NEW in Version 12.7.3 (July 14, 2016)

New file structure for preferences
The new preference file, called Bookends Preferences and stored in the ~/Library/Application Support/Bookends folder, is much smaller than the old, will not grow in size over time, and is resistant to corruption. Existing preferences as far back as Bookends version 11.0 will be converted to the new schema automatically. If you are upgrading from Bookends 10.x or earlier, preference settings will be reset to the defaults.

Find a group
Use the Action pop-up menu under the groups pane or click on the group list header to search for a specific group. If a match is found Bookends will select that group and scroll to it. If you type in only a partial name, Bookends will search for a group that begins with those letters and select the first one it finds. You can't search for the three mandatory groups: All, Hits, and Attachments.

Improved single column reference list
Bookends remembers the field the list is sorted by when you click on the column header to toggle between descending and ascending sorts. Cosmetic changes.

Improved drag visual feedback
The textual content in the drag of items in the reference list will be displayed (e.g. either the temporary citation or, if the Option key is held down, the formatted reference). The pdf proxy icon will be displayed when it is dragged. Previously, only the rectangular outlines of these items were displayed.

Improvements to OpenURL
Bookends now supports arguments that specify the DOI or PMID: rft_id=info:doi/ and rft_id=info:pmid/, respectively.

Bug fixes
Fixed a bug in Autofill From Internet that uses the ISBN where an editor's name was missed. Fixed a bug where some in-text citations could be missed when scanning a NWP document that as pictures. Fixed several bugs in formatting that affected sorting and numbering of references in a bibliography. Fixed a bug that prevented an online search from being performed if you selected the terms from the search history pop-up menu while the search button was disabled. Fixed an issue that caused an error to be thrown when scanning with certain formats. Fixed a bug that could cause an error when loading preferences. Fixed a bug in the default field settings for the Newspaper Type. Fixed a bug that could cause edited format settings to be saved to the wrong Type if the Type pop-up was used before the information had been saved.

NEW in Version 12.7.2
(June 18, 2016)

The way that format files are created, used, and saved has been entirely rewritten
As a result, any format you create or edit in 12.7.2 cannot be used by older versions of Bookends. This means that if you use Bookends on more than one Mac you should update to 12.7.2 on all of them. There are many advantages to the new format files, being much smaller, faster to load and execute, much less likely to become corrupted, and insensitive to anti-virus software.

Swap the position of half-width fields in the reference edit pane
Command-drag and drop the label of one of a pair of half-width fields on the other to swap positions. The pairs are Authors-Editors, Journal-Volume, and Pages-Date.

When importing directly from EndNote, Bookends will ensure that attachment names are unique

Changing the reference sort status in preferences will be reflected immediately in the library window

If the path to the custom folders becomes invalid, Bookends will revert to the default location

Bug fixes
Fixed a bug that could cause a malformed URL error to be thrown with some advanced PubMed searches. Fixed a bug that could cause an error with some arXiv searches. Fixed a problem with arXiv boolean searches, which once more work. Fixed an error that could be thrown if you Rebuilt a library twice in a row. Fixed a bug in downloading cover art from Amazon when autofilling an ISBN. Fixed a bug that could cause an error message when declining to convert a very old Bookends database to Bookends 12. Fixed a bug in Go To URL where Bookends would ignore the selection and use the first reference in the list.

NEW in Version 12.7.1
(May 21, 2016)

Improvements to Database Maintenance -> Rebuild and Repair
If these operations are successful, the original library will be moved to the Trash with a date and time stamp added to its name. The newly rebuilt or repaired copy will be given the name of the original, making the entire process transparent to you. If there are problems, the original file will be left where it is and you'll find the rebuilt or repaired version in the same folder.

Integration with Manuscripts
Manuscripts ( is a word processor that handles its own formatting of references and bibliographies. If Manuscripts is selected as your linked word processor, Copy Citation will send the reference information in a form that Manuscripts can convert to its internal citation scheme. In addition, Manuscripts can now request reference metadata from Bookends (please see Manuscripts documentation for details). These features require Manuscripts v1.1.3.

Improved AppleEvent support
If you use an AppleScript to retrieve formatted references (the GUID event), you can ask that the references be returned as EndNote XML instead of in a formatted form. In this case a request to return the information as RTF will be ignored.

Online Search has been upgraded to use the HTML/1.1 protocol

The boolean setting (AND/OR) for how to combine search results when multiple are selected is remembered between launches

Bookends can use a DOI in any field to find the reference online
If you have one or more DOIs in any field in the edit pane (e.g. Keywords, Notes, the DOI field, etc.), right-clicking on that field will bring up a list of the DOIs that you open in your browser. Each DOI must be on its own line.

Improved single column reference list
The field used to sort the list is shown in the list header. You can now sort by Rating.

Italics in book titles will toggle to plain text if the format calls for the field to be italicized

The extension .ris will be added to a file exported as plain text using the RIS format

Improved detection of keywords when importing from PubMed via Online Search

Bug fixes
Fixed an issue where a Rebuilt synced library would perform an unnecessary cloud sync when it was closed. Fixed a problem where a DOI in a PDF could be mistakenly found on PubMed and the wrong metadata imported. Fixed a spurious error that could occur when checking for a new version. Fixed a bug that could cause an error when syncing with Bookends On Tap. Fixed an error message that could appear after doing an autocomplete paper using Web of Science. Fixed multiple issues with Bookends Server. Fixed an issue where reference sync status was included when copying a reference from one library to another. Fixed a bug where Autofill From Internet could increment the disambiguating letter in the Key field if BibTeX was enabled. The date modified will not be changed when dragging a reference from one library to another. Fixed a bug that could cause an error when using Global Change -> Modify PDF Tags. Fixed a bug that in rare cases could cause a spurious number to be added to a citation date during disambiguation when formatting. Fixed an issue where importing many references from the watch folder using a slow Internet connection could have unpredictable consequences. Fixed a bug where drags from a Term List were not being displayed in the reference field. Fixed several bugs dealing with formatting metatypes. Super- and subscripts will render properly when sending a bibliography to disk as styled text.

NEW in Version 12.7 (April 23, 2016)

Sync reference libraries via the cloud
Bookends uses iCloud Drive—all you need is your Apple ID and password to log in, then you don’t need to think about it again. Refer to the User Guide (Help menu) for instructions on setting up cloud sync. Cloud sync requires OS X 10.10 (Yosemite) or later.

Sync new or edited formats, import filters, and journal glossaries in the cloud
Bookends creates “custom” folders for newly created or edited formats, import filters, and journal glossaries. Their default locations are in your user Library: ~/Library/Application Support/Bookends/. You can cloud-sync these files between computers by moving them to the folder created by a cloud storage and backup service such as DropBox, Google Drive, Microsoft OneDrive, etc. On each computer where you use Bookends, go to Bookends preferences (General tab) and tell Bookends where these sync-service folders are on the local drive. In that folder Bookends will create a new folder called Bookends (if it doesn't already exist) and place the custom folders in it. Bookends will use that folder to save or access any custom files. Note that you must allow read/write permissions to the shared folder or you will get an error when Bookends tries to save to it.

The old mechanism for syncing Bookends databases has been removed
If you are using a pre-Yosemite version of OS X, you can sync libraries via a file-sync service like iCloud Drive, Dropbox, Google Drive, Microsoft OneDrive, etc.

Refactored DOI detection in Bookends Browser
In addition to DOI detection being faster and more accurate, metadata will be imported from PubMed when possible.

Improved DOI detection in PDFs

Display author first names as initials in the reference list
This option is set in preferences (Lists tab).

Italicized words in a title will toggle to plain text if the format calls for an italicized title
For example, if your format outputs titles in italics and there is an italicized species name in a title, that name will be output in plain text and the rest of the title in italics.

Importing from Google Scholar will work when you have set the language in Google Scholar to Turkish

The arXiv id will be imported into User1
If you are using this field for the BibTeX key, in the arXiv import filter position the tag "arXiv:" in front of another field to hold this id.

If TeX markup is enabled, smart open and close apostrophes will be converted to ` and ', respectively

When using Bookends Browser, Command-] and Command-[ will move forward and back, respectively

Updated Google Scholar search to deal with changes made by Google
Imported references will once again represent the best metadata Google Scholar has.

Improved retrieval of conference proceeding metadata from CrossRef

Bookends will use an en dash rather than a hyphen in a citation group with a sequential range of reference numbers

Modified formats will be copied, not moved, to the Custom Formats Folder
This means that if you want to revert from an edited version of a format to the version we distribute, all you need to do is delete the format in the Formats Manager (select it in the Formats Manager and press the Delete key) and the original format will be shown. Formats that are in the Custom Formats Folder are shown in bold.

Global Change -> Modify PDF Tags has an updated UI

If an attachment or library is on an external volume such as a server, Bookends will not attempt to mount the volume if it's not already available
Trying to mount an unavailable volume can result in an apparent hang.

Improvements in the generation of BibTeX keys
If you have told Bookends to warn you if a key is not unique and also have asked Bookends to create keys when importing, Bookends will simply create the keys when importing without asking for every non-unique key field. If you have more than 26 references with the same base key (author + year) Bookends will use as many lowercase letters in the key as are necessary to disambiguate them. The key field will be disambiguated if necessary when duplicating a reference.

Limit the length of the file names Bookends suggests for attachments
Limit the length of file names suggested for attachments by Bookends. This is useful if you have Bookends automatically rename attachments. This value is set in preferences (General tab) and the range is 20–200 characters (excluding the extension).

Added smart quotes for Polish
Set in preferences (Scan & Bib tab).

Citation identifiers in Sente XML files will be imported into the User20 field
This will make it possible for you to scan documents that have temporary citations inserted by Sente.

Bookends will ignore images in notes when importing references from Sente XML

Made changes to the Bookends Browser JSTOR parser to deal with changes made by JSTOR

The update notification dialog is much more informative
This will be used to notify you of future updates.

Detection of accented capital letters for services such as small caps is much improved

Drag a browser's PubMed reference link onto a static group to import to that group

Remove a PDF Finder tag associated with a library
This allows you to remove incorrect tags (e.g. typos) and tags you no longer use.

