Scipion-pyworkflow

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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

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- Hotfix: Fix resume single. Protocol was reset.

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users:
- New optional config variable: SCIPION_MAIN_COLOR. Any medium tone color name or hexadecimal should work(like in CSS)
- New optional config variable: SCIPION_BG_COLOR. Any light tone color name or hexadecimal should work(like in CSS)
- Control + Plus (numpad) will increase the font of the logs. Control + subtract will restore it.
- Toolbar and actions refactored: Most of them have shortcuts and appear in the toolbar without text, but have tooltips showing the shortcut
- Plugins in devel mode are shown with a delta suffix after the package name.
- Green lines in log are lighter, colored lines are back in the log.
- Commands in the log are "announced" by "** Running command: **"
- Project list window: F5 on the filter box will refresh the list.
- Project list window: Auto refresh on window activate when data is older than 60 seconds
- New actions: Copy (Control+c) and Paste (Control +v) will allow to copy the selection to and from the clipboard.
- File browser thumbnail: Writes if the file is a link
- Protocol in devel mode is shown prefixing the protocol in the box and shown in log
- Unused graphical gui nodes are cleaned up upon protocols deletion and graph painting (to clean up old projects)
- Error in host.conf for clusters better described.
- Fixed a bug related to organizing the workflow when importing a template(Import workflow template option)
- Terminal where Scipion is being launched only shows ERROR level info. Rest goes to scipion.log shown by the Scipion log menu.
- Scipion windows of the same process are now grouped under the same icon. Window Tooltip says Scipion framework instead of Toplevel
- Refactoring Restart & Continue workflow option. Allowing to continue and restart a workflow from a protocol


developers:
- Plugin.inDevelMode(): returns true is plugin installed in devel mode.
- Shortcut for devel mode is now Control+D since Control+d is for duplicate (old copy)
- Protocol.getClassPlugin deprecated. Use instead getPlugin()
- Protocol._cleanExtraFiles(): optional method to clean files other than tmp folder.
- Config.isScipionRunning(): To distinguish from just importing or running.
- Set implements copy() leaving mapper_path out.
- TaseCase: compareSetProperties() added to compare 2 set's properties.
- Add debugging messages to check the job status and add renameGpuIds method in the StepQueueExecutor