Bug 24187. Fix case in cmph5tools.py merge where the input file is also supplied as the output file. Fix several places where an PBH5ToolException is raised with an incorrect signature. Close the input cmp.h5 file handles as the files are merged.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132134]
Bug 24187. Roll back some of the changes from 13214. Need to investigate the file handle closing more closely. Adding real unittests.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132152]
Bug 24187. Add unitest for input files specified as output file in cmph5Merge. Fixed cram test.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132153]
Bug 24187. Switch to raising an ValueError.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132154]
Remove pbtools pseudonamespace from pbh5tools

examples.t seems broken, I have asked John Harting to fix it

[Bug 24835]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132253]
Fix unit tests

[Bug 24835]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132254]
Bug 24835 - revision for pbh5tools pseudoname checking

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132261]
Bug 24835 - Bug 24050 - refactor the pip uninstall and revise the pbtools pseudoname handling

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132262]
Bug 24835 - fixing clean rule problem instroduced by dir reorg

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132264]
bug 24837.  Fixed examples.t with updated barcodes in aligned_reads_ss.cmp.h5.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132273]
bug 24885 Update to cmphtools.py select to allow for groupByCsv.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132647]
bug 24885  include grouped.csv file for cram test.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132711]
bug 24885 fixed groupCsv function to remove carriage returns, which are in cmph5tools.py stats output csv files for some reason.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 132881]
bug 24885 don't export NotInCsv.cmp.h5 file for groupByCsv.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 133010]
New chemistry information passing regime: 

chem barcode triple is piped "end-to-end" all the way into the cmp.h5, left to the application level 
to be decoded.

This change involves:
 - addition of a new tool "loadChemistry.py" to pbalign, which is responsible for transfering the triple
 - addition of a LoadChemistryService to pbalign that is run under --forQuiver
 - fixing pbalign tests
 - get SMRTpipe mapping modules to do loadChemistry.py as part of loadPulses step
 - cmph5tools merge needs to properly merge new columns in MovieInfo table

[Bug 24737]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 133135]