OBO-Edit 2.0 beta release notes: Difference between revisions
mNo edit summary |
No edit summary |
||
(2 intermediate revisions by one other user not shown) | |||
Line 1: | Line 1: | ||
[[Category:OBO-Edit]] | |||
<h3>Release Name: 2.000-beta25</h3> | <h3>Release Name: 2.000-beta25</h3> | ||
<b>Notes:</b> | <b>Notes:</b> | ||
Line 22: | Line 22: | ||
* Removed option to create a desktop link from installer (SF 1845378) | * Removed option to create a desktop link from installer (SF 1845378) | ||
<h3>Release Name: 2.000-beta23</h3> | <h3>Release Name: 2.000-beta23</h3> | ||
<b>Changes:</b> | <b>Changes:</b> |
Latest revision as of 15:35, 30 June 2014
Release Name: 2.000-beta25
Notes: Bye, y'all!
Changes:
- Graph DAG Viewer succinct mode is fixed! (SF 1829694)
- Fixed some layout problems in Configuration Manager
- Added a "has multiple roots" search criterion (SF 1833117)
- Modification stamps are now optional (SF 1820650)
- Made a stab at stabilizing progress window size (SF 1816415)
- Fixed bug where Configuration Manager would not save if window close button (as opposed to titlebar close button) was clicked
- Fixed bug where invisible zombie components could be trapped in a layout if an undocked component was closed using the window close button (rather than the titlebar button)
- Fixed minor bug in search configuration
- Rebuilt image plugin
Release Name: 2.000-beta24
Changes:
- (See beta23 release notes for many other changes)
- Fixed bug where menus would not appear (SF 1845378)
- Removed option to create a desktop link from installer (SF 1845378)
Release Name: 2.000-beta23
Changes:
Added framework to attach help topics to components. If a component has a help topic attached, a little question mark button appears in the title bar. When the button is clicked, help for that component is displayed. Text edits no longer lost when a new search item is selected (SF 1844991) Fixed numerous bugs in custom verification checks Fixed bug where Graph Editor would not properly display explanations for some links (thanks to Chris for fixing this) Fixed bug where the save dialog would appear when there were fatal errors in the ontology (all the more ironic because it appeared after a message explaining that you will not be allowed to save until these errors are fixed) Redundant and implied links once again have a distinctive appearance - you will need to delete ~/.oboeditbeta/filter_prefs.xml to get the new default settings (SF 1844745) Many changes to text editor quickfix system (SF 1844885): * Added quickfix for "no punctuation at end of sentence" error * Added quickfix for "non-url characters in dbxref" error * In text editor panes, errors are highlighted in red. Errors that can be quickfixed are also underlined. * In list editors (like the dbxref editor or the synonym editor), items that contain errors are listed in red. Items that can be quickfixed display a quickfix icon next to them. Quickfixes can be applied by right-clicking an item and selecting a fix from the menu. * Quickfixes are now available in the synonym text text editor.
Release Name: 2.000-beta22
Changes:
Global renderers are now used to display search results Fixed problem where live verification data would not be updated properly when definition dbxref problems have been fixed (SF 1844213) The big, distracting text editor error message panel has been removed. Now error messages appear in the text editor's title bar. Mousing over the title bar will display a tooltip listing the errors. Remove redundant links problem (SF 1844193) and associated reasoned link deletion bugs are fixed. Platform independent launcher bug fixed (SF 1843989) Log files are being generated correctly again (SF 1844183) Garbage tabs no longer appear if OBO-Edit is shut down with search results still visible (SF 1844184) Fixed disappearing global/local selection mode buttons (SF 1838678) Added new log messages to aid in diagnosis of rogue popup menu problem (SF 1839411) Fixed problem where list editors (like the synonym editor) could cause unexpected changes if the selection changed while the editor panel was still open (SF 1837056)
Release Name: 2.000-beta21
Changes:
Fixed bug where synonym dbxrefs would be lost on synonym edit (SF 1843460) Added editor for synonym dbxrefs Dbxref listing is now always the same size in synonym editor (SF 1843405) Live error highlighting in the text editor now works properly All TableList editors (like the dbxref editors and the synonym editor) now commit their changes the minute they are unfocused, which should make them easier to use
Release Name: 2.000-beta20
Changes:
