NEW in Version 13.0.8 (April 14, 2018)


Updated database engine
Note that you must now use quote marks (" ") rather than square brackets ( [ ] ) when performing an SQL search for the fields "type" and "pages" or you'll get an error.

You will be notified if a PDF you are attaching already has a matching reference in the library
Bookends uses a DOI, JSTOR stable URL, or arXiv id in the PDF to determine if the reference is in your library.

PDF page display settings (e.g. single page vs. two pages) are remembered when switching between references

Updated the JSTOR parser to deal with changes made by JSTOR

Bookends will import the year posted on arXiv if the reference has no date of publication

Copy has been added to the View Formatted contextual menu

When formatting Bookends will use the capitalization rules dictated by the preferred language setting in System Preferences -> Language & Region

Improved determination of PDF page number when creating a notecard
Bookends will add the page's relative number in the PDF to the page entered for the reference if the latter is the first of a range. If it's a single number, Bookends will assume it's the total page count for the reference and ignore it.

URLs imported from Amazon will be shortened to the minimum necessary length

Finding orphaned attachments is considerably faster

Updated import from Amazon Japan to deal with changes made by Amazon

A number of free OpenURL servers will be be installed in preferences when Bookends is first run
If you have already run Bookends, you can find the server information for these services in the User Guide and enter them yourself in preferences (Metadata tab).

Change an Inspector parent by double clicking on a reference
This applies only when the Inspector has a parent reference (i.e., the Links and Cited Inspectors).

A new preference option that tells Bookends to ignore a double click on a reference has been added

Bug fixes
Fixed a bug in the Attachment Inspector where the Action pop-up Open menu selection did not work. Prevented a situation where an empty attachment name caused an error to be thrown. Fixed a bug that caused an error to be thrown when canceling the conversion of an older library to the current schema. Fixed a bug where having an en dash in an ISBN while doing a QuickAdd would cause an error. Fixed a problem with sync of recently viewed reference data. Fixed a bug in importing of keywords from Google Books. Fixed a bug where the library window wasn't being repositioned when only a few pixels were showing at the right edge of the screen. Fixed a bug introduced in 13.0.7 where clicking on a reference after a Rebuild would cause an error message to be shown. Fixed a bug in dragging references where it could take a long time to assemble the drag information if you have many attachments. Fixed a bug where names imported from Amazon (China) were sometimes improperly parsed. Fixed a problem where a parsing error would occur when evaluating replies from Crossref.org. Fixed a bug in the PDF viewer where the page number could stop updating. Fixed a bug where the default PDF reader selected in preferences was ignored when using Shift-Command-O to open the PDF in the lower display pane.


NEW in Version 13.0.7
(March 17, 2018)


Recently Viewed group
This is a permanent group that displays the references you have viewed in descending order (i.e. most recent being at the top). A reference is added to this group if you click on it or a PDF tab and the selection remains showing for a specified interval. In preferences (List tab) you can tell Bookends how long to wait after a click to consider the reference as "viewed", and the maximum number of references to keep in this group. When the maximum is reached the oldest reference will be removed when a new one is added. Clicking on a reference while viewing this group will make it the most recently viewed, but to avoid confusion the list won't redraw until the Recently Viewed group is selected again. If you are using cloud sync, the Recently Viewed group will be synced between Macs but not iOS devices.

Import metadata from PubMed with some style information
If text is super- or subscripted, Bookends will surround it with the corresponding metacharacters used in Bookends to denote these, otherwise the style information (e.g. italics) is removed. Note that due to limitations in PubMed a space before or after the styled text may be missing.

Made changes in JSTOR parsing to deal with changes made by JSTOR

Made changes to PubMed searches so that you can retrieve 500 or more references in a search

Updated automated PDF downloads from ScienceDirect to deal with changes made by Elsevier

Refs -> Replicate As Book Chapter will be enabled for references with a user-defined Type
It's up to the user to determine if this is a meaningful option for that Type.

Improved Wi-Fi sync
To decrease the time it takes to sync, Wi-Fi sync will no longer check for orphaned attachments each time it is performed. If heretofore unfound local attachments are can now be found (e.g., they were relocated, or the maximum sync size of attachments was changed), click on the gear icon in the sync window and select “Check for orphaned attachments”.

