manubot
Continuous integration build not working
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
@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.
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 [email protected] 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 https://github.com/manubot/rootstock/issues/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 https://github.com/manubot/rootstock/issues/405#issuecomment-753326185, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABPHYUZ6NPMAIDCR64TPJFLSXXPF5ANCNFSM4VPY5Z5Q .
Hi, The selected folder should be /root rather than /doc. Updated.
Paul
On Fri, Jan 1, 2021 at 12:56 PM Thodiyil, Paul [email protected] 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 [email protected] 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 https://github.com/manubot/rootstock/issues/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 https://github.com/manubot/rootstock/issues/405#issuecomment-753326185, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABPHYUZ6NPMAIDCR64TPJFLSXXPF5ANCNFSM4VPY5Z5Q .
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
Many thanks. Nice suggestion for private collaborator access to manuscript.
Paul
On Sat, Jan 2, 2021 at 8:57 AM Anthony Gitter [email protected] 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 https://github.com/manubot/rootstock/issues/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/
/blob/gh-pages/manuscript.pdf — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/manubot/rootstock/issues/405#issuecomment-753476834, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABPHYUYSLPBCHLZITZ7HB4LSX4Q4VANCNFSM4VPY5Z5Q .