Python3.10

[Matthew-Jennings]

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[Matthew-Jennings]

So I think we have some success!

• imageio now seems to work unpinned due to changes in lib/pymedphys/_losslessjpeg/__init__.py
• docs build works on Windows with Python 3.10 by replacing sphinxcontrib-napoleon with sphinx.ext.napoleon in lib/pymedphys/docs/_config.yml.
• I can now successfully run poetry install -E dev locally using Python 3.10. CI is also successful.

[SimonBiggs]

Some brilliant work here :)

There seems to be a few CI items that are a little unhappy still though...

[Matthew-Jennings]

Some brilliant work here :)

There seems to be a few CI items that are a little unhappy still though...

Latest changes might do the trick.

• pylint appears to be throwing false positive E1101s (no-member) for pathlib.Path.joinpath() (see similar Github issue). I think its safe to disable these inline. COuld maybe disable more broadly, but not sure how best to do so.

• pylint is suddenly throwing [E0601 (used-before-assignment) errors too. I've put in dummy assignments to satisfy pylint, but wonder whether it is acceptable to just simply disable E0601..

• doctests were failing due to streamlit and an incompatibly version of protobuf. streamlit is pinned and updating it might help and is possibly a better long-term solution but I didn't investigate this due to a warning in pyproject.toml indicating the need for its pin.

• no idea about the cypress tests..

[SimonBiggs]

This need for no-member has me confused...

[Matthew-Jennings]

One possibility is that pylint somehow recognises that pathlib.Path(np.__file__).parents[4] could return an Exception (IndexError) and so joinpath() would not be a "member". Dunno.

[Matthew-Jennings]

I think I got everything except the Mosaiq tests passing (notwithstanding that not every combination of test task, python version and OS are being tested!).

I'm likely not going to be able to spend any longer on this for a couple of days, but understand that:

• the Mosaiq tests may need addressing before the merge
• we'll need a changelog entry.

I'll try to revisit midweek. In the meantime, if anyone (@SimonBiggs, @dg1an3?) has a quick fix for the Mosaiq stuff they can add, I'd be very much obliged!

[SimonBiggs]

• pylint is suddenly throwing [E0601 (used-before-assignment) errors too. I've put in dummy assignments to satisfy pylint, but wonder whether it is acceptable to just simply disable E0601..

My rule of thumb, if a new pylint error is added I will initially add it to the list of ignored errors in the config file, and then at a later date decide whether or not to scour the repo and fix up all of those.

• doctests were failing due to streamlit and an incompatibly version of protobuf. streamlit is pinned and updating it might help and is possibly a better long-term solution but I didn't investigate this due to a warning in pyproject.toml indicating the need for its pin.

Streamlit is okay to be upgraded, it just needs to stay pinned for end user installation for now. But, streamlit is stabalising significantly. So this might not be an issue. But if upgrading streamlit doesn't cause CI issues, it's fair game.

[nlambriICH]

Or @nlambriICH, might you be interested in taking a swing at this?

@SimonBiggs I could give it a try, but I think someone more experienced than me might be more suitable.

As a sidenote, I see that here the tests Library / Tests (ubuntu, updates) (pull_request) and Library / Tests (windows, docs) (pull_request) are passing, whereas in #1638 they are failing, possibly due to Python3.9?

[SimonBiggs]

possibly due to Python3.9?

Not actually due to 3.9. @Matthew-Jennings actually did quite a bit of work in here fixing the various tests by updating the required dependencies.

[Matthew-Jennings]

Or @nlambriICH, might you be interested in taking a swing at this?

@SimonBiggs I could give it a try, but I think someone more experienced than me might be more suitable.

As a sidenote, I see that here the tests Library / Tests (ubuntu, updates) (pull_request) and Library / Tests (windows, docs) (pull_request) are passing, whereas in #1638 they are failing, possibly due to Python3.9?

Hi @nlambriICH, if you're up for it, you could have a go! I'm likely out until next week now - I won't have access to a suitable workstation for coding. But I can still review PRs, etc.

I think the way to go would be to:

1. create a new branch/pull request from this branch (python3.10)
2. try removing the sqlalchemy pin in pyproject.toml and run poetry update and poetry install -E dev. You may need to specifically run poetry update sqlalchemy
3. Push to Github and see whether the Mosaiq tests fail and, if so, begin troubleshooting
   • if it does fail, it may be because of a different reason that it's failing now. I.e. it may fail because upgrading sqlalchemy broke the Mosaiq database test code, as opposed to whatever reason the test is failing now (which upgrading sqlalchemy may fix!)
   • If upgrading sqlalchemy does make it fail (differently), have a look at the sqlalchemy release notes. They may have introduced some relevant breaking changes between our currently pinned version and the latest version. See if you can identify a culprit - with luck it might be fairly simple - e.g. a change in function name/parameters?

Don't worry about all of that if you're not keen. I only write this since you expressed interest in trying!

[Matthew-Jennings]

Hi @nlambriICH, if you're up for it, you could have a go! I'm likely out until next week now - I won't have access to a suitable workstation for coding. But I can still review PRs, etc.

I think the way to go would be to:

1. create a new branch/pull request from this branch (python3.10)

2. try removing the sqlalchemy pin in pyproject.toml and run poetry update and poetry install -E dev. You may need to specifically run poetry update sqlalchemy

3. Push to Github and see whether the Mosaiq tests fail and, if so, begin troubleshooting

   • if it does fail, it may be because of a different reason that it's failing now. I.e. it may fail because upgrading sqlalchemy broke the Mosaiq database test code, as opposed to whatever reason the test is failing now (which upgrading sqlalchemy may fix!)
   • If upgrading sqlalchemy does make it fail (differently), have a look at the sqlalchemy release notes. They may have introduced some relevant breaking changes between our currently pinned version and the latest version. See if you can identify a culprit - with luck it might be fairly simple - e.g. a change in function name/parameters?

Don't worry about all of that if you're not keen. I only write this since you expressed interest in trying!

I had a small stab at this to no avail. Though my SQL skills are little more than "beginner" level.

[SimonBiggs]

I had a small stab at this to no avail. Though my SQL skills are little more than "beginner" level.

Alright, having these tests not pass is blocking other PRs being able to be merged. I'll give this a crack.

[SimonBiggs]

Given this is merging into the other Python 3.10 branch, I'll merge this into there and work on it further there.