Blog

New features:

• Export notes directly to Keep It (replaces Together)
• Privacy update: removes Hockey App crash reporting framework and adds privacy policy

Minor improvements:

• Lots of memory improvements
• The underline power tool can now handle multiple unnumbered references across multiple pages
• Fixed issue where moving or renaming files could crash the app due to sandbox issue with sidecar markdown files
• Fixed issue where manual metadata lookups could result in a crash

New features:

• Smoother experience when annotating on macOS Sierra and High Sierra
• Interface now remembers size and position of both window and split view dividers

Minor improvements:

• Fixes glitches when adding/removing annotations
• Fixes issue with permission for saving sidecar files

New features:

• Improves compatibility with macOS High Sierra (10.13)
• Adds support for MultiMarkdown equations using MathJax (Disabled by default. Preferences –> Markdown)
• Adds compatibility for exporting to the new version of Ulysses

Minor improvements:

• Fixes an issue where the app would get very slow when sorting annotations spanning multiple text columns
• Lots of bug fixes

Highlights has not seen any updates in the last year and many of you have been rightfully concerned about the future of this app. However, if you came here looking for bad news, I will have to disappoint you. Highlights is live and well with several exciting things on the horizon, none of them being a sunset.

Apple released macOS High Sierra (version 10.13) to the public on Monday and if you are one of the brave people who updated straight away, you will know that Highlights still works. However, there are some known bugs¹ and a fix is on the way. In macOS Sierra (version 10.12) Apple changed a lot of the underlying PDFKit framework in macOS resulting in a lot of issues. Highlights has had its own share of problems under Sierra due to this² and I have communicated poorly to you how these issues were being addressed.

While the changes to PDFKit gave me and other developers a headache, they were not the real reason Highlights did not see any updates in the last year. 2016 was a very busy, but rewarding year for me personally. We had a baby, got married and I handed in my PhD thesis. Doing all of those things in a single year meant something had to give. Being an indie developer on the side, that unfortunately meant Highlights had to give.

After defending my thesis this spring, I have finally had some development time back on my hands. I was suspecting that the changes to PDFKit meant that the framework was being ported to iOS, and surely enough, with the introduction of iOS 11 at WWDC in June, PDFKit became cross platform. As I am a heavy user of Highlights myself, but love annotating on the iPad Pro with the Apple Pencil, this is something I have been hoping for for a long time.

After countless hours of work, it is therefore my pleasure to announce Highlights for iOS. Highlights for iOS will be a universal app (iPhone and iPad) written from the ground up in Swift with the Apple Pencil in mind. It is not ready yet, but if you have read this far chances are you would like to have Highlights on your iOS devices today. I believe dedicated users make the best beta testers and would love for you to test it with me. If you are interested, please go to the beta signup page.

New features:

• Tabs in macOS Sierra

Minor improvements:

• Improved support for macOS Sierra
• Better search highlighting
• Link to Tutorials in Help-menu

Fixes:

• Fixes issue where only one reference was showing when multiple unnumbered references were underlined

Highlights comes with some special power tools for academics. The PDF underline tool for reference lookups is a super fast and easy way to get to the source of a reference without touching the keyboard.

How do I enable it?

Go to Preferences –> PDF –> Underlining power tools and select a color for your reference lookups:

This color should be a color you do not use for other types of annotations as it will no longer be extracted along aside your regular annotations.

How do I use it?

To look up a reference, select the text in the PDF and underline it using the color you set in the preferences:

If the references are ordered by number you can include the numbering:

Underlined references show up at the bottom in the notes panel:

Highlights will do an online search for the reference and if successful link it to the source:

If you enabled integration with Papers or Bookends the link will send you to your reference manager otherwise it will open in your default browser.

If the reference number is included in the underlined text, Highlights will look for this number in your notes. Here is an instance of it in a highlighted section:

..and replaces it with a footnote-link to the reference at the bottom:

Highlights can be integrated with the popular referene management apps Papers and Bookends (tutorial here) on the Mac.

