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Bio7 Changelog

What's new in Bio7 2.6.0

Oct 19, 2017
  • NEW FEATURES:
  • General:
  • Improved the dark theme for Bio7 2.6
  • Improved the default Bio7 theme
  • Improved the theming of some Bio7 views (e.g., tables, text editors)
  • Added a new shortcut for Windows and Linux to show or hide the Bio7 main menus – CTRL(CMD)+2, CTRL(CMD)+3). By default the application frame, toolbar and the status bar can be hidden, too.
  • Bio7 2.6 is based on Eclipse 4.7.1a
  • Added the ‘Project Explorer’ view to many perspectives and deleted the ‘Navigator’ view in some of the perspectives (the ‘Project Explorer’ view displays errors and warnings and supports pasting of clipboard Java code, etc.)
  • Added a break and interrupt action for the windows shell to end ,e.g., a ssh connection (CTRL+BREAK) or interrupt an ongoing shell process (CTRL+C)
  • Added an API to send commands to the Windows/Linux/MacOSX shell
  • Added SSH for Windows
  • Added the embedded SSH application path to the shell
  • Added a new ‘ImageJ Edit’ perspective to execute ImageJ scripts, macros side by side with the ImageJ-Canvas (see ImageJ section below)
  • Added a easy to use R API for Java/BeanShell/Jython/Groovy/JavaScript to execute R commands or scripts in an extra job (thread)
  • Improved several import/export scripts (now with Groovy) with the new Bio7 R API.
  • Improved the Linux shell (added the default xterm path)
  • The R package install script now works with a native R shell connection.
  • Shiny applications can now be tested from all folders (not only project folder – e.g.; from Git folders)
  • R Editor:
  • Added an action to surround selected code with a “try and catch” skeleton
  • Added an Project view/Navigator view popup action to start a shiny app in a arbitrary folder
  • Added an action to open and insert a hex color in the editor
  • Added a hoover dialog to display and replace selected hex and R colors
  • Added an action in the hoover dialog to select hex colors
  • Added an action in the hoover dialog to select default R colors by name
  • Added a new database view to the R perspectives to store or apply database profiles and connections
  • Added SSH support for the database view (also for Windows!). Bio7 comes bundled with the latest SSH version of Windows
  • Improved the code completion of the R-Shell
  • Improved the default R package install script for Bio7
  • Restructured the R editor context menu
  • ImageJ:
  • The ImageJ view menu is now right aligned and foldable to the left
  • Updated ImageJ to version 1.51r
  • Several bugfixes for the ImageJ compatibility
  • Added a full featured ImageJ macro editor with the following features:
  • Dynamic error detection (grammar derived from the ECMA grammar by Bart Kiers)
  • Toolbar action to execute ImageJ macros
  • Syntax highlightening
  • Editor debugging support (reusing and implementing interfaces and methods from – same keyboard shortcuts)
  • Code completion (with browser help)
  • Code templates (add you own templates)
  • Info popups (text hoover)
  • Outline view (var variables, variables, methods and macros)
  • Automatic closing of braces, parentheses and strings
  • Automatic indention of functions,loops, etc.
  • Code folding
  • Code formatting (based on the Eclipse-javascript-formatter by Sebastian Moran)
  • Resize fonts functions (with Ctrl++ or CMD++, CTRL+- or CMD +-)
  • Font preferences
  • Mark occurences (scope independant)
  • A copy function for the ImageJ forum

New in Bio7 2.4.0 (Jul 19, 2016)

