GitHub Actions workflow for building and deployment #297

dhimmel · 2020-01-02T20:15:23Z

Switch to GitHub actions as the primary CI service for new manuscripts, while retaining backwards compatibility with existing Travis manuscripts.

Todo:

update manubot python package to detect GitHub CI variables

to test github actions

Prototyping manubot/rootstock#297 Use manubot.yaml from https://github.com/manubot/rootstock/blob/27462d4eea1f1ce961e25d9e043460b55b42ea68/.github/workflows/manubot.yaml

Based on code prototyped at greenelab/iscb-diversity-manuscript@36af311 greenelab/iscb-diversity-manuscript@f6f921f greenelab/iscb-diversity-manuscript@571e561

Based on the in-progress GitHub Actions workflow in manubot/rootstock#297

merges #4 closes #3 Based on the in-progress GitHub Actions workflow in manubot/rootstock#297

dhimmel · 2020-01-14T20:30:29Z

.github/workflows/manubot.yaml

+          github.event_name == 'push' &&
+          job.status == 'success')
+        env:
+          MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }}


perhaps we can also test if secrets.MANUBOT_SSH_PRIVATE_KEY is set and if not, provide a better error message

Yes, better error messages would be valuable. Setting up CI has been a common source of errors.

Okay I will save this for a subsequent PR. Possibly that also removes the legacy travis deploy key method of deployment.

dhimmel · 2020-01-14T23:01:01Z

This action is alive and working (including deployment) at:

One question is whether we want to switch to GitHub Actions as the primary method CI method for rootstock and future clones. I think we probably do, since it reduces the setup from using two services (GitHub and Travis) to just one (GitHub). It's also more aligned with the longterm roadmap.

Unfortunately, we still have to manually generate a deploy key to push to GitHub until since secrets.GITHUB_TOKEN only triggers GitHub Pages pages builds on private (not public) repos.

One option if we switch to actions as the primary CI going forward, is that we can add something like the following to the cleanup step of setup:

git rm .travis.yml .appveyor.yml ci/install.sh

Or do we want to remove this files from rootstock, thereby nudging existing users to switch?

vincerubinetti · 2020-01-15T15:08:04Z

.github/workflows/manubot.yaml

@@ -0,0 +1,40 @@
+name: Manubot


Maybe this could have a more descriptive name, since the user's might theoretically poke around and see it?

Maybe Manubot Continuous Integration or Manubot CI or just Manubot Build and Deploy Manuscript

Maybe the file name could be manubot-ci.yml or manubot-build-and-deploy.yml

Finally, is "manubot" necessary in these names since we're already in the context of manubot, being in a manubot repository.

is "manubot" necessary in these names since we're already in the context of manubot

I am thinking about the situation where someone creates a repository with a manuscript as well as other stuff. The other stuff may need additional workflows. Those other workflows may have nothing to do with Manubot... for example perhaps one runs an R analysis, another one spellchecks pull requests, another makes sure PR authors have signed a contributor license agreement, another one automatically merges approved PRs. In these cases, I envision you want workflow names that best differentiate the specific workflow.

Since the name "Manubot" is used in the context of a workflow, I think adding CI or "Continuous Integration" afterwards is a bit redundant. My understanding is that workflows are basically CI, and perhaps GitHub wanted to get away from the CI terminology because it's a bit confusing.

One final point is that I see the GitHub action workflow as become the main way people run manubot. The rest of the manuscript repo will be their content / config files. The action is actually "the manubot", or at least the place where "the manubot" runs.

vincerubinetti · 2020-01-15T15:09:17Z

.github/workflows/manubot.yaml

@@ -0,0 +1,40 @@
+name: Manubot


Maybe you want to add a status badge to the readme:
![](https://github.com/manubot/rootstock/workflows/manubot/badge.svg)

Oh wait, that wont refer to the specific manuscript. Would a relative image link work? ![](workflows/manubot/badge.svg)

The relative image link won't work, first because it's an SVG and second because that is not a file path relative to the repo content.

We could use the absolute URL. It would get rebranded to the manubot instance from manubot/rootstock during setup. Do you think badges are important given that you can now see the check or fail mark from the main page? I guess it makes it more clear for those unfamiliar with CI / GitHub actions?

I do think that badges are more obvious to a larger audience that may not know to look for the pass/fail icons.

vincerubinetti · 2020-01-15T15:11:21Z

.github/workflows/manubot.yaml

+      - master
+jobs:
+  build:
+    name: Build Manuscript


Maybe Build and Deploy Manuscript to be more accurate, and to avoid duplicate name of the Build Manuscript step below.

FWIW I think you can omit this and in the Actions tab it will just show up as the config file name at the top.

vincerubinetti · 2020-01-15T15:12:31Z

.github/workflows/manubot.yaml

+        with:
+          name: output
+          path: output
+      - name: Deploy


Maybe Deploy Manuscript to keep in line with the [verb] [noun] pattern of the other step names above.

Yes, I like this suggestion too

ci/deploy.sh

resovle conflicts

AppVeyorBot · 2020-01-15T18:14:52Z

AppVeyor build 1.0.86 for commit 70398be by @dhimmel is now complete. The rendered manuscript from this build is temporarily available for download at:

agitter

These changes look good to me, and I support the decision to make GitHub Actions the default but leave optional instructions for using Travis CI.

