Release Notes for Papers2 - version 2.1

Overview of the Changes

This update focuses on bringing back most of the features that were in Papers 1.9 but went missing in Papers 2.0, as well as bringing significant performance improvements. Finally, Papers 2.1 is jam packed with 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'):

  • Support for search tokens in repository search (aka 'The Return of the Blue Tokens')
  • Support for highlighting and making notes on your PDFs
  • Improved interaction of 'Magic Manuscripts' with MS Word
  • Improved management of column settings
  • Significant performance increases throughout the entire app
  • 64-bit support

highlight_preview_normal.png

Highlight and create notes in your PDFs. The blue search tokens are back.


New Features

  • Return of the blue search tokens:

    • much more advanced query parsing and translation to search engine specific syntax
    • now supports au: and [au] syntax, supported by all search fields
    • automatic detection of dates, dois, pmids, arxiv and ADS IDs, etc
    • auto-complete of journal and author names and keywords from your library
    • added support for the search syntax to the library search field in the filterbar as well
    • google Scholar now uses high quality match
    • improved Google Books search engine (making use of official API)
    • return of the option to automatically continue when a single match is found
    • improved ranking algorithm to put publications with matching titles on top
    • status bar now shows total number of hits, hovering over the toggle button shows total hits per search engine
    • option to display parsing warnings for search queries
    • command-F now works in search section
    • selecting a search engine now starts editing in the search field
    • after matching we now return to the tab and collection previously selected
    • return of the match button to the inspector without having to go in edit mode
    • added DBLP, ERIC and Espacenet search plugins
    • added ability to use a custom Scopus or WOS url in the respective settings for these search engines
    • added holding configuration property to Pubmed search engine
    • added ability to search local amazon store fronts (UK, JP, DE, FR, CA)
    • wider and larger search fields throughout the application
  • Notes and highlighting (annotations):

    • you can now highlight selections and create notes on PDFs
    • highlights can be created by selecting while holding the Command key down, or by selecting a piece of text and right clicking it, or via the View -> Annotate menu
    • notes can be created by right-clicking or command-double clicking anywhere on the PDF, or using the View -> Annotate menu
    • works in preview, tab and fullscreen mode
    • notes and highlights are synced between your Mac and iOS devices
    • export PDF with annotations in File > Export -> PDF Files
  • Return of author merging, including a new UI for deciding which metadata the merged author should have

  • Return of Papers1 archive import (export will come in 2.2)

  • Improved behavior of the action 'Copy as... Papers Link' so that more apps are able to use the content on the pasteboard

  • New menu items in View..Columns allow copy and paste of column settings between collections; column settings include which columns are shown/hidden and in what order, and which column is used for sorting
  • New option in the 'Papers' preference pane: column settings can be shared by all collections when disabling the option to 'Remember column settings'; the default behavior is to enable that option, so that each collection can have distinct and persistent settings; column settings include which columns are shown/hidden and in what order, and which column is used for sorting
  • Added support for emailing with Sparrow and Sparrow Lite
  • Added rating mode to library search field
  • Added tooltips to first columns of tableview to explain read status and entity types
  • Added tooltips to search results tableview to explain read status and show in which repositories the paper was found when hovering over the 2x, 3x etc buttons
  • Added tooltips to Livfe collection tableview to explain read status and show the number of comments when hovering over the 2, 3 etc buttons
  • Added the PDF outline also to fullscreen mode
  • Added tooltips to sources tableviews to explain first column
  • Editing: added review and other article type filters to article category
  • Editing: added the option to define a subtitle for a journal article
  • Editing: removing the URL in the inspector now removes all URLs for that paper
  • Editing: add possibility to paste a string of authors into the author editor
  • Editing: added abstract as kind to journal article and anecdote as kind to personal communication

Performance

  • Up to 25% improved application startup time
  • Papers2 now runs in 64-bit in Macs that support the architecture
  • Overall better responsiveness by using multiple CPU cores more effectively (Grand Central Dispatch)
  • Overall performance improvement (especially 64-bit version)
  • Overall decreased memory footprint (especially 64-bit version)
  • Smaller memory footprint during importing
  • Smaller memory footprint during syncing
  • Improved stability during library indexing (creation of index files that are later used to search PDF contents)
  • Substantially improved reloading of smart and search collections:
    • collections are only reloaded when the property that has been updated is actually involved in the rules set for the collection, leading to significant performance improvements
    • collection reloading no longer shows the annoying flash where the collection becomes empty and repopulated again
    • when a second update for the same collection comes in, the ongoing reloading is being cancelled
    • collection reloading is now thread safe and better managed from a performance perspective
  • Animations above the serial number and student discount sheets are now movies instead of Quartz Composer compositions with lower CPU usage

Magic Manuscripts

  • Support for the following citekey modifiers (available with the default Papers citekey format):

