Bio7 2.7 Bugfix Release for MacOSX

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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

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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

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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 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.

ImageJ Plugin with Eclipse Macro Editor Updated

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16.11.2017

I released a new version of the ImageJ plugin which comes bundled with a feature complete ImageJ macro editor.

For an overview of the plugin please consult the github page:

https://github.com/Bio7/EclipseImageJ1Plugin

Release notes:

  • Updated ImageJ plugin to version 1.51.s24
  • Code completion (templates) 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 attribute)
  • MacOSX extra menu disabled (avoids a cluttered menu)
  • Macros can now be executed within an external ImageJ instance in a separate Java process (if enabled in the preferences – see screenshot 2 below). Tested on Windows only!
  • Added JavaFX library reference for Java9

Installation:

To install the plugin the latest Eclipse Java version 4.7 (Oxygen) is required (I tested this plugin with 4.7.1a). Open the Help->Install new Software dialog and add the following update site:

https://bio7.github.io/imagej/

The plugin is also availabe from the Eclipse Marketplace Client:

Help->Eclipse Marketplace… (search for ImageJ)

Install Useful Eclipse Plugins in Bio7 for R, Data Science and Programming

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20.10.2017

Beside a massive of amount of R packages and ImageJ plugins Bio7 can be extended with Eclipse plugins useful for data science and programming.

Some of them could also be very useful for R related developments (e.g., to develop R packages or distribute Shiny apps).

Installation of Eclipse Plugins

One  way to install Eclipse plugins is by using the Update Manager in the help menu (Help->Install New Software).

Thus the first step to install a plugin is to open the Update Manager and selecting the category “Eclipse Repository – http://download.eclipse.org/releases/neon” (see screenshot below!)

Another handy way of searching and installing Eclipse plugins is by using the Marketplace Client plugin which must be installed firstly with the Update Manager.

Search for the Marketplace Client (e.g., “marketplace”) plugin to filter, select and install the Marketplace Client.

The following plugins can be installed using either the Marketplace Client or the Update Manager.

Database Remote Files and Shells

EGit

https://marketplace.eclipse.org/content/egit-git-team-provider
The powerful Eclipse Git plugin to connect Bio7 with Git repositories.

TM-Terminal

http://marketplace.eclipse.org/content/tcf-terminals
A true native terminal with SSH,Telnet and Serial line support. Bio7 comes already with a pseudo-terminal but lacks the support of a pty connection and ANSI escape sequences (but can be controlled from a Bio7 API interface). The terminal can also be installed with the Update-manager searching for “tm” (see screenshot below).

Remote System Explorer

https://marketplace.eclipse.org/content/remote-system-explorer-ssh-telnet-ftp-and-dstore-protocols
A plugin to connect Bio7 with SSH, Telnet, FTP and DStore protocols.This plugin work very well with a remote connection and makes it easy to transfer data from a local workspace to a remote server. Remote files can be opened, edited and stored with the available Bio7 editors (e.g., a *.html file with the JavaFX editor – see screenshot below).
Apropos, please use an OpenSSH key for, e.g. a SFTPconnection!). It works great together with the TM-Terminal plugin.

DBWeaver

https://marketplace.eclipse.org/content/dbeaver
“DBeaver is free universal SQL client/database tool for developers and database administrators. It can work with any database server which has JDBC driver.” (source: website DBWeaver)
DBWeaver is a great database tool and plugin for Eclipse and can also be installed into Bio7 to control and edit R database connections.

Scripting Editors with Bio7 interpret support

The following three editors can be used within the current Bio7 process to execute scripts using the Bio7 interface. It is important however to create a language project first to profit from the advanced editor features.

Bio7 will recognize the opened editor type and interpret the current opened script with the embedded script interpreter of Bio7 when using the dedicated toolbar action.

Please use the context menu action “Open with” to open the scripts with the installed editors instead of the default Bio7 editors (Groovy, Jython/Python editors are available by default in Bio7).

Here a video installing and using the JavaScript editor as an general example.

JSDT

https://eclipse.org/webtools/jsdt/
JavaScript editor and development tools. Install with the Update-manager (search for JavaScript – see video above).

PyDev Editor

https://marketplace.eclipse.org/content/pydev-python-ide-eclipse
A very powerful Python editor which can be used to execute Bio7 Jython and Python scripts instead of the Bio7 default editor.
In addition Bio7 can use the PyDev editor to execute scripts running on the Bio7 Java classpath. If you open Jython/Python scripts with the PyDev editor the default Bio7 action will be visible to execute the scripts on the Bio7 classpath.

Groovy Editor

https://github.com/groovy/groovy-eclipse/wiki
(Add site: http://dist.springsource.org/snapshot/GRECLIPSE/e4.7/ to the Update Manager)
A more powerful Groovy editor. Can also be used with the Bio7 classpath if scripts are opened with this editor instead.

General programming editors and extensions

Eclipse CDT

https://marketplace.eclipse.org/content/eclipse-cdt-cc-development-tooling
Powerful C/C++ editor and development tooling.

Arduino C++ IDE:

https://marketplace.eclipse.org/content/arduino-c-ide
A great Arduino extension of the C++ editor of Eclipse. See this video for an introduction. Bio7 embedds some Java libs to communicate with an Arduino (see Bio7 examples).

Photran (comes with PTP)

https://eclipse.org/ptp/
http://www.eclipse.org/photran/
An Integrated Development Environment and Refactoring Tool for Fortran

Julia Editor

https://github.com/JuliaComputing/JuliaDT
A Julia editor in an early stage. But very promising.

Bash Editor

https://marketplace.eclipse.org/content/bash-editor
A bash editor for bash scripts. Perfect for the use with the above linked TM-Terminal and Remote Systems Explorer.

Jeeeyul’s Eclipse Themes

https://marketplace.eclipse.org/content/jeeeyuls-eclipse-themes
To install more themes into Bio7.

pde-tools

https://github.com/jeeeyul/pde-tools#crazy-outline
A plugin which adds clipboard history support and a crazy outline view.

WindowBuilder

https://marketplace.eclipse.org/content/windowbuilder
A very powerful builder for Graphical User Interfaces for SWT, etc.
In Bio7 a wizard is available to create a template for the builder (File->New->Bio7 Java Projects->Bio7 Java Project (WindowBuilder template)).
You can then open this template with the WindowBuilder to create interfaces (e.g., to create R interfaces using the new Bio7 R API). The created interface can be compiled dynamically with Bio7 (compiling the main class) and executed instantly in the current Bio7 process (see screenshot below)

More plugins can be found with the Eclipse Marketplace Client. It depends however how useful the plugins are in the context of Bio7.