Version History

Restored direct downloading of PDFs from publishers that use ScienceDirect

• This requires access privileges.

Drag files from the marooned attachment list

• Dragging the selected files is like dragging the files in the Finder. You can move them to another folder, drag them into an “Open File” dialog, drop them on a Bookends library window to attach them, etc. If the files are moved the list will automatically update.

Right-click to refresh the list of files in the marooned attachment list

• This may be useful if, for example, you’ve opened another library that has attachments and want to regenerate the list without having to close and reopen it.

Attaching multiple files to the selected reference has been streamlined

• When you drop more than one file on the library window, one of the options in the resulting dialog is "Attach To Selected Ref". If you select this option a second dialog will offer to rename the files and/or move or copy them to the default attachment folder. These options will be applied to all the files in the drag without further user intervention. In previous versions this dialog would appear for every file in the drag.

Create a notecard with a title from a PDF's table of contents

• When the PDF's table of contents is showing, right-click on an entry to add it to the note stream as the title of a new notecard. If the note stream is showing the notecard will be opened for editing, so you can add content if you want.

When formatting as BibTeX Markup, institutional names (i.e. those terminated with a comma) will be surrounded by curly brackets

Bookends will identify damaged PDF attachments and offer to show them to you in the Finder

• Previously, trying to display a damaged PDF would result in a cryptic error message which could be mistaken for a crash.

When searching a PDF, pressing Shift-Command-G will find the previous match

• As before, Command-G fill finds the next match.

medRxiv was added to the Bookends Browser bookmarks

• This will be seen in new installations of Bookends.

The last run date for a saved search won't be updated if an error occurs

Group names in the manual remove duplicates window are read-only, and an explanatory dialog will appear if you try to do edit them

Preferences changes to library window fonts/sizes are updated immediately

You can show URLs created with OpenURL in the library window browser (default), Bookends Browser, or your preferred macOS standalone browser

• These options are available in the Metadata tab in preferences.

The Action pop-up menu below the reference list has been removed

• These functions and more are provided by a right-click hierarchical menu.

Bug fixes

• Fixed a bug in exporting references to a tab-delimited file.

• Fixed: a bug where a space was used instead of an underline in front of the disambiguating number when renaming attachments.

• Fixed: pressing the cancel button when attaching multiple files at once cancels the entire process, not just the attachment of that one file.

• Fixed:=a bug that prevented the progress window from showing when exporting selected references with a format.

• Fixed: a bug that caused Bookends to add a non-PDF attachment to the selected reference even if you indicated it should be added to a new reference.

• Fixed: a bug where selecting “Open” from the hierarchical menu would not open graphic attachments such as jpgs.

• Fixed: a problem that could cause an error in some situations if the color picker wasn't manually closed.

• Fixed: a bug in manual verification of remove duplicates where a modified attachments field wasn't updated in the database.

• Fixed: a cosmetic problem when switching from a boolean search to Bookends Browser in the Online Search window

File -> Export References provides more flexibility and a cleaner user interface

• You can now use a hierarchical menu to export the selected references or the Hits, decreasing the number of dialog windows that need to be dealt with. Previously you could only export the Hits. These options have also been added to the reference list right-click contextual menu.

Improved marooned attachment manager

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

Bookends will select the default reference Type, set in preferences, when populating the Type pop-up menus in the Format Manager

Previously it selected Journal Article regardless of the user’s preference setting.

New color picker

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

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

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

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

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

Clickable email links work in Bookends Browser

Use swipe gestures to change pages in Bookends Browser

• Swipe between pages with one finger can be enabled in System Preferences -> Mouse -> More Gestures.

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

Updated database engine

Bug fixes

• Fixed a bug where Bookends would misidentify a file as marooned if it contained certain characters, such as parentheses or question marks.

• Fixed a bug where file bundles (e.g. TextEdit RTFD files) were treated as folders and their internal contents identified as marooned attachments.

• Fixed a bug that could cause a hang when performing an Autocomplete Paper using Google Books.