    • support for prefix and suffix: {see also Smith:1997ww}, {Smith:1997ww has more on this}
    • support for page numbers: {Smith:1997ww p89}, {Smith:1997ww p 89-102}, {Smith:1997ww pp89-210}, {Smith:1997ww p. 89}
    • author and year suppression: ...as shown by Smith {*Smith:1997ww}, ...as shown in 1997 {Smith:1997ww*}, ...as shown by Smith in 1997 {*Smith:1997ww*}
    • all can be combined: ...as shown by Smith in 1997 {see for instance *Smith:1997ww* pp89 with more on this}
    • escaping commas (normally used to separate citekeys) in suffix/prefix can be done using a double-comma, e.g. ...as shown by Smith {see his recent works,, for instance *Smith:1997ww pp89}...
  • Improved support for various cite key formats (as set in the Manuscripts preferences):

    • More tolerant parsing of Papers citekeys to account for small variations in spacing
    • More tolerant parsing of BibTeX citekeys to account for small variations in spacing and for command variants and modifiers
    • Ignoring comment lines when parsing LaTeX documents
    • Support for Pandoc citekey format, e.g [@Smith:1999cd], with tolerant parsing to take into account other variants
    • Support for MMD citekey formats, with the 3 options [#Smith:1999cd], [][#Smith:1999cd] and [#Smith:1999cd][], with tolerant parsing to take into account other variants
    • Support for ConTeXt citekey format, e.g \cite[Smith:1999cd], with tolerant parsing to take into account other variants
    • Autodetection of the citekey format of the manuscript (bypassing the default setting in the preferences if applicable)
    • Mix/match citekey formats in the same document (current limitation: the only suffix/prefix/modifiers properly formatted are those in the Papers2 citekey format, since other format are typically used in conjunction with BibTeX)
    • Proper locking of citekeys for all citekey formats except the Papers format
  • Merge consecutive citekeys, so that e.g. {Smith:1999cd}{Doe:2001ad} is interpreted as {Smith:1999cd, Doe:2001ad}

  • Flexible author disambiguation (e.g. in APA): 2 names are presumed equivalent, and thus not disambiguated, unless unequivocally proven different. In Papers 2.0.9, 2 names were presumed different unless all their components were exactly identical, which lead to unwanted addition of first names or initials depending on the authors used in a manuscript

  • Now properly only recognizes the ctrl-ctrl keyboard shortcut if no other keys are used at the same time; this should please emacs users, but also more generally reduce the risk of false negatives that trigger invocation of the Magic Manuscripts window

  • Improved behavior when emptying the search field in the MM floating window, either after editing or after pressing the 'esc' key, so that the option to "Insert Citation" becomes available again when several papers are already entered, instead of expecting a new query string from the user
  • Improved behavior to keep the selection in the list of results even as more results come in (in the past, the selection would annoyingly be reset to the top as new results come in)
  • New design of the 'Copy As…' submenu to allow copy-paste of the citekey(s) of the selected paper(s), via either the 'Magic Citation' (alt-cmd-M), or the 'BibTeX Cite Command' (alt-cmd-C) menu items. The BibTeX menu item is adjusted based on the Manuscripts preferences, to be for instance 'BibTeX \cite command' or 'MMD citation', etc...
  • Similar changes in the options for the 'Drag Papers As' option in preferences, and in the citekey field popup menu in the inspector

  • Bug fix: spurious 'U.S. Patent' are no longer inserted in the bibliography generated by some of the CSL styles

  • Bug fix: no more crash of Magic Manuscript when using some keyboard input sources like Romaji
  • Bug fix: remote servers with previously used manuscripts are not forcibly mounted anymore just by invoking Magic Manuscripts
  • Bug fix: the Magic Manuscripts process would sometimes be disabled when starting the Papers2 main application
  • Bug fix: in some cases, the ouput URL in bibliographies included the proxy

  • Pages support: paragraph formatting of the bibliography

  • Bug fix in Pages support: in some cases, formatting a manuscript in Pages in Mac OS X 10.7 Lion could 'freeze' Pages, and lead to the dreaded beach ball of death, which would require to force-quit Pages
  • Improved support for the iA Writer application to allow formatting of manuscript
  • Basic support for the Sublime Text application to allow insertion of formatted references and citekeys
  • Basic support for the DEVONthink application to allow insertion of formatted references and citekeys
  • Basic support for the Texpad application to allow insertion of formatted references and citekeys

  • Magic Manuscripts interaction with Word:

