerful features and good design choices, 
>> which is why I recently migrated to it. Also, I understand that this is an 
>> open-source project, but is there any special reason for this feature not 
>> being available? It looks like a basic feature that we can find in almost 
>> all PDF readers, including Preview.
>> 
>> Regards,
>> 
>> Arthur
> 
> 
> The thumbnail table selects the page that is currently focused. The PDF view 
> has only one currently focused page. So there is only one page selected at 
> any time.
> 
> Christiaan


In the next release you will be able to do this in the Overview mode.

Christiaan

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Re: [Skim-app-users] Extracting pages from thumbnails

[Christiaan Hofman]

> On 28 Apr 2023, at 01:50, Arthur Pinheiro via Skim-app-users 
>  wrote:
> 
> Hello! 
> 
> Searching this mailing list, I've found a thread claiming that extracting 
> multiple pages from the thumbnail view was not possible. I'm new to Skim, yet 
> I recognize that it has some powerful features and good design choices, which 
> is why I recently migrated to it. Also, I understand that this is an 
> open-source project, but is there any special reason for this feature not 
> being available? It looks like a basic feature that we can find in almost all 
> PDF readers, including Preview.
> 
> Regards,
> 
> Arthur


The thumbnail table selects the page that is currently focused. The PDF view 
has only one currently focused page. So there is only one page selected at any 
time.

Christiaan

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Re: [Skim-app-users] Search display suggestion

[Christiaan Hofman]

> On 28 Mar 2023, at 07:20, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> No, that is not possible.That is what the search pdf feature does.
>> Finding all matches is a potentially slow, and therefore
>> asynchronous, process. So this cannot work together with quick
>> single match. (And searching just a page is not possible).
> 
> I'm quite puzzled.
> 
> Why is it possible to display all of the hits on a page under
> Option-Command-F but not Command-F?
> 
> Why can't the hits on a page be colored by "current" (green) and
> "other" (magenta)?
> 
> Why can Option-Command-F report all hits and current location but not
> Command-F?
> 
> That is, is it possible to have Command-F do what Option-Command-F
> does, but not have the bulky display on the left?
> 
> Thanks,
> 
> Tom

You can’t do both at the same time. If you would do it in the Cmd-F UI, then 
the other UI is not possible, and you would loose a lot of functionality of 
that feature (like the overview of the hits and all that you can do with it). 
The other thing is that you should also be able to get rid of the highlights, 
and if we would do that in the Cmd-F feature (because off the way it works), 
that would be very hard, and would functionally interfere with the “quick hit” 
nature of the feature.

Christiaan



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Re: [Skim-app-users] Search display suggestion

[Christiaan Hofman]

> On 28 Mar 2023, at 00:13, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> It is the default. For that feature. In the other featur, it is
>> impossible, as it would interfere.For insurance, arrows generally
>> have a function in many contexts.
> 
> I'm viewing without Option-Command-F.
> 
> I prefer to use the Command-F (the search bar appears at the top)
> because it takes up less screen space.
> 
> With Command-F only one search match shows up at a time.  Is there a
> way to show all of them on the current page?  Like Firefox the main
> one could be green and the others magenta.  That would be super
> useful.
> 
> Also, the Command-F mode doesn't tell me the total number and the
> number I'm on (like Firefox does).  That would be highly useful too.
> 
> Regards,
> 
> Tom

No, that is not possible.That is what the search pdf feature does. Finding all 
matches is a potentially slow, and therefore asynchronous, process. So this 
cannot work together with quick single match. (And searching just a page is not 
possible). 

Christiaan



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Re: [Skim-app-users] Search display suggestion

[Christiaan Hofman]

It is the default. For that feature. In the other featur, it is impossible, as 
it would interfere.For insurance, arrows generally have a function in many 
contexts.

Christiaan

> On 26 Mar 2023, at 19:30, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> The only thing here Skim does not do is tell you which number of the
>> hits you have selected.You can select all or multiple hits (also by
>> page, see the second view option) to select several hits, and move
>> through them using the arrow keys.
> 
> Ok, fabulous!  How about making the multiple hits and moving by arrows
> the default?
> 
> Tom



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Re: [Skim-app-users] Search display suggestion

[Christiaan Hofman]

The only thing here Skim does not do is tell you which number of the hits you 
have selected.You can select all or multiple hits (also by page, see the second 
view option) to select several hits, and move through them using the arrow keys.

Christiaan

> On 26 Mar 2023, at 04:07, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan
> 
>> To some extent, you can get this with the Search PDF feature.
>> Yes, the search field on the left, Option-Command-F. 
> 
> Ok, thanks.  The main thing I am enamored about in the Firefox display
> is how it shows multiple hits simultaneously on the page and also how
> it reports the number of hits and which hit one is looking at.  This
> could help people using Skim.
> 
> Tom



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Re: [Skim-app-users] Search display suggestion

[Christiaan Hofman]

> On 26 Mar 2023, at 00:07, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> To some extent, you can get this with the Search PDF feature.
> 
> I only know about command-F that provides a search feature.  It does
> not mark all hits.  Is there another search feature?  If so, where do
> I find it?
> 
> Tom


Yes, the search field on the left, Option-Command-F.

Christiaan

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Re: [Skim-app-users] Search display suggestion

[Christiaan Hofman]

To some extent, you can get this with the Search PDF feature.

Christiaan

> On 25 Mar 2023, at 22:54, Thomas Schneider via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
> The search function that Skim provides is better than most since it
> shows the new location in a bright yellow box before subsiding to a
> blue highlight.
> 
> The Firefox browser has a fabulous search match display method.  When
> one does command-F a box shows up in the lower left.  I turn on
> 'Highlight All'.  When a search is done by entering a term, it says,
> for example, '1 of 14 matches'.  Then the term gets a highlight in
> blue and others that are not on are magenta.  As one moves through the
> matches (using up and down arrows), the current one is always blue and
> the others are magenta.  This keeps one oriented.  There is also a
> strip on the side that shows magenta lines corresponding to all hits
> in the entire document and a grey oval that shows the currently
> displayed page.  This allows one to be completely oriented as to the
> locations of the matches in the document.
> 
> It would be great if the highlighting (and maybe the strip) were in
> Skim!
> 
> Thanks for all your great work.
> 
> Tom
> 
>  Thomas D. Schneider, Ph.D.
>  Senior Investigator
>  National Institutes of Health
>  National Cancer Institute
>  Center for Cancer Research
>  RNA Biology Laboratory
>  Biological Information Theory Group
>  Frederick, Maryland  21702-1201
>  schne...@mail.nih.gov
>  alum.mit.edu/www/toms
>  https://alum.mit.edu/www/toms
> 



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[Skim-app-users] SkimNotes 1.6.15

[Christiaan Hofman]

A correction to the previous message, with the correct release notes. A new 
version of Skim is available for download at > or using the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.15

New Features
  *  Display edited form fields in Skim notes documents.
  *  Simplify Lines panel.

