Re: [Bioc-devel] New Package Submission Workflow Updates!

[Martin Morgan]

Hi Lluís --

We'll try to incorporate your comments. If you can, it would be great to make 
specific pull requests on 
https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md or 
https://github.com/Bioconductor/bioconductor.org, e.g., at 
https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md
 . There's a dockerfile for processing the Bioconductor web site in the 
repository, but having the web site build correctly is not a requirement for a 
useful pull request!

Thanks for your attention to detail; it's very valuable for the project.

Martin



On 7/8/20, 11:59 AM, "Bioc-devel on behalf of Lluís Revilla" 
 wrote:

Hi Lori and Core Team,

Hope this change will make it easier for all to submit packages to
Bioconductor (and review them).

I have a couple of comments on the documentation. I think that the
extensive documentation available can be confusing and a bit circular.
The README of github.com/Bioconductor/Contributions says: "Review the 
package
submission 
process"
While on that page under Submission it says: "Submit by opening a new issue
in the *Bioconductor* Contributions
 repository,
following the guidelines  of
the README.md file.".
Perhaps a more lineal documentation will be easier to follow and understand
for new and old contributors.

Another thing that caught my attention: on the README under "What to
expect" there is a link to the new package workflow

where it is explained how to set up the local repository to be able to
update the package for the submission. However, it isn't linked from the
package submission website and it only mentions that it is for
modifications **after moderation**. I think this is the ideal situation
(first time submitted packages pass all the check the first time), but
often new submissions must update the package so that the package passes
all the checks in order to be reviewed/moderated. I think this needs to be
mentioned too.

Best,

Lluís

On Wed, 8 Jul 2020 at 17:03, Shepherd, Lori 
wrote:

> Hello Bioconductor Development Community,
>
> The team has made a significant change to the single package builder
> process for submitting new packages to Bioconductor.
>
> Previously, when submitting a new package, the process was to submit on
> github, add a webhook for interactive building on version bump, 
acceptance,
> addition to the git.bioconductor.org repository system, and addition to
> the daily builder manifest.
>
> Now upon submission of your package to github, the preapproval process
> will involve immediately adding packages to git.bioconductor.org.
> Subsequent builds of the package during the review process will be
> triggered by a version bump and push to the upstream repository at
> g...@git.bioconductor.org:packages/. Upon acceptance your
> package will be added to the daily builder manifest for official inclusion
> in Bioconductor.
>
>
> The webhook will be deactivated and no longer trigger builds during the
> review process.
> Any package that was previously submitted (Before July 7th, 2020) will not
> have to worry about the new workflow. You can continue your new package
> review as you have been and we will deactivate your webhook once you are
> through the submission process.
> This will only affect packages newly submitted.
>
> Please ask any questions or concerns you may have.
>
> Thank you
> Lori Shepherd on behalf of the Core Team
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] New Package Submission Workflow Updates!

[Lluís Revilla]

Hi Lori and Core Team,

Hope this change will make it easier for all to submit packages to
Bioconductor (and review them).

I have a couple of comments on the documentation. I think that the
extensive documentation available can be confusing and a bit circular.
The README of github.com/Bioconductor/Contributions says: "Review the package
submission 
process"
While on that page under Submission it says: "Submit by opening a new issue
in the *Bioconductor* Contributions
 repository,
following the guidelines  of
the README.md file.".
Perhaps a more lineal documentation will be easier to follow and understand
for new and old contributors.

Another thing that caught my attention: on the README under "What to
expect" there is a link to the new package workflow

where it is explained how to set up the local repository to be able to
update the package for the submission. However, it isn't linked from the
package submission website and it only mentions that it is for
modifications **after moderation**. I think this is the ideal situation
(first time submitted packages pass all the check the first time), but
often new submissions must update the package so that the package passes
all the checks in order to be reviewed/moderated. I think this needs to be
mentioned too.

Best,

Lluís

On Wed, 8 Jul 2020 at 17:03, Shepherd, Lori 
wrote:

> Hello Bioconductor Development Community,
>
> The team has made a significant change to the single package builder
> process for submitting new packages to Bioconductor.
>
> Previously, when submitting a new package, the process was to submit on
> github, add a webhook for interactive building on version bump, acceptance,
> addition to the git.bioconductor.org repository system, and addition to
> the daily builder manifest.
>
> Now upon submission of your package to github, the preapproval process
> will involve immediately adding packages to git.bioconductor.org.
> Subsequent builds of the package during the review process will be
> triggered by a version bump and push to the upstream repository at
> g...@git.bioconductor.org:packages/. Upon acceptance your
> package will be added to the daily builder manifest for official inclusion
> in Bioconductor.
>
>
> The webhook will be deactivated and no longer trigger builds during the
> review process.
> Any package that was previously submitted (Before July 7th, 2020) will not
> have to worry about the new workflow. You can continue your new package
> review as you have been and we will deactivate your webhook once you are
> through the submission process.
> This will only affect packages newly submitted.
>
> Please ask any questions or concerns you may have.
>
> Thank you
> Lori Shepherd on behalf of the Core Team
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] New Package Submission Workflow Updates!

[Shepherd, Lori]

Hello Bioconductor Development Community,

The team has made a significant change to the single package builder process 
for submitting new packages to Bioconductor.

Previously, when submitting a new package, the process was to submit on github, 
add a webhook for interactive building on version bump, acceptance, addition to 
the git.bioconductor.org repository system, and addition to the daily builder 
manifest.

Now upon submission of your package to github, the preapproval process will 
involve immediately adding packages to git.bioconductor.org. Subsequent builds 
of the package during the review process will be triggered by a version bump 
and push to the upstream repository at g...@git.bioconductor.org:packages/. Upon acceptance your package will be added to the daily builder 
manifest for official inclusion in Bioconductor.


The webhook will be deactivated and no longer trigger builds during the review 
process.
Any package that was previously submitted (Before July 7th, 2020) will not have 
to worry about the new workflow. You can continue your new package review as 
you have been and we will deactivate your webhook once you are through the 
submission process.
This will only affect packages newly submitted.

Please ask any questions or concerns you may have.

Thank you
Lori Shepherd on behalf of the Core Team



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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