Fix the app deployments #41

vedhav · 2023-08-01T10:45:19Z

Changes made

Removes renv from all the nine apps
Adds front-end tests for these seven apps (all except early-dev and python):
RNA-seq, basic-teal, efficacy, exploratory, longitudinal, patient-profile, safety
Updates the deploy.yaml workflow:
1. Runs the cypress tests when they are present in the app directory
2. Deploy two versions of apps to RSConnect. NEST_<APPNAME>_main and NEST_<APPNAME>_release. The _main suffix apps install the teal packages from https://insightsengineering.r-universe.dev while the _release suffix apps install the teal packages from https://pharmaverse.r-universe.dev
Updates to the _internal/utils/sourceme.R to install the packages from r-universe instead of renv.lock.
Changes to the appropriate readme files.

… app

…ratory app

…ories

Merge branch 'main' into 447_remove_formatters@main # Conflicts: # DESCRIPTION # staged_dependencies.yaml

… deploy-apps@main # Conflicts: # early-dev/app.R

_internal/utils/sourceme.R

# Conflicts: # README.md # _internal/quarto/demo-template.ejs

vedhav · 2023-09-01T15:02:45Z

Created two separate issues blocking this PR #67 and #68

donyunardi · 2023-09-20T16:45:40Z

@pawelru @cicdguy

We have a scheduled workflow that deploys the teal.gallery from the main branch, which results in the demo app page pointing to the *_main suffix. The GIF featured on the Demo page utilizes material from the deploy-apps@main branch, as all updates related to the logo are located there.

The current strategy I observe is that every time we make a push to main, we perform a merge from main to this branch. I followed the same process when completing the nest logo update.

The main branch does not contain the updated workflow to publish the app to _stable and _dev. During my update, I manually ran the publish workflow from deploy-apps@main, but as expected, it was overwritten when the scheduled workflow was triggered.

Until this PR is merged, should we turn off the scheduled workflow so that Demo App can start pointing to "_stable" and "_main" suffix?

For awareness: @lcd2yyz

Signed-off-by: walkowif <[email protected]>

Closes #69 #68 and #67 And remove unused assets from the demo apps as we've moved to a remote logo path The fix for the cypress tests to work (#67) was to move the JS dependency lock files inside the `tests` directory instead of the dedicated `js` directory as it was before. The deployment failure issues (#68) were caused by a new dependency added to some package in the `renv.lock` file and once we update the renv.lock file with the new package dependency it started to work fine.

cicdguy · 2023-09-26T21:59:32Z

Until this PR is merged, should we turn off the scheduled workflow so that Demo App can start pointing to "_stable" and "_main" suffix?

Yeah I think that should be fine. We'll need to remove it from the workflow definition in the main branch. I can do that for you guys.

Disabling per #41 (comment) Signed-off-by: cicdguy <[email protected]>

pawelru · 2023-10-03T08:52:00Z

Hey @vedhav. Can you please tell what's the status of this PR? In your previous message you created new issues that blocks this PR but all of them are resolved now. Is there any other blockers?

vedhav · 2023-10-03T08:56:06Z

The only thing wrong with the deployment is that the mcr package is archived from CRAN, making the longitudinal app deployment fail.
But, we can merge it regardless. WDYT?

Signed-off-by: Vedha Viyash <[email protected]>

pawelru · 2023-10-03T09:07:59Z

Thanks. I'm ok with merging. Please have a chat with @donyunardi. I have seen somewhere that he reached out to the mcr package author. If there is a chance that it will be addressed soon then I am also ok with waiting a few days or so.

…ally

donyunardi · 2023-10-06T18:12:36Z

I've been in contact with author and he's in the process of resubmitting the package.
Let's wait until next week.

donyunardi · 2023-10-11T20:07:12Z

mcr package is back online.

We can merge this now?

cicdguy · 2023-10-11T20:08:55Z

Yes let's do it!

donyunardi · 2023-10-11T20:09:24Z

I ran the workflow again:
https://github.com/insightsengineering/teal.gallery/actions/runs/6487483463

I will merge once all green.

donyunardi · 2023-10-11T22:00:35Z

The workflow failed because @vedhav changed the branch name on 878437e
It should be okay once we merge.
Merging.

