No requirements.txt dependency file about sherlock HOT 19 OPEN

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:

1. Install and update ubuntu, along with git, pip, and virtualenv.
2. install graphviz with sudo apt-get install graphviz libgraphviz-dev pkg-config
3. Clone sherlock.
4. 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

1. Install and update an ubuntu 17 vm
2. Install and update ubuntu, along with git, pip, and virtualenv.
3. Run sudo apt-get install graphviz libgraphviz-dev pkg-config python-tk python-dev
4. Go to the server directory.
5. Create a virtual environment using virtualenv --python=/usr/bin/python2.7 venv. Activate the environment.
6. Run pip install --install-option="--incude-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz" pygraphviz.
7. 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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