Version History
Version 14
February 3, 2024
Citation Inspectors enhanced
Filter the list of references "cited in" or "cited by" to show only those that are articles or have a PMID or PMCID. You can also view the selected publication's abstract, if available.
Filter your own works in My Publications to see only those that have a PMID, a PMCID, or are articles
Open an attachment that Bookends can't display in a compatible app of your choosing
Right-click on the "Can't display" message to generate and select a list of installed apps that can open the attachment. The first option is "Default", which will open the Finder's default app.
Extract each reference's PDF annotations to disk as an individual file
If you are saving extracted annotations to disk, check "Create one file per reference" in the configure window and the output for each reference will be saved to a separate file. This is useful for those exporting information for use in personal knowledge management systems that store each idea or concept as an individual "card" (e.g. Zettelkasten).
Sort PubMed search results by Most Recent, Relevance, Authors, or Journal
Previously, searches were always sorted by Most Recent.
Bibliographies created by exporting the selected references will be sorted according to the current format
If the format doesn't sort the bibliography, the references will be listed in the same sort order as the reference list.
References added by dropping files onto a library window will be added to the single selected static group, if any
If that is not the case, they are added to All.
When scanning with a format that replaces temp citations with numbers, non-breaking hyphens will be used when there is a consecutive sequence
This prevents a word processor from using the hyphen as word-break character and displaying the first and last numbers on different lines.
OpenAlex is bookmarked in Bookends Browser
Code optimizations and cosmetic improvements
Fixes
Fixed a bug in the Citation Inspector where the retraction indicators were not removed when subsequent references were analyzed.
Fixed a rare problem where a PDF that was moved to the Finder Trash could be shown again if a PDF with the same name was attached immediately afterward.
Fixed an issue where the assignment of extensions to files containing formatted references was erratic.
Fixed a bug in the Format Manager Types pop-up menu where there was an incorrect limit on the maximum number of Types that could be shown.
The right-click display of the basic Finder tags in the PDF toolbar was restored after being broken by macOS upgrades.
Fixed bugs in setting and saving hypertext links in notecards.
January 13, 2024
Discover yourself
If you have an ORCID identify (https://orcid.org/) you can instantly explore your own publications and their relationships with others. Enter your ORCID ID in Settings (Internet tab) and Bookends will query OpenAlex.org for the number of times your publications have been cited and your h-index. You can choose to receive a notification when new citations are added. The OpenAlex database is updated once a month, so you may find that more than one new citation appears at the same time. Use Windows -> My Publications (ORCID ID), which will bring up a list of all your publications and the number of times each has been cited. Select a publication and in an adjacent list you will see all of the papers that have cited it, the most recent at the top. You can filter this list to show just articles, or just articles with PMIDs or PMCIDs. You can also choose to show the abstract of the selected work, if available. Double click on a publication to open it in your browser, and import publications into your library via a right-click contextual menu or drag and drop. Citing references that have been retracted will be flagged. Note that not all ORCID IDs are found by OpenAlex, and for those that are you may need to curate your publication history at ORCID.org to make sure it is accurate and up-to-date.
Global speed improvements
Optimizations in the Bookends framework and numerous functions have resulted in snappier performace throughout. This is especially noticeable with large libraries.
A DOI's structure will be validated before attempting to use it to Autofill from Internet
Added additional protections to prevent commas from being set as the citation separator when enabling and then disabling BibTeX and using citekeys with Copy Citation
Fixes
Fixed an issue in importing references from an EndNote XML export where attachment subfolders could be added to the ad hoc attachment list.
Bookends won't sync with a .bib file that has been made invisible.
Fixed an error that could occur when formatting Mellel documents.
Fixed a bug that caused some automated DOI searches on PubMed fail.
Attempts to access reference information from OpenAlex when offline will result in an explanation rather than an error warning.
Fixed an error that occurred when importing a reference from Google Scholar with an arXiv DOI.
There will be no message that a bibliography is in the clipboard after an Apple Pages proofreading scan.
Fixed a bug in Copy Formatted Citation.
December 16, 2023
Vastly improved citation discovery
The Citation Inspector lets you identify works cited in, or that cite, references in your library. It has been completely rewritten, and now uses as its online source OpenAlex (https://openalex.org/), an index of hundreds of millions of interconnected reference entities. This means that you will find many more citations and receive better metadata. Furthermore, OpenAlex covers more academic disciplines than were available before, including many in the humanities (e.g., philosphy, education, etc). To make citation discovery easier to access, there is a menu Refs -> Find Cites, which is enabled if the selected reference contains a DOI, PMID, or PMCID. These options are also available via a right-click contextual menu. The Citation Inspector UI has also been updated, with sortable independent columns for author, date, title, and source.
Import citations from the Citation Inspector
This is done via the import button (share icon with downward arrow), a right click contextual menu, or drag and drop. The first two allow you to import the references with or without a link to the parent, such as Work: Work Cited. Citations that are already in your library will have a yellow background. A right click menu will show you if it is already linked, and if not will offer the option Link To Parent.
Retraction detection
If a reference found in the Citations Inspector has been retracted, you will be notified. If the publication is the parent, the color of its outline will turn from blue to red. If it is a citing reference, you see a red flag and "Retracted" will be inserted in front of the title. According to OpenAlex, because retractions may not be reported in a timely manner if at all, there may be false negatives. However, a reference that is flagged has almost certainly been withdrawn.
There is a predefined smart SQL group called Retracted
Output the number of times a reference has been cited in bibliographies
A question mark (?) in a format's field order will tell Bookends to query OpenAlex in real time and output the number of times the reference has been cited. If OpenAlex finds a reference that has not yet been cited, a 0 will be output. If OpenAlex cannot locate the reference, nothing will be output. This is an example of how the preceding literal text in a format will be output only if the the reference is found: $Times cited: $?.
OpenAlex replaces Dimensions.ai as a source for the edit pane citation count
Clicking on the number of times cited opens the Citation Inspector to the cited-by pane. A right click on the number in the edit pane brings up a menu that lets you view the citation metrics on the Dimensions.ai web site. Note that although OpenAlex must have indexed the publication, it is possible that Dimensions.ai has not.
Bookends imports higher quality metadata for references found on Google Scholar if they have a DOI
In such a case, after the initial import Bookends will immediately query Crossref and update the metadata with its content.
Quick Add is much faster when importing multiple references at once
Dropping text containing a DOI on a library window while a static group is selected will import the reference to that group
Bookends Browser identifies more DOIs in web pages
Bookends compares Unicode character values when sorting lists
The option to sort by ASCII values has been removed.
You can avoid the annotation popover when selecting PDF text by holding down the Command key
An empty reference added when the list is sorted on a numeric field in descending order will be inserted at the beginning, not the end, of the list
Fixes
Fixed a bug that could prematurely close the PDF selection popover window.
The pressed state of the buttons along the bottom of the library window are now updated when the layout is changed in the View menu.
Fixed a error in the placement of a PDF proxy icon contextual menu when the PDF is showing in the edit pane Attachments tab.
Fixed bugs in the handling of BibTeX super and subscripts.
Fixed a bug where in some cases the search field text did not scroll to the right when needed.
Fixed a bug where no reference was selected after moving references to the trash using Command-Delete.
Fixed a bug in the Markdown link created when copying a PDF annotation's content and link.
Fixed a bug where a new empty reference in a standalone window was populated by the selected reference is a group was showing.
Fixed a bug that could cause an error when a color was assigned to slot 9 but not slot 8 in Settings.
November 11, 2023
Copy a PDF annotation's content and hypertext link in one step
When right-clicking on a PDF highlight, underline, or note, the contextual menu will let you copy its link as well as textual content to the clipboard. This can also be done with a right-click on the annotation's notecard. The human-readable link text will show the name of the PDF and the page on which the annotation appears.
Use Live Search to find references with a specific color label
You can search using the color label's text (e.g. 'red' or 'important') or its order number in Settings (e.g., a number from 0 to 9). In many cases this may be more convenient than using Find or a smart group.
Performance improvement: Extracting and formatting large notes containing styled text is much faster, in some cases over 1000-fold
Performance improvement: Sorting the reference list when there are many selections is much faster
Global Change -> Add/Remove PDF Tags autocompletes as you type
The Label popup menu in smart groups and the Find dialog displays the label color in addition to the text
Bookends will not allow you to set a color label's text to an empty string
This prevents errors that occur when the color has no textual definition.
Citekey punctuation is preserved when the output style is BibTeX
Fixes
Fixed a bug where moving reference list columns could generate and error under certain conditions.
Edit -> Select All will select all web page content when Bookends Browser has the focus.
Fixed several cosmetic issues in the Online Search window.
Fixed a bug where PDF deep links created in a standalone reference window were malformed.
Fixed a cosmetic bug where text fields were not correctly sized and positioned when a standalone reference window was opened.
Fixed a bug in the dialog informing users that Semantic Scholar doesn't support boolean searches.
Fixed a minor cosmetic flaw in the standalone reference window Attachments pane.
Fixed a bug in Global Change -> Modify PDF Tags where batch changes failed.
Fixed a problem where closing the Bookends Browser window during a search for a DOI would cause an error.
Fixed a bug where some references that were in the database were not highlighted in yellow after importing from the Inspector.
The result of using Copy Formatted -> Citation will be automatically pasted into a linked Nisus Writer Pro document.
October 7, 2023
Display the number of times a reference in the scientific literature has been cited and link to publication and citation metrics
When the Times cited checkbox in Settings (Refs tab) is ticked and the edit pane is open, Bookends will query Dimensions.ai, a comprehensive scientific research database, and display the number of times a reference in the scientific literature has been cited. The display is a live link that takes you to more detailed information about the reference's publication and citation metrics. This is information is obtained in real time and requires an active Internet connection. Right-click on the link to select the browser to use: your default browser or Bookends Browser (this setting is saved, so changing it is only necessary if you want to change the current choice). This feature works with references that have a PMID from PubMed or DOI from Crossref, and if their citation metrics are available from Dimensions.ai. If these criteria are not met, the letters "N/A" (not available) will be displayed instead of the link.
Added an import filter that lets you search and import from the Common Library Network (K10plus)
This is a database with contents contributed from over 2000 German institutions. Many of the resources are in English and other languages, making it a valuable source for scholars regardless of their nationality or language.
If Bookends finds a JSTOR or arXiv unique identifier when attaching a PDF, it will use the corresponding site rather than Crossref.org when importing the metadata
Metadata from JSTOR and arXiv is generally more complete than that provided from Crossref.org.
