Cope with strange GenPept files with CONTIG and ORIGIN lines.

These may be a temporary oddity from the NCBI Entrez API,
but currently breaking test_SeqIO_online.py -- see example
file Tests/GenBank/NP_416719.gbwithparts
Test new GenBank fix with online example
Fix typos
Deprecated Bio.Motif as discussed on the mailing list
Bump versions for planned Biopython 1.62 beta
Fix epydoc warning, use doctest style
Remove trailing spaces in docstrings
Fix epydoc paragraph indentation warnings
Post release version bump

Documentation change only, no need for testing [ci skip]
fixed two typos. Ignoring deprecation warning in test_Motif
PyPy 2.0 has numpy.dot now, but not numpy.linalg
Add comment to tutorial doctest regarding PyPy

No need for TravisCI [ci skip]
One central import for this test
Test Bio.Motif & Bio.motifs PSSM with alternative alphabet.

Addresses this issue: http://www.biostars.org/p/73500/
http://lists.open-bio.org/pipermail/biopython-dev/2013-June/010639.html
Fix motif alphabet instance bug

Previous commit was a test for this bug, addresses
http://www.biostars.org/p/73500/
http://lists.open-bio.org/pipermail/biopython-dev/2013-June/010639.html
Remove now redundant imports
Updating Bio.Entrez DTDs; see bug #3444
Now using GitHub issues not RedMine
Update issue tracker URL in Entrez DTD message
Test EMBL file with missing sequence type in ID line.

Based on a bug report from Peter Thorpe.