    • Adds the option to 'Unformat Manuscript' and revert to the original unstyled format with just citekeys, e.g. reverting to '{Smith:2009aa}'; these are still kept as Word fields, but that still allows manual editing of the cited papers, see below. The 'Unformat Manuscript' option will appear after the first time the manuscript is formatted (if you had already formatted the manuscript prior to Papers 2.1, you can simply format it again to get the new option)
    • Detects 'plain text' citekeys in the text, so that citekeys can be copy-pasted from Papers (with the menu item 'Copy as... Magic Citation') or from another non-Word manuscript (e.g. exported from Pages)
    • Detects changes in citekeys in unformatted citations, including in fields, which allows manual editing of the list of cited papers in a citation
    • Removes empty invisible fields that could sometimes be left over in a Word document and would reappear unexpectedly when formatting the manuscript
    • Fix issue related to 'Track Changes' that could result in '?' strings when formatting a manuscript
    • Smarter handling of manuscript formatting to avoid spurious changes when using 'Track Changes'
    • Proper output of small caps when formatting a manuscript in MS Word (also already supported in Pages; unsupported in TextEdit)
    • Shows percent progress when scanning large documents in Word
    • Hidden preference to work around rare cases where Word styles result in formatting of citations and bibliography different from the surrounding text (disabled by default, as it impacts performance)
  • Manuscript styles:

    • Adds user interface for simple duplication of a style, within the style browser in Manuscripts preferences (the style browser is displayed when choosing the 'More Styles' option in the popup menu for the 'Favorite Styles'); this allows to simply add a style for a journal that is not present in the default bundled styles, but follows the same guidelines as another style, for instance 'Vancouver' or 'APA'; it is not a style editor, but a straightforward way to add styles for journals that have simple requirements
    • Adds support in the Papers2 CSL engine for the papers2-specific variables papers2_pmid, papers2_pmcid and papers2_notes; the PMCID will be used to generate an NIH-compatible CSL stylesheet that outputs the PMCID (forthcoming)
    • Removing the publication styles that don't have a corresponding CSL file anymore in built-in and user-defined styles folders (previous behaviour was that the style would still be listed, but not functional). This 'clean-up' is done every time Papers starts

Syncing

  • Up to 50% faster library syncing with Papers for iPad and iPhone
  • Change tracking is only activated if an iOS device has been linked
  • Added the option to ignore the maximum publication count limit
  • Added the option to sync the whole Papers2 library with the iPad
  • Improved reliability in handling sync startup and cancellation
  • The port used to sync with Papers for iOS has changed from 3795 to 3895
  • Bug fix: sync authors and bundle edits from Papers for iOS correctly
  • Bug fix: fixed re-adding of collections that were previously not selected for syncing (could cause paper duplication for some users)
  • Bug fix: fixed "Mac to mobile device" syncing which was broken in previous 2.1 betas
  • Bug fix: fixed removing of unsynced papers in the "Mac to mobile device" mode from the iOS library (could cause paper duplication for some users)
  • Bug fix: prevented a crash during syncing when importing papers from iPad with missing journal information
  • Bug fix: prevented a crash during syncing with libraries with certain types of smart collections
  • Bug fix: prevented a crash if the syncing view was interacted with when syncing is finished
  • Bug fix: prevented showing the uninformative "General CFSocket error" dialogs in certain cases when pairing with iOS device
  • Bug fix: when using automated syncing, stop the countdown when Sync button is pressed manually
  • Bug fix: syncing no longer occasionally hangs at "Connecting..." after a failed sync
  • Bug fix: syncing no longer fails because of "Previous sync operation already running"
  • Bug fix: note and highlight related syncing failure fixed (syncing would fail if certain kinds of annotations were present)
  • Bug fix: corrected syncing authors for publications between the iPad and the Mac
  • Bug fix: improved syncing reliability after failed or cancelled syncing

Search & Match

  • Bug fix: Mathscinet now shows the total number of results and allows to fetch more results
  • Bug fix: crossref search results now show correctly
  • Bug fix: corrected a bug in IEEE search where more than 1000 results would be reported as no results at all
  • Bug fix: correct author parsing in IEEE where some authors were missed if the query terms would appear in them
  • Bug fix: batch sizes set in the preferences are no longer ignored
  • Bug fix: wikipedia and OAIster now fetch more results due to corrected duplicate detection
  • Bug fix: high quality search engine results are now considered matched
  • Bug fix: proper layout and resizing of search engine toggles
  • Bug fix: ranking based on metadata like the title is only done during matching
  • Bug fix: fixed last author searches in ADS
  • Bug fix: solved an issue where the match search field would stay empty after adding a token
  • Bug fix: espacenet now properly handles spaces in search queries
  • Bug fix: prevent a crash with certain arXiv queries
  • Bug fix: solved an issue where adding an additional search engine to an existing query would hide the search field content
  • Bug fix: ACM query parsing now works correctly
  • Bug fix: IEEE link out is now more robust
  • Bug fix: Google Scholar parsing no longer removes links and URLs
  • Bug fix: tokens created by selecting text in a PDF replace previous tokens if no results were found
  • Bug fix: searching in tab now correctly shows "no matches" if nothing is found
  • Bug fix: added more failsafe mechanisms when google scholar advanced matching fails
  • Bug fix: fixed search field selection in the match tab controller
  • Bug fix: the local library search is now included in the default active and favorite set of search engines

