Bio7 2.8 Released

Leave a reply

30.05.2018

A new and improved release of Bio7 is available. The new Bio7 2.8 release comes with a plethora of new R features and bugfixes.

Release Notes:

General:

  • Updated Eclipse RCP to 4.7.3
  • Windows R update to version 3.5.0
  • ImageJ plugin updated to version 1.52d7
  • Added the ImageJ Edit perspective to the default opened perspectives
  • The R perspective is now selected as the opened perspective after startup of Bio7
  • Added an option to save all editors on close (default enabled on MacOSX)
  • Improved the main ‘Scripts’ menu to allow nested custom scripts in folders and subfolders which form new submenus
  • Improved the Table and R-Shell context scripts menu
  • Added some example scripts to the new scripts menu
  • Added an script to open the default script location in the OS file explorer
  • Simplified the different script locations (reduced to four locations in the Bio7 preferences)
  • Spatial import, export scripts moved to the main ‘Scripts’ and R-Shell script context menu (Deleted import, export script locations)

R:

  • Simplified the Bio7 R-Shell interface
  • Added a new view for some R templates
  • Code completion from loaded R packages can now be imported from the R-Shell or the R editor (both completions will be updated!)
  • Improved the reload code completion by only considering R functions (cleaner seperation of functions and datasets)
  • The updated R-Shell context menu can now dynamically be extended with custom scripts (updated dynamically). Folder and subfolders form new submenus.
  • Improved, bugfixed and extended the ‚Evaluate Line‘ action which was renamed to ‚Evaluate Line or Selection‘  action which now interprets selected R code, too.
  • Improved MacOSX ImageJ interaction (editor hoover focus)
  • Improved the call of the default plot device (quartz) in a native R connection on MacOSX (now default opened when, e.g., plotting, debugging, etc.)
  • Added a new menu to install Rserve for R > 3.5.0
  • New shutdown option to execute R code at shutdown (e.g., to save the current R workspace – a reload with the already existing startup option is possible, too!)
  • Improved the general error messages of the R-Shell view and the R editor evaluation. Now much simpler and printed cleaner!
  • Added an option to print the error stream of the Bio7 console to the R-Shell view (to the right output panel to get an output if the console is hidden!)
  • Fixed a bug with the shiny execution (removed annoying dialog)
  • Fixed many other bugs (unnecessary error messages, execution errors, MacOSX bugs, etc.)
  • R-Shell code completion improved (see editor code completion improvements below)
  • Removed the use of temporary files of the R-Shell and R editor code completion
  • Added an preference option to add arguments to the source command
  • Multiple selected R-Shell variables are now available in the R workspace (‘.r_shell_vars’ – a character vector) for the use in custom R scripts (e.g., to extend the R-Shell script context menu!)

R Editor:

  • Added a detection/quickfix function to install missing packages when a package load definition is in the editor file but the package is not installed

  • Added a quickfix to add a library definition when an unknown function is called (not defined and loaded but package with function is installed)
  • Added support for the the magrittr piping operator in code completion to autocomplete a given dataframe in the workspace (column completion)

  • Added code completion support for dataframes columns and rows, named list elements and named arrays (of arbitrary dimension)

  • Improved code completion to display current workspace variables
  • Classes of R objects are now displayed in the code completion context dialog
  • Editor variables and functions are now emphazised in code completion, too
  • Added a directory dialog to easily create a directory string for the editor file
  • Created new submenus for the organization of the context menu
  • Improved the hoover dialog (improved offset)
  • Improved the completion context of R objects (current workspace objects)
  • The styler package can now be used for an improved code formatting (requires UTF-8 Bio7 workspace on Windows – see preferences!)
  • Improved code completion for S3 and S4 objects (correctly display current cursor completion)

ImageJ:

  • Updated ImageJ plugin to version 1.52d7
  • Updated ImageJ2 libraries
  • Added new ImageJ macro functions to the code completion of the macro editor
  • Added the ImageJ Edit perspective to the default openend perspectives
  • Improved the editor hoover activation on MacOSX
  • Improved the ImageJ MacOSX touchpad resizing of the ImageJ panel

Java:

  • Updated JRE to 1.8.71
  • Improved the creation of Java projects and project imports (no annoying dialog anymore)
  • Improved the ‘Add Selected Libraries’ preference to add multiple Java libraries for dynamic compilation (e.g., to compile more embedded Eclipse library functions)
  • Now ImageJ2 libs have to be added to the dynamic compilation libraries for compilation (removed as default libraries)
  • Added a key shortcut (STRG + ‚+‘) to increase the SceneBuilder panel (2x)

Download and Installation:

Windows:

Just download the *.zip distribution file from https://bio7.org and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.

