Re: [Bioc-devel] Multiple projects for submission to Bioconductor

[Ali Sajid Imami]

Hi,

Thank you for the detailed response. I’ll make sure I dot all the I’s and
cross all the T’s. I’ll also reach out to the author of Biocthis to cross
verify things.

Looking forward to the submission process and thank you and the
bioconductor team for this amazing service.

On Mon, Jan 2, 2023 at 8:12 PM Vincent Carey 
wrote:

>
>
> On Mon, Jan 2, 2023 at 7:51 PM Ali Sajid Imami 
> wrote:
>
>> Hi Colleagues,
>>
>> I am currently a PhD student in Bioinformatics at the University of
>> Toledo,
>> College of Medicine and Life Sciences. I am working in the cognitive
>> disorders research lab (https://cdrl-ut.org) and we have been actively
>> developing multiple packages. We are particularly interested in
>> building data and analysis packages for Kinase Activity analysis.
>>
>> We have a number of packages that we would like to submit to Bioconductor
>> for acceptance. I am currently in the process of streamlining the
>> packages,
>> making sure their dependencies are clearly defined and extracting large
>> datasets into their own data packages.
>>
>> I had a couple of questions regarding the submissions:
>>
>> 1. At our lab we rely heavily on Github Actions for continuous integration
>> and delivery. Are the actions outlined in the biocthis (
>> https://bioconductor.org/packages/release/bioc/html/biocthis.html)
>> package
>> up to date and something we can reliably build on?
>>
>
> Thank you for your note.
>
> I would say the answer here is "yes", but you could also check with the
> author of biocthis to see whether there are any concerns to be aware of.
>
>
>> 2. We have quite a few packages and there may be some packages that would
>> be better to go into the same release. Is it possible to submit them all
>> separately but have their review process be streamlined, collectively?
>>
>
> It is impossible to say without more information.  We have limited
> personnel
> for reviewing.  There is an approach for submitting related packages, see
> here
> 
> .
>
> 3. Is Bioconductor's git infrastructure set up to update from our github
>> repo or is there a solution we can build to push our new "release" to the
>> bioconductor git infra after the integration tests in github actions are
>> completed?
>>
>
> I suspect you could accomplish update-git-on-push-to-github but perhaps
> further discussion is needed.  At this time our build system works with git
> repositories that are jointly managed by us and by the package maintainer.
> Maintainers are responsible for ensuring that the git repository is up to
> date.
>
> Sincerely,
> Vincent Carey
>
>
>> Thank you.
>>
>>
>> Regards,
>> Dr. Ali Sajid Imami
>> LinkedIn 
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> The information in this e-mail is intended only for th...{{dropped:23}}

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Re: [Bioc-devel] Multiple projects for submission to Bioconductor

[Vincent Carey]

On Mon, Jan 2, 2023 at 7:51 PM Ali Sajid Imami 
wrote:

> Hi Colleagues,
>
> I am currently a PhD student in Bioinformatics at the University of Toledo,
> College of Medicine and Life Sciences. I am working in the cognitive
> disorders research lab (https://cdrl-ut.org) and we have been actively
> developing multiple packages. We are particularly interested in
> building data and analysis packages for Kinase Activity analysis.
>
> We have a number of packages that we would like to submit to Bioconductor
> for acceptance. I am currently in the process of streamlining the packages,
> making sure their dependencies are clearly defined and extracting large
> datasets into their own data packages.
>
> I had a couple of questions regarding the submissions:
>
> 1. At our lab we rely heavily on Github Actions for continuous integration
> and delivery. Are the actions outlined in the biocthis (
> https://bioconductor.org/packages/release/bioc/html/biocthis.html) package
> up to date and something we can reliably build on?
>

Thank you for your note.

I would say the answer here is "yes", but you could also check with the
author of biocthis to see whether there are any concerns to be aware of.


> 2. We have quite a few packages and there may be some packages that would
> be better to go into the same release. Is it possible to submit them all
> separately but have their review process be streamlined, collectively?
>

It is impossible to say without more information.  We have limited personnel
for reviewing.  There is an approach for submitting related packages, see
here

.

3. Is Bioconductor's git infrastructure set up to update from our github
> repo or is there a solution we can build to push our new "release" to the
> bioconductor git infra after the integration tests in github actions are
> completed?
>

I suspect you could accomplish update-git-on-push-to-github but perhaps
further discussion is needed.  At this time our build system works with git
repositories that are jointly managed by us and by the package maintainer.
Maintainers are responsible for ensuring that the git repository is up to
date.

Sincerely,
Vincent Carey


> Thank you.
>
>
> Regards,
> Dr. Ali Sajid Imami
> LinkedIn 
>
> [[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] Multiple projects for submission to Bioconductor

[Ali Sajid Imami]

Hi Colleagues,

I am currently a PhD student in Bioinformatics at the University of Toledo,
College of Medicine and Life Sciences. I am working in the cognitive
disorders research lab (https://cdrl-ut.org) and we have been actively
developing multiple packages. We are particularly interested in
building data and analysis packages for Kinase Activity analysis.

We have a number of packages that we would like to submit to Bioconductor
for acceptance. I am currently in the process of streamlining the packages,
making sure their dependencies are clearly defined and extracting large
datasets into their own data packages.

I had a couple of questions regarding the submissions:

1. At our lab we rely heavily on Github Actions for continuous integration
and delivery. Are the actions outlined in the biocthis (
https://bioconductor.org/packages/release/bioc/html/biocthis.html) package
up to date and something we can reliably build on?
2. We have quite a few packages and there may be some packages that would
be better to go into the same release. Is it possible to submit them all
separately but have their review process be streamlined, collectively?
3. Is Bioconductor's git infrastructure set up to update from our github
repo or is there a solution we can build to push our new "release" to the
bioconductor git infra after the integration tests in github actions are
completed?

Thank you.


Regards,
Dr. Ali Sajid Imami
LinkedIn 

[[alternative HTML version deleted]]

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