Bugs Fixed
  *  Fix remembering of export options in export panel.
  *  Avoid a slowdown in opening of documents with many pages.
  *  Prevent jump when scrolling using keys.
  *  Scroll to current page also on 10.12.
  *  Fix glitch in first presentation page transition.
  *  Make sure selected font wells control the font panel.

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[Skim-app-users] Skim 1.6.15

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.15

New Features
  *  Add option to display line script and go script command to not select text.
  *  Allow resizing freehand notes, press Shift to resize proportionally.
  *  Expose preference for using sequential rather than logical page numbers.
  *  Expose preference for adding author name to new notes, also through 
AppleScript.

Bugs Fixed
  *  Don't draw page shadows when not showing page breaks.
  *  Fix freehand note selection highlight on rotated pages.
  *  Try to target current page on low zoom when scrolling to a page.
  *  Clear user name for new Skim notes by default.
  *  Highlight full line for reading bar.
  *  Fix export panel on macOS 13.

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[Skim-app-users] SkimNotes 1.5.5

[Christiaan Hofman]

For those interested in the SkimNotes framework or tools, I'd like to say that 
there is a new version 1.5.5 released. This version also allows building the 
frameworks for iOS. It can be downloaded from the Skim web page.

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Re: [Skim-app-users] Change note colors in context menu

[Christiaan Hofman]

You can do that in the Display preferences, using the control(s) aneart the 
bottom.

Christiaan

> On 20 Feb 2023, at 17:24, Rasmus Malver  
> wrote:
> 
> Hi,
> 
> Is it possible to change the six colors in the context menu? The help page 
> points to the preferences, where the default note color can be set, but that 
> doesn't change the six in the context menu. If I select a note, and choose 
> “note color” in the context menu, I can define my own palette, but the “Skim” 
> palette is locked to “Favorite Color” 1 through 6.
> 
> I have searched the wiki, the mailing list and tried downloading and 
> searching the source code to find any definition of the colors, but I can't 
> seem to find it.
> 
> Thanks,
> 
> Rasmus Malver
> 



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Re: [Skim-app-users] Skim URLs to specific notes...?

[Christiaan Hofman]

That is only for markup. Apart from tha, this is not available in PDFKit. 
Moreover, a creation date does not (uniquely) identify a note.

Christiaan

> On 13 Feb 2023, at 13:12, Mark Roberts  wrote:
> 
> In v. 1.7 of the PDF spec, § 12.5.6.2 for Markup Annotations specifies a 
> CreationDate.
> 
> Not applicable?
> 
> Thanks,
> 
> M.
> 
> On Mon, Feb 13, 2023 at 6:51 PM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> The point is that they don’t. See the Adobe specifications.
> 
> Christiaan
> 
>> On 13 Feb 2023, at 03:15, Mark Roberts > <mailto:mroberts1...@gmail.com>> wrote:
>> 
>> I set this idea aside for a while, but then I had an idea...
>> 
>> As it stands now, each Skim note includes a modification date. What if it 
>> also included a UUID, or a creation date that never changes? 
>> 
>> If one of these were added to the note structure, then they could also be 
>> referenced in a URL. In this fashion, a Skim URL could resolve to a specific 
>> note.
>> 
>> The use case I have in mind is another app reading the Skim notes sidecar 
>> file, and generating hyperlinks that could resolve to the same note.
>> 
>> Thanks again
>> 
>> M.
>> 
>> 
>> 
>> On Thu, Jan 26, 2023 at 6:41 PM Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> 
>> 
>>> On 26 Jan 2023, at 05:17, Mark Roberts >> <mailto:mroberts1...@gmail.com>> wrote:
>>> 
>>> I'm using the "Deep Links Using Skim URLs" feature, to open a PDF file in 
>>> Skim.
>>> 
>>> I can use a "page=" fragment to open to a particular page, but I'm 
>>> wondering if there's a way to open to both a page and to select one of my 
>>> notes (highlighted text) on that page.
>>> 
>>> Possible?
>>> 
>>> TIA
>> 
>> No, that is not possible. It wouldn’t even be possible, there is no reliable 
>> way to identify a note.
>> 
>> Christiaan

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Re: [Skim-app-users] Skim URLs to specific notes...?

[Christiaan Hofman]

The point is that they don’t. See the Adobe specifications.

Christiaan

> On 13 Feb 2023, at 03:15, Mark Roberts  wrote:
> 
> I set this idea aside for a while, but then I had an idea...
> 
> As it stands now, each Skim note includes a modification date. What if it 
> also included a UUID, or a creation date that never changes? 
> 
> If one of these were added to the note structure, then they could also be 
> referenced in a URL. In this fashion, a Skim URL could resolve to a specific 
> note.
> 
> The use case I have in mind is another app reading the Skim notes sidecar 
> file, and generating hyperlinks that could resolve to the same note.
> 
> Thanks again
> 
> M.
> 
> 
> 
> On Thu, Jan 26, 2023 at 6:41 PM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> 
> 
>> On 26 Jan 2023, at 05:17, Mark Roberts > <mailto:mroberts1...@gmail.com>> wrote:
>> 
>> I'm using the "Deep Links Using Skim URLs" feature, to open a PDF file in 
>> Skim.
>> 
>> I can use a "page=" fragment to open to a particular page, but I'm wondering 
>> if there's a way to open to both a page and to select one of my notes 
>> (highlighted text) on that page.
>> 
>> Possible?
>> 
>> TIA
> 
> No, that is not possible. It wouldn’t even be possible, there is no reliable 
> way to identify a note.
> 
> Christiaan

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Re: [Skim-app-users] Skim URLs to specific notes...?

[Christiaan Hofman]

> On 26 Jan 2023, at 05:17, Mark Roberts  wrote:
> 
> I'm using the "Deep Links Using Skim URLs" feature, to open a PDF file in 
> Skim.
> 
> I can use a "page=" fragment to open to a particular page, but I'm wondering 
> if there's a way to open to both a page and to select one of my notes 
> (highlighted text) on that page.
> 
> Possible?
> 
> TIA

No, that is not possible. It wouldn’t even be possible, there is no reliable 
way to identify a note.

