Parse error in open-sir CLI using Windows cmd command line

[felipehuerta17]

A good amount of Python users who use Windows as their operating system have Python installed using Anaconda. By default, the Anaconda Prompt is a cmd shell and most python commands are run in the conda environment embedded in a cmd shell.

When trying to use the open-sir CLI in windows cmd

pipenv run python open-sir.py -p '[0.95,0.38]' -i '[341555,445,0]' -t 6

An error is obtained

Traceback (most recent call last):
  File "open-sir.py", line 39, in <module>
    run_cli()
  File "open-sir.py", line 35, in run_cli
    sol.set_params(p, w0).solve(**kwargs).export(sys.stdout)
  File "C:\open-sir\models\sir.py", line 60, in set_params
    self._set_params(p, initial_conds)
  File "C:\open-sir\models\model.py", line 54, in _set_params
    if len(p) != num_params or len(initial_conds) != num_ic:
TypeError: len() of unsized object

@jia200x thinks that this is caused because of not making the CLI full POSIX.

I haven't tried this in Powershell, but the issue is persistent on cmd.

[felipehuerta17]

Hi all,

I tried the above on anaconda prompt in Powershell with my new laptop and works fine. It is something related to windows cmd.

[jia200x]

I think this happens because of the ugly input format for the parameters. That's absolutely not portable.

Maybe we should think of an input file?

[sasalatart]

@jia200x If that is the case, I think we should support both options. If no parameters are found, then assume it is in a file, or something like that?

[felipehuerta17]

@gwenzel had an installation issue with pipenv.

For some reason his local version added a package python==3.7 and that raised an installation error. We should keep an eye on it.

[jia200x]

@jia200x If that is the case, I think we should support both options. If no parameters are found, then assume it is in a file, or something like that?
I read this comment a little bit late, sorry :(

I'm using for now an "input param" file that can be read from STDIN or a CLI param (see #34 ).
If we need to add these params to the CLI args (as @sasalatart proposes), we can indeed do it.

[jia200x]

@felipehuerta17 is this issue still present?

[felipehuerta17]

@jia200x made an excellent improvement on #34.

However, I just realized that our CLI documentation has a small error.

It is not immediately obvious that

usage: opensir-cli [-h] [-m {sir,sirx}] [-t TIME] [-f FILE] [-s] [-d DELIMITER] 

Has to be prefixed by python if it's intended to be run from a CLI.

In the example below,

opensir-cli --model sir --time 6 --file input_file.txt

Will not run (at least in Win10) unless it is called from a Jupyter Notebook or from a python shell. My suggestion is to update the documentation to:

python opensir-cli --model sir --time 6 --file input_file.txt

I just tested again in PS and CMD and works fine as long as python is explicitely mentioned before. I don't know whether the bash preamble enables to run opensir-cli directly on Linux/Mac @jia200x ?

In any case, the full form should be reproducible in all Windows, Linux and Mac

[jia200x]

Has to be prefixed by python if it's intended to be run from a CLI.

It shouldn't be prefixed with a python command. The CLI is an executable file with a proper python shebang

Will not run (at least in Win10) unless it is called from a Jupyter Notebook or from a python shell.

Did you install the package using pip?

In theory one should be able to do this:

pip install .
open-sir-cli --help

If this is not working under Windows, there's something wrong with the setuptools package and IMO we should fix that instead of updating the documentation. Calling an executable without the python prefix is intended

[jia200x]

(I'm 100% sure python executables are compatible with Windows. If this is not working, maybe I did something wrong with the package)

[felipehuerta17]

@jia200x testing:

No luck in PS

And CMD just complains

[jia200x]

hmmm there might be something wrong with the deployment setup. I will give it a look.

Thanks for testing!