If you use a custom reference Type whose name contains the characters "[Book]" or "[book]", Bookends will enable the Refs -> Replicate As Book Chapter menu item

Bug fixes
Fixed a bug that could in some cases cause a crash when manually removing duplicates. Fixed a bug that could cause a crash when importing a tag beginning with an asterisk. Fixed a bug in drawing the Term List pushpin on Retina displays. Fixed a bug that prevented Refs -> Insert Date from working in the Additional Fields tab. Fixed a bug in Autocomplete Paper using Google Scholar where some search characters could cause the search to hang. Fixed a bug in which the Type column in the reference list where there are multiple selected lines was not updated immediately after a global change. Fixed a bug where some characters could be output as UTF-8 even though BibTeX conversion of Unicode to TeX was enabled. Fixed a bug where the "Generate a bibliography" checkbox could be disabled when doing a Mellel scan. Fixed a bug that could cause an error to be thrown when importing an existing bibliography using CrossRef. Fixed a problem where the Word 2016 AppleScripts were not installed when the user's machine didn't have an Application Scripts folder. Fixed a bug that could cause a hang when importing some MARC records. Fixed a bug in searching notecards for character strings enclosed quote marks. Fixed a cosmetic bug in File -> Go To URL where the online search window controls might not be rendered properly. Fixed a bug that prevented windows from being moved to the top of the screen when System Preferences -> General -> Automatically hide and show the menu bar was checked. Fixed an issue with RIS imports where the starting and ending pages numbers could be reversed.

NEW in Version 12.6.5 (January 30, 2016)

Quickview of notecard contents
If a notecard contains more text than can be displayed at once, move the mouse over it with the Option key held down. The entire notecard (or as much as can be displayed on the screen) will be shown.

Improved Sente XML import
Bookends will reduce multiple Returns in a single quote or comment to one so that they appear in one notecard in Bookends, and will convert HTML entities to normal punctuation. If there are two consecutive Returns the second will be replaced with a space + Return to maintain the line spacing in a Bookends notecard.

Bookends looks at the first and last page of a PDF for the DOI when attaching

Improved detection of references in a web page by Bookends Browser

The setting in Biblio -> Bibliography for where to send the bibliography (window or disk) is preserved between launches

Updated File -> Import From Existing Bibliography to deal with changes made by CrossRef

Edit -> Copy As Hypertext Link will switch to a linked application and try to paste in the link

Bug fixes
Fixed a bug in changing columns with a right-click that could occur when the reference list was scrolled horizontally. Fixed a bug in single column view that caused an entry to look empty if you changed its color label. Fixed some issues that could cause Autofill From Internet to fail to retrieve information from PubMed. Fixed a problem where a BOM at the beginning of a UTF-8-encoded file could cause Bookends to ignore the first reference when importing. Fixed a number of problems that could arise when there is a Label column in the reference list. Fixed a bug where the rating stars were not updated properly in the reference editing pane.

NEW in Version 12.6.4 (January 2, 2016)

The number of references imported will be reported with a notification

Words in the Concise view or the Online Search window that match a search are shown as black on a yellow background
Previously, the color of the letters was changed to red.

Menu option Refs -> Mark -> Mark Selected References menu
This is similar to Shift-clicking on the checkbox of a reference or right-clicking on a reference when more than one is selected.

In a format, output the date a reference was added to the library
Use the letter w to represent this information.

Improved import of Sente XML web citations

Show text of a color label in the library window reference list
The text can be edited in preferences.

Bug fixes
Fixed several bugs that could cause window illegal cast exception errors to be thrown. Fixed a bug in author-date citations with condensed years where a differentiating lowercase letter after the year was omitted. Fixed a bug in Term Lists that could prevent filtering from working properly. Fixed an issue in El Capitan where some progress windows appeared in black. Fixed a bug in Flatten Group Hierarchy that prevented folders from being emptied. Fixed a bug that could hang an unscan if a temp citation has spurious second open curly bracket before the closing curly bracket. Fixed an encoding problem that could occur when doing an Autocomplete Paper with Google Scholar. Fixed a bug in Sente XML import that prevented multiple attachments from a single reference from being imported. Fixed a bug in scanning Pages documents were temp citations in the body of the text were sometimes not found. Fixed a problem where "find in this reference" would not work if the reference list had the focus. Fixed a bug in Autofill From Internet -> This Field so that it no longer autofills all fields. Fixed a bug that could cause the Find sheet to open in the wrong window. Fixed an error that could happen when dropping an attachment on an empty library window.

NEW in Version 12.6.3 (December 5, 2015)

If a word in the live search box is found in a notecard, the word will be displayed in red

Obtaining PDF tags is faster
This is especially noticeable if you are using the tag cloud to show attachment tags. Because each PDF has to be surveilled, however, there will still be a noticible delay if you are creating a tag cloud from thousands of attachments, whether they have tags or not.

Bookends will display the text of attached .docx files
The unformatted text will be shown.

When importing Sente XML, a Report's "publicationTitle" field will be mapped to the Bookends Title field

The path used for attachments in exported EndNote XML has been changed to improve interoperability with other reference managers

Bug fixes
Fixed a bug that prevented the watch folder from working. Fixed several problems with groups that could cause some groups to be hidden. Fixed a problem where a reference added to a group in Bookends On Tap was not added to the group in Bookends after syncing. Fixed a bug where the tag "[doi]" was imported from PubMed into the DOI field. Fixed a bug in "Flatten Group Hierarchy" when dealing with smart folders. Fixed a problem that could cause reference imports into DEVONthink Pro to time out. Fixed a bug in that could cause the wrong import text encoding to be used when importing a reference.

NEW in Version 12.6.2 (November 15, 2015)

Smart folders (nested smart groups and more)
A smart folder is actually a smart group that can contain other groups and folders. If a smart folder has no content, clicking on it is the same as clicking on a smart group. However, if you have placed other groups inside it, when you click on the smart folder all the searches it contains will be executed. The result will be an AND or and OR of all the searches, depending on your setting in the Action pop-up menu beneath the groups pane (also accessible with a right-click in the Groups pane). This is a powerful feature that lets you nest searches. And if you open the smart group by clicking on its disclosure triangle, you can click on any of the groups or folders it contains to perform just that subset of searches. Note that smart folders, just like normal folders, do not sync with Bookends On Tap.

Make Quoted Highlight From Selection
This option, available in the PDF Action pop-up menu in the lower display pane, will highlight the selected text and add metadata to it: the page (e.g. @5) and the text as a quote (i.e. preceded by a >), which will be displayed in a notecard. Press Return or Enter immediately after performing this command to add to or edit the notecard. Be aware that the contents are stored in the PDF, not the Bookends database, and so can have multiple consecutive Returns. This replaces the older option "Make Quoted Note From Selection".

If you select a PDF highlight or note and the note stream is visible, Bookends will select the corresponding notecard

Set default PDF highlight color
Set this value in the PDF Action pop-up menu, or by right-clicking on the color indicator in the PDF toolbar.

Malformed URLs will be ignored when importing XML

Improved import of DOIs from BibTeX text files

If you omit "http://" in a Bookends Browser URL, Bookends will add it when doing a search

Right-click on a picture attachment to zoom in or out

Bug fixes
Fixed a bug in the notecard Find in PDF function that could prevent quoted text from being found. Fixed several problems with the display of picture attachments in the standalone reference window.

NEW in Version 12.6.1 (October 24, 2015)

New scripts for Word 2016
These scripts will be automatically installed if you have Word 2016 installed on your Mac, and will appear in the Add-ins tab in the Word ribbon. If for some reason they are not installed you can do that manually, the scripts and instructions being available in ~/Library/Application Support/Bookends/Scripts for MS Word. Note: these scripts are a temporary solution. Microsoft is developing a new mechanism for adding third party add-ins to the ribbon, and when it is available we'll transition to it.

Many enhancements in the handling and display of PDF annotations in the note stream
(1) If a line in a notecard begins with >, Bookends will consider it to be quoted and display it as indented text in gray to indicate that fact. (2) New menu option: Make Quoted PDF Note From Selection. When you select text in a PDF, this option will create a new note (in the PDF) and begin each line with > to indicate that it is quoted text. You can add comments on the line immediately following the last line of quoted text. (3) New menu option: Highlight Selected Text and Make Bookends Notecard. This will highlight the selected text and import it into Bookends as a quote. The corresponding notecard will include the page (e.g. @23). Press Enter immediately after this if you want to add comments to the notecard. (4) When adding a PDF annotation or a notecard, Bookends will automatically scroll to in the note stream. (5) Find notecard in PDF will use quoted text, if any, for the search. This means that if a line begins with >, indicating quoted text, that will be used for the search. If one doesn't exist, the first line of text (excluding a header) will be used.

Improved importing of Sente XML
If you have quotes in Sente notes, they will be converted to Bookends quotes when imported (e.g. a > will be placed in front of each line).

Improved display of headers in notecards
For notecards that contain both a header and text, the header will take up only a quarter of the display, leaving more room for the text.

Improved ability of Bookends to find a DOI in an attached PDF

When a library is opened, Bookends will select the reference that was showing when it was last closed
Returns interfere with Google Scholar searches.

Bug fixes
Worked around a bug in El Capitan to restore Show In Finder. Fixed a bug in Mellel scans where before and after quoted text in a citation was ignored. Fixed a bug in scanning a Mellel document where consecutive reference numbers weren't converted to a range if italicized numbers were being output (e.g. Science format). Fixed an problem that could occur when parsing an EndNote XML file yielding an "The path passed into new FolderItem was invalid" error. Fixed a bug in Mellel scanning where Ibid could be incorrectly used when a citation matched the last citation of a preceding group.

NEW in Version 12.6.0 (October 3, 2015)

File -> Import References From EndNote
EndNote must running with an open database. The options are to import All references or just the Selected references. Any EndNote attachments will be moved to a subfolder in the Bookends default attachment folder called "EndNote Attachments" (the EndNote file/folder organization will not be preserved). You can import references from EndNote into a Bookends group by selecting that group in the Bookends library window before initiating the import. Note that if a PDF with the same name is already in the Bookends folder called "EndNote Attachments", the EndNote PDF not be moved and the existing PDF will be considered the attachment.

New UI for comparing duplicates and references
This applies to the side-by-side comparisons you see with Refs -> Remove Duplicates -> Preview and Verify and with Refs -> Compare References. Clicking on the symbol in front of a field will bring up a control containing that field from both references. You can quickly copy the field from one reference to the other with arrowhead buttons, or you can copy/paste only selected text from one to the other. Changes are not committed until you click the Save button (or you can click Close to exit without changes). Command-clicking on the symbol immediately moves that field's contents to the corresponding field in the other reference, no other clicks are required, and this is undo-able.

After a notecard search, Bookends will switch to the note stream view in the right pane if it is not already selected

New option to generate BibTeX citekeys as lowercase only
This setting is in the BibTeX tab in preferences.

Bookends now works with Mellel Lite
Mellel Lite must be specified as the default word processor in preferences for full functionality.

Return characters will be automatically removed from searches done in Autocomplete Paper
Returns interfere with Google Scholar searches.

If CrossRef returns malformed XML when attaching a PDF, Bookends will alert you to this and attach the PDF to an empty reference

Updated PubMed import function to deal with changes made by PubMed
This corrects a problem where the reference Type was set to Artwork.

Updated Bookends Browser detection of JSTOR reference information to deal with changes made by JSTOR
Note that because of the variability in the way different reference types can be displayed, Bookends cannot detect and/or import all references.

