From 806c60f23a349918c5763484e8bf677c01dbadb3 Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Mon, 13 Jan 2025 09:20:26 -0500 Subject: [PATCH 01/11] Update config_automation.yml Switch underscores back to dashes --- config_automation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config_automation.yml b/config_automation.yml index da4d39f..6dc3708 100644 --- a/config_automation.yml +++ b/config_automation.yml @@ -23,5 +23,5 @@ render-coursera: no # What docker image should be used for rendering? # The default is jhudsl/base_ottr:latest -rendering_docker_image: 'jhudsl/ottr_jupyter:latest' +rendering-docker-image: 'jhudsl/ottr_jupyter:latest' From 33470206972da40000eaa9ad783192472e1c708d Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 13 Jan 2025 16:21:22 -0500 Subject: [PATCH 02/11] Print out the image --- .github/workflows/pull_request.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 091af95..f4eca34 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -174,7 +174,9 @@ jobs: - name: Render quarto version id: quarto if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }} - run: Rscript -e "quarto::quarto_render('.')" + run: | + echo ${{needs.yaml-check.outputs.rendering_docker_image}} + Rscript -e "quarto::quarto_render('.')" # This checks on the steps before it and makes sure that they completed. # If the renders didn't complete we don't want to commit the file changes From 2d52cf2626a0275c350efd678a9df2f4b0650b79 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 13 Jan 2025 16:28:10 -0500 Subject: [PATCH 03/11] Looking for clues --- .github/workflows/pull_request.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index f4eca34..80af1af 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -162,6 +162,8 @@ jobs: git fetch --all git checkout $branch_name git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories + quarto --version + quarto check shell: bash # Run bookdown rendering @@ -175,8 +177,9 @@ jobs: id: quarto if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }} run: | - echo ${{needs.yaml-check.outputs.rendering_docker_image}} - Rscript -e "quarto::quarto_render('.')" + quarto check + quarto::quarto_render('.') + shell: Rscript # This checks on the steps before it and makes sure that they completed. # If the renders didn't complete we don't want to commit the file changes From f826cc104c0f6db165b15c5b9ae80eb563fc2309 Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Mon, 13 Jan 2025 16:46:21 -0500 Subject: [PATCH 04/11] Update pull_request.yml update rscript shell --- .github/workflows/pull_request.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 80af1af..353ee9b 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -179,7 +179,7 @@ jobs: run: | quarto check quarto::quarto_render('.') - shell: Rscript + shell: Rscript {0} # This checks on the steps before it and makes sure that they completed. # If the renders didn't complete we don't want to commit the file changes From eeff5b4889269fec07179bf6c6f768210c2b0c8a Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Mon, 13 Jan 2025 16:54:19 -0500 Subject: [PATCH 05/11] Update pull_request.yml look for path and add an explicit library(quarto) --- .github/workflows/pull_request.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 353ee9b..385f6cf 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -177,7 +177,8 @@ jobs: id: quarto if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }} run: | - quarto check + library(quarto) + quarto_path() quarto::quarto_render('.') shell: Rscript {0} From b77933268fba13de4ae1e6a14e11a5357809bf69 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 14 Jan 2025 08:17:25 -0500 Subject: [PATCH 06/11] What if we directly install quarto here? --- .github/workflows/pull_request.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 80af1af..6ab9195 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -177,6 +177,7 @@ jobs: id: quarto if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }} run: | + install.packages("quarto", repos='http://cran.us.r-project.org') quarto check quarto::quarto_render('.') shell: Rscript From e81df8785cb57a1f1c9a6e9d08f0e32da24fab48 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 14 Jan 2025 08:34:54 -0500 Subject: [PATCH 07/11] Update without install.packages() --- .github/workflows/pull_request.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index bf66237..26aa87a 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -177,7 +177,6 @@ jobs: id: quarto if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }} run: | - install.packages("quarto", repos='http://cran.us.r-project.org') quarto::quarto_render('.') shell: Rscript {0} From 7df1d59ca37d74bb90bf6fbed86ed5c9202af18c Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 14 Jan 2025 08:40:05 -0500 Subject: [PATCH 08/11] bring install back --- .github/workflows/pull_request.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 26aa87a..bf66237 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -177,6 +177,7 @@ jobs: id: quarto if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }} run: | + install.packages("quarto", repos='http://cran.us.r-project.org') quarto::quarto_render('.') shell: Rscript {0} From a06ff28359ab3216d5ee1cbfef6efdd5dc1a063e Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 14 Jan 2025 08:48:02 -0500 Subject: [PATCH 09/11] I have quarto reinstalled on the image now --- .github/workflows/pull_request.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index bf66237..26aa87a 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -177,7 +177,6 @@ jobs: id: quarto if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }} run: | - install.packages("quarto", repos='http://cran.us.r-project.org') quarto::quarto_render('.') shell: Rscript {0} From 72f23b984ce8c7d9721486d201a34cd66fd83566 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 14 Jan 2025 08:51:43 -0500 Subject: [PATCH 10/11] get rid of bread-crumbs: false --- _quarto.yml | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/_quarto.yml b/_quarto.yml index 551ecd0..6bbbf4d 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -7,14 +7,13 @@ book: author: Howard Baek date: "4/3/2024" favicon: img/favicon.ico - bread-crumbs: false page-navigation: true search: true repo-url: https://github.com/fhdsl/OTTR_Quarto - repo-actions: [edit] + repo-actions: [edit] issue-url: https://docs.google.com/forms/d/e/1FAIpQLSfBvVELBg8lcynKj0TrzMlov1zil-Sbkh9VhMKRcSpeo1xo6g/viewform - + chapters: - index.qmd - intro.qmd @@ -29,27 +28,27 @@ book: - third-section-new-chapter.qmd - conclusion.qmd - references.qmd - - sidebar: + + sidebar: logo: "img/logo.png" logo-href: "https://hutchdatascience.org/" foreground: "#1B365D" - + page-footer: left: | - This book was built with Quarto using + This book was built with Quarto using OTTR. center: | All illustrations CC-BY.
All other materials CC-BY unless noted otherwise. - right: + right: - icon: github href: https://github.com/ - icon: slack href: https://fhdata.slack.com/join/signup#/domain-signup - + bibliography: references.bib @@ -60,17 +59,17 @@ format: css: style.css linkcolor: "#00C1D5" mainfont: "Karla" - + sidebar: true toc: true - + code-link: true code-copy: true - + link-external-newwindow: true - + image: img/favicon.ico license: "CC BY" knitr: opts_chunk: - fig.path: "resources/images/figure/" \ No newline at end of file + fig.path: "resources/images/figure/" From 31107873c05d9cdb4cbed386f551b7569a1b15ae Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 14 Jan 2025 08:52:59 -0500 Subject: [PATCH 11/11] Make it main --- config_automation.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/config_automation.yml b/config_automation.yml index 5695c01..e946aa4 100644 --- a/config_automation.yml +++ b/config_automation.yml @@ -25,5 +25,4 @@ render-coursera: no # What docker image should be used for rendering? # The default is jhudsl/base_ottr:latest -rendering-docker-image: 'jhudsl/ottr_jupyter:latest' - +rendering-docker-image: 'jhudsl/ottr_jupyter:main'