NEW in Version 13.5.4 (May 1, 2021)
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File -> Export References provides more flexibility and a cleaner user interface
You can now use a hierarchical menu to export the selected references or the Hits, decreasing the number of dialog windows that need to be dealt with. Previously you could only export the Hits. These options have also been added to the reference list right-click contextual menu.

Improved marooned attachment manager
Right-click on the list to move the selected files to a folder or the Trash. Press Delete to move the selected files to the Trash. Moving many files at once is much faster.

Bookends will select the default reference Type, set in preferences, when populating the Type pop-up menus in the Format Manager
Previously it selected Journal Article regardless of the user’s preference setting.

New color picker
The color picker has been modernized and is now asynchronous. That means that changes in a color are immediately reflected in the associated control. In addition, the new color picker fixes a problem some Big Sur users experienced where selecting a color resulted in sluggish behavior.

Swap columns in the reference list by right-clicking in the column and choosing the column to swap with

The full URL will be displayed in the concise views (Summary and All), not a truncated version

Added "More than one attachment" to the pre-defined Smart (SQL) groups

You will receive a warning if the default attachment folder is unavailable (e.g. on an unmounted server) and has been reset to the factory default

Clickable email links work in Bookends Browser

Use swipe gestures to change pages in Bookends Browser
Swipe between pages with one finger can be enabled in System Preferences -> Mouse -> More Gestures.

Improved trapping of illegal characters entered in the Autocomplete Paper text fields

Updated database engine

Bug fixes
Fixed a bug where Bookends would misidentify a file as marooned if it contained certain characters, such as parentheses or question marks. Fixed a bug where file bundles (e.g. TextEdit RTFD files) were treated as folders and their internal contents identified as marooned attachments. Fixed a bug that could cause a hang when performing an Autocomplete Paper using Google Books. Fixed a bug that prevented the PDF annotation color icon from changing appearance immediately after the color was edited. Fixed a bug in Wi-Fi sync of attachments. The lack of an annotation modification date will no longer cause an error when filling out the note stream.

NEW in Version 13.5.3 (April 3, 2021)
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Marooned Attachments Manager
A marooned attachment is a file in an attachments folder that is not attached to any references. File -> Show Marooned Attachments generates a list of files that aren't attached in any open library. It is important to note that Bookends can only check open libraries for the presence of an attached file -- if you have unopened libraries the "marooned" file may actually be attached in one of those. It's up to you to make sure all your libraries are open when you invoke this function. Once identified, you can press the space bar to open a file in Quick Look, double click to open it in your PDF reader, or show it in the Finder. A pop-up menu lets you move the selected files to a specified folder or the Trash. Some users may have attachments on the Desktop, making the Desktop an ad hoc attachment folder. Because the Desktop will undoubtably have files unrelated to Bookends, by default Desktop files aren't listed. However, there is an option to show potentially marooned Desktop files if you want to see them.

When attaching to a PDF to new reference with Autocomplete Paper, Bookends will import the PDF's title and subject if they are found in its metadata
If Autocomplete Paper is successful these will be replaced by the information imported from the online source.

Images (non-PDFs) in the display pane can be moved to the Finder or another app by drag and drop
A copy of the original will be delivered to the dropped location. To create an alias of the image, hold down the Option and Command keys and then drag.

When an image is showing in the display pane, the right-click hierarchical menu has options to open the image, zoom the image, and show the image file in the Finder
Opening the image with a double click has been removed because it conflicts with drag and drop.

The jpg files of cover art imported from Google Books will be named using the same rules as when renaming attachments
Previously, they were named "Download" followed by a random number.

Bookends Browser detects DOIs for articles from The Lancet journals and does a better job downloading their PDFs

When searching PubMed in Bookends Browser, Bookends will find a PDF's metadata even if it hasn't been assigned a DOI

Set the font and font size for PDF comments in Preferences

References of Type Review will be treated as Journal Articles when formatting an entry in the Vol (Issue) field
That is, the volume and issue can be output together or independently.

Live Search will perform a string (character) search for characters enclosed in quote marks
Previously this search would only match whole words.

Added PDF Viewer as an option for viewing in PDFs in another application

Bookends Browser will now allow you to download PDFs from OVID via the PDF proxy icon or the paper clip

If an article found on PubMed with a direct search lacks page numbers but has an electronic location, the latter will be inserted in the Pages field on import

Updated the PubMed parser to import the correct DOI when the data provided by PubMed contain multiple DOIs of cited references

Bug fixes
Fixed a bug in which a name with an apostrophe caused an error when generating a BibTeX key. Fixed a bug in "Make PDF note from selection". Fixed an error that could occur when attaching hundreds of PDFs at once. Fixed a bug in cloud sync that caused an error when linking to an existing library in the cloud. Fixed a bug that caused an error when attaching a PDF whose contents could not be read. Fixed an error that occurred when doing a find again in a PDF with after changing the selection. Fixed a bug where the secondary order field in a format wasn't used unless the scan generated a bibliography. Fixed a bug that could cause an image in the display pane to persist when a search found no matching references. Fixed an error that could occur when switching references with an attachment being shown. Fixed a bug when deleting references from very large libraries. Fixed several problems with Wi-Fi syncing of attachments. Fixed a problem where using the Temporary folder as an ad hoc attachment folder generated errors in Catalina and later.

NEW in Version 13.5.2 (March 6, 2021)
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Major code refactoring of many core functions
The code has been modernized and streamlined.

The icons in the PDF thumbnail view are larger, making it easier to distinguish the contents of one page from another

Subject Bibliographies now display super/subscripts when sent to the Bibliography Window

When Bookends is watching the Downloads folder for PDFs, files ending in ".pdf.part" will be ignored
These files represent partial downloads in progress and should not be attached until they are complete.

Spotlight queries now search ad hoc attachments folders as well as the default folder/subfolders

You are able to use default attachment folder subfolders to any depth when attaching files
This was previously limited to just root level subfolders.

When searching PubMed in Bookends Browser, Bookends will find a PDF's metadata even if it hasn't been assigned a DOI

Added a keyboard shortcut for New Static Group: Option-Command-G

Added PubMed Central to the Bookends Browser default bookmarks
This will appear only for new installs. If you are upgrading, have not previously edited the bookmarks, and want this entry in your bookmarks, remove the Bookmarks file from the Bookends folder. The new default settings will appear after the next launch.

The modification dates shown for annotations in the note stream now include seconds

Changed the Term List keyboard shortcut to Option-Command-; to avoid a conflict with the Check Spelling Now menu

Attaching a file in the Trash is no longer allowed

Updated database engine

Bug fixes
Fixed a bug where moving to another reference using the Links Inspector could cause edits to a reference field to be discarded. Fixed a bug where creating a new format based only on the first Type of the selected format would result in an error. Fixed a bug that prevented Bookends QuickLook from working. Fixed bugs in scanning with formats that have a secondary order field for citations. Refs -> Generate BibTeX Key works again. Fixed a problem in Bookends Browser where trying to download a .docx file would cause Bookends to hang. Fixed a bug that could prevent a PDF from being moved to the trash via a menu option if a file with the same name was already there. Fixed a bug that was introduced in 13.5 where importing from Zotero failed to import attachment file names. Fixed a bug in the column view where the first time it was used the indicated sort order was incorrect. Fixed a problem where an error could be generated when closing the online search window in the middle of a search. Fixed a bug in the watch folder where the same PDF could be added to the library multiple times when files were copied rather than moved. Fixed a bug in scanning .odt files where the presence of hard returns (line breaks) would result in an error. Fixed a bug that caused operations that opened PDFs in the default viewer to fail. Fixed a bug in Spotlight Search where Bookends ignored attachments whose names contained a slash. Fixed a problem with scanning some Mellel documents on M1 Macs. Fixed a bug that prevented bibliographies from being placed in the clipboard after scanning RTF files. Fixed a bug that allowed the addition of the default attachment folder and subfolders to the ad hoc attachment folder list. Fixed a bug that prevented hypertext links in notecards from showing with right-click. Fixed a bug in notecard word wrap.

NEW in Version 13.5.1 (January 23, 2021)
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Fixed a number of issues that arose with the new universal build
These are itemized in the bug fix list below.

Improved AppleEvent communication with Word

Bug fixes
Fixed a problem with labels where editing one in preferences would cause an error. Fixed a related problem where extra label names were added to the label list for the default reference Type. Fixed the failure for some to find and display PDFs containing Unicode characters. Fixed a bug in switching from Groups to Term Lists in the library window. Fixed a bug that prevented Z39.50 searches (the Library of Congress and universities) from working on Apple Silicon Macs if the filter was set to use Direct Access Z39.50. Fixed a bug that caused an error when upgrading from Bookends 13.5 or early versions of Bookends 12 or older.

NEW in Version 13.5 (January 16, 2021)
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Bookends is a Universal Binary
That means it is optimized for both Apple Silicon- and Intel-based Macs.