• Fixed a bug that prevented the PDF annotation color icon from changing appearance immediately after the color was edited.

• Fixed a bug in Wi-Fi sync of attachments. The lack of an annotation modification date will no longer cause an error when filling out the note stream.

Marooned Attachments Manager

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

When attaching to a PDF to new reference with Autocomplete Paper, Bookends will import the PDF's title and subject if they are found in its metadata

• If Autocomplete Paper is successful these will be replaced by the information imported from the online source.

Images (non-PDFs) in the display pane can be moved to the Finder or another app by drag and drop

• A copy of the original will be delivered to the dropped location. To create an alias of the image, hold down the Option and Command keys and then drag.

When an image is showing in the display pane, the right-click hierarchical menu has options to open the image, zoom the image, and show the image file in the Finder

• Opening the image with a double click has been removed because it conflicts with drag and drop.

The jpg files of cover art imported from Google Books will be named using the same rules as when renaming attachments

• Previously, they were named "Download" followed by a random number.

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

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

Set the font and font size for PDF comments in Preferences

References of Type Review will be treated as Journal Articles when formatting an entry in the Vol (Issue) field

• That is, the volume and issue can be output together or independently.

Live Search will perform a string (character) search for characters enclosed in quote marks

• Previously this search would only match whole words.

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

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

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

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

Bug fixes

• Fixed a bug in which a name with an apostrophe caused an error when generating a BibTeX key.

• Fixed a bug in "Make PDF note from selection".

• Fixed an error that could occur when attaching hundreds of PDFs at once.

• Fixed a bug in cloud sync that caused an error when linking to an existing library in the cloud.

• Fixed a bug that caused an error when attaching a PDF whose contents could not be read.

• Fixed an error that occurred when doing a find again in a PDF with after changing the selection.

• Fixed a bug where the secondary order field in a format wasn't used unless the scan generated a bibliography.

• Fixed a bug that could cause an image in the display pane to persist when a search found no matching references.

• Fixed an error that could occur when switching references with an attachment being shown.

• Fixed a bug when deleting references from very large libraries.

• Fixed several problems with Wi-Fi syncing of attachments.

• Fixed a problem where using the Temporary folder as an ad hoc attachment folder generated errors in Catalina and later.

Major code refactoring of many core functions

• The code has been modernized and streamlined.

When attaching to a PDF to new reference with Autocomplete Paper, Bookends will import the PDF's title and subject if they are found in its metadata

• If Autocomplete Paper is successful these will be replaced by the information imported from the online source.

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

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

When Bookends is watching the Downloads folder for PDFs, files ending in ".pdf.part" will be ignored

• These files represent partial downloads in progress and should not be attached until they are complete.

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

You are able to use default attachment folder subfolders to any depth when attaching files

• This was previously limited to just root level subfolders.

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

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

Added PubMed Central to the Bookends Browser default bookmarks

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

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

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

Attaching a file in the Trash is no longer allowed

Updated database engine

Bug fixes

• Fixed: a bug where moving to another reference using the Links Inspector could cause edits to a reference field to be discarded.

• Fixed: a bug where creating a new format based only on the first Type of the selected format would result in an error.

• Fixed: a bug that prevented Bookends QuickLook from working.

• Fixed: bugs in scanning with formats that have a secondary order field for citations.

• Fixed: Refs -> Generate BibTeX Key works again.

• Fixed: a problem in Bookends Browser where trying to download a .docx file would cause Bookends to hang.

• Fixed: a bug that could prevent a PDF from being moved to the trash via a menu option if a file with the same name was already there.

• Fixed: a bug that was introduced in 13.5 where importing from Zotero failed to import attachment file names.

• Fixed: a bug in the column view where the first time it was used the indicated sort order was incorrect.

• Fixed: a problem where an error could be generated when closing the online search window in the middle of a search.

• Fixed: a bug in the watch folder where the same PDF could be added to the library multiple times when files were copied rather than moved.

