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vatlab / sos

SoS workflow system for daily data analysis
http://vatlab.github.io/sos-docs
BSD 3-Clause "New" or "Revised" License
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Outdated SoS conda packages #1544

Closed gaow closed 5 months ago

gaow commented 6 months ago

Here is the list of outdated packages on conda-forge that we would need to fix, comparing pypi vs conda-forge:

gaow commented 5 months ago

Just to let you know that we are taking a look into this with help from @danielnachun, hopefully pushing a fix soon.

danielnachun commented 5 months ago

An important update here - many of the feedstocks are out of date because the issue with ipkernel.tests identified in https://github.com/vatlab/sos-notebook/issues/354. As of now I believe the follow conda-forge feedstocks are affected:

Of the remaining outdated feedstocks:

BoPeng commented 5 months ago

For the kernels, maybe we can comment out the tests and check only if the modules can be imported.

gaow commented 5 months ago

Okay we'll do that and send in PR

danielnachun commented 5 months ago

@BoPeng I think all the kernel recipes already have an import check. For most of them we'll just end up deleting the run_test.py file from the feedstock as its only purpose is to run that unit test. I believe the only exception to this is sos-notebook which has some other test in that script, so I'll just delete the part that needs ipykernel.test.

danielnachun commented 5 months ago

@BoPeng I have made the PRs to address all but one feedstock. Can you merge the following PRs:

I will create a separate set of PRs after these are merged to add myself as a feedstock maintainer, because right now the CI would fail for most of the feedstocks.

The only remaining issue now is I don't see a version 0.20.9 of sos-pbs on PyPI - the newest version is 0.20.8, the same as in conda-forge. If a version 0.20.9 does exist, it will need to be uploaded to PyPI before we can update in conda-forge. Otherwise if 0.20.8 is newest version we'll just want to get auto-merge enabled, which I will make a new PR for.

BoPeng commented 5 months ago

Thanks. I have merged the PRs and released sos-pbs 0.20.9. It contains a few bug fixes that I am not sure if it is the fault of sos-pbs or my local configuration, but I made the release anyway.

danielnachun commented 5 months ago

Thank you so much! I made a PR for sos-pbs 0.20.9 - can you merge it as well: https://github.com/conda-forge/sos-pbs-feedstock/pull/14.

The only remaining question brought up by @gaow was the version of jupyterlab-transient-display-data. The latest version on PyPI is 0.4.4, but @gaow mentioned seeing version 0.5.3 in commit messages. Is there a plan to release a new version on PyPI. Now that we have auto-merge enabled for the feedstock, it should update itself automatically after a new PyPI release.

gaow commented 5 months ago

Thanks! To clarify, we should not have arch specific release for these packages right? Still here for example: https://anaconda.org/conda-forge/sos-notebook I see the noarch is up to date but there are arch specific releases.

BoPeng commented 5 months ago

Regarding transient-display-data, a commit message for the release of version 0.4.3 has a tupo for version 0.5.3. Then version 0.4.4 for Jlab 4.x was released without an explicit "release" message. The current pypi (and conda) release of 0.4.4 should work.

danielnachun commented 5 months ago

Thanks! To clarify, we should not have arch specific release for these packages right? Still here for example: https://anaconda.org/conda-forge/sos-notebook I see the noarch is up to date but there are arch specific releases.

Both conda-forge and bioconda don't allow the deletion of old packages unless they contain malicious code or constitute license violations. So the arch-specific packages won't disappear, but won't be updated anymore. They can just be ignored - the only time they'd be an issue is if the user wanted to use the old version that was still arch specific on a platform that didn't support it, and I don't think for this type of software someone is going to need to do that.

danielnachun commented 5 months ago

Regarding transient-display-data, a commit message for the release of version 0.4.3 has a tupo for version 0.5.3. Then version 0.4.4 for Jlab 4.x was released without an explicit "release" message. The current pypi (and conda) release of 0.4.4 should work.

Thanks @BoPeng for clarifying this, in that case we are good to go for transient-display-data. All of the outdated conda-forge packages are now fully up to date with what is on PyPI, so I think we can close this issue. I am going to open a separate set of PRs tomorrow to add myself as a feedstock maintainer for these feedstocks, but that won't have any affect on the packages. Once those PRs are merged, I'll be able to merge another set to add @gaow as a maintainer and then the 3 of us will all be to help maintain the feedstocks for the foreseeable future.

BoPeng commented 5 months ago

Thanks for taking care of this mess.