Manage Ad Hoc Attachment Folders
A folder is added to this list automatically when you attach a file and tell Bookends to leave it where it is. A new button in the Preferences General tab opens a window listing the paths of all such ad hoc attachment folders. If a folder's path cannot be resolved (e.g., if it is on an unmounted server) you'll see the words "Folder Unavailable" or "Path can't be resolved" in red. You can remove folders that are no longer used for attachments by selecting them and clicking the minus button or pressing the Delete key. This may make UI operations a bit faster in some cases because Bookends will no longer search in that folder for attachments.

Updated database engine

Bookends looks for illegal Unicode from Internet sources and prevents them from causing crashes when they are normalized

Attachment Flow view removed

When generating a unique citekey, detection of existing citekeys is case-insensitive

Refactored many internal operations, including a full rewrite of Wi-Fi sync

Bug fixes
Fixed a bug in scanning where the secondary order field could be ignored in some cases. Fixed several bugs in the Works Cited Inspector that affected the UI and the hierarchical pop-up menu. Fixed a bug in Google Books online search where the book cover art was not being displayed. Fixed an error that could occur when trying to add a notecard when no reference was selected. Fixed a bug in OpenURL where searches using the token did not work. Fixed a bug where Edit -> Copy Hypertext Link might not be enabled when clicking in the groups pane. Fixed a bug where Bookends would be off by one in identifying the group a reference was dropped on.


NEW in Version 13.4.8 (December 5, 2020)
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New Send Feedback menu
This is under the Help menu and creates an email to support@sonnysoftware.com in your default email client.

Invalid responses from Google Books will be ignored instead of being reported as an error

The Cited Works Inspector has been updated for Dark Mode

Messages in the PDF viewer are word wrapped and displayed in their entirety even if the width is narrow

Live searches will update immediately if you change the search field while text is entered

The currently active search field is checked in the Live Search menu

Improved connection error detection when downloading PDFs

Add a PDF underline annotation to the Bookends database with a right-click in the note stream
Previously, this was only available for highlighted text.

Updated the JSTOR parser to deal with changes made by JSTOR

Bug fixes
Fixed a bug where a newly created reference didn't immediately appear in the reference list if a smart group was selected. Fixed a bug where the background color obscured the white text when editing a PDF note in Dark Mode. Fixed a bug where the font of a field could be changed to the System default when consolidating terms in a Term List.


NEW in Version 13.4.7 (November 8, 2020)
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Restored importing from JSTOR
Importing references that weren't available via free access had been broken because of changes made by JSTOR.

Requests to Crossref are faster and more reliably return a DOI

The PDF command "Make Notecard from Selection and Page #" places the quoted text on a new line

Bookends will offer to unlock a PDF that is locked in the Finder when you try to add or edit a PDF tag, or click on the lock icon in the PDF toolbar

Updated automated download of PDFs from ScienceDirect to deal with changes made by the publisher

Improvements in scanning LibreOffice .odt files

Improved handling of cases where you try to register Bookends on a new Mac with a registration code whose 2 years of free updates has expired

Author names terminated with a comma will be output as entered for Author-Date citations

In the Attach dialog the pop-up list of subfolders to which the file could be moved is sorted alphabetically
This fixes a problem introduced by the APSF file system. Only top level subfolders will be shown.

Close the Quick Look PDF display with Command-W without closing the library window

Bug fixes
Restored detection of drag and drop of PDFs and other files types onto the Bookends icon in the Dock. Fixed a bug in Live Search that allowed Spotlight searches to be initiated with every keypress instead of when a Return is pressed. The contents of the edit pane attachment tab will be emptied when no reference is selected. Fixed a bug that prevented Live Search of notecards from finding tags (i.e. when the tag word is preceded by %). Fixed a bug where PDFs with slashes in their names weren't displayed in the edit pane Attachments tab. Fixed an error that could occur when searching Google Books. Fixed a bibliography bug were references could be output in small caps if the default bibliography and reference font sizes were 3 points apart. Fixed a bug in secondary citations where "et al." was output after the surname even if Surname Only was selected. Fixed a bug where any groups selected in the groups pane were deselected when a PDF was dropped on it.


NEW in Version 13.4.6 (October 3, 2020)
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The maximum number of columns in the reference list has been increased to 10

Bookends has been updated to use modern file system APIs
Because of this, there is a change in the way file names with slashes are handled. The names are now stored with slashes replaced by colons. When you open an older library in 13.4.6. or later the conversion of existing attachments names will be done for you automatically. Note that means if you open such a library in a version of Bookends prior to 13.4.6 attachments with slashes in their names will not be found.

Improved Bookends Browser handling of PDFs
This should result in faster downloads and better compatibility with proxy servers.

Faster reference navigation when the edit pane is visible

Updated automated download of PDFs from ScienceDirect to deal with changes made by the publisher

Improved the appearance of lists

Safeguards put in place to prevent Bookends Browser from hanging when validating DOIs if Crossref requests time out

Updated unscanning of Nisus Writer Pro documents to deal with changes made in Nisus Writer Pro 3.1

Improvements in Wi-Fi sync

Bookends treats files with the extension of .org as text files for the purpose of scanning

Bug fixes
Fixed a bug that could cause an error message when closing the library window. Reduced cursor flicker when mousing over a PDF. The width of field labels adjusts to the width of the label text, ensuring that clicks on labels on the right don't open the enlarged window for the field on the left when the edit pane is very narrow. Fixed an error that prevented some users from opening the Registration Window. Fixed a problem when attaching some PDFs from JSTOR where the publisher's name was promised but was actually missing. Fixed problems in unscanning documents in which citations had non-default styles.


NEW in Version 13.4.5 (September 5, 2020)
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Select Hits Group is a new menu item in the Hits menu
The keyboard shortcut is Shift-Command-H.

When searching a PDF, all matches will be highlighted as they are in Preview
Note that in some cases the highlight will be blue, not yellow, until you scroll to another page and back. This is a cosmetic bug in macOS.

Command-Option drag of the PDF proxy icon in the PDF toolbar will create an alias of the PDF when dropped
This is in addition to the normal behavior where dragging without keyboard modifiers will create a copy of the PDF when dropped.

When searching PubMed, the lower pane in the Online Search window will show the article on the publisher's web site if it can
If not (entries in PubMed may lack that link), Bookends will default to the article on the PubMed web site.

Improvements in the PDF toolbar when the width is too narrow to display all controls

Bookends can insert a space in front of a semicolon separating multiple citations in a group
This option is in the format's Citation Options -> Common Settings section.

If Bookends can't search the PDF for a unique identifier when attaching because it is corrupted or perhaps just an image, the alert dialog will include the name of the PDF

Autofill will accept JSTOR URLs that use jstor.com in addition to those using the standard jstor.org

Improvements in Wi-Fi sync

Attachment Inspector improvements
You can resize the list showing attached files. The contents of an attached folder are sorted alphabetically (this is now true in the attachment display pane pop-up menu as well). Reordering attachments by drag and drop is disabled when a folder is attached (the list is always sorted).

When editing a PDF note in Dark Mode the background color will be made black (instead of yellow) to make reading the white text easier

When updating PubMed references with Autofill From Internet, Bookends will remove HTML tags for italicized text from titles

Added a confirm dialog before performing a Global Change Move or Change

Improved the detection and correction of invalid DOI candidates when using Bookends Browser


Bug fixes
Fixed a bug that caused the PDF page number and the highlighted text to run together when adding a highlight to the Notes field. Unlike highlights, clicking on a note card showing a PDF underlined text annotation will not permit its import into the library. Fixed a bug where the Add Note pop-up menu under the note stream was enabled when no reference was selected. Fixed a bug that caused some fields in the edit pane to incompletely refresh their contents when moving between references. Adding cited pages to a BibTeX citation in the Copy Citation With Modifiers dialog now works. Fixed a bug where tag cloud stop words were applied to file tags. Fixed a bug where a Finder tag might not be refreshed when switching between PDFs. Fixed a bug in Compare References where the field from the wrong reference might be moved when Command-clicking on the field symbol. Fixed a bug in scanning a text file with BibTeX citations where a citation wasn't found if it was preceded by a modifying metacharacter (e.g., ^, %, etc.). Fixed a bug that prevented a right-click on a display pane image of a file in an attached folder from bringing up the hierarchical menu that allows zooming. Bookends will add the extension .bdb to any Bookends 9 library that is converted to the current database schema. Fixed a problem that could cause Bookends to incorrectly identify the default email client. Fixed a bug in Global Change where an error occurring when moving date from a styled text field to one without styles. Fixed an issue in Bookends Browser where you might be prompted to save login credentials when no login as done.


NEW in Version 13.4.4 (August 2, 2020)
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Widescreen layout
A menu option in the View menu lets you toggle between the compact view, where the display pane for PDFs, formatted references, etc. is shown beneath the reference list, and the new widescreen view, where the display pane is shown between the reference list and the right info pane. You may prefer the widescreen view when, for example, reading PDFs with the note stream open. Unlike the compact view, when in Full Screen all library window panes will be available while you work.

New Speech toolbar icon
This icon is not in he default control set, to use it you must right-click on the toolbar and customize it. Place the cursor in a text field and click the Speech button. Bookends will read the field's contents, or just the selected text, if any. Click on the Speech button again to stop Bookends from speaking.