  • GENERAL:
  • Updated Bio7 to use Eclipse 4.6 (Neon) as RCP basis
  • Updated the embedded Java Runtime Environment to version 1.8.92
  • Updated embedded R for Windows to R 3.3.1
  • Improved the toolbar layout and action alignments (CSS can be edited!)
  • Added a new ImageJ R analysis perspective
  • rimagejpersp:
  • Added a new R debug perspective
  • Added a new and easy to use text preference field to execute Groovy script commands at startup (beside any scripts in the startup folder!) to open, e.g., a custom perspective, or startup R if enabled.
  • preferencestartup:
  • The Quadgrid, Linechart, Piechart and the Points view are now embedded in a Swt JavaFX panel and can be fullscreened (F1, F2, F3, F4, F5 – F1 key is Windows only!)
  • Added a terminate (Java controlled) and kill R process (OS controlled) action to the main toolbar of Bio7.
  • terninatetoolbar:
  • At R/Rserve startup a new check for a running R instance is executed with an option to kill all running R instances (to avoid a wrong connection to a running instance from an crashed Bio7 R session).
  • Added many new Bio7 R command key shortcuts
  • Added an install R packages script to install some useful default R packages for Bio7
  • R EDITOR:
  • The R editor has been transferred to it’s own Github repository and can be updated as a plugin
  • Improved and formatted the display of the error messages
  • Improved massively the speed for parsing and marker creation
  • Added many new R editor key shortcuts to speed up editing
  • Added an action to the context menu to open the plot preferences
  • Added an action to the context menu to open the font preferences
  • Added a RServe formatR action to the context menu
  • Added a Profile script action for the profvis package to the context menu
  • Added a Profile script selection action for the profvis package to the context menu
  • Added a color dialog to the context menu. A selected R,G,B color will be displayed and set in the editor
  • Added an “Reload Package Completion” action to the context menu to load completion help for loaded packages (decrease warnings by known methods, increase available code completion templates – The same action is available in the R-Shell view evaluation textfield).
  • contextRmenu:
  • The Load/Remove packages(s) dialog has a new action to transfer available selected package names to the R editor (as ‘library(package)’)
  • Now warnings and errors are displayed more consistently. If a quick fix is available it will be indicated with a warning/error quick fix icon instead of a default warning/error icon
  • Added new quick fixes to the R editor
  • Quick fixes and warning messages can now be displayed and fixed by hoovering over the underlined editor marker
  • Added the automatic close of {braces}, (parentheses), [brackets], “strings” and ‘strings’. It can be disabled in the preferences
  • Improved the speed of the ‘Mark selected word’ action (scope independant) which can be enabled in the preferences
  • R editor refactoring:
  • Added an ‘Extract Method’ action which parses and extract a method from a selected text if valid
  • refactordialog:
  • Added an ‘Extract Variable’ action which parses and extracts a variable from a selected text if valid
  • Added a ‘Create new File from Clipboard’ action which parses and creates a new file from the clipboard text if valid in the project folder and opens the R file for editing
  • Added an ‘Extract Editor Selection to File’ action which parses and creates a new file from a selection if valid in the project folder and opens the R file for editing
  • R EDITOR CODE ANALYSIS:
  • Added an analysis function to detect Unused Functions
  • Added an analysis function to detect if a function is available
  • Added an analysis function to detect if a variable is used
  • Added an analysis function to detect if a variable is available
  • Added an analysis function to check for wrong constants (na, true, false, null)
  • Added an analysis function to check for functions if a function (or variable) with that name is already defined
  • Added an analysis function to check for variables if a variable (or function) with that name is already defined
  • Added an analysis function to check if a function call argument is missing
  • Added an analysis function to check if a function call has to many arguments
  • Added an analysis function to check if the name of a variable assignment in a function call is wrong
  • Added an analysis function to check a function call with parameter on a parameterless function
  • Added an analysis function to check variables in function calls and square brackets
  • Added options in the preferences to enable/disable the code analysis functions
  • R Outline View:
  • Added the display of loop variables to the outline view
  • Added the display of function call variable assignments to the outline view
  • Added the display of S3,S4, References and R6 classes to the outline view (S3 classes are only detected with class(x), References classes and R6 classes functions are not displayed nested!)
  • R editor code completion:
  • The sorting of the code completion dialog has been improved
  • The code completion dialog now displays local defined variables and methods available in the current scope
  • Added a new function in the code completion popup dialog to open the template preferences faster
  • codecompletionvar:
  • If the code completion is opened in a method call the arguments of the function will be displayed in a new table dialog. However if an function or variable is started within the method call the regular code completion is shown (for nested functions or variables call)
  • codecompletioninfun:
  • Added two actions in the hoover help dialog to open the help browser (?) or search in the Rdocumentation website
  • hooveractions:
  • The code completion dialog can now be configured in the preferences to open automatically on key typing (number of typed chars and chars can be configured, too).
  • R-Shell view:
  • The R text is now validated with the Bio7 default R code parser
  • Added an error marker to the textfield if a parsing error occurs
  • Added code completions to the evaluate expression textfield (Ctrl+Space). Code completion is only available in nested calls after open parentheses
  • rshellparse:
  • A help file browser can now be opened from selected text (e.g., nested function).
  • Native connection commands can now be executed in the evaluate expression textfield
  • R Markdown:
  • Now JavaScript is enabled for the HTML-Browser by default
  • Added a new option to scale the JavaFX browser content if enabled (handy for R markdown presentations). The JavaFX browser can be fullscreened (F1,F2,F3 – secondary monitor…..)
  • Table view:
  • Improved massively the speed of the close operation of a table sheet
  • Improved the CSV importer with more options to import data with a dynamic preview
  • The CSV importer now accepts clipboard data if selected
  • The preview table is now updated dynamically if changes occur
  • ImageJ:
  • Updated ImageJ to version 1.51d
  • Added a subset of ImageJ2 libraries in a new ImageJ2 Eclipse plugin
  • Improved the ROI image pixel data transfer methods. Now selected ROI’s pixels are transferred. If no selection is available all ROI‘s will be transferred!
  • The ROI transfer methods now also accept points and lines (please note that line pixels are interpolated in the ImageJ results table by default)
  • The Bio7 ImageJ plugin can now be updated or installed individually
  • ImageJ panels can now be opened in a JavaFX panel embedded in SWT (experimental) if enabled in the preferences
  • Other:
  • Updated all Java libraries
  • Update the JavaFX SceneBuilder to version 2.2
  • The JavaFX SceneBuilder controller class created variables and methods are now ‘public’ by default.
  • Added support for LibreOffice 5. Now the Bio7 LibreOffice functions work again with LibreOffice 5.

New in Bio7 1.7.1 RC 3 (Oct 11, 2013)

  • Fixed a deadlock when a plot is opened from R in ImageJ (e.g. from the R-Shell)
  • PDF and SVG R plots are now created and opened with the default registered application on MacOSX
  • Rescaled some dialogs
  • Fixed a deadlock in ImageJ when converting images to a stack

New in Bio7 1.7.1 RC 2 (Oct 8, 2013)

  • This upload bundles a JRE so you don’t have to install the lates Java yourself.
  • In adition i fixed some bugs related to the Update Manager (Now you can install e.g. the EGit plugin) and adjusted some default paths for the Mac (default LibreOffice location, default R location)

New in Bio7 1.5 Beta (Aug 13, 2011)

  • Improved configuration of start parameters.