Scipion-pyworkflow

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")"...

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users:
- Boxes from Plugins in devel mode are prefixed with * now (not delta anymore)
- Partial exporting/copying will carry also the input of those protocols not being exported
- Partial importing/pasting will be linked to existing protocols in the project with the same id.
- Fix: Scheduling failed with direct pointers (impossible to get form GUI but programming or tests)
- tests: possible to use " tomo." (e.g.) to test just a plugin. Unfortunately needs adaptation in the launcher
- "Return" keypress "clicks" the active button in a window
- Avoid adding the same viewer twice

developers:
- Control and Shift keypress are captured when clicking in analyze result button and passed to the viewer.
- Project.getProtocol() has a fromRuns mode to prevent going to the db. Used in a couple of calls.(performance)
- Plotter.createSubPlot: allow plots without axis passing xlabel and ylabel as None
- Tolerate type change in attributes in protocol execution processes.
- Fixing an error when loading a project where it is not possible to retrieve the current version of an installed plugin

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users:
- Templates validate booleans properly (false, true, 0 or 1)
- Labels and box positions are saved after Labels being edited.
- scipion3 project list (or without list) should list existing projects.
- Windows are grouped by project under the project name.
- Do not allow empty Config variables unless is the default value
- SCIPION_MAIN_COLOR: If not valid, fallsback to Firebrick
- Project names: Only accepts digits, "letters", - or _. Rest are turned into -
- Fix wrong PARALLEL_COMMAND in hosts.conf created during tests.
- SCIPION_USE_QUEUE: New variable (default=False). If defined to anything else than False, new protocols will be sent to queue by default.

developers:
- Tolerate loading of extra set properties but WARN the developer.
- ListDialog: allows for a preview panel on the right if previewCallback is passed.
- SQL DEBUG deprecated: active when regular debug is on.
- Boolean Config variables refactored to be "reversible".
- Show info id debug mode (print) when an infinite loop happens in the protocols graph