• Fixed: a bug in scanning .odt files where the presence of hard returns (line breaks) would result in an error.

• Fixed: a bug that caused operations that opened PDFs in the default viewer to fail.

• Fixed: a bug in Spotlight Search where Bookends ignored attachments whose names contained a slash.

• Fixed: a problem with scanning some Mellel documents on M1 Macs.

• Fixed: a bug that prevented bibliographies from being placed in the clipboard after scanning RTF files.

• Fixed: a bug that allowed the addition of the default attachment folder and subfolders to the ad hoc attachment folder list.

• Fixed: a bug that prevented hypertext links in notecards from showing with right-click.

• Fixed: a bug in notecard word wrap.

Fixed a number of issues that arose with the new universal build

• These are itemized in the bug fix list below.

Improved AppleEvent communication with Word

Bug fixes

• Fixed: a problem with labels where editing one in preferences would cause an error.

• Fixed: a related problem where extra label names were added to the label list for the default reference Type.

• Fixed: the failure for some to find and display PDFs containing Unicode characters.

• Fixed: a bug in switching from Groups to Term Lists in the library window.

• Fixed: a bug that prevented Z39.50 searches (the Library of Congress and universities) from working on Apple Silicon Macs if the filter was set to use Direct Access Z39.50.

• Fixed: a bug that caused an error when upgrading from Bookends 13.5 or early versions of Bookends 12 or older.

Bookends is a Universal Binary

• That means it is optimized for both Apple Silicon- and Intel-based Macs.

Manage Ad Hoc Attachment Folders

Updated database engine

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

Attachment Flow view removed

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

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

Bug fixes

• Fixed: a bug in scanning where the secondary order field could be ignored in some cases.

• Fixed: several bugs in the Works Cited Inspector that affected the UI and the hierarchical pop-up menu.

• Fixed: a bug in Google Books online search where the book cover art was not being displayed.

• Fixed: an error that could occur when trying to add a notecard when no reference was selected.

• Fixed: Refs -> a bug in OpenURL where searches using the token did not work.

• Fixed: a bug where Edit -> Copy Hypertext Link might not be enabled when clicking in the groups pane.

• Fixed: a bug where Bookends would be off by one in identifying the group a reference was dropped on.

New Send Feedback menu

• This is under the Help menu and creates an email to support@sonnysoftware.com in your default email client.

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

The Cited Works Inspector has been updated for Dark Mode

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

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

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

Improved connection error detection when downloading PDFs

Add a PDF underline annotation to the Bookends database with a right-click in the note stream

• Previously, this was only available for highlighted text.

Updated the JSTOR parser to deal with changes made by JSTOR

Bug fixes

• Fixed: a bug where a newly created reference didn't immediately appear in the reference list if a smart group was selected.

• Fixed: a bug where the background color obscured the white text when editing a PDF note in Dark Mode.

• Fixed: a bug where the font of a field could be changed to the System default when consolidating terms in a Term List.

Restored importing from JSTOR

• Importing references that weren't available via free access had been broken because of changes made by JSTOR.

Requests to Crossref are faster and more reliably return a DOI

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

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

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

Improvements in scanning LibreOffice .odt files

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

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

In the Attach dialog the pop-up list of subfolders to which the file could be moved is sorted alphabetically

• This fixes a problem introduced by the APSF file system. Only top level subfolders will be shown.

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

Bug fixes

• Fixed: restored detection of drag and drop of PDFs and other files types onto the Bookends icon in the Dock.

• Fixed: a bug in Live Search that allowed Spotlight searches to be initiated with every keypress instead of when a Return is pressed.

• Fixed: the contents of the edit pane attachment tab will be emptied when no reference is selected.

• Fixed: a bug that prevented Live Search of notecards from finding tags (i.e. when the tag word is preceded by %).

• Fixed: a bug where PDFs with slashes in their names weren't displayed in the edit pane Attachments tab.

• Fixed: an error that could occur when searching Google Books.