Christiaan

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Re: [Skim-app-users] skim 1.6.14 not found at sourceforge repository

[Christiaan Hofman]

> On 19 Jan 2023, at 14:35, Daniel Macêdo Batista via Skim-app-users 
>  wrote:
> 
> Hi all!
> 
> I tried to update to 1.6.14 on macOS, but the embedded updater is returning:
> 
> "Update error! An error occurred while downloading the update. Please try 
> again later."
> 
> Probably because the file is not available at sourceforge? (When I try to get 
> the .dmg at https://sourceforge.net/projects/skim-app/files/ 
>  I am receiving 'Unable to 
> find any mirror information for the "/Skim/Skim-1.6.14/Skim-1.6.14.dmg"')
> 
> Is there any other mirror from where I can get the .dmg?
> 
> Best!
> Daniel

Yes, it looks like the last year and a half of release files are missing on 
sourcefrorge! It is obviously a problem of source forge, as it seems to be the 
case for every project (their bugreporter is filled with bugs about this). I 
really hope they have a backup to restore them.

Christiaan

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Re: [Skim-app-users] Problem using SKIM on two computers

[Christiaan Hofman]

Yes, that is what it most often means. But it also means that you did preserve 
the notes in the separate .skim files, so you can just get them by answering 
YES. (You can suppress the dialog by setting a hidden preferences, see the Wiki 
for details).

Christiaan

> On 18 Jan 2023, at 11:24, Mark Roberts  wrote:
> 
> I have had some similar issues when moving PDF and Skim files between 
> computers. It sounds like it might(?) be because the file attributes were not 
> preserved.
> 
> The symptom is that when I open xyz,pdf from mac A on mac B, I get an error 
> message:
> 
>  Unable to read notes for xyz.pdf, but a Skim notes file with the same 
> name was found. Do you want Skim to read notes from this file?
> 
> Does this error mean the file attributes could not be found?
> 
> TIA
> 
> On Tue, Jan 17, 2023 at 12:25 AM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> The extended attributes are file attributes. It depends on the file system 
> implementation exactly where they are saved, that cannot be controlled. It is 
> not a question of “saving in DropBox” (DropBox is not a location), but rather 
> whether DropBox copies the attributes (which nit doesn’t). Attributes are not 
> like separate files, so “save it in another folder” does not make sense. BTW, 
> in the current default format iCloud should preserve the Skim note attributes.
> 
> Christiaan
> 
> > On 16 Jan 2023, at 16:09, Stéphane Coudé  > <mailto:stephane.co...@gmail.com>> wrote:
> > 
> > Dear Thomas and Christiaan, thanks for you help !!!
> > 
> > Actually, by activating the .skim file in the general setting (it was 
> > activated by default in the former version of SKIM) I solved my problem. 
> > Since the .skim file is saved at the same location as my .pdf file, which 
> > is in my Dropbox, both files are now saved on both computers. I just have 
> > to ensure that once I have finished working from one computer that I close 
> > the file. Then when I reopen it on my other computer, SKIM automatically 
> > detects that there is a .skim file related to my document and ask me if I 
> > want to integrate the notes from the .skim file. That way, I have access to 
> > my notes on both computers and I can update and modify them from both 
> > computers.
> > 
> > Just a curiosity Christiaan, you are probably right about the fact that 
> > Dropbox doesn’t synchronize the extended attribute of the pdf files. It may 
> > be all depends on where that information is saved. Is there a way I can 
> > save such information in my Dropbox ? In other words, where is the extended 
> > attributes of the file are saved ? And can we decide to save it in another 
> > folder (that could be on my Dropbox as an example) ?
> > 
> > Many thanks again,
> > 
> > Stephane
> > 
> >> Le 16 janv. 2023 à 04:36, Christiaan Hofman  >> <mailto:cmhof...@gmail.com>> a écrit :
> >> 
> >> 
> >> 
> >>> On 16 Jan 2023, at 02:07, Stéphane Coudé  >>> <mailto:stephane.co...@gmail.com>> wrote:
> >>> 
> >>> Hi,
> >>> 
> >>> I have a desktop computer and a laptop (both recent Apple products 
> >>> purchased in 2022) and work on the same document from both computers. I 
> >>> have installed SKIM on both computers. But I recently have to work on a 
> >>> large document (more than 200 pages) and I have had the following problem 
> >>> :
> >>> 
> >>> If I annotate my file with SKIM from my desktop computer, when I open the 
> >>> same document on my laptop, I cannot see my annotation anymore ???
> >>> My documents are saved and synchronized with Dropbox.
> >>> 
> >>> I have been using SKIM for almost 10 years (great product by the way) on 
> >>> my previous computers, always with a desktop and a laptop computer for 
> >>> scientific reading annotation as well as scientific article review but 
> >>> not much during the last three years. Previously (I don’t remember from 
> >>> which version this change happened), every time I was creating annotation 
> >>> with SKIM on a document, it was creating a « .skim » file beside my 
> >>> original file. Therefore, it was easy to find my notes and to see it from 
> >>> any of my computers or even when I change computer. Considering the 
> >>> problem I have now by restarting doing such kind of work, I am concerned 
> >>> about that issue because when I will change my computers in the future, 
> >>> is that mean I will lose al

Re: [Skim-app-users] Problem using SKIM on two computers

[Christiaan Hofman]

The extended attributes are file attributes. It depends on the file system 
implementation exactly where they are saved, that cannot be controlled. It is 
not a question of “saving in DropBox” (DropBox is not a location), but rather 
whether DropBox copies the attributes (which nit doesn’t). Attributes are not 
like separate files, so “save it in another folder” does not make sense. BTW, 
in the current default format iCloud should preserve the Skim note attributes.

