Author: Mike Arthur

Mendeley Desktop 0.6.3

Mike Arthur

The moons have once more aligned and we would like to announce the release of a new version of Mendeley Desktop for your software-using pleasure, including the Word plugin.

Thank-you all for your feedback, it’s really helped to shape this release. If you have any problems with Mendeley or you wish to request cool new stuff for us to add please visit our feedback forum, which is accessible through the Help menu.

New Features
  • PDF file organisation and renaming tool
  • Automatic extraction and retrieval of metadata for ArXiv papers
  • Lookup metadata for documents based on their PubMed ID
  • Invite other researchers who are not Mendeley contacts to join Shared Document Groups from within the program
  • Store and sync paper abstracts
  • Link to your Mendeley profile and online library in Mendeley Desktop
Improvements to Existing Features:
  • Author extraction improvements in the PDF importer – This release lays the groundwork for future metadata extraction improvements
  • Faster startup with large libraries
  • Reduce the number and duration of pauses during synchronisation, especially with large libraries
  • Improved auto-completion of authors
  • Allow deletion of documents in Recently Added and Ungrouped views
  • Display the number of documents in groups next to the group name
  • Warn the user if they accidentally try to add papers to ‘My Publications’ if they do not appear in the author list for that paper
  • Show number of PDFs uploaded/downloaded from Mendeley Web while syncing
  • More informative progress updates during PDF import
  • Import tags from Bibtex, RIS files
  • Export tags to Bibtex files
  • Word plugin installer integrated into Mendeley Desktop (Tools menu)
  • More citation styles for citation view and Word plugin
  • Bibliographies in Word plugin have hanging indents for certain styles
  • Various improvements to citation formatting
Bug Fixes (General)
  • More robust synchronisation – fixed many bugs which could occur whilst syncing
  • Various citation formatting improvements
  • Various Bibtex import fixes – Bibtex files generated by Google Scholar and Web of Science now import correctly
  • Support RefWorks-generated RIS files
  • Prevent pasting rich text into metadata fields which do not support it
  • Use case insensitive sorting in fields list and table view
  • Strip XML tags when exporting notes to Bibtex or RIS
  • Fix ‘Save’ button not being enabled when viewing un-corrected metadata until at least one of the fields had been changed
  • Removed in-line editing in table view as it was accidentally activated too easily
  • Fixed problems entering ISBN, ISSN information
  • Made several error messages less scary
  • Fix current article selection being lost when sorting library
  • Fixed imported documents being added to different groups if the user changed the selection while the import was in progress
  • Fixed searching for exact phrases using quotation marks
  • Stop trying to upload PDF files if account quota is reached
  • Fixed bug causing scary message about UUID clash
Bug Fixes (Windows)
  • Fixed crashes when importing certain PDFs on Windows
  • File auto-renamer could create file names which were too long on Windows
Bug Fixes (Mac)
  • Fixed crash during online metadata retrieval when importing PDFs
  • Now works on OSX systems which have Qt/KDE installed (fix possible crash on startup)
Bug Fixes (Linux)
  • Make Ubuntu package require the Qt 4 SQLite plugin
  • Now compatible with Qt 4.5

Mendeley Desktop: The About Dialogue (and the Refactor)

Mike Arthur3 Comments


New About Dialogue and it’s even closable on Mac! How on earth did we get to this point?

Let me tell you a story…

Since my last post the Mendeley Desktop team has been very busy indeed!

Our “rewrite of some of the internal Mendeley code” has turned into a rewrite of almost all the code.

Why are we rewriting our code you may ask? Like many other small companies, Mendeley started with their software being written by external contractors. By the time I started in May 2008 a significant amount of code had been written which was then ported to Linux and Mac. What started life as a prototype had turned into a product which was then released to the world when we hit open beta. This means we lacked a solid architecture, any real documentation, coding standards or unit testing.

In the past few months the team has rewritten basically everything except the metadata extraction and the Citation Style Language parser (although these two have both been improved also and will probably be incrementally rewritten for further releases). As a result, we now have a much smaller, easier to read, unit-tested, documented, faster and just plain better codebase by any software engineering metric you would care to throw at it. My slightly obsessive insistence that the team meets the coding standards document and our continuous integration tool has resulted in a far higher quality product.

You might be asking why on earth you should care about everything I said above. Well the answers are in the features/bugfixes that you’ll see in the new release:

  • Better performance and lower memory usage
  • Adding sub-groups
  • Folder monitoring
  • Encrypted data transfer
  • Only uses standard HTTP ports (i.e. 80 and 443) and uses your system proxy settings
  • Less interface slowdown on network/import operations
  • A closable “About” window on Mac, as featured at the top of this post (No, I’m not joking. To close it in 0.5.9 or below, press Escape)
  • More native and more usable user interface
  • More traditional Mac packaging

Anyway, I hope that is enough to get you excited about the next release. We will be retaining feature parity with 0.5.9 (i.e. no features currently existing in 0.5.9. will be dropped in 0.6.0) and 0.6.0 will fix a lot of outstanding bugs with 0.5.9.

