create PyPI package from package

GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification

https://w3id.org/mixs

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create PyPI package from package #245

Open wdduncan opened 3 years ago

wdduncan commented 3 years ago

A python file is produced as part of the output by LinkML. In the NMDC, we produce a PyPI package from this python file. This automated using a github workflow when a new release is created. Doing this for mixs could be quite useful too.

@ramonawalls I tried to post this ticket on mixs-source, but didn't have permission to do so. Perhaps you can transfer this issue?

cc @cmungall @turbomam

ramonawalls commented 3 years ago

It seems that one cannot create issues in forks. I had no idea, but I guess that kind of makes sense. Anyway, I will transfer this issue to the main MIxS repo so we don't loose it.

ramonawalls commented 2 years ago

@ramonawalls needs to add the pypi generation when making the release.

ramonawalls commented 2 years ago

mixs.py is already being generated as part of the release. I'll leave this issue open until we decide about hosting PyPi.

turbomam commented 2 years ago

I think we have been talking about a could of different ways to make the location of MIxS files clear to the public

merge the MIx6 branch into main, so that the MIxS LinkML is available via a GH URL, or even GH submodules
get the MIxS OWL artifact into BioPortal
start using w3id resolution, to that the MIxS files will be available via non-GH urls
get the MIxS module published to PyPI. It would be great if that included the YAML files. If not, I think the YAML can be regenerated from the Python file(s) with gen-yaml.

Is there anything I can do to push any of these forward?

ramonawalls commented 2 years ago

@turbomam, I can take care of the first three, but if you can help with preparing the PyPi module, that would be great, and provide some documentation in MAINTAINERS.md so we know how to do it in the future.

turbomam commented 2 years ago

I'm glad to. I just need to know whose PyPI credentials to use. I don't think they have formal support for organizational accounts. I could do it under my PyPI account and delegate to you and a few other GSC people. It definitely shouldn't be just me.

PyPI is pretty easy with poetry

We also have to agree on a name. Would you want just "mixs"? Or mixs-schema?

wdduncan commented 2 years ago

@turbomam I think you can use your credentials, but add Chris, Ramona, and myself as admins (like I did for you and Sujay for the nmdc-schema module).

@ramonawalls do you a PyPI account?

ramonawalls commented 2 years ago

I don't, but I will sign up for one ASAP.

On Tue, Mar 22, 2022 at 2:31 AM Bill Duncan @.***> wrote:

@turbomam https://github.com/turbomam I think you can use your credentials, but add Chris, Ramona, and myself as admins (like I did for you and Sujay for the nmdc-schema module).

@ramonawalls https://github.com/ramonawalls do you a PyPI https://pypi.org/ account?

— Reply to this email directly, view it on GitHub https://github.com/GenomicsStandardsConsortium/mixs/issues/245#issuecomment-1075118338, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAZIHLR7DHSHQVRCQPWWWIDVBG4QJANCNFSM5CKYML3A . You are receiving this because you were mentioned.Message ID: @.***>

ramonawalls commented 2 years ago

I now have a PyPi account using my gmail address. My username is ramonawalls,

ramonawalls commented 1 year ago

@wdduncan and @turbomam I think this issue is obsolete. Can we close it?

wdduncan commented 1 year ago

I don't know. Are we still interested in deploying a pypi package?

turbomam commented 1 year ago

see

https://github.com/GenomicsStandardsConsortium/mixs/issues/630