Python 3.8 incompatible typehints in components/harvester.py

[marcus-oscarsson]

@woutdenolf noticed that the there are some Python 3.8 incompatible type-hints used.

Originally reported in issue #1383

mxcubeweb-server -r $(pwd)/mxcubeweb/demo/ --static-folder $(pwd)/mxcubeweb/ui/build/ -L debug

Traceback (most recent call last):
  File "/home/denolf/.local/wdnbashutils/virtualenvs/mxcubeweb/bin/mxcubeweb-server", line 3, in <module>
    from mxcubeweb import main
  File "/home/denolf/projects/sb/mxcubeweb/mxcubeweb/__init__.py", line 14, in <module>
    from mxcubeweb.app import MXCUBEApplication as mxcube  # noqa: E402
  File "/home/denolf/projects/sb/mxcubeweb/mxcubeweb/app.py", line 36, in <module>
    from mxcubeweb.core.components.harvester import Harvester
  File "/home/denolf/projects/sb/mxcubeweb/mxcubeweb/core/components/harvester.py", line 14, in <module>
    class Harvester(ComponentBase):
  File "/home/denolf/projects/sb/mxcubeweb/mxcubeweb/core/components/harvester.py", line 189, in Harvester
    def get_sample_info(self, sampleID: str) -> dict[str]:
TypeError: 'type' object is not subscriptable

[marcus-oscarsson]

Can be solved but using from __future__ import annotations or from typing import Dict

[marcus-oscarsson]

Perhaps @jbflo can have a look when he is back :) ?

[marcus-oscarsson]

:), I'm wondering if this however is a development that we only have on our internal GitLab. @woutdenolf, you checked out the GitLab code right. Because the GitHub test action should have caught this issue, however we are not testing against Python 3.8 on GitLab ?

[marcus-oscarsson]

Actually just double checking and the code is pretty much identical, so this line is the same here on GitHub:

mxcubeweb/mxcubeweb/core/components/harvester.py

Line 189 in 4ce5472

def get_sample_info(self, sampleID: str) -> dict[str]:

So its strange that this passes the tests, or am I overlooking something ?

[jbflo]

did not have python 3.8 en in place
just Setup a python 3.8 env and had the issue that @woutdenolf raised.

[marcus-oscarsson]

Yes, I found the issue. I'm not sure how this was meant to work:

mxcubeweb/.github/workflows/build_and_test.yml

Line 48 in 4ce5472

environment-file: conda-environment.yml

As far as I can see this never uses the interpreter specified in the matrix :

mxcubeweb/.github/workflows/build_and_test.yml

Line 15 in 4ce5472

python-version: ["3.8"]

I guess we could perhaps add something here:

mxcubeweb/.github/workflows/build_and_test.yml

Line 46 in 4ce5472

with:

[marcus-oscarsson]

@jbflo, thanks If you run pytest the tests are still failing because there is the same issue in mxcubecore. Do you think you can make a PR for mxcubecore as well

[jbflo]

@jbflo, thanks If you run pytest the tests are still failing because there is the same issue in mxcubecore. Do you think you can make a PR for mxcubecore as well

yes, i did it as well mxcube/mxcubecore#1031

[marcus-oscarsson]

Oh, yes I got lost in the issue "cross-over" Thanks alot @jbflo 👍