Improvements in the way that Bookends detects PDF highlights for display as notecards

Output the text representation of a reference's color label in a formatted reference
Use the & symbol in the format's Order field.

Bug fixes
Fixed a bug where Hits menu options were disabled after doing a Refs -> Remove Duplicates and choosing to put the duplicates in the Hits List. Fixed a problem where dropping a reference from the Online Search window onto the library window to import would result in a hang. Fixed a formatting bug where using ^^ to tell Bookends what to output if there are two or more editors gave incorrect results. Fixed a bug where attaching a file to multiple references at once failed if the file was copied or moved to the default attachments folder. Fixed a bug in Title Case where a letter after a smart apostrophe or en dash was always converted to lower case. Fixed a bug in Pages scanning that could cause a hang for certain footnote citations. Fixed a bug in the Mellel scan where arbitrary punctuation that came after cited pages (e.g. @p\,\} was repeated. Fixed a bug in Concise View where clicking on a link to another reference took you to the wrong reference. Fixed several display issues in the Concise View where some text was mistakenly underlined. Fixed an issue with Google Scholar that prevented some references from being identified if there was only one match and Google Scholar thinks may not be correct. Fixed a problem in Bookends Sync where sync wasn't being offered on database open even if that option was checked in the Sync Configure window. Fixed a bug where Bookends would not recognize .gloss (journal glossary) files created in another application. Fixed a bug in scanning where the option to have no punctuation before and a closing parenthesis after a citation was ignored. Fixed a bug that caused a return to be output in citations where multiple references are grouped under one number.

NEW in Version 12.5.9 (August 22, 2015)

File -> Import References From Sente
Sente must running with an open database. This command will switch from Bookends to Sente where you select the references you want to import (Command-A selects all). When finished, either press Command-Y or click the Select button in the dialog Sente puts up. You will switch back to Bookends and the references will be imported. Any Sente attachments will be moved to a subfolder in the Bookends default attachment folder called "Sente Attachments" (the Sente file/folder organization will not be preserved). You can import an individual collection from Sente into a Bookends group by selecting that group in the Bookends library window before initiating the import.

Improved Remove Duplicates -> Preview & Verify Duplicates
(1) Red arrowheads will appear in front of fields that differ between duplicate references. Clicking on an arrowhead will move the field from one reference to the other, allowing you to extract the information from a reference before it is deleted. (2) In the lower reference display pane, the reference that will be saved will always appear on the left and the one to be removed on the right.

Improvements in emailing references and attachments
You can now send attachments via Microsoft Outlook if that is your default email client (set in Apple Mail preferences).

The Bibliography Window UI has been updated
Superscripts and subscripts are now rendered, hanging indents are shown, and you can use a toolbar and ruler to adjust the bibliography.

The formatted view pane displays superscripts and subscripts

Double-click a tag word to create new tag cloud based upon the references displayed
This is much faster than using the corresponding menu to drill down through your references to find useful related tags.

Static group names are sorted in the smart group definition window

DOIs that are part of a URL will be extracted and imported if the import filter has a corresponding tag

The Compare References window is now read-only, it doesn't support copying of text from one reference to another

Improved detection of DOIs in PDFs from Science

Attach a file to more than one reference at a time
When using drag and drop or Refs -> Attach File, the file will be added to all selected references, not just the first selected reference. This may be useful, for example, if you have a PDF of entire journal and want to add it to each individual article in that issue.

Bug fixes
Fixed a bug where a file tag search would fail if the path to the default attachment folder had been changed in preferences. Fixed a bug the prevented importing of pdfs from Bookends Browser when you right-clicked on the PDF proxy icon. Fixed a bug in setting the bibliography output style in preferences. Fixed a bug where the value of the "PDFs only" checkbox was was not set correctly in the watch folder configure window. Fixed a bug in Remove Duplicates where the reference list did not scroll when using the arrow keys or the buttons to change the selection. Fixed a problem in BibTeX imports where an internal quote mark could cause an imported field to be truncated. Fixed a problem in Yosemite where Bookends couldn't determine the default email client.

NEW in Version 12.5.8 (August 1, 2015)

Show the groups a reference belongs to in the reference list display
You can add a column called Groups in preferences (Lists tab) or by right-clicking on a column. Bookends will show all static groups that each reference belongs to, separated by commas.

When selecting a folder in the groups pane, Bookends will honor the boolean AND/OR setting for virtual groups when displaying the folder's contents
This means that you can tell Bookends to display any reference in any group in that folder, or just the references that are in all of the groups in that folder. The pop-up menu "Virtual Groups" was changed to "Multiple Selections" to better reflect its function.

Improvements in extracting notes from notecards
When right-clicking on a notecard, Copy Notecard or Copy Notecard With Citation will copy just the styled text of the note to the clipboard, ignoring any headers, cited pages, or tags. The latter will not automatically switch and paste into a linked Mellel document, but will do so with all other word processors.

Improved downloading with Bookends Browser
The UI has been simplified, so that if only one library is open an import button is shown, otherwise a pop-up menu is available that allows you to select the library to import into. A "download PDF" checkbox tells Bookends whether to try to import the PDF or not.

Add a reference to a group in the All Concise View
Click on the label "Groups" and create a new group for the reference or select from the existing groups.

Remove Duplicates has the option to "Put Duplicates in Hits List"
This will make hits of all replicates and display them in the library window reference list.

Bug fixes
Fixed a bug that could cause SQL errors to be thrown if a folder containing certain smart group combinations was selected. Fixed a bug in the direct Google Scholar search that caused a single hit to be ignored. Fixed a bug in "Flatten Group Hierarchy" that could cause folders to retain false information about their contents. Fixed a problem using the watch folder where when the default attachment folder was on a different volume. Fixed a bug in applying Refs -> Replicate as Book Chapter to a reference of Type Book Chapter. Fixed a problem where rare DOIs were not imported with Online Search. Fixed a bug in Sente XML export where an attachment name could be imported twice. Fixed an error that could be thrown during a Sente XML import if the author had a first name but no surname. Fixed a bug that would sometimes cause a message to be shown when opening the standalone reference window. Fixed a bug in Global Change -> Change Field where a leading return character in the text to be added could be ignored. Fixed a bug where outputting complete last pages in a format was applied to Roman numerals (it is now restricted to Arabic numbers). Fixed a bug where straight apostrophes typed into SQL searches were converted by the system to smart apostrophes, causing SQL errors to be thrown. Fixed several issues with Autofill from Amazon.

NEW in Version 12.5.7 (July 3, 2015)

Improved importing of reference metadata and attachments exported from Sente as Sente XML

Include final citation in formatted bibliography reference
If you enter the + (plus) symbol in the Bibliography Options order field, Bookends will replace it with the citation that was inserted for that reference during a scan. The enclosing punctuation (e.g. parentheses) are not included. This works for author-date and custom but not numbered citations. If the + is entered in the Citation Options order field it will be ignored.

Spotlight used from within Bookends will search webarchives

Updated the PMID -> PMCID converter
Bookends uses the latest and very fast NCBI APIs, which are much better at finding PMCIDs than the older versions.

If available, the PubMed Central ID (PMCID) will be imported from PubMed searches

Updated importing of JSTOR metadata when using Bookends Browser to deal with changes made by JSTOR

Go To URL will show the URL of each selected reference in your default browser
Previously, only the URL of the first selected reference was shown.

The menu Generate BibTeX Key is enabled even when BibTeX is not enabled in preferences
This means you can now create a "citekey" in the User1 field for your own purposes.

The obsolete designations for user1 through user4 (w, x, c, and g) in formats are no longer valid
Use u1 through u4 in the format instead.

Bug fixes
Fixed a bug in scanning where using ^ in an author-date format beginning with the letters "APA " did not cause " and " to be used instead of " & ". Fixed a bug in scanning Pages where enclosing punctuation (e.g. parentheses) around an italicized number were also italicized (i.e. the Science format). Fixed a bug in scanning where an author-date citation in which the name was supposed to be italicized came through as marked up plain text. Fixed a bug when scanning with the Science format where consecutive references weren't being consolidated into a range. Fixed a bug in automated PubMed search where previously found references were not ignored in subsequent searches. Fixed an error that was thrown when drag-reordering searches in an import filter. Fixed a bug where the URL for Web Of Science was outdated. Fixed a bug where text enclosed in backslashes in cited pages did not replace the text specified in the format for "after cited pages". Fixed a bug that moved the folder containing an .odt document to the Trash if you aborted a scan of that file. Fixed a bug where the break binding character in a format could cause the preceding field to be output twice. Fixed a bug in scanning .odt files where the punctuation separating citations in a group could sometimes be omitted.

NEW in Version 12.5.6
(June 7, 2015)

Unchecking "Automatically Resize" in the PDF annotation view display the PDF at its actual size
This setting is remembered between launches and will be used when the same or a new PDF is displayed (the setting is used for the PDF display pane in the lower part of the library window and the Attachment tab in the edit reference pane/window). If you want to toggle between the actual and the resized display without setting that as the default, right-click on the PDF and select "Automatically Resize" or "Actual Size" from the hierarchical menu.

You can choose to open PDFs with the application Highlights

If you click on the metadata of a PDF in the application Highlights, Bookends will come to the front and show the corresponding reference in Bookends
If the reference is not found in the Bookends library, the link to the reference will be opened in Bookends Browser, where you can read and/or import the reference. Note that Highlights and Bookends use DOIs to identify references, so if it is missing (in Bookends) or not registered by CrossRef these functions won't work.

Export PDFs without annotations
The Action pop-up menu in the PDF annotation view lets you export the PDF being displayed with annotations (i.e., "as is") or without annotations. When using the latter, Bookends will remove all markup: notes, comments, highlights, and line drawings (circles, squares, etc.).

Email PDFs without annotations
If this option is set in preferences (Internet tab), when emailing a reference with a PDF Bookends will make a copy of the PDF in the Trash and send that link to Appe Mail. The duplicated PDF will be deleted when you next empty the Trash. The original PDF attachment will not be touched.

When emailing a single reference, Bookends will tell the email client to use the article's title as the Subject

Bug fixes
Fixed a bug in importing unicode characters from a Google Scholar search. Fixed a bug in Copy Citation with Scrivener where the temporary citation wasn't being automatically inserted. Fixed a bug where a reference could be formatted incorrectly if there was no format Type corresponding to the reference Type. Fixed a bug in Spotlight OR searches. Fixed a problem where Copy Citation or Copy Formatted didn't paste into the linked Scrivener application. Fixed a bug where super/subscripted metacharacters were not being resolved in the bibliography when scanning a Pages document. Fixed problems in the note stream when copying cited pages in notecards with a header and tags. Fixed a bug in parsing author names when importing a BibTeX file. When scanning a document with an author-date format and asking for the authors to be placed before the citation with the ^ metacharacter, an " and " will be substituted for an " & " if the format name begins with "APA" (this previously worked with custom, but not author-date, citations).

