search

openworm / tracker-commons

Compilation of information and code bases related to open-source trackers for C. elegans
11 stars 12 forks source link

Detailed setup instructions broken for fresh Ubuntu 14.04 LTS install via Virtualbox #81

Closed cheelee closed 8 years ago

cheelee commented 8 years ago

Broken Steps:

  1. sudo pip install wcon - results in:

File "wcon/wcon_parser.py", line 21, in

import jsonschema

ImportError: No module named jsonschema

  1. Attempting to fix this with sudo pip install jsonschema - results in:

File "wcon/wcon_parser.py", line 25, in

idx = pd.IndexSlice

AttributeError: 'module' object has no attribute 'IndexSlice'

Weirdness Issues:

  1. numpy installed twice ... once through pip, another through apt-get.
  2. the long apt-get line installs a ton of stuff as dependencies, including TexLive. Are the dependencies for what we need actually minimal?

    Alternative Success:

I have had success (i.e. was able to run python tests.py and get 23 successes) using a git clone with Miniconda3, and with the following environment dependency file for python3 (environment.yml). Have not tested against python 2 for Ubuntu yet, but I had done something similar on Mac OS X and it worked for python 2 (and fails for python 3 because something about psutil appeared to be broken on Mac OS X):

name: wcon3
dependencies:
  - python=3.*
  - scipy
  - pandas
  - jsonschema
  - psutil
MichaelCurrie commented 8 years ago

AttributeError: 'module' object has no attribute 'IndexSlice' is the error you get if your pandas is out of date.

Great point about the INSTALL.md not handling this or the jsonschema install. I will now try to work out a clean Miniconda3 set of install steps (probably mirroring what the .travis.yml is doing).

MichaelCurrie commented 8 years ago

OK I have updated (and tested from scratch!) the new install instructions. Thanks for pushing me on this, I appreciate it.

Commits 9b5bad85702f4385f16c62b94d524256911c69b4 and 91db15263bfed2e18c5b7ebb4347b426d578ada6.