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.

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.