Updated the initial installation process to enable the new versions of the Chicago and Turabian formats
Updated the arXiv filter to import DOIs, if available
Extracted live links are now separated from the corresponding annotation by a space, not a Return
When attaching a PDF with a DOI, Bookends will remember the setting for the "Attach to a new reference" checkbox in the attach dialog
Previously, this option was automatically checked, which meant you had to uncheck it every time you wanted to add a PDF to an existing reference.
Bug fixes
Fixed a bug where an error could be reported when drag-reordering field labels in Settings.
Fixed a Dark Mode bug where the color and ratings indicators would overlap with the Type popup menu when the edit pane was too narrow.
Importing references from an existing bibliography works again.
September 9, 2023
Bookends Browser will detect and import references from more online repositories
Examples include NASA/ADS and European PMC.
Show annotations in the note stream only if they have assocated notes
If you have chosen to show PDF annotations in the note stream, this option can be toggled by right-clicking on a notecard. When enabled, only annotations that contain user-supplied content (i.e. notes) will appear. This applies to standalone note annotations, highlights, and underlines. The setting applies for the duration of the current session.
The SQL search windows have a pop-up menu listing the field labels and their actual database field names
If you select one it will be inserted into the search field. The field labels of the default Type are shown.
Removed obsolete subject options from PubMed Advanced Search
Added the formats Turabian Notes (9th ed) and Turabian Author-Date (9th ed)
Populating the reference list is faster
If Highlight owning groups always is enabled in Settings it is much faster.
When attaching a PDF that has a DOI, Bookends will automatically tick the Attach to a new reference checkbox
Uncheck it to attach the PDF to the selected reference.
When finding marooned attachments, a dialog will show the number being verified and give you the option to stop by pressing Command-
A subtitle will be included when importing a reference metadata from Crossref
Cosmetic improvements in the display of information in dialogs and the edit pane
Bug fixes
Fixed a bug that caused an error when creating a subject bibliography with a group whose name contains an apostrophe.
Fixed a bug where the final scanned Word document did not contain the bibliography when scanned on some systems were the language was set to Japanese or Korean.
Only files with a .xml extension can now be selected in the Open File dialog when you tell Bookends to import XML.
Fixed a bug that could cause an error when searching Google Books.
August 5, 2023
Improvements in PDF annotation creation, display, and appearance in the note stream
The UI for adding content and user interactions is more natural. Among the improvments are (1) animated text boxes with compatible colors are used for adding/editing content, (2) there is a visual indicator that a highlight or underline contains content, (3) standalone notes open with a single click, (4) notes can be added to underlines, (5) right-click on highlights or underlines to add or remove notes, and (6) right-click to change the color of a standalone note.
Notecard appearances are more pleasing. A color bar will match the annotation's color. Notes belonging to highlights or underlines are inset, and their color will be a muted version of the parent's. Note annotations can be edited in the note stream (there is no lock icon) and the PDF itself will be updated if you do.
Improved integration of PDF annotations with the note stream. Notecards containing the text from the reference's notes are listed first, and a light blue line separates the last from any PDF annotaion notecards. PDF annotations are listed in the order in which they appear, regardless of type. Notes belonging to markup annotations are listed immediately below their parents. Moving to the selected annotation in the PDF or note stream is much calmer — if you click on an annotation or notecard and the target is already visible, no scrolling will occur.
New features and enhancements to the extraction of PDF annotations (and now reference notes)
File -> Extract Notes And PDF Annotations has two submenus: Extract Now and Configure Then Extract. The first extracts the data immediately, using the current output settings. The second lets you adjust the settings before performing the extraction.
Extract reference notes as well as PDF annotations. Note text styles and live links will be preserved when the output is Styled Text. These will be converted to their appropriate equivalents if the output style is Markdown or HTML.
Output the extracted information to a new window or a file. If you repeatedly save a file to the same location, you can specify it in the configuration window. If you do, the file will be saved immediately, bypassing the Save dialog. If there is an existing file with the same name it will be overwritten. This can be useful if you repeatedly extract information to a file for processing by other apps.
Extract from references in particular groups. If the Groups pane has the focus, only the references in the selected groups will be processed.
Create hypertext links to the references themselves as well as the extracted annotations.
Extracted PDF page numbers will reflect the true publication page number if it is available, or if you have entered the page range in the reference's Pages field. Otherwise, page numbers begin at 1.
Notes added to markup annotations will be output immediately after the highlighted or underlined text. If colors are extracted, highlight notes will have a softer color than the highlight itself.
Information extracted to a new window can be saved to disk with a right-click contextual menu.
You can initiate an extraction with an AppleScript
AppleScripts can specify Markdown as the output style
Added a bookmark for Dimensions.ai in Bookends Browser
An excellent source for references in the sciences and engineering and thier PDFs.
System-enabled conversion of straight quotes to smart quote is automatically disabled in the SQL search window
SQL does not allow smart quotes in searches.
The different Chicago A and B formats have been renamed to Chicago (Author-Date) and Chicago (Notes), respectively
If you have modified the ones we ship, they will remain in your Custom Formats folder and be shown in bold face. The new factory default formats will appear as well in plain text.
Bookends will import only the attachment name from .ris files that contain the L1 tag
This is useful when importing references with attachments from apps that export the full pathname such as PaperPile, because Bookends cannot use the pathname to locate attachments.
Minor changes to output style names and menu shortcuts to simplify and clarify the UI
Support for Refbase has been removed because Refbase.org is now offline
Bug fixes
Clicking on an embedded hypertext link in the Summary view now takes you to the destination.
Fixed a bug where reordering rows by drag and drop did not work if they were accessed by using the horizontal scrollbar.
Fixed a bug where reordering rows caused an error if sorting of the reference list was unchecked in Settings.
Fixed a bug where adding multiple PDFs at once when using a database-specific attachment subfolder caused an error.
Fixed a bug where the old reference list columns settings reverted to the factory default when updating to 14.2.2 or later.
Fixed a bug in saving the extracted annotations as styled text.
The annotation popover can now be dismissed by pressing Escape.
Fixed an error message that could rarely happen when the reference list was filled out.
Fixed a bug where a newly created group folder was treated as a normal group until the pane was refreshed.
Fixed a bug where text styles were removed when formatting a short title terminated by a comma.
Fixed a problem where the final selection was not detected when rapidly clicking on different file names in the Formats or Import Filter Manager.
Fixed a bug in syncing to a BibTeX file where citekeys beginning with certain punctuation symbols would cause an error.
Fixed a conflict with the Hookmark preference setting "Show current item's number of hooks in menu bar icon" that prevented edited formats from being saved.
An open SQL search window will now close when the associated library window is closed.
July 1, 2023
Drag-reorder the reference list with animation
The way that columns are handled in the multi-column reference list has been entirely revised. Columns can be dragged and dropped to place them in any order. The sort status of the dragged column will be preserved as will all column widths except for the last. The last column always extends to the right border, and a column dropped into the last position will assume that width.
The right-click options for manipulating reference columns have been rewritten to provide a consistent UI regardless of how they are added, removed, or reordered
You now tell Bookends which fields to show and in what order by right-clicking a column header and using the contextual menus or by drag and drop. The Settings -> List options for manipulating columns have been removed.
The default reference list columns can be restored in Settings -> Lists
Right-click the column header to select a sort option for the single-column reference list
Group by Color is a separate contextual menu item that preserves the order of the unlabeled references. Previously, these options were buried in the reference list's large contextual menu.
Improved UI for the PDF annotation popover
The options are grouped by function, and the groups are separated by double vertical lines. Members of the first group create annotations, those in the second copy to the clipboard, and those in the third create notecards.
Bibliographies with hanging indents that are generated when scanning a Word document will assume the paragraph style settings at the point of insertion
Exceptions are the font and text size, which you specify in Bookends Settings, and the spacing of the hanging indent.
Bug fixes
Corrected the tooltip explanation for the Copy Link option in the PDF annotation popover.
Updated the RIS.fltr so that it recognizes PDFs exported by Zotero with the Export Library menu option.
Fixed an error that occurred when editing labels in Settings and the reference pane had never been opened in the library window.
June 3, 2023
Facilitated importing from Zotero Desktop
You can repeatedly import from Zotero by creating a special watch folder that notifies Bookends when it detects an export. To do this, assign a folder action item to a folder (e.g. one on the Desktop). This is done by right-clicking on the folder and selecting Services -> Folder Action Setup, then clicking the Run Service button when prompted. Tick the checkbox "Enable Folder Actions" and the ones next to the name of the folder and the script "Bookends - Import Zotero export.scpt". Close the window. In Zotero, select the references to export, right-click, and choose "Export Item(s)…". In the export dialog select the format "RIS", and under Translator Options check the other items you want Bookends to import (Export Notes, Export Files, Include Annotations). Export to the Zotero watch folder (do not change the name of the data folder Zotero creates, it must be "Exported Items"). Zotero does not provide feedback during the export, so be patient. Once Bookends has been notified, the import will begin and a progress window will keep you informed. Bookends will import the data, move the attachments to the Bookends default attachment folder, and then move the exported data folder to the Trash. If a Bookends static group was selected, the imported references were added to it. Bookends uses the import filter "Zotero RIS.fltr", which adds "Imported from Zotero" to each imported reference's Keywords. You can modify this behavior. If the Zotero attachments are on your local HD, you will have two copies after importing into Bookends, one in the Zotero and one in the Bookends attachment folder. If you no longer want them in Zotero, delete them in the Zotero app or in the Finder.
New badge options in the groups pane
There are four options for showing badges: None, Folders, Groups, and Folders and Groups. These options can be selected with a right click or the Action pop-up menu at the bottom of the library window. The setting is library-specific, previously it was a global property.
Use a modified or the default RIS filter when importing .ris files
If you have more than one enabled filter with the letters "RIS" in the name, Bookends will offer an import dialog and you can select which filter to use. If you have only one filter containing "RIS", Bookends will automatically use it to import .ris files. Previously Bookends automatically used the filter named "RIS.fltr".
Assign the PDF annotation author name
Selecting Annotation Author from the PDF Action pop-up menu will produce a dialog in which you can specify the currently active user (default) or any name you choose.
File-> Extract PDF Annotations has the option to display annotation authors
In the PDF viewer, Add Text and Add Note replace Make Comment and Make Note
The use of Text to refer to free-standing moveable annotations conforms to usage in other apps. Edit replaces Comment in the PDF note contextual menu. "Comment" refers to content added to highlighted text.
The size of PDF thumbnails has been increased
Use the space bar to close as well as open the Quick Look window in the Floating Citations window
Previously you had to close it by clicking the window's close button.