Autofill from Internet will merge existing notes with any imported notes

Bookends will remove spaces before semicolons in formatted references

Cloud Sync normalizes times zones when determining modification dates

Bug fixes
Fixed a bug in the import filter Source parser that prevented some metadata from being imported. Fixed a bug where the setting for using an underscore for spaces when renaming PDFs was not shown properly when preferences was opened. Fixed a rare problem with Mellel Live Bibliography where inserting the same citation multiple times could cause an error to be thrown. Fixed a problem in Bookends Browser where an invalid DOI on the web page could cause an error to be thrown when clicking on the downward arrow icon. Fixed a problem in references found on PubMed where the title or abstract was truncated if style information was included. Fixed a problem where an error was thown when displaying references with no titles for import in Bookends Browser. Fixed a bug in finding and attaching a local PDF when there was a single match. Fixed a bug in the Term List live search where the reference metadata was not updated if there were no matching references. Fixed a bug when attaching PDFs in batch where the metadata was not imported even though a DOI was present. Fixed a bug where the reference list's single column heading was incorrect when sorting by Date Added. Fixed a bug in Global Change -> Remove Orphaned Attachments where the affected references were not updated properly and marked for sync.


NEW in Version 13.0.6
(February 18, 2018)


Updated database engine

Copy Citation and Copy Formatted will insert the corresponding text automatically in Apple Pages documents

Improved metadata found with Crossref searches
The results will include abstracts and the number of times an article has been cited, if available.

Rotate PDFs in the PDF viewer

Improved Cited Inspector
Drag and drop references cited in the paper, or select them and use a right-click, to import them into your library. References that are already in your library or that have no DOI will be ignored.

The names of temporary libraries created during a Rebuild will not be added to the Open -> Recent menu

Replace spaces with underscores ( _ ) when renaming a PDF
This option is available in preferences.

Created a workaround for a problem with the Science web site so that automatic PDF downloading works again

Bookends will offer to automatically fetch the metadata when attaching a PDF from arXiv.org
This will work when importing the PDFs from the watch folder, too.

Bug fixes
Fixed a bug that caused an error to be thrown if you tried to attach a PDF or delete a reference immediately after doing a Rebuild. Fixed a cosmetic bug where the toolbar wasn't being drawn correctly when switching to the PDF view when in viewing in full screen. Fixed a bug where PDF tabs for different PDFs in the display pane and the attachments of a single reference could become confused. Fixed a bug that added the name of the temporary file created during a Rebuild to the Open -> Recent menu. Fixed a bug that caused the select PDF pop-up in the Attachments tab to be hidden when viewing in full screen mode. Restored the ability of Bookends to insert the formatted document into Word 15.x at the end of a scan. Fixed a bug in the Cited In Inspector where dragging the mouse extended the selection. Fixed a bug that caused an error to be thrown when closing a library window while the Inspector was open.


NEW in Version 13.0.5
(January 27, 2018)


Scanning is now fully compatible with Word 2016 16.9

PDFs remember their scrolled positions in the Attachments tab (right pane) when switching between references

PDF tabs can be used in the Attachments tab (right pane)
These tabs are independent of PDF tabs in the PDF view in the lower pane.

Drag and drop PDF thumbnails from Preview to the Bookends library window to create a new PDF that will be attached in Bookends

Improved find and attach of local PDFs
The search based on the reference metadata is less stringent, resulting in fewer cases where no match is found. Furthermore, rather than always searching the entire drive, you now select the folder (and its subfolders) that Bookends searches for the matching PDF. This decreases search time and reduces the number of spurious matches. Double-click on the full path name to show the PDF in the Finder. There have also been cosmetic improvements in the UI for displaying multiple matches.

Updated "Print to Bookends" to work in High Sierra

Each format must have at least one Type
You will receive a warning if you try to delete all Types.