NEW in Version 12.5.5
(May 16, 2015)

Improvements in the ability and speed of Bookends to resolve DOIs

Improved Watch Folder that can be used by multiple users
The watch folder behavior has changed in several important ways. It now registers each addition of a file to the watch folder, rather than repeated examining the watch folder for the presence of files. A new option in the watch folder Configure dialog is to move or copy files to the default attachments folder. If you tell Bookends to copy files, the original will be left in the watch folder. This makes it possible for more than one person in a group to watch the same folder (e.g. on a server), providing an easy mechanism to distribute the same PDF and references to many people. Note that this also means that when you "start watching", any files already in the watch folder will be left alone -- you would have to drag them out and then back in for Bookends to register their addition and then move or copy them to the default folder.

Add multiple PDF tags at once
You can add more than one tag at a time by clicking in the Tag field (PDF annotation view toolbar) and pasting a Return-delimited list of tags. Note that this will not work when editing an existing tag.

Importing from Google Scholar will work when you have set the language (in Google Scholar) to something other than English
Supported language settings are: Arabic, Catalan, Chinese, Croatian, Danish, Dutch, English, French, German, Hebrew, Italian, Japanese, Portuguese, Spanish, and Serbian.

Enhancements to the manual remove duplicates window
The window is now a sheet instead of modal dialog, and the unique ID of each reference is displayed.

Add references and attachments to a library via an AppleScript
This feature will be used by an upcoming release of DevonThink Pro. See the User Guide for the syntax if you want to use it with your own scripts.

New import filter file format
Import filters created in or edited by Bookends 12.5.5 cannot be used by earlier versions of Bookends.

Bug fixes
Fixed a bug that caused an error to be thrown when viewing a reference with multiple attachments in the editable reference window and selecting an item in the attachment pop-up menu. Fixed a bug that prevented entry or editing of tags in the reference edit pane/window. Fixed a bug in locating PubMed references with the Bookends Browser data detector. Fixed a bug in importing using a PDF doi that was found on PubMed. Shift-Command-O now opens the PDF showing in the standalone reference window Attachments tab. Fixed a cosmetic bug that prevented the top of the window the directly abut the bottom of the menu bar. Window -> Term LIst menu options are now enabled when the standalone reference window is in front. Fixed a bug introduced in 12.5.4 where autofill from internet could fail for references found on PubMed. Fixed a bug in scanning where styled numbers in citations were incorrectly applied if there was preceding literal text. Fixed a bug where on rare occasions the name order for "others" did not correspond to the format setting. Fixed a bug in importing an internet reference Type from Bookends browser where the URL could be incorrect. Fixed a bug that under some conditions could result in data entered into a new reference to be added to an existing reference. Fixed a bug where scanning of text files could cause a hang. Fixed a bug where the unscan dialog was not closed after scanning a document.

NEW in Version 12.5.4
(April 5, 2015)

Integrated PDF tags
If you are running OS X 10.9 (Mavericks) or later, tags will appear in the toolbar in the annotated PDF view. Click on the field labeled Tags to enter a new tag manually, or right-click to choose from a list of tags already defined in the Finder or in the database (you can use the keyboard or the arrow keys to quickly locate the tag you want in the list). Click on a tag name to bring up a pop-up menu that lets you edit or remove it from the PDF. Any of these operations can be applied to all selected references as well. Refs -> Global Change -> Modify PDF tags is another way to Add or Remove tags from the selected references, the Hits List, or the entire database. If attachments are displayed in the Summary view (set in Preferences), any tags will be shown in parentheses after the attachment names.

Consolidate attachments
This Global Change option will move attachments that are outside of the default folder to the default folder or a subfolder you select. Attachments already in default attachment subfolders will not be moved. This operation can be applied to the selected references, the references in the Hits List, or to all the references in the library.

PubMed improvements
Bookends will import accented (Unicode) characters, and you can import full first names (rather than initials) by using the FAU tag in the import filter.

Greatly decreased the time needed to save very large note streams

Bookends will ensure that new database file names end with the extension ".bdb"

Added \citenum as a recognizable citation delimiter for BibTeX scans

Updated parser for importing existing bibliographies to deal with changes made by CrossRef

Bug fixes
Fixed a bug in Autocomplete Paper when using the standalone editable window. Fixed an error message in Sente XML import that could occur if some expected metadata wasn't there. Fixed a bug where specifying a Type other than default when creating a new reference wasn't honored. Fixed a bug that would cause an error to be thrown if you generated a subject bibliography based on groups twice in a row. Fixed a bug in scanning where the last digit of a cited page could be omitted if the ^ metacharacter was used in the temp citation. Fixed a bug in the concise view where attachments could be shown twice instead of links. Fixed a bug where "Rename PDF" didn't work in the standadlone editing window. Fixed a bug where the sort preference for the one column view was not always used.

NEW in Version 12.5.3
(March 7, 2015)

Bookends 12.5.3 is compatible with Yosemite 10.10.3

Display or hide the Notes field in the main tab of the reference edit pane/window
This setting in preferences (Refs tab) tells Bookends whether or not to display the Notes field on the main tab (there is already a separate tab devoted to Notes). If you elect to hide it, the Abstract field becomes twice as large and will expand more rapidly when the window height exceeds that necessary to display all fields. Hiding the Notes field is a good option for those with small screens who want to maximize the amount of text they can see in the main tab without scrolling.

Add attachments when using the standalone reference window
Use Refs -> Attach -> File or Folder.

Better migration of references from Sente to Bookends
When exporting from Sente, Sente XML files contain more information than EndNote XML (for example Sente XML includes notes, comments, and the date the reference was added). This information can now be imported into Bookends, the notes and comments becoming notecards.

Changes to navigation in the reference list
The Refs menu navigation commands (First, Next, etc.) now apply to the order of the references in the list (previously the internal order of the reference in the database was used). This is a much more natural way to use these commands to move through the list. The Hits navigation menu items have been removed because they are redundant.

Combine cited pages and a header in the same notecard
This is an example: #@12 This is a header. The # tells Bookends this is a header, the @12 (which must end with a space or a return) is the cited page.

When editing a notecard, pressing Enter will close the field and save the changes

Bug fixes
Fixed a bug where text style could be missing in the Summary pane when using a format to create the display. Fixed a bug where the editable reference window wasn't updated properly when replicating a book as a book chapter. Fixed a bug in scanning citations in author-date format where the author was placed in front and cited pages were used. Fixed a bug where the default reference font was not used in the standalone reference editing window. Fixed a bug that could cause Bookends to miss citations in NWP documents with many images. Fixed a bug where text in an active edit field was lost if the user moved to another reference via the Refs menu. Fixed a bug that could cause a scan to hang on rare occasions. Fixed two bugs with New Ref and the editable reference window where either it didn't open or it opened with the contents of another reference showing. Fixed a bug where the ! metacharacter in a temp citation was ignored during a scan. Fixed a bug in Global Find and Replace where an error could be thrown when operating on a single field. Fixed a bug where EZProxy settings were ignored by Bookends Browser if you entered the URL manually.

NEW in Version 12.5.2
(February 21, 2015)

Add/edit references in a standalone window
The setting for this is in preferences (Refs tab). There is also the option to have one editing window open at a time (which can stay open while you change references, or can be closed and reopened), or a separate editing window for each reference you add/edit.

Rearrange the order of reference fields

Bug fixes
Fixed a bug where groups were not immediately shown after a Rebuild, but were when the database was closed and reopened. Fixed a bug where using the enlarged field view to enter text in an empty field would result in setting the text to the wrong size. Fixed a bug in formatting Word and NWP documents that prevented numbers from being italicized or bolded in final citations.

NEW in Version 12.5.1
(February 16, 2015)

Open an attached PDF in your default PDF viewing application by clicking on the paper clip
If you have more than one PDF, right-click on the paper clip and choose from the attachments in the hierarchical list.

Improved recognition of pdf attachments in Zotero exports

Bug fixes
Fixed a bug on retina Macs where dragging a reference over a static group would cause an error. Fixed a bug where the list of groups was truncated. Fixed a bug where Bookends Sync settings weren't being saved. Fixed a cosmetic issue with the Automated Search window, and a problem where a reference could be imported into the wrong library if more than one was open. Fixed a cosmetic bug in drawing the numbers of items in a folder in the Groups pane. Fixed several issues that could cause scanning and unscanning of Word and NWP files to fail. Fixed a cosmetic issue with toolbar icons and labels when resizing the window. Fixed a bug where editing a field in the enlarged view would increase the font size by 2 points. Fixed a problem where opening very long notes in the Notes pane could take a long time. Fixed a bug where the | delimiter wasn't recognized when scanning. Fixed an error that was reported with doing a Global Change -> Change Reference Type. Fixed a bug that prevented renaming of smart groups. Fixed a bug in Subject Bibliography that prevented the use of groups. Fixed a bug where an incorrect DOI could be returned from a PDF that does not contain a DOI.

NEW in Version 12.5
(February 8, 2015)

New icons for the application and library files, and an updated user interface
Removed: (1) the standalone reference window, (2) setting font, font size, and colors for the note stream, concise views, and the Term List pane in the main library window.

Merge or replace multiple Terms at once
To merge Terms, drag and drop one or more items in a Term List onto another and Bookends will offer to merge them (i.e. replace them with the one that received the drop). To replace Terms with new rather than existing text, select all the Terms you want to change, right-click on the Term List, and select “Replace…” from the hierarchical menu.

Show live linked references in the concise view
You can have Bookends display a list of references the selected reference is linked to (e.g. a book linked to a book chapter) in the concise view pane on the right. The unique ID of the linked references will be shown and act as hypertext links that take you directly to the linked reference.

Open any browser web page or PDF in Bookends Browser
Sonny Software provides a bookmarklet, labeled “Open In Bookends”, that you can install in your browser’s bookmark bar by drag-and-drop. If the page has references that Bookends can import, or contains a PDF you want to import, click on “Open In Bookends” and the same web page/pdf will be automatically opened in Bookends Browser. You can install the bookmarklet from this web page.

The functions that scan Word and RTF files and for handle groups have been entirely rewritten
These changes will allows us to more easily deal with bugs and add features going forward.

Omit names from final citation is improved
Using - in front of a temp citation results in removal of the author and editor names in the final citation. If the reference is a Book Chapter, only the authors’ names will be removed.

Pressing Escape while editing a notecard or the concise view no longer closes the edit field and discards edits
To ensure data aren’t lost inadvertently, only clicking the Cancel button will do that.

