Continuous integration build not working

[Thodiyil]

Hi,
I am new to Manubot and have set up a local repository on my windows (10, 64bit) that syncs well with the remote repository. I have removed travis appveyor.yml following instructions in setup.md.

Unfortunately, I do not see any manuscript builds in either the local or remote repositories. When I run the build command from the repo root, this is the error:
$ bash ./build/build.sh
Retrieving and processing reference metadata
./build/build.sh: line 16: manubot: command not found

I then ran this command from a conda prompt with the following errors:

conda env create --file build/environment.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

• cairocffi=0.8.0
• pango=1.40.14

When I try to check status:
$ git status
sh: __git_ps1: command not found

Would appreciate any help
Paul

[agitter]

@Thodiyil we can definitely help get your manuscript working in your remote repository because it does not depend on your local environment. Is your repository public? I saw you forked the try-manubot and rootstock repositories, but I did not see a public manuscript repository that you created. Did you start with the configuration step of the setup and then create a new GitHub repository?

Local Manubot builds are not currently supported in Windows. I'm looking into this in #406, but it does not look easy to set up.

[Thodiyil]

Hello Anthony, Thanks for your comments. My repository is private. I finally figured out how to get the manuscript published. I noticed that GitHub actions generated a warning that GitHub pages was not found. I solved this problem by pointing to gh-pages as the source files for GitHub pages under the settings for the repository. This step is not explicitly described in the setup doc and so I proposed the following changes to the setup.md doc. ```` #### Set up GitHub pages In order to enable GitHub Actions to generate and publish the manuscript, it requires you to specify the gh-pages branch as the build source for GitHub Pages. Go to the repository's settings, and then down to GitHub Pages. Select gh-pages as source and /doc as the folder and then save. Your manuscript will then be published at https://$OWNER.github.io/$REPO/. Note that this manuscript will be public even if your repository is private. Once a commit is pushed to the remote site, GitHub Actions automatically takes care of the rest of publishing the manuscript, but the process may take several minutes. ```` One outstanding issue I have not been able to address is how to keep an incomplete manuscript private while still visible to collaborators. It is useful to get a visual of the manuscript as it progresses while still not ready for the public. Your help is much appreciated. Best wishes for the new year. Paul Thodiyil

…

On Fri, Jan 1, 2021 at 9:57 AM Anthony Gitter ***@***.***> wrote: @Thodiyil <https://github.com/Thodiyil> we can definitely help get your manuscript working in your remote repository because it does not depend on your local environment. Is your repository public? I saw you forked the try-manubot and rootstock repositories, but I did not see a public manuscript repository that you created. Did you start with the configuration step <https://github.com/manubot/rootstock/blob/main/SETUP.md#configuration> of the setup and then create a new GitHub repository? Local Manubot builds are not currently supported in Windows. I'm looking into this in #406 <#406>, but it does not look easy to set up. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#405 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPHYUZ6NPMAIDCR64TPJFLSXXPF5ANCNFSM4VPY5Z5Q> .

[Thodiyil]

Hi, The selected folder should be /root rather than /doc. Updated. Paul

…

On Fri, Jan 1, 2021 at 12:56 PM Thodiyil, Paul ***@***.***> wrote: Hello Anthony, Thanks for your comments. My repository is private. I finally figured out how to get the manuscript published. I noticed that GitHub actions generated a warning that GitHub pages was not found. I solved this problem by pointing to gh-pages as the source files for GitHub pages under the settings for the repository. This step is not explicitly described in the setup doc and so I proposed the following changes to the setup.md doc. ```` #### Set up GitHub pages In order to enable GitHub Actions to generate and publish the manuscript, it requires you to specify the gh-pages branch as the build source for GitHub Pages. Go to the repository's settings, and then down to GitHub Pages. Select gh-pages as source and /doc as the folder and then save. Your manuscript will then be published at https://$OWNER.github.io/$REPO/. Note that this manuscript will be public even if your repository is private. Once a commit is pushed to the remote site, GitHub Actions automatically takes care of the rest of publishing the manuscript, but the process may take several minutes. ```` One outstanding issue I have not been able to address is how to keep an incomplete manuscript private while still visible to collaborators. It is useful to get a visual of the manuscript as it progresses while still not ready for the public. Your help is much appreciated. Best wishes for the new year. Paul Thodiyil On Fri, Jan 1, 2021 at 9:57 AM Anthony Gitter ***@***.***> wrote: > @Thodiyil <https://github.com/Thodiyil> we can definitely help get your > manuscript working in your remote repository because it does not depend on > your local environment. Is your repository public? I saw you forked the > try-manubot and rootstock repositories, but I did not see a public > manuscript repository that you created. Did you start with the configuration > step > <https://github.com/manubot/rootstock/blob/main/SETUP.md#configuration> > of the setup and then create a new GitHub repository? > > Local Manubot builds are not currently supported in Windows. I'm looking > into this in #406 <#406>, but > it does not look easy to set up. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#405 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABPHYUZ6NPMAIDCR64TPJFLSXXPF5ANCNFSM4VPY5Z5Q> > . >

[agitter]

The first GitHub Pages deployment is a bit erratic. Sometimes it works without any modification to the settings. Sometimes it requires reselecting "gh-pages branch" as the source. We have a note about that in this setup step, but we can consider recommending selecting the source as the default process. This is a frequent source of confusion.

For private manuscripts (e.g. #358) the best option for sharing with collaborators but not sharing publicly is to give the collaborators access to the private repository and point them to the PDF version of the manuscript in the gh-pages branch: https://github.com/Thodiyil/<my-manuscript>/blob/gh-pages/manuscript.pdf

[Thodiyil]

Many thanks. Nice suggestion for private collaborator access to manuscript. Paul

…

On Sat, Jan 2, 2021 at 8:57 AM Anthony Gitter ***@***.***> wrote: The first GitHub Pages deployment is a bit erratic. Sometimes it works without any modification to the settings. Sometimes it requires reselecting "gh-pages branch" as the source. We have a note about that in this setup step <https://github.com/manubot/rootstock/blob/main/SETUP.md#github-actions>, but we can consider recommending selecting the source as the default process. This is a frequent source of confusion. For private manuscripts (e.g. #358 <#358>) the best option for sharing with collaborators but not sharing publicly is to give the collaborators access to the private repository and point them to the PDF version of the manuscript in the gh-pages branch: https://github.com/Thodiyil/<my-manuscript>/blob/gh-pages/manuscript.pdf — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#405 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPHYUYSLPBCHLZITZ7HB4LSX4Q4VANCNFSM4VPY5Z5Q> .