Better visual feedback and control when dragging pane splitters
Copy a reference or group link text as a Markdown link or just a URL
Edit -> Copy Link (formerly Copy Hypertext Link) places two verions of the link in the clipboard, a native link and a text link. Which is used depends on the app into which it is pasted. The default text link is in Markdown format. If you want just the link URL, hold down the Option key and Edit -> Copy Link becomes Copy Link Text as URL. This is true of contextual menus that offer Copy Link as well.
Bug fixes
Fixed a bug in Bookends Browser that could cause some sites not to load.
Fixed a bug where the command to generate a citekey failed after updating from an older version.
Cleaned up conflicting and rarely used keyboard shortcuts.
Fixed a bug that could cause some Autocomplete Paper searches of Semantic Scholar to generate an error.
Fixed a bug that could result in misidentification of the macOS system version.
May 6, 2023
Introducing Floating Links
Floating Links lets you readily connect one reference to another, a group, or a folder. Select a word or phrase in an edit field that supports styled text (including the Notes tab) and (1) right-click and choose "Search Library To Create Link" or (2) double-tap the same trigger key that invokes Floating Citations (the Control key by default). Use the resulting floating window to search for references or groups/folders. Select a target and click the Set Link button or double-click to create a live link. If a reference has an attachment, click on the thumbnail to open it, or press the space bar to view it in Quick Look. This option is not available when editing in the standalone reference window. View a short video tutorial demonstrating how hypertext links are created and used.
Quickly alternate between linked references
After clicking a link,use Refs -> Back (Command-[) to go back. If done, Refs -> Forward (Command-[) will be enabled and can be used to return to the linked reference. This link relationship lasts until you select a reference outside of that pair.
The destination of a hypertext link will appear when you mouse over it
Previously this required that the Option key be held down. The help tag will be repositioned, if necessary, to ensure it's not truncated if it is near the right edge of the display.
Searches for PDF file tags will locate matching attachments in any ad hoc attachment folder
Previous they were only found if they were stored in the default attachment folder.
Entering text that is not a URL in Bookends Browser will invoke a Google search
If you enter text in the URL field that does not begin with "http://" or "https://", Bookends Browser will submit the search to google.com.
Generate citekeys using a format
If none of the preset citekey options suit you, you can create your own with a format. Enabled formats whose names begin with "Citekey" can be selected in Settings -> BibTeX tab. An example, Citekey.fmt, is included with this release.
Improved detection of DOIs in web pages
Newly added references will be selected after importing to the Hits List
A number of menu items and shortcuts were changed or removed for clarity and compatibility
Improvments in Autocomplete Paper
If the search finds a reference that is already in the library (i.e., has a yellow background), right-click and use the contextual menu to go directly to that reference in the library.
Improvements in Extract Annotations
Links to the annotation will be shown in the form consistent with the current output style: Styled Text -> embedded native links, Markdown Syntax -> Markdown links, HTML Markup -> HTML links, and destination URLs for the rest. If you save the extracted annotations to disk, the file extension will be consistent with the output style.
Select a reference with an attachment in the floating citations window and press the space bar to view it in Quick Look
This replaces the previous keyboard shortcut, Command-Shift-L.
Bug fixes
Semantic Scholar server errors will not trigger a Bookends warning.
Fixed a bug in attaching where moving a file to a subfolder could fail.
You can no longer begin of the name of a cloud library with an underscore.
Changing the output style in Biblio -> Default Format & Output Style will work even when the library window is not in front.
Fixed a bug where on rare occasions the wrong PDF could be used when extracting annotations.
Attachments that Bookends can't display can now be detached with a right-click in the edit pane Attachments tab.
Fixed a bug that prevented Bookends from running in macOS 13.3.1 (a) when the system language was set to Japanese.
April 1, 2023
Hypertext links to PDFs have changed
Previously, Bookends relied on the creation date stored in the PDF itself. We have learned, however, that PDFKit changes the creation date when a PDF is modified and saved. Bookends will now use the PDF file creation date the Finder uses. Note that most of the older PDF and deep PDF links will continue to work. The exception will be links made to a second PDF attached to a reference. These links will need to be remade.
Format references in Markdown syntax
If Markdown Syntax output is selected, Bookends will convert bold, italic, superscript, and subscript to their Markdown equivalents. It will also generate Markdown hypertext links that are created by a format. There are variants of Markdown — Bookends uses Obsidian as a benchmark. Hypertext links embedded in reference fields will not be converted to Markdown links. In the Biblio -> Bibliography dialog, if you choose a format whose name contains "Markdown" Bookends will offer to switch the output to Markdown Syntax for you.
Use Markdown syntax in formats that create a hypertext link
These can include data from fields (e.g. the URL) or literal text that you enter. For example: [$link text$]($link URL$) and [t](z). Bookends will continue to support the legacy syntax <<link text><link URL>>.
Several Markdown template formats are included with this release
You can use these as configured and/or modify them for your needs.
Biblio -> Default Format & Output Style lets you set the name and the output style (e.g. Styled Text, Markdown Syntax, etc.) from one submenu
Previously the output style could only be set in the dialog preceding the generation of a bibliography or exporting formatted references.
Hypertext links to references, groups, and folders have been improved
The links now include the type of link and the name of the library. This means the library will automatically be opened if necessary when the link is used in another app. In addition, Bookends will copy a Markdown link to the clipboard as text, along with the live link information, so that apps that can't accept styled text will still receive the link URL. Therefore, Copy Hypertext Link As Text has been removed.
To see the contents of a hypertext link in an edit field, hold down the Option key and move the pointer over it
If the link is to a reference in the same library, the tooltip will display the formatted reference, otherwise it will display the destination URL. The tooltip is generated by the Tooltip format, which you can edit in the Formats Manager.
The User Guide (Help menu) contains a new chapter that discusses hypertext links in detail: what they are, how to create them, and how to use them inside and outside of Bookends
Implemented the macOS-native Window menu
This means that window management options provided by macOS are now available in the Window menu.
Improvments in Autocomplete Paper
If a DOI can't be found in the attached PDF and you have entered metadata for the reference, Bookends will pre-fill Authors (first author surname), Title, and Year.
If a single reference is selected, it can be deselected with a Command-click
Text font and size in the Inspector Cited In and Cited By panes conform to preference settings, along with other cosmetic improvements.
The Extract Annotations movable modal dialog includes two new options
Prefix each reference with a number (default is yes), and show references that have PDF attachments even if they have no annotations (default is no).
The Bookends Browser back button contextual menu (right click or left click and hold) sorts the viewing history from most recent to oldest
Clicking on an inactive library window will activate it without selecting the reference or group you may have clicked
The watch folder works properly with very large downloads using the Vivaldi browser
If enabled in Preferences, Bookends will force attachments in subfolders of the iCloud Drive attachment folder to be downloaded if they had been moved to iCloud
Previously, only attachments at the root level would be touched.
If Import From Existing Bibliography finds a mix of publications on PubMed and other sites, it will import them all, not just those on PubMed
Updated Bookends Browser to be compatible with sites that block access from old versions of Safari
Bug fixes
Fixed several cosmetic bugs that occurred when the formatted reference pane was open in the single column view.
Fixed an error that occurred when trying to edit a hypertext link to a file or folder.
Fixed a cosmetic bug in the Attachment Inspector.
Fixed a bug that could cause extracting PDF annotations to fail in some circumstances.
Fixed a cosmetic bug where the edit pane field height weren't set properly when the library window opens.
The Save dialog properly shields the file extension when exporting saving a bibliography to disk.
Fixed flicker issues when the mouse pointer was over the edit pane.
Fixed a bug where the internal name of a smart group didn't match the true name if it was renamed during a paste.
Floating citations window searches will not find references in the trash.
Fixed a bug where exporting the selected references using a non-sorting format would result in the hits being exported.
Fixed a bug where Biblio -> Bibliography would output marked references that were in the trash.
Fixed a bug in Wi-Fi sync where an attachment wasn’t placed to the Bookends for Mac library-specific attachment subfolder, if present.
Very short DOIs in PDFs will be recognized.
Searches for file tags that contain apostrophes now work.
March 4, 2023
Add a hypertext link to any word or phrase
Select the text you'd like to link then right-click and select Add Link. You'll be prompted to add the link, which must contain the characters "://" (without the quote marks) preceded and followed by text. The selected text will now be blue with an underline, and clicking on it will open the URL you entered. Note that this works for application-specific links, too. You are responsible for making sure the link is valid, Bookends can't determine that. Right-clicking on such a link provides four new options: Open Link, Copy Link, Edit Link, and Remove Link.
Create links to attached PDFs
Select Copy Link from the PDF Action pop-up menu to copy a hypertext link to the PDF page being viewed. Paste into a compatible third-party application like TextEdit, Scrivener, Obsidian, etc., or into a style-savvy Bookends edit field or the Notes tab, to insert a live link.
New toolbar button "Open With App"
This button is enabled when the selected reference has an attachment that Bookends can locate. If the attachment is a PDF, clicking the button will open it in the PDF reader selected in preferences (if none is selected, the PDF reader chosen by the Finder, usually Preview, will open). If the attachment is not a PDF it will be opened by the app the Finder chooses (e.g. TextEdit, Microsoft Word, etc.). Hover the pointer over the toolbar button to see the name of the app that will be used.
Added AppleEvents that deal with the PDF currently displayed in the library window
The new commands elicit information about the displayed PDF: (1) the name, (2) the file path, (3) the selected text contents, (4) a hypertext link (URL) to the PDF, (5) a hypertext link to the selected text, and (6) descriptive information about the link to the selected text. This will allow greater integraton with third party applications like Hookmark.
Option to exempt Title words with multiple capital letters when applying Title Case or Sentence case
In the preferences Scan & Bib tab there is the option to leave words with 2 or more capital letters as is. If checked, acronyms like UK and chemical symbols like H2O will retain their case when the Title is changed to Title Case or Sentence case. This is in addition to the list of words that should always appear in the specified case. The new option allows you to exclude an entire class of words (those with multiple capital letters) without having to enter them individually in the "don't change" list.
The preferences BibTeX option "Bracket "don't change case" will bracket words entered in the Scan & Bib -> Sentence & Title Case list containing at least one capital letter, regardless of where it appears
For example: {mRNA}, {iPhone}, and {Paris}.
The default when adding a static group is to create it without entries (make empty)
You can have the hits automatically added with "add Hits" pop-up menu option. This setting is remembered between uses in the same session. Previously the default was "add Hits" if hits were present .
The setting for putting newly imported references in the Hits List is remembered between launches
The Hits group will be shown immediately after importing to the Hits List
If you want any existing hits to be removed before adding the newly imported references, hold down the Option key when clicking the Import button.
