Updates to Readme #222

vsmalladi · 2024-10-24T21:17:11Z

Updates to Readme and cleanup of documentation for ease of contribution to code base.

…lopment.

uniqueg · 2024-10-28T13:55:25Z

CONTRIBUTING.md

+
+This version replaces references to Travis CI with GitHub Actions while maintaining the original meaning and intent.


Do we need this? Travis hasn't been in use for a long time, so I don't think anyone will complain about this info changing without this disclaimer.

If you wanna keep it, it probably makes sense to place it as a comment/quote (with >) below the links that follow the colon from the previous statment.

uniqueg · 2024-10-28T13:56:58Z

CONTRIBUTING.md

 The post v1.0.0 voting group include stakeholders, such as server and client implementors.
 The membership of this group will be established as part of the v1.0.0 release.


We should probably actually do this and check with the Cloud WS to make sure it's in line with GA4GH regulations. For example, I think GA4GH DPs might need to retain voting rights.

Also, I think we can remove the pre-TES v1.0.0 stuff, because we're already passed that. And then we can remove the explicit "post" as well, and can just name the section "Voting Procedure".

Finally, we might want to move the entire section to GOVERNANCE.md and only keep the reference here (because, as it is, this very important info is now missing from GOVERNANCE.md).

Fix this too

uniqueg · 2024-10-28T13:57:52Z

GOVERNANCE.md

+
+| Name               | Organization       | github                  |
+|:-------------------|:-------------|:------------------
+| Kyle Ellrot        | oregon health and science university | [kellrott](https://github.com/kellrott) |


Maybe capitalize Oregon Health and Science University?

Might also be good to add links, e.g., https://www.ohsu.edu/

Actually, at second thought: Perhaps we should replace the "API Champions" with "Product leads" and link to the current product leads at https://www.ga4gh.org/product/task-execution-service-tes/

That way, we don't have to update this file when leads change (which we might forget).

And for getting in contact, we could put the TES email address I think we have (the mailing list).

uniqueg · 2024-10-28T13:58:38Z

GOVERNANCE.md

+|:-------------------|:-------------|:------------------
+| Kyle Ellrot        | oregon health and science university | [kellrott](https://github.com/kellrott) |
+| Venkat Malladi     | Microsoft        | [vsmalladi](https://github.com/vsmalladi) |
+| Alex Kanitz        | ELIXIR        | [uniqueg](https://github.com/uniqueg) |


If you wanna keep this table, please replace ELIXIR with "Swiss Institute of Bioinformatics / ELIXIR Switzerland" and use this URL: https://www.sib.swiss/

uniqueg · 2024-10-28T14:05:11Z

CONTRIBUTING.md

@@ -13,7 +13,11 @@ Suggested changes to this schema can be initiated as [**Issues**](https://github

 Even those with write access to the main repository should in general create pull request branches within their own forks. This way when the main repository is forked again, the new fork is created with a minimum of extraneous volatile branches.

-> To facilitate review of external pull requests, users are encouraged to activate [**Travis CI**](https://travis-ci.org/) to monitor the build status (documentation, Swagger UI) of their fork. By following the documentation for [deployment to GitHub Pages](https://docs.travis-ci.com/user/deployment/pages/) and adding a `$GITHUB_TOKEN` environment variable to their repo configuration, pushes to the forked repo should be viewable relative to `https://[user-or-org].github.io/workflow-execution-service-schemas/preview/<branch>/`:
+
+> To facilitate the review of external pull requests, users are encouraged to activate [**GitHub Actions**](https://github.com/features/actions) to monitor the build status (documentation, Swagger UI) of their fork. By following the documentation for [deployment to GitHub Pages](https://docs.github.com/en/actions/publishing-packages/deploying-to-github-pages) and adding a `$GITHUB_TOKEN` environment variable to their repository configuration, pushes to the forked repository will be viewable at `https://[user-or-org].github.io/workflow-execution-service-schemas/preview/<branch>/`:


I think it would actually be good if you did that so that we could see how the built docs look like with this PR, @vsmalladi ;-)

uniqueg · 2024-10-28T14:09:11Z

README.md

-![release_badge](https://img.shields.io/github/v/tag/ga4gh/task-execution-schemas)
+![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg) [![release_badge](https://img.shields.io/github/v/tag/ga4gh/task-execution-schemas?label=latest%20release&logo=github&style=flat)](https://github.com/ga4gh/task-execution-schemas/releases)
+
+`master` branch status


Do we maybe wanna use the migration to v1.0.0 as an opportunity to rename master to main to be in line with current naming trends?

Good idea. I think we need to create main and then delete master first

uniqueg · 2024-10-28T14:11:54Z

README.md

+
+| Build  | CI  | Open API Validator |
+|------------------------|-----------|--------------------|
+| ![Build Status](https://github.com/ga4gh/task-execution-schemas/actions/workflows/build.yml/badge.svg?branch=master) | ![CI Status](https://github.com/ga4gh/task-execution-schemas/actions/workflows/ci.yml/badge.svg?branch=master) | [![Open API Validator](https://img.shields.io/badge/OpenAPI-Validator-blue)](http://online.swagger.io/validator?url=https://raw.githubusercontent.com/ga4gh/task-execution-schemas/master/openapi/task_execution_service.openapi.yaml) |


Replace http with https

uniqueg · 2024-10-28T14:15:38Z

README.md


-The [Global Alliance for Genomics and Health](http://genomicsandhealth.org/) is an international coalition, formed to enable the sharing of genomic and clinical data.
+[GA4GH](http://genomicsandhealth.org/) is an international coalition, formed to enable the sharing of genomic and clinical data.


