Problem installing pygraphviz

[biotom]

When I try and run 'pip install -r requirements.txt', it fails with the error: ERROR: Command errored out with exit status 1: command: /Users/ittd/climatemind-backend/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/setup.py'"'"'; __file__='"'"'/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/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 /private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-record-9cpocl9v/install-record.txt --single-version-externally-managed --compile --install-headers /Users/ittd/climatemind-backend/venv/include/site/python3.7/pygraphviz cwd: /private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/ Complete output (33 lines): running install Trying dpkg Failed to find dpkg Trying pkg-config Package libcgraph was not found in the pkg-config search path. Perhaps you should add the directory containing 'libcgraph.pc' to the PKG_CONFIG_PATH environment variable No package 'libcgraph' found Traceback (most recent call last): File "<string>", line 1, in <module> File "/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/setup.py", line 93, in <module> tests_require=['nose>=1.3.7', 'doctest-ignore-unicode>=0.1.2', 'mock>=2.0.0'], File "/Users/ittd/climatemind-backend/venv/lib/python3.7/site-packages/setuptools/__init__.py", line 163, in setup return distutils.core.setup(**attrs) File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/setup_commands.py", line 44, in modified_run self.include_path, self.library_path = get_graphviz_dirs() File "/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/setup_extra.py", line 162, in get_graphviz_dirs include_dirs, library_dirs = _try_configure(include_dirs, library_dirs, _pkg_config) File "/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/setup_extra.py", line 117, in _try_configure i, l = try_function() File "/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/setup_extra.py", line 72, in _pkg_config output = S.check_output(['pkg-config', '--libs-only-L', 'libcgraph']) File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 376, in check_output **kwargs).stdout File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 468, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['pkg-config', '--libs-only-L', 'libcgraph']' returned non-zero exit status 1. ---------------------------------------- ERROR: Command errored out with exit status 1: /Users/ittd/climatemind-backend/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/pygraphviz/setup.py'"'"'; __file__='"'"'/private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-install-56vasmf8/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 /private/var/folders/3j/dq8385xs2b3gr_w7yxrqbvjr0000gs/T/pip-record-9cpocl9v/install-record.txt --single-version-externally-managed --compile --install-headers /Users/ittd/climatemind-backend/venv/include/site/python3.7/pygraphviz Check the logs for full command output.
This happens also when I try and run pip install pygraphviz

[rodriguesk]

You don't need pygraphviz to run the app. I suggest looking back to an earlier versions of the repo before visualize.py was added to the knowledge_graph folder.

@ppython I'm thinking it might be good to move the visualize script to a different repo, one that's internal only, especially since the visualize.py script isn't going to be run by the app.

[rodriguesk]

@biotom if you do want to install graphviz and you have a mac, then follow these directions to fix the dependency issue:

I had issues getting pip install pygraphviz to work on my mac. I had to download pygraphviz from the zip file on their website, then unzip and include the special arguments in the install command to include the proper path to Graphviz installed on my mac.

For mac, after installing Graphviz, to install pygraphivz providing path to graphviz (from the install documentation for pygraphviz):

We tried our best to discover graphviz location automatically, but if you
would like specify specific location for graphviz you may provide additional parameters to specify graphviz location in the setup.py file in the zip or tar file.
include-path= path to graphviz include files
library-path= path to graphviz library files
For example
::
python setup.py install --include-path=/usr/local/Cellar/graphviz/2.38.0/include/graphviz --library-path=/usr/local/Cellar/graphviz/2.38.0/lib

Note that Graphviz is different than the pygraphviz python package. Graphviz is separate software that can be downloaded if you have a mac and have homebrew by doing brew install graphviz. If you have a PC try to follow the instructions here to get pygraphviz and Graphviz working.

[rodriguesk]

@biotom Try using this state of the repo to work off of for Swagger:
b8d8b3a#diff-d7b6a4b835cd70aa17e6993900a57dbe

[biotom]

Thanks, after brew install graphviz, it worked! However, I'm now getting ModuleNotFoundError: No module named 'pandas' when I try and do flask run... @rolandoldengarm is it worth dockerising this now?

[rodriguesk]

Pip install pandas

…

On Sun, Aug 16, 2020 at 11:49 AM Tom Deadman ***@***.***> wrote: *External Email* Thanks, after brew install graphviz, it worked! However, I'm now getting ModuleNotFoundError: No module named 'pandas' when I try and do flask run... @rolandoldengarm <https://github.com/rolandoldengarm> is it worth dockerising this now? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEXL62V72Z7ETPQXWIGVFALSBAS4TANCNFSM4QA572YQ> .

[biotom]

Yes, I've done this- and so has pip install -r requirements.txt

[rodriguesk]

Is some code written import pandas as pd? Instead of just import pandas as pandas?

…

On Sun, Aug 16, 2020 at 11:57 AM Tom Deadman ***@***.***> wrote: *External Email* Yes, I've done this- and so has pip install -r requirements.txt — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEXL62RODDBUB2J2ZWKSGJDSBAT3JANCNFSM4QA572YQ> .

[biotom]

With the docker container developments, and the fact that installing graphviz fixed this, I think we can close this issue.