bug: flopy.utils.binaryfile.HeadUFile.get_ts() gives error for idx= 0

[giovannifi]

I am trying to run this script:

import flopy
import flopy.utils.binaryfile as bf

path_exe = r'C:\modflow'
path_model = r'c:\models'
modelname = 'mymodel'

heads = bf.HeadUFile(path_model + '\\' + modelname + '.hds')  # hds file generated with the software mf-usg

print(heads.get_ts(idx=0))

and I get the following error message:

{IndexError}index -682005 is out of bounds for axis 0 with size XXXX

If I use any number between 1 and (XXXX - 1), I get a timeseries without any problem. I have the feeling that the command does not read node 0.

PS I am running flopy v 3.3.5 on a python 3.9 environment.

[wpbonelli]

Hey @giovannifi, this should be fixed by #1510. To get around this until a new release you can work from the head of the develop branch.

[wpbonelli]

Hi @giovannifi was this problem resolved for you? I rechecked some of flopy's example .hds files and didn't encounter the issue. Wanted to confirm before closing as there is a new release coming shortly.

[giovannifi]

I am currently using python 3.9. I tried to run pip install flopy --upgrade but it does not give me the possibility to get the latest version of flopy (3.3.6). So I cannot really verify. Do I need to run python 3.10 to be able to install the latest version of flopy?

[cnicol-gwlogic]

Try to add the --force-reinstall switch

...just noticed you aren't pointing it to the develop branch. Use this:
Pip install https://github.com/modflowpy/flopy/zipball/develop -U --force-reinstall

[giovannifi]

tried that, it installs version 3.3.5.

[cnicol-gwlogic]

See my edited comment

[giovannifi]

The command does not work for me due to SSL certificate limitation imposed by my company policies. it seems I can get the package only from the official repository. I have to work out with IT how I can run your command. For the moment this is the error message I get:

Collecting https://github.com/modflowpy/flopy/zipball/develop
  WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate signature failure (_ssl.c:1123)'))': /modflowpy/flopy/zipball/develop
  WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate signature failure (_ssl.c:1123)'))': /modflowpy/flopy/zipball/develop
  WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate signature failure (_ssl.c:1123)'))': /modflowpy/flopy/zipball/develop
  WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate signature failure (_ssl.c:1123)'))': /modflowpy/flopy/zipball/develop
  WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate signature failure (_ssl.c:1123)'))': /modflowpy/flopy/zipball/develop
ERROR: Could not install packages due to an OSError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /modflowpy/flopy/zipball/develop (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate signature failure (_ssl.c:1123)')))

[cnicol-gwlogic]

Not sure on that one. You could try this instead:
Pip install -U --force-reinstall git+https://github.com/modflowpy/flopy@develop

[wpbonelli]

@giovannifi if you're on mac and haven't previously installed certificates for your Python distribution, this might help

[giovannifi]

Thanks all for the suggestions. I have finally managed to bypass the SSL issue by downloading the zip flopy package and manually install version 3.3.6. I re-run my script and it does not throw any error. So, yes this can be closed.

Thanks

[mbakker7]

For future reference, @giovannifi, how did you manage to install it?

[giovannifi]

@mbakker7 I used the link provided by @cnicol-gwlogic in the post above (https://github.com/modflowpy/flopy/zipball/develop). This allowed me to download a zip file. Then I simply run the command: pip install <zipfilename>.zip

As you are asking, I take advantage of this to say the things I do not understand:

• why is the zip file called modflowpy-flopy-3.3.5-215-g00757a4.zip, i.e. why does the file name contain the old flopy version? I can confirm that after the installation I had version 3.3.6 installed.
• why is not posible to install the upgrade from the official repository (pypi.org)? if you check this page https://pypi.org/project/flopy/ the latest version is still 3.3.5.