I think the canonical link is https://ga4gh.org/, so maybe better to use that (in the line above as well).

uniqueg · 2024-10-28T14:16:41Z

README.md


 Cloud Work Stream
 -----------------

-The [Cloud Work Stream](https://ga4gh.cloud) helps the genomics and health communities take full advantage of modern cloud environments.
-Our initial focus is on “bringing the algorithms to the data”, by creating standards for defining, sharing, and executing portable workflows.
+The [Cloud Work Stream](https://ga4gh.cloud) helps the genomics and health communities take full advantage of modern cloud environments. Our initial focus is on “bringing the algorithms to the data”, by creating standards for defining, sharing, and executing portable workflows.g


Since the launch of the new GA4GH website, the official link for the Cloud WS is https://www.ga4gh.org/work_stream/cloud/, so best to replace.

uniqueg · 2024-10-28T14:19:04Z

README.md

+
+You can also examine the specification in the [Swagger Editor](https://editor.swagger.io/?url=https://ga4gh.github.io/task-execution-schemas/openapi.yaml).  
+
+*If you are using a version from a non-develop branch, please load the JSON manually.* You can preview the documentation from the [gh-openapi-docs](https://github.com/ga4gh/gh-openapi-docs) for the development branch [here](https://ga4gh.github.io/task-execution-schemas/preview/develop/docs/index.html).


I would probably remove the

[...] from the gh-openapi-docs [...]

part, because the average user doesn't need to check out that branch (or even know about it). A reference to the built docs for the development branch should be enough.

Also, you can merge that statement with the next section as an example for how people can get branch-specific previews of the docs.

vsmalladi · 2024-10-28T17:06:39Z

Take a look now

vsmalladi added 16 commits October 24, 2024 12:18

Update to be linked to the latest tag.

42bb695

Fix repo.

a0da756

Add back build and spec badges.

93b1e3a

Check with develop.

0c05b27

Testing ci badge.

d04eca1

Testing ci badge.

6288dc4

check validtor.

c4f8d98

Make a table and visualize all on the status for both master and deve…

244a8b8

…lopment.

Change the develop branch name.

4bf02c6

Reword description.

f6495ef

Fix formating and full stops.

d9ebe9c

Add rewording.

c02bcb9

Update JSON.

a248cde

Remove Possible future enhancemnts section.

b287476

Add Governance.

7f253a0

Add in license.

9b19cf7

vsmalladi requested a review from uniqueg October 24, 2024 21:17

Fix badges.

8614de7

uniqueg requested changes Oct 28, 2024

View reviewed changes

vsmalladi added 11 commits October 28, 2024 09:25

Simplify build.

07cbe93

Build in PR.

aab9eba

Change the plugin to be used so doesnt require secrets.

a55038c

Fix security.

ab2f679

Fix spelling error.

7e0f90c

update for security.

15c3088

Update links.

31dbd36

Fix some wording.

6834190

Fix build.

3d1733b

Fix build.

6209a56

Fix build.

fc905dd

Fix build syntax.

e482eac

vsmalladi requested a review from uniqueg October 28, 2024 17:06

Add in push.

04550ed

uniqueg approved these changes Oct 28, 2024

View reviewed changes

Fix voting.

4592b2a

vsmalladi merged commit 639ca06 into ga4gh:develop Oct 28, 2024
7 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Updates to Readme #222

Updates to Readme #222

vsmalladi commented Oct 24, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

vsmalladi Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

vsmalladi Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

uniqueg Oct 28, 2024

vsmalladi commented Oct 28, 2024


		This version replaces references to Travis CI with GitHub Actions while maintaining the original meaning and intent.

		The post v1.0.0 voting group include stakeholders, such as server and client implementors.
		The membership of this group will be established as part of the v1.0.0 release.


		The [Global Alliance for Genomics and Health](http://genomicsandhealth.org/) is an international coalition, formed to enable the sharing of genomic and clinical data.
		[GA4GH](http://genomicsandhealth.org/) is an international coalition, formed to enable the sharing of genomic and clinical data.


		You can also examine the specification in the [Swagger Editor](https://editor.swagger.io/?url=https://ga4gh.github.io/task-execution-schemas/openapi.yaml).

		If you are using a version from a non-develop branch, please load the JSON manually. You can preview the documentation from the [gh-openapi-docs](https://github.com/ga4gh/gh-openapi-docs) for the development branch [here](https://ga4gh.github.io/task-execution-schemas/preview/develop/docs/index.html).

Updates to Readme #222

Updates to Readme #222

Conversation

vsmalladi commented Oct 24, 2024

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

vsmalladi commented Oct 28, 2024