Release Notes for Papers2 - version 2.2

Overview of the Changes

This update focuses on bringing back some of the remaining features that were in Papers 1.9 but went missing in Papers 2.0, as well as fixes to some long standing issues. Finally, Papers 2.2 also brings a number of exciting new features and improvements to existing features. Here is a brief summary of the highlights (but be sure to read the full list of the 'Detailed Changes'):

  • Recent papers search for Authors and Periodicals
  • Auto-complete of authors and sources in the inspector
  • Editing of multiple papers at once and duplicate merging of papers
  • Merge and split any duplicate or incorrectly merged sources
  • Displaying and navigation of notes and highlights in the inspector
  • Addition of tools to allow page rotation and hiding a PDF coverpage
  • Creating of collection hierarchies upon import of folders
  • Return of column mode for search results in the search section
  • Support for inserting footnotes in Microsoft Word
  • Improved Papers for iOS syncing


Search for the most recent papers published by your favorite authors and journals.

New Features

  • Recent papers search for Authors and Periodicals

    • search for recent papers across all your search engines in one go
    • results are grouped by year or issue
  • Auto-complete of authors and sources in the inspector

    • fast auto-complete while editing authors and periodical information in the inspector
  • Editing of multiple papers at once and duplicate merging of papers and periodicals

    • edit the properties of multiple papers at once
    • merge duplicate papers into a single entry
    • much improved duplicate resolving workflow
  • Merge and split any duplicate or incorrectly merged sources

    • merge of duplicate authors, periodicals, conferences and websites
    • split authors and sources into two separate items
  • Support for Lion fullscreen mode

    • take your Papers window fullscreen for distraction free working
  • Displaying and navigation of notes and highlights in the inspector

    • filter to show highlights or notes only or show both at the same time
    • navigate to a highlight or note in the text
    • quickly copy a highlight or a reference to the highlight
    • added ability to email PDFs with and without annotations
    • sticky notes are now spotlight indexed
  • Addition of tools to allow page rotation and hiding a PDF coverpage

    • rotate the individual pages of a PDF in a non-destructive manner
    • hide the cover page of a PDF in a non-destructive manner
    • available through a menu option under the new tools menu, or via right-click on the PDF
  • Creating of collection hierarchies upon import of folders

    • collections are now created when you drag-and-drop or import a folder of files
    • duplicates are automatically detected and replaced by the copy already in your library
  • Return of column mode for search results in the search section

    • switch between a single or multi-column viewing of search results
  • Support for inserting footnotes in Microsoft Word

    • insert footnotes in your word document with Magic Manuscripts
  • Improved Papers for iOS syncing

    • more reliable and faster syncing of your Papers library with Papers for iOS

Magic Manuscripts

  • Support for footnotes/endnotes in Microsoft Word:

    • the first insertion of a citation in an empty document gives the option to 'Insert Citation', 'Insert Footnote' or 'Insert Endnote' (press the option key for that latter option)
    • footnotes are inserted already formatted (not just the citekey like with 'in text' citations), but they can still be unformatted using 'Unformat Manuscript'
    • a style can either be used for 'in text' citations (like 'Nature', 'APA', 'Cell', etc...) or for 'notes' (like some of the 'Chicago' styles)
    • switch between 'in text' citations and 'footnotes' when selecting a style (the user interface will clearly warn about the switch when you select a style)
    • for 'notes' layout, switch between footnotes and endnotes using the corresponding action in the document action list
    • insertion of bibliography is optional for 'notes' styles (for 'in text' styles, it is automatically added at the end of the document, if not present yet)
    • known limitation: footnotes can only be inserted using the Magic Manuscripts floating window, but not pasted from the main Papers application using the menu item Copy As > Magic Citation ((support will be added in next 2.2 update)
    • known limitation: 'in text' citations cannot be mixed with citations in footnotes when using a style for 'in text' cites (support will be added in next 2.2 update)
    • known limitation: support only available with MS Word (support in Pages forthcoming, but timeframe not yet known)
  • Improvements to the CSL engine:

    • support for the page-range-format CSL attribute (affecting at least APA and Chicago)
    • support for CSL variable page-first (affecting at least APA and Chicago)
    • fix output of CSL terms when used in multiple forms in the same style sheet (affecting at least APA and Chicago)
    • fix CSL output to avoid having a space after a parenthesis in some cases (e.g. in APA)
    • bug fix in bibliography output: the 'edited by' and similar labels are properly output before the editor names, instead of after, where applicable (for instance in the Chicago style)
    • bug fix in bibliography output: no more extra editor names inserted in the middle of a reference (for instance in the Chicago style)
    • bug fix in bibliography output: no more duplicated titles for some of the publication type (e.g. websites, books, for instance in IEEE style)
  • New styles (now 2010 built-in styles):

  • Improvements in text editor interaction:

    • improved support for Latexian
    • basic support for insertion of citekeys in nvALT
    • better behavior with 'Track Changes' in MS Word when it is set to 'Final Showing Markup'; in some cases, Magic Manuscripts was wrongly 'resuscitating' deleted citations when formatting
    • fix rare bug with Word interaction: wrong removal of some non-Papers-related fields (like cross-references) in some documents with unexpected field layout (the bug would happen after seeing a message 'Adjusting Inconsistent Citations...')
    • fix rare bug with Word interaction: similar to a previous bug, there were still cases where formatting a manuscript would lead to inconsistent citations and 'ERROR' strings in the cites
    • fix rare bug with Pages: in some cases, manuscript formatting would stop half way, and Pages refusing to save or auto-save the document; Pages would also occasionally get stuck, and fail to react at all, or get the beach ball of death, while filling the console with exceptions
    • use of Pandoc cite key format ([@citekey]) instead of \cite in some empty tex documents
    • use of \cite instead of \citep in empty tex documents despite the user's preferences
  • Improvements to style handling:

    • support for drag-and-drop install of CSL files
  • Misc improvements to Magic Manuscripts:

    • fix issue with search in Magic Manuscripts where the use of the word 'a' was resulting in empty results
    • fix issue with citekeys sometimes exported to BibTeX with an extra 'a' suffix
    • improved warning messages in magic manuscripts
    • various crash fixes, for instance that could occur during search, or that could happen when inserting a citation in Pages


  • Previously duplicated annotations are cleaned up during syncing
  • Fixed an issue where annotations would get duplicated if syncing is aborted at a certain stage
  • Fixed an issue where notes made on the iOS device would override notes made on the Mac.
  • Fixed an issue with choosing collections for syncing in hierarchical collections deeper than four levels.
  • Fixed a rare crash with cleaning up library before syncing with Papers for iOS
  • Fixed a rare crash when merging changes to notes or highlights between Papers2 for Mac and iOS.
  • Fixed a rare crash when cleaning up related metadata between Papers2 for Mac and iOS.
  • Fixed a network connection timeout handling issue affecting some users where subsequent syncing would fail until restarting Papers2 for Mac.
  • Fixed a network pairing related issue where in some circumstances the Papers for iOS would not appear in the source list even after a successful link.

Search & Match

  • Added ability to populate a paper with metadata from the clipboard while editing  in the inspector or by dragging a citation file on the file view in the bottom right corner
  • Imported articles are now considered matched if a crossref record is found
  • Fixed an issue where hitting delete during matching would trash the paper
  • Fixed a crash that would happen after matching an article, or cancelling matching an article
  • Hitting escape during matching now cancels the matching process
  • Pubmed searches now correctly handles quotes  in terms like Alzheimer's and O'Donnell
  • Added indication when Google Books search engine hits API quotum
  • Updated link out url for Web of Science search results
  • Temporarily retracted project muse search engine due to website changes
  • Exit the store, scanner and matching process by changing selection in the source list
  • Matching should no longer reset the flagged status of an article
  • Matching should now preserve the DOI if it would otherwise be erased
  • Removed the need to confirm automatic matches upon import, added reset option instead
  • Added an unmatch option available while editing in the inspector
  • Automatically continue with single match dialog remembers also when you don't want to be asked again
  • Updating metadata from citation files now maintains the matched status
  • Fixed the IEEE search engine plugin
  • Improved query generation for IEEE, arXiv, ADS
  • Improved parsing of results from arXiv

Import & Export

  • Importing papers directly to a collection by drag and drop no longer switches to the last imported collection but keeps the collection selected
  • Downloading metadata now imports the publication automatically
  • Improved duplicate detection and handling
  • Added support for Pubmed Citation files (nbib files)
  • New from clipboard now works correctly for RIS files
  • Fixed an issue with author import from RIS files from JSTOR
  • Fixed an issue where the last import and library collections would show mixed up content after coming from a selected open tab
  • Fixed a crash when importing a folder of publications
  • Fixed an intermittent crash when merging or batch editing large numbers of publications together
  • Fixed a crash that would happen when importing non-PDF files