• Fixed: a bibliography bug were references could be output in small caps if the default bibliography and reference font sizes were 3 points apart.

• Fixed: a bug in secondary citations where "et al." was output after the surname even if Surname Only was selected.

• Fixed: a bug where any groups selected in the groups pane were deselected when a PDF was dropped on it.

The maximum number of columns in the reference list has been increased to 10

Bookends has been updated to use modern file system APIs

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

Improved Bookends Browser handling of PDFs

• This should result in faster downloads and better compatibility with proxy servers.

Faster reference navigation when the edit pane is visible

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

Improved the appearance of lists

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

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

Improvements in Wi-Fi sync

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

Bug fixes

• Fixed: a bug that could cause an error message when closing the library window.

• Fixed: reduced cursor flicker when mousing over a PDF.

• Fixed: the width of field labels adjusts to the width of the label text, ensuring that clicks on labels on the right don't open the enlarged window for the field on the left when the edit pane is very narrow.

• Fixed: an error that prevented some users from opening the Registration Window.

• a problem when attaching some PDFs from JSTOR where the publisher's name was promised but was actually missing.

• Fixed: problems in unscanning documents in which citations had non-default styles.

Select Hits Group is a new menu item in the Hits menu

• The keyboard shortcut is Shift-Command-H.

When searching a PDF, all matches will be highlighted as they are in Preview

• Note that in some cases the highlight will be blue, not yellow, until you scroll to another page and back. This is a cosmetic bug in macOS.

Command-Option drag of the PDF proxy icon in the PDF toolbar will create an alias of the PDF when dropped

• This is in addition to the normal behavior where dragging without keyboard modifiers will create a copy of the PDF when dropped.

When searching PubMed, the lower pane in the Online Search window will show the article on the publisher's web site if it can

• If not (entries in PubMed may lack that link), Bookends will default to the article on the PubMed web site.

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

Bookends can insert a space in front of a semicolon separating multiple citations in a group

• This option is in the format's Citation Options -> Common Settings section.

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

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

Improvements in Wi-Fi sync

Attachment Inspector improvements

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

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

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

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

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

Bug fixes

• Fixed: a bug that caused the PDF page number and the highlighted text to run together when adding a highlight to the Notes field.

• Fixed: unlike highlights, clicking on a note card showing a PDF underlined text annotation will not permit its import into the library.

• Fixed: a bug where the Add Note pop-up menu under the note stream was enabled when no reference was selected.

• Fixed: a bug that caused some fields in the edit pane to incompletely refresh their contents when moving between references.

• Fixed: adding cited pages to a BibTeX citation in the Copy Citation With Modifiers dialog now works.

• Fixed: a bug where tag cloud stop words were applied to file tags.

• Fixed: a bug where a Finder tag might not be refreshed when switching between PDFs.

• Fixed: a bug in Compare References where the field from the wrong reference might be moved when Command-clicking on the field symbol.

• Fixed: a bug in scanning a text file with BibTeX citations where a citation wasn't found if it was preceded by a modifying metacharacter (e.g., ^, %, etc.).

• Fixed: a bug that prevented a right-click on a display pane image of a file in an attached folder from bringing up the hierarchical menu that allows zooming.

• Fixed: Bookends will add the extension .bdb to any Bookends 9 library that is converted to the current database schema.

• Fixed: a problem that could cause Bookends to incorrectly identify the default email client.

• Fixed: a bug in Global Change where an error occurring when moving date from a styled text field to one without styles.

• Fixed: an issue in Bookends Browser where you might be prompted to save login credentials when no login as done.

Widescreen layout

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

New Speech toolbar icon

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

Double click a reference to toggle the edit or attachment pane open or closed

• Which pane a double click opens is set in preferences. Previously, a double click would only open the selected pane.

The text size for the Summary view will be the same as for the Note Stream

• Both are set in Preferences with the Note Stream & Summary pop-up menu.

