pytz dependency not met in recent builds of conda environment
cnluzon opened this issue · 4 comments
I recently created a conda minute environment by using the command:
mamba create -n minute minute
And then during a minute run got the following error:
No module called pytz
I am uncertain which was the tool that now has this dependency, it seems to come from pandas. Either way, it might need to be made explicit in the environment.yaml file at this point so we guarantee that minute runs from a fresh install.
Edit to say that this easily fixes with pip installing it on the active environment:
pip install pytz
Since minute itself doesn’t use pytz, the problem would be that one of the dependencies does not correctly list pytz among its own dependencies.
That said, I tried to reproduce this and wasn’t able to. Which command gave you the error?
I got it when I did a minute run. But now I have noticed a different but related thing, which is that the bioconda recipe for minute is not updated to the latest tagged version which is 0.6.0, it installs minute 0.4.0. And in the recent changes we did fix things in the environment.yaml. Things seem to run ok if I install from the repository instead of bioconda.
I keep forgetting about this, should I notify you when I tag a new version? I thought the bioconda bot would notify you. Now I am thinking that maybe it's because we moved the repository to elsasserlab on those times.
If this is an inconvenience, I can also find out how to become a bioconda member and be able to maintain the bioconda recipes myself.
It appears the bioconda autobump bot was changed recently and no longer knows how to update the minute recipe. I have opened a PR and CC'ed you.
You don’t have to become a Bioconda member (but of course feel free if you want to). It is not an inconvenience for me to merge a PR once every couple of months. And when the bot works, any other Bioconda member can also do it.
Simplest for now would be to check the list of Bioconda PRs about an hour after you made a new Minute release. If working as it should, the bot will have noticed the release and opened a PR. You can comment on the PR in case there is anything important. In particular, when the versions of any dependencies have changed, this needs to be updated in the recipe manually because the bot doesn’t do it.