Added customizable heat maps Right-clicking a component's title bar allows you to change the title Search control now remembers last settings Search results text is now customizable in search control settings Added new Icons & Colors tab in configuration manager (SF 1838664) Added icons for OBO-Edit application and installer The Mac OS "Quit" and "About" menus are now properly handled by OBO-Edit Text edits now autocommit if another edit occurs (for example, if you have pending text edits and you create a new term, your text edits are no longer lost) Changed Parent Editor appearance to make things fit on the screen better Fixed unhandled exceptions when clicking "classes", "properties", etc (SF 1840390) Fixed undo/redo failures (SF 1839564, SF 1839564) Fixed shortcut key bugs (SF 1838830, SF 1836524) Fixed bug where "<new term>" did not appear correctly after new terms were created (SF 1838829) Made "working" popup look a little better (SF 1838787) Fixed bug where search results disappeared between layout switches (SF 1838784) Fixed bug where panels would not update correctly after new ontology load (SF 1838764), and for good measure fixed some other screen update bugs in the graph editor, including bugs that left stray arrows floating around Fixed graphical artifacts and switched-around button behaviors in term change tracker (SF 1838679) Fixed problem where a change in the autocommit setting did not cause "commit" and "revert" buttons to immediately appear (SF 1838673) Fixed parent editor drag and drop button (SF 1838669) Fixed bug where namespace changes would not be saved (SF 1838656) Fixed icon browsing problem (SF 1838651) Fixed bug where OBO-Edit would not display installer-generated memory settings on Mac OS (SF 1838648) Installer now WILL create a desktop icon if you ask it to (SF 1838648) If there are unsaved changes to an ontology, a special message appears in the quit confirmation dialog (SF 1838644) (note that this message will appear whether or not you have "confirm on exit" checked, on the theory that anyone would want to know about this potential disaster) Fixed spurious "unsaved changes" message (SF 1837005) It is now possible to re-select already selected search results (SF 1836549)
Release Name: 2.000-beta19
Changes:
Added Import... to the file menu Added Fix ids... to the file menu Added a verification system check for bad ids. The id fix options are all available as quickfixes Added a new system for installing custom graph decorators
Release Name: 2.000-beta18
Changes:
Fixed OBO 1.2 save bug (SF 1827542) Fixed bugs when saving filtered files with range & domain defined Changed method of starting load/save operations
Release Name: 2.000-beta17
Changes:
Added new rendering system Added Image Display Component Added Configurable Message Component You can now autotype individual words in an autocomplete box using Ctrl+Space (on any platform) or Command+Shift+Space (on macs only) or Ctrl+Shift+Space (on non-mac-platforms only) Fixed problem where arrowheads would drift around while scrolling the ontology editor panel Changed wording of "load" menu item to Load Ontologies (SF 1826388) Changed default ordering of data adapters to something sensible (SF 1826388) Added clearer error messages when a file of the wrong type is loaded by the serial adapter (SF 1826388) Fixed broken autocomplete in Cross Products panel (SF 1825311) Fixed bugs in list editors (SF 1824736 + others) Fixed "change relationship type" bug (SF 1824731) Disabled autopanning in the graph editor (SF 1820642) Fixed "multiple globe icons" problem (SF 1820621 & 1820134) Fixed graph dag viewer problems (SF 1820621)
Release Name: 2.000-beta16
Notes: To use the new image saving plugin, create the following folder:
~/.oboeditbeta/extensions
and put the jar file in there. When you start OBO-Edit, every component will have a tiny camera icon in the title bar that lets you save an image of the component in a number of different formats. Also, when you right-click in the graph editor, you have the option to save an image of the current graph (unlike the title bar button, the image will contain the entire graph, even if the whole graph doesn't fit on the screen).
Changes:
Added lots o' hotkeys, see release notes on sourceforge Reworded obsolete warning message (SF 1810837) Fixed bugs in ancestor & descendant searching (SF 1811624) Fixed commit keyboard shortcut (SF 1811771) Fixed save bug (SF 1811658) Added ability to expand the full path to a term in the Graph Editor (this can be disabled in the configuration screen) (SF 1811581) When multiple child terms are added, they are assigned to the parent namespace (SF 1814547) Default id rule is no longer broken (SF 1811685) Text edit hotkey now works (SF 1811771) Fixed problem where table lists in the text editor did not autocommit pending edits when their values are requested. This manifested as bugs in the dbxref and synonym editing lists (SF 1814568). Added add/remove buttons to renderer lists in Global Filter Manager Load/save error details are once again displayed Created image saving plugin No more flickers of movement in graph no-animations mode Added option to hide "Search results" prefix for search results (SF 1816398)
Release Name: a>
Changes:
Added ability to remove consider/replaced-by terms with the right-click "delete" option Added in-panel "popup-window" that appears when a parent/child expansion control is clicked in the graph editor Disabled default spell checking when saving Fixed icon configuration bugs Fixed text editor bugs Fixed drag and drop bugs Fixed autocommit bugs Fixed right-click editing menu bugs Fixed expanding children when right-clicking in graph editor
Release Name: 2.000-beta14
Changes:
Fixed Save As lockups Fixed autocomplete bugs Changed autocomplete box in search control to initiate a search if enter is pressed when the autocomplete popup is hidden Added lightbulb tooltips in new search controls Graph editor tooltips are no longer animated in no-animations mode Fixed bugs in reasoning over intersections with sub-properties Graph editor now only pans to a newly selected node if it is not currently on the screen Fixed bug where OBO-Edit would not exit properly if closed from the window controls Added possible fixes for Windows XP problems - if problems persist, try the command-line switch -J-DuseModalProgressMonitors=false to disable a potentially problematic feature on Windows Improved animation disabling code Animations can now be disabled in the graph dag viewer Added unicode character searching Progress windows now automatically choose the correct size Added better progress bar updating for long-running tasks Added support for plugins
Release Name: 2.000-beta13
Changes:
Faster graph relayout Changed expand/collapse graph editor controls Graph editor node boxes are now sized to just fit the node label Link lines in graph editor will no longer appear above term boxes Changed default font size to 12 point Fixed bugs in reloading saved renderers User-added links are no longer trimmed by the reasoner
Release Name: 2.000-beta12
Changes:
Fixed bugs where sometimes screen would go blank when showing a new component Big reasoner speedups BIG editing speedups New search interface Updated filtering interface in most places (old filtering system is still in use for filtered saves) Graph Editor now supports filtering (but not rendering)
Release Name: 2.000-beta11
Changes:
Fixed bugs in obo2obo Fixed bug in dbxref checking that greatly increases speed of verification checks Fixed bug where links don't work properly in verification results page Dbxref verification no longer reports % as a non-dbxref character Added resizable graph overview panel to the graph editor Added "Remove redundant links..." menu item Fixed bug where panning the graph editor would cause view to jump wildly Dbxref library buttons now work Fixed bug where dag graph view would be disconnected if there were many is_a links between the selected term and the first non-is_a link in a transitive path Graph editor now does text wrapping OBO-Edit no longer applies font changes to menus - instead it uses the system default. This should allow better integration with a given platform's look and feel
Release Name: 2.000-beta10
Changes:
Improved Graph DAG Viewer display Fixed bugs in search panel selection that would make it impossible to select search results if many intersection definitions were loaded Dangling relationship types are now supported Fixed bugs in displaying dangling references in the intersection editor Changed implementation of links in OBO-Edit so that most link objects should use about half the space they used to use (this is significant, particularly when the reasoner is running, because there are *far* more links than terms) Fixed reasoner bugs that would manifest with certain kinds of redundant links Improved support for reading in links implied by an external reasoner Platform independent OBO-Edit launcher now reads memory settings correctly Font changes update immediately. No need to restart! Fixed inconsistencies in typeface, background colors and button colors
Release Name: 2.000-beta9
Changes:
Added scale bar to graph editor Changed the way toolbar is added to the graph editor to save space
Release Name: 2.00-beta8
Changes:
Fixed bugs in implied link expansion menu Fixed search bugs Fixed bug where Configuration Manager settings were lost Greatly sped up save of Configuration Manager settings Individual component settings now save properly Added OWL URL reader adapter
Release Name: 2.000-beta7
Changes:
Beta versions now write settings to the .oboeditbeta directory
Release Name: 2.000-beta6
Changes:
obomerge now properly merges consider and replaced_by tags New memory settings screen in installers
Release Name: a>
Changes:
Added global selection controls to component title bars Added filter control button to component title bars Reinstated autosave; autosave files are now in OBO format Disabling graph editor animations now disables tooltip popup animations as well Added ability to right-click highlighted errors in text editor and choose a quick fix from the popup menu obo2obo now supports dangling links in loaded-in files
Release Name: 2.000-beta4
Notes: Known issues:
- Some text edit errors are reported too many times
- Modal progress boxes (like the reasoner progress box) sometimes do not disappear properly on Mac OS
- Autocommit mode is always on
Changes:
Fixed search Changed to IDW docking framework Changed the way automatic error reporting works Changed synonym editor to list-based editor Enabled basic perspective switching in the text editor Added quick configuration buttons to docking headers
Release Name: 2.000-beta3
Changes:
- Fixed swing-based memory leaks
- Added an option to turn off graph editor animations
Release Name: 2.000-beta2
Notes: Known issues:
* The text edit tool graph editing tool may have problems * Text-edit error checking is disabled * Some quick-fixes are not available * The automatic error loader will occassionally report a non-existent error, usually one about definitions with no dbxrefs, even though they're there * The user's guide is totally out of date
Changes:
Fixed some problems in graph-based editing Added the javadocking system Added some spellcheck features Added dynamic error checking displays The settings directory can now be specified with the "-Dprefsdir=" option
Release Name: 2.000-beta1
Notes: This is the first beta release of OBO-Edit 2.0. It's going to be buggier than you're used to in an OBO-Edit release, but we need user feedback on the new graph editor.