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

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

Added bioRxiv to the Bookends Browser default bookmarks list

• This will only be available when performing a new install.

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

Bug fixes

• Fixed: an error that occurred when switching a reference list column header to Date Added.

• Fixed: a bug that caused Bookends to hang if the Delete button was removed from the library window toolbar.

• Fixed: a bug where the bibliography was output with white text when scanning a Word document in Dark Mode and using a numbered format.

• Fixed: a bug in scanning a NWP document when in Dark Mode where NWP would treat the bibliography as simply text and couldn't unscan it.

• Fixed: a cosmetic issue where in specific cases the selected reference could be displayed as white text when the list lost the focus.

• Fixed: a problem when importing multiple PDF in batch where matching references already exist.

• Fixed: a permissions problem in Catalina where a PDF annotated in iOS wasn't downloaded by wi-fi sync.

• Fixed: a rare problem where when opening a non-PDF in a third-party app Bookends would try to use the default PDF reader.

Improved Bookends Browser

• Bookends can display web pages and PDFs with atypical URIs, has more safeguards to prevent Google Scholar from thinking you're a robot, and can resolve Google Scholar reCAPTCHAs if you are challenged to prove you're a human.

Import PDF attachment names with import filters

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

Insert attachment names from any field into the Attachment field with Global Change -> Move Field

• This is for power users and may be useful if you imported attachments names from another source into a normal Bookends field. This feature will allow Bookends to recognize them as attachments, and if the file of that name is in the default attachment folder Bookends will display it.

Updated the JSTOR parser to deal with changes made by JSTOR

Improved error handling when a PDF download times out

New preference option to allow/disallow Bookends from forcing downloading of attachments in iCloud Drive that were moved to iCloud

• This option is in the iOS tab and the default is "allow".

Updated the COinS parser for WorldCat

When responding to a hypertext link from another app, Bookends will initially search the current list of references

• If not found, all references will be displayed and the matching reference selected. This will prevent you from being taken out of a group if it isn't necessary.

The group All will be selected if you import references with a non-static group selected

• This ensures that the imported references will be highlighted. If a static group is selected, they will be added to that group.

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

Different Title Case settings can be specified for the titles of a book chapter and the book it is in

• This option appears when you select the Book Chapter Type in the Formats Manager.

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

Database engine updated

Bug fixes

• Fixed: a bug where the top of the reference list could obscure the PDF toolbar in full screen view.

• Fixed: two bug where the text in bibliographies generated for Nisus Write Pro or saved directly to disk as RTF was in Dark Mode was white.

• Fixed: an issue with some imports from JSTOR where titles were truncated if they contained a quote mark.

• Fixed: improved trapping (ignoring) of invalid entries in the Quick Add dialog.

• Fixed: Bookends will now work if you mistakenly remove the live search field from the toolbar.

• Fixed: a bug in cloud sync that could prevent the library from being opened with a "record locked" error message.

• Fixed: a bug in the reference list view where the sort after pressing the header was not in the correct direction.

• Fixed: a bug in editing or copying of notecards where some characters, including smart quote marks and apostrophes, were lost.

• Fixed: an error that occurred when using the keyboard shortcut to go to the PDF find box.

• Fixed: a problem where having the location of cited pages specified in the citation options tab would result in the removal of any text styles if cited pages weren't included in a temp citation.

• Fixed: a problem where some Unicode characters didn't appear in the formatted reference.

• Fixed: a bug when using a menu to move groups to a nested folder where the UI would initially show the groups in the wrong folder.

• Fixed: a bug in wi-fi sync where an error sometimes occurred when syncing a new Mac library with one that existed on the iOS device.

Automated group repair

• Bookends will determine the integrity of the group hierarchy when a library is opened. If irregularities are found they will be repaired. A repaired group may be moved out of a folder and placed at the root level if its intended location couldn't be determined.

Bookends will force PDFs in the iCloud Drive folder to appear on the hard drive if you have Optimize Mac Storage turned on

• This is necessary because Bookends can't find PDFs that were removed by macOS and stored only in the cloud.