In addition to my small comments, there are a few open comments from @vincerubinetti we can resolve before merging.

agitter · 2020-01-17T19:17:14Z

.github/workflows/manubot.yaml

+          GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
+        shell: bash --login {0}
+        run: bash build/build.sh
+      - name: Upload Artifacts


Will this eventually replace the AppVeyor artifacts and notification messages?

The main difference now is that it doesn't provide notification messages (possibly it could not sure). Although I'm not sure I love the messages since they get overwhelming.

So yeah, I think it is a satisfactory substitute, but requires users are aware of the feature, since you have to navigate to it.

agitter · 2020-01-17T19:20:55Z

README.md

@@ -4,7 +4,6 @@

 [![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://manubot.github.io/rootstock/)
 [![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://manubot.github.io/rootstock/manuscript.pdf)
-[![Build Status](https://travis-ci.com/manubot/rootstock.svg?branch=master)](https://travis-ci.com/manubot/rootstock)


I like the suggestion to include a GitHub Actions badge here. Because we can't adaptively show the Travis or GitHub Actions badge based on which CI service is being used, would we default to GitHub's?

I think it's okay to have both. Travis CI fails gracefully

GitHub's doesn't. Note I'll have to merge to even see whether the GitHub badge works.

agitter · 2020-01-17T19:23:46Z

SETUP.md

+
+GitHub Actions is the default service for new manucripts since it's easiest to setup.
+We recommend using either GitHub Actions or Travis CI, but not both to avoid deploying manuscripts multiple times.
+AppVeyor can be used in addition to GitHub Actions or Travis CI to comment on pull request with download links to renderred PDFs.


"renderred" -> "rendered" here and in the next line.

agitter · 2020-01-17T19:25:58Z

SETUP.md

+# Print the URL for adding the private key to GitHub
+echo "https://github.com/$OWNER/$REPO/settings/secrets"
+
+# Print the encoded private key for copy-pasting to Travis CI


"Travis CI" -> "GitHub"

agitter · 2020-01-17T19:27:31Z

SETUP.md

+
+### GitHub Actions
+
+If you plan on only using GitHub actions, you can remove configuration files for other CI services:


I think this is fine for now instead of removing the files from rootstock. Some users may prefer to continue using Travis CI for reasons we can't anticipate.

agitter · 2020-01-17T19:28:04Z

SETUP.md

 Check the "Allow write access" box below.
 Finally, click "Add key".

-#### Add the private key to Travis CI
+#### Add the private key to GitHub


I didn't test these steps, but they are easy to understand.

merges manubot/rootstock#297

dhimmel added 4 commits January 2, 2020 15:14

Add github workflow

a63b2b0

to test github actions

Upload PDF artifact

2ed24a5

rename workflow

915b2fc

Add deployment

27462d4

dhimmel added 2 commits January 14, 2020 14:36

Fix deployment

771a9ea

Based on code prototyped at greenelab/iscb-diversity-manuscript@36af311 greenelab/iscb-diversity-manuscript@f6f921f greenelab/iscb-diversity-manuscript@571e561

Fix artifacts .zip.zip

84df9b3

dhimmel mentioned this pull request Jan 14, 2020

Setting up GitHub actions to build the manuscript data2health/contributorship#3

Closed

dhimmel added a commit to data2health/contributorship that referenced this pull request Jan 14, 2020

Enable GitHub actions

2f3ad78

Based on the in-progress GitHub Actions workflow in manubot/rootstock#297

dhimmel mentioned this pull request Jan 14, 2020

Enable GitHub actions data2health/contributorship#4

Merged

dhimmel added a commit to data2health/contributorship that referenced this pull request Jan 14, 2020

Enable GitHub actions (#4)

8ef2847

merges #4 closes #3 Based on the in-progress GitHub Actions workflow in manubot/rootstock#297

dhimmel changed the title ~~Add github workflow to test github actions~~ GitHub Actions workflow for building and deployment Jan 14, 2020

dhimmel commented Jan 14, 2020

View reviewed changes

dhimmel added 2 commits January 14, 2020 17:13

GITHUB_PULL_REQUEST_SHA

dccf6df

simplify line

c5f0007

dhimmel requested review from agitter and vincerubinetti January 14, 2020 23:01

vincerubinetti reviewed Jan 15, 2020

View reviewed changes

dhimmel added 2 commits January 15, 2020 13:09

Update docs for GitHub Actions default

20dac58

Merge branch 'master' into actions

70398be

resovle conflicts

dhimmel mentioned this pull request Jan 15, 2020

A simplified & minimal template for manuscripts manubot/template#1

Open

vincerubinetti approved these changes Jan 17, 2020

View reviewed changes

agitter reviewed Jan 17, 2020

View reviewed changes

Revisions based on PR reviews

16d9caa

dhimmel merged commit f072e93 into manubot:master Jan 17, 2020

dhimmel deleted the actions branch January 17, 2020 20:35

ploegieku added a commit to ploegieku/2023-functional-homology-paper that referenced this pull request Aug 6, 2024

GitHub Actions workflow for building and deployment

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merges manubot/rootstock#297

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GitHub Actions workflow for building and deployment #297

GitHub Actions workflow for building and deployment #297

dhimmel commented Jan 2, 2020 •

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		### GitHub Actions

		If you plan on only using GitHub actions, you can remove configuration files for other CI services:

GitHub Actions workflow for building and deployment #297

GitHub Actions workflow for building and deployment #297

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dhimmel commented Jan 2, 2020 •

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