How do I enable it?

To enable the integration in Highlights go to Preferences –> Customize –> Reference Manager and select “Papers”:

For the best experience you should set Papers to open PDFs in Highlights by default. To do this, select Highlights in the list of applications in the “Open PDF files:”-preference of Papers in Preferences –> Papers:

How does it work?

When enabled, clicking links to references (DOI-links) in the notes pane of Highlights will redirect you to Papers. This includes the link in the header after fetching metadata:

and any references looked up using the underline power tool:

If Papers has the PDF for the specific reference in its library it will open it:

If Highlights is set as the default reader, it will bounce back to Highlights and open it there directly.

If Papers does not have the PDF, it will open the link in the built-in browser so you can download it:

This allows for seemless reading and checking of references in Highlights without using the keyboard or downloading the same article twice.

The integration works for both Papers.app version 2 and version 3 as it is based on URL-schemes. If you have multiple versions of Papers installed, Highlights will talk to the currently open version of Papers first. If no instance of Papers is running, Highlights will open the most recent version of Papers installed on you Mac.

Highlights can be integrated with the popular referene management apps Bookends and Papers (tutorial here) on the Mac.

How do I enable it?

To enable the integration in Highlights go to Preferences –> Customize –> Reference Manager and select “Bookends” from the list:

For the best experience you should set Bookends to open PDFs in Highlights. As Bookends does not have a default reader preference, you will have to do this at the system level. Keep in mind that this will make Highlights as the default application for opening all PDFs on your Mac.

To do this, right-click any PDF file in the Finder and go to “Get Info”. In the window that opens go to “Open with” and select Highlights from the list of applications:

Select “Change All…”:

Select “Continue” in the dialog:

How does it work?

When enabled, clicking links to references (DOI-links) in the notes pane of Highlights will redirect you to Bookends. This includes the link in the header after fetching metadata:

and any references looked up using the underline power tool:

If Bookends has the PDF for the specific reference in its library it will open it:

If Highlights is set as the default reader, it will bounce back to Highlights and open it there directly.

If Bookends does not have the PDF, it will open the link in the built-in browser so you can download it:

This allows for seemless reading and checking of references in Highlights without using the keyboard or downloading the same article twice.

New features:

• Improved PDF reading on large screens: display two pages side-by-side
• Better PDF browsing experience: back and forward buttons
• Both the sidebar and notes panel can now be collapsed
• PDF Thumbnails resizes as you change the width of the sidebar
• Use DEVONthink PDF-links when exporting (Install AppleScript in Preferences–> Export)

Minor improvements:

• Cleaned up keyboard shortcuts for managing layout of elements in window
• Cleaned up toolbar buttons
• Duplicate PDF when saving Adobe ClearScan files (to prevent destroying OCR layer of original file)

Fixes:

• Fixes Yosemite bug where the window would display nothing due to a partially collapsed sidebar

New Features:

• Export to Quiver: each annotation is exported as a Quiver-cell + support for images and tags
• Split files: Export annotations as individual HTML/Markdown-files to a folder or directly to DEVONthink
• Tagging split files: tag individual annotations using “@tag” syntax in the annotations note field
• MultiMarkdown Citekey: copy metadata for current PDF as MultiMarkdown Citekey to pasteboard
• MultiMarkdown Reference: copy metadata for current PDF as MultiMarkdown Reference to pasteboard
• Preference: file name based on document or metadata title when exporting

Minor Improvements:

• Underlined references that have not been cited in the text now show up in Preview (not only in Edit)
• Preference to automatically lowercase all tags
• “Export to PDF” now adds a “Highlights” to the suggested name to prevent overwriting the currently open PDF
• Improved speed when handling PDFs with many pages
• Improved speed when handling PDFs with many references
• Added custom Finder file icon for when Highlights is set as system PDF reader

Fixes:

• Export to nvALT now support multiple tags
• Change annotation color using keyboard is now working again
• Page number now show up in annotation headers as expected

New Features:

• Collapsible sidebar

Fixes:

• Fixes bug where the split view panes would be collapsed when opening a PDF
• Fixes bug where export to Textbundle would not include Markdown text
• Stability improvements (threading issues)

Improvements:

• Better UI performance
• Custom plaintext format with direct export to pasteboard (CMD+Y)
• Faster image grabbing from PDF

Fixes:

• Bugs from the future

This version of Highlights drops support for 10.9 to enable use of new interface frameworks in OS X.

