Running setup.py install doesn't install requirements in Alpha0.5

[slarson]

For some reason running setup.py install, the requirements.txt packages are not actually installed. Tried this on a fresh virtualenv and it complained that networkx wasn't installed, even though it is in the requirements.txt file. Running pip install -r requirements.txt works, and have added this to the INSTALL.md instructions but this should be improved to happen in one step.

[mwatts15]

This is working in the latest alpha. I've noticed all the requirements are pinned to a specific version. Is this necessary for the one-step install?

[slarson]

@mwatts15 this is done to avoid future versions of each lib that may come out but be incompatible with this version of PyOpenWorm and mess up the build

[msasinski]

I would hope that the transitive dependencies in the default configuration are resolved by setup.py with the requirements.txt.

Let's see.

Installing alpha0.5 only (clean ubuntu machine..)

#sudo apt-get install git
#git clone https://github.com/openworm/PyOpenWorm.git
#cd PyOpenWorm
#git checkout alpha0.5

at this point we need to install pip

#sudo apt-get install python-pip
#sudo pip install -r requirement.txt

no go..

#sudo apt-get install python-dev
#sudo pip install -r requirement.txt

nope.. need libxml

#sudo apt-get install libxml2-dev
#sudo pip install -r requirement.txt

again not working.. need libxslt

#sudo apt-get install libxslt1-dev

another try

#sudo pip install -r requirement.txt

nope.. need zlib

#sudo apt-get install zlib1g-dev

that worked...

#sudo python setup.py install
./runtests

passed let's see if we can pythonize

#python
  >>> import PyOpenWorm as P
  >>> P.connect('PyOpenWorm/default.conf', data='OpenWormData/out.n3', dataFormat='n3')

Nope.. no data.

#sudo rm -r PyOpenWorm
git clone https:/github.com/openworm/PyOpenWorm.git --recursive #thanks @wilzh40
#cd PyOpenWorm
#python
  >>> import PyOpenWorm as P

no module neuroml.. but it's in requirements.txt?? let's try setup again

#sudo python setup.py install
#python
  >>> import PyOpenWorm as P
  >>> P.connect('PyOpenWorm/default.conf', data='OpenWormData/out.n3', dataFormat='n3')

still no cookie. data missing.

cd OpenWormData
#git clone https://github.com/mwatts15/OpenWormData.git .
#cd ..
#python 
  >>> import PyOpenWorm as P
  >>> P.connect('PyOpenWorm/default.conf', data='OpenWormData/out.n3', dataFormat='n3')

still no go. data missing.

cd OpenWormData
#git clone https://github.com/mwatts15/OpenWormData.git .
#cd ..
#python 
  >>> import PyOpenWorm as P
  >>> P.connect('PyOpenWorm/default.conf', data='OpenWormData/out.n3', dataFormat='n3')

it's doing something.. but it's really slow. .... ... .. . connected.. that's good enough for me.

so it's time to create a 'one liner' for this:

sudo apt-get install git python-pip python-dev libxml2-dev libxslt1-dev zlib1g-dev &&
git clone https://github.com/openworm/PyOpenWorm.git --recursive && cd PyOpenWorm &&
git checkout alpha0.5 &&
cd OpenWormData && 
git clone https://github.com/mwatts15/OpenWormData.git . && cd .. &&
sudo pip install -r requirements.txt && sudo python setup.py install && ./runtests.sh &&
echo "PyOpenWorm installed. Enjoy"

[mwatts15]

I believe this issue was addressed in df0ecc4f. The specific requirements of lxml have been removed, requirements are being installed through setup.py, and the README and INSTALL files have been updated to reflect steps perhaps not typically expected in a software install.

If you continue to experience the problem, please reopen this ticket if necessary or create a new ticket with your related issue, referencing this one (#36).