The maximum height of edit pane fields is capped
This prevents drawing artifacts when fields contain enormous amounts of text.
Bookends will no longer implicitly convert the output to ASCII when Convert to TeX is enabled in BibTeX preferences
Citekeys generated by Bookends willl allow some Unicode characters
This reverts the changes made in the last update.
All else being equal, Remove Duplicates will remove the duplicate reference without a DOI or, if both had one, with the shorter Abstract
Updated the JSTOR parser to deal with changes made by JSTOR
Decreased CPU usage when downloading many PDFs at once
Removed the confirmation dialog when detaching attachments that can't be found
References in the trash will be ignored when exporting references in the Hits lists
The Floating Citations display of Books will include the volume number, if present
Small cosmetic improvements
Bug fixes
Fixed a bug that could cause a crash when an edit field contained a great deal of text.
Fixed a bug where the citekey unique id was set to 0 when it was created on import.
Fixed a bug where a terminating comma in the pages field wasn't removed when the reference was formatted.
Fixed a bug where a double-click on an unknown attachment type in the display pane was ignored instead of opening the attachment.
Fixed a bug that could slow the opening of a library with thousands of reference links.
Fixed mouse pointer flickering over the groups pane when there are many references.
Fixed a bug in BibTeX Markup where the output of back-to-back superscripted characters could be malformed.
Fixed a number of inaccurracies in the library window that could occur immediately after removing duplicates.
Fixed a bug where making a bibliography from the selected references ignored the sorting options specified in the format.
Added checks to ensure that a right-click on a PDF won't cause an error if incorrect parameters are passed from the OS.
February 4, 2023
Include live hypertext deep links to annotations when using File -> Extract Annotations
Paste live hypertext links into Bookends notecards
This works with links to references, groups, folders, and PDF text and annotations, as well as those created by third-party apps.
Invoke hypertext links in notecards without opening them for editing
If a notecard contains a live hypertext link, a small image of a link will appear in the upper right corner. Right-click and select the link from the contextual menu to navigate to it. This applies to live hypertext links to references, groups, folders, annotations, and those created by third-party apps.
Copy a hypertext link to an annotation from the note stream
Right-click on the annotation's notecard and choose Copy Link from the contextual menu.
Clicking on a hypertext link to a PDF annotation in another app will launch Bookends if it is not running, open the library, and navigate to the annotation.
Bookends will automatically open a closed library if it can be found in the File -> Open -> Recents menu. Previously Bookends had to be running with the correct library open for links to work.
Much improved detection of uncommon URLs (i.e. those not prefixed with http:// or https://) when right-clicking on a notecard
View and navigate to crosslinked references (not hypertext links, but internal links made with the Inspector) from the reference list
Use Refs -> Linked References or use a right click to obtain a list of all references to which the selected reference is crosslinked. Select a linked reference to navigate directly to it. This is a more convenient than using the Link Inspector for this purpose.
A comma will be used to separate keywords when they are output as BibTeX Markup
A semicolon is used for other output styles.
The PubMed Automated Search window will use the List font and font size you have selected in Preferences
The option to Select References With Orphaned Attachments is now available in the Refs menu
Previously it was only accessible from a contextual menu.
Insert Date has been removed from the Refs menu
Copy Formatted -> Citation will include styled text. Multiple citations will be separated by returns
Non-ASCII characters will be removed from citekeys generated by Bookends
Bug fixes
Fixed a bug where modifying the note stream could cause Bookends to lose any hypertext links that were pasted into the notes field.
Fixed a bug where links to libraries whose names contained spaces failed.
Fixed a cosmetic issue with extracted annotations when there was more than one PDF attachment for a reference.
Bibliographies exported to disk as Styled Text (RTF) will have hanging indents if called for by the format.
Fixed a bug where a reference list column added via a right-click couldn't be resized until the window was closed and reopened.
Fixed a bug in BibTeX markup where the parentheses surrounding an insitutional name could mistakenly include the conjuction between multiple authors.
January 7, 2023
Introducing deep PDF links
You can create a hypertext link to any PDF text or annotation and insert in into 3rd party applications like Scrivener, DEVONthink, and Obsidian, or into Bookends reference fields themselves (e.g. Notes). Deep links to selected text are created in the annotation popover window (Copy Link). You can create links to annotations in two ways: (1) right click on the annotation, select Copy Link from the contextual menu, and paste it into a compatible app, or (2) Command-drag the annotation to a window in a compatible app. Annotation links work with Highlight, Underline, Note, and Comment annotations created in Bookends or any other PDFKit-compliant application. If the corresponding Bookends library is open when the link is clicked, you will be taken to the reference/PDF and the linked text or annotation selected. In the copy or drag Bookends will also include a markdown link in the form [descriptive text](link). This allows you to use links with apps such as Obsidian and Bear, which do not recognize native links. You can rename the PDF without breaking the link. However, if you move a linked PDF Note or Comment on the page Bookends won't be able to locate it. In this case Bookends will still open the PDF of the linked reference and take you to the correct page, it just won't select the annotation. Note that to paste a live link into a reference field, it must support styled text and you must perform a plain Paste, not Paste And Match Style. If you set Command-V to use Paste And Match Style in Preferences, paste the link with Edit -> Paste or the keyboard shortcut Shift-Option-Command-V.
Compatible with macOS Ventura 13.2 (a)
Clicking on an underline annotation will select the corresponding notecard if the note stream is open and the option to show PDF annotations is active
Swap two PDF tabs by holding down the Command key and dragging and dropping one tab onto the other.
Added the option to remove duplicates from selected references (Refs -> Remove Duplicates). Previously Bookends would only search the entire library for duplicates.
The Preferences list containing field labels (Refs tab) has a new column that displays the default (original) values
This is useful if you have renamed and/or rearranged labels and need to know what metadata is intended for the corresponding field. You can reset a label to its default with a right-click, or edit it manually.
Updated import of nonstandard EndNote XML files exported from Mendeley.
Bug fixes
References in the Trash will not be used when creating or syncing a linked BibTeX file.
Fixed a bug where the first column in the reference list couldn't be sorted by clicking on the header.
Fixed a bug where the middle pane's width couldn't be changed in widescreen view.
Fixed a bug where the library window panes sometimes didn't update when a reference was selected.
Fixed several bugs in how the edit pane Notes field is displayed when switching between Light and Dark Mode.
Fixed a bug where edits made in an edit field would be lost if you immediately right-click on the field and choose Change Case.
Fixed a bug where Bookends didn't properly account for references in the Trash, resulting in a spurious warning that some references didn't have citekeys when creating a synced BibTeX file.
Fixed a bug where opening a PDF in LiquidText would also launch Highlights.
Fixed a bug where a short title created with a right-click on the title field could be shown in gray.
Fixed a bug where trying to remove a reference from a group could fail when the browser pane was open.
Fixed a bug in Compare References where the text could turn blue after saving changes.
December 3, 2022
Improvements in library window reference list sort behavior
The sort column and direction (ascending vs. descending) is saved independently for each library when it is closed and restored when it is opened. Previously, when a library was opened an ascending sort was performed on the first column.
Add and/or remove reference list columns in the UI
Right-clicking on a list column header brings up a contextual menu that lists all of the possible options (e.g. Authors, Title, Added, Attachments, etc.) that can be displayed, with those currently showing being checked. Select a checked value to remove it from display, select an unchecked value to add it as a column immediately preceding the header that was clicked on. The minimum number of columns is 3, the maximum is 10. The options to add or remove columns still exist in Preference, this new feature is a convenient shortcut.
Scroll PDF tabs horizontally
When there are too many tabs to view all at once, place the mouse pointer over the PDF toolbar or the "no attachment" image, if showing, and swipe left or right to scroll horizontally. This works with track pads and the Apple Magic Mouse.
When a PDF tab is selected using a right-click contextual menu the PDF tabs will scroll, if necessary, so that it is visible.
PDF highlight and underline page numbers are now shown in the note stream.
The PDF Action pop-up option Show Annotation Modification Date in Notecards now applies to highlights and underlines
Previously it applied only to notes. Be aware that modification date for some annotations is not available in older versions of macOS.
Sort notecards by page number
Right-click on the note stream to open contextual that lets you sort notecards from the Notes field (not PDF annotations, which are already sorted by page number) if they have a page number indicated by "@". Notecards without page numbers will be left in their original position. This contextual menu option will appear if the note stream contains two or more notecards created from Notes.
Removed Copy As Hypertext Link from the note stream contextual menu
This option was misleading because it copied a link to the reference, not to selected the notecard. There is already an option to copy the link to the reference in the Edit menu.
Quickly navigate between pages you've viewed in Bookends Browser
Click and hold or right-click on the forward/back navigation buttons to open a contextual menu that will let you quickly go to web pages visited in the current session.
Improved detection of DOIs in PDFs from PNAS
Updated how automatic PDF downloads from eLife are handled to deal with changes made by the publisher
When formatting, the BibTeX Markup setting will only be applied if the format name contains the word BibTeX
If it does not, the reference will be output as styled text. This means you can switch between conventional formats and BibTeX.fmt without having to explicitly adjust the output style.
BibTeX keys are now referred to as Citekeys throughout the UI
When formatting with BibTeX Markup, superscripts will be indicated by \textsuperscript{}
When you right-click on the note stream and Copy Notecard and Citation, any headers, page numbers, and tags will be removed
Added LiquidText as an optional PDF reader
Bug fixes
Fixed a cosmetic bug in the widescreen view when changing the groups pane width while the formatted reference was being displayed.
Fixed a bug where an error could occur when switching between the library window and a standalone reference window when the Formats Manager was open.
Updated Copy Citation from the floating citation window to work with Scapple.
Fixed a bug where PDFs automatically fetched from PubMed Central were downloaded twice.
Fixed a bug in the note stream where moving a PDF annotation notecard into the list of database field notecards could cause notecards to merge.
BibTeX bracketing of acronyms will no longer bracket runs of capital letters that occur inside a string.
Fixed a bug where having a space in the PMID field could cause an error when using it to search for the PDF.
November 5, 2022
Minor adjustments for macOS 16 Ventura
Automatic downloading works with many more PDFs
If you attempt to download a PDF whose URL can't be resolved or is behind an unaccessible paywall to a reference that has a DOI, Bookends will query Unpaywall (https://unpaywall.org) to obtain it from a repository on which it has been legally uploaded. You can learn more about Unpaywall, which keeps track of repositories containing millions of articles from thousands of publishers, in their FAQ: https://unpaywall.org/faq.
