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 annotations are not always drawn correctly on High Sierra. This can result in highlighted selections obscuring the text and deleted annotations showing after being removed. While the annotations are correctly added and removed behind the scenes, the changes are not displayed correctly on the screen. You can force the page to redraw correctly by going to another page in the PDF and then back, but this is annoying and a permanent fix is on the way. ↩
For example, macOS Sierra made it impossible to use the thumbnails in the sidebar to navigate the PDF. Apple fixed this bug in High Sierra. ↩
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:
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:
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).
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).
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.