If you close the library but leave Bookends running, Bookends will open that library again automatically if you click on its icon in the dock

The Import Filter Manager and Journal Glossary windows now have a File -> Save menu (Command-S)

References found with a search of Google Scholar that have DOIs matching references in your library will be highlighted in yellow
This may be useful when outputting reference metadata in formats such as RIS or EndNote (Refer) that are intended for import into other reference managers. The symbol is m, and multiple attachments will be separated by returns.

The list of saved searches in the Online Search window can be sorted by name or date of last search by clicking on the corresponding column header

The full title will not be substituted for an empty short title in a conditional group
This means that if a conditional group is {s}, nothing will be output if the short title is empty. If you want the full title output in such a conditional group, you'd use this: {s^t}.

Add URL to bookmarks
Whenever you are using Bookends Browser, you can bookmark the current URL by clicking on the bookmark icon and selecting Add URL As Bookmark.

Updated JSTOR online search and the search in Bookends Browser to deal with many changes made by JSTOR

Updated Google Scholar search and autocomplete to deal with changes made by Google

On launch, Bookends won't automatically open a library that was moved to the Trash

If Bookends has to use CrossRef to validate DOIs, Bookends Browser will show up to 10 references found by the DOI data detector on a single page
This is to prevent excessive waits for verification by CrossRef when there are many dozens of DOIs on a page.

Bug fixes
Performing a proofreading scan on a text file containing BibTeX-style temporary citations is no longer allowed. The - metacharacter in temporary citations now works with .odt author-date scans. Fixed a rare bug where literal text in a temporary citation could be repeated in a subsequent citation. Fixed a bug that could cause a crash when adding a PDF highlight annotation to the note stream. Fixed a bug where the PDF popup menu had the options for note stream display were available when it was invoked in the reference edit window Attachment pane. Fixed a bug where newly highlighted text was not added immediately to the note stream. Pressing tab when editing a notecard saves any changes before closing the field being edited. Fixed a bug where rich text in a field would lose the style information when edited in the Concise View. Fixed a bug that could cause a crash when updating a term list for an empty library. Fixed a crash that could occur when the import text encoding was set to UTF-8 and an invalid character was found. Fixed a bug in obtaining DOIs from CrossRef that could slow down or prevent retrieval of PDFs from some sites using Bookends Browser. Fixed a bug in which edits in an enlarged Notes field were not immediately updated in the Notes tab. The View -> Attachment option is now correctly checked when the selected reference has no attachment. Fixed a bug that could cause the number before a bibliography reference to be output in bold if the authors were bolded. Fixed a bug in which the tag cloud pop-up menu text was not updated when a group changed. Fixed a bug that could truncate the document when doing an author-date scan with year-only after multiple cites by the same author enabled. Fixed a rare bug that could cause autocompletion of heavily used terms to fail. Fixed a bug where an incorrect DOI would be returned from a PDF that does not contain a DOI.

NEW in Version 12.2.4
(November 15, 2014)

A more appropriate error message will be shown if you use the watch folder to import more than 50 references when running in demo mode

You can’t annotate or markup a locked PDF in the annotated pdf viewer
A small lock icon will appear in the PDF display toolbar to tell you that the PDF is locked. In this case you cannot add a note, comment, highlight, or underline to the PDF. You can make an unlocked copy of the PDF in Preview or Acrobat and attach that if you want an editable copy.

Updated Bookends Browser to deal with changes made by ScienceDirect and the American Chemical Society

Updated CrossRef parser so that titles that contain colons will be imported in their entirety

Removed keyboard shortcut for Fonts -> Show Colors
It conflicted with the shortcut for Autocomplete Paper.

Improved the identification of PDF highlighted text for display in the note stream

If a temp citation consists of only literal text (e.g. is between backslashes), that text will be output in the final citation as if it were a reference
Note that you will get unpredictable results if this is used with a format that outputs numbers rather than text for final citations.

Duplicate references without attachments
This option in the Refs menu lets you make a duplicate reference that is identical to the original except that it will not have any attachments.

The relative widths of the Abstract and Keywords (or Notes) field in the editable reference pane are remembered between launches

Output attachment full path names in a formatted reference
This may be useful when outputting reference metadata in formats such as RIS or EndNote (Refer) that are intended for import into other reference managers. The symbol is m, and multiple attachments will be separated by returns.

Modified the CrossRef importer to correctly deal with DOIs and URLs
This was broken because of changes made by CrossRef.

Bug fixes
Fixed a bug that could cause text to be output in tiny sizes when metatypes were used. Fixed a crash that could occur when importing and attaching a PDF based on its DOI. Fixed a problem where right-clicking to remove styles from a reference field would cause the text to be deleted if had not first been automatically saved. Fixed a bug in the Online Search window where the Search button could be mistakenly disabled. Fixed a case where an error would be thrown if a word whose case was not to be changed contained an open but not a closed bracket. Fixed a bug where two open parentheses were output for citations by number where there was quoted text between backslashes at the beginning of the temporary citation. Fixed a bug in scanning .odt files where the * metacharacter in a temp citation resulted in the output of only the year for Author-Date formats. Fixed an error message that could be thrown if an attachment has an illegal file name. Fixed a bug that interfered with the setting of ratings with a click if they were in the first column of the reference list. Fixed a bug that caused an error to be thrown if you imported a PDF to an empty reference when a static group was selected in the library window. Fixed a bug in the hierarchical menu that appeared when you right-clicked on a URL field that had more than one URL. The paper clip attachment icons now appear correctly on Retina displays. EndNote XML references for web pages are now correctly imported as type Internet.

NEW in Version 12.2.3
(September 13, 2014)

Open an attached graphic in the program that created it by double clicking on it in the library window

Improved citation handing
If a citation ends with a period and a quote mark, the period will be suppressed for all citations in a group except the last.

Improved speed when saving notecards edited in the note stream

Bug fixes
Fixed several bugs in which an error could be thrown when manipulating an annotated pdf in the standalone reference window. Fixed an error that could be thrown when performing a Bookends Sync. Fixed a bug in metatypes where a return was not placed after a metatype reference output in the bibliography. Fixed a bug where an editor name might not be placed in front of a citation even if the ^ metacharacter was used. Fixed a cosmetic issue with misalignment of the reference list in the library window. The option to import references exported from Bookends to the Hits List option works again. Fixed a bug where the attachment tab wasn't updated correctly in some circumstances. A period following the cited pages after an Ibid. will be suppressed for all citations in a group except the last. Fixed a bug in Global Change where the ¬ character was not being converted to a Return. Bookends will no longer try to download pdfs of books from JSTOR via the direct search (they are not supported by JSTOR). Fixed a bug that could distort the UI when resizing the library window and require a force-quit. Fixed an error in drag and drop of a pdf onto a group folder and attaching the pdf to a new reference. Fixed a bug in adding a new reference when Hits was selected in the group pane. Subject bibliographies work again (broken in 12.2). Fixed a bug that could cause bibliographies to be output in hit order instead of sorted in some cases. Fixed a bug where an extra empty notecard was added when adding a notecard to the note stream. The list of reference Types shown in the library window will be updated instantly if it is edited in preferences. Fixed a bug in Option-Shift where smart groups that were not supposed to find references in static groups were highlighted in yellow by mistake.

NEW in Version 12.2.2, Mac App Store Only
(July 29, 2014)

Fixed several bugs in which an error could be thrown when manipulating an annotated pdf in the standalone reference window

Fixed an error that could be thrown when performing a Bookends Sync

Fixed a bug in metatypes where a return was not placed after a metatype reference output in the bibliography

Fixed a bug where an editor name might not be placed in front of a citation even if the ^ metacharacter was used

Fixed a cosmetic issue with misalignment of the reference list in the library window

NEW in Version 12.2.1
(July 12, 2014)

Show highlighted PDF text in notecards
If this option is turned on in the pdf view Action popup menu, any text highlighted in the PDF will be shown as a virtual notecard when the note stream is visible. The notecard will be the same color as the highlighted text, and a small lock icon at the upper left indicates that it cannot be edited. If the highlighted text has an associated note, the text of each (the highlighted text and the note) will be shown in its own notecard. If you select a notecard representing highlighted text and press the Delete key, the highlight will be removed from the PDF.

Show PDF note modification dates in the note stream
This option can be toggled on/off in the pdf view Action popup menu.

Maximize/Minimize PDF Pane
Expands or diminishes the height of the PDF display pane in the library window. Available via the PDF Action popup-up menu and keyboard shortcuts.

Updated the Google Scholar parsing to deal with changes made by Google

Name suffixes (e.g. Jr.) will be omitted when the secondary order is used to create a custom citation.

Bug fixes
Fixed a rare bug that could cause two reference imported from PubMed to be placed into the same record. Setting fields User5 through User20 with an AppleScript no longer generates an error. Fixed a bug that could cause an error to be thrown when adding a new reference. Fixed a bug is Cited Pages that resulted in failure to move a preceding comma before a closing quote mark. Fixed a bug that could cause an error to be thrown when editing a reference and then clicking on the Inspector button. The library window can no longer be dragged when in full screen view. Fixed a bug in scanning a text file where a numbered final citation could include the author's name. Fixed a bug that could cause an error to be thrown when right-clicking in the Attachment tab to detach a pdf that couldn't be found. The paper clip attachment images now update properly when moving the library window between a non-retina and a retina display. Fixed a bug in printing the selected references.

NEW in Version 12.2
(May 24, 2014)

New PDF viewer with search, markup, and annotation
The new PDF rendering engine has the following features: (1) search for words and phrases in the pdf, (2) thumbnail page view, (3) markup PDF text with highlighting and underlining, (4) create and edit PDF notes and comments, (5) create a note associated with highlighted text, and (6) position and reposition notes and comments on the PDF page. Any markups or annotations that you create in Bookends will be visible in any applications that uses PDF Kit (e.g Preview and Adobe Acrobat). To use the new PDF viewer in the library window, select “Use Annotation View for PDFs” in the Action pop-up menu underneath the reference list.

Tight integration between PDF notes and the Bookends note stream
When using the PDF annotation view, PDF notes will automatically appear as virtual notecards at the end of the note stream (highlighted in a color different from reference notes, which is configurable in preferences). Clicking on a virtual notecard will instantly take you to the note in the PDF. Any edits you make in the PDF note will appear in the corresponding virtual notecard, and any edits you make in the virtual notecard will be written back to the PDF. Text selected in the PDF can be imported into Bookends as a permanent and searchable notecard. You can also right-click on any notecard and search for its text in the PDF.

Move groups between folders with a hierarchical menu
Select one or more groups (static or smart) in the groups pane and right click. You will have the option to move the groups to an existing folder or to a newly-created folder. If anything other than a static or smart group is selected this option will not appear.