Import & Export

  • Less memory hungry publication importing
  • Improved ENW parsing
  • Improved dpi detection and parsing of DOIs from APS PDFs
  • BibTeX export: Papers notes are now mapped to the annote field instead of note
  • Prevented sorting of the collection and the CoverFlow view during importing
  • Added checkbox in PDF import dialog to enable importing embedded PDF metadata fields
  • Bug fix: memory leak during importing bibtex data
  • Bug fix: proper import of PDFs defined in the local-url variable in bibtex, e.g. generated by Sente
  • Bug fix: importing files without a file extension no longer hangs the app

Livfe

  • Bug fix: entering an institution in the Livfe profile sheet now updates the information correctly.
  • Bug fix: changing the institution in the profile sheet now correctly updates the affiliation of the me author
  • Bug fix: correct name parsing in profile sheet for names like Paul W. de Bruin

Other bug fixes

  • Bug fix: find next/previous now works properly in tabs
  • Bug fix: we now remove "- " hyphens from pasted sentences
  • Bug fix: the title of a website should no longer override the manually edited metadata
  • Bug fix: workaround for the typo in the mime type send by Springerlink pro cite citation files
  • Bug fix: added more safety measures to prevent crashes with keyword selector
  • Bug fix: now correctly handles Dutch last names like in 't Veld
  • Bug fix: corrected an issue where login into Livfe would modify the users name incorrectly
  • Bug fix: proper behavior of the add author button in the author editor
  • Bug fix: the menus are now correctly set when a tab is opened in the background
  • Bug fix: opening the library website in a tab now selects the tab upon opening
  • Bug fix: deleted keywords are now removed from smart collection configurations
  • Bug fix: dismissing the smart collection configuration sheet with the keyword selector visible no longer leads to a crash
  • Bug fix: smart collections now correctly filter out manuscripts and papers in the trash
  • Bug fix: fixed issues with showing help content
  • Bug fix: made certain kinds of calendar date access thread safe
  • Bug fix: made creation of character sets thread safe
  • Bug fix: the author editor now correctly handles key events (for instance when tabbing when editor name field not in focus)
  • Bug fix: the author editor and keyword selector no longer crash when on screen and done is pressed
  • Bug fix: added workaround for crashes during spotlight indexing
  • Bug fix: the quick look panel now shows again for supplemental files
  • Bug fix: book chapters are now displayed correctly again and new ones can be added
  • Bug fix: the collection column is now updated when a collection is removed or renamed
  • Bug fix: dismissing the notes panel using the keyboard shortcut now correctly saves the notes
  • Bug fix: fixed an issue where PDF thumbnails were not loaded in fullscreen mode
  • Bug fix: the enabled status of the fullscreen button is now set correctly
  • Bug fix: updating the keywords in a tab now directly updates the inspector
  • Bug fix: the bottom status text now displays the correct item count
  • Bug fix: improved status text for search results
  • Bug fix: added more precautions to prevent issues with the quick look window not showing in combination with certain video cards
  • Bug fix: ignore duplicate now updates status bars
  • Bug fix: memory leak in metadata parsing from some PDF documents
  • Bug fix: author names are now correctly parsed upon import of new papers from public live collections
  • Bug fix: added workaround to issue with replacing the scrollers that would prevent the preview to show up
  • Bug fix: addressed an issue where the library website or login page would open a previously downloaded PDF each time
  • Bug fix: PDF outlines that contain multiple levels no longer crash
  • Bug fix: a beep sound is no longer played when using option-return to open a paper in an external editor
  • Bug fix: correct placeholder string in searchfield when changing to All mode
  • Bug fix: the keyword mode in the main search field now only searches user defined keywords
  • Bug fix: drag handles of the source list and inspector split views not responding
  • Bug fix: source list could annoyingly take over the full window
  • Bug fix: missing 1px line below sourcelist and inspector now showing correctly

Migration

  • Migration from Papers1: create aliases instead of hard links when migrating PDF files that are stored outside of the Papers 1 library
  • Migration from Papers1: fix issue where in some cases, the migration would slow down and come to a halt because of failed requests

Changes

  • Crash reports now send more detailed information
  • Email address is now sent by default with the crash report, user can opt-out by unchecking the checkbox
  • Selection in the quick look pdf (instead of dragging) is now trigger by the shift key
  • Papers window can now be resized to smaller size, for instance for use on an 11inch macbook

Papers for iOS

We advise to upgrade to Papers for iOS 1.9.9, 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:
https://mekentosj.tenderapp.com/kb/roadmap/papers-for-mac-roadmap