From a22f5c9f25fd2f4c488b1ceec8151b3bc60f24b9 Mon Sep 17 00:00:00 2001 From: Julia Bowden <117294751+juliambowden@users.noreply.github.com> Date: Wed, 21 Jun 2023 15:05:55 -0400 Subject: [PATCH 01/13] Update sync.yml Enrolled PracticalGenomics/cogaps-on-sciserver repository for OTTR updates --- .github/sync.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/sync.yml b/.github/sync.yml index 40b46a7b..29c87446 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -54,6 +54,7 @@ group: mccoy-lab/hgv_modules griffithlab/pVACtools_Intro_Course griffithlab/CIVIC_SVI_Course + PracticalGenomics/cogaps-on-sciserver ###ADD NEW REPO HERE following the format above# From 7feb95e56991bed05c004058b73697b284af316e Mon Sep 17 00:00:00 2001 From: Carrie Wright <23014755+carriewright11@users.noreply.github.com> Date: Wed, 12 Jul 2023 10:32:26 -0400 Subject: [PATCH 02/13] Update sync.yml adding AI course to sync --- .github/sync.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/sync.yml b/.github/sync.yml index 40b46a7b..3839b4bf 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -54,6 +54,7 @@ group: mccoy-lab/hgv_modules griffithlab/pVACtools_Intro_Course griffithlab/CIVIC_SVI_Course + fhdsl/AI_for_software ###ADD NEW REPO HERE following the format above# From 7889d5327915a093a1a2e828f08e3346412b3f89 Mon Sep 17 00:00:00 2001 From: AM Hoffman Date: Thu, 13 Jul 2023 08:09:34 -0700 Subject: [PATCH 03/13] Update README.md w/ course --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index cf31a254..743969f3 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,7 @@ _This template and guide helps you_: ## To Get Started - Go to the [ottrproject.org](https://www.ottrproject.org/). - Check out the [rendered version of the template](https://jhudatascience.org/OTTR_Template/). +- Check out our [course on using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html) for help publishing on this platform. - Please take a look at the [code of conduct](./code_of_conduct.md). - If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated. From fac01cd7a35d312f86bfa62eeeff45252b16bf68 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 20 Jul 2023 09:12:50 -0400 Subject: [PATCH 04/13] Update sync.yml --- .github/sync.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/sync.yml b/.github/sync.yml index c459e0cd..6e2e1782 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -47,7 +47,7 @@ group: fhdsl/NIH_Data_Sharing fhdsl/FH_Cluster_Guide fhdsl/Using_Leanpub - fhdsl/Overleaf_Tutorial + fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles fhdsl/Design_of_Data_Analysis fhdsl/Tools_for_Reproducible_Workflows_in_R fhdsl/Introduction_to_reproducible_research From 636a806612fcc2e249c145b674a3a5d5bbf5e8c7 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 20 Jul 2023 09:17:41 -0400 Subject: [PATCH 05/13] Update sync.yml for Ethical Data Handling --- .github/sync.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/sync.yml b/.github/sync.yml index 6e2e1782..e4901723 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -29,7 +29,6 @@ group: jhudsl/Documentation_and_Usability jhudsl/Informatics_Research_Leadership jhudsl/Data_Management_for_Cancer_Research - jhudsl/Ethical_Data_Handling_for_Cancer_Research jhudsl/Computing_for_Cancer_Informatics jhudsl/Adv_Reproducibility_in_Cancer_Informatics jhudsl/Reproducibility_in_Cancer_Informatics @@ -47,6 +46,7 @@ group: fhdsl/NIH_Data_Sharing fhdsl/FH_Cluster_Guide fhdsl/Using_Leanpub + fhdsl/Ethical_Data_Handling_for_Cancer_Research fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles fhdsl/Design_of_Data_Analysis fhdsl/Tools_for_Reproducible_Workflows_in_R From 9a8169efac3f44f00eb4ff40183cab5116935d00 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Thu, 10 Aug 2023 11:08:48 -0400 Subject: [PATCH 06/13] add README template for courses (#667) --- .github/course_README_template.md | 24 +++++++++++++++++++++ .github/workflows/starting-course.yml | 1 + README.md | 30 --------------------------- 3 files changed, 25 insertions(+), 30 deletions(-) create mode 100644 .github/course_README_template.md diff --git a/.github/course_README_template.md b/.github/course_README_template.md new file mode 100644 index 00000000..1c9ccdf7 --- /dev/null +++ b/.github/course_README_template.md @@ -0,0 +1,24 @@ +# {Course Name} + +This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template). + +You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.