Double click a reference to toggle the edit or attachment pane open or closed
Which pane a double click opens is set in preferences. Previously, a double click would only open the selected pane.

The text size for the Summary view will be the same as for the Note Stream
Both are set in Preferences with the Note Stream & Summary pop-up menu.

When using unique id in a reference to create a hypertext link in a concise view, Bookends will ensure that what follows the # is a number before creating the link

Renaming an attachment via a right-click on the reference list will allow you to edit the proposed name if there is only one reference selected and it has only one attachment

Added bioRxiv to the Bookends Browser default bookmarks list
This will only be available when performing a new install.

Updated Quick Add to accept URLs from jstor.com as well as jstor.org

Bug fixes
Fixed an error that occurred when switching a reference list column header to Date Added. Fixed a bug that caused Bookends to hang if the Delete button was removed from the library window toolbar. Fixed a bug where the bibliography was output with white text when scanning a Word document in Dark Mode and using a numbered format. Fixed a bug in scanning a NWP document when in Dark Mode where NWP would treat the bibliography as simply text and couldn't unscan it. Fixed a cosmetic issue where in specific cases the selected reference could be displayed as white text when the list lost the focus. Fixed a problem when importing multiple PDF in batch where matching references already exist. Fixed a permissions problem in Catalina where a PDF annotated in iOS wasn't downloaded by wi-fi sync.Fixed a rare problem where when opening a non-PDF in a third-party app Bookends would try to use the default PDF reader.


NEW in Version 13.4.3 (July 3, 2020)
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Improved Bookends Browser
Bookends can display web pages and PDFs with atypical URIs, has more safeguards to prevent Google Scholar from thinking you're a robot, and can resolve Google Scholar reCAPTCHAs if you are challenged to prove you're a human.

Import PDF attachment names with import filters
Import filters now accept tags that tell Bookends to put the contents of the field into the internal attachment field. This is useful if you are exporting from another reference manager with a tagged format like RIS and want the attachments transferred to Bookends (previously this was only possible when exporting/importing EndNote XML). Note that you should import only the file name, not its path. If you import a path Bookends won't find it. After import, move the actual attachment files to the Bookends default attachment folder so they can be found.

Insert attachment names from any field into the Attachment field with Global Change -> Move Field
This is for power users and may be useful if you imported attachments names from another source into a normal Bookends field. This feature will allow Bookends to recognize them as attachments, and if the file of that name is in the default attachment folder Bookends will display it.

Updated the JSTOR parser to deal with changes made by JSTOR

Improved error handling when a PDF download times out

New preference option to allow/disallow Bookends from forcing downloading of attachments in iCloud Drive that were moved to iCloud
This option is in the iOS tab and the default is "allow".

Updated the COinS parser for WorldCat

When responding to a hypertext link from another app, Bookends will initially search the current list of references
If not found, all references will be displayed and the matching reference selected. This will prevent you from being taken out of a group if it isn't necessary.

The group All will be selected if you import references with a non-static group selected
This ensures that the imported references will be highlighted. If a static group is selected, they will be added to that group.

Enabling the PDF continuous highlight marker will highlight any text already selected

Different Title Case settings can be specified for the titles of a book chapter and the book it is in
This option appears when you select the Book Chapter Type in the Formats Manager.

PDFpenPro was added to the list of external PDF readers that Bookends will offer as an option to open a PDF

Database engine updated

Bug fixes
Fixed a bug where the top of the reference list could obscure the PDF toolbar in full screen view. Fixed two bug where the text in bibliographies generated for Nisus Write Pro or saved directly to disk as RTF was in Dark Mode was white. Fixed an issue with some imports from JSTOR where titles were truncated if they contained a quote mark. Improved trapping (ignoring) of invalid entries in the Quick Add dialog. Bookends will now work if you mistakenly remove the live search field from the toolbar. Fixed a bug in cloud sync that could prevent the library from being opened with a "record locked" error message. Fixed a bug in the reference list view where the sort after pressing the header was not in the correct direction. Fixed a bug in editing or copying of notecards where some characters, including smart quote marks and apostrophes, were lost. Fixed an error that occurred when using the keyboard shortcut to go to the PDF find box. Fixed a problem where having the location of cited pages specified in the citation options tab would result in the removal of any text styles if cited pages weren't included in a temp citation. Fixed a problem where some Unicode characters didn't appear in the formatted reference. Fixed a bug when using a menu to move groups to a nested folder where the UI would initially show the groups in the wrong folder. Fixed a bug in wi-fi sync where an error sometimes occurred when syncing a new Mac library with one that existed on the iOS device.




NEW in Version 13.4.2
(June 3, 2020)
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Automated group repair
Bookends will determine the integrity of the group hierarchy when a library is opened. If irregularities are found they will be repaired. A repaired group may be moved out of a folder and placed at the root level if its intended location couldn't be determined.

Bookends will force PDFs in the iCloud Drive folder to appear on the hard drive if you have Optimize Mac Storage turned on
This is necessary because Bookends can't find PDFs that were removed by macOS and stored only in the cloud.

Underlined PDF text will be shown as underlined in the corresponding notecard

Improved visuals in Dark Mode

The text color in reference list rows with color labels is dynamically adjusted to be more readable

Text dragged and dropped into a reference field will be appended to the end of any existing content

Perform recent and smart SQL group searches from the SQL search window
An action pop-up menu will display saved smart SQL group searches and any recent ad hoc searches you have done, which when selected will be performed instantly. The list of recent searches is temporary and is reset between launches. If you want to use these searches between sessions, create a smart SQL group.

If you are running Catalina and you encounter an error when converting an old library, Bookends will offer to open System Preferences -> Privacy so you can give Bookends Full Disk Access permission

Updated the way Bookends Browser finds PDFs when importing from Google Scholar to deal with changes made by Google

When a reference is changed or refreshed, the browser view in the bottom pane will not reload if the URL in the URL field is the same as the one for the reference
PubMed users note that the stored URLs that worked with the old PubMed site are no longer valid. You can correct that with Global Change -> Find And Replace, searching the URL field for https://www.ncbi.nlm.nih.gov/pubmed/ and replacing with https://pubmed.ncbi.nlm.nih.gov/ . The PubMed import filter has been updated to use the new URL prefix for newly imported references.

Importing from PubMed by dropping a URL on the library window has been updated to work with the new PubMed servers

Bookends will treat *.md (markdown) files as text files for the purpose of scanning

Increased constraints on Google Scholar searches. This should decrease the chances that frequent searches will trigger Google Scholar's robot detector and block your access.

Folder names are sorted alphabetically when using a right-click to add groups to a folder

Improvements in the arXiv parser
The tags primary_category and category will be listed in the summary pane. You can edit the arXiv import filter to import them into the fields of your choice.

If you invoke a smart SQL group containing invalid syntax, Bookends will send you a notification with the diagnostic information rather than a modal dialog

Database engine updated

Bug fixes
Fixed a bug where the top of the reference list could obscure the PDF toolbar in full screen view. Fixed two bug where the text in bibliographies generated for Nisus Write Pro or saved directly to disk as RTF was in Dark Mode was white. Fixed an issue with some imports from JSTOR where titles were truncated if they contained a quote mark. Improved trapping (ignoring) of invalid entries in the Quick Add dialog. Bookends will now work if you mistakenly remove the live search field from the toolbar. Fixed a bug in cloud sync that could prevent the library from being opened with a "record locked" error message. Fixed a bug in the reference list view where the sort after pressing the header was not in the correct direction. Fixed a bug in editing or copying of notecards where some characters, including smart quote marks and apostrophes, were lost. Fixed an error that occurred when using the keyboard shortcut to go to the PDF find box. Fixed a problem where having the location of cited pages specified in the citation options tab would result in the removal of any text styles if cited pages weren't included in a temp citation. Fixed a problem where some Unicode characters didn't appear in the formatted reference. Fixed a bug when using a menu to move groups to a nested folder where the UI would initially show the groups in the wrong folder. Fixed a bug in wi-fi sync where an error sometimes occurred when syncing a new Mac library with one that existed on the iOS device.




NEW in Version 13.4.1
(May 2, 2020)
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Updated the PDF toolbar and added new graphic elements

PDF Table Of Contents
An icon or menu option (Shift-Command-T) in the PDF Action pop-up menu opens the table of contents (TOC) in a popover window. Select an entry (click or use the arrow keys), to go to the corresponding point in the PDF. If an entry contains a destination URL, it will open in your browser.

Right-click on the PDF proxy icon in the PDF toolbar to pop-up a menu listing each folder in the pathname
Select a folder to open it its enclosing folder in the Finder and select it. This works just like the window proxy icons.

Manage continuous PDF highlighting via the keyboard
When a PDF is showing and has the focus, pressing Control-1 through -5 (without the Command key being pressed) will turn on continuous highlighting with the color corresponding to the number. Any text selected when this is done will be highlighted. Pressing the Control key and the same number as the current color will turn off continuous highlighting.

