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py2cytoscape

Python utilities for Cytoscape and Cytoscape.js

https://github.com/cytoscape/py2cytoscape

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    3 of 16 committers (18.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Python utilities for Cytoscape and Cytoscape.js

Basic Info
Statistics
  • Stars: 176
  • Watchers: 17
  • Forks: 46
  • Open Issues: 29
  • Releases: 0
Created almost 12 years ago · Last pushed over 4 years ago
Metadata Files
Readme License

README.md

py2cytoscape Build Status PyPI version ReadtheDocs DOI

DEPRECATION

Please note that this project has been superceded by the py4cytoscape project. py2cytoscape is not currently maintained.

Installation

py2cytoscape can be installed using conda, pip.

conda

conda installs igraph with py2cytoscape. You do not need to install igraph by yourself.

shell conda install -c conda-forge py2cytoscape

Latest stable release (pip)

shell pip3 install py2cytoscape

Development version (pip)

shell pip3 install git+https://github.com/cytoscape/py2cytoscape.git

Dependencies (extra): igraph

``` git clone https://github.com/igraph/python-igraph/ cd python-igraph

git clone https://github.com/igraph/igraph igraphcore cd igraphcore ./bootstrap.sh mkdir build && cd _build ../configure --prefix=$PWD/../install make make install cd ../../

CPPFLAGS="-I$PWD/igraphcore/install/include/igraph ${CPPFLAGS}" export CPPFLAGS LDFLAGS="-L$PWD/igraphcore/install/lib ${LDFLAGS}" export LDFLAGS PKGCONFIGPATH=igraphcore/install/lib/pkgconfig/ export PKGCONFIG_PATH

python3 setup.py install --user ```

Documentation

Package documentation can be found on https://py2cytoscape.readthedocs.io.

For contributing please check the wiki.

Full workflows can be found on the cytoscape/cytoscape-automation repo. The following workflows include cyrest usage:

Contributing

Please do all your development in our development docker image:

docker pull mpgagebioinformatics/py2cytoscape:latest

  • Create a folder to map to the container's user home folder mkdir -p ~/py2cy-container ----
  • Start the container from the latest version of the image sudo docker run -d -p 8787:8787 -p 8888:8888 \ -v ~/py2cy-container:/home/mpiage --name py2cy-container \ -it mpgagebioinformatics/py2cytoscape:latest ----
  • Alternatively you can start the container from a specific tag/version of the image sudo docker run -d -p 8787:8787 -p 8888:8888 \ -v ~/py2cy-container:/home/mpiage --name py2cy-container \ -it mpgagebioinformatics/py2cytoscape:<tag> ----
  • Connect to the running container sudo docker exec -i -t py2cy-container /bin/bash ----
  • Stop the container sudo docker stop py2cy-container ----
  • Jupyter

Once you have connected to the running container you can start jupyter with module load jupyterhub jupyter notebook --ip=0.0.0.0 A URL will be presented to you, and it should be pasted into your host's browser (Chrome recommended).

  • RStudio-server Once you have connected to the running container you can start Rstudio server with module load rlang sudo rstudio-server start You can then get access by connecting on your host's browser to http://localhost:8787.

For stopping the server use: sudo rstudio-server stop

  • X forward to enable Cytoscape

On a Mac install socat and xquartz: brew install socat brew install xquartz Open Xquartz: open -a Xquartz Then navigate to XQuartz > Preferences > Security and tick the box 'Allow connections from network clients'.

Check your ip address: IP=$(ifconfig en0 | grep inet | awk '{ print $2 }') Start socat: socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\" an then start the container by adding the -e DISPLAY=${IP}:0 argument.

Complete example call: IP=$(ifconfig en0 | grep inet | awk '{ print $2 }') && \ socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\" & \ docker run -d -e DISPLAY=${IP}:0 -p 8787:8787 -p 8888:8888 \ -v ~/py2cy-container:/home/mpiage --name py2cy-container \ -it mpgagebioinformatics/py2cytoscape:latest

  • User account

User: mpiage

Pass: bioinf

Citing

Ono, K. et al. (2015) CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res, 4, 478

Note to repository maintainers: Please *DO NOT* move this page ... the Cytoscape Automation paper refers directly to it.

Owner

  • Name: Cytoscape Consortium
  • Login: cytoscape
  • Kind: organization

GitHub Events

Total
  • Watch event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Fork event: 1

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 211
  • Total Committers: 16
  • Avg Commits per committer: 13.188
  • Development Distribution Score (DDS): 0.531
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jorge Boucas J****s@a****e 99
Keiichiro Ono k****o@g****m 56
Kozo Nishida k****a@g****m 28
Zachary Juang z****2@m****m 6
Rasmus Scholer r****r@g****m 3
Guido Pio Mariotti g****v@g****m 3
pkrezel p****l@g****m 3
Daewon Lee D****e 3
Barry Demchak i****k@g****m 2
James Pino j****o@v****u 2
andorsk a****r@g****m 1
romainstuder r****r 1
U-ICSN\elie n****e@f****r 1
Moritz Schaefer m****l@m****e 1
Kyle Kelley r****k@g****m 1
Rundong Du r****u@g****u 1
Committer Domains (Top 20 + Academic)
gatech.edu: 1 moritzs.de: 1 free.fr: 1 vanderbilt.edu: 1 me.com: 1 age.mpg.de: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 71
  • Total pull requests: 29
  • Average time to close issues: 5 months
  • Average time to close pull requests: 5 months
  • Total issue authors: 34
  • Total pull request authors: 17
  • Average comments per issue: 1.63
  • Average comments per pull request: 0.55
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kozo2 (14)
  • jorgeboucas (11)
  • dotasek (5)
  • mwang87 (4)
  • Niveda-S (2)
  • empet (2)
  • shaaaarpy (2)
  • zachary822 (2)
  • brownmk (2)
  • moritzschaefer (2)
  • Benito-chem (2)
  • keiono (1)
  • cs48a (1)
  • 229668880 (1)
  • sauloal (1)
Pull Request Authors
  • zachary822 (5)
  • scholer (3)
  • dwgoon (3)
  • pkrezel (3)
  • moritzschaefer (2)
  • gmariotti (2)
  • cs48a (1)
  • nicolaselie (1)
  • jorgeboucas (1)
  • andorsk (1)
  • adamlawr-cisco (1)
  • DnlRKorn (1)
  • rundong08 (1)
  • romainstuder (1)
  • JamesPino (1)
Top Labels
Issue Labels
enhancement (10) bug (7) help wanted (4) question (1) invalid (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 4
  • Total versions: 2
conda-forge.org: py2cytoscape
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 4
Rankings
Dependent repos count: 16.1%
Forks count: 26.1%
Stargazers count: 27.6%
Average: 30.3%
Dependent packages count: 51.6%
Last synced: 12 months ago

Dependencies

setup.py pypi
  • networkx *
  • pandas *
  • pydot *
  • pydotplus *
  • pyparsing *
  • requests *