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* Update Staging branch with what's in main (#438)

* Return to pre-gist method of spell check (#409)

* Return to pre-gist method of spell check

* Get rid of gist stuff on delete-preview too

* Temporarily add spelling errors to test

* Commit before testing

* Switch to use -z

* Fix git diff step

* Just look at the local main since it should be up to date

* make it simple

* Get rid of double bracket

* No brackets?

* Revert "Temporarily add spelling errors to test"

This reverts commit 9e9a932.

* Update screenshot for new repo (#410)

* Update template button screenshot (#411)

* Update screenshot for new repo

* Update template button too

* See if `fetch-depth: 0` fixes the shallow problem (#412)

* Update screenshot for new repo

* Update template button too

* fetch it all

* Switch to devtools::session_info()

* Render bookdown

* Update screenshot for git-secret.png (#414)

* Update screenshot for git-secret.png

* Crop off irrelevant git secrets

* syntax updates

* Needed a semicolon

* Fix branch handling

* Update spell check set up

* Update main

* add brackets

* set shell intentionally

* fix if statements

* Create PR if it can't push directly

* Make sure it merges

* Alter branch test

* quote the 0?

* switch to -z

* Delete extra then

* This should work

* Change to preview- again whoops

* Add a push step

* Update starting course

* set upstream

* Set to bash intentionally (#419)

* set to bash

* Update

* no workflow dispatch

* Test leanpub from here (#420)

* Test leanpub from here

* Update comments

* Add check quizzes too

* Couple edits

* Shut them off for now

* Update comments

* Render leanpub

* Minor polishing of steps (#421)

* Test leanpub from here

* Update comments

* Add check quizzes too

* Couple edits

* Shut them off for now

* Update comments

* Note which places needed to be uncommented

* Just making the step clearer

* Add a git fetch

* Add quizzes to spell check

* Update README.md

* Render leanpub

* Add new repository to sync

* Polish Examples in Rmds (#426)

* Echo false in examples

* Updating wiki

* Render bookdown

* Render bookdown (#427)

* Prep for ottr rename (#428)

* Render bookdown

* Make docker unfail (#431)

* Make docker not fail

* Add Dockerfile example

* Get rid of extra line

* Skip build for this test

* comment out push part too for this test

* undo test Dockerfile

* Render bookdown

* Try out screenshot creator as a part of the new Leanpub set up  (#422)

* Try out screenshot creator

* Fix spacing

* Get rid of typo

* fix argument spec

* Fix git pat handling

* Add copy over assets step

* Try this

* Try installing just the packages we need

* Add install of remotes

* Try using devtools instead

* try set environ

* Try to install R first

* Add prereqs

* Try rocker r-base

* Put installations in script

* Try different strategy

* Switch to tidyverse

* Make directory in bash

* I guess I'm making this its own docker image

* This isn't working but I want it in case I come back to it

* Switch to wkhtmltopdf

* Lets' try it

* Trying leanbuild steps on their own dockerfile

* Test build of leanbuild docker image

* Try out webshot r package

* fix file path to script

* Oh. Actually fix it

* Try installing webshot::install_phantomjs

* Try installing phantomjs on its own first

* Set this up

* Build from jhudsl/course_template

* Switch back to main dockerfile

* assets problem

* It works!

* Revert "assets problem"

This reverts commit 2aada9b.

* Add markdown maker basics

* Push this version before I delete things

* Clean up

* Delete the pdfs

* Reconfig with latest ottr package changes

* Turn on render again

* Add PR instead

* Move copying step

* Add an :: that was missing

* Fix arguments for getting pages url

* misplaced quotes

* Add make_book_txt = TRUE

* It's working! Undo the commenting part

* Set base to main

* Revert "It's working! Undo the commenting part"

This reverts commit 92e5081.

