From e37c5e8deae69f55efcad7d3171a1ba24b06741d Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:15:29 -0300 Subject: [PATCH 01/13] fix name dir --- exercises/projects.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/exercises/projects.qmd b/exercises/projects.qmd index d520ced..8e48a48 100644 --- a/exercises/projects.qmd +++ b/exercises/projects.qmd @@ -15,7 +15,7 @@ We are going to practice setting up an RStudio Project to get oriented with the 2. Click on the drop-down menu and select the first option: "New Project..." - Alternatively, navigate to the top left corner, click "File", and then click "New Project..." 3. Select "New Directory", then "New Project" -4. Name the directory "2023-CSEE-workshop-projects" and navigate to the subdirectory in your computer where you want the folder to appear +4. Name the directory "reproducible-workflows-workshop" and navigate to the subdirectory in your computer where you want the folder to appear 5. Minimize RStudio and using your file navigation system, navigate to the place on the computer where your project is saved (e.g., Downloads) 6. Open the folder (you should see one file in there, an .Rproj file with the name you gave the folder) - Create five folders within your project folder: From da7f83d27d163addb9392c7d7a612665e741a571 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:15:35 -0300 Subject: [PATCH 02/13] more build ignore --- .Rbuildignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.Rbuildignore b/.Rbuildignore index 77cd445..b917cbf 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,3 +11,5 @@ ^quarto\.yml$ ^_targets\.R$ ^index\.qmd$ +^.*\.Rproj$ +^\.Rproj\.user$ From 87eff7641f3d66a1c5c0b3239005116ae64c6a78 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:15:42 -0300 Subject: [PATCH 03/13] fix name rproj --- ...ws-workshop.Rproj => reproducible-workflows-workshop.Rproj | 4 ++++ 1 file changed, 4 insertions(+) rename 2023-CSEE-reproducible-workflows-workshop.Rproj => reproducible-workflows-workshop.Rproj (70%) diff --git a/2023-CSEE-reproducible-workflows-workshop.Rproj b/reproducible-workflows-workshop.Rproj similarity index 70% rename from 2023-CSEE-reproducible-workflows-workshop.Rproj rename to reproducible-workflows-workshop.Rproj index d96a2b3..49f2092 100644 --- a/2023-CSEE-reproducible-workflows-workshop.Rproj +++ b/reproducible-workflows-workshop.Rproj @@ -13,3 +13,7 @@ RnwWeave: Sweave LaTeX: pdfLaTeX StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source From c4007ef403c7513bcc297a66d3b972769c59f5fe Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:15:48 -0300 Subject: [PATCH 04/13] fix title --- _quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_quarto.yml b/_quarto.yml index 5b5c3ab..56c891d 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -12,7 +12,7 @@ project: - "!paper/manuscript.qmd" website: - title: "2023 CSEE Reproducible workflows workshop" + title: "Reproducible workflows workshop" sidebar: tools: From 138c5f8724442584f13b936dd56e86d6fc716859 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:15:55 -0300 Subject: [PATCH 05/13] fix gh link --- _quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_quarto.yml b/_quarto.yml index 56c891d..f6ecbc4 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -17,7 +17,7 @@ website: sidebar: tools: - icon: github - href: https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop + href: https://github.com/robitalec/reproducible-workflows-workshop contents: - text: "Home" file: index.qmd From 518bf5448f499e206498e269702200a520222763 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:16:04 -0300 Subject: [PATCH 06/13] fix pkg title --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2592cc5..23181a5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ -Package: CSEE.reproducible.workflows.workshop -Title: Workshop for CSEE 2023 On Reproducible Workflows In R +Package: reproducible.workflows.workshop +Title: Reproducible Workflows Workshop Version: 0.0.0.9000 Authors@R: c(person(given = "Alec L.", From b40e349d3d34458addb04625b75660f53c6225ec Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:16:07 -0300 Subject: [PATCH 07/13] fix pkg url --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 23181a5..32f8fde 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,7 +16,7 @@ License: GPL-3 Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 -URL: https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop, https://robitalec.github.io/2023-CSEE-reproducible-workflows-workshop +URL: https://github.com/robitalec/reproducible-workflows-workshop, https://robitalec.github.io/reproducible-workflows-workshop Depends: R (>= 4.0) Imports: targets, tarchetypes, From d971f731bcddc8fa4e8ed161eb3d944ca6c8e1b0 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:17:18 -0300 Subject: [PATCH 08/13] fix readme, note originally dev for csee --- README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 4686abb..8a9f805 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,10 @@ # Reproducible workflows workshop -Workshop at [CSEE 2023](https://www.beepeg2023.ca/): developing a reproducible workflow in R using functions, {targets} and {renv} +## Developing a reproducible workflow in R using functions, {targets} and {renv} + +Originally developed for a +[workshop](https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop) +at [CSEE 2023](https://www.beepeg2023.ca/) Developed and delivered by: @@ -120,11 +124,11 @@ library(usethis) # (Set your own destination directory) use_course( - 'https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop/archive/refs/heads/participant.zip', + 'https://github.com/robitalec/reproducible-workflows-workshop/archive/refs/heads/participant.zip', destdir = '~/Documents') ``` -Or by downloading and unziping the ZIP file at this link: . +Or by downloading and unziping the ZIP file at this link: . Then open up the RStudio project. @@ -223,5 +227,5 @@ Link to data (CSV): ## LICENSE -This project is released under the GNU General Public License v3.0. Read it [here](https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop/blob/quarto/devel/LICENSE). +This project is released under the GNU General Public License v3.0. Read it [here](https://github.com/robitalec/reproducible-workflows-workshop/blob/quarto/devel/LICENSE). From 1867e23cf3b4e3c586bcf583de39a1a320fbf76e Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:20:38 -0300 Subject: [PATCH 09/13] turn off quarto workflow on pull requests --- .github/workflows/quarto-render-pages.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/quarto-render-pages.yaml b/.github/workflows/quarto-render-pages.yaml index c33dbe3..2716536 100644 --- a/.github/workflows/quarto-render-pages.yaml +++ b/.github/workflows/quarto-render-pages.yaml @@ -9,8 +9,6 @@ on: push: branches: [main, master] - pull_request: - branches: [main, master] release: types: [published] workflow_dispatch: @@ -50,4 +48,4 @@ jobs: - uses: quarto-dev/quarto-actions/publish@v2 with: target: gh-pages - render: false \ No newline at end of file + render: false From 269d7c7b5f0e76825f0ff10bfa42c78960882a77 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:21:26 -0300 Subject: [PATCH 10/13] use usethis --- R/packages.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/packages.R b/R/packages.R index 05cd757..1d0d3c3 100644 --- a/R/packages.R +++ b/R/packages.R @@ -12,7 +12,7 @@ library(conflicted) library(palmerpenguins) library(visNetwork) library(quarto) - +library(usethis) library(fs) library(parameters) From 5662a0658f3243b44fa0375e081a3b392d8f9589 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:29:27 -0300 Subject: [PATCH 11/13] minor --- README.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/README.md b/README.md index 8a9f805..66b6233 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,7 @@ Originally developed for a [workshop](https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop) -at [CSEE 2023](https://www.beepeg2023.ca/) - -Developed and delivered by: +at [CSEE 2023](https://www.beepeg2023.ca/) by: - Alec L. Robitaille (Memorial University of Newfoundland and Labrador) - Isabella C. Richmond (Concordia University) From b868d6d4258e4d524720701b34551ec5e75abc7a Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:29:34 -0300 Subject: [PATCH 12/13] bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 32f8fde..0b3a4e9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: reproducible.workflows.workshop Title: Reproducible Workflows Workshop -Version: 0.0.0.9000 +Version: 0.0.1 Authors@R: c(person(given = "Alec L.", family = "Robitaille", From cd66235c4d9ccdf4d0be079adeffaf07f39e5965 Mon Sep 17 00:00:00 2001 From: "Alec L. Robitaille" Date: Fri, 19 Apr 2024 11:37:58 -0300 Subject: [PATCH 13/13