Added more publications as targets for automatic PDF downloading
If an online search finds references you already have (e.g. they are highlighted in yellow), right-click to select and display them in your library window
When importing a duplicate reference when attaching a PDF, Bookends will offer to show you the existing copy even when it's in the trash
The online search display of references will use the list text font and size selected in preferences
Copy live hypertext links to folders in the groups pane
Send formatted references to the bibliography window
The pop-up menu listing attachments will be enabled even if there is only one
Previously it would be disabled and you couldn't see the entire name if it exceeded the width of the menu.
Bug fixes
Fixed an error that occurred when using the PDF action pop-up in a standalone editing window.
Fixed an error that occurred with the Summary view.
Fixed a bug that prevented hanging indents from showing in the bibliography window.
Fixed a bug where the right reference might not be selected when using a right-click -> Show This Reference In Library in the Online Search window.
The Summary pane updates immediately when its font size is changed in preferences.
Fixed a cosmetic bug where attachment names shown in the reference list weren't immediately updated when renamed.
Fixed a problem in the registration code window where the dates weren't parsed as intended for some non-English System languages.
Fixed a bug where the year was incorrect in exported XML when the Date field contained styled text.
Fixed a bug in Get DOI where the search failed when the title or journal name contained characters that should be escaped.
Fixed a bug where the setting to not include the PDF pathname with extracted annotations was ignored.
Fixed a bug where showing edit pane hints was turn on by default when a new library was made.
October 8, 2022
Much improved extraction of PDF annotations
The ability of Bookends to extract and export PDF annotations has been rewritten from the ground up, and is now reference- rather than PDF-centric. This means that the annotations "know" which reference the PDF is attached to. Now each annotation block, which contains the annotations from all PDFs attached to a reference, is headed by information about the reference. This information is created using the default format (Biblio -> Default Format) and style (e.g., Styled Text, Plain Text, BibTeX Markup, etc.). This means you can include any information the formatter can access, including the unique ID, linked references, etc. Extracted highlights can be shown in the same color as in the PDF (light mode only). Annotations are output to a new Annotation Window, which gives you instant access to your annotations while working in Bookends itself. Search the contents of the annotation window using Command-F. You can copy and paste the contents into other applications, or save the contents to disk using File -> Save PDF Annotations.
Improved file downloading in Bookends Browser
Bookends Browser now works for download links for many file types, not just PDFs. It's intelligent, meaning that Bookends will offer to attach downloaded PDFs and Word files (as well as some other document types), whereas .zip files will be directly downloaded to your Downloads folder. How files are handled depends upon the MIME type assigned by the server. Requires macOS Big Sur 11.3 or later.
Text styles are now included when you drag notecards to another app with the Option key held down
Color label pop-up menus now show the color along with the assigned text
More graceful handling of the Inspector if the user-selected format for the display of references is deleted
HTML markup for text styles will be removed from PubMed abstracts, if present
Changes to the content obtained when you copy or drag a notecard
When you drag a notecard with the Option key held down or copy it to the clipboard, all text and formatting cues (e.g. # for header, @ for page, etc.) will included. This makes it possible to manipulate the header, tags, quotes, etc. with a macro or script in the receiving app. Any styles you may have applied will be preserved. To be compatible with markdown, when Bookends adds a # to a new notecard to indicate the line is a header it will be followed by a space.
Minor cosmetic enhancement to the standalone Term List window
The pop-up menu listing attachments will be enabled even if there is only one
Previously it would be disabled and you couldn't see the entire name if it exceeded the width of the menu.
Bug fixes
Fixed an error that occurred when using the PDF action pop-up in a standalone editing window.
Fixed an error that occurred with the Summary view.
Fixed a bug that prevented hanging indents from showing in the bibliography window.
Fixed a bug where the right reference might not be selected when using a right-click -> Show This Reference In Library in the Online Search window.
The Summary pane updates immediately when its font size is changed in preferences.
Fixed a cosmetic bug where attachment names shown in the reference list weren't immediately updated when renamed.
Fixed a problem in the registration code window where the dates weren't parsed as intended for some non-English System languages.
Fixed a bug where the year was incorrect in exported XML when the Date field contained styled text.
Fixed a bug in Get DOI where the search failed when the title or journal name contained characters that should be escaped.
Fixed a bug where the setting to not include the PDF pathname with annotations was ignored.
September 3, 2022
Print PDFs
The PDF Action pop-up menu has the option to print the PDF you are viewing.
Copy/paste multiple smart groups at once
Improved display of exported PDF annotations
When a reference is moved to the trash, the preceding reference will be selected
Previously the list scrolled to the top and first reference was selected.
Better handling of corrupted PDFs
If you try to attach a PDF that cannot be read, Bookends will alert you and offer to move it to the Finder trash, show it in the Finder, or simply continue without attaching.
Right-click on the Abstract field to create a new notecard from the selected text
Set the defaults for viewing PDF highlights in the note stream when in the edit pane attachments tab
Previously they could only be set from the dedicated PDF display pane.
When a file is added via the watch folder, Bookends will only add the comment that the metadata wasn't found online if it is a PDF
If identical authors in sequential bibliography references are to be replaced with dashes, edited book editors will be considered to be authors
The JAMA format has been renamed AMA (American Medical Association)
Bug fixes
Fixed a bug in Remove Duplicates.
Fixed a bug in scanning using metatypes.
Fixed a bug that prevented Bookends from launching on some Macs where the system language is set to Japanese.
Fixed an error caused by clicking on white space in the note stream with the Option and Command keys pressed.
Fixed a bug in the Summary view where a background color at the beginning of the text (caused by a live search match) would bleed through when clicking on a field to edit it.
Fixed an error that would occur when editing in the Summary view.
August 6, 2022
Refreshed Bookends app icon
New Trash group
When you delete a reference it is placed in the trash rather than being deleted from the database. If you drag a reference to the trash or press Command-Delete you will bypass the warning message. You can restore references from the trash or permanently delete them from the library. References in the trash can still be used, with a few exceptions: Live Search will find references in the trash only when the trash group is selected and scanning won't find matches with references in the trash. In addition, you can't extend group selections that include the trash, meaning that it can't participate in virtual groups. If you're syncing with Bookends for iOS, trash will sync automatically for cloud sync, but Wi-Fi sync requires version 3.7.6 or later.
Formatted reference examples include secondary citations
Custom citation formats can output different results depending on whether the reference is cited for the first time or a subsequent time. For such formats, the examples in the Format Manager and in the library window formatted reference pane include the first (1°) and secondary (2°) forms. If the format has no entry for subsequent citations, these will be identical.
Use Copy Formatted for citations
Previously Copy Formatted only allowed you to copy the formatted bibliography output.
Perform smart change text case operations in the edit pane
Right-click on a field in the edit pane and select Change Case. The options are Sentence case, Title case, Uppercase, and Lowercase. Unlike the now-removed Transformations menu options, these operations leave any text styles intact and honor the words entered in preferences that are to be excepted (e.g., articles and proper nouns). This is identical to the Global Change-> Change Case function but much more convenient if you simply want to change one or a few references.
Use Delete (the key or the menu options) to move references in smart groups or the Recently Viewed group to the trash
Improved display of the groups you have created
Improved automatic detection and correction of some database problems
If a library is stored on a service like Dropbox, iCloud Drive, etc. you will receive a warning notification when it is opened
Databases are prone to corruption when entire files are synced. If you receive this warning, move the library file out of file sync folder and use Bookends cloud sync instead. It is much faster, more robust, and can serve as a backup mechanism if the library file itself becomes damaged.
The option to exclude leading parts of authors names when sorting will honor smart apostrophes, for example d’
Improved compatibility with PopClip
The PDF annotation popover window should remain open when PopClip is active.
Bug fixes
Fixed a problem that prevented the color pickers in preferences from working.
Fixed a bug where renaming corrupted a smart group.
Fixed a bug where a new reference wasn't automatically added to the selected static group.
Fixed a bug where the standalone edit window didn't update its contents when another reference was opened for editing.
Fixed a bug where the standalone edit window title was incorrect when first opened.
Fixed a bug where the wrong reference could be shown in the edit pane when the library was opened or a group changed.
Fixed a bug that prevented some information found with an online search from being imported.
Fixed an error caused by editing the "Replace repeated authors with" in a format.
Fixed a bug where compound words in the author sort ignore list weren't used.
Fixed a bug where new annotations weren't extracted unless the PDF had been saved.
Fixed a bug where the subfolder selection pop-up menu wasn't updated immediately after creating a new subfolder.
Fixed a problem where a terminal period before Cited Pages wasn't removed if it was followed by a Return.
Fixed a bug where a right-click on a keyword tag incorrectly offered to add it to the stop list.
Fixed a problem with Mellel verification of citations containing both literal text and a metacharacter.
July 2, 2022
Completed a multi-year effort to refactor and modernize large amounts of the code base
New UI for searching Notes
When the edit pane Notes tab is showing, use Refs -> Find -> In Notes (Command-F) to bring up a search bar with an option to replace text as well.
Search Semantic Scholar
Semantic Scholar is a research discovery resource that covers over 200 million papers in all fields of science. Its strength is that it uses a variety of AI-driven tools to return highly relevant results. Its limitations are that it doesn't allow boolean searches, doesn't search behind paywalls, and doesn't return volume or page numbers. It does, however, provide abstracts and information about the number of citations a paper has received.
Smart SQL groups can be duplicated
Available with a right-click on the group or a click on the Action pop-up menu.
Click and hold or right-click on the Bookends icon in the dock to select from a list of recently opened libraries
Bookends must be running at the time.
Import filter tags can contain commas
Commas are used to separate multiple tags that map to the same field. Previously, you therefore couldn't import metadata whose tag contained commas. Now you can do that by escaping the comma in the import filter like this: \, . Thus, the tag "Abstract, Summary" in the text could be imported with this import filter tag: "Abstract\, Summary" (without the quote marks). Fixed an error in logic in the restore default font and styles function.
Most contextual menu options in the Attachment Inspector will operate on multiple attachments at once
The exception is Rename Attachment, which works with the first selected attachment.
Added more group pane Action pop-up menu options
Improved instructions for file sharing in the dialog the participant sees when accepting a share invitation
Improvements in the Autocomplete Paper dialog UI
Updated the notification subsystem to work more reliably with macOS 12 Monterey and later
In the Online Search window, changing the site to search clears the results of a previous search
Removed Substitutions and Transformations from the Edit menu
Global Change -> Restore Default Font and Style is much faster
The process by which Bookends determines if a reference field contains styled text has been improved
Hypertext links to other apps invoked with a right-click now work in all user-defined fields
Previously they only worked in fields up to User4.
Bug fixes
Fixed a bug in the ! formatting directive that outputs the library name.
