Comments (19)
I fixed pygraphviz’s graphviz dependency issue by specifying installation options in requirements.txt. Let me know if anyone runs into related bugs.
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Hey everyone, here's the link to our Slack group.
https://join.slack.com/t/bakerstconsulting/shared_invite/enQtMzM3MzU4NjQyMDIxLWIyZTNjZDBmNmQ0ZTM3ODEwZGU0NTIwMWU5MWMyYjAzMTRiYjcyMTkxY2RkMjJiZDM1Y2NjMDlmMGIyNzIxNzQ
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Just added people to the issue who want to solve it
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Looks like the current requirements.txt file has a bunch of stuff that my virtualenv doesn't have. I don't know whether that's due to differences between my machine and Benjamin's. Here is my requirements.txt created by running pip freeze > usipeusrequirements.txt
.
backports.functools-lru-cache==1.5
cycler==0.10.0
decorator==4.2.1
kiwisolver==1.0.1
matplotlib==2.2.0
networkx==2.1
numpy==1.14.1
pandas==0.22.0
Pillow==5.0.0
pkg-resources==0.0.0
pydot==1.2.4
pygraphviz==1.3.1
pyparsing==2.2.0
python-dateutil==2.6.1
pytz==2018.3
reportlab==3.4.0
scikit-learn==0.19.1
scipy==1.0.0
seaborn==0.8.1
six==1.11.0
sklearn==0.0
subprocess32==3.2.7
This may solve the issue where ccsm
version 0.9.12.2 can't be installed by pip. I ran a search for ccsm
on the pypi website and it's not listed as a package.
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Doing some digging and realizing that the script being python 2 is creating some REALLY nasty issues with the virtual environment, looking for fixes...
For some insight into the issue, here's a link.
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New requirementst.txt pushed, pull it and let me know if it works. 2 packages are slightly upgraded and one is missing compared to what you posted above.
Okay, so here's what I found:
make a virtualenv with with the following command:
virtualenv --python=/usr/bin/python2.7 venv
install dependencies with:
pip2 install -r requirements.txt
Sherlock seems to be buggy, but works (except for part 3, but that was broken before anyway).
EDIT: Sherlock is NOT buggy, clarified in issue 2.
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The requirements.txt was updated to include flask, please let me know if it's functional.
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Running the latest requirements file I receive this error:
Collecting subprocess32=.3.2.7 (from -r requirements.txt (line26))
Using cached subprocess32.3.2.7.tar.gz
Complete output from command python setup.py egg_info:
This backport is for Python 2.x only.
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-_8y3ufrr/subprocess32/
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The new requirements.txt works on my end.
EDIT: It is NOT working on my end, I believe this is because scikitlearn uses scipy as a dependency but requirements.txt files are organized alphabetically. I'll poke around.
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@inp2 is what you were describing an error or warning? Are you sure you're using pip2 specifically?
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@suspiciousCloud the update you made to requirements.txt breaks dependency installation on my machine. Could you specify the issue you're having with the requirements.txt in commit 16075e1?
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pygraphviz requires graphviz which my Ubuntu VM didn’t have so i received this error:
Running setup.py install for pygraphviz ... error
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-build-Rueu87/pygraphviz/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-ZzPFrj-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
running install
Trying pkg-config
Failed to find pkg-config
Trying dotneato-config
Failed to find dotneato-config
Failed to find dotneato-config
library_dirs=None
include_dirs=None
error: Error locating graphviz.
----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-build-Rueu87/pygraphviz/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-ZzPFrj-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-Rueu87/pygraphviz/
So i implemented the fix described here which cleared up the issue:
https://www.lesinskis.com/tag/python.html
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Could you try running
sudo apt-get install graphviz libgraphviz-dev pkg-config; pip2 install -r requirement.txt
in a new vm and see if sherlock will run?
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It works for me now
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Okay, so I think I got it.
Do the following:
- Install and update ubuntu, along with git, pip, and virtualenv.
- install graphviz with
sudo apt-get install graphviz libgraphviz-dev pkg-config
- Clone sherlock.
- Go to the server directory and type
pip install -r requirements.txt --no-cache-dir
EDIT: Having issues. I also need to apt install python-tk, but now I'm having issues with pygraphviz.
EDIT 2: Ok, I think I solved it. You have to install the dependencies and then specify some options. So you have to install pygraphviz independently using pip install --install-option="--incude-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz" pygraphviz
EDIT 3: Also need to sudo apt install python-tk
I'll look into getting this into the requirements file, after a quick triple check that this works.
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Mkay, here are cohesive instructions to get sherlock running
- Install and update an ubuntu 17 vm
- Install and update ubuntu, along with git, pip, and virtualenv.
- Run
sudo apt-get install graphviz libgraphviz-dev pkg-config python-tk python-dev
- Go to the server directory.
- Create a virtual environment using
virtualenv --python=/usr/bin/python2.7 venv
. Activate the environment. - Run
pip install --install-option="--incude-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz" pygraphviz
. - Run
pip install -r requirements.txt --no-cache-dir
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I was testing out these installation instructions using a fresh Ubuntu 17.10 VM and I got it to work without steps 5 and 6 but I did need to run sudo apt-get install python-dev
for step 7, because it was complaining about a missing Python.h
header file.
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@usipeus thanks for the feedback! Steps 5 and 6 are taken as a python coding best practice. I'll explain more in person today.
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Quick update: use pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/"
to install pygraphviz.
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