Adds NetCDF Databases

[PaulTalbot-INL]

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Pull Request Description

What issue does this change request address? (Use "#" before the issue to link it, i.e., #42.)

Closes #1320
Closes #1463

What are the significant changes in functionality due to this change request?

Adds NetCDF as a database storage option.

• Cleanup and modularization of Databases module
• Differentiation between base class Database and HDF5
• Implementation of Database.NetCDF
• Addition of NetCDFDiffer for testing
• Moves NetCDF writing compatibility from DataSet to new database

Also

• Extends some of the rook documentation for user clarity
• Renames obtuse variables in Simulation for easier comprehension and maintenance

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For Change Control Board: Change Request Review

The following review must be completed by an authorized member of the Change Control Board.

• 1. Review all computer code.
• 2. If any changes occur to the input syntax, there must be an accompanying change to the user manual and xsd schema. If the input syntax change deprecates existing input files, a conversion script needs to be added (see Conversion Scripts).
• 3. Make sure the Python code and commenting standards are respected (camelBack, etc.) - See on the wiki for details.
• 4. Automated Tests should pass, including run_tests, pylint, manual building and xsd tests. If there are changes to Simulation.py or JobHandler.py the qsub tests must pass.
• 5. If significant functionality is added, there must be tests added to check this. Tests should cover all possible options. Multiple short tests are preferred over one large test. If new development on the internal JobHandler parallel system is performed, a cluster test must be added setting, in XML block, the node <internalParallel> to True.
• 6. If the change modifies or adds a requirement or a requirement based test case, the Change Control Board's Chair or designee also needs to approve the change. The requirements and the requirements test shall be in sync.
• 7. The merge request must reference an issue. If the issue is closed, the issue close checklist shall be done.
• 8. If an analytic test is changed/added is the the analytic documentation updated/added?
• 9. If any test used as a basis for documentation examples (currently found in raven/tests/framework/user_guide and raven/docs/workshop) have been changed, the associated documentation must be reviewed and assured the text matches the example.

[alfoa]

The PR and Modifications for the NetCDF database are good as they are. No comment there. Modifications that are not functional to this PR should be reverted (addition of diffs that are just cosmetic)

[alfoa]

@PaulTalbot-INL , is the error in #1320 caught now ? PS. Can you add an issue specific for the addition of netCDF support and tag it with "future RAVEN v 2.1"?

[PaulTalbot-INL]

That's a good point, it doesn't prevent that error if the user applies HDF5. I changed the "close" to a new issue.

[alfoa]

@PaulTalbot-INL do you think it is possible to error out in case of HDF5? (It should be something like if DO.type not in ['PointSet','HistorySet']: self.raiseAnError() right?

[PaulTalbot-INL]

Yup, think I caught both. This would be a much better cross-test for a good validator, but for now at least the user should get a reasonable error.

[alfoa]

PR Approved...

Checklist passed...

Merging once tests pass...

[alfoa]

Test passed.

Merging...