} + +If you would like to contribute to this course material, take a look at the [OTTR documentation](https://www.ottrproject.org/). + +## About this course + +This course introduces {info on what this course introduces} + +## Learning Objectives + +This course will teach learners to: + +- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here} +- {More learning objectives} + +## Encountering problems? + +If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}. + +Creative Commons License
All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise. diff --git a/.github/workflows/starting-course.yml b/.github/workflows/starting-course.yml index d1683f28..5ded0b20 100644 --- a/.github/workflows/starting-course.yml +++ b/.github/workflows/starting-course.yml @@ -30,6 +30,7 @@ jobs: - name: Cleanup run: | # Cleanup + mv .github/course_README_template.md README.md rm -rf \ .github/workflows/report-maker.yml \ .github/workflows/send-updates.yml \ diff --git a/README.md b/README.md index 743969f3..04db84a6 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,3 @@ - - ## Open-source Tools for Training Resources - OTTR Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada: @@ -33,31 +31,3 @@ _This template and guide helps you_: - Please take a look at the [code of conduct](./code_of_conduct.md). - If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated. - - -# {Course Name} - -[![Render Bookdown and Coursera](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-all.yml/badge.svg)](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-all.yml) - -This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template). - -You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.} - -If you would like to contribute to this course material, take a look at the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki). - -## About this course - -This course introduces {info on what this course introduces} - -## Learning Objectives - -This course will teach learners to: - -- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here} -- {More learning objectives} - -## Encountering problems? - -If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}. - -Creative Commons License
All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise. From 140f60641b75620c6f0bc7fa594e8bf724b5215d Mon Sep 17 00:00:00 2001 From: "Thomas B. Mooney" Date: Wed, 20 Sep 2023 12:57:13 -0500 Subject: [PATCH 07/13] Update sync.yml (#665) Add griffithlab/Immuno_workflow_Course --- .github/sync.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/sync.yml b/.github/sync.yml index e4901723..d0f474ca 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -56,6 +56,7 @@ group: griffithlab/CIVIC_SVI_Course PracticalGenomics/cogaps-on-sciserver fhdsl/AI_for_software + griffithlab/Immuno_Workflow_Course ###ADD NEW REPO HERE following the format above# From e64a2aba54e6b133697ab5099e12a47b270ed47d Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Wed, 20 Sep 2023 13:58:16 -0400 Subject: [PATCH 08/13] add C-MOOR_Template to sync.yml (#666) Co-authored-by: Candace Savonen --- .github/sync.