Mendeley Desktop 0.6.0: Coming soon!

Mendeley Desktop: The MVC strikes back

Mike Arthur1 Comment

Firstly, thanks to all of you who have filed feature requests or flagged up bugs on our bug tracker, your feedback has been really useful.

After thinking about how to best accommodate your needs we’ve deciding to do a rewrite of some of the internal Mendeley code in order to get it running snappier and work better with larger libraries.

As a result of some work Fred has done on his music player we’ve decided that using Qt’s MVC framework maps extremely well to our needs and should bring us far greater performance when dealing with large libraries as well as keeping the code cleaner, better separated and making it much easier to write unit tests with decent coverage levels.

So where are we with this at the moment? Currently we have implemented most of the new non-GUI code with just our local/remote database code to finish. For those interested in this sort of thing, we are 100% documented with Doxygen (both private and public members) and have every class’s method unit-tested with around 85% test coverage.

Without revealing too much you should be excited about this and some of the new features that will see the light of day around the same time as the new, better-performing internal code. This will hopefully mean we can feasible support much larger collections than currently with a slimmer/faster application and quicker bug turnaround with less regressions than our previous releases.

Get excited, I am! 😀

HOWTO: Mendeley on OS X/Linux/Toaster

Mike Arthur7 Comments

Update: We now have native versions for Windows, OS X and Linux, so I have crossed out the instructions on how to run Mendeley using WINE and Darwine. The instructions for running Mendeley on your toaster remain valid.

—————————————————————

[June 13, 2008]: My name is Mike and I’m a software engineer. No, I won’t fix your computer. However I will get Mendeley running on it because you’re such a nice person.

I’m hard at work at the moment making Mendeley work on Linux. For those who care this involves moving from a Visual Studio based build-system to one using CMake and also fixing some of the inane rubbish that the the MSVC++ compiler seems to think should be valid C++.

At the moment you can use WINE on Linux/FreeBSD, Darwine on Apple OS X and Mendeley-shaped bread in your toaster to fulfil all your unsated academic document management needs.

Running Mendeley on Apple OS X

  • Install Darwine from http://www.kronenberg.org/darwine/ into the Applications directory.
  • Install TRiX from http://mike.kronenberg.org/?p=69 into the Applications directory.
  • Run TRiX from Applications.
  • Make sure the following options are selected: In the “General” tab: “MS Arial, Courier, Times fonts“, “MS Tahoma font (not part of corefonts)”. In the “Libraries & Runtimes” tab: “vc6redist from VS6sp4 (mfc42, msvcp60, msvcrt)”
  • Press the “Install” button.
  • When done (i.e. Terminal displays “All done, no errors”) install Mendeley (double click on .exe file – Darwine will do the rest. Allow it to install into the default directory: i.e. “C:Program FilesMendeley Beta”). If “All done, no errors” did not appear then try and click “Install” again until it does.
  • Open a new Terminal.
  • Run the following commands: “cd ~/.wine/drive_c/Program Files/Mendeley Beta/; /Applications/Darwine/Wine.bundle/Contents/bin/wine Mendeley.exe“
  • The last command should have launched Mendeley! If it didn’t or you are having any other problems then post them here and we’ll try and help.
  • KNOWN Problems: Depending on your language, “Program Files” may be something like “Programme” instead. If the above command doesn’t work then try to run “ls ~/.wine/drive_c/” and use the results to see where you should “cd” to.

Running Mendeley on Linux/FreeBSD/BeardOS

  • Install Wine from your package manager.
  • Download Winetricks from http://www.kegel.com/wine/winetricks.
  • When downloaded run “sh winetricks” from a terminal, when in the same directory as Winetricks.
  • Select “allfonts” and “vcrun6” and press “OK“. Press “OK” when the VC6 installer pops up.
  • When done (i.e. the terminal displays “All done, no errors”) run “wine Mendeley-0.5.4.0.exe” when pointing at the correct downloaded installer and change the version number to be correct. Allow it to install into the default directory: i.e. “C:Program FilesMendeley Beta”).
  • Run the following commands: “cd ~/.wine/drive_c/Program Files/Mendeley Beta/; wine Mendeley.exe“
  • The last command should have launched Mendeley! If it didn’t or you are having any other problems then post them here and we’ll try and help.
  • KNOWN Problems: Depending on your language, “Program Files” may be something like “Programme” instead. If the above command doesn’t work then try to run “ls ~/.wine/drive_c/” and use the results to see where you should “cd” to.

Running Mendeley on your Toaster

  • Get a piece of Bread.
  • Cut the piece of Bread into the shape of the Mendeley logo.
  • Insert into Toaster and set heat to at least 5.
  • Wait patiently for the Toast (toasted bread) to pop out of the toaster.
  • Optional step: Use a Knife and a Spread (any bread-compatible spread will do) and combine them on the toast.
  • Consume the toast.
  • The last command should have launched Mendeley made you less hungry! If it didn’t or you are having any other problems then post them here and we’ll try and help.