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

Improved visuals in Dark Mode

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

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

Perform recent and smart SQL group searches from the SQL search window

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

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

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

When a reference is changed or refreshed, the browser view in the bottom pane will not reload if the URL in the URL field is the same as the one for the reference

• PubMed users note that the stored URLs that worked with the old PubMed site are no longer valid. You can correct that with Global Change -> Find And Replace, searching the URL field for https://www.ncbi.nlm.nih.gov/pubmed/ and replacing with https://pubmed.ncbi.nlm.nih.gov/ . The PubMed import filter has been updated to use the new URL prefix for newly imported references.

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

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

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

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

Improvements in the arXiv parser

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

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

Database engine updated

Updated the PDF toolbar and added new graphic elements

PDF Table Of Contents

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

Right-click on the PDF proxy icon in the PDF toolbar to pop-up a menu listing each folder in the pathname

• Select a folder to open it its enclosing folder in the Finder and select it. This works just like the window proxy icons.

Manage continuous PDF highlighting via the keyboard

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

Added a warning dialog when a damaged format is detected

• It instructs you to move the damaged format file to the trash and select another.

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

The list selection color is now the macOS accent color

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

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

Improved detection of PDFs in some web pages

There is an option to hide group pane folder badges

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

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

Preference settings for openURL will be synced between computers

Bug fixes

• Fixed: a problem where the top of the library window could appear offscreen.

• Fixed: removed extraneous HTML from the Abstract of Google Scholar results when sorting by date.

• Fixed: many fixes for cosmetic issues in Dark Mode.

• Fixed: a bug where bibliographies created for Mellel in Dark Mode were white.

• Fixed: a bug in the generation of formatted citation examples.

• Fixed: a bug in the height of the PDF in the edit pane's Attachment tab.

• Fixed: a problem where some users weren't able to select options in the Inspector's segmented button.

• Fixed: a bug that caused errors when opening libraries after customizing some of the toolbar elements.

• Fixed: a bug where styled text changes weren't saved in dark mode.

• Fixed: a bug in the automated PubMed search window where selected a library from a number that are open failed to import the references.

• Fixed: several bugs in Wi-Fi sync.

• Fixed: a bug that prevented Autofill From Internet from working with ISBNs.

• Fixed: a bug in Remove Duplicates that prevented changes made in the Verify process from being saved.

• Fixed: tool tips for the buttons in the library window bottom strip were restored.

• Fixed: an issue where the selection could change in the reference list after doing an Autofill From Internet.

• Fixed: several instances where changes in the database weren't synced.

• Fixed: a bug where bibliographies created by scanning a Pages files in Dark Mode where output in white instead of black.

• Fixed: restored the dialog asking you to paste in the bibliography after a Pages scan.

Bookends is Dark Mode compatible

• There are a few minor changes in the UI to make the appearance work well in light and dark mode.

The library window now has a macOS-native toolbar

• This means that you can use a right click to configure

Detach attachments in the Inspector by pressing the Delete key

• Menu items available in the old Action pop-up are now available with a right-click.

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

You can select multiple citations at once in the floating citations window

• This makes it possible to perform operations like Copy Citation on several references at once to create a citation group.

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

Improved SQL search

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

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

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

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

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

Amazon France and Amazon Germany searches have been removed

• These sites finally caught up with Amazon.com and began throttling searches, rendering them useless for Bookends.

Updated database engine

Bug fixes

• Fixed: a bug where the default output style was set to Styled Text after scanning a Word document regardless of the setting in preferences.

• Fixed: a bug where removal of attachments in the Inspector wasn't marked for sync.

• Fixed: a problem with an atypically-encoded en dash in an ISBN used in Quick Add.

• Fixed: a bug where a duplicated reference wasn't automatically added to the original's group, if any.

• Fixed: a bug in where the short title created from the full title via a right-click wasn't saved.

• Fixed: a bug in opening and displaying attached Mellel files.