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/.github/sync.yml b/.github/sync.yml index d0f474ca..c5815fb9 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -112,3 +112,25 @@ group: dest: style-sets/fhdasl/ repos: | jhudsl/AnVIL_Template + + - files: + - source: config_automation.yml + dest: config_automation.yml + - source: .github/workflows/ + dest: .github/workflows/ + deleteOrphaned: true + - source: .github/switch_sync_repo.R + dest: .github/switch_sync_repo.R + - source: .github/automatic-issues/ + dest: .github/automatic-issues/ + - source: assets/box_images/ + dest: assets/box_images/ + - source: assets/style.css + dest: assets/style.css + - source: assets/toc_close.css + dest: assets/toc_close.css + - source: scripts/ + dest: scripts/ + deleteOrphaned: true + repos: | + C-MOOR/C-MOOR_Template From 259d7d8ca0562993cdeb9a5efd4e2d684f4d3d98 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 20 Sep 2023 13:59:53 -0400 Subject: [PATCH 09/13] Make it so courses are re-rendered when quizzes are changed (#668) --- .github/workflows/render-all.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml index 083817ac..b9b19728 100644 --- a/.github/workflows/render-all.yml +++ b/.github/workflows/render-all.yml @@ -10,6 +10,7 @@ on: paths: - '**.Rmd' - assets/* + - quizzes/* jobs: From b894e412dd003a518feadd3b306ca7bd300ccbc2 Mon Sep 17 00:00:00 2001 From: Chris Lo Date: Wed, 20 Sep 2023 11:01:40 -0700 Subject: [PATCH 10/13] Update sync.yml (#672) added fhdsl/Intro_to_Command_Line for sync Co-authored-by: Candace Savonen --- .github/sync.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/sync.yml b/.github/sync.yml index c5815fb9..637580ae 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -57,6 +57,7 @@ group: PracticalGenomics/cogaps-on-sciserver fhdsl/AI_for_software griffithlab/Immuno_Workflow_Course + fhdsl/Intro_to_Command_Line ###ADD NEW REPO HERE following the format above# From 7484b65f43347d530cfa22fb6f281f62714a2b3a Mon Sep 17 00:00:00 2001 From: Chris Lo Date: Tue, 24 Oct 2023 05:14:18 -0700 Subject: [PATCH 11/13] Update sync.yml (#684) added fhdsl/S1_Intro_to_R --- .github/sync.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/sync.yml b/.github/sync.yml index 637580ae..2748ab25 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -58,6 +58,7 @@ group: fhdsl/AI_for_software griffithlab/Immuno_Workflow_Course fhdsl/Intro_to_Command_Line + fhdsl/S1_Intro_to_R ###ADD NEW REPO HERE following the format above# From 92fdd1dfd8157aa3086a491927432f22c3ea2d9a Mon Sep 17 00:00:00 2001 From: AM Hoffman Date: Tue, 24 Oct 2023 08:20:17 -0400 Subject: [PATCH 12/13] Update w analytics reminder (#691) Co-authored-by: Candace Savonen --- .github/automatic-issues/add-feedback-method.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/automatic-issues/add-feedback-method.md b/.github/automatic-issues/add-feedback-method.md index 4e9b0150..a69be417 100644 --- a/.github/automatic-issues/add-feedback-method.md +++ b/.github/automatic-issues/add-feedback-method.md @@ -1,4 +1,8 @@ To help users report issues or areas of improvement for your course, you should provide a clear method of feedback for your users to route their concerns through. -[Read this chapter from an OTTR-made course about how to obtain user feedback](https://jhudatascience.org/Documentation_and_Usability/obtaining-user-feedback.html). +- [ ] [Read this chapter from an OTTR-made course about how to obtain user feedback](https://jhudatascience.org/Documentation_and_Usability/obtaining-user-feedback.html). + +It's also a good idea to collect passive feedback via Google Analytics. + +- [ ] [Read our guide to Google Analytics here](https://www.ottrproject.org/more_features.html#google-analytics). From dbb0b381fc2db30ec7094e36194fcd53f6b42861 Mon Sep 17 00:00:00 2001 From: Chris Lo Date: Tue, 24 Oct 2023 05:24:14 -0700 Subject: [PATCH 13/13] Update sync.yml (#692) Co-authored-by: Candace Savonen --- .github/sync.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/sync.yml b/.github/sync.yml index 2748ab25..de89e922 100755 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -57,8 +57,9 @@ group: PracticalGenomics/cogaps-on-sciserver fhdsl/AI_for_software griffithlab/Immuno_Workflow_Course - fhdsl/Intro_to_Command_Line fhdsl/S1_Intro_to_R + fhdsl/S1_Intro_to_Command_Line + fhdsl/S1_Intro_to_Git_GitHub ###ADD NEW REPO HERE following the format above#