The pygenstability cli#
Command line interface.
cli#
App initialisation.
cli [OPTIONS] COMMAND [ARGS]...
plot_communities#
Plot communities on networkx graph.
cli plot_communities [OPTIONS] GRAPH_FILE RESULTS_FILE
Arguments
- GRAPH_FILE#
Required argument
- RESULTS_FILE#
Required argument
plot_scan#
Plot results in scan plot.
cli plot_scan [OPTIONS] RESULTS_FILE
Arguments
- RESULTS_FILE#
Required argument
run#
Run pygenstability.
graph_file: path to either a .pkl with adjacency matrix in sparse format, or a text file with three columns encoding node indices and edge weight. The columns need a header, or the first line will be dropped. Notice that doubled edges with opposite orientations are needed for symetric graph.
See https://barahona-research-group.github.io/PyGenStability/ for more information.
cli run [OPTIONS] GRAPH_FILE
Options
- --constructor <constructor>#
Name of the quality constructor.
- Default:
linearized
- --min-scale <min_scale>#
Minimum scale.
- Default:
-2.0
- --max-scale <max_scale>#
Maximum scale.
- Default:
0.5
- --n-scale <n_scale>#
Number of scale steps.
- Default:
20
- --log-scale <log_scale>#
Use linear or log scales.
- Default:
True
- --n-tries <n_tries>#
Number of Louvain evaluations.
- Default:
100
- --NVI, --no-NVI#
Compute the normalized variation of information between runs.
- Default:
True
- --n-NVI <n_nvi>#
Number of randomly chosen runs to estimate the NVI.
- Default:
20
- --postprocessing, --no-postprocessing#
Apply the final postprocessing step.
- Default:
True
- --ttprime, --no-ttprime#
Compute the ttprime matrix.
- Default:
True
- --spectral-gap, --no-spectral-gap#
Normalize scale by spectral gap.
- Default:
True
- --result-file <result_file>#
Path to the result file.
- Default:
results.pkl
- --n-workers <n_workers>#
Number of workers for multiprocessing.
- Default:
4
- --tqdm-disable <tqdm_disable>#
disable progress bars
- Default:
False
- --method <method>#
Method to solve modularity, either Louvain or Leiden
- Default:
louvain
- --with-optimal-scales, --no-with-optimal-scales#
Search for optimal scales
- Default:
True
- --exp-comp-mode <exp_comp_mode>#
Method to compute matrix exponential, can be ‘spectral’ or ‘expm’
- Default:
spectral
Arguments
- GRAPH_FILE#
Required argument