Added a warning dialog when a damaged format is detected
It instructs you to move the damaged format file to the trash and select another.

There is a separate Dark Mode setting for the color required BibTeX fields in preferences

The list selection color is now the macOS accent color
This requires macOS 14 (Mojave) or later. For High Sierra the selection color is blue, as was previously the case.

Updated Bookends Browser import from JSTOR and WorldCat to deal with changes made by these sources

Improved detection of PDFs in some web pages

There is an option to hide group pane folder badges
Right-click or use the group action pop-up menu to show (default) or hide the badges that tell you how many items are in a folder.

Newly created scanned files will have the word "scanned" instead of "formatted" in their names

Preference settings for openURL will be synced between computers

Bug fixes
Fixed a problem where the top of the library window could appear offscreen. Removed extraneous HTML from the Abstract of Google Scholar results when sorting by date. Many fixes for cosmetic issues in Dark Mode. Fixed a bug where bibliographies created for Mellel in Dark Mode were white. Fixed a bug in the generation of formatted citation examples. Fixed a bug in the height of the PDF in the edit pane's Attachment tab. Fixed a problem where some users weren't able to select options in the Inspector's segmented button. Fixed a bug that caused errors when opening libraries after customizing some of the toolbar elements. Fixed a bug where styled text changes weren't saved in dark mode. Fixed a bug in the automated PubMed search window where selected a library from a number that are open failed to import the references. Bug fixes for Wi-Fi sync. Fixed a bug that prevented Autofill From Internet from working with ISBNs. Fixed a bug in Remove Duplicates that prevented changes made in the Verify process from being saved. Tool tips for the buttons in the library window bottom strip were restored. Fixed an issue where the selection could change in the reference list after doing an Autofill From Internet. Fixed several instances where changes in the database weren't synced. Fixed a bug where bibliographies created by scanning a Pages files in Dark Mode where output in white instead of black. Restored the dialog asking you to paste in the bibliography after a Pages scan.



NEW in Version 13.4
(April 2, 2020)
Download


Bookends is Dark Mode compatible
There are a few minor changes in the UI to make the appearance work well in light and dark mode.

The library window now has a macOS-native toolbar
This means that you can use a right click to configure the toolbar as you like. The only control that can't be removed is the live search field.

Detach attachments in the Inspector by pressing the Delete key
Menu items available in the old Action pop-up are now available with a right-click.

The Google Scholar and arXiv search results can be returned ordered by relevance or date

You can select multiple citations at once in the floating citations window
This makes it possible to perform operations like Copy Citation on several references at once to create a citation group.

The Links column in the library window is updated immediately when links are added or removed

Improved SQL search
Newly created or edited SQL searches will be checked for validity before the dialog is closed. If there is an error the dialog will remain open so that you can fix the problem and try again. The group pane hierarchical menu will offer to edit a saved SQL search rather than rename it.

Duplicate a smart group with a right-click or the Groups Action pop-up menu

Delete terms from the library with a right-click in the Term List window

Scanning of Apple Pages has been updated to work with Pages version 10

Import References from the Online Search window with File -> Import References -> Import Selected References (Shift-Command-I)

Amazon France and Amazon Germany searches have been removed
These sites finally caught up with Amazon.com and began throttling searches, rendering them useless for Bookends.

Updated database engine

Bug fixes
Fixed a bug where the default output style was set to Styled Text after scanning a Word document regardless of the setting in preferences. Fixed a bug where removal of attachments in the Inspector wasn't marked for sync. Fixed a problem with an atypically-encoded en dash in an ISBN used in Quick Add. Fixed a bug where a duplicated reference wasn't automatically added to the original's group, if any. Fixed a bug in where the short title created from the full title via a right-click wasn't saved. Fixed a bug in opening and displaying attached Mellel files. Fixed several issues with the Watch folder. Fixed an error in Bookends Browser caused by missing data returned from CrossRef. Fixed a bug where the Import Reference menu was enabled inappropriately.



NEW in Version 13.3.2
(February 23, 2020)
Download


Bookends 13.3.2 requires macOS 10.13 (High Sierra) or later
This is necessary to have access to APIs used by the updated Bookends Browser.

Bookends Browser
Storing and retrieving surname and password in Keychain works with the new browser API.

Bookends Browser
You are able to download PDFs accessed through a proxy server such as EZProxy. If for some reason Bookends can't download the PDF file, the PDF may actually still be displayed in the browser window. If so, you can open it in Preview with a right-click or by using the HUD and then attach it to a Bookends reference by dragging and dropping the PDF proxy icon in the Preview window title bar.

Bookends Browser
If the link to a PDF triggers a file download (rather than being displayed in the browser window), the attach dialog will appear and let you attach the PDF to the frontmost library's selected reference, a new reference with autofill Autocomplete Paper, etc. If no library window is open, the PDF will be downloaded to the Downloads folder and opened in the default PDF reader (e.g. Preview).

Bookends Browser
The "open PDF" head-up display (HUD) works. When viewing a PDF, if you move the mouse to the bottom of the page a HUD appears. If you click on the third icon from the left, the PDF will be opened in Preview. You can attach the PDF to the selected reference in Bookends by dragging the file proxy icon (in the Preview window title bar) and dropping it on the Bookends library window.

Autocomplete Paper works when the attachment is a webarchive

Added a format for The Generic Style Rules for Linguistics

Bug fixes
Fixed a bug that caused an error message when opening the Bookends Browser window. Fixed a scanning bug when using an author-date format with year-only for repeated authors and there is preceding literal text in a citation group. Fixed a bug in Wi-Fi sync. Fixed a bug in which creating a notecard with page # from an annotation didn't calculate to true page number correctly.



NEW in Version 13.3.1
(February 8, 2020)
Download


Bookends Browser has been completely rewritten
Bookends Browser now uses a more modern macOS API that has many advantages, including faster page loading, much better compatibility with web sites using complex Javascript, no interference by the Adobe PDF plug-ins, the ability to display webarchives, and fixes a problem some people had with logging into iCloud to use sync. One feature has been removed: automatic fill-in of login name and password is no longer available.

The warning about the presence of Adobe PDF plug-ins has been removed because they no longer interfere with Bookends (see above)

Much improved importing from Papers 3
Bookends will now import reference citekeys and manual collections from Paper 3. Limitations: (1) collection hierarchies will not be preserved (i.e. the manual collections will be converted to Bookends static groups at the top level), and (2) if you have nested manual collections, the references will be imported into a single static group that has the name of the topmost collection.

Enable/disable EZProxy while in Bookends Browser
Click on the bookmark icon to use EZProxy to access web information. Bookends will use the preference settings for the EZProxy address. If there are none entered, you will be asked to provide the information in Bookends Browser. This is handy if you want to mix searches that do and do not go through your university's authentication servers.

Various enhancements and fixes were made to the reference list in the library window
In addition, the dates added and modified are now shown in the form YYYY-MM-DD + time.

Updated database engine

Bookends will import a reference if its URL from the updated PubMed web site is dropped onto the library window
The base URL of this site is "https://pubmed.ncbi.nlm.nih.gov".

Bug fixes
Fixed a bug in citation disambiguation when scanning with an author-date format. Fixed a bug that prevented direct import from Google Scholar if you are using EZProxy. Fixed a bug in Standardize Journal Names. Fixed a bug in the tag cloud search for authors and editors that have periods after initials. When changing a selection in the tag cloud any text in the live search field will be taken into account in filtering references. Fixed a bug in the Links Inspector where clicking on an empty row would deselect all references in the library window. Hyperlinks to unique IDs in the Summary view will only be created if the # in the abstract or notes is followed by a number.



NEW in Version 13.3
(January 3, 2020)
Download


Updates for Catalina
Fixed a problem where some default fonts, such as Times New Roman, weren't recognized as such and were substituted with Helvetica in formatted references. Fixed an issue where the style of literal text in a format (e.g. bold) was not carried through to the formatted reference. Fixed a problem when clicking on PDF text that was highlighted in Papers 3. Fixed a hard crash that occurred when formatting thousands of references as BibTeX.

Import from Google Scholar in Bookends Browser
This feature requires that Google Scholar is configured to export citation information, which is indicated by a link below each reference with the words "Import into" followed by a destination, If you do not see this, use Bookends Browser to go to Google Scholar and click on the preferences icon (3 horizontal bars at the upper left, and then either the word Settings or the gear icon). Check the option to "Show links to import citations into" and select RefMan (preferred), EndNote, or BibTeX as the destinations from the pop-up menu. When you subsequently use Bookends Browser to search Google Scholar, each result will have the link "Import Into Bookends". Click it to import the reference into the frontmost Bookends library. Sometimes Google Scholar has the URL of the PDF. If so, and you have access privileges to the PDF, it will be automatically downloaded.

Improved detection of the correct URL for a reference in a Google Scholar web page

Reference metadata will be imported from a direct search of Google Scholar even if Google thinks you are a robot
In this case the data are scraped from the web page and may not be complete.

Sort groups and folders
Right-click on the groups pane or use the groups pane Action pop-up menu and select "Sort Groups". All groups and folders, including their contents, will be sorted alphabetically.

