Scipion-em

Users:
- Fix: importing non cubic volumes could render 0 elements in dimensions. Now minimum is 1.
Developers:
- ImageHandler.getDimensions uses ImageReader registry and its readers (Xmipp, Tiff, Eman, ...) image
- tiff dimensions (gain, eer, tif, tiff) are swap. They original y were opposite to xmipp and others convention.
- User subset: ready for new metadata viewer using txt files with ids.
- classifyItems method of SetOfClasses updates an existing output set than can be utilized for streaming protocols
- New metadata viewer(BETA). To use it run 'scipion3 pip install metadata-viewer mrcfile'. Right click on outputs should show "Scipion metadata viewer"

Users:
- New viewer: "Basic MD viewer" to allow doing manual subsets on those sets where before it wasn't possible (Coordinates2D, FSCs)
- ImageJ filehandler: Set IMAGEJ_BINARY_PATH to the ImageJ or Fiji binary.
Developers:
- SetOfCoordinates tweaks: better use of micrographs pointer

Users:
- New Angular distribution viewer (right click on any SetOfParticles or SetOfSubtomograms will list it)
- Use main color config variable
- New variable: CHIMERA_OLD_BINARY_PATH: Full path to chimera binary. If defined, it will offer BASIC visualization of pdb and volumes
- Set editor: summary show the formula
- Join sets: clones all attributes, not only 1st level ones.
- New protocol box size checkpoint to validate an estimated particle size.
- The browser thumbnail show origin info for mrc files
- Import volumes set the volume comment to the original file.
- Fix subset: Scheduling waits when subset uses other set
- ChimeraViewer: Handle also set of volumes and 3d classifications

Developers:
- SCIPION_CANCEL_XMIPP_BINDING_WARNING defined in the environment will cancel the warning about xmipp binding missing
- SCIPION_CANCEL_XMIPP_BINDING_WARNING defined in the github action
- function readFromPDBDatabase tries to download an atomic structure up to 5 times before returning an error (before it tried only once)
- function retry search for fatal error messages in the output and if found, it aborts instead of trying several times.
- plotter.py uses logging
- Plotter.plotAngularDistribution refactored: uses scatter instead of plot fo each point. It may improve performance.
- Plotter.plotAngularDistributionFromSet new: To plot sets with items.getTransform()
- Volume.getHalfMaps: receives optionally "asList" to return the list instead of the string
- Volume.fixMRCVolume, now receives (optionally) a boolean to set the header's sampling rate of the MRC file it refers
- showj.py: uses logger
- showj.py: javaVersion cached, javaBin taken from Config.JAVA_HOME o "java"
- showj.py: SCIPION_JAVA_HOME takes priority over JAVA_HOME (pycharm debugging case)
- Use new Config.isScipionRunning to register file handlers.
- Use new Config.isScipionRunning to print xmipp ghost message.
- SetOfImages._samplingRateStr extracted to convert sampling rate to a str

- Hot fix: Assign angles assign full shifts by default. Warns about loosing xFrac and yFrac comming from extract coordinates.