Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Thank you all for your suggestions! Can anyone from the Bioconductor team comment on whether David's approach to use the .Rbuildignore file is valid for submission to Bioconductor? Obviously, this will would the least work so if possible, I would like to use this. Kind regards, Alan. From: David Jimenez-Morales Sent: 06 April 2021 17:53 To: Andris Jankevics Cc: Murphy, Alan E ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor This email from biodavi...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Hi there, What about including the "_pkgdown.yml" file in the ".Rbuildignore" file? Would this somehow help "avoiding any issues with these external configurations and Bioconductor"? Thanks David On Tue, Apr 6, 2021 at 5:05 AM Andris Jankevics mailto:a.jankev...@bham.ac.uk>> wrote: Haven't used this, but I think you could use Github Action to merge master branch in the branch for pkgdown whenever changes on master are made. https://github.com/marketplace/actions/merge-branch BW, Andris -Original Message- From: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> On Behalf Of Murphy, Alan E Sent: 06 April 2021 16:24 To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor Hi all, I'm working on the development of (EWCE)[https://github.com/NathanSkene/EWCE] and have a question regarding a reviewer note. My package currently uses pkgdown to create a website through the master branch. I also create and push a new docker image from the main branch when the package successfully builds on travis. My reviewer has asked to remove the related files _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues with these external configurations and Bioconductor. My reviewer has suggested to put these in another branch. It's not clear to me how best to do this? Ideally, if they are in a separate branch, is there a way to run them once there is an update and successful build on the master branch? If this isn't possible, is there a way to avoid manually duplicating new changes in the master branch in this separate branch and instead, just push the changes from master to this separate branch and trigger pkgdown and docker build that way? Sorry, I realise this last part more so relates to github commands but I was thinking someone else has probably already foudn a way around this issue. Kind regards, Alan. Alan Murphy Bioinformatician Neurogenomics lab UK Dementia Research Institute Imperial College London [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Hi there, What about including the "_pkgdown.yml" file in the ".Rbuildignore" file? Would this somehow help "avoiding any issues with these external configurations and Bioconductor"? Thanks David On Tue, Apr 6, 2021 at 5:05 AM Andris Jankevics wrote: > Haven't used this, but I think you could use Github Action to merge master > branch in the branch for pkgdown whenever changes on master are made. > > https://github.com/marketplace/actions/merge-branch > > BW, > Andris > > -Original Message- > From: Bioc-devel On Behalf Of Murphy, > Alan E > Sent: 06 April 2021 16:24 > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor > > Hi all, > > I'm working on the development of (EWCE)[ > https://github.com/NathanSkene/EWCE] and have a question regarding a > reviewer note. My package currently uses pkgdown to create a website > through the master branch. I also create and push a new docker image from > the main branch when the package successfully builds on travis. > > My reviewer has asked to remove the related files > _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any > issues with these external configurations and Bioconductor. My reviewer has > suggested to put these in another branch. It's not clear to me how best to > do this? Ideally, if they are in a separate branch, is there a way to run > them once there is an update and successful build on the master branch? If > this isn't possible, is there a way to avoid manually duplicating new > changes in the master branch in this separate branch and instead, just push > the changes from master to this separate branch and trigger pkgdown and > docker build that way? Sorry, I realise this last part more so relates to > github commands but I was thinking someone else has probably already foudn > a way around this issue. > > Kind regards, > Alan. > > Alan Murphy > Bioinformatician > Neurogenomics lab > UK Dementia Research Institute > Imperial College London > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Hi Alan,
Here is my solution: https://github.com/jianhong/HMMtBroadPeak/tree/staging.
Hope this help.
You may want to add one more step after check and before pkgdown to push to
your dockerhub by:
- name: push to docker
- uses: docker/build-push-action@v1
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_TOKEN }}
repository: your/docker/path
tag_with_ref: true
tag_with_sha: true
tags: latest
[https://avatars.githubusercontent.com/u/5640707?s=400=4]
jianhong/HMMtBroadPeak
call broad peak by a modified Baum_Welch algorithm that supports
multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak
github.com
From: Bioc-devel on behalf of Murphy, Alan E
Sent: Tuesday, April 6, 2021 10:24 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Hi all,
I'm working on the development of
(EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$
] and have a question regarding a reviewer note. My package currently uses
pkgdown to create a website through the master branch. I also create and push a
new docker image from the main branch when the package successfully builds on
travis.
My reviewer has asked to remove the related files
_pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues
with these external configurations and Bioconductor. My reviewer has suggested
to put these in another branch. It's not clear to me how best to do this?
Ideally, if they are in a separate branch, is there a way to run them once
there is an update and successful build on the master branch? If this isn't
possible, is there a way to avoid manually duplicating new changes in the
master branch in this separate branch and instead, just push the changes from
master to this separate branch and trigger pkgdown and docker build that way?
Sorry, I realise this last part more so relates to github commands but I was
thinking someone else has probably already foudn a way around this issue.
Kind regards,
Alan.
Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
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https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Haven't used this, but I think you could use Github Action to merge master branch in the branch for pkgdown whenever changes on master are made. https://github.com/marketplace/actions/merge-branch BW, Andris -Original Message- From: Bioc-devel On Behalf Of Murphy, Alan E Sent: 06 April 2021 16:24 To: bioc-devel@r-project.org Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor Hi all, I'm working on the development of (EWCE)[https://github.com/NathanSkene/EWCE] and have a question regarding a reviewer note. My package currently uses pkgdown to create a website through the master branch. I also create and push a new docker image from the main branch when the package successfully builds on travis. My reviewer has asked to remove the related files _pkgdown.yml,Dockerfileanddocker_push from my master branch to avoid any issues with these external configurations and Bioconductor. My reviewer has suggested to put these in another branch. It's not clear to me how best to do this? Ideally, if they are in a separate branch, is there a way to run them once there is an update and successful build on the master branch? If this isn't possible, is there a way to avoid manually duplicating new changes in the master branch in this separate branch and instead, just push the changes from master to this separate branch and trigger pkgdown and docker build that way? Sorry, I realise this last part more so relates to github commands but I was thinking someone else has probably already foudn a way around this issue. Kind regards, Alan. Alan Murphy Bioinformatician Neurogenomics lab UK Dementia Research Institute Imperial College London [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