Improvements:

• Bookends integration
• Preference to set Reference manager
• Keyboard shortcut for sorting annotations by color

Fixes:

• No preference pane was selected when opening preferences
• Performance improvements

New features:

• Popup PDF annotation tools
• Export to nvALT
• Export to Together
• Icon makeover

Minor improvements:

• Toolbar now shows currently selected annotation color
• Improved control over export format
• Option to disable headers completely
• Option to turn off text wrapping
• Option to turn on automatic tab-switching (Markdown-mode)
• Cleaned up preference-window

Fixes:

• Page range now uses en-dash, not a hyphen
• Exporting to Ulysses now removes page breaks (horizontal lines)
• Missing Export to Ulysses-option in main menu

New features:

• Export to Ulysses

Minor improvements:

• The sticky note tool is now automatically deselected after use
• The image selection tool is now automatically deselected after use

Fixes:

• Annotation spacers not included on first launch
• One character long highlighted text causing a crash
• Scroll sync glitches when near top of preview and edit views
• Fixes issues with exporting Markdown with MMD-metadata included as header
• Popup-elements only added to annotations with attached comments

Improvements:

• Markdown/TextBundle sidecar-files are only saved if enabled in Preferences
• More robust syntax for sticky notes using horizontal line elements instead of italics
• Underlined text is turned into bold text when extracting
• Tagging/References power user features are only active if enabled in Preferences
• HockeyApp integration for crash reporting

Fixes:

• Text notes outside annotations are turned into sticky notes (text no longer disappears)
• “Fetch metadata”-dialog no longer reappears after hitting cancel
• “Fetch metadata”-dialog only presented if PDF has a DOI
• App no longer shows a blank window when the default PT Mono font is unavailable
• Black annotation color replaced with gray
• Improved insertion point selection for annotations with spacers
• If a PDF-file is moved, the URL-scheme bookmark for the file is updated

Minor improvements:

• Link to FAQ from help menu
• Link to Release notes from help menu
• Link to Feedback submission from help menu

Fixes:

• Insertion point improvements
• Tags not showing up in Finder for PDFs
• RGB values for color categorization refined

Fixes:

• Sticky notes resetting to “New comment” placeholder
• Markdown comments were in some cases not synced to the PDF
• More accurate insertion point selection in text editor for newly added annotations
• Reading PDFs with blank annotations could in some cases crash the app
• Purple and pink was sorted as one color

New features:

• PDF search
• Page-links:
  • clicking links in the Preview-window will scroll the PDF to that page
  • clicking link in exported HTML-file/Evernote/DEVONthink, will open Highlights and scroll to linked page
• URL-scheme (backend for page-links):
  • Open file: highlights://Users/test.pdf
  • Open file on a specific page: highlights://Users/test.pdf#page=3
• Performance improvements:
  • New MultiMarkdown parser: should handle books and PDFs with lots of annotations better
  • Improved asynchronous PDF saving (no interface lockup)
  • Snappier Markdown-to-PDF sync

Fixes:

• Adding an annotation to a page with no other annotations resulted in wrong text selection in the editor
• Incorrect meta-tag for UTF-8 charset in HTML caused issues on some systems
• Annotation could in some cases end up on the previous or next page when scrolled far down or up as the page being annotated was not accurately determined
• Lots of crash-fixes

I want atx-header style Markdown headers, is this possible?

Yes, go to Preferences –> Markdown and turn on “Use # for title/author headers”

Can I have a standard color for each type of annotation?

