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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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Basic continuous integration #63

Closed bcipolli closed 8 years ago

bcipolli commented 8 years ago

Highly recommend to have some very basic unit tests and use travis.ci to validate that a merge doesn't break the build. Matters less now before release, but post-release it could help a lot, and it doesn't take too much to do...

bcipolli commented 8 years ago

Chatted with @binarybottle , and decided this is a priority. I'm working on this here: https://travis-ci.org/bcipolli/mindboggle

binarybottle commented 8 years ago

Thank you for recommending travis-ci -- what an incredible resource!

I have been using Continuum's miniconda's python and to install some python libraries, including vtk:

conda install --yes numpy scipy matplotlib pandas nose networkx traits vtk ipython VTK_DIR=${INSTALL_PREFIX}/lib/vtk-5.10

I see with travis, you are specifying a python version and trying to install vtk independently after wget: "$ tar xzvf vtk-precise64.tar.gz -C ~". I have found vtk to be difficult to install. Can we use miniconda's version?

bcipolli commented 8 years ago

Sure; I had no idea how to best install VTK, so I found a sample travis script and copied that. Your way sounds more reliable!

binarybottle commented 8 years ago

travis supports testing on quite a few different versions of python, but miniconda's downloads include only 2.7 and 3.4 (http://conda.pydata.org/miniconda.html). Should I simply copy mindboggle/setup_mindboggle.sh and replace the miniconda download version when I wish to test 2.7 vs. 3.4?

bcipolli commented 8 years ago

Yep. You can also call the setup script from .travis.yml; they will have cloned your repo by that point.

binarybottle commented 8 years ago

How do you call the setup script from within .travis.yml?

On Fri, Oct 23, 2015 at 2:04 AM, Ben Cipollini notifications@github.com wrote:

Yep. You can also call the setup script from .travis.yml; they will have cloned your repo by that point.

— Reply to this email directly or view it on GitHub https://github.com/nipy/mindboggle/issues/63#issuecomment-150485314.

bcipolli commented 8 years ago

I do everything by finding examples. Try calling the script in the before-install block: https://github.com/nipy/nibabel/blob/master/.travis.yml#L47

satra commented 8 years ago

also see: https://github.com/Theano/Theano/blob/master/.travis.yml

then you can also do: conda install vtk

binarybottle commented 8 years ago

I have written high-level doctests for almost all of mindboggle's functions. Functions pull test data from http://media.mindboggle.info/data/ where necessary:

>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> label_file = fetch_data(urls['left_freesurfer_labels'])

Travis worked great for all but a couple functions in the features directory, because they take more than 10 minutes to complete. On @satra's recommendation, I would like to move over to circleci so that it will enable continuous integration for all of mindboggle's functions.

binarybottle commented 8 years ago

Circleci.com error for build #331 (python 3.5):

conda install cmake pip numpy scipy matplotlib pandas networkx vtk ipython Fetching package metadata: .... Solving package specifications: ....

The following specifications were found to be in conflict:

satra commented 8 years ago

vtk7 is not available on conda yet - that's what is causing your issues.

binarybottle commented 8 years ago

And no version of vtk comes up for "conda list" for miniconda3, for linux or macosx. Should I try to install vtk from scratch? If so, I wonder why I even bother with miniconda, since vtk is the most unreasonable of dependencies?

satra commented 8 years ago

because vtk7 was just released and the issue as to it's packaging is still open.

binarybottle commented 8 years ago

Now that I am able to run the python 3 version of mindboggle on linux with vtk 7, why am I still getting the error on circleci.com:

python -c "import vtk"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named 'vtk'

python -c "import vtk" returned exit code 1
satra commented 8 years ago

@binarybottle - i don't know - this would be a good thing to debug with their ssh debugging.

binarybottle commented 8 years ago

When I SSH into circleci.com, I continue to get the above error when I try to import vtk, even when I try to set the PATH, PYTHONPATH, or LD_LIBRARY_PATH to /home/ubuntu/miniconda3/lib/cmake/vtk-7.0. Any suggestions?

satra commented 8 years ago

on circleci where is vtk getting installed? i'm assuming that's happening without an error. it is possible that vtk is not getting installed in the same python as the python you are using to run the tests. so when you ssh, find out which python you are calling and check it's site-packages. also check the site-packages of the other python binaries on the system.

binarybottle commented 8 years ago

You are absolutely correct about the discrepancy in pythons. I have been in communication with the folks at Clinical Graphics about their conda vtk installation (https://anaconda.org/clinicalgraphics/vtk).

