Outdated SoS conda packages

[gaow]

Here is the list of outdated packages on conda-forge that we would need to fix, comparing pypi vs conda-forge:

• https://anaconda.org/conda-forge/jupyterlab-sos Not all platforms have the same version of build. Need a fix.

• https://github.com/conda-forge/jupyterlab-transient-display-data-feedstock is 0.4.3, is 0.4.4 at https://pypi.org/project/transient-display-data/, should be 0.5.3 based on GitHub commit message

• https://github.com/conda-forge/sos-bash-feedstock is 0.20.0, should be 0.21.0 at https://pypi.org/project/sos-bash/

• https://github.com/conda-forge/markdown-kernel-feedstock is 0.2.1, should be 0.2.2 https://pypi.org/project/markdown-kernel/

• https://github.com/conda-forge/sos-matlab-feedstock is 0.18.8, should be 0.20.3

• https://github.com/conda-forge/sos-rmarkdown-feedstock is 0.1.3, should be 0.1.4

• https://github.com/conda-forge/sos-python-feedstock is 0.18.4, should be 0.18.5

• https://github.com/conda-forge/sos-pbs-feedstock is 0.20.8, should be 0.20.9

[gaow]

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

[danielnachun]

An important update here - many of the feedstocks are out of date because the issue with ipkernel.tests identified in vatlab/sos-notebook#354.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

• sos-bash
• sos-julia
• sos-matlab
• sos-notebook
• sos-python
• sos-r

Of the remaining outdated feedstocks:

• sos-rmarkdown and sos-pbs have no apparent issues and I'll rerender those
• markdown-kernel has a linting issue with its recipe which I will fix in the update PR.
• jupyterlab-transient-display-data had some missing dependencies and an issue with its source URL, which I will push a fix for.
• jupyterlab-sos had some missing dependencies and an issue with properly installing its extension, as discussed here: JupyterLab SoS kernel missing right panel kernel selections jupyterlab-sos#72. See that issue for more details on the fixes.

[BoPeng]

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

[gaow]

Okay we'll do that and send in PR

[danielnachun]

@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]

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

• jupyterlab-sos 0.10.1 conda-forge/jupyterlab-sos-feedstock#26
• jupyterlab-transient-display-data 0.4.4 conda-forge/jupyterlab-transient-display-data-feedstock#8
• rerender sos-bash 0.21.0 conda-forge/sos-bash-feedstock#11
• sos-notebook 0.24.4 conda-forge/sos-notebook-feedstock#87
• sos-python 0.20.2 conda-forge/sos-python-feedstock#10
• sos-rmarkdown 0.1.4 conda-forge/sos-rmarkdown-feedstock#4
• sos-matlab 0.20.2 conda-forge/sos-matlab-feedstock#15
• markdown-kernel 0.2.2 conda-forge/markdown-kernel-feedstock#3
• [ci skip] [skip ci] ***NO_CI*** rerender sos-r 0.20.1 conda-forge/sos-r-feedstock#9
• [ci skip] [skip ci] ***NO_CI*** rerender sos-julia 0.20.0 conda-forge/sos-julia-feedstock#9

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]

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]

Thank you so much! I made a PR for sos-pbs 0.20.9 - can you merge it as well: conda-forge/sos-pbs-feedstock#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]

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]

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]

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]

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]

Thanks for taking care of this mess.