Annotating a PDF will update the date modified field for the corresponding reference in the library

Improved detection of JSTOR stable URLs when attaching a PDF

Bug fixes
Fixed a bug in Rebuild that could cause errors to be thrown after the process was complete. Fixed a bug when using the "Add To Group" menu. Fixed a bug where converting some OpenURL configurations to the new format could result in an error. Fixed a bug that could cause the PDF page count to fail to update when switching between PDFs. Fixed a bug that could cause a mouse click in the PDF toolbar or built-in PDF view to initiate a window drag. Fixed an error that occurred if you clicked on a PDF and then pressed Return. Fixed a bug in rendering PDFs in full screen view on a second monitor and in split-view on any monitor. Fixed a bug where the last sorted heading wasn't remembered if it was the 7th column in the list. Fixed a bug where an & in a group name was not shown in the Add To Group submenu. Fixed a problem where spaces in front or after the reference identifier in Quick Add would cause the search to fail. Fixed a bug in Global Change -> Find and Replace where searching for and/or replacing a Return character did not work. Fixed a bug where clicking a PDF tab wouldn't take you to the reference if the live search field had content. Fixed a bug where exiting full screen PDF viewing by clicking the paper clip icon didn't make the live search box visible. Fixed a bug that could cause some accented characters in a Word document to be misinterpreted during a scan. Fixed a bug that caused an error to be thrown if you tried to edit a reference after Rebuilding the library.


NEW in Version 13.0.4
(January 19, 2018)

Critical Cloud Sync bug fix
Suspend Syncing for your current library and then quit Bookends. Install this update and download your library from the cloud: File -> New Library -> Download From Cloud. Open this freshly downloaded library and Resume Syncing.



NEW in Version 13.0.3
(January 6, 2018)


Quick Look
Pressing the space bar will display the selected reference's attachments. Press the spacebar again or the Escape key to dismiss the Quick Look display.

Thumbnails of attached files are shown in the single column reference list
Double click on the thumbnail to open the attachment in your default PDF reader.

Quick Add new references
If you have a reference's DOI, PMID, ISBN, or JSTOR stable URL you can import its metadata by invoking Quick Add (Refs -> New Reference -> Quick Add or the New pop-up menu icon in the toolbar). Bookends will notify you if you already have the reference. Note that Bookends may not identify the identical reference in your library if the signature information differs (e.g. the ISBN you are looking for has no hyphens but does in your library, or if your library has the ISBN 10 version and you are doing a Quick Add with the ISBN 13 form).

Improved OpenURL
Each OpenURL server you add in preferences (Internet tab) now has its own name and query parameters. This means that if you have access privileges you can search sites such as Web of Science, Scopus, and Semantic Scholar. You can specify any Bookends field in the query by enclosing the field name in angled brackets, such as < title>. There are two convenience exceptions: < doi> and < pmid> will be mapped to their correct internal names, user17 and user18, respectively. Please see the User Guide for free and commercial OpenURL services you may find useful.

Automatically import arXiv PDFs when you import the references's metadata

Bug fixes
Fixed a bug that prevented File -> Export References (Hits) from being enabled if you marked references via the Refs menu. Fixed a bug that sometimes prevented the reference list from being updated when necessary. Fixed a bug in group search. Fixed a bug that could cause a drag in the Online Search window splitter to move the entire window. Fixed a bug in Google Scholar importing where a field's leading quote mark was not imported. Fixed an issue where in some circumstances clicking on an already selected reference would cause its PDF to scroll to the beginning. Fixed several cosmetic bug in the full screen PDF view.



NEW in Version 13.0.2
(December 22, 2017)


Automated repair of damaged indexes
If Verify detects a problem with the library, Bookends will reindex it without user intervention. This will result in fewer problems being reported and fewer suggestions to Rebuild.

Changes in cloud sync should result in fewer requests for authentication from Apple

Copy Citation and scanning have been updated to work with Microsoft Word version 16.x

Updated import from Google Scholar to deal with changes made by Google
Bookends will import the best information it can obtain from Google Scholar.

Better detection of a linked word processor
Bookends will now recognize the linked word processor if its name has been changed in the Finder.

Improved scanning of text files
Bookends will assume the scanned text file has the same encoding as the bibliography output (e.g. plain text, UTF-8, or UTF-16). If the output is incompatible with plain text files (e.g. Styled Text), the text file will be assumed to be encoded as UTF-8.

Improved scanning of LibreOffice .odt files

Click on the Term List header in the library window to filter the list
This is now analogous to the groups search, except it is "live" (filtering occurs as you type), no need to press Return.

Improved metatag searches
All searches for metatags are now "by character" exact matches so that they work when tags contain spaces. Note that in the Find dialog the setting of the search type (e.g. "word beginning with") will be ignored if the search term is a metatag.