Korijn Van Golen:

When you are setting up your python environment, you should do so through Miniconda. Once you've installed it, you can create a python environment to work with and install your libraries in it. Like this:

C:\Development\Projects>conda create -n my_env -c clinicalgraphics python vtk
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment C:\Users\Korijn\Miniconda3\envs\my_env:

The following packages will be downloaded:

package build
setuptools-20.6.7 py35_0 765 KB defaults

The following NEW packages will be INSTALLED: 

msvc_runtime:   1.0.1-vc14_0    defaults         [vc14]                                                   
pip:            8.1.1-py35_1    defaults                                                                  
python:         3.5.1-4         defaults                                                                  
setuptools:     20.6.7-py35_0   defaults                                                                  
vs2015_runtime: 14.00.23026.0-0 defaults                                                                  
vtk:            7.0.0-py35_2    clinicalgraphics                                                          
wheel:          0.29.0-py35_0   defaults

Proceed ([y]/n)? y

Fetching packages ...
setuptools-20. 100% |###############################| Time: 0:00:01 442.58 kB/s
Extracting packages ...
[ COMPLETE ]|##################################################| 100%
Linking packages ...
[ COMPLETE ]|##################################################| 100%

To activate this environment, use:

> activate my_env

C:\Development\Projects>activate my_env
Deactivating environment "C:\Users\Korijn\Miniconda3"...
Activating environment "C:\Users\Korijn\Miniconda3\envs\my_env"...

[my_env] C:\Development\Projects>python
Python 3.5.1 |Continuum Analytics, Inc.| (default, Feb 16 2016, 09:49:46) [MSC v.1900 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

import vtk

On Codeship we use the following:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh bash ~/miniconda.sh -b -p $HOME/miniconda export PATH="$HOME/miniconda/bin:$PATH" conda config --set show_channel_urls yes --set always_yes yes conda config --add channels clinicalgraphics conda update conda --quiet conda install conda-build anaconda-client --quiet conda env create --quiet

source activate export PYTHONPATH="$PYTHONPATH:$HOME/miniconda/envs//lib/python3.5/site-packages/vtk"

Note the PATH changes, we prepend the New conda environment to the PATH, so if you type Python, it finds the right version.

Ivo Flipse:

Looking at the logs from Circle CI:

The bash ~/miniconda.sh step reports:

You currently have a PYTHONPATH environment variable set. This may cause unexpected behavior when running the Python interpreter in Miniconda3. For best results, please verify that your PYTHONPATH only points to directories of packages that are compatible with the Python interpreter in Miniconda3: /home/ubuntu/miniconda3

So you might want to verify that it is correct. Judging by your circle.yml I guess that it is.

Given that all your conda commands work though, it seems that up to there everything is working as intended.

python setup.py install though runs on your system Python and not the conda python. So I reckon Miniconda is added to the end of the path, not at the beginning. When it looks up conda, it can't find it in your system Python install, whereas looking for python does.

Running the more specific commands does seem to work.

Here's what Ilastik does: https://github.com/ilastik/ilastik/blob/master/circle.yml

binarybottle commented 8 years ago

Finally -- All paths are finally working on build #498!: https://circleci.com/gh/nipy/mindboggle/498

Thank you for your help! I have updated the circle.yml file after following the excellent advice on http://stiglerdiet.com/blog/2015/Nov/24/my-python-environment-workflow-with-conda/

The https://github.com/ilastik/ilastik/blob/master/circle.yml and https://circleci.com/docs/config-sample/ links were also helpful. Now the dependencies are in an environment.yml file, as per https://github.com/conda/conda-env:

name: mindboggle-env
channels:
    - clinicalgraphics
dependencies:
    - python=3.5.1
    - vtk=7.0.0
    #-------------------------------------------------------------------------
    # nipype:
    #-------------------------------------------------------------------------
    - scipy
    - networkx
    - lxml
    - simplejson
    - future
    - nose
    - pip
    - pip:
        - nibabel
        - prov
        - traits
        - xvfbwrapper
        - https://github.com/nipy/nipype/archive/master.zip
    #-------------------------------------------------------------------------
    # mindboggle's remaining dependencies:
    #-------------------------------------------------------------------------
    - cmake
    - matplotlib
    - numpy
    - pandas
    #-------------------------------------------------------------------------
    # additional testing tools:
    #-------------------------------------------------------------------------
    - ipython
    - pytest
    - coverage
binarybottle commented 8 years ago

As of build 541, all tests for the python 3 version of mindboggle are passing (when the circleci service doesn't time out)!