m7pr and others added 25 commits July 18, 2023 19:36

remove formatters

5f82eb3

feat: update the deploy workflow to test deployment for exploratory…

9a41c12

… app

fix: using the release version of R instead of relying on lockfile

5475cc4

fix: provide reproducible package versions and remove renv from explo…

ef89aaf

…ratory app

feat: deploy all the apps and remove the renv from all the sub-direct…

5f703f4

…ories

feat: adding front end tests for two apps

5a0372e

feat: adding deployments for main and release versions

c249587

fix: increase the timeout so the elements are loaded in time

13f637f

feat: adding front end tests for all the other apps

d293cda

fix: adding a system dependency for python virtual env

d6cf957

fix: increase the startup timeout

fac5b07

chore: validate the correct number of tabs in the safety app

23bc8f2

merge main

0c262e6

Merge branch 'main' into 447_remove_formatters@main # Conflicts: # DESCRIPTION # staged_dependencies.yaml

teal.widgets -> teal.data

c4a43b9

formatters_var to col_

d94a288

Merge remote-tracking branch 'origin/main' into deploy-apps@main

d41dcba

Merge branch 'main' into 447_remove_formatters@main

24ec23d

revert: remove front-end tests for python and early-dev apps

af17610

Merge remote-tracking branch 'origin/447_remove_formatters@main' into…

dcf98fb

… deploy-apps@main # Conflicts: # early-dev/app.R

fix: explicitly deploy the app.R file

69d9351

feat: update source script to install dependencies from r-universe

0a52bb1

docs: update the readme files with new install instructions

23a55df

fix: provide the cdisc data

f93412f

Merge branch 'main' into deploy-apps@main

3fe4510

fix: also install and update the package dependencies

acb8c40

vedhav force-pushed the deploy-apps@main branch from 0e1cbf4 to acb8c40 Compare August 4, 2023 05:57

Merge branch 'main' into deploy-apps@main

0ff4830

vedhav requested a review from pawelru August 4, 2023 05:59

Merge branch 'main' into deploy-apps@main

047259b

pawelru reviewed Aug 7, 2023

View reviewed changes

_internal/utils/sourceme.R Outdated Show resolved Hide resolved

vedhav added 4 commits August 30, 2023 14:10

chore: bundle only the app.R and static files for the deployment

3264004

Merge branch 'main' into deploy-apps@main

1f94193

# Conflicts: # README.md # _internal/quarto/demo-template.ejs

fix: update renv env for the python app

655fd7c

fix: stash and apply changes before checkout

d053a82

vedhav and others added 2 commits September 5, 2023 17:28

Merge branch 'main' into deploy-apps@main

abf44c0

Merge branch 'main' into deploy-apps@main

7d27aa0

donyunardi mentioned this pull request Sep 20, 2023

[Question]: Why are filters for all datasets shown in patient profile modules insightsengineering/teal.modules.clinical#817

Closed

3 tasks

walkowif and others added 4 commits September 22, 2023 17:36

Update deploy.yaml

3c24cff

Signed-off-by: walkowif <[email protected]>

Update deploy.yaml

c7570c7

Signed-off-by: walkowif <[email protected]>

Update deploy.yaml

980eaa2

Signed-off-by: walkowif <[email protected]>

cicdguy mentioned this pull request Sep 26, 2023

Disable scheduled deployments for now #74

Merged

vedhav pushed a commit that referenced this pull request Sep 27, 2023

Disable scheduled deployments for now (#74)

6e3e424

Disabling per #41 (comment) Signed-off-by: cicdguy <[email protected]>

Merge branch 'main' into deploy-apps@main

9ffee72

Signed-off-by: Vedha Viyash <[email protected]>

feat: update the renv.lock file during restore and runing the app loc…

138ec6b

…ally

[skip deploy] update branch references

878437e

cicdguy approved these changes Oct 11, 2023

View reviewed changes

donyunardi merged commit dd77baf into main Oct 11, 2023

donyunardi deleted the deploy-apps@main branch October 11, 2023 22:01

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Fix the app deployments #41

Fix the app deployments #41

vedhav commented Aug 1, 2023

vedhav commented Sep 1, 2023

donyunardi commented Sep 20, 2023

cicdguy commented Sep 26, 2023

pawelru commented Oct 3, 2023

vedhav commented Oct 3, 2023

pawelru commented Oct 3, 2023

donyunardi commented Oct 6, 2023

donyunardi commented Oct 11, 2023

cicdguy commented Oct 11, 2023

donyunardi commented Oct 11, 2023

donyunardi commented Oct 11, 2023 •

edited

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Fix the app deployments #41

Fix the app deployments #41

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vedhav commented Aug 1, 2023

Changes made

vedhav commented Sep 1, 2023

donyunardi commented Sep 20, 2023

cicdguy commented Sep 26, 2023

pawelru commented Oct 3, 2023

vedhav commented Oct 3, 2023

pawelru commented Oct 3, 2023

donyunardi commented Oct 6, 2023

donyunardi commented Oct 11, 2023

cicdguy commented Oct 11, 2023

donyunardi commented Oct 11, 2023

donyunardi commented Oct 11, 2023 • edited Loading

donyunardi commented Oct 11, 2023 •

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