Christiaan

> On 16 Jan 2023, at 16:09, Stéphane Coudé  wrote:
> 
> Dear Thomas and Christiaan, thanks for you help !!!
> 
> Actually, by activating the .skim file in the general setting (it was 
> activated by default in the former version of SKIM) I solved my problem. 
> Since the .skim file is saved at the same location as my .pdf file, which is 
> in my Dropbox, both files are now saved on both computers. I just have to 
> ensure that once I have finished working from one computer that I close the 
> file. Then when I reopen it on my other computer, SKIM automatically detects 
> that there is a .skim file related to my document and ask me if I want to 
> integrate the notes from the .skim file. That way, I have access to my notes 
> on both computers and I can update and modify them from both computers.
> 
> Just a curiosity Christiaan, you are probably right about the fact that 
> Dropbox doesn’t synchronize the extended attribute of the pdf files. It may 
> be all depends on where that information is saved. Is there a way I can save 
> such information in my Dropbox ? In other words, where is the extended 
> attributes of the file are saved ? And can we decide to save it in another 
> folder (that could be on my Dropbox as an example) ?
> 
> Many thanks again,
> 
> Stephane
> 
>> Le 16 janv. 2023 à 04:36, Christiaan Hofman  a écrit :
>> 
>> 
>> 
>>> On 16 Jan 2023, at 02:07, Stéphane Coudé  wrote:
>>> 
>>> Hi,
>>> 
>>> I have a desktop computer and a laptop (both recent Apple products 
>>> purchased in 2022) and work on the same document from both computers. I 
>>> have installed SKIM on both computers. But I recently have to work on a 
>>> large document (more than 200 pages) and I have had the following problem :
>>> 
>>> If I annotate my file with SKIM from my desktop computer, when I open the 
>>> same document on my laptop, I cannot see my annotation anymore ???
>>> My documents are saved and synchronized with Dropbox.
>>> 
>>> I have been using SKIM for almost 10 years (great product by the way) on my 
>>> previous computers, always with a desktop and a laptop computer for 
>>> scientific reading annotation as well as scientific article review but not 
>>> much during the last three years. Previously (I don’t remember from which 
>>> version this change happened), every time I was creating annotation with 
>>> SKIM on a document, it was creating a « .skim » file beside my original 
>>> file. Therefore, it was easy to find my notes and to see it from any of my 
>>> computers or even when I change computer. Considering the problem I have 
>>> now by restarting doing such kind of work, I am concerned about that issue 
>>> because when I will change my computers in the future, is that mean I will 
>>> lose all my SKIM work ?
>>> 
>>> Is anyone can please help me with that issue ?
>>> 
>>> Thanks in advance,
>>> 
>>> Stephane
>> 
>> DropBox (probably) does not synchronize the extended attributes of the 
>> files, where we save the Skim notes. So this will not work. You could either 
>> save your PDFs as PDF bundles, which should synchronize them properly. Or 
>> you can always save a .skim file backup of the notes (you can set this in 
>> the General preferences), and synchronize that with the PDF. (But be aware 
>> that changing notes on both systems may b=not be seen on the other when you 
>> do this). Our you can synchronize files with embedded notes, but that has 
>> other problems. See also the FAQ on the Wiki.
>> 
>> Christiaan



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Re: [Skim-app-users] Skim notes in XML plist format ?

[Christiaan Hofman]

> On 16 Jan 2023, at 11:15, Mark Roberts  wrote:
> 
> As always, I'm happy to be Skimming PDFs !
> 
> Recently, I have been working on some scripts to extract information from my 
> Skim notes.
> 
> For this, I use:
> 
>  skimnotes get -format plist xyz.pdf | plutil -convert xml1 -o xyz.pdf - 
> 
> ...to get XML files, and it seems to work fine.
> 
> In the release notes to the latest update of the skimnotes framework, I 
> notice "Allow Skim notes in XML plist format".
> 
> Is this another way to generate XML? How does it work? If I use this feature, 
> what happens with any existing .skim files?
> 
> Thanks!
> 
> M

No, it just says that when you attach skim notes (e.g. using skimnotes set) and 
the notes are in xml format rather than binary plist, we  are able to read 
them. So it is for the opposite action.

Christiaan

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Re: [Skim-app-users] Problem using SKIM on two computers

[Christiaan Hofman]

> On 16 Jan 2023, at 02:07, Stéphane Coudé  wrote:
> 
> Hi,
> 
> I have a desktop computer and a laptop (both recent Apple products purchased 
> in 2022) and work on the same document from both computers. I have installed 
> SKIM on both computers. But I recently have to work on a large document (more 
> than 200 pages) and I have had the following problem :
> 
> If I annotate my file with SKIM from my desktop computer, when I open the 
> same document on my laptop, I cannot see my annotation anymore ???
> My documents are saved and synchronized with Dropbox.
> 
> I have been using SKIM for almost 10 years (great product by the way) on my 
> previous computers, always with a desktop and a laptop computer for 
> scientific reading annotation as well as scientific article review but not 
> much during the last three years. Previously (I don’t remember from which 
> version this change happened), every time I was creating annotation with SKIM 
> on a document, it was creating a « .skim » file beside my original file. 
> Therefore, it was easy to find my notes and to see it from any of my 
> computers or even when I change computer. Considering the problem I have now 
> by restarting doing such kind of work, I am concerned about that issue 
> because when I will change my computers in the future, is that mean I will 
> lose all my SKIM work ?
> 
> Is anyone can please help me with that issue ?
> 
> Thanks in advance,
> 
> Stephane

DropBox (probably) does not synchronize the extended attributes of the files, 
where we save the Skim notes. So this will not work. You could either save your 
PDFs as PDF bundles, which should synchronize them properly. Or you can always 
save a .skim file backup of the notes (you can set this in the General 
preferences), and synchronize that with the PDF. (But be aware that changing 
notes on both systems may b=not be seen on the other when you do this). Our you 
can synchronize files with embedded notes, but that has other problems. See 
also the FAQ on the Wiki.

Christiaan

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[Skim-app-users] SkimNotes 1.5.4

[Christiaan Hofman]

For those interested in the SkimNotes framework or tools, I'd like to say that 
there is a new version 1.5.4 released. It can be downloaded from the Skim web 
page.

Christiaan

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[Skim-app-users] Skim 1.6.14

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.14

New Features
  *  Add option to display line script and go script command to not select text.
  *  Allow resizing freehand notes, press Shift to resize proportionally.
  *  Expose preference for using sequential rather than logical page numbers.
  *  Expose preference for adding author name to new notes, also through 
AppleScript.

Bugs Fixed
  *  Don't draw page shadows when not showing page breaks.
  *  Fix freehand note selection highlight on rotated pages.
  *  Try to target current page on low zoom when scrolling to a page.
  *  Clear user name for new Skim notes by default.
  *  Highlight full line for reading bar.
  *  Fix export panel on macOS 13.

