psycopg2 not found

[undercertainty]

Notebook 08.1 raises the error with the cell:

# Run the database cleanup script

!./sql_initial_state.py

raises:

Traceback (most recent call last):
  File "./sql_initial_state.py", line 3, in <module>
    import psycopg2 as pg
ModuleNotFoundError: No module named 'psycopg2'

Problem with the PATH in the script perhaps? There's no problem with just doing import psycopg2 in a cell.

[psychemedia]

I haven't tested this yet but it raises an important question: I guess by default you are trying to run that script in a different python environment to the one in which everything was installed. So we maybe need to find a way to ensure that scripts are run in the correct environment by tweaking paths, or explicitly setting a hashbang at the start of the file?

[psychemedia]

@undercertainty Did you add a test case for this your test file? We should perhaps create a .tests/ dir to run build tests in that is then deleted in the final container or left hidden?

[psychemedia]

Simplest way to invoke it might be to run:

!python ./sql_initial_state.py or even better %run ./test.py. The latter will run in the same Python environment as the notebook kernel.

rather than !./sql_initial_state.py

[undercertainty]

Agree, I think that a test notebook that's called with %run would be better than a standalone python script.

Also easier for the students to see what's going on if they decide to look it up. The version I'm using at the moment attached here. Weirdly, GH doesn't allow notebooks to be attached, so I'm afraid it's zipped. reset_databases.zip

[undercertainty]

BTW, my online behaviour’s likely to be a bit odd for a bit ‘cos my Mac’s on the blink and I’m having to learn how to use my Windows machine for the first time.

From: Tony Hirst notifications@github.com Sent: 07 August 2020 16:40 To: innovationOUtside/tm351vm-binder tm351vm-binder@noreply.github.com Cc: undercertainty undercertainty@gmail.com; Mention mention@noreply.github.com Subject: Re: [innovationOUtside/tm351vm-binder] psycopg2 not found (#16)

@undercertainty https://github.com/undercertainty Did you add a test case for this your test file? We should perhaps create a .tests/ dir to run build tests in that is then deleted in the final container or left hidden?

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[psychemedia]

@undercertainty Ah, good, we can maybe make some progress on debugging windows docker commands then:-) (I really should by myself a dev windows machines...)