Scipion-pyworkflow

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- Empty sections/subsection (without protocols) in the left tree will not be shown

Developers:
- Allow pointers to be defined with a list of classes instead of a string: "SetOfParticles, SetOfAverages" or [ SetOfParticles, SetOfAverages ]
- Two "utils" functions: hasAnyFileChanged, hasFileChangedSince to check if a file/s have changed since a "time" passed.
- BaseTest now has: setupTestOutput exposed --> self.setupTestOutput()
- Allow getting an item in a set not only by id but by a query: myset["_tsId=tomo1"].

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- Scalar parameters pointing to outputs now works also when scheduling
- Fix: outputs after a Scalar output (boxSize from pickings) weren't offered to the chosen
- Defining a new format to handler the log
- Creating in the config new constants to prevent sqlite locks when updating any set
- SCIPION_UPDATE_SET_ATTEMPTS: Number of attempts when trying a set update. The default value is 3
- SCIPION_UPDATE_SET_ATTEMPT_WAIT: Time in seconds to wait between updates. The default value is 2 seconds

Developers:
- In _showWizard, passing the paramName as a form variable so the wizard can check from which parameter it was called

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- Fixed GUI errors:
- fixing the workflow collapse/expand nodes
- resetting nodes with manual subset looses the parent
- reporting the protocol wall time
- finished protocol can't be modified
- Fixed: execute a protocol directly that is not streaming and that has an open input must be scheduled
- Close all sets when stopping a protocol
- fixing an error closing some viewers(the action of closing some viewers closes Scipion completely)
- fixing an error drawing the protocols step tree
- fixing an error deleting a protocol by the keyboard
- logging DEBUG mode will be activated when toggling debug mode
- A dramatic plugin import error will be tolerated. Plugin will not be loaded.
- Possible outputs definition is now possible. Protocols can define possible outputs to allow designing
a workflow in advance without executing them.
- New variable added: SCIPION_STEPS_CHECK_SEC. Defaults to 3 (seconds). It represents how often new input is checked in streamified protocols. Increasing this
value will relax the stress in the system, but will feel less "alive".
- Workflow templates can now be imported into an existing project

Developers:
- Possible Outputs allowed: dict or enum definition possible, see Protocol._possibleOutput
- Allow readonly parameters in protocols. Useful in combination with wizards or just informative parameters.
- Added the variable SCIPION_PRIORITY_PACKAGE_LIST that is used in the view
protocols in order to load first the plugins that contains the main
protocols.conf sections. This variable is defined as string with the packages names separated by a space.
e.g: SCIPION_PRIORITY_PACKAGE_LIST = "pwem tomo cistem"

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- Second tab of logs have just error messages (stderr output)
- Tests show stderr output too (last lines)
- Report host.conf submit command problems when parsing/formatting fails

Developers:
- Logging mechanism closer to a standard way. import logging + logging.getLogger() whould work in any module

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- Do not suggest deleteing hosts-conf when parsing fails
- "Select from" option in context menu to select all protocols hanging from the current selection.
- Schedule optimized
- dataset download more verbose
- pyworkflow version shown in main project window
- new color chooser. More user friendly
- Viewers are not asked to open outputs generated by themselves. In case a viewer creates an output.
- File browser shows links
- File browser allow multiple file handlers for the same extension

Developers:
- weakImport tool: context manager to tolerate import errors

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- Cancel fastcopy of shutil if SCIPION_CANCEL_FASTCOPY is defined (fix GPFS copying errors)
Developers:
- Allow renaming parameters using pyworkflow.protocol.params.DeprecatedParam

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