Finding and displaying attachments is up to 3 times faster
This will be noticeable when you have many attachments.

Formatting references as BibTeX is much faster

New Library of Congress online search
The new search is UTF-8 compliant, meaning that non-Roman (e.g. accented) characters will be returned correctly.

Updated detection and removal of the Adobe PDF Viewer plug-ins
These plug-ins (AdobePDFViewer.plugin and AdobePDFViewerNPAPI.plugin) can cause serious problems when displaying or downloading PDFs in Bookends Browser. Because of increasingly stringent security protections implemented by Apple, Bookends can no longer remove them for you. If detected, Bookends will alert you and offer to show them in the Finder. You can then either trash them or remove them from the Internet Plug-ins folder.

Direct import from Papers 3 will work even if Papers isn't running

Updated "Import From Existing Bibliography" to deal with changes made by CrossRef

Bookends no longer scans documents created with Pages '09 or earlier
Refs -> Scan Open Apple Pages Document will not be enabled unless a more recent version of Pages, version 5 or later, is running.

The super- and subscript metacharacters will be removed from the title when submitting an OpenURL search

PDFs added from the watch folder will not be renamed if their metadata is not found online
You can now tell Bookends to "Rename imported files if metadata are found" in the Configure window. This is the reverse of the previous setting, which was "Don't rename imported file".

Updated the JSTOR import with Bookends Browser to deal with changes made by JSTOR

Renamed Live Search option from "Spotlight" to "Attachments (Spotlight)" to make this search capability clearer

Automatic import of reference from files with uniquely identifying extensions
If you drop a file that has an unambiguous identifying extension Bookends will import the references without asking which filter to use. This applies to files sent to Bookends by other applications, like Firefox, as well. The extensions Bookends recognizes are .ris, .bib, .nbib, .enw, and .ciw. In such cases the current settings for adding the imported references to the Hits List, and if the file should be moved to the Trash, will be used. To change these, use File -> Import References and the configurable import dialog will appear. Import dialog settings are saved even if you cancel the import.

Improved DOI detection in web pages

Simple arXiv searches are by word
This means that if you search for "solar eclipse", references that contain both words will be found, even if they aren't in that order. Boolean searches will continue to search by phrase.

Added the ability to detect and automatically download PDFs from several chemistry journals and the ACM Digital Library

Updated database engine
Fixed a bug that caused a crash when using "cast" in an SQL group.

Bug fixes
Fixed a bug that prevented the creation of PDF comments. Fixed a bug in the Summary view where extra returns were added around styled characters in the abstract or notes and \par would be shown in place of returns. Fixed a bug that prevented styled text information added when editing a notecard to be saved. Fixed a bug that prevented the Browse button in the Attachment dialog from setting the pop-up menu to the selected subfolder. Fixed several bugs in opening of spring loaded group folders. Fixed a bug that could prevent some PDF DOIs from being resolved. Fixed a bug that prevented the last PDF highlight from appearing in the note stream. Fixed a bug in Wi-Fi sync. Fixed an issue that will make importing direct importing of references from Papers 3 more reliable.



NEW in Version 13.2.8
(November 30, 2019)
Download


Updated database engine

Improved update notification
This version does a better job of indicating that a license with two years of free updates has expired and the current update is not free.

Bug fixes


NEW in Version 13.2.7
(October 26, 2019)


Catalina compatibility fixes
Opening PDFs in a non-default app works. Scanning an open Apple Pages document works even when Bookends is not given Full Disk Access. Searching for DOIs in certain PDFs when attaching no longer causes a crash.

When file renaming is done using a format, Bookends will make sure only one period precedes the extension

Bookends can perform BibTeX scans on files with the extension .tex

Changed the keyboard shortcut for "Make Quoted PDF Highlight From Selection" to Control-Shift-Command-Q. The old shortcut, Control-Command-Q, is now used by macOS to lock the screen.

Added a keyboard shortcut for Sync Now: Control-Command-S

A trailing return will be removed when performing Copy Formatted

Improved JSTOR URL detection of older URL schemes when attaching PDFs

Identification of invalid DOIs in web pages is much faster

Only straight quote marks will be output when generating HTML-formatted references

Bug fixes
Fixed a bug where a file's extension was repeated when it was automatically renamed. Fixed a bug that caused an error when doing a file tag search and there were no hits. Fixed a bug where there would be a long delay when trying to access a server that is no longer mounted. Fixed a bug where the attachment pane wasn't updated properly when displaying a text or rtf file. Fixed a bug in Window -> Reset Position where the tops of the Format and Import Filters Manager would be offscreen. Fixed a problem where on occasion the word processor wasn't returned to the front after a scan. Fixed a bug in Find where references could be found and made hits when doing a search for both text and Spotlight when the latter found no matches. Fixed a bug in creating a new standalone reference window when that preference option was selected. Fixed a bug where the author/editor capitalization rules could be ignored if there was no first name and the output was surname last. Fixed a bug in the concise view where the coloring of a file tag was offset by 2 characters. Fixed a bug that caused unnecessary updating of database fields. Fixed a bug that could cause an error when syncing references for which an attachment was modified. Fixed a problem in syncing of groups with iOS when the parent folders have non-Roman names. Fixed a bug in the attachments inspector where the contents of an attached textual (non-image) file wasn't refreshed properly. Fixed a bug that could corrupt a format when the "repeated authors" field was updated. Fixed an issue in HTML markup where replacing a < with its HTML entity prevented the creation of hypertext links. Fixed a bug in the display of attached Mellel documents containing images.


NEW in Version 13.2.6
(September 14, 2019)


Updated the JSTOR importing function to deal with changes made by JSTOR
In addition, when JSTOR provides editors names Bookends will import them.

Updated parsing of Google Scholar URLs to deal with changes made by Google

When you launch Bookends and there's a second copy of Bookends on the network, you will be offered the choice of quitting the remote copy, in which case you can continue to work on the local machine, or the local copy
Previously you had to quit the local copy.

Bookends will include qualifiers when importing PubMed MESH headings (keywords)

Updated database engine

You can permanently remove references from the library itself when in a group, virtual group, or folder by holding down the Shift key when you Delete

Right-clicking an image (not a PDF, which has its own Action pop-up menu option) in the display pane or Attachment tab of the edit pane will offer to Move it to the Trash.
This is in addition to Detach, Zoom In, and Zoom Out.

Backward compatibility
Bookends will no longer convert formats made for, or import files exported from, versions prior to 11.2. Bookends won't offer to convert libraries made with versions 8 or earlier. Bookends no longer creates a special folder to store custom formats made with Bookends 11 or earlier.

BibTeX scans will recognize complex citations where modifying instructions are inserted between the citation beginning and the cite key, such as \citep[see][chap.~2]{smoth2019}
Note that if you are having Bookends insert final citations when you scan, the modifying instructions will be ignored.

Mellel will be brought back to the front after the verifying references process has completed

When attaching a PDF Bookends will look for its DOI on the second page if there is none on the first

When automatically renaming PDFs slashes (/) will be removed from file names
Slashes are allowed in macOS but not iOS.

Bug fixes
Fixed a bug when adding a PDF via the watch folder to an existing reference where it would replace any attachments already there. Fixed a problem where Bookends wouldn't recognize temporary citations in Scrivener footnotes. Fixed a bug where Bookends couldn't find a file inside an attached folder. Prevented an error that could occur when closing the Online Search window when a browser search was in progress. Fixed a bug in the Links Inspector where the comment field was locked when it should be editable. Fixed a bug that could cause text to become temporarily invisible when coloring required BibTeX fields. Fixed a bug where no field got the focus when exiting the Key field while BibTeX citekey duplicate checking is enabled. Fixed a bug in renaming attachments where Bookends would use a space before a random number even when the user asked for underscores in preferences. Fixed an error that could occur when trying to import metadata for some references from CrossRef. Fixed a problem when using tag cloud file tags and the PDF name included a slash. Fixed a hard crash that could occur when closing the library window after using tag cloud file tags. Fixed problems in the Compare References window where changes in the marked or ratings status of references weren't being updated in the database of the UI. Fixed a problem when doing an Autofill From Internet for multiple references at once via PubMed where references weren't updated. Fixed a bug in AppleEvents that could cause a search of some SQL groups to always return 0 references.


NEW in Version 13.2.5
(July 20, 2019)


Bookends code is hardened and notarized
This is in preparation for the upcoming macOS 10.15 (Catalina).

Embed links to web pages in formatted references
This is controlled by the format by the use of < and > punctuation – see the section on formatting in the User Guide for details. Embedding links to external web pages works with Microsoft Word 2016 (version 15.x) or later and Nisus Writer Pro. It does not work with Mellel at this time. It will not work with Pages or LibreOffice.

Global Change -> Standardize Journal Names
This option is enabled if you are using a journal glossary. You can choose to have all journal names found in the glossary be changed to the short name (e.g. J. Biol. Chem.) or the full name (e.g. Journal of Biological Chemistry), and/or have periods removed (e.g., J Biol Chem). It is not necessary to have the same journal name be identical in all corresponding references because the glossary will substitute the required form at the time of formatting. However, some users want uniformity in the library itself and in the Journal Term List.

