Closed vpnagraj closed 3 years ago
system()
callreticulate
to manage python call AND dependencies (https://rstudio.github.io/reticulate/articles/python_dependencies.html)required python pkgs per https://github.com/reichlab/covid19-forecast-hub/blob/master/visualization/requirements.txt
pandas
requests
pymmwr
click
urllib3
selenium
webdriver-manager
pyyaml
PyGithub
git+https://github.com/reichlab/zoltpy/
https://github.com/hannanabdul55/pykwalify/archive/master.zip
the functionality from validate_single_forecast_file.py
is now implemented in two ways:
validate_forecast()
R wrapperdigging in here and basically all that the single forecast vaildation script did was call a function from single py module (zoltpy
). that was made it very easy to wrap in a function and call using reticulate
.
there is more to validation though ... the other python scripts that C19FH maintains (and are now pulled into the misc/validation dir in this repo) do things like checking metadata files, looping over many forecast files, etc.
there are also the R scripts (no longer maintained by C19FH?) but pulled over and working (for now?) in this repo
we can revisit validation workflows later. for now, this wrapper function works to make sure the quantile csv format is not broken
see https://github.com/signaturescience/focustools/issues/6
this function should wrap the validation
.py
script provided by C19FH:https://github.com/reichlab/covid19-forecast-hub/blob/master/code/validation/test_formatting.py
we can call it with a
system()
command orreticulate
(eventually?)