Fixed a bug where the field in which a notecard was being edited remained visible after the right pane was closed.
Fixed a bug in Autofill From Internet where some DOIs weren't found on PubMed.
Fixed a bug where the Notes field hint text itself could be saved to the database.
Fixed a bug in the Online Search recent searches pop-up menu.
Fixed a bug in the where the edit pane wasn't updated correctly when references were imported.
Fixed a bug where the edit pane fields weren't resized properly when the library was opened.
Fixed a bug in which the a reference field text style could become "stuck" when switching between references.
June 4, 2022
Color labels for groups and folders
Groups and folders can be assigned a color defined in Preferences (Lists tab). Select a group color from a right-click contextual menu, the action pop-up menu beneath the groups pane, or the keyboard shortcut Control-Command-# (the number of the color is defined in the preferences Lists tab). You can only assign colors to groups and folders you create; the color of default groups (All, Hits, Attachments, and Recently Viewed) can't be modified .
Ignore citation delimiter metacharacter
When the open citation delimiter, typically a curly bracket, is immediately followed by a tilde (~), Bookends will ignore it during a scan. This is useful if you need to use the citation delimiter in another context, such as a mathematical formula, and don't want Bookends to mistakenly think it is the beginning of a temporary citation. When ready to submit the manuscript, do a search/replace in your word processor and replace the open delimiter plus ~ with the open delimiter (for example, replace {~ with { ).
Perform a live search for a unique ID by preceding it with the # character (e.g. #43237)
You can already select Unique ID as a field to search in using the live search field pop-up menu; this is another way to do so that is arguably more convenient.
The library name output by the formatter will no longer include the file extension, .bdb
A colon will be used in place of an underscore before the unique ID when generating a citekey as Author + Year + UniqueID
If a file in the destination folder has the same name as an exported attachment, Bookends will move it to the Trash and then proceed with the export
Small UI tweaks
Updated Help menu wording. The right-click contextual menu for references in static group reads "Remove From Group" instead of "Delete". Improved display of edit pane when no reference is selected.
The note steam will scroll to a newly-imported notecard
Added a warning that importing from Papers 3 can't be done when running a macOS version later than Big Sur 11.2
Bookends will import issue numbers exported from Mendeley as EndNote XML.
Right-clicking on empty space in the groups pane will bring up the contextual menu
Previously you had to right-click on a group.
Bug fixes
Dumb quote marks won't be escaped when BibTeX Markup is used for formatting references.
Fixed a bug where a right click on empty space in the reference list caused an error warning.
Unicode characters in the WiFi sync list are now rendered correctly.
Fixed a bug where the BibTeX "don't change case" status wasn't correctly shown when preferences was opened. Fixed several bugs in generating citekeys.
Fixed a bug that prevented smart SQL groups with predefined content from being created.
Fixed a bug in the format window where changing the Type in one tab didn't update the field names pop-up menu in the other.
Fixed problems with the display of scrollbars in the library window right pane.
Fixed a bug on library open where the various panes weren't updated to reflect the first selected reference's content.
You can once again change the color of text in the edit pane.
Fixed a problem where searching for some DOIs failed to find the reference or generated an error.
Fixed a bug where the wrong reference was shown in the edit pane.
Fixed a bug where the Notes tab could contain light gray hint text. The PDF tag enter field expands if necessary to accommodate pasted text.
Fixed a bug where the reference list would become invisible when invoking full screen while the library was in the widescreen view.
Fixed a bug where searches for PDF tags could incorrectly match a PDF with a similar name.
Fixed a bug where the issue number wasn't imported if it was identical to the volume number.
Fixed a reference duplication bug where the new reference was selected but edits were recorded in the original.
May 7, 2022
Changes in importing data from JSTOR
Changes in importing data from JSTOR. JSTOR has made substantial changes that require modifications in how their data are accessed. First, note that if you should log into JSTOR, even into a free account you create, because you may then have access to more references. Second, if you then accept the terms and conditions in your profile, the Accept Terms and Conditions pop-up won't appear each time you download PDFs in a session. Third, access to some references requires IP authentication. Therefore the results are often better if you are using Bookends on your institution's network or via a VPN connection. Bookends will no longer offer to attempt to automatically download JSTOR PDFs. Downloading JSTOR PDFs can still be done, however. If you are using direct JSTOR search, select the reference you want to import and then open Bookends Browser in the bottom pane. Click the Download PDF button (if offered), agree to the Terms and Conditions if necessary, and download the PDF. Import the metadata and PDF using the import pop-up menu at the bottom of the window. If you search with the full screen Bookends Browser and see the down arrow at the top right, click it and import the metadata as usual. Then click the JSTOR Download PDF button in the web page (if offered), agree to the Terms and Conditions if necessary, and download the PDF to Bookends Browser. Once downloaded, either drag and drop the PDF proxy icon onto the Bookends library window, or right-click on the PDF proxy icon and choose among the options. Because of restrictions enforced by JSTOR, Bookends direct search is more likely to be able to download metadata from JSTOR than the Bookends Browser search.
BibTex: improved protection of capitalized words in title
When you are outputting text as BibTeX Markup, Bookends will compare each title word to the list of words whose case is not to be changed (Scan & Bib preferences). If there is a match, and the word begins with a capital letter, Bookends will output it surrounded by curly brackets (e.g. {Paris} or {United States}). This option can be enabled in preferences, BibTeX tab: Bracket "don't change case" words in title.
BibTeX: customize citekeys
In BibTeX preferences tab, you can configure Bookends to create the following citekeys: Author + Year, Author + Year + UniqueID, Author + Year + Partial Title (first 5 meaningful characters), and Author + Year + Library Name. The second and fourth options ensure that the citekey is unique among all of your libraries.
Output linked reference information using a format
To access linked reference information independently of the Inspector, use the % character in a format. Bookends will output the unique id and reference relationship for each linked reference. If there is more than one, they will be separated with semicolons. This could be useful, for example, if you want to obtain linked references using AppleScript. The % character was previously used to output the absolute reference position in the database, which is now obsolete.
Bookends will recognize Markdown URLs in notecards
Select the notecard and right-click, then select the URL from the contextual menu to open it in your browser. If the URL begins with www, https:// will automatically be added.
A right-click now selects the format or import filter in the Formats Manager and Import Filter Manager, respectively
The option to show the import filter in the Finder now only works for items in the Custom Import Filters folder.
Updated right-click behavior in the references, groups, and term lists
A right-click now selects the row and immediately brings up the contextual menu. Previously you had to left-click to change the selection and then right-click to activate the contextual menu.
Bug fixes
Fixed: an error when scanning with an Author-Date format or when adding Types to a format.
Fixed: the formatting function replaced repeated authors with an en-dash or em-dash failed.
Fixed: when in dark mode, some PDF tags in the summary view were displayed in black (i.e. invisible).
Fixed: the reference selected in the library window could change when switching to another app or the Finder while in the process of creating a new reference.
Fixed: selecting nothing from the contextual menu in the groups pane could cause it to resize.
Fixed: the same ad hoc attachment folder could be added multiple times.
Fixed: eliminated some unnecessary UI updating when syncing references after the library window is deactivated.
Fixed: Proofreading Word documents, which was broken in the last update, works again.
Fixed: group names changed via AppleScript weren't saved.
Fixed: group names changed via AppleScript weren't saved.
Fixed: scanning a document containing only citations that were excluded from the bibliography would generate an error.
April 9, 2022
Type pop-up menus no longer display Unused Types
When the name of an Unused Type is changed in preferences it will appear in Type pop-up menus. If the name is changed back to name beginning with Unused it will no longer be shown. The exception is that if a reference was assigned a Type that was later changed back to Unused, that Unused Type will be shown when that reference is selected.
The punctuation settings for Cited Pages are now Type-specific
That means that what is output before and/or after cited pages in the final citation can be different for different reference Types.
Show all references in the library window when filtering by Term List
IWhen filtering the library with Term Lists instead of groups, right-click and select "Deselect All Unpinned Terms" to have Bookends show all references. This is useful if you want to add Terms like Keywords to your references by drag and drop on the Term List.
Add Terms to references by dropping them on the Term List
When showing a Term List in the left pane you can drop one or more references on an item in the list and it will be added to all of the references. This is especially useful as a quick way to add keywords. If a reference already contains the keyword, it won't be added again. Note that you must right-click and "Deselect All Unpinned Terms" so that the list shows all references, not just those that already contain the term.
Add keywords to references via a contextual menu
Right-clicking on the keywords field will bring up an Add Keyword option that lists all of the keywords in the library. As with all pop-up menus, typing will take you to the closest corresponding item in the list. Bookends will add the chosen to all of the selected references. If a selected reference already has tha keyword, it will not be added again.
The selection in a PDF will remain when the annotation popover window closes
This means that utilities that cause the popover to close, like PopClip, can be used with Bookends.
Added a keyboard shortcut for Edit -> Copy Hypertext Link -> Copy As Link
Shift-Option-Command-L.
Fields in the edit pane accept dropped text
Enhanced readability of the PubMed automated search results
Type and labels cannot be set to empty in preferences
Bug fixes
Fixed: a rare bug in BibTeX file sync where in certain conditions the contents of the file could be deleted.
Fixed: a bug where the name of the selected Type above the preferences label list wasn't immediately updated after it was edited.
Fixed: right-clicking on an edit field when the library has no references no longer shows a hierarchical menu.
Fixed: a bug where under certain conditions the Type in the popup menu didn't match the data for that Type when the Format Manager was opened.
Fixed: the progress window will now be shown when exporting the selected references using a bibliography format.
Fixed: a bug that caused edit field hints to be drawn when changing Types even if they were turned off in preferences.
Fixed: a rare problem where an error message was displayed when the library window was closed.
March 11, 2022
Improved JSTOR imports
When using a JSTOR URL to identify the reference to import, Bookends will use the JSTOR APIs to obtain higher quality information. This requires that you have access privileges to JSTOR, and does not work with JSTOR Research Reports (a limitation enforced by JSTOR). A byproduct of this is that Bookends will use the JSTOR.fltr settings to import JSTOR data when it is obtained via the JSTOR URL. If you've modified JSTOR.fltr you should remove it from the Custom Import Filters folder and use the new default filter provided by Bookends.
Improved edit pane display
Changes in label placement and spacing allow more text to be shown in each field.
Showing edit field hint text is optional
A setting in preferences, Refs tab, lets you show or hide hints in edit fields.
Added more escaped BibTeX characters to the Unicode conversion table
Bookends will now import text in cases where the tag and the textual content are separated by a tab
When doing a live search for words surrounded in quote marks, the matching phrase in the Summary view will be highlighted in yellow
Previously each word in the phrase would be highlighted even if they weren't found together.