Watch folders work when the default attachment folder is not on the boot HD

Use AppleScripts to set the contents of a field

Bibliography generation is faster

Set text output style (e.g. Styled Text, BibTeX, HTML, etc.) in Preferences, Scan & Bib tab
This can also be done in Biblio -> Bibliography.

Worked around a Mendeley XML incompatibility with EndNote XML so that reference Types are imported correctly

The keyboard shortcut for Autofill From Internet has been changed to Shift-Command-A

If Bookends can't find an assigned attachment folder, the factory default folder will be used

JSTOR search and Autocomplete Paper were updated to deal with changes made by JSTOR

The number of references you can import from Google Scholar at once has been reduced from 50 to 20
This is to prevent Google Scholar from thinking that you are a web bot and banning your i.p. address.

Updated Google Scholar parsing to deal with changes made by Google

Existing font styles will be preserved when pasting decomposed Unicode text into a text field

Smarter handling of Title Case
Bookends will not capitalize a letter if it occurs immediately after a number or a period.

New menu item Refs -> DOI -> Copy DOI

Bug fixes
Fixed a bug in the Import Filter Manager that prevented the hierarchical menu option Show Filter in Finder from working. Fixed several small bugs dealing with using "\cite" with BibTeX citations. Fixed a number of bottlenecks that caused delays when formatting fields with many text styles. Fixed a bug that could cause the first reference returned in a Google Scholar search to be skipped. Fixed a bug that could cause references already found by an automated PubMed search to be displayed in subsequent automated searches. Fixed a bug where the space between the author and date would be omitted when using the ^ to place the author in front of unenclosed Author-Date citations. Fixed a bug that caused the key field and the reference Type to be ignored when importing a BibTeX file. Fixed a bug that caused the wrong reference to be edited when creating a new reference with a smart group selected. Fixed a bug where using a right-click to add a reference to a group could result in the wrong group being modified. Worked around a bug in the framework that could cause an exception to be thrown when formatting styled text. Fixed a bug in setting proxy information in preferences. Fixed some mis-mappings of accented characters in BibTeX output. Accented characters are now really replaced by their ASCII counterparts when the BibTeX Key field is generated. Fixed a bug where a trailing comma in the title could be included in the formatted output.

NEW in Version 12.1.2
(April 5, 2014)

Amazon Spain ( has been added to Online Search

The last conditional group in a series will be used even if it has fields that are empty

Better handling of the warning you receive when using Mellel's Live Bibliography and the Bookends database is not open
Requires Mellel 3.3.2 or later.

The size of PDFs synced with Bookends On Tap can be limited to 2 MB

Bug fixes
Fixed a bug where trying to make a new filter based on an existing one would silently fail. Fixed a drawing artifact that could occur when resizing the Online Search window. Fixed a bug that could cause Online Searches using the Library of Congress gateway to fail. The browser in the main window now uses any EZProxy settings. Fixed an AppleEvent timeout delay that occurred when opening a Mellel document that used Live Bibliography and no Bookends database was open. Fixed a bug where small caps weren’t used in citations that had Cited Pages. Fixed a bug in EndNote XML output where the Book Chapter fields Book Title and Series Title were not exported. Fixed several problems with Refs -> Find In This Note. Fixed several cosmetic issues with Add to Group menus. Fixed a problem where scanning an RTF file would appear to hang after the bibliography was generated. Fixed a scanning bug where using Surname only in the secondary order could result in mishandling of the “et al.” settings. File -> Print References will now generate a sorted bibliography if the format calls for it.

NEW in Version 12.1.1
(March 1, 2014)

Bookends will find many more pdf attachments for references in EndNote XML files exported from Sente

Title words beginning one or two spaces after a semicolon or period will be capitalized when Title Case is used, even if they're on the exclude list
Previously, only words beginning one space after the semicolon or period were capitalized.

Library of Congress and Google Scholar searches were updated to work around changes made by those services

If a format calls for the last two digits of the second page in a page range be output, a leading 0 will be ignored

The right-click contextual menu in the group pane has an option to rename the selected group

Bug fixes
Fixed a bug that could cause mangled reference metadata to appear in the reference list. Fixed a bug where editing the Notes field on the main tab would not update the Notes field in the Notes tab. Fixed a bug that could cause an error to be thrown if you edited a tag while the tag cloud was showing and then clicked on the tag cloud. Fixed a scanning bug that prevented the year from being output when a citation used the year-only modifier (%) and had cited pages. Fixed a bug where the font size of scanned in-text citations would be different from that of the paragraph's style sheet. Fixed a bug in excluding words from capitalization where words consisting of a single accented character were ignored. Fixed several bugs in case conversion that affected Title Case and Sentence case. Fixed a bug that resulted in malformed citations if you scanned a Word document twice in the same session with an Author-Date format. Rating stars in the list view can no longer appear as white on a white background in refs that have been assigned a color label. Fixed a bug in Find in This Reference. Fixed a problem that prevented dropped text onto a note stream from being added to the new notecard. Cited Pages once again work in scanned text files. Bookends Server works once again. Fixed a problem where a Find/Replace with styles could change the style for an entire field. Fixed an issue with JSTOR where the search would have to be done a second time for it to succeed. Corrected the escaped BibTeX output for é. Importing metadata from Web of Science in Bookends Browser works again. The Key field, if shown in the reference list, will update automatically if you use Refs -> Generate BibTeX Key. Fixed a bug where an author's surname was always used if a secondary order field in the format had content, even if the popup told Bookends to use the same name format as the first time.

NEW in Version 12.1
(January 5, 2014)

Bookends 12.1 requires OS X 10.7 (Lion) or later
This is necessary because OS X 10.6 (Snow Leopard) is no longer supported by our development tools. Databases created with Bookends 12.1 and later (until the database schema changes at some time in the future version), however, are still compatible with Bookends versions 12.0 through 12.0.7.

Attachment Flow
Like Apple’s Cover Flow, this view will present a carousel showing the first page of all files attached to the selected references. Move to the attachment (usually a pdf) that you want and press Return, click Select, or double click on it to have that reference selected with the attachment shown in the lower pane. Press Escape or click Cancel to exit the Flow view. Attachment Flow is presented in a movable modal window with the same dimensions as the library window to make reading the contents easier.

Drag and drop creation of a static group in a specific folder
A folder in the groups list will highlight if you drag one or more references over it. When you drop, Bookends will offer to create a new group that will be placed in the folder. If you drop on any line that is not a folder or a static group, Bookends will add the new group outside of any folder.

Spring-loaded group folders
If you drag references and hover over a closed folder for a second, the folder will flash and then expand to reveal its contents. If you hold the Option key down while hovering, all subfolders will expand as well. The folders will not automatically collapse if you move the cursor away without making a drop.

Improved automatic installation of a format or import filter
If you double click on a format or filter, or drop one on an open Bookends library, and the format or filter already exists in the corresponding Custom folder, Bookends will offer to replace an existing format or filter of the same name, keep both, or cancel the operation. Previously, the format or filter already existed, it would automatically keep both. If there is no existing format or filter of the same name in the Custom folder, the new item will simply be moved there.

OpenURL 1.0 compatibility
If you enter "url_ver=Z39.88-2004&" (without the quote marks) in the Search Arguments (Preferences, Metadata tab) Bookends will understand that the query should be OpenURL 1.0-compliant. Bookends will then add the prefix "rtf." before any field name when the query is sent (you should not enter that in the query string yourself, Bookends will do that for you).

The "Bibliography Formatter" menu item has been renamed "Bibliography"

Bug fixes
Fixed a bug that prevented certain Chinese and Korean characters from being output in citations or bibliographies when styled text is applied. Fixed a bug in the Import Filter Manager that prevented Bookends from finding a filter selected in the list pane. Fixed a bug where the Preferences password field for an authorized proxy server was invisible. Fixed some BibTeX accented character escape sequences. Smart groups can once again be used for Subject Bibliographies.

NEW in Version 12.0.7
(November 24, 2013)

UI update completed
Major changes in preferences, minor tweaks elsewhere.

Scan Pages 5 documents
Bookends is unable to directly scan saved Apple Pages 5 documents, which have an undocumented file format, no APIs, and limited AppleScript support. However, if you have a document open in Pages 5, you can use Biblio -> Scan Open Apple Pages Document to scan it. The scanned document will be saved in Pages '09 format, which Pages 5 will automatically open and convert to its native format. Note that the bibliography will not be automatically added to the scanned document, but will be in the clipboard. After the scan, scroll to where you want the bibliography to appear (usually at the end) and press Command-V (Edit -> Paste).

Improved small cap handling in bibliographies
When small caps are used in bibliographies, Bookends will output them to your word processor in sizes relative to the style sheet font size settings, as is already the case for citations. This works with Word, Nisus Writer Pro, and Mellel (version 3.2.7 or later).

Placing a comma at the end of the Date field will cause Bookends to output it without parsing

Bug fixes and improvements
Fixed a cosmetic bug where the left edge of a color label was too far to the right when showing attachment icons was turned off in preferences. Fixed a bug that prevented cited pages in an author-date citation from being displayed in Nisus Writer Pro. Fixed a bug that caused bibliographies to be omitted from scanned RTF files. Autocomplete works again when editing a field with a term list in the concise view. Fixed a number of bugs that interfered with metatypes. Fixed a bug in small caps where the last initial of a name might be output as a small cap instead of a true cap if the surname was output first. Fixed a bug that prevented small caps from being displayed in scanned citations if cited pages were used. Fixed a bug in hanging indents in scanned Nisus Writer Pro bibliographies. Pasting a bibliography copied from the Bibliography Window into a word processor document will once again appear with a hanging indent if specified in the format. Fixed a bug that could cause unwanted punctuation to be output before “et al.” when a reference was cited more than once. Fixed a cosmetic bug where color of a notecard being edited would revert to white if the library window lost and then regained the focus. All Greek letters are now correctly converted to their capitalized form when displayed in small CAPS or ALL CAPS. Fixed a rare problem with syncing pdfs with accented characters in their names with Bookends On Tap.

NEW in Version 12.0.6
(November 2, 2013)

Updated user interface
Includes changes to the library, online search, standalone reference, and Inspector windows.

Updated the Google Scholar parser to deal with changes made by Google

New formatting option: surname in small caps

Improved small cap handling in Word and Nisus Writer Pro citations
When small caps are used in citations, Bookends will output them not in absolute point numbers but in relation to the style sheet font size settings.

Rename Attachments has been added to the library window right-click menu and Action pop-up
This option is available when the first reference selected has attachments, and will apply to all selected references that have attachments. To rename just the attachment you are viewing in the display pane, use the Action pop-up menu or a right click on the attachment (if Use WebKit to display pdfs is unchecked) and choose "Rename Attachment…"). You can also rename attachments in bulk with Refs -> Global Change -> Rename Attachments.

When using an APA format, if the editors name is the first item output its surname/first name order will be that set for authors
This only applies to APA formats, which Bookends detects by the presence of the 3 letters “APA” at the beginning of the format name.