PDF comments imported from Sente will be separated from the corresponding quote, if any, by an empty line

Bug fixes
Fixed a bug where Bookends failed to quit when another copy using the same license was running. Fixed a bug where the + button to add a PDF tab was visible in the Attachments pane of the reference edit display. Fixed a bug that prevented PDF page numbers from being updated in the reference edit pane/window. Fixed a bug in the scanning dialog where bibliography output settings as UTF-8 and UTF-16 were not shown correctly. Fixed an error when multiple PDFs were imported into a static group at once. Fixed a bug where the Bookends Browser window was dragged by clicking and holding a toolbar button. Fixed a bug in Author-Date scans where the % and - metacharacters were applied to all citations in a group instead of individual ones. Fixed a drawing artifact caused by opening the PDF pane while working in full screen. Fixed a bug where the buttons in the Inspector window would stop responding to mouse clicks. Fixed a bug where the groups pane might not appear in full screen view if the PDF pane was closed. Removed extraneous commas in the authors names when a reference has more than one institutional author and is displayed in the single column or summary view. Fixed a bug where a right-click would offer to detach an attachment from a reference that had no attachments.



NEW in Version 13.0.1
(December 3, 2017)


The consequence of a reference double click is a preference option
In preferences (List tab) you can tell Bookends what to do when you double click a reference: open the PDF display pane and add the PDF to the toolbar, or open the reference's edit pane/window.

The PDF toolbar shows the page number
Click on to bring up a dialog that lets you go to a specific page

The PDF tabs have been moved to the bottom of the toolbar

Choose your own PDF highlight colors
In the PDF highlight color selector, Option-click on the color you want to change. To restore a color to the factory default, Shift-Option click on it.

To change the color of an existing highlight, select it and choose a new color from the PDF highlight color selector
The default highlight color will not be affected.

More flexible handing of repeated citations
You can tell Bookends to output literal text (e.g. "Ibid.") when a citation is repeated, or to output reference data (e.g. the author). This is determined in the format: Citation Options -> Custom Citation -> Common Settings. The option to output the author when a citation is repeated is used in the new Chicago 17th A format, included in this release.

Open multiple reference windows at once
If you edit references in a standalone window and each reference opens in a separate window, selecting up to 5 references and pressing Return or Enter will open them all at once.

Import copied text when in Bookends Browser
If a library is open and you copy text to the clipboard while in Bookends Browser, selecting File -> Import References From File or Clipboard (Shift-Command-I) will bring up the import dialog with the clipboard option selected. Click OK to import to your library.

Bookends does a better job at restoring the original library window pane heights when exiting full screen

Double-click on the PDF proxy icon in the PDF viewer to open it in your default PDF reader

Bug fixes
Fixed a bug that could cause an error message when attaching a file. Fixed an error that occurred when using Command-' to copy the Pages information from the previous reference. Fixed a problem with updating of the progress window when doing a Global Change -> Rename Attachments. Fixed a problem where typeahead scrolling didn't work for several lists. Fixed a problem with windows being moved off screen. Fixed a bug where the groups pane would appear under the thumbnail view when viewing a PDF in full screen. Fixed an issue that prevented the Bookends library icon from showing correctly in the Finder. Fixed a bug that could cause a live search error when Label is used as a column. Fixed a bug that would cause an error when doing a BibTeX scan. Fixed a problem in finding attachments in High Sierra when the file named contains a non-breaking space. View -> Edit Reference now brings up the standalone editing window if it is specified in preferences. Fixed a rare bug where in some cases a group wasn’t placed in the parent folder after cloud sync. Fixed a bug that caused an attached jpeg to be shown after another reference was selected.



NEW in Version 13.0
(November 10, 2017)


Bookends is a 64-bit application

Bookends requires macOS 10.9 (Mavericks) or later

The longstanding problem of improper rendering of large PDFs has been resolved

Updated database engine

Import references and PDFs with annotations from Papers 3
File -> Import From Papers 3 imports all of the references being displayed in the Papers 3 library window. If a static group is selected in Bookends, the references will be imported into that group. Important: so that your attachments retain annotations you made in Papers 3, you must follow these instructions. In Papers 3, make sure Preferences -> Library -> "Rename files in library folder" is checked. If you don't the PDFs that Bookends imports may lose any annotations that you added in Papers. Perform a File -> Export PDF Files and Media, and in the resulting Save Dialog click the Option button and make sure that "Include annotations" is checked. Export the PDFs to the Bookends default attachment folder (not a subfolder). In Bookends choose File -> Import From Papers 3. The imported references will be selected in the Bookends library window, and if you like you can immediately rename their attachments with Refs -> Global Change -> Rename Attachments -> selected references. This feature requires macOS 10.10 (Yosemite) or later. Special thanks to Matthias Steffens for creating the AppleScript.