PDFs can be downloaded automatically from more journals

Updated database engine

Refs -> OpenURL Search will display the results in the library window browser view (lower pane)
This makes it easier to click through links to a PDF and then attach it to the reference. Previously Bookends opened the results in an external browser.

Bibliographies in Word can contain colored text

The "show thumbnails" setting in the PDF viewer will stick when moving between references that do and don't have PDF attachments

Bookends will move a format file to the Custom Formats folder and enable it for you when you drop it on a library window or double click on it

When using Biblio-> Bibliography and sending the output directly to disk, the suggested file name will include the name of the format (e.g. Bibliography (Turabian).rtf"

Bug fixes
Fixed a bug in full screen view where the live search field showed inappropriately when a PDF was on display. Fixed a bug where the PDF lock icon could be shown when the PDF was not locked. Fixed a bug that prevented scanning of BibTeX citations. Fixed a bug when using smart caps SURNAME for formatting. Fixed a bug in QuickAdd that caused searches for ISBNs with hyphens to fail. Fixed a bug that caused hanging indent settings to be ignored when the bibliography contained colored text. Fixed a bug in which the OK button was not enabled when renaming a static group. Fixed a bug in deleting references from a group where Bookends would mistakenly offer to delete them from the library. Fixed a crash in Bookends Browser when checking DOIs with CrossRef. Fixed a bug that could cause an error when searching for a unique id in the Find window.


NEW in Version 13.2.4
(June 22, 2019)


Most Amazon search sites (including Amazon.com) have been removed
Amazon is enforcing a new policy that reduces (throttles) the number of searches that can be performed over a period of time based on the number of sales generated. Because Bookends uses Amazon for obtaining metadata, not referral for sales, this means that Bookends is effectively prevented from using Amazon as a source of metadata. Amazon.de and Amazon.fr are working as before for now and remain. If/when they stop working they will be removed, too.

Google Books is added as source of book metadata when using an ISBN with Quick Add and Autofill From Internet
You can choose between it and Amazon (France) and Amazon (Germany) as your preferred source in preferences, Internet tab. If an ISBN isn't found at the preferred source Bookends will query the other sources until it succeeds or the ISBN can't be found.

Added an AppleEvent that will return the file path of the default attachments folder
This is useful if you want to use AppleScripts to add attachments to references and need to move the files to the default folder.

When launching Bookends after a crash the user will be asked if he wants to open the last-used library
This prevents an endless cycle of crashes if a corrupted library is at fault. Previously, the library would not open automatically after a crash and the user would have to use the Open -> Recent menu to use it.

A lock icon will appear when viewing read-only PDFs and the annotation tools will be disabled
Click on the lock icon to have Bookends unlock the PDF by assigning read/write permissions to the PDF.

Added a workaround for problems caused by some anti-virus software when creating a new library

Bug fixes
Fixed a bug that could cause the Types and Labels preferences to be reset to the factory default when updating to a new version when cloud sync is not enabled. Fixed a bug that could cause text to be invisible in the edit pane when using BibTeX and indicating required fields with color. Fixed a bug in the replacement of an older Word .dotm file with a newer version. Fixed a bug that prevented Bookends from telling you that you can't remove a reference from a smart group with the Delete key. Fixed a bug in handling of the AppleScript command to get the selected references. The PDF highlight marker color updates immediately when the user selects a different one. Fixed several wi-fi sync bugs involving groups. Fixed a bug in cloud sync. Fixed a bug that prevented Bookends from fetching and syncing the PMCID.


NEW in Version 13.2.3
(May 25, 2019)


Automatically obtaining PDFs for PubMed references works again
This function had been broken by changes made by PubMed.

Copy Hypertext Link As Text is a pop-up menu option in the floating citations window

When a PDF from the watch folder is attached to an existing reference the modification date of the reference will be updated

Tab-delimited files exported from Bookends will include the names of attachments

Minor cosmetic changes in the Inspector floating window

Minor cosmetic improvements to the Bookends tab in the Microsoft Word ribbon

Bug fixes
Fixed a problem where the DOI found on a web page had the wrong encoding. Fixed a bug that prevented users from removing a color label. Fixed a bug that prevented Edit -> Copy Hypertext Link as Text from switching to the linked app, if any. Fixed an issue where some menu options were inappropriately enabled when editing a reference. Added more accented characters to the BibTeX conversion table. Fixed a bug that caused the Term List window to be dragged when clicking and holding the Action pop-up menu. Fixed a bug where the old Word Add-in wasn't removed if Word was open. Fixed a bug in the Chicago 17th A format. Fixed a bug that prevented the groups pane from being resized. Fixed a bug that prevented the Link menu from checking the linked app if it was first in the list. Fixed a memory leak that could affect performance.


NEW in Version 13.2.2
(May 11, 2019)


Some global preference settings will be synced via the Cloud
The synced settings are: the default reference Type (Mac and iOS), the names of reference Types and field labels (Mac and iOS), the temporary citation delimiter (Mac and iOS) and separator (Mac), the EZProxy URL (Mac and iOS), PDF annotation colors (Mac and iOS), color label names and values (Mac and iOS), super- and subscript metacharacters (Mac), the floating citations trigger key (Mac), and author and title ignore lists (Mac). We will add more global preference settings in future updates. Use of synced preferences by Bookends for iOS requires version 3.3.6 or later.

Modernized Bookends options in the ribbon for Word 2016 or later/Office 365
The macros that interact with Bookends now appear in their own tab, the Add-ins tab is no longer used.

The menu Refs -> Mark Selected References toggles the marked (hit) status of the selected references
If the first selected reference is unmarked, all selected references will be marked. If it is marked, all selected references will be unmarked.

Updated direct download of PDFs from ScienceDirect to deal with changes made by Elsevier

Updated PubMed web viewer to deal with changes made by PubMed

Perform boolean Spotlight searches for phrases (i.e. text enclosed by quote marks)

Live search for text between quote marks now searches for whole words

New citation delimiter option: (+ +)

Bug fixes
Fixed a bug that could make the library window invisible. Fixed a problem on systems running anti-virus software where the Types and field labels reverted to the factory defaults. Fixed a hang that could happen when highlighting a reference's owning groups and one of the groups was not visible. Fixed a bug that prevented the pop-up menu listing all attachments from appearing at the bottom of the Attachments tab in the reference edit pane. Fixed a bug in Reset Window Position where the library window wasn't the full screen height. Fixed a bug in the display of en dashes in the Format Manager examples and of en dash display in scanned Mellel files. Fixed a bug that could cause PDF tags to overlap when viewed in the Attachments tab. Fixed a bug that could cause an error when saving an edited format. Fixed an issue with Bookends Server where the default formSat was used to generate a bibliography even though a different format was requested. Fixed several bugs in coloring of required BibTeX fields. Fixed a bug that prevented italicized numeric citations from displaying in a scanned Mellel document. Fixed a bug in the registration window display of dates for some countries where the day rather than the month appeared. Fixed a bug where Refs -> Replicate As Book Chapter -> Include Attachments was enabled inappropriately.


NEW in Version 13.2.1
(March 29, 2019)


A new AppleEvent lets you get the selected references in the library window
Example Applescript: set myRefs to selected publication items of front library window.

Restrict PubMed searches to articles for which the PDFs are free for you
The references that are free for you may depend on your current IP address and may differ in different locations (e.g. work vs. home). This setting in the Online Search window applies to both normal and advanced PubMed searches.

Automatic detection and removal of the Adobe PDF Viewer plug-ins
Adobe products can install two plug-ins that provide their own tools for viewing PDFs in browsers such as Safari. These plug-ins are incompatible with Bookends and can result in faulty PDF displays, failure to download PDFs, and even crashes. When you open Bookends Browser or activate Autocomplete Paper, Bookends will check for the presence of these plug-ins and, if found, offer to remove them. If you accept, Bookends will move the plug-ins to the Trash. If you don't accept, Bookends will allow you to proceed but warn you again the next time you run Bookends. Note that removing these plug-ins will have no effect on Adobe Acrobat or Reader.

Set the font size for groups and the note stream in preferences
The font face is not configurable.

When entering a PDF tag, pressing Return or Enter accepts the tag
Pressing Tab accepts the tag and places the cursor in a new empty tag field so you can enter another.

Copy Notecard And Citation will place the plain as well as the styled text in the clipboard because some apps only recognize the former

The reference list sort is by first column then title if there is no date column
As before, if there is a date column the sort is by first column/date column/title column.

Faster population of fields in the reference edit pane

Use the keyboard shortcut Shift-Command-M to mark (make hits of) the selected references

Improved UI for changing field labels in preferences
Selecting a row in the Type list automatically fills out the corresponding fields in the field label list.

