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 exeeds 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 intgernal 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 authort’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 veriified Mellel citation that was preceeded 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.