When importing from bioRxiv in Bookends Browser, Bookends will put 'biorXiv' in the Journal field
Something similar will happen when importing from medRxiv, which had been broken by changes made on their server.
Attach a picture in the clipboard
Use the Refs menu or right-click in the reference list and select Attach -> Picture In Clipboard.
When fetching Google Books cover art, Bookends will change the URL provided by Google to use "https"
Bug fixes
Fixed: the Notes tab will once again have an asterisk if the Notes field has content and you are not showing it on the Main edit pane tab.
Fixed: a cosmetic issue in the edit pane where the hint color would be incorrectly applied to metadata.
Fixed: a bug where the PDF annotation popover didn't close when it should.
Fixed: a bug where double clicking on white space in the note stream would cause an error
Fixed: a bug where the hyphen-containing citekey in two references weren't identified as duplicates.
Fixed: a rare problem with importing references Sente.
Fixed: a bug where downloading the same reference with cover art from Google Books caused a hang.
Fixed: a bug where the edit field hints reflected those of the last-viewed reference.
Fixed: a bug in the standalone editing window where hint text could be saved as the content of the empty field.
Fixed: a bug in the standalone editing window where resizing the window didn't resize the text fields.
Fixed: a bug where the Action pop-up menu under the group pane didn't fire unless there were user-added groups.
Fixed: a problem where in some cases there were duplicate entries for the same folder in the ad hoc folder list.
Fixed: a problem with edit field hints were a & in the label name was output twice.
Fixed: a bug in the build process where Bookends was incorrectly marked as supporting non-English languages.
Fixed: a bug in Mellel scans when the first character in a citation is @.
February 13, 2022
Share synced libraries with others (requires macOS 11 Big Sur or later)
After uploading your library to the cloud, the cloud pop-up menu will have a new option, Share Library. Use it to send an invitation to other Bookends users to allow read/write or read-only access to the library. Once accepted, you (the owner) and others (the participants) can work with the same library. To share attachments, point the library’s attachment subfolder (set in the File menu) to a file sync service folder (e.g. iCloud Drive, Dropbox, Microsoft OneDrive, etc.) that contains the attachments, and use that service’s method to share the folder. If you are sharing with Bookends for iOS, the folder must be in iCloud Drive. Bookends will automate much of this for you when you use the cloud pop-up menu Prepare Shared Attachment Folder.
Specify a library-specific attachment folder outside of the default attachment folder
Use File -> Set Default Attachment Subfolder to bring up a dialog that let's you set an attachment folder for the open library. Click Browse and select the folder you would like to use, and its full pathname will be shown. Note that if you use the pop-up menu instead of the Browse button you will only be offered subfolders in the global default attachment folder. You must use Browse if you want a folder outside of that hierarchy.
Improvements in the edit pane
In Light Mode, the field label text is shown in empty fields as light gray "hint" text. This is not done in Dark Mode, in which the fields are a darker shade that provides guidance. The height of the edit field will adjust as you type if you're autocompleting and the suggested text is too long to fit on one line. Finally, label text size will adapt if you change the size of reference text in preferences. If the reference text size is set to 12 points, the label text size will be 12 points. If the reference text size is 13 points or greater, the label text size will be 13 points.
Improvements in importing authors when a JSTOR PDF is attached
Drag-reorder field labels with a simple click and drag
This previously required that the Command key was pressed.
If Postbox is your email client, sending an email from Bookends will now include attachments
Sending attachments already works with Mail and Microsoft Mail.
Floating citation references will include the volume number of edited books
The annotation popover window will close if you copy the selected text with Command-C or the Edit -> Copy menu
Bookends will search up to the first 5 pages of a PDF for a DOI when it is attached
Bug fixes
Fixed: a bug in the automated search window "find" function.
Fixed: a bug in preferences where restoring the factory default for the Summary views set incorrect values.
Fixed: a bug that could result in "record locked" errors.
Fixed: a crash that occurred if you closed the preferences window with a listbox edit cell active.
Fixed: a bug where changing some labels would cause an error.
Fixed: a bug in editing very large fields where deleting text could cause the view to become truncated.
Fixed: a bug that in rare circumstances could cause the attachments folder to be moved to the Trash.
Fixed:a bug where the text color would be black after editing a field in Summary view while in Dark Mode.
Fixed: an issue with saving edited text in Dark Mode.
January 8, 2022
All-new reference edit pane
All fields are in a vertical scrolling list. Field sizes automatically adjust to accommodate their content. You can reorder the fields in preferences (Refs tab) or by Command-dragging a field's label and dropping it on the label of another (the dropped field will be moved to the position before the receiving field). You will have to recreate the field order if you had changed it in previous versions of Bookends. If the contents of a field exceed a certain height, a disclosure triangle will allow you to expand or collapse the field. If more than one field has a disclosure triangle, all will expand or collapse together. Cloud Sync will sync the field order between Macs. The All concise view has been removed as it is now redundant.
File -> Export PDF Annotations
This operation exports annotations in PDFs attachments. You can choose to work with PDFs attached to the selected references, those in the Hits List, or all references in the library. Annotation contents can be sent to the clipboard or a text file, and you can specify the kind of annotations you want extracted (highlights, underlines, and/or notes), and the metadata associated with the annotations (PDF pathname, the page on which the annotation occurs, and/or the date it was last modified). The page label is extracted from the PDF itself, and may or may not correspond to the page of the published article. Annotations with content (e.g. Notes) usually have modification dates; those without content (e.g. plain highlights) usually do not.
Right-click on the PMID or PMCID fields and obtain a contextual menu that will open the article in your browser
This already exists for the URL and DOI fields.
If you try to sync a BibTeX file but none of your references have citekeys a message will explain why nothing was saved
In the edit pane, clicking on the color label name at the top will bring up the pop-up menu allowing you to change colors
Improvements in importing metadata from JSOR when attaching a PDF
Note that the data can be incomplete because JSTOR is inconsistent in providing it. The direct JSTOR search imports higher quality information.
Bug fixes
Fixed: a bug that caused Bookends to mistakenly create the folders /Bookends/Attachments when the default folder was set to iCloud in preferences.
Fixed: Fixed a bug where a right-click on an underline notecard offered the possibility of editing it.
Fixed: a bug in BibTeX sync where extra @ characters were added at the beginning of the first reference.
Fixed: JSTOR PDFs will no longer be attached to the wrong reference if there is an error when trying to import the metadata.
Fixed: a bug where Global Change -> Move Attachments of the selected references didn't work.
Fixed: a bug where an error was thrown when moving attachments to a top level folder.
Fixed: a crash in the Online Search window when a search hadn't been performed and the Find -> Done button was clicked.
December 11, 2021
Manipulate PDF annotations with a contextual menu
Right-click on an annotation type that Bookends supports and you’ll see a contextual menu that lets you delete, copy, edit contents, or change the color, depending on the type of annotation selected.
Turn on continuous highlighting and set the selected text to the desired color by pressing Control-1 to 5 when the annotation popover window is active
Global Change -> Move Attachments
This function lets you move or copy the attachments in your selected references, the Hits List, or in the entire library to a folder of your choice. There is also the option to remove annotations from PDF attachments as they are moved or copied. This would be useful if, for example, you created a library-specific attachment folder and wanted to move all the attachments in that library to the new folder.
Watch folder improvements
Bookends will create only one reference when downloading very large files from a browser to the watch folder..
The author/editor separator field is disabled in the BibTeX import filter
BibTeX expects names to be separated with " and ".
Created a keyboard shortcut for Copy DOI (Shift-Command-G) and added this option to the reference list right-click contextual menu
The default attachment folder pop-up menu in preferences now offers “Bookends iCloud Folder” as an option
This was previously “iCloud Folder For iOS Sync”, but was changed to reflect the fact that because Bookends 14 uses native cloudKit, it can create this special dedicated folder itself.
When present, subtitles will be added to the title of books found on Google Books
Bug fixes
Fixed: a bug that could corrupt the preference file containing the reference Types and labels.
Fixed: added an extra check to prevent an ad hoc attachment folder from being added more than once.
Fixed: a bug where libraries weren't being synced on open.
Fixed: a bug where the PDF comment size setting in preferences wasn’t saved.
Fixed: a bug in the Formats Manager where the controls for setting case options could be invisible if the window was resized.
Fixed: a problem with custom formats where the bibliography example in the format window would be empty if the citation example was empty.
Fixed: a bug with the BibTeX sync file where the leading @ of an edited reference was stripped off.
Fixed: a bug where the wrong crosslink type was added to a reference when the link preference default was changed from Book:Book Section.
Fixed: a bug where resetting the concise views to the factory defaults in preferences wasn't saved.
Fixed: a problem where syncing preferences could result in a "503" error.
Fixed: a bug in the automated PubMed search window where the entire metadata field could have a background yellow color.
November 6, 2021
New PDF annotation popover
When you select text in a PDF, a small floating window allows you to set the highlight color (or none) and offers the following choices: Highlight, Underline, Copy, PDF Note, Notecard, Quote. Clicking Highlight, or double-clicking a highlight color, will highlight the selection (if no color is selected, the window will simply close). PDF Note will create a new PDF note that contains the selected text. Notecard will make a new notecard containing the page number and the selected text as the body, and Quote will make a new notecard with the page number and use the selected text as a quote. If the PDF is displayed in the PDF view pane, Notecard and Quote will open the note stream and display the new notecard. If the PDF is displayed in the edit pane Attachments tab, the selection will be added but the edit pane will remain. The floating window is dismissed when you click a button or click outside of the window. The items in the old Action pop-up menu that performed these functions have been removed.
Improved UI for setting PDF highlight colors
This function lets you move or copy the attachments in your selected references, the Hits List, or in the entire library to a folder of your choice. There is also the option to remove annotations from PDF attachments as they are moved or copied. This would be useful if, for example, you created a library-specific attachment folder and wanted to move all the attachments in that library to the new folder.
Added a keyboard shortcut for Make Note in the PDF viewer: Shift-Command-E
Automatic retrieval of PDFs from PubMed Central
If Bookends is unable to fetch a PDF from the publisher for an article imported from PubMed (e.g., if you don’t have journal access privileges), it will check to see if it's available from PubMed Central and, if so, download it from there.
Certain types of errors in a format will be automatically repaired when it is opened in the Formats Manager
A sync warning will be issued if your library is stored in iCloud Drive even if it is not in the Bookends iOS sync folder
Sync will be suspended for the current session, and can be re-enabled after you move the library file in the Finder.
