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
[Bioc-devel] Best practice use pkgdown, docker with Bioconductor
6 messages · Murphy, Alan E, Andris Jankevics, Jianhong Ou, Ph.D. +2 more
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 <bioc-devel-bounces at r-project.org> On Behalf Of Murphy, Alan E Sent: 06 April 2021 16:24 To: bioc-devel at 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 _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 at v1 with: username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_TOKEN }} repository: your/docker/path tag_with_ref: true tag_with_sha: true tags: latest [https://avatars.githubusercontent.com/u/5640707?s=400&v=4]<https://github.com/jianhong/HMMtBroadPeak/tree/staging> jianhong/HMMtBroadPeak<https://github.com/jianhong/HMMtBroadPeak/tree/staging> call broad peak by a modified Baum_Welch algorithm that supports multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak github.com ?
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Murphy, Alan E <a.murphy at imperial.ac.uk>
Sent: Tuesday, April 6, 2021 10:24 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Sent: Tuesday, April 6, 2021 10:24 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Hi all, I'm working on the development of (EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$ ] 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 at r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPX4panddY$
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 <A.Jankevics at 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 <bioc-devel-bounces at r-project.org> On Behalf Of Murphy, Alan E Sent: 06 April 2021 16:24 To: bioc-devel at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 <biodavidjm at gmail.com>
Sent: 06 April 2021 17:53
To: Andris Jankevics <A.Jankevics at bham.ac.uk>
Cc: Murphy, Alan E <a.murphy at imperial.ac.uk>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
Sent: 06 April 2021 17:53
To: Andris Jankevics <A.Jankevics at bham.ac.uk>
Cc: Murphy, Alan E <a.murphy at imperial.ac.uk>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor
This email from biodavidjm at 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 <A.Jankevics at bham.ac.uk<mailto:A.Jankevics at 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 <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>> On Behalf Of Murphy, Alan E Sent: 06 April 2021 16:24 To: bioc-devel at r-project.org<mailto:bioc-devel at 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 at r-project.org<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Thank you Jianhong for the clean solution. I would encourage Alan to check out the biocthis::use_bioc_github_action to set up the Docker build and pkgdown. Best, Marcel
On 4/6/21 12:48 PM, Jianhong Ou, Ph.D. wrote:
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 at v1 with: username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_TOKEN }} repository: your/docker/path tag_with_ref: true tag_with_sha: true tags: latest [https://avatars.githubusercontent.com/u/5640707?s=400&v=4]<https://github.com/jianhong/HMMtBroadPeak/tree/staging> jianhong/HMMtBroadPeak<https://github.com/jianhong/HMMtBroadPeak/tree/staging> call broad peak by a modified Baum_Welch algorithm that supports multi-dimensional Student's t emission. - jianhong/HMMtBroadPeak github.com ?
________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Murphy, Alan E <a.murphy at imperial.ac.uk> Sent: Tuesday, April 6, 2021 10:24 AM To: bioc-devel at r-project.org <bioc-devel at r-project.org> Subject: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor Hi all, I'm working on the development of (EWCE)[https://urldefense.com/v3/__https://github.com/NathanSkene/EWCE__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPXEq7ZeFM$ ] 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 at r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPX4panddY$ [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
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