fix #780 - Update do.sh

[drtamermansour]

Fix #780 :In the do.sh script, the old argument --savehash has been updated to --savetable

[ged-jenkins]

Can one of the admins verify this patch?

[ged-jenkins]

Can one of the admins verify this patch?

[mr-c]

Jenkins, add to testlist

[mr-c]

Hey, @drtamermansour can you add the line bash -ex 'cd examples/stamps/; ./do.sh' to jenkins-build.sh as part of this pull request?

[mr-c]

You'll also need to change the mode of the 'examples/stamps/do.sh' file. This can only be done at the command line (via mode u+x examples/stamps/do.sh)

[drtamermansour]

I can not see a special format of the jenkins-build.sh file so I just added the line of code to the end of the file. Also I assume that you meant chmod

[mr-c]

Jenkins, test this please

[mr-c]

mea culpa; add -c after -ex

[mr-c]

@drtamermansour can you paste in the checklist and fill it out? http://khmer.readthedocs.org/en/latest/dev/coding-guidelines-and-review.html#checklist

[mr-c]

Jenkins, test this please

[drtamermansour]

• Is it mergable?
• Did it pass the tests?
• If it introduces new functionality in scripts/ is it tested?
  Check for code coverage.
• Is it well formatted? Look at make pep8, make diff_pylint_report,
  make cppcheck, and make doc output. Use make format and manual
  fixing as needed.
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Is it documented in the ChangeLog?
• Was a spellchecker run on the source code and documentation after
  changes were made?

[drtamermansour]

When I try: make doc test pep8

This is what I get:
./setup.py build_sphinx --fresh-env
/mnt/home/mansourt/env/lib/python2.7/site-packages/setuptools/dist.py:291: UserW
arning: The version specified ('1.3-204-gd89c575-dirty') is an invalid version,
this may not work as expected with newer versions of setuptools, pip, and PyPI.
Please see PEP 440 for more details.
"details." % self.metadata.version
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help

error: invalid command 'build_sphinx'

Note: I am working on MSU-HPC using the virtual environment. I installed the dependencies and the make test passed ok

[mr-c]

Turns out that the HPCC used an old version of virtualenv; local upgrade fixed that.

Next he ran into python-versioneer/python-versioneer#52 which he fixed via multiple pip uninstall screeds followed by pip install bz2file; pip install -i https://testpypi.python.org/pypi --pre screed

[drtamermansour]

ready for review

[mr-c]

Oh, I just had an idea: if this test doesn't work there won't be a good indication of why

if you add || { echo examples/stamps/do.sh no longer runs; /bin/false } to the end of line 68 that will fix this.

[drtamermansour]

ready for review

[mr-c]

Wrapped lines should be indented to match the line above. In this instance you need three space before --savetable

[mr-c]

Otherwise this is ready to merge

[drtamermansour]

@mr-c
I do not know why Jenkins failed !!
When I run: make pep8, it gives me
pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/ || true
Is this an error?

[ctb]

This passes 'make test' and 'make pep8' on my laptop; looks like Jenkins may be barfing on it.

Jenkins, test this please.

[ctb]

please test this

[drtamermansour]

I think you need to mention "Jenkins" in the test request

[mr-c]

jenkins-build.sh: line 69: syntax error: unexpected end of file

[drtamermansour]

Jenkins, test this please

[mr-c]

Jenkins, test this please

[mr-c]

Thanks, @drtamermansour