The h-index option in Online Search has been removed

Turn off automatic check for updates on launch
This option, which is on by default, can be turned off in preferences, General tab. If Bookends was purchased from the Mac App Store this option is disabled because Apple has its own update notification system.

Curly brackets will be removed from fields imported with the BibTeX filter
This requires that you check Convert from TeX in the BibTeX tab in preferences.

A Google Scholar advanced search will be noted as such in the Online Search window

The color palette for reference labels has been updated
Completely new installations of Bookends will show these colors. If you are an existing Bookends users, you can install this new color palette by clicking Set To Default button under the color display in preferences (Lists tab).

Display the contents of attached TaskPaper documents in the display pane and the Attachment Inspector

Removed support for Microsoft Word 2004 and X add-ins
If you need to use these old versions of Word, write to Sonny Software and request the corresponding add-ins and/or templates.

Bug fixes and improvements
The attachment icon in the reference list is now displayed properly on Retina-enabled machines and when sorting by a column with numeric entries, such as Ref #. Fixed a bug in journal glossaries where short journal names were not being output when called for. Fixed a bug that prevented periods in journal names from being removed if the journal name was not in an enabled glossary. Fixed a bug where repeated citations with a secondary order could have "et al." output twice. Fixed a bug where cited pages would be output in italic if the preceding text were italic in Word and Nisus Writer Pro scans. Fixed a bug where scanned footnotes would use the bibliography default size. Fixed a problem where using a watch folder would result in very high CPU activity. When the insertion point is in the live search field, clicking on a reference will immediately give the list the focus. Fixed a rare bug where a translator's name could be output as dashes if the author's name was. Fixed an error message that could be thrown when clicking on a group folder that contained a smart group returning no hits. Fixed a bug when outputting formats in plain text where metacharacters in quoted text (e.g. ++ and ^^) were ignored and they were output as is. Bibliographies in Nisus Writer Pro documents once again use the default bibliography font. Fixed a bug in scanning that prevented hanging indents to be automatically added for Nisus Writer Pro and Pages documents. Fixed a bug in bibliography sorts by first author and then date. Fixed a number of bugs with metatypes. BibTeX fields beginning with protected characters (in curly brackets) will not be truncated. Fixed a bug in scanning Nisus Writer Pro documents that contain pictures. Fixed a bug in scanning Word and NWP where unicode characters would be mangled in unmatched citations. Fixed several issues concerning the use of “Idem” when scanning. Cited pages once again work with Author-Date citations. Fixed a bug that prevented the library window Action pop-up menu Copy Text To…hierarchical menu from working when text was selected in the browser. Fixed a bug in Bookends On Tap sync where multiple keywords would considered as a single keyword. Fixed an error that occurred when adding or removing a virtual tag with a right-click. Fixed a bug that prevented a right-click on the pdf proxy icon in Bookends browser from importing the pdf or web archive being viewed. Fixed a bug that prevented cited pages from being added to "ibid." citations.

NEW in Version 12.0.5
(September 28, 2013)

Updated user interface

Bookends will import attachments from the watch folder even when it is in the background

A new option to include or remove page ranges in footnotes that use Cited Pages
The default behavior is to remove a specified page range when Cited Pages are present. Set this option in the Cited Pages section of the format.

If a format calls for the short title and that field is empty, the full title will be substituted

Empty lines created by doing a Find/Replace in the Authors, Editors, and Keywords fields will be automatically removed

A new menu item and keyboard shortcut for enter/exit full screen
View -> Enter Full Screen (Control-Command-F). This menu item will not appear if you’re running Bookends on Snow Leopard, which doesn’t support the full screen view.

Hits -> Prev/Next shortcuts have been changed to [ ] (so Option-Command-F switches focus to Live Search again)

If a journal glossary is enabled it will be used for the Book Series Title field as well as the Journal field
If the glossary entry matches, it will be used as entered in the glossary. If no match is found, the usual title capitalization rules set in the format will be used.

If Cited Pages contain non-numeric characters other than a space, dash, or en dash, Bookends will not try to adjust an ending page number as specified in the format
This means that nonstandard or complex cited pages will be output as entered.

The text font for any converted order in a pre-12.x format that has styled text will be set to Arial
This is important because in Cocoa only fonts that have italic and bold faces will show these variations (e.g. avoid fonts like Geneva and Lucida Grande). The font in the order field is not used when creating a formatted reference, but the face (bold, italic, and/or underlined) is.

Bug fixes and improvements
Fixed a bug that would cause APA citations to always use just the first name plus et al. the second time a reference was cited. Fixed the enlarged field view so that it is the same text style but 2 points larger than the normal field. Fixed a bug with the watch folder feature where Bookends would have very high CPU use when in the background. Fixed a bug that could cause an error to be thrown when a watch folder pdf was damaged. Fixed a bug that caused an error with watch folders when renaming the pdf according to a format. Fixed a bug that would cause an error to be displayed if you changed the reference in the standalone reference window with a right-click. Fixed a bug that could cause an attached pdf downloaded with the library browser to contain two periods in the name. Fixed a bug that could cause an error when entering large amounts of text in the Notes field. Fixed a bug that could cause Bookends to output an author or author/title for a citation even when directed not to and the field had styled text. Fixed a bug that caused an error when removing styled text from a field with a right-click in the standalone reference window. Fixed a bug that could cause an error to be thrown when styled text data was incomplete. Fixed a problem where styled text saved in a format's notes field would appear as naked RTF when the format was next opened. Fixed bugs in scanning with metatypes. When generating initials from an author’s name, accented capital letters will be included. Superscripted characters in scanned citations will appear properly. Fixed a bug that caused cited pages to be output twice when an en dash was used between the starting and ending page number. Fixed a bug that prevented Bookends from creating a correct reference when using “Replicate as Book Chapter” in the standalone reference window. Fixed a formatting bug where Bookends would obey the setting for "last author at end" even when "use et al." was unchecked. Fixed a bug that could cause a return character to be inserted in a verified Mellel citation that was preceded by a metacharacter. Fixed a situation where an error could be thrown when clicking on a folder in the groups pane. Fixed incorrect application of smart quotes that appeared before or after other punctuation marks. The library window pane settings are now saved when you quit Bookends without closing the window first. Fixed a bug in APA 7th where only the first and last authors were output if there were more than six. Fixed a problem with generating large bibliographies during a Nisus Writer Pro scan. Fixed a bug in which a trailing period in a series titles was stripped out when formatting. Fixed a error that could be thrown if you closed the library window while doing a PubMed search.

NEW in Version 12.0.4, Mac App Store Only
(September 3, 2013)

Fixed a bug that could cause a crash when doing a live search within the library

NEW in Version 12.0.3
(August 4, 2013)

Introducing watch folders
When a new file is detected in a watch folder, Bookends will attach it to a new empty reference and, if a file is a pdf and Bookends can locate a doi for it, import the metadata from online sources. The file will be moved to the default attachments folder and renamed according to the specifications in preferences. If the metadata cannot be found, the title of the new reference will contain the name of the original file, prior to renaming. Watch folder settings apply to individual libraries, so different libraries can watch different folders. Settings are managed in File -> Import From Watch Folder -> Configure. You must tell Bookends what folder to watch, whether Bookends should watch for just PDFs, and if any imported attachments should be added to a particular group. Once a valid folder has been specified, Bookends will begin watching. You can stop (or restart) watching with File -> Import From Watch Folder -> Stop/Start Watching. Bookends will temporarily suspend watching when it is not the active application or the library window is moved to the background, and will resume when brought to the front. Note that if a file in the watched folder can't be moved (e.g. you don't have read/write privileges), Bookends will stop watching, as it will if the watch folder is renamed, moved, or deleted. To avoid distracting updates to the UI while you are working, newly added references will not be displayed until the list is refreshed naturally (for example, by clicking the group All). An exception is that if you are importing to a group and that group is selected, the reference list will be updated in real time.

Improved online metadata detection when attaching a pdf
When you drop a pdf on a library window, Bookends first looks for a doi in the pdf. If none is found, Bookends will search PubMed for a reference that matches the initial text of the pdf. If a single match is found, Bookends will retrieve the doi from PubMed. This allows Bookends to find more references online. One example would be a preprint of a paper submitted to a journal that was accepted (and is now on PubMed), but the pdf you have doesn't contain the doi.

Greatly speeded up opening and saving the enlarged field view for fields with styled text and the standalone Notes field

For APA formats, an & will be replaced with "and" when author names are placed in front using the ^ metacharacter and there are 2-5 authors

New option for Cited Pages
In the Cited Pages portion of a format, you can tell Bookends to "Move leading punctuation inside of a preceding quote". This means that if a cited page is separated from the rest of the citation with a comma or a period and the preceding text ends with a single or double quote mark, the punctuation in front of the cited pages will be moved inside the quote: "The Example," p. 14. If unchecked, the same citation might look like this: "The Example.", p. 14. The former (the default) is standard for American English, the latter for British English.

Select references that have orphaned attachments

If a specific field is selected in Live Search, its name will be displayed underneath

Updated formats for American Society of Microbiology journals

When disambiguating citations by title, if quotes are called for Bookends will use the form of smart quote selected in preferences
If none is selected, English will be used. This is primarily used by the MLA format.

Navigation through the hits is available in the library window
These functions are available in the Hits menu. Note that the order of the hits is arbitrary (e.g., it might be the order of citations in a scanned document), usually not the same order as the sorted reference list.

The keyboard shortcut for Hits -> Next has been changed to Command-Option-F
This avoids a conflict with the OS X Universal Access Zoom shortcut.

Bug fixes and improvements
Fixed a bug that could cause problems with fields with returns and styled text when converting a database to Bookends 12. The author settings in a format's second order are honored again. Editors names will not be replaced with --- if the format calls for the authors names to be replaced in consecutive works by the same authors and editors, unless the reference is an Edited Book. Fixed a bug that could cause references to be sorted in the bibliography even when not called for when scanning a Mellel or Nisus Write Pro document. Fixed a bug that prevented citation disambiguation by author initials, names, or short title from working. Fixed a bug with journal glossaries where the full name was not substituted for the short name when the short name was not found. Fixed a bug that would cause the standalone reference window to appear when using Hits -> Go To Hit # when the library window was in front. Fixed a problem where reference copied to the clipboard with Copy Formatted could not be pasted into some applications. Notecard headers now appear in the correct color.

NEW in Version 12.0.2
(July 20, 2013)

Correct APA formatting for two authors in front of a citation
When scanning with an APA format, if there are two authors in a citation and they are to be placed in front, " and " instead of " & " will be used to separate them. This occurs when the temp citation begins with the ^ metacharacter and the name of the format begins with the letters APA.