* rm manuscript folder

* Just commit to main

* Delete old manuscript files

* Copy over assets

* Render bookdown

* Remove manuscript if it is there

* Set group and user id to get rid of permissions probs

* Forgot \ 's

* Render bookdown

* Make it force push

* only force manuscript dir

* Render Leanpub

* Render Leanpub

* Render Leanpub

* Add to transfer PRs

* Delete manuscript folder

* Add to sync.yml

* Render Leanpub

* Remove _Template bit

* Add coursera bit and _Quizzes

* Clean out manuscript folder when starting new course

* Make transfers go to the right folder

* add /

* Update sync.yml with OTTR_Template_Website (#437)

Co-authored-by: jhudsl-robot <itcrtrainingnetwork@gmail.com>

Co-authored-by: GitHub Actions <actions@github.com>
Co-authored-by: jhudsl-robot <97678365+jhudsl-robot@users.noreply.github.com>
Co-authored-by: Tiffany Miller <tiffanym@broadinstitute.org>
Co-authored-by: jhudsl-robot <itcrtrainingnetwork@gmail.com>

* Delete packages.bib

* Minor edits to index.Rmd

* Delete extraneous files

* Consolidate and config a pull request GHA  (#448)

* Create config_automation.yml

* Update style-and-sp-check.yml

* Update the filename 😑

* Checking dependency

* Update style-and-sp-check.yml

* Testing that file is carried over

* Add toggle to second check

* Change config to test

* Test removal of some extra text

* Change config to test (again)

* Update config_automation.yml

* What does the output look like with more checks added?

* Fix spacing

* Forgot "steps:"

* BIG YAML

* Get rid of other ones

* Fix names

* Add needs

* Try adding docker to it

* Fix syntax

* Gotta check it out first

* Extra "if" lying around

* Set logically differently

* Testing change

* Add Ava's suggestions!

Co-authored-by: AM Hoffman <avamariehoffman@gmail.com>

* Consolidate and config a rendering GHA  (#449)

* Create config_automation.yml

* Update style-and-sp-check.yml

* Update the filename 😑

* Checking dependency

* Update style-and-sp-check.yml

* Testing that file is carried over

* Add toggle to second check

* Change config to test

* Test removal of some extra text

* Change config to test (again)

* Update config_automation.yml

* What does the output look like with more checks added?

* Fix spacing

* Forgot "steps:"

* BIG YAML

* Get rid of other ones

* Fix names

* Add needs

* Try adding docker to it

* Make a render-all yaml

* Fix syntax

* Gotta check it out first

* Extra "if" lying around

* Set logically differently

* Echo no branch to delete if there is none to delete

* Update sync.yml

* fix syntax

* Fix name of render-all

* Add names

Co-authored-by: AM Hoffman <avamariehoffman@gmail.com>

Co-authored-by: GitHub Actions <actions@github.com>
Co-authored-by: jhudsl-robot <97678365+jhudsl-robot@users.noreply.github.com>
Co-authored-by: Tiffany Miller <tiffanym@broadinstitute.org>
Co-authored-by: jhudsl-robot <itcrtrainingnetwork@gmail.com>
Co-authored-by: AM Hoffman <avamariehoffman@gmail.com>
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6 people authored Feb 11, 2022
1 parent 80af9ed commit 13c6897
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34 changes: 16 additions & 18 deletions .github/sync.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,20 +3,22 @@

group:
- files:
- source: .github/workflows/render-bookdown.yml
dest: .github/workflows/render-bookdown.yml
- source: .github/workflows/render-preview.yml
dest: .github/workflows/render-preview.yml
- source: .github/workflows/render-leanpub.yml
dest: .github/workflows/render-leanpub.yml
- source: .github/workflows/docker-build-test.yml
dest: .github/workflows/docker-build-test.yml
- source: config_automation.yml
dest: config_automation.yml
- source: .github/workflows/
dest: .github/workflows/
deleteOrphaned: true
- source: scripts/
dest: scripts/
deleteOrphaned: true
- source: .github/workflows/pull-request.yml
dest: .github/workflows/pull-request.yml
- source: .github/workflows/render-all.yml
dest: .github/workflows/render-all.yml
- source: .github/workflows/docker-build.yml
dest: .github/workflows/docker-build.yml
- source: .github/workflows/transfer-rendered-files.yml
dest: .github/workflows/transfer-rendered-files.yml
- source: .github/workflows/style-and-sp-check.yml
dest: .github/workflows/style-and-sp-check.yml
- source: .github/workflows/url-checker.yml
dest: .github/workflows/url-checker.yml
- source: .github/workflows/release-notes.yml
dest: .github/workflows/release-notes.yml
- source: .github/workflows/delete-preview.yml
Expand All @@ -29,8 +31,6 @@ group:
dest: scripts/make_screenshots.R
- source: scripts/spell-check.R
dest: scripts/spell-check.R
- source: scripts/get_spell_errors.R
dest: scripts/get_spell_errors.R
- source: scripts/git_repo_check.R
dest: scripts/git_repo_check.R
- source: code_of_conduct.md
Expand Down Expand Up @@ -62,10 +62,8 @@ group:

### This is a custom group for this repo which doesn't want syncing on all the files ###
- files:
- source: .github/workflows/style-and-sp-check.yml
dest: .github/workflows/style-and-sp-check.yml
- source: .github/workflows/url-checker.yml
dest: .github/workflows/url-checker.yml
- source: .github/workflows/pull-request.yml
dest: .github/workflows/pull-request.yml
- source: scripts/spell-check.R
dest: scripts/spell-check.R
repos: |
Expand Down
116 changes: 0 additions & 116 deletions .github/workflows/check-quizzes.yml

This file was deleted.

11 changes: 4 additions & 7 deletions .github/workflows/delete-preview.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,9 @@

name: Delete Preview

#---TRIGGER-START---#
on:
pull_request:
types: [closed]
#---TRIGGER-END---#

jobs:
delete-preview:
Expand All @@ -19,8 +17,7 @@ jobs:
shell: bash

# Delete the branch!
- name: Delete branch
uses: dawidd6/action-delete-branch@v3
with:
github_token: ${{ secrets.GH_PAT }}
branches: preview-${{ github.event.pull_request.number }}
- name: Delete branch locally and remotely
run: |
git branch -d preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
Original file line number Diff line number Diff line change
@@ -1,26 +1,18 @@
# Candace Savonen Apr 2021

name: Build of Docker
name: Build Docker


#---TRIGGER-START---#
on:
release:
types:
- created
pull_request:
branches: [ main, staging ]
paths: [ docker/Dockerfile, docker/github_package_list.tsv ]
workflow_dispatch:
inputs:
dockerhubpush:
description: 'Push to Dockerhub?'
required: true
default: 'false'
#---TRIGGER-END----#

jobs:
build-docker:
name: Build Docker image
runs-on: ubuntu-latest

steps:
Expand All @@ -33,18 +25,15 @@ jobs:
git config --local user.name "jhudsl-robot"
- name: Don't re-test if this is a sync branch
if: ${{ github.head_ref == 'repo-sync/OTTR_Template/default' }}
run: |
echo This was tested on OTTR_Template no need to re-run
# Set up Docker build
- name: Set up Docker Buildx
if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
uses: docker/setup-buildx-action@v1

# Setup layer cache
- name: Cache Docker layers
if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
uses: actions/cache@v2
with:
path: /tmp/.buildx-cache
Expand All @@ -58,12 +47,10 @@ jobs:
uses: docker/setup-buildx-action@v1

- name: Get token
if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt

# Build docker image
- name: Build Docker image
if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
uses: docker/build-push-action@v2
with:
push: false
Expand All @@ -86,14 +73,6 @@ jobs:
run: docker push jhudsl/course_template

- name: Get the version
if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
id: get_version
run: |
echo ::set-output name=version::$(echo $GITHUB_REF | cut -d / -f 3)
# Push the Docker image if it is a release
- name: Push Docker image if release
if: ${{ github.event_name == 'release' }}
run: |
docker tag jhudsl/course_template:latest jhudsl/course_template:${{ steps.get_version.outputs.version }}
docker push jhudsl/course_template:${{ steps.get_version.outputs.version }}
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