Linux:

Download and extract the installation file from https://bio7.org.
For Linux you have to install R and Rserve (see Rserve installation below!).

MacOSX:

Download and extract the installation file from https://bio7.org.

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition for MacOSX you have to install R and Rserve (see below!).

Linux and MacOSX Rserve (compiled for cooperative mode) installation:

To install Rserve open the R shell and then execute the menu action “Options -> Install Rserve (coop. mode) for R …” for different R versions. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!). In cooperative mode only one connection at a time is allowed (which we want for this Desktop appl.) and all subsequent connections share the same namespace (default on Windows)!

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the R-Shell context menu “Packages” action:

R-Shell context menu->Packages->Install_Default_R_Packages

Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.

 

R Improvements for Bio7 2.8

Leave a reply

18.05.2018

The next release of Bio7 adds a lot of new R features and improvements. One minor change is that the default perspective after the startup of Bio7 now is the R perspective to emphazise the importance of R within this software.

The R-Shell view has been simplified and the R templates have been moved in it’s own simple view for an improved usability (see screenshot from R perspective below).

In addition the context menu has been enhanced to allow the creation of submenus from scripts found in folders and subfolders (recursively added) which you can create for a menu structure.
Scripts can be added created in R, JavaScript, Groovy, Jython, BeanShell, ImageJ Macros.
Java (with dependant classes) can be dynamically compiled and executed like a script, too.

Several improvements have also been added to the R-Shell and the R editor for an easier generation of valid R code. The R-Shell and the R editor now display R workspace objects with it’s class and structure in the code completion dialog (marked with a new workspace icon – see below).

R-Shell:

R editor:

In the R editor a new quick fix function has been added to detect and install missing packages (from scanned default packages folder of an R installation – has to be enabled in the Bio7 R code analysis preferences).

Also the detection of missing package imports are fixable (when a function is called but the installed package declaration is missing in the code but the package is installed to deliver the function).

The code assistance in the R-Shell and in the R editor now offers completions for, e.g., dataframes (columns) in the %>% operator of piped function calls:

In addition code assistance is available for list, vectors, dataframes and arrays of named rows and columns, etc., when available in the current R environment.

Code completion for package functions can now easily added with the R-Shell or the R editor which loads the package function help for both interfaces. The editor will automatically be updated (see updated editor marking unknown functions in screencast below).

Numerous other features, improvements and bugfixes have been added, too.

Bio7 2.8 will hopefully be available soon at:

https://bio7.org

Overview videos on YouTube

 

 

Bio7 2.7 Bugfix Release for MacOSX

Leave a reply

26.02.2018

Last week I released a new bugfix version of Bio7 which fixes some annoying bugs on MacOSX and updates some plugins.

  • Updated ImageJ to version 1.51v1
  • Improved the import of Java projects (No annoying dialog anymore)
  • Improved the execution of Shiny apps (No dialog when stopping the server)
  • Fixed several bugs and possible deadlocks regarding the swt_awt bridge and the OpenGL panel
  • Fixed a swt_awt key listener bug (ImageJ panel) to restore key events on the panel
  • Fixed a Mac bug in the R editor color dialog (hoover dialog of name R colors)
  • Huge fontsize for Swing (e.g., ImageJ dialogs) can be corrected for Retina displays (Bio7 ImageJ preferences – ‘-6’ for Retina displays fits well)
  • Bio7 editors and the Bio7 Workspace will be automatically saved before application shutdown

 

Download here

Bio7 2.7 Retina-Display Fix for MacOSX

2 Replies

08.01.2018

I recently discovered on a high dpi display (Retina-Display) enabled 13’’ notebook that the latest release of Bio7 for MacOSX is not displayed in high dpi but in a lower resolution which makes text and icons blurry (scaled) and unnecessary strains the eyes when editing R scripts with the R editor.

So I uploaded a new, fixed version for MacOSX.

However, to fix an already downloaded version of Bio7 you have to open open the ‘/Bio7.app/Contents/Info.plist’ file with a text editor (right-click on Bio7.app, execute ‘Show Package Contents’ and open ‘/Contents/Info.plist’) and add the following lines before the </dict> tag:

<key>NSHighResolutionCapable</key>
<true/>

In addition to update the Info.plist file for the Operating System you have to open the Terminal (in ‘Applications/Utilities’) and execute the following command (default install directory – shell command is one line!):

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -v -f /Applications/Bio7.app

Here some screenshots from before and after the fix was applied on a Retina-Display (zoom in for details):

Before:

After:

An updated version with the fix already applied can be downloaded here

See also:

Release notes for Bio7 2.7

 

Bio7 2.7 Released

3 Replies

02.01.2018

A new version of Bio7 is available. The application Bio7 is an integrated development environment for ecological modeling scientific image analysis and statistical analysis. Over the years Bio7 evolved to a platform useful for a broad scientific context.