Spotlight searches for exact matches can be performed by surrounding the search text with quote marks

If you drop a pdf on a static group, the group will be selected

You can batch import pdfs into a static group by dropping them onto the group name

The pdf image in the Attachment Inspector can no longer be dragged and dropped

The Inspector window is now a floating palette

The results of an advanced PubMed search will be labeled as such in the Online Search window

If a specific field is selected in Live Search, its name will be displayed underneath

Bug fixes and improvements
Fixed a bug that could cause unwanted styles to be applied to punctuation in a formatted reference. Fixed a bug that could insert repeated cited pages in a scanned Mellel citation. Fixed a Word and NWP scanning bug that would cause Bookends to think two citations were back-to-back and combine them if the intervening text had no spaces and was entirely in Unicode. Fixed a highlight that wouldn't go away after dropping a pdf on a static group. Database Maintenance operations now work on libraries that have an ampersand (&) in their names. Fixed a bug that caused a delay when double-clicking on a pdf in the Attachment inspector. Fixed a bug that would cause all but the last reference in a bibliography grouping (i.e. under one number) to lose styled text. Fixed a bug that would cause the authors to be formatted incorrectly in a bibliography after dashes were used to replace repeated authors. A comma at the end of a title once again means that no special casing will be applied to that title. The bibliography for a scanned text file is now properly placed in the clipboard. Fixed a bug that caused Global Change -> Change Field to malfunction. Fixed a bug that caused text entered in the Concise View to sometimes be bolded. Fixed a rare bug where under certain conditions the font size of the title in a formatted reference would be incorrect. Fixed a bug that could cause citations in a group to be sorted by author incorrectly. Refs -> New is enabled when the standalone reference window is in front. The keyboard shortcut preference setting for Paste vs. Paste and Match Style is remembered between launches. References with titles containing returns will be displayed correctly in the single column view. Fixed a bug in syncing with Bookends On Tap where one might have to repeatedly move the mouse or press a key to get the sync to progress. Fixed a bug in the Bookends On Tap where some edited pdfs on the Mac were not transferred to the iOS device when subsequently synced. The BibTeX conversion of several accented characters has been fixed. Fixed a bug in the AppleScript handlers that respond to requests by DevonThink and Tinderbox in which an error was reported if the library name began with a number. Fixed a bug where a reference transferred from one library to another by drag and drop would not be synced with Bookends On Tap. The Greek letter ∆ is once again output correctly. Fixed a bug in dropping multiple pdfs on a library window with the Hits group selected.

NEW in Version 12.0.1
(July 4, 2013)

Many functions are faster, including scanning documents and outputting XML

For Book Chapters, the format's title case setting will be applied to the Volume field as well as the Title field

Bookends will ignore a colon pasted into the Rename field by the user when attaching a file

Attachments will be exported when File -> Export References -> Export Attachments Too is checked and a bibliography format is used

Improvements in syncing pdfs with Bookends On Tap (requires BOT 2.1 or later)

The Autocomplete Paper sheet is resizable

Bug fixes and improvements
Fixed a bug that prevented the secondary order field from being used when an in-text citation or footnote was cited more than once. Fixed a bug that prevented scanned footnotes from displaying styled text. Fixed a bug where cited pages were not being included when creating citations from notecards. Importing a reference into DevonThink Pro using the Bookends template works again. Fixed a bug that caused the Editors to be omitted when replicating an Edited Book as a Book Chapter. Fixed a formatting problem where the punctuation between last and first names wasn't honored when the full name was output. The menu Edit -> Copy Formatted text is properly restored after removing the selection from a notecard. Fixed a bug that prevented keywords from being output in formatted references. Fixed a bug that could cause an entry in a Term List to be shown in RTF. Styles assigned to punctuation in the format are now conserved when a reference is formatted. A Return character in a format will once again be output even if the field in front of it is empty. Fixed several bugs that prevented citation disambiguation by a letter appended to the year from working when scanning. Improved the handling of styled text so that italics and bold text in a reference field will adopt the default bibliography format font more reliably. The "Go To Ref" button in the ambiguous citation window that can appear during a scan works again. Fixed a bug that caused the text in the find field in the find/replace dialog to disappear when exiting the field. Fixed a bug that prevented Bookends from scanning long Mellel documents. Fixed a bug that prevented Bookends from inserting the bibliography in scanned RTF files. The text enlarge/decrease buttons for the web view in the Online Search window work again. Emptying a field in the concise view will no longer cause an error. Fixed a bug where "et al." would sometimes be preceded by a comma even if none was specified in the format. Worked around a situation in which .doc or .html attachments had problems with text encoding that could cause an error message. Fixed tabbing between fields in the Autocomplete Paper sheet. Citations in scanned Pages documents once again include cited pages and quoted text. Printing references works again. Fixed a bug that could cause an error when scanning and using metatypes. Fixed a bug in the formatter where two $ in a row would cause Bookends to consider the rest of the order field as quoted text. Fixed a bug that could cause an error when doing a drag and drop copy of references from one library to another. Returns are now shown properly in scanned LibreOffice documents. Fixed a bug that caused styled text to be removed from references after a Rebuild. Fixed a bug that could in some cases cause a question mark to be output after a unicode character in a scanned Word or NWP document. Fixed a situation where a closing quote mark could be omitted in a citation containing cited pages. Imports from the Online Search window will now work with databases whose extensions are hidden in the Finder. Hanging indents work properly for unnumbered bibliographies. Fixed a bug in hits list sort.

Version 12.0 released
(June 15, 2013)

New or Improved:

Import references and pdfs from the Web while in the library window
The browser pane has the same features as Bookends browser in the Online Search window. Use the green proxy icon to import references and pdfs (if they can be identified) from Web pages that include PMIDs, DOIs, or whose references are encoded as COinS. Use the browser paper clip button to attach any pdf or Web page that you can navigate to.

Updated database engine with journaling (protects against database corruption)
When run, Bookends will create a temporary copy of your database with the same name but with the extension .journal. When the database is closed, this temporary database will be deleted. However, if the program crashes the temporary file will remain, and when you next open the database any data that was lost or corrupted because of the crash will be restored. You can manually delete the .journal file, but if you do it will not be available to ensure the integrity of the database when it is opened again.

Spell checking
Use the Edit menu or right-click in a reference field in the editing pane. Set fields you want to be spell checked automatically in preferences.

Multi-level Undo/Redo

Improved library window toolbar
A right-click in the toolbar gives you several options: Icons and Text, Icons Only, and Text Only.

Advanced PubMed search lets you limit the results to a particular language (e.g. English)

Improved detection of DOIs on Web pages

Improved sorting of citation groups
If the sort is by author, Bookends will ignore punctuation between the last authors and "et al.". In rare cases, such additions could cause the sort to be out of name-order.

New formatting option "cap SURNAME"
First names(s) will not be modified.

New formatting option "titles in SMALL CAPS"
Bookends will preserve any capitalized letters in their normal size and the rest will be output as small caps.

Improved author capitalization
For author capitalization options, the text between the last two names, if any, is output as entered in the format except for small CAPS, in which case it is output as all small capitals.

Remove styles from text in reference field with a right-click
Use Global Change if you want to do this on multiple fields and/or multiple references.

Open attachments in the application of your choice with a right-click
Open attachments in the Finder's default application, Preview, Acrobat Reader, Skim, or PDFPen with a right-click on the reference in the library window or by using the Action pop-up menu.

New Help menu option: Show Bookends Folder in Finder
This will take you to the Finder and open the folder ~/Library/Application Support/Bookends. This folder is the default location for your library (you may have selected another) and is where support folders and files that you may want easy access to are located.

In the Edit Bookmarks window you can specify which Web page should be automatically opened by Bookends browser
This only applies to the Online Search window. The browser in the library window always automatically opens the URL of the selected reference.

File -> Open Location
This is enabled whenever a window has a browser open, and will move the focus to the URL field.

Right-click on a column in the reference window to select a different field to display
This will update Preferences as well. If you want to add or remove columns (not just change the heading), you must use Preferences, List tab.

Easier creation of new references from multiple attachments
If you drag and drop more than one file on the library window (or a folder containing more than one file), a dialog will appear asking if you want to create a new reference for each one and import the metadata from the Internet, or if you want to attach them all to the selected reference.

Type-ahead in Term Lists and the Groups pane
Go to a specific term or group by typing its first few letters. In the groups pane, the search is only for groups and folders whose names are showing.

Bookends PDF attachments that were edited in Bookends On Tap and then synced with Bookends will be placed back in their original folder


Super/Sub in bibliographies no longer will end the style when a space is encountered
You must terminate the super/subscript yourself: H|2|O and ^3^H.

Reference exporting to versions of Bookends prior to 10 has been removed
Reference exported to versions 10-11.3.7 will contain text but not styled text information.

The keyboard shortcut for duplicating a reference is Command-D

"type" is now a reserved word in SQL searches
To perform an SQL search for a reference Type you must enclose this word with square brackets: [type]

For the GUID AppleEvent, multiple refs will be separated by a return (ASCII 13), not a null character
This is because RTF does not allow null characters.

Command-M will minimize the front window
Command-Option-M is the new shortcut for Mark/Unmark references.

If the short title field is empty it will be treated as such when formatting
Previously, the full title was used in this instance.

Window -> Attachments replaces the Window -> Groups menu


Import/export of EndNote 7 XML schema no longer supported
Import/export of XML files compatible with EndNote 8 or later (including all X versions) is supported.

Quick Font toggle

Show Clipboard

There is no keyboard shortcut for deleting a reference being viewed in the standalone reference window
Use Refs -> Delete. When viewing references in the library window, use the Delete key to delete references with a confirmation dialog, or Command-Delete to delete without confirmation.


If you are upgrading to Bookends 12, the first time you run it any existing custom formats will be moved to ~/Library/Application Support/Bookends/Custom Formats Before Bookends 12
You can use these older, non-upgraded formats, if you need them with your pre-Bookends 12 version of Bookends.

When converting an older Bookends database to version 12, all reference field text will be set to black

Bug fixes
Fixed a bug that would result in an error message if you dragged text onto a library window and selected Bookends Tab-Delimited File to import it. Fixed a bug that caused an error if you invoked Copy Formatted while a field was being edited. Fixed a bug in which a pdf shown in the reference pane was not removed when the selection changed and no reference was selected. Fixed a bug that prevented AppleEvent searches for escaped characters from finding the correct references. Fixed a bug that would cause an error to be thrown when doing an Autocomplete Paper with the Term List window open. Fixed several bugs in the formatting of metatypes in scanned documents. Fixed a bug that would yield incorrect hits when doing a boolean OR Find that was limited to references in the Hits List. Meaningless punctuation marks at the beginning of a temporary citation will be removed from the scanned citation. Fixed a bug that could cause an error to be thrown when scanning a .odt (LibreOffice) document.