Updated Bookends Browser to maintain compatibility with certain sites
The $ sign won't be escaped with formatting using BibTeX Markup
Updated database engine
Editing PDF file tags works in Monterey
Bug fixes
Fixed: a rare bug where using a legitimate format could result in an error.
Fixed: a problem where EndNote PDFs weren't being transferred when importing from EndNote.
Fixed: a bug where the tag was still added after canceling the addition of a PDF tags to multiple selected references.
Fixed: a bug in the concise views where the name of file tags could be colored incorrectly.
Fixed: a rare problem where the first reference list column could be hidden.
October 10, 2021
Create peer-to-peer reference links directly in the library window
When two or more references are selected, the menu option “Link Selections (Peers)” will be enabled in the Refs menu and the right-click contextual menu. This option will create peer-to-peer links even when the Links Inspector is not open. Note that if the references already have a link relationship, it will be changed to peer-to-peer.
Create a synced .bib file containing all your references in BibTeX format
This is a one-way (Bookends -> file) sync on demand, which may be useful to those who use Bookends references with other apps such as LaTeX, Pandoc, or TeXstudio. To initiate, use File -> Create Synced BibTeX File. Once created, the menu will read Sync Linked BibTeX File. When this is invoked, Bookends will update the file with references added, deleted, or edited. Note that Bookends stores the .bib file's alias, so you may rename it or move it to another location on the HD and Bookends will still find it. If the file has been deleted or is stored on an external drive that is not mounted, the menu will revert to Create Synced BibTeX File. Bookends identifies references by their citekey, so any references without citekeys will not be synced to the linked BibTeX file. This function uses the format "BibTeX.fmt". If you have created an alternative BibTeX format with a different name, you must rename it to BibTeX.fmt to be used for syncing. Note that this function has nothing to do with cloud sync -- it just maintains a local .bib file that can be synced (updated) on demand to match your library.
BibTeX format updated
Fields with missing content will no longer be output, which in many cases will improve processing speed and reduce the size of export files.
The names of saved advanced PubMed searches can be of any length
Previously they were limited to 31 characters.
If an error occurs during sync, Bookends will offer to "Force Full Sync", which will often override the problem and allow the sync to finish
You will also have the option to temporarily suspend syncing during the current session.
When an item from a term list for a non-scrolling field (e.g. Journal) is dropped on a reference, the contents of the corresponding field will be replaced
Previously, the item was appended to the existing text.
Bug fixes
Fixed: a bug that prevented AppleScripts from working.
Fixed: a bug in floating citations where pressing Return or Enter didn't insert the temp citation of the selected reference.
Fixed: a bug in the inspector's Rename Attachment function.
Fixed: an error that would occur when clicking on the inspector’s import icon when there were no references in the list.
Fixed: a bug where duplicating a reference could cause and error on sync.
Fixed: a rare problem where the online search list of references could become unresponsive.
Fixed: eliminated an unnecessary dialog in the inspector asking permission to detach a PDF that was moved to the Trash.
Fixed: the characters " and # will be excluded from citekeys generated by Bookends.
September 10, 2021
Bookends 14 has a new bundle id
This means that older versions of some apps that integrate with Bookends (e.g., Mellel, Nisus Writer Pro, DEVONthink, and Tinderbox) will not be able to send AppleEvents to Bookends 14. We have worked with each of these companies and they have released updates that work with Bookends 14: Mellel 5.0.8, NWP 3.2.2, Tinderbox 9, and DEVONthink3 3.8 work with Bookends 14.
Introducing cloud sync version 2 (v2)
The original Bookends cloud sync (version 1) used Apple's CloudKit JS APIs, which give web apps access to iCloud. Bookends now uses Apple's native CloudKit. You must be signed into iCloud and have enabled iCloud Drive in System Preferences to sync. The major advantage at this time is that v2 uses your macOS iCloud account information, meaning that there is no need to log in separately to iCloud in Bookends. Importantly, native CloudKit will allow us to expand Bookends' sync capabilities in future releases.
Much improved PDF search results
The results of a PDF search will be listed, with the bolded search word shown in context along with page where it was found. Clicking on an item in the list will take you to its location in the PDF.
New Cited By Inspector
If the parent reference has a PMID this inspector will use PubMed to find all of the references in which it has been cited. You can view a reference in your browser by double clicking on it, or import it by clicking the download button, right-clicking, or drag and drop. When using the first two methods, you have the option to automatically link the imported reference to its parent. Note that the references found by PubMed may or may not correspond to other sources that track citing references. Hover the pointer over a reference to see the full contents in the help tag.
Cited In Inspector adds PubMed as a source
If the parent reference has a PMID Bookends will use PubMed to find which references are cited in the parent reference. PubMed has much more information about cited references than CrossRef and the results are resolved much more quickly. If there is no PMID and the parent reference has a DOI, Bookends will use Crossref as before. From the inspector you can view a reference in your browser by double clicking on it, or import it by clicking the download button, right-clicking, or drag and drop. When using the first two methods, you have the option to automatically link (work: work cited) the imported reference and its parent. Hover the pointer over a reference to see the full contents in the help tag.
The two Cited Inspectors won't change the parent when used to import references
The way that Link Inspector relationships are created and synced has been completely rewritten
Although transparent to users, this will make it easier to add improvements in the future.
The Attachments Inspector now shows each attachment’s path name
Added a peer-to-peer relationship to reference links
This is useful if you want to link references that do not have a hierarchical relationship, for example references cited in a paper (article-to-article) or chapters in a book (chapter-to-chapter).
Various modifications to the Link Inspector
The ability to add comments to individual linkages has been removed. Cosmetic improvements.
Double clicking on a reference will not toggle the edit pane or PDF viewer if the Links, Cited In, or Cited By Inspector is open
In those cases it will simply set the Inspector parent to the reference clicked on. Previously, it would do both.
Show attachment names in the reference list column view
You can set this in preferences (Lists tab) or with a right-click contextual menu in the reference list. Names of multiple attachments belonging to the same reference will be separated with semicolons.
Use Bookends Browser to replace an orphaned attachment
Select the reference with the orphaned attachment and open Bookends Browser in the display pane. Depending on the URL stored with that reference, the browser will display either the PDF or the reference's web site from which you can navigate to the PDF. Click the paper clip attach icon and the PDF will be downloaded and replace the existing orphaned attachment. Note that if you have more than one attachment, orphaned or not, Bookends will simply add the PDF to the attachment list and you should detach the orphaned attachment yourself.
The reference list contextual menu "Sort By Label" has been changed to "Group By Color"
This reflects the difference between sorting the Label column, which is ordered by the text assigned to each color, and this function, which groups references with the same color.
Bibliographies sent to disk as UTF-8 or UTF-16 will have the extension .txt
If output as Plain Text, the extension will be set to .ris if the RIS format is used.
There is a new AppleScript property to get the path to a library's default attachment subfolder, if any (library attachments subfolder path)
If no library subfolder has been set, Bookends will return the path to the default attachment folder itself.
Typographic quote marks will be converted to their BibTeX equivalents when "BibTeX Markup" is specified for the formatted output
A reference’s unique ID can no longer be changed by the user
Too many features that depend on the unique ID and would break if it were changed.
On launch Bookends will check for and "forget" ad hoc attachment folders that are in the Trash
The reference list right-click contextual menus have been modified
Right-clicking on the paper clip icon now only shows options relevant for attachments.
Improved user control when downloading PDFs
A Skip button in the PDF -> Download From Internet dialog immediately stops the attempt to get the current PDF and moves to the next selected reference, if there is one. This is useful if the online source is slow to respond or hangs, and is more reliable than pressing Command-.
Online searches can be stopped by clicking the progress wheel
This is more reliable than pressing Command-.
Improved Autocomplete Paper UI
The sheet remembers its dimensions between openings during a session. When references are found, the default button changes from Search to Import, and import will be triggered by pressing the Return key.
When fetching metadata using PDFs downloaded from pre-print servers like bioRxiv and medRxiv, Bookends places the name of the pre-print server in the Journal field
Note that once the paper is published that version will receive a new DOI.
Any text in the live search field will be selected after you select and group and the reference list is updated
This makes it easier to delete if you no longer want to filter the results.
If present, the following characters will be removed from automatically-generated BibTeX keys: ’\&^
When attaching a PDF whose reference already exists in the library, you will still have the option to attach to a new reference and import the metadata
This is be useful if, for example, you are adding separate PDFs for a book and its chapters.
Bug fixes
Fixed: the format of the date in the Added column when duplicating a reference.
Fixed: a cosmetic fix for the display of the selected reference’s text in the Link Inspector when it is in the background.
Fixed: a crash that could occur in Big Sur when running the Bookends demo on the same machine where there was an old version from the Mac App Store.
Fixed: a bug where failure to close the color picker in preferences could lead to an error message.
Fixed: the Google Books online search now responds to Command-.
Fixed: a bug that prevented changes to Types and field labels from being synced via the cloud.
Fixed: a bug where styled text in the Short Title field wasn't toggled to plain when it should be when formatting.
Fixed: a bug where the Attachments Inspector and pop-up menu of attachments weren't updated immediately after reattaching a file.
Fixed: the Attachment dialog subfolder pop-up menu will no longer show folder aliases the user placed in the default folder.
Fixed: a bug where the links column didn't update immediately when replicating a book as a book chapter.
Fixed: a bug where starting the watch folder without it first would result in the import of hundreds of files from the Bookends bundle.
Fixed: several bugs in the marooned file inspector that could cause a file to be listed as marooned even if it wasn't.
Fixed: a bug in several printing functions that resulted in white text on a white background when in Dark Mode.
Fixed: a bug in Pages scanning where the format's hanging indent setting was only honored for numbered bibliographies.
Fixed: two bugs in creating a bibliography in Dark Mode where the output was either black text on a black background or the file sent to disk was empty.
Fixed: a leading > for a comment will be excluded when copying the contents of a notecard.
Fixed: an error that could occur when the library was synced as it was closed.
Fixed: the color for a color label is now positioned correctly in the Summary view.
Fixed: an error that could occur when clicking on certain types of PDF annotations.
Fixed: a bug that in rare instances would cause an “illegal cast” error.
Fixed: a bug where user-defined Term List weren't remembered between launches.
Fixed: a bug in the PDF search field when a recent menu item was selected.
Fixed: a bug that prevented autofilling of individual fields from working.
Fixed: a bug that could cause a PDF to be scrolled to the end when opened by changing references using the arrow keys.
Fixed: a bug that caused the text of a field edited in the enlarged field window and then saved in Dark Mode to be 2 points too large and black.
Fixed: an error that could occur when dragging a reference from the floating citation window to a Mellel document.