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Re: [Skim-app-users] Export

[Christiaan Hofman]

> On 2 Jan 2023, at 07:32, HumanEngr  wrote:
> 
> Hi Christiaan, 
> 
> Am I right that the "With Embedded Notes” option disappeared in OS 13.1?
> 
> humanengr
> Version 1.6.13 (143)
> 
> _


It shouldn’t. But there seems to be a problem with export in macOS 13.1, but I 
have no idea what it is, and I cannot check it myself. 
So what do you actually see? Do you see the 3 options below the format popup, 
or do you only get the popup?

Christiaan

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Re: [Skim-app-users] question about note margin

[Christiaan Hofman]

> On 12 Dec 2022, at 06:06, Donald Williams  
> wrote:
> 
> Dear Skim developers,
> 
> I have been using Skim for a long time, and thank you so much for developing 
> such a great tool. 
> 
> There is one thing about note margin that has been bothering me for a long 
> time. I checked the FAQ, Tips and Tricks on the Skim Wiki, Hidden 
> Preferences, past mail archive, feature request, and searched all entries 
> related to note margin, but didn't find any similar request.
> 
> I have many notes written on pdfs using Skim version <= 1.5.6, and the note 
> margins are very small, so I can fit many words in a note. This is also 
> helpful when correcting some typo in the pdf so that I can use a 0-margin 
> note to cover the typo. Since some version after 1.5.6, the note margins 
> become quite large, especially vertically. All the notes that I have taken 
> before now appear overflowed. For this reason, I have been stuck at version 
> 1.5.6. However, recently I need to switch to the new macOS Monterey (since 
> the El Capitan I have been using is getting too old to have many softwares 
> unsupported). Now it seems that even for version 1.5.6, the note margin is 
> very wide. 
> 
> Is there any way to reduce the note margin to 0, and if so, in which version? 
> I tried the latest version, and I cannot seem to find such an option. 
> 
> Thank you so much,
> Don

I assume you are talking about text notes? The notes are drawn by Apple’s 
PDFKit, we don’t (and can’t) influence how they are drawn. So this is not about 
the Skim version, but rather your OS version. And as we cannot influence the 
drawing, we also cannot change the margin. This really is a question for Apple, 
not us.

Christiaan

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Re: [Skim-app-users] Selection with AppleScript

[Christiaan Hofman]

> On 4 Dec 2022, at 09:20, Detlef Beyer  wrote:
> 
> Hi,
> 
> I’m new to Skim and I play around trying to add highlights (note type = 
> highlight note) with AppleScript.
> 
> I got a position and page from a Kindle export of the highlights made there 
> (position = a location comprises around 125 characters, spacing included, or 
> 23 words). The kindle export looks like:
> 
> 
>Highlight(yellow) - page 10 · 
> Position 124
> 
> 
>Überseeische Siedlungskolonisation.
> 
> 
> So first thing I tried:
> 
> set theText to "Überseeische Siedlungskolonisation."
> set kindleLocation to 124
> set startOfLocation to (kindleLocation * 125)
> set endOfLocation to startOfLocation + (length of theText)
> set aSelection to {a reference to characters startOfLocation thru 
> endOfLocation of text of document 1}
> set theSel to find text theText from aSelection
> 
> worked sometimes. But the position value I got from the Kindle seems to be 
> calculated in a way I can’t predict. So I tried the page value.
> 
> set aSelection to {a reference to text of page kindlePage of document 1}
> 
> now aSeletion contains "every text of page 8 of document 1“. The result of 
> the find returns "characters 34 thru 47 of text of page 9 of document 
> „mydemopdf“"???
> 
> Why does the find return something located out of the selection? Any idea how 
> to use the values of the kindle export in Skim?
> 
> Thanks a lot,
> 
> Detlef


As for the location Kindle reports, I have no idea as I don’t know what Kindle 
does.

As for your last question, what do you mean with the find result? Are you 
trying to use the find command from the selection of the whole page? That would 
search starting *after* that page (after the selection), the way it works when 
you choose Find Next from the UI when you have selected text. It would be 
better to start from a selection of just the first character on the page, 
something like

tell document 1
set aSelection to find theText from {character 1 of page kindlePage}
end tell

It won’t find it when it happens to start at the first character. You could 
then also start from the last character of the previous page.

Christiaan

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Re: [Skim-app-users] Skim/Latex Next Page button grayed out on first page sometimes

[Christiaan Hofman]

As I said, Skim updates its UI (including button validation) in response to 
PDFKit telling us about page changes. And that is the only way for us to know 
how and when to update. So when the UI is not properly updated, it means that 
PDFKit its not notifying us. That’s Apple’s bug, and unfortunately there is no 
way for us to fix that, only Apple can. I have absolutely no idea why it fails 
to notify, as I know nothing about what Apple does b behind the scenes.

Christiaan

> On 20 Nov 2022, at 15:29, Themis Matsoukas via Skim-app-users 
>  wrote:
> 
> This is a follow up on my previous post, because it seems to me that the 
> issue here is actually with Skim, not just with the page info sent by Apple.
> 
> In this example,   latex  apparently is telling Skim that we are on the last 
> page of the document, hence the next-page button is grayed out. However, Skim 
> thinks it is displaying the first page of the document and even though the 
> next button looks active, it does not respond to clicking. If I scroll to a 
> different page using the mouse, Skim continues to say that we are looking at 
> "page 1 of 11” regardless of the page displayed, and both buttons 
> “Previous/Next” are unresponsive. Somehow Skim becomes unaware of page 
> scrolling and of the page that is currently displayed, even when that page 
> changes.
> 
> This is a beamer document with a lot of  transitions. The problem occurred 
> when I turned off the transitions by running the handout mode in beamer. With 
> the transitions on the document has 34 pages, but with the transitions off it 
> only has 11. This change in the size of the document may have confused Skim.
> 
> Themis
> 
> 
> 
> 
>> On Nov 13, 2022, at 4:14 AM, Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> 
>> There are also some bug reports about this. But as I said there, there is 
>> nothing we can do about it, as it is Apple reporting the wrong page to us. 
>> And we have to rely on them top tell us right. This is Apple’s bug, and only 
>> they can fix this.
>> 
>> Christiaan 

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Re: [Skim-app-users] change font size of all existing text notes at once?

[Christiaan Hofman]

AppleScript is notoriously bad at interpreting its own language, especially if 
terms can have multiple meanings (like ’type’). In this case you can use a 
slightly different filter that usually does work. Replace ‘whose type’ with the 
equivalent (or it should be) ‘where its type’, then it should work. 