Online Search of arXiv will retrieve the id and import it to the pages field

A slightly darker yellow will be used for groups that are selected when highlighting groups a reference belongs to

Added a delay in automated PubMed searches with multiple queries to deal with new restrictions imposed by PubMed

Bug fixes
Fixed a bug that prevented hypertext links into Bookends from other apps and the browser bookmarklet from working. Fixed a bug in adding text to a reference via AppleEvents. Fixed a cosmetic bug where the progress window didn't update properly when removing orphaned attachments or exporting references as XML. Fixed a bug in Autocomplete Paper from arXiv. Fixed a bug where the contents of the Notes field were not completely removed when moving from one reference to another. Fixed an error that could occur in Online Search when switching too quickly between references found on Google Scholar. Fixed a bug in Wi-Fi sync. Fixed a bug that prevented saving import filter searches. Fixed a bug that caused a right-click on an import filter saved search to fill out the search fields. The online source icon updates properly when a new site is selected. Fixed a bug in a Google Books search where the cover art display wasn't updated when there was no picture. Fixed a bug that prevented Autofill from importing text to a field that already contained styled text. Fixed a problem with some Japanese Word documents where the ending number of a citation span wasn't output. Fixed a bug in floating citations where dragging a row would actually drag the entire window. Fixed a bug in citekey generation that would cause a disambiguating letter to be inappropriately added. Fixed a bug that caused PDF tags to overlap when the library window opened with the PDF pane showing.


NEW in Version 13.2
(February 18, 2019)


Bookends is AppleScript-able
Bookends has an AppleScript dictionary with properties and commands that let you retrieve and set reference metadata, add and populate groups, fetch formatted references, and more. See the User Guide for details. Note that this supersedes the previous AppleScript mechanism, which is retained for backward compatibility but is no longer under development.

Place cited pages inside a final citation
In previous versions Cited Pages were always placed at the end of the final citation. Now, however, you can insert them anywhere in a custom format by placing the @ character in the Field Order field where you want them to go. For example, if you create a format with the order a. t. @ (d). Bookends will replace the @ with the Cited Pages you have entered in the temp citation. Bookends will add any pre- and post-characters specified for Cited Pages in the format definition (for example, "p. "). Using the example above this might be output as: author. title p. 12 (2019). If you use such a format and do not specify Cited Pages in the temporary citation, the @ character will be removed in the final output. Note that when you use such a format outside of scanning (i.e. it is not possible to add Cited Pages), the @ will be replaced by @@ to indicate where the Cited Pages would be placed when provided.

The format symbol for Unique ID has been changed to = (was @, which is now used for Cited Pages)

Continuously highlight a reference's owning groups
If this option is selected in preferences (Lists tab), Bookends will always highlight in yellow any groups to which the selected reference belongs. The default option is to show such groups only when Option-Shift is pressed.

Updated importing from JSTOR to deal with changes made by JSTOR

Cloud sync will be halted and the user notified if Bookends detects that the library file is in a file sync folder (e.g. Dropbox, iCloud Drive, or Google Drive)
Combining Bookends cloud sync (which updates just the metadata that have changed) and file sync (which uploads/downloads the entire library) can cause problems. The solution is to move the library file to another folder (the Bookends default is ~/Library/Application Support/Bookends).

Added the option to create temporary citations as Author, Date, PMID
This may be useful to those in biomedical professions who are writing papers with collaborators using EndNote, which should recognize these citations. If a reference does not have a PMID entered the Author and Date will be used.

Bookends will replace a / with a - if necessary when naming a library for sync on iCloud Drive

Added Shift-Command-L keyboard shortcut for Copy Hypertext Link in the floating citations window

The Pages script "Find in Bookends" has been removed because Apple Pages no longer supports this AppleEvent functionality

If the recently viewed list is corrupted, Bookends will empty it rather than generating an error that prevents the library from being opened

Added an option that tells the Watch Folder to leave an attachment's name as is when moving or copying it to the default attachment folder
This setting is in the Watch Folder -> Configure window.

Formatting a reference that has a field with an unclosed superscript or subscript will no longer cause the baseline of all subsequent references to be affected

Bookends Browser should now load URLs that contain accented (Unicode) characters

Added @conference as a valid BibTeX reference Type

Slashes (/) are not allowed when renaming attachments. Slashes are not allowed in iOS file names

If Bookends can't display an attachment it will suggest you double click on the (empty) display pane to open it in a compatible app, if available

You can now import the Epub date from PubMed by using the tag DEP in the import filter

You can email references and attachments via the Airmail app

Bug fixes
Fixed a bug in Mellel scans where the & metacharacter was removed during a Verify and the instruction (exclude authors and title) ignored. Fixed bugs that would cause the focus to move to the reference list after editing keywords and move to the authors field when clicking out of live search box to an editable field. Fixed a bug that incorrectly recreated the formatted view if the reference was edited while that display pane was open. Fixed a bug where citekeys generated by Bookends might not sync via the cloud. Fixed a situation where the floating citation window could be off screen if it had been used on a second monitor that was then disconnected. Fixed a bug that would cause a malformed final citation group when the author was being placed in front and the format sorted the citation group. Fixed a bug in Sente XML import where the first character of a comment could omitted. Fixed a bug that could cause the Online Search window to appear more than once in the Windows menu. Fixed a bug in drag-reordering of groups. Fixed a bug where styled text information in a format's quoted text was ignored when the output was marked up as HTML or BibTeX. Fixed a rare bug in sorting of the reference list. Fixed a bug with saving bibliography generation defaults from the "export formatted references" dialog. Fixed a bug in Quick Add where some valid PMIDs were not found. Worked around a problem where opening a library caused a "-47" error when running antivirus software. Fixed a bug in Option-Shift group highlighting where the wrong item would be highlighted if a preceding folder was opened and then closed. Fixed a bug in cloud sync where spurious references could be added to the library. Fixed a bug in Mellel Synchronize Databases where references would be imported from a document even if they were already in your library. Fixed a rare error that could occur when saving text from the concise view field.


NEW in Version 13.1.5
(November 23, 2018)


Updated database engine

Bookends will display Google's reCAPTCHA page when Google Scholar thinks you are a web robot
Google Scholar will sometimes think you're a web robot based upon your search and downloading activity and refuse further service. If this happens when you're searching in the Online Search window, Bookends will show the Google confirmation page with a reCAPTCHA asking you to confirm you're not a robot. Once completed your search rights will be restored, although the time this takes is variable and can be up to 24 hours.

When importing malformed XML, Bookends will alert you and show the lines generating the error
This information may help you correct the XML in a text editor or, if exported from another reference manager like Sente or Papers, delete the reference whose metadata is incorrectly represented.

Bookends will prevent duplication of keywords in a reference

Added a "include attachments" option when replicating a reference as a Book Chapter
This is useful, for example, if you have the PDF of the entire book and you want each chapter to have that as an attachment.

Increased the timeout setting for Bookends Server to deal with problems with network latency

HTML-formatting of references has been improved and is now compatible with XHTML

The "generate bibliography" setting in the Scan dialog is remembered throughout a session
It is always "true" when Bookends is relaunched.

The upper limit of references that Bookends will detect on a web page in Bookends Browser has been increased to 100

The menu item "Synced iOS Device Info…" has been renamed "Wi-Fi Synced iOS Devices…", and is disabled if there are none

Quote marks will be removed from PDF names when they are being automatically renamed by Bookends

Export Attachments is a right-click option if any selected reference has attachments
Previously this function was only available if the first selection had attachments.

Bookends won't show a recently opened library in the Open menu if it was moved to the Trash

Bug fixes
Fixed a bug in BibTeX export where a close instead of an open smart quote could be output by mistake. Pressing Option when invoking Copy Citation or Copy Formatted copies to the clipboard but no longer switches to a linked word processor. Fixed a bug in EndNote XML import where the URL could be imported into the wrong field. Fixed a rare bug that could cause an error if you changed a field label and then did a live search on that field. Command-+ and Command-- keyboard shortcuts now zoom in or out PDFs displayed in the edit pane's attachment tab. Fixed a bug that prevented Bookends from importing titles beginning with a superscript from PubMed. Fixed a bug where the Hits menu wasn't enabled after a Spotlight live search.


NEW in Version 13.1.4
(October 13, 2018)


Bookends 13.1.4 requires OS X 10.10 (Yosemite) or later

Import references from multiple files at once with drag and drop
If you drag and drop more than one text file onto the library window Bookends will import the references contained in all. Note that the references in each file must be in the same format (e.g. RIS, PubMed, XML, etc.) or some of the references will not be imported. If any of the files is not a text file Bookends will offer to attach them all (the previous behavior).

Styled text information in the Abstract and Notes will be preserved when importing EndNote XML files even if more than one EndNote field is combined

When attaching a PDF to an existing reference that is showing in the list (e.g. in a group), Bookends will not change the group selection to All

Bookends will generate a more useful error notification when the PubMed network connection is dropped
PubMed is having intermittent connection problems that affect some users.

Export PDFs attachments with or without annotations via the File menu or by using a right-click

Copy Hypertext Links from the floating citations window
Note that many apps, including Word, do not accept hypertext links.

The rarely-used non-editable PDF viewer has been removed
PDFs are now always displayed in the more versatile PDF annotation view.