PDF tabs
This feature allows you to quickly go back and forth between references and their PDFs. When viewing PDFs in the library window there is a plus sign at the upper left hand corner of the PDF toolbar. Clicking it will add a link to that PDF in the toolbar (a tab), which is denoted by the author/editor name and the date. Hovering over the tab will display the PDF's name. Clicking on the link will take you to the corresponding reference and display the PDF. Clicking the "x" to the left of the tag name will close it – if you click it with the Shift key held down all tabs will close. When viewing a tabbed PDF, the tab text will be blue and the add-tab plus sign will be disabled. Right-click on a tab to bring up a pop-up menu with the names of all tabbed PDFs and select one to navigate to it. If the Option key is held down when you select a reference from the pop-up menu the tab will be removed. The PDF tabs are remembered between launches.

Double-clicking on a reference opens the lower PDF display pane and, if the reference has a PDF, creates a tab

Bookends remembers PDF scroll positions
This means that you can work on PDFs from multiple references, and when you return to one Bookends will display the PDF at the point you left it. The scroll positions are not remembered between launches.

Toggle continuous PDF highlighting
A highlighter icon in the PDF annotation toolbar that acts as a toggle. When continuous highlighting is off (the icon has no color) you can make selections in the PDF and apply actions to them (highlight, underline, import into Bookends as a notecard, etc.). Click on the highlighter icon to turn on continuous highlighting, at which point the icon will assume the highlight color (the default is yellow). Any selections you make in the PDF while this is enabled will instantaneously be highlighted. You can change the highlight color by clicking on the chevron (downward arrow) next to the highlighter icon and selecting from the pop-up menu.

Fresh PDF annotations are saved before opening the PDF in another application

PDF underline annotations can be selected with a click and removed with the Delete key

Work with PDFs in full screen mode
When a PDF is showing in the lower display pane, invoking View -> Enter Full Screen (Control-Command-F) will cause the PDF to take up the entire window excluding the right pane, if open. When working with PDFs, Bookends will exit full screen mode when you invoke View -> Exit Full Screen or its menu shortcut, click the window maximize (green) button, or perform a Find (Command-F). Note: the PDF scroll position will be maintained if you use View -> Enter/Exit Full Screen (Control-Command-F), but will only be approximated if you use the window's green button.

Double-click on the PDF proxy icon in the PDF viewer to open it in your default PDF reader

Bookends will use the starting page entered for the reference to calculate the correct page for a notecard
If the publisher has included the actual instead of the relative page number as PDF metadata, Bookends will use that.

Get PDF from Internet is improved
Bookends uses the PMID, DOI, ISBN, or JSTOR stable URL to get a reference's PDF from an online source. If the reference has none of these, Bookends will try to find its DOI first and then fetch the PDF.

Automated downloading of PDFs works with BioMed Central (BMC)-series, Sage, and Elsevier ScienceDirect journals

Improved format catalogs
Format catalogs now contain examples of final in-text citations in addition to the bibliography output. Because they are Type-independent, if the citation is "by number" or "author-date" an example is given for only the first Type. If the citations are custom they will be shown for each Type. The time it takes to generate a format catalog has been shortened by about 50%.

Much improved automated PubMed search
When performing an automated search, Bookends will import the results into a temporary database. Words in the lower detail pane that match search words will be shown with an orange background highlight. Press Command-F to reveal a live search field that lets you search among the references. Any text in the lower pane of the search window that matches your ad hoc search will be highlighted with a blue background. Click on the search box pop-up triangle to select a specific field to search; the default is All Fields. Note that the PubMed import filter determines which metadata are imported, and you can edit the filter if you want information other than the default to be imported (e.g. to import MESH headings to Keywords). The search field pop-up triangle also lets you select previous searches, which are remembered when you press Return while the cursor is in the search field. If you have retrieved the same reference with different searches in one session, importing one will cause all to be colored yellow.

