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