[Bioc-devel] New Package Submission Workflow Updates!

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Fri Jul 10 18:57:08 CEST 2020


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" <bioc-devel-bounces using r-project.org on behalf of lluis.revilla using gmail.com> 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 <https://bioconductor.org/developers/package-submission/>
    process"
    While on that page under Submission it says: "Submit by opening a new issue
    in the *Bioconductor* Contributions
    <https://github.com/Bioconductor/Contributions/issues/new> repository,
    following the guidelines <https://github.com/Bioconductor/Contributions> 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
    <https://bioconductor.org/developers/how-to/git/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 <Lori.Shepherd using roswellpark.org>
    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
    > git using git.bioconductor.org:packages/<Your Package>. 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
    >
    >
    >
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