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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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Python issues #43

Closed mw55309 closed 7 years ago

mw55309 commented 7 years ago

Hey

I'm using Python 3.4. I get the error:

./blobtools/blobtools create --help File "./blobtools/bloblib/create.py", line 105 print BtLog.warn_d['0'] ^ SyntaxError: Missing parentheses in call to 'print'

Is this a Python 2 vs 3 issue?

Cheers Mick

DRL commented 7 years ago

Hi Mick,

yes, unfortunately I haven't massaged the code to be Python3 compatible yet...

If you use Python2.7 all things should work.

cheers,

dom

mw55309 commented 7 years ago

Hmmm. Not on eddie3:

ip install matplotlib Collecting matplotlib Downloading matplotlib-2.0.0-1-cp27-cp27mu-manylinux1_x86_64.whl (14.6MB) 100% |████████████████████████████████| 14.6MB 88kB/s Collecting pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib) Using cached pyparsing-2.2.0-py2.py3-none-any.whl Requirement already satisfied: numpy>=1.7.1 in /exports/eddie3_homes_local/mwatson9/.local/lib/python2.7/site-packages (from matplotlib) Exception: Traceback (most recent call last): File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/site-packages/pip/commands/install.py", line 335, in run wb.build(autobuilding=True) File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/site-packages/pip/wheel.py", line 749, in build self.requirement_set.prepare_files(self.finder) File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/site-packages/pip/req/req_set.py", line 380, in prepare_files ignore_dependencies=self.ignore_dependencies)) File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/site-packages/pip/req/req_set.py", line 666, in _prepare_file check_dist_requires_python(dist) File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/site-packages/pip/utils/packaging.py", line 48, in check_dist_requires_python feed_parser.feed(metadata) File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/email/feedparser.py", line 177, in feed self._input.push(data) File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython2.7/lib/python2.7/email/feedparser.py", line 99, in push parts = data.splitlines(True) AttributeError: 'NoneType' object has no attribute 'splitlines'

gah!

DRL commented 7 years ago

Interesting.

Are you using a virtualenv for installing the dependencies?

mw55309 commented 7 years ago

I'm using conda as per the ECDF instructions: https://www.wiki.ed.ac.uk/display/ResearchServices/Anaconda

DRL commented 7 years ago

Oh, I did not know about this ...

you could do this though:

wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py --user
pip install --user virtualenv
mkdir virtualenvs
virtualenv virtualenvs/blobtools
source virtualenvs/blobtools/bin/activate
pip install matplotlib
pip install docopt
git clone https://github.com/DRL/blobtools.git
blobtools/blobtools -help

I have tested it and it works. For proper running you still need to download the NCBI taxdumps, though.

Since it is installed at the user level admins shouldn't be upset ...

cheers,

dom