Tabs & Editing

  • The tab bar now hides automatically when no tabs are available (can be switched off in preferences)
  • Added a new tab button that triggers the open location button
  • Added a copy as notes option under the edit menu
  • Added iTunes like linkout arrow next to periodical name that brings you directly to the bundle
  • Added warning when bookmarklet is used on a loaded PDF in Safari
  • Added a warning upon entering a proxy url in the Library Website URL preference field
  • Added an indicator icon for when the ezproxy is not used to load a webpage
  • Replaced the ezproxy selection popup button by a searchable combo box
  • Tab closing behavior is now similar to Safari (select tab to the right if present)
  • Reopening tabs from last session no longer closes tabs you have already open
  • Fixed tab order issues upon dragging of tabs
  • Fixed a crash upon closing all tabs
  • Fixed an issue where restoring the previous tabs would trigger all content to scroll down
  • Fixed an issue where PDF zoom factor and viewing mode were not correctly saved and restored
  • Fixed an issue where editing in the inspector would trigger actions every 2 seconds
  • Fixed an issue where the focus ring would sometimes be drawn in the inspector on Lion
  • Improved row heights for large text setting
  • Improved layout in the inspector when using larger font sizes
  • Conference proceedings can now have editors
  • Fixed an issue where the wrong menus were set when switching between help center and paper opened in a separate tab
  • Fixed tooltips for switching between website and PDF in a tab
  • Fixed an issue where metadata for search results was not updated properly while navigating the website
  • Shortened the time for automatically mark as read down to 20s
  • Supplements inspector header now shows the number of supplemental files

Authors & Sources

  • Added displaying of papers in your library for periodicals, conferences and websites
  • Authors shown in the author inspector can now be dragged to collections
  • Improved author merging
  • The source column now lists a chapter's book title or the publisher/body where appropriate
  • Fixed an issue where the full name would be incorrectly parsed if the author was marked as institutional
  • Fixed an issue with merging and editing of last names with suffices
  • Fixed a crash when deleting an author in the author editor
  • Removed the von part in the placeholder for new authors


  • Fixed the reordering of smart collections after renaming
  • Fixed a bug where the collection column was not updated after deleting a collection

Papers for Windows

  • Added an option to create Windows XP compatible (short) filenames
  • File naming on Mac is now excluding characters that cause Windows incompatibilties

Registration & Activation

  • Fixed an issue with the serial number upgrade sheet not dismissing
  • Fixed an issue where requesting the upgrade discount request sheet would hang or crash
  • Added warning to not use hotmail for coupon requests
  • Added warning during purchase if cookies are blocked

Performance & Stability

  • Added property list value to force Papers to use the integrated GPU to safe battery life on MacBook Pro models with a dual GPU setup
  • Papers now also collects crash report information for Magic Manuscripts
  • Added option to automatically send crash reports in background
  • Fixed a crash related to thumbnail generation
  • Fixed a crash when attempting to export a PDF after the file had been replaced outside of Papers. WARNING! You still should not replace the PDF on disk outside of Papers, this simply makes Papers more resilient to crashing when this has happened
  • Improved thumbnail generation with less storage space requirements

Other bug fixes & changes

  • Improved network detection
  • Improved warning messages when the database fails to open
  • Fixed an issue where the notes in fullscreen would jitter or loose parts of text
  • Fixed an issue where the preview would cause switching spaces
  • Manual check for updates now also shows previously skipped updates
  • Contextual menu now works in coverflow
  • Pubmed thumbnails are now generated without the ugly javascript warning
  • Fixed an issue where the database migration would accidentally run twice for certain users
  • Fixed a crashing bug when opening the same paper in fullscreen twice but with closing and reopening a tab in between
  • Fixed an issue where the information of which papers are marked as duplicate was not being updated after a paper has been moved to Trash
  • The database verification in the maintenance now verifies duplicate marking information
  • Added request to help us with the automatic matching database

Papers for iOS

We advise to upgrade to Papers for iOS 1.9.12, this free update is available now in the iTunes App Store.

Up next

Have a look at our roadmap to see what's up next:

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