Improvements were made in the way AppleEvents are handled in macOS 10.14 (Mojave)

Adding terms to references via the Term List window will not bring up a confirmation dialog
A notification will be sent after the terms are added.

The floating citations window height will adjust accordingly if "always show scrollbars" is selected in System Preferences

Bug fixes
Fixed a bug where some Google Scholar searches could cause an error message. Fixed a bug where the reference edit pane might not scroll back to the top correctly when the window height was increased. Fixed a bug in preferences where the superscript character was shown as = when it was actually set to None. Fixed a scanning error that could occur in some situations when a reference has no author or editor. Fixed a bug that prevented the online search window from showing the references found if a library window was not open. Fixed a bug where pressing Command-+ on some non-US keyboards would not zoom the PDF. Fixed a spurious error that could occur when trying to automatically import metadata from arXiv. Bookends Server Query searches are once again case-insensitive.


NEW in Version 13.1.3
(August 25, 2018)


Use floating citations to copy the attached file (PDF) to another application by dragging its icon

The floating citation window will appear when the active application is in full screen mode

The setting "No Enclosing Delimiters" was added to the floating citations window
If checked, when performing a Copy Citation Bookends will not add place citations delimiters (typically curly brackets) around the temporary citation it creates. This setting is saved between launches, and may be useful to some people using BibTeX who create the required citation delimiters themselves and simply want the cite key to be inserted.

Updated the JSTOR parser to deal with changes made by JSTOR

Add arXiv references with QuickAdd
The arXiv id must be entered in the form: arxiv: followed by the id. Example: arxiv:astro-ph/0405136

PDFs with newly created annotations will be saved before being exported or emailed

The modifier key used to trigger floating citations has been changed to Control for new installs
If you've already installed Bookends 13.1.2 this must be changed by you in preferences, Scan & Bib tab.

Bug fixes
Fixed an issue where the modifier keys on the right side of the keyboard could not be used to call up the floating citations window. Fixed a problem where Control-clicking on a reference in the floating citations window did not activate the hierarchical menu. Fixed a problem where a spurious SQL error could be thrown by the floating citation window when working in another application. Fixed a bug that could cause BibTeX imports to hang. Fixed a bug where Shift-Command-O failed to open the attached PDF when in the standalone reference window Attachment tab. Fixed several problems with the display of webarchives in the lower pane. Fixed a bug where after removing duplicates the number of references in the database shown at the bottom of the library window could be incorrect. Fixed a rare problem where a PDF could be duplicated when performing an Autocomplete Paper. Fixed an error message that occurred when Crossref returned a file type of nil. Fixed a bug in import where the wrong Type was assigned if there were multiple possible comma-delimited tag names specified in the import filter. Fixed a crash that could occur when responding to a link sent from Highlights.


NEW in Version 13.1.2
(July 28, 2018)


Introducing Floating Citations
With floating citations you can search your reference library, read PDF attachments, create and insert temporary citations, and more, without leaving your word processor. To use floating citations, Bookends must be running and a library must be open. The floating citation window is triggered while in another application (typically a word processor, but it can be Scrivener, DEVONthink, Tinderbox, or any other application) by double tapping a modifier key. This feature can be enabled/disabled in preferences (Scan & Bib tab), where you can select the trigger key you prefer: Shift, Control, Command, Option, or Caps Lock (Shift is the default). Refer to the User Guide (Help menu) for complete details on the use of floating citations.

A preview of the temporary citation Bookends will insert updates in real-time as you enter modifiers in the Copy Citation And Modifiers dialog

Use Quick Add to import multiple references at once
The reference identifiers (DOIs, PMIDs, ISBNs, or JSTOR URLs) must be separated with commas.

Import multiple references at once by dragging and dropping a single DOI or a list of DOIs on the library window
DOIs in a list should be separated by Returns or commas.

Bug fixes
Fixed several circumstances where "et al." was not italicized properly. Fixed edge cases where a space could follow or precede the open/close parenthesis in the MLA format.


NEW in Version 13.1.1
(July 7, 2018)


Display both citation and bibliography styles in the formatted display pane
The pop-up menu that holds the names of the enabled formats when you "view formatted" has an option to show the bibliography output only (default) or the citation and the bibliography outputs. You can also switch between these options with a right-click in the view formatted display pane itself. The citation output will be shown first, then the bibliography output. This is most useful for displaying custom citations (e.g. Chicago, Turabian, etc.). Superscripted numbers (e.g. Nature format) will be shown without the superscript.

PDFs automatically imported from the watch folder will be attached to an existing reference if the DOI, JSTOR stable URL, or the arXiv ID matches

Move references from one static group to another with drag and drop
If you drag and drop from one static group to another with the Option key held down, Bookends will remove it from the original and add it to the destination (without the Option key the reference would have been copied and exist in both groups). This may be useful in cases where a reference's status changes and you want to move it between mutually exclusive groups, such as Read vs. Unread or In Preparation vs. Published.

Get PDF from arXiv works even if the reference only has the URL for the arXiv abstract, not the PDF

Proofreading Word documents preserves quoted text and cited pages in the temporary citations

The minimum database cache has been increased to 20 MB

More accented characters were added to the BibTeX conversion table

Bug fixes
Fixed an error message that could be thrown if Bookends Browser couldn't parse a web page. Fixed a crash that could occur when autofilling a reference from Amazon and downloading the associated jpg. Fixed a bug that prevented the "Find in PDF" keyboard shortcut (Option-Shift-Command-F) from working. Fixed a bug in Bookends Browser that could cause a spurious error message to be shown. Fixed a rare bug that could cause a blank error dialog to appear when opening preferences. Fixed a error that was generated if the identifying information in the quick add dialog contained spaces. Fixed a bug where scanning a BibTeX file with an empty citation caused the scan to terminate at that point.


NEW in Version 13.1
(June 9, 2018)


Bookends Browser uses Keychain to save and autofill login name and password fields
When you log into a site Bookends Browser will offer to store the name and password in Keychain. If you revisit the site you will either be asked to allow Bookends to autofill these fields, or if you have already given permission to allow this always, the login fields will be populated automatically for you. You can toggle this feature on/off in preferences (Internet tab). The saved names and passwords can be viewed and deleted in Keychain Access. Note that this feature will fail in some cases where scripts are used to display the login fields or in which the server actively empties the password field. In these cases you must enter the information manually.

Added 20 more Unused Types
The maximum is now 40.

A new AppleEvent (ADTG) lets you add references to an existing static group
Details of how to use this AppleEvents are in the User Guide.

When using the ADDG AppleEvent to add a new group, Bookends will return the name of the group added
This is helpful when you specify a name that is already in use and Bookends appends a number to make it unique.

Pressing Return or Enter while entering a PDF tag will save it and automatically enable a new tag entry field so that you can enter another tag

The internal database cache maximum has been increased to 200 MB

If a PDF is corrupted, Bookends will offer to show it in the Finder so that you can delete it

Cosmetic improvements in the Bookends Browser window

Bug fixes
Fixed a bug in arXiv import where some words in the Abstract could be run together. Fixed a bug where the window could not be dragged by clicking in the toolbar after clicking on a PDF in the edit pane Attachments tab. Fixed a bug where applying a new field label to all Types only worked for the selected Type. Fixed a bug in disambiguating BibTeX keys when the author's name is in capital letters and there is no year.


NEW in Version 13.0.9
(May 12, 2018)


Back and Forward commands have been added to the PDF viewer
This means that you can go back and forth between a link and the location it takes you to in the PDF.

If Automatically Resize is inactive, a PDF's zoom level will be remembered when switching between references

New AppleEvents have been added that let you get and set the contents of multiple reference fields at once, set reference Types, and get the Bookends version number
Details of how to use these AppleEvents are available in the User Guide.

Bookends will import the Status field in a Sente XML file to User19

Option-clicking on the Online Search button forces Bookends to open the Online Search window with Bookends Browser selected

Updated automatic downloading of PDFs from PubMed Central to deal with changes made by PubMed

Window -> Reset Window Position can be applied to any window that appears in the Window menu
This is useful for those with multiple screens where for some reason a window's title bar may not be visible. For non-library windows the position will be set to the top left of the screen.

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.

Updated Open PDF with PDFPen to work with currently shipping versions of PDFPen

Bug fixes
Fixed an erroneous error message you could get with reindexing or rebuilding a library. Fixed a bug when saving an SQL search for the fields Type or Pages. Fixed a problem with automated PubMed search where some searches failed to return any results when they should. Fixed an issue where searching some PDFs for DOIs could result in a crash. Fixed a bug where a PDF in the watch folder could be attached to the wrong reference if the extracted DOI was incorrect. Fixed a bug where locating an attachment that resided on the top mounted volume and not in a subfolder would result in an error. Fixed a bug in Term Lists where after a drag and drop all items would be pinned. Fixed a bug in the Unmatched Citation window where clicking Go To Ref would show the wrong reference. Fixed a regression introduced in the last update that could cause Bookends to hang on launch if it couldn't find a previously-used server.


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 thrown 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.