• Fixed: several issues with the Watch folder.

• Fixed: an error in Bookends Browser caused by missing data returned from Crossref.

• Fixed:a bug where the Import Reference menu was enabled inappropriately.

Bookends 13.3.2 requires macOS 10.13 (High Sierra) or later

• This is necessary to have access to APIs used by the updated Bookends Browser.

Bookends Browser

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

Bookends Browser

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

Bookends Browser

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

Bookends Browser

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

Autocomplete Paper works when the attachment is a webarchive

Added a format for The Generic Style Rules for Linguistics

Bug fixes

• Fixed: a bug that caused an error message when opening the Bookends Browser window.

• Fixed: a scanning bug when using an author-date format with year-only for repeated authors and there is preceding literal text in a citation group.

• Fixed: a bug in Wi-Fi sync.

• Fixed: a bug in which creating a notecard with page # from an annotation didn't calculate to true page number correctly.

Bookends Browser has been completely rewritten

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

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

Much improved importing from Papers 3

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

Enable/disable EZProxy while in Bookends Browser

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

Various enhancements and fixes were made to the reference list in the library window

• In addition, the dates added and modified are now shown in the form YYYY-MM-DD + time.

Updated database engine

Bookends will import a reference if its URL from the updated PubMed web site is dropped onto the library window

• The base URL of this site is "https://pubmed.ncbi.nlm.nih.gov".

Bug fixes

• Fixed: a bug in citation disambiguation when scanning with an author-date format.

• Fixed: a bug that prevented direct import from Google Scholar if you are using EZProxy.

• Fixed: a bug in Standardize Journal Names.

• Fixed: a bug in the tag cloud search for authors and editors that have periods after initials.

• Fixed: when changing a selection in the tag cloud any text in the live search field will be taken into account in filtering references.

• Fixed: a bug in the Links Inspector where clicking on an empty row would deselect all references in the library window.

• Fixed: hyperlinks to unique IDs in the Summary view will only be created if the # in the abstract or notes is followed by a number.

Updates for Catalina

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

Import from Google Scholar in Bookends Browser

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

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

Reference metadata will be imported from a direct search of Google Scholar even if Google thinks you are a robot

• In this case the data are scraped from the web page and may not be complete.

Sort groups and folders

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

Finding and displaying attachments is up to 3 times faster

• This will be noticeable when you have many attachments.

Formatting references as BibTeX is much faster

New Library of Congress online search

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

Updated detection and removal of the Adobe PDF Viewer plug-ins

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

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

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

Bookends no longer scans documents created with Pages '09 or earlier

• Refs -> Scan Open Apple Pages Document will not be enabled unless a more recent version of Pages, version 5 or later, is running.

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

PDFs added from the watch folder will not be renamed if their metadata is not found online

• You can now tell Bookends to "Rename imported files if metadata are found" in the Configure window. This is the reverse of the previous setting, which was "Don't rename imported file".

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

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

Automatic import of reference from files with uniquely identifying extensions

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

Improved DOI detection in web pages

Simple arXiv searches are by word

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

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

Updated database engine

• Fixed a bug that caused a crash when using "cast" in an SQL group.

Bug fixes

• Fixed: a bug that prevented the creation of PDF comments.

• Fixed: a bug in the Summary view where extra returns were added around styled characters in the abstract or notes and \par would be shown in place of returns.

• Fixed: a bug that prevented styled text information added when editing a notecard to be saved.

• Fixed: a bug that prevented the Browse button in the Attachment dialog from setting the pop-up menu to the selected subfolder.

• Fixed: several bugs in opening of spring loaded group folders.

• Fixed: a bug that could prevent some PDF DOIs from being resolved.

• Fixed: a bug that prevented the last PDF highlight from appearing in the note stream.

• Fixed: a bug in Wi-Fi sync.

• Fixed: an issue that will make importing direct importing of references from Papers 3 more reliable.

Updated database engine

Improved update notification

Bug fixes