New AppleEvent for creating a new group and (optionally) populating it with references
The AppleEvent ID is ADDG, and is invoked like this: return «event ToySADDG» "flashy new group!" given string:"82469". If a group with the requested name already exists, Bookends will make the new name unique by appending a number. Separate multiple unique IDs with a comma or Returns (ASCII 13).

New AppleEvent for getting the name and paths of attachments
The AppleEvent ID is GETA, is invoked like this: return «event ToySGETA» "18012,92167", where the parameter contains the unique IDs of the references. Separate multiple unique IDs with a comma or Returns (ASCII 13). The POSIX pathnames of the attachments will be returned in an ASCII 10-delimited list. If the attachment name in the library can't be found an empty string will be returned.

Ad hoc suppression of number styles in citations
When scanning with formats that cite by superscripted (e.g. Nature) or italicized (e.g. Science) numbers, use the _ metacharacter at the beginning of a citation group to remove styling. Previously this applied only to superscripts. This doesn't yet work with Mellel.

You can scan Pages documents stored in iCloud

ASCII-only characters in attachment names generated by Bookends
When ASCII-only names (remove accents) is checked in preferences, Bookends will convert non-ASCII characters to ASCII when PDFs are being attached or renamed (i.e. é becomes e).

Add tags to metatags while viewing the tag cloud
Right-click on a tag name and select the metatag you want to add it to. If the metatag already has this tag it won't be added again. You may find this method more convenient than opening preferences to add tags.

When scanning, Bookends will recognize BibTeX citations in the form \footcite{key}

Improved removal of accents and non-ASCII characters from BibTeX keys Bookends generates

Smarter Global Change -> Change Field
When putting text before or after the contents of a scrolling field (e.g. Authors, Editors, or Keywords), Bookends will automatically add a Return where appropriate so that the inserted text appears on its own line. In addition, if you insert text that begins with a Return (the ¬ character) into an empty field, Bookends will remove the Return.

Faster transfer of PDFs from Bookends for iOS to Bookends for macOS via wi-fi

Automatically attach PDFs to matching references when attaching more than one PDF
When attaching many PDFs at once, if a DOI or stable JSTOR URL is found Bookends will try to match the PDF to an existing reference and, if found, attach it. If there is no match in your library Bookends will download it from the Internet if it's available and then attach the PDF

Improved Links Inspector
Navigation between linked references is easier (one-click instead of double-click) and cosmetic changes were made.

You can set a reference's color label and attachment names via the SFLD AppleEvent

Output of references as unstyled text via an AppleScript (the GUID AppleEvent) is faster

When autofilling from CrossRef, the full journal title will be imported if available

Importing from the watch folder will autofill metadata if a JSTOR stable URL is found in the PDF

Double clicking on a reference in the library window will open the edit pane or the standalone reference editing window
If the edit pane is already open a double click will open the pdf viewing. To use the keyboard to open just the edit pane or standalone reference window press Return or Enter.

Use Live Search to search by Unique ID
Because partial matches are not possible, the search will be performed only after Return or Enter is pressed.

More informative window titles for standalone reference editing windows
If you have configured macOS to open documents as window tabs and are using one standalone reference window per reference in Bookends, each open reference will appear in the main library window in a tab.

Bookends sets the default import option to PubMed when you import a .nbib file

Selected rows in lists are more readable when the list does not have the focus.

Help -> Read Me had been changed to Help -> Release Notes
Using this will take you to the Version History page on the Sonny Software web site where you can see what has changed in every Bookends release, starting with the most recent.

The Society Bib Lit glossary has been updated to the SBL Handbook of Style, 2nd ed (2014)
Thanks to Danny Zacharias and Nhaps for contributing their work.

Bug fixes
Fixed a bug in handling of import filter names that contain an ampersand. Fixed a bug in Refs -> Global Change -> Consolidate Attachments that could generate an error message. Fixed a bug that caused a Term List search to switch the focus to the list. Fixed a bug in importation of RIS files in which the "ending page" tag EP is listed before the "starting page" tag SP. Fixed a bug in scanning Pages documents where punctation after a citation was not removed when cited pages began with punctuation.