Christiaan

> On 14 Nov 2022, at 20:04, Glenn Hollingsworth  wrote:
> 
> When I tried this, I get the result: "Skim got an error: Can’t make type into 
> type specifier." number -1700 from type to specifier
> 
> I'm using Monterey 12.6 and updated Skim app (1.6.13). I've tried looking at 
> the examples of other scripts in the wiki or whatever but not found anything 
> that makes it work.
> 
> I"m asking because sometimes when I export a Skim-annotated PDF with embedded 
> notes, then later convert those notes back into skim notes, it makes the font 
> larger in text notes. Not sure if there's a different fix for preventing that 
> in the first place, but I thought I'd throw it out there. 
> 
> Thank you. 
> 
> 
> On Sun, Jun 12, 2022 at 7:31 AM  <mailto:skim-app-users-requ...@lists.sourceforge.net>> wrote:
> Send Skim-app-users mailing list submissions to
> skim-app-users@lists.sourceforge.net 
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Skim-app-users digest..."
> Today's Topics:
> 
>    1. change font size of all existing text notes at once?
>   (Glenn Hollingsworth)
>2. Re: change font size of all existing text notes at once?
>   (Christiaan Hofman)
> 
> 
> 
> -- Forwarded message --
> From: Glenn Hollingsworth mailto:wghwo...@gmail.com>>
> To: skim-app-users@lists.sourceforge.net 
> <mailto:skim-app-users@lists.sourceforge.net>
> Cc: 
> Bcc: 
> Date: Sat, 11 Jun 2022 12:14:51 -0500
> Subject: [Skim-app-users] change font size of all existing text notes at once?
> Is it possible to change the font size of all (or even a portion) existing 
> text notes in a PDF at once? 
> 
> Thanks.
> Glenn
> 
> 
> 
> -- Forwarded message --
> From: Christiaan Hofman mailto:cmhof...@gmail.com>>
> To: Skim users list  <mailto:skim-app-users@lists.sourceforge.net>>
> Cc: 
> Bcc: 
> Date: Sat, 11 Jun 2022 19:26:05 +0200
> Subject: Re: [Skim-app-users] change font size of all existing text notes at 
> once?
> 
> 
>> On 11 Jun 2022, at 19:14, Glenn Hollingsworth > <mailto:wghwo...@gmail.com>> wrote:
>> 
>> Is it possible to change the font size of all (or even a portion) existing 
>> text notes in a PDF at once? 
>> 
>> Thanks.
>> Glenn
> 
> This can be done using AppleScript. For instance, this simple script:
> 
> tell document 1 of application "Skim"
>   set font size of notes whose type is text note to 12
> end tell
> 
> Christiaan
> 

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Re: [Skim-app-users] Skim/Latex Next Page button grayed out on first page sometimes

[Christiaan Hofman]

> On 13 Nov 2022, at 01:27, Themis Matsoukas via Skim-app-users 
>  wrote:
> 
> I use Skim with sublime text for latex. Recently I encountered the following 
> problem that happens frequently but I cannot reproduce reliably:
> 
> Upon typesetting, Skim displays the first page of the document but thinks it 
> is the last page and grays out the “Next Page” button. In the attached 
> example Skim displays the title page of a 5-page beamer presentation but at 
> the bottom of the screen it says Page 5 of 5 and the Next button is grayed 
> out. If I scroll the screen manually towards the next page Skim reads the 
> correct page number and the Next button is activated as it should. 
> 
> I am not sure what exactly triggers this behavior and I cannot reproduce at 
> will, although I have seen it several times. It is some combination of where 
> I initiate the built (each page of my slides is a different source file ) and 
> the magnification in the Skim window. 
> 
> Skim Version 1.6.13 (143)
> 
> Themis
> 
> 
> ___

There are also some bug reports about this. But as I said there, there is 
nothing we can do about it, as it is Apple reporting the wrong page to us. And 
we have to rely on them top tell us right. This is Apple’s bug, and only they 
can fix this.

Christiaan

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Re: [Skim-app-users] In PDF-TeX Sync is there a way to turn of the blue highlighting?

[Christiaan Hofman]

> On 3 Nov 2022, at 11:00, Leon Simon  wrote:
> 
> In PDF-TeX Sync is there a way to turn of the blue highlighting? I find it is 
> a hindrance to initally viewing the pdf file
> 


You can instead of the selection have a (temporary) reading bar. Call the 
display line with the -b argument if you want that. Otherwise, the point isn 
top indicate the location you are requesting, so that is what we do. So there 
is no way of doing neither.

Christiaan

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[Skim-app-users] Skim 1.6.13

[Christiaan Hofman]

A new version of Skim is available for download at 
> or using 
the built-in updater.

Thanks to those of you who submitted reproducible bug reports and comments 
along with the exception reports; as always, please continue to submit bug 
reports at >.

For those interested in what is fixed, release notes follow.

Release notes for Skim version 1.6.13

New Features
  *  Move reading by by double clicking on it.

Bugs Fixed
  *  Workaround for initial auto resizing problems.
  *  Only show reading bar when there are lines to highlight.
  *  Write text representations of URLs to the clipboard.
  *  Improve scrolling bug workarounds.
  *  Fix reading pacer at higher zoom.
  *  Improve workarounds to restore scroll position.
  *  Make sure magnify is updated in some cases.

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Re: [Skim-app-users] skim failing to display figures

[Christiaan Hofman]

> On 18 Oct 2022, at 18:53, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> This can only be a limitation of Apple’s PDFKit, which we use to
>> display the PDF. You should see the same problem in Preview.
> 
> You are right!  I suppose I'll have to write to Science to report the
> issue.  Or maybe Apple?
> 
> Tom


I guess Apple.

Christiaan

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Re: [Skim-app-users] skim failing to display figures

[Christiaan Hofman]

> On 18 Oct 2022, at 16:57, Thomas Schneider via Skim-app-users 
>  wrote:
> 
> Dear Christiaan:
> 
> In this intriguing paper:
> 
> @article{Keizer.Steg2008,
> author = "K. Keizer
> and S. Lindenberg
> and L. Steg",
> title = "{The spreading of disorder}",
> journal = "Science",
> volume = "322",
> pages = "1681--1685",
> pmid = "19023045",
> note = "\url {https://doi.org/10.1126/science.1161405};,
> year = "2008"}
> 
> The figures do not display in Skim 1.6.12 (142) under
> macOS 12.6 on a laptop and an iMac pro.
> 
> The figures DO show up in Adobe Acrobat Reader.
> 
> I downloaded the latest version of the paper from Science and this
> did not correct the problem.
> 
> So something is strange about these figures from 10 years ago.
> Why won't Skim show them?
> 
> Since this is copyright, if you don't have access I could send you the
> PDF privately if you want.
> 
> Thanks for all your efforts on the fabulous Skim!!!
> 
> Tom


This can only be a limitation of Apple’s PDFKit, which we use to display the 
PDF. You should see the same problem in Preview.