This release includes a plethora of new features and improvements for the R editor, RShell, RMarkdown editor and the ImageJ plugin.

Release Notes:

General:

  • Bundled with Java 1.8.52
  • Updated bundled R to version 3.4.3 (Windows)
  • Improved PDF rendering (PDF.js) with Java 1.8.52 (fixed rendering)
  • Updated the Windows SSH client
  • Simplified the dynamic java compilation
  • Updated the Java compiler infrastructure

R

  • Improved the context information when opening code completion (R-Shell and R editor)
  • Added an improved context information when openening code completion in the R-Shell
  • Context information of a function is shown when using code completion inside function calls
  • Added code completion for function arguments in the R-Shell
  • Added code completion help for ‘library’, ‘require’, ‘data’,’::’ and ‘:::’ functions in the R-Shell and in the R editor

Screencast code completion:

Screencast code completion with particle analysis:

  • Improved code completion for S3 and S4 nested attributes (e.g., x@y$z) also in function calls when cursor is set inside of a composite call
  • Implemented a code completion filter (when typing)
  • Added an option to select different key combinations for the R-Shell code completion (Strg+Space can already be occupied on MacOSX)
  • Added dark theme support for the help browser when opened from the R-Shell help (?)
  • Added a matching brackets selection action to the R-Shell view (Key+Mouse-click before opening or closing bracket)
  • Added an action to transfer the R-Shell history to an opened R editor (see R-Shell help (?))
  • The R-Shell and code completion fonts can now be changed and the size increased
  • The R-Shell is now faster if long text is printed (removed automatic text wrapping)
  • Added the Eclipse Spell Checking infrastructure to the R editor (can be enabled in the preferences)

Screencast spell checking:

  • Spell checking errors can now be fixed in the R editor (hoover action available)
  • Added a preference to enable/disable spell checking
  • Added a ‘Load packages tab’ in the ‘Packages’ view as an UI replacement for the Load packages dialog (improved usability)
  • Added an action to update the display list of installed packages (also triggered if you activate the tab)
  • Added an ‘Attached Packages’ tab to the ‘Packages’ view
  • Added an action to update all packages (‘Load Packages’ tab)

Screencast R Packages view:

  • Improved the R-Shell code completion in general
  • Improved the hoover display layout (for warnings and errors)
  • Fixed several bugs (Reenabled loop parsing and fixed a bug to restore code folding after using code completion in the R editor!)
  • Updated ANTLR parser to version 4.7
  • Added „require“ for package code completion
  • Reduced the memory footprint of the R editor (OS handles)
  • Added missing roxygen tags for code completion of the R editor
  • Created a wizard to support a project template (default folders and files) for reproducible projects
  • Changed key binding of ‘<-‘ and ‘%>%’ operators to make them available in the R-Shell, too (see help in R-Shell)
  • Improved the “Evaluate Selected Line” Action for Rserve (Evaluated when successfully parsed!)

R Markdown editor

  • Spell checking errors in the R markdown editor can now be fixed with a hoover action
  • Added a decent markdown parser (flexmark) to the editor which fixes some minor display problems
  • Added a format action for selected text to the markdown editor

Screencast format markdown selection

ImageJ:

  • Updated ImageJ plugin to version 1.51.t16
  • Code completion (template) action now displays the macro documentation when typing
  • Code completion context information improved
  • Images from macros are now opened fast (before had a 2s delay because of a missing ImageJ attribute)
  • Cluttered MACOSX menus are now closed (added from opened application windows and frames). Some default added menus are disabled in the Bio7 preferences by default
  • Macros can now be executed within an external ImageJ instance in a separate Java process (if enabled in the preferences). Windows only!
  • Added Macro debugging context menus to the macro editor

Screencast ImageJ macro debugging:

  • Added an context actions to copy the Macro Recorder code to the current editor
  • Added an „Evaluate Line“ action
  • Reenabled CTRL+X as default „Cut“ text action.

Download and Installation:

Windows:

Just download the *.zip distribution file from https://bio7.org and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.

Linux:

Download and extract the installation file from https://bio7.org.
For Linux you have to install R and Rserve (see Rserve installation below!).

MacOSX:

Download and extract the installation file from https://bio7.org.

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition For MacOSX you have to install R and Rserve (see below!).

Linux and MacOSX Rserve installation:

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!).

The special version of Rserve can also be downloaded here:

https://bitbucket.org/maustenfeld/bio7-new/downloads

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the main menu “Scripts” action:

Scripts->R-Scripts->InstallDefaultRPackages

Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.