Scipion-pyworkflow

users:
- Inform when a plugin does not import properly
developers:
- Handling the name and the suffix to be used for a new output
- New method: Config.isCondaInstallation

users:
- Add protocol is an icon.
- Right clik on canvas offers to add a protocol on the clicked location.
- Scipion log is a project.log (only for project events)
- Variables window saves non default variables changed (bug)
- Queue interoperability review:
- jobs cancelled in the queue are detected in scipion
- job and pids handling improved, pids = 0 when use queue for protocol rely on jobid
- Change Protocols Lock to Rlocks objects to avoid concurrency when updating the protocols jobid
- add information in the protocol log regarding execution type (pid or jobid)f
- Streaming protocols based on new streaming (generation steps) are resumable
- Avoiding a double process when launching a workflow using the protocol form
- pyworkflowtest tests fixed
- GUI will detect when protocols processes have been killed(cancelled) in all cases?
- fix outdated pyworkflow scripts
- scipion3 template (template manager) lists workflows at workflowhub.eu from "Scipion CNB" organization
- Join heterogeneous sets are possible for tomography objects TS and tomograms.
developers:
- Canvas has a testing method: _drawGrid to draw a grid on the canvas (unused now)
- String.toSeconds:converts to seconds any "duration" string like "1h 4m 34s" -> 3600 + 240 + 34.
- ListDialog has a refresh method to refresh the content taking into account the filter
- Improve the DDBB lock in the method "_store". If Protocol._lock is locked, a nullcontext is used instead of another
Protocol._lock context, which causes a permanent lock.
- XmlMapper removed.
- FlatMapper instanatiation centralized:
New variable: SCIPION_MAPPER_USE_TEMPLATE. By default uses the template as it was now. If deacivated, instantiation happens on each iteration (less performant) but dev friendly
- Adding a parameter to launch jobs (e.g: bash)
- Handling item-click event in the treeview dialog
- Method copyAttributes expanded to manage the complex sets properly

users:
- Window to see/edit config variables. Launched from Project menu in project window.
- Fix installation error: matplotlib imported at installation time
- Fixing an error drawing the graph
developers:
- FileBrowser window tweaks: Can be called from a dialog.
- Windows can be called as dialogs with show(modal=True)
- askPath: Method to ask for a path (PATH, FOLDER or BASENAME)
- backup: Method in pyworkflow.utils.path to backup files
- All variables are centralized and Plugin._defineVar or _defineEmVar accept variable description, and type (VarTypes enum) to better describe the variable.
- ProgressBar handles the step in combination with increase method call
- Set.aggregate more flexible and versatile.
Accepts strings or lists in operations, labels or groupby args.
Accepts id or _objId ar fields
- String.getListFromValues: works now with strings with an x inside (e.g.: _x _y)
- New utils method: valueToList (converts the argument into a list if is not a list): Useful for "dual type arguments) that can be a list or not

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users:
- New Icons.
- Icons based on sprites, easier to resize or customized
- New variable: SCIPION_SPRITES_FILE to point to a custom sprite. It should be compatible with sprites.png at pyworkflow/resources.
- Scipion GUI log moved to the log tabs and removed from menu
- New variable: SCIPION_SHOW_TEXT_IN_TOOLBAR, set it to anything to show the text of the icons below
- New variable: SCIPION_ICON_ZOOM, defaults to 50 (percent) to show icons at 16x16. 100 will set them to 32 or 75 to 24.
- Icons in toolbar grouped. Better row height adjustment in trees.
- Improved handling of the case where protocols steps are send to the queue, fix stop protocol functionality
developers:
- ProjectConfig class removed
- New methods in path: hasChangedSince and isFileFinished
- New method in utils: strToDuration (useful to translate "1h 35m" to seconds). For duration parameters.
- New class Variable to be tested in Config class. A step towards a Config editing GUI.
- SCIPION_DEBUG_SQLITE rescued to activate SQL clauses in debug.
- Active jobs are stored in the 'jobIds' protocol variable. Iteration through these job IDs allows for canceling each active job sent to the queue.
- Implemented cleaning of old protocol job IDs and PIDs.
- Extending the ToolbarDialog buttons. Now is possible to define a tooltip and a shortcut
- Viewers has getName class method.
- Object.getClassName is now a class method
- Validating the Close method in the Dialog class. Now we can to reimplement de validateClose method.
- Better case-specific implementation of pID and jobID. Three scenarios: normal execution, sending the entire protocol to the queue, or sending individual steps.
- Object.clone a copy optionally clones the enable flag
- Set.getItem: returns the first item with a value in the fields passed. Useful for querying by TsId in tomo.
- Correctly update the protocols in streaming workflows when the input pointer points to a protocol, the protocol points to a set (i.e., classes), and this set points to another set (i.e., particles).

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users:
- Prevent cyclic loops in protocols. Cannot chose as input, as output that is derived or will be derived from the current protocol.
- Tolerate cyclic loops saved projects projects, disconnecting the "problematic" protocol.
developers:
- Dialog class: add lockGui input to allow the viewers to prevent getting the screen focus if desired.

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users:
- Steps window can force finish steps too. Useful for some CS cases.
- "Continue workflow" from improved. Works with more cases.
- Fix output deletion when right-clicking on an output compatible with this option.
developers:
- Set class has isItemEnabled to be used as callback based on item.isEnabled()
- config.py.OS class (not for GUI): to return distro info (isCentos or isUbuntu) or isWSL (--> new dependency "distro")"...