Yes, go to Preferences –> PDF and set what color you want for each type of annotation.

Is there tagging support in Highlights?

Yes, Highlights supports per file tagging. Select a color for Tags in Preferences –> PDF –> “Underlining power tools”. Underline the words or short sentences in the PDF you want to use as a tag with the selected color. Tags will be embedded as PDF keywords and exported as Finder-tags when saving.

In addition, Highlights supports per annotation tags “Split files” is enabled in Preferences –> Export. To use this feature as add tags as comments to the annotation using the syntax @tagname e.g. @important or @review. The tags will be added as Finder-tags to the file representing that annotation when exporting as split HTML/Markdown files or to DEVONthink.

Does Highlights integrate with any reference managers?

Yes, Highlights integrates with Bookends (tutorial here) and Papers (tutorial here).

Is Highlights scriptable?

No, not yet.

My extracted annotations show up with redundant text, why?

This happens when the PDF is exported from Skim as it saves a backup of the highlighted text in the comment-field of the annotation.

Highlights can not find the correct metadata for my PDF, can I manually lookup a DOI?

Yes, if you select the text containing the DOI-link and selecting “Lookup metadata” in the View-menu (Cmd+Alt+R) Highlights will use the selection for fetching metadata.

Highlights crashed on me, what do I do?

Please email me with as much information as you can provide on when/how/why it crashed (crash reports and screenshots are very helpful).

Is there a trial version?

Yes, you can download it here. The demo has the same features as the full version, but only extracts annotations from every other page of the PDF.

Can Highlights extract annotations made with other apps?

Yes, Highlights uses standard embedded annotations which are supported by most PDF readers on both OS X and iOS.

Some PDF apps (including Skim) and most reference managers use non-standard annotations which are not compatible with Highlights. However, most of these apps allow you to export the PDFs with embedded annotations which will work in Highlights.

How do I customize what is included in each annotation?

Under Customize in Preferences, you can set which information should be included in each annotation (including author, modification date and color category).

How do I use reference lookups?

Check out this tutorial.

How do I use color coding?

Color coding allows for categories of annotations sorted by color. By going to Preferences –> Colors you can see the current order in which the colors will be sorted. You can reorder the sorting and rename the each color to represent a category.

New features:

• New PDF tool: sticky notes
• Scroll positions in sync
  • changing the page of the PDF, scrolls the extracted annotations list to the same page
  • scroll position of view and edit are kept at the same point
• Annotation colors
• Color-coding: give each color a name and sort annotations by their color
• Improved sync between extracted annotations and PDF annotations:
  • removing an annotation in the text editor, removes it in the PDF as well
  • adding a note in the text editor, adds a sticky note in the PDF
• Annotation headers: include subheading over each annotation with page, category, color, type, author and/or date information
• Annotation spacers: separate annotations by a horizontal line
• ATX-style Markdown headers (#h1# and ##h2##)
• Papers.app integration: open links in Papers. If the PDF is present in your Papers library it will be opened directly, otherwise Papers will attempt to fetch the article
• Better cursor visibility in text editor: cursor changes color to white when over the dark background of the text editor

Fixes:

• Tags are now written to both PDF and Markdown files when “Embed tags” preference is selected
• Performance improvements

Fixes:

• Links inside the PDF are clickable again
• Issue with parsing of PDF Text-notes to italics resolved
• The “Fetch metadata”-dialog no longer keeps popping back after hitting cancel
• PDF metadata is not written unless it is different from the empty header
• Document no longer shows edited status before actually being edited
• Switching between View and Edit mode is now per document
• Maximum length of suggested tags (underlined words) set to 30 characters, to prevent mixup with bad references
• Added export-icon for TextBundle-files
• Username and modification date metadata added to annotations modified or created in Highlights

Initial release:

• New app icon and interface redesign
• Native TextBundle support (see http://textbundle.org)
• Preference for setting default font and size for Markdown editing
• New introduction guide
• Minor bugfixes