Christiaan

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Re: [Skim-app-users] Hyperlinks to PDF and a specific page

[Christiaan Hofman]

> On 15 Oct 2022, at 13:15, std300  wrote:
> 
>> That shows indeed that there is a URL on the clipboard. The other apps you 
>> mention then apparently don’t know how to handle URLs. TextEdit does.
> 
> The obvious feature request would be if the URL can also be
> represented as a text. But as I said, I don't know much about the
> macOS clipboard, so I don't know if this makes sense.
> 
> Thank you anyway
> 
>  Dirk
> 


I added a seciotn on skim uRLs too the Wiki. And we will also put text 
representation on the clipboard.

Christiaan

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Re: [Skim-app-users] Hyperlinks to PDF and a specific page

[Christiaan Hofman]

> On 15 Oct 2022, at 11:19, std300  wrote:
> 
> Clipboard: I have tried VS Code, the terminal and a few other programs
> which showed nothing. But text edit works (= inserts the correct URL).
> 
> I can confirm that the clipboard viewer contains the correct text
> (from Finder -> Edit -> Show Clipboard) with Copy URL from Skim, but I
> could not paste it with the mentioned programs. Even pbpaste does not
> paste anything in the terminal.
> 
> See the attached clipboard view (another clipboard viewer than from
> the finder) - perhaps the copied types are
> incompatible with the to be pasted text (but I don't know much about
> the clipboard types, so you just might ignore my comment here)
> 
> Dirk
> ___

That shows indeed that there is a URL on the clipboard. The other apps you 
mention then apparently don’t know how to handle URLs. TextEdit does.

Christiaan

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Re: [Skim-app-users] Hyperlinks to PDF and a specific page

[Christiaan Hofman]

> On 14 Oct 2022, at 19:58, Patrick  wrote:
> 
> Hello Christiaan, thank you for the reply. Linking to the page works
> great! However the copy url does "nothing" here, i.e. when I have an
> PDF open (for example the PDF reference), I click on Edit -> Copy URL
> but the clipboard seems to be empty. Also I have searched the Wiki for
> URL (https://sourceforge.net/p/skim-app/wiki/search/?q=url) but this
> did not give any relevant results as far as I can see.
> 
> Thanks again
> Dirk
> 


You are right about the Wiki, I though I had put an item on it there, but 
apparently not.It only seems to be discussed on this list, and mentioned in the 
release notes.

However the Copy URL does work for me. Are you sure it is not on the clipboard? 
Where did you try to paste?

Christiaan

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Re: [Skim-app-users] Hyperlinks to PDF and a specific page

[Christiaan Hofman]

> On 14 Oct 2022, at 11:51, Patrick  wrote:
> 
> Hello all,
> I try to open a PDF file on a specific page from my markdown document.
> 
> I can insert a link such as
> 
> skim:///Users/dirk/stuff/doku/pdf/PDFReference17.pdf
> 
> and clicking on the link opens the PDF file.
> 
> I am not sure if this is a Skim feature or not. My question is: is
> there a way to open the PDF document on a specific page?
> 
> Dirk


Yes, this is a SKim feature, specifically to allow things like opening the PDF 
at a specific page. You can do that by adding a #page=N fragment to the URL. 
You can easily copy such a URL using Edit > Copy URL. See also the Wiki.

Christiaan

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Re: [Skim-app-users] Skim popup problem

[Christiaan Hofman]

> On 30 Sep 2022, at 19:25, Thomas Schneider via Skim-app-users 
>  wrote:
> 
> Dear Skim Experts:
> 
> Maybe someone can help me with a Skim popup problem.
> 
> The computers toot (iMac) and lap (MacBook Pro) are:
> macOS Monterey Version 12.6 (up to date)
> Skim 1.6.12 (up to date)
> 
> On toot there is no problem.  The issue only happens on lap, but I
> don't know why.
> 
> On lap in the trash directory (~/.Trash) I have a pdf file named a.aw.
> (The actual name has a date-time stamp and the file is coming from
> another computer but the example below can be done by hand so that is
> not relevant.)
> 
> cp a.aw a.pdf
> open a.pdf
> (Skim opens the file.)
> cp a.aw a.pdf
> 
> Skim OBJECTS with a pop up message:
> 
> The file "a.pdf" couldn't be opened because you don't have 
> permission to view it.
> 
> To view or change permissions, select the item in the Finder and 
> choose File > Get Info.
> 
> OK
> 
> I must click OK.
> 
> I have full read-write permissions for the files (chmod u+rw *)!  This 
> even happens when I give everybody permission (chmod a+rw *)!
> 
> I have been doing this kind of move in the Trash for YEARS.
> Suddenly it fails on one computer but not on the other.
> 
> Normally Skim would update the PDF since I have the Preferences for
> Sync to be 'Check for file changes' and 'Reload automatically'.  This
> scheme allows me to create a PDF on one computer, transfer it to my
> laptop and display the new version.
> 
> The problem is apparently not related to the attributes marked by '@'
> in the long ls listing.  The attributes can be removed using the 
> command "xattr -c *" and this does not prevent the popup.
> 
> This does not happen if I work in /tmp or another directory,
> only in ~/.Trash
> 
> Does anyone have a clue what's going on?
> 
> Tom


I actually have no idea. But it has almost certainly got something to do with 
how the system treats the trash. I am actually suprised you are able to do what 
you can top, as for me that does not work. Most file operations (like cp) just 
fail with “operation not permitted”  in .Trash. Also the alert message you get 
is coming from the system, so it is just a system objection.

Christiaan

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Re: [Skim-app-users] zoom to fit

[Christiaan Hofman]

> On 6 Sep 2022, at 19:51, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
>> That does not have any immediate effects. That only saves the
>> settings for newly opened PDFs in the future. So you probably saved
>> that with a tiny zoom factor. You can choose that with a larger zoom
>> factor, or with Automatically Resize checked. Or you can set the
>> default settings in the General preferences.
> 
> I don't see what the settings should be in General preferences.
> It's not clear what they do.
> 

What is not clear? If you want the zoom level to automatically adapt to the 
view size, then you check Automatically Resize. Otherwise, you enter a specific 
zoom level in the Scale field. 

And this is a *preference*, i.e. settings that will be used for newly opened 
documents. It is not the settings used for currently open documents.

>> When it is checked, then the PDF view should just resize the PDF to fit the 
>> view.
> 
> I resized my postage stamp.  I closed skim.  It was still tiny when I
> reopened.  In General I clicked on 'Normal'.  Nothing changed
> apparently when I did that (no check box or any other change).
> 

Why would you expect anything to change this way? You changed the setting for 
an opened document. That will not apply to the next opened document, even if it 
is the same. If you want to change the setting for newly opened documents, you 
should change the default settings by clicking Normal in General Preferences, 
set the settings, and hit OK. What did you do after clicking Normal? Did you 
confirm any changes?

> I closed and opened Skim.  Now it is big but although PDF/Auto Resize
> is checked, the PDF is too big and not fitting the window.  Zoom to
> Fit is greyed out so I can't do that!!!
> 

If this is the case, then it must be auto sized. I think your expectation about 
what the automatic size should be is wrong. Note also that how the page is 
sized depends on the display mode (single page, continuous scrolling, …). It 
may either fit the width or the height of the page, depending on the display 
mode. note that this is how Apple’s PDFKit works, not our choice.

> I'm quite lost and still running around in circles.
> 
> Tom
> 


Please try to understand the difference between default settings and settings 
for an open document.

Christiaan

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Re: [Skim-app-users] zoom to fit

[Christiaan Hofman]

> On 5 Sep 2022, at 13:51, Schneider, Thomas (NIH/NCI) [E] via Skim-app-users 
>  wrote:
> 
> Christiaan:
> 
>> There is currently a system bug that has the automatic zoom level a
>> bit off (basically it does not take the titlebar into account). That
>> will is fixed for the next release. But that should not disallow
>> page navigation.
> 
> Ok.
> 
 This is called Automatically Resize, in the PDF menu (or the toolbar
 if you have the button). It is also is indicated whether it is on or
 off.
>>> 
>>> I have that on.  One PDF opened properly and is zoomed properly (so I
>>> can scroll to switch pages) - but I had set that up previously.  So I
>>> opened another PDF and I had to click 'Zoom to fit' to be able to
>>> scroll through the pages.  I suspect this will not keep working ...
>> 
>>> What did not work in the other case? How could you not scroll? And
>>> what display mode have you set?
> 
> Ok, my current status is that at some point I shrank the PDF to be
> small like a postage stamp.  Now new PDFs are tiny too.  So I make
> them bigger to fit my screen and under 'PDF' I 'Use Current View
> Settings as Default'.  There is no response to this.  Nothing gets
> checked.  So I never know if it does anything or what the settings
> happen to be that it is recording.
> 

That does not have any immediate effects. That only saves the settings for 
newly opened PDFs in the future. So you probably saved that with a tiny zoom 
factor. You can choose that with a larger zoom factor, or with Automatically 
Resize checked. Or you can set the default settings in the General preferences.

> When I do that the next PDF is still tiny!
> 
> PDF/'Automatic Resize' is checked.
> 

When it is checked, then the PDF view should just resize the PDF to fit the 
view.

> I am still totally confused as to what gets set, and how to set things
> so they do what I want.  It works for awhile and then doesn't.
> 

Then you probably reset some setting.

> Thanks again for your great program and your help.
> 
>>> What did not work in the other case? How could you not scroll? And
> 
> When zoom to fit has decided not to be zoomed to fit, then I cannot
> scroll page to page with my mouse rotating wheel.  I have to click
> 'zoom to fit and then can do it.  Sometimes this happens but I cannot
> predict when so I'm always stumbling.
> 
> I think that would help to put all the page controls in one place and
> to show what the current status is without the window going away.
> 
> Tom


There are different controls for different functions.And they are controlled in 
the appropriate places for the function.

Christiaan



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Re: [Skim-app-users] Changing export to notes?

[Christiaan Hofman]

Yes, you can generate a hyperlink, including to the page. You can use a tag for 
the <$skimURL/> of the note, which gives a special URL that also links to a 
specific page. You select the text (or tag) you want to have a link for, and 
add a link (in TextEdit, select it and hit Edit > Add Link). Then set the URL 
to <$skimURL/>.

There are simple shorthands to directly add a link, like <$skimURLlinkedIcon/> 
or <$skimURLlinkedText/>, but those use an icon or the URL

<$fileName/> should work. Perhaps you used it inside a notes collection tag?

Generally, <$string/> is the text/label of any note. However, <$text/> is the 
larger rich text in the text view area (or the expansion in the note table) for 
an anchored note.

Christiaan


> On 3 Sep 2022, at 03:51, Mark Roberts  wrote:
> 
> Hi,
> 
> Thanks for the pointer. I was able to create a new template to do some of 
> what I wanted to do.
> 
> However, I can't figure out if it's possible to generate a hyperlink in the 
> exported RTF file.
> 
> Also, reading over the wiki page, I find that some basic things are unclear. 
> E.g., the wiki page says:
> 
> An example of a template tag is <$fileName/>, which represents the file name 
> (path) of the document.
> 
> But when I add this tag at the head of my template, nothing happens.
> 
> Similarly, the difference between <$string/> and <$text/> is unclear.
> 
> Thanks
> 
> On Fri, Sep 2, 2022 at 5:34 PM Christiaan Hofman  <mailto:cmhof...@gmail.com>> wrote:
> 
> 
>> On 2 Sep 2022, at 03:31, Mark Roberts > <mailto:mroberts1...@gmail.com>> wrote:
>> 
>> When I export annotations to RTF notes, they always have the format:
>> 
>> • Highlight, page 46
>> My Note Text.
>> 
>> Is there some way that I can change this, so that each note is exported like 
>> this:
>> 
>> My Note Text. (46)
>> 
>> Also, it would be cool if the page # (e.g., 46) could be a hyperlink that 
>> opens the Skim app to the PDF and advances to the page.
>> 
>> Is any of this possible?
> 
> 
> You can replace the template that is used for text export. You can find the 
> details on how to do this on the Wiki.
> 
> Christiaan

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