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ictr / covid19-outbreak-simulator

Population-based Forward-time Simulator for the Outbreak of COVID-19
https://ictr.github.io/covid19-outbreak-simulator/
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Cannot run simulator #12

Closed wuben2602 closed 4 years ago

wuben2602 commented 4 years ago

Description

The outbreak simulator cannot complete the simulation I think maybe because i didn't install the requirements.txt but everytime I try to run pip install -r requirements.txt, it can't find the file or directory.

What I Did

conda create -n covid19simtest conda activate covid19simtest pip install numpy,scipy pip install covid19-outbreak-simulator cd covid19-outbreak-simulator (covid19simtest) [u235123@soshub covid19-outbreak-simulator]$ outbreak_simulator --popsize A=2000 B=500 --rep 10 --handle-symptomatic quarantine_14 1 --susceptibility A=1.2 --symptomatic-r0 A=1.2 B=0.8 --logfile hetero.log --stop-if 't>40' --plugin stat --interval 1 --plugin insert A=5 --prop-of-infected 0.5 --interval 1 | python contrib/report2csv.py > hetero.csv

Error Message: ` Traceback (most recent call last): File "contrib/report2csv.py", line 7, in import pandas as pd ModuleNotFoundError: No module named 'pandas' Traceback (most recent call last): File "/home/bwu/.conda/envs/covid19simtest/lib/python3.8/site-packages/covid19_outbreak_simulator/simulator.py", line 36, in load_plugins obj = getattr(mod, plugin_name)(simulator) AttributeError: module 'stat' has no attribute 'stat'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/bwu/.conda/envs/covid19simtest/bin/outbreak_simulator", line 8, in sys.exit(main()) File "/home/bwu/.conda/envs/covid19simtest/lib/python3.8/site-packages/covid19_outbreak_simulator/cli.py", line 175, in main load_plugins(args.plugin) File "/home/bwu/.conda/envs/covid19simtest/lib/python3.8/site-packages/covid19_outbreak_simulator/simulator.py", line 38, in load_plugins raise ValueError( ValueError: Failed to retrieve plugin stat from module stat: module 'stat' has no attribute 'stat' (covid19simtest) [u235123@soshub covid19-outbreak-simulator]$ `

BoPeng commented 4 years ago

This is perhaps because 

pip install covid19-outbreak-simulator

installs the last released version, which does not have plugins/stat. Please try

pip install -e .

to install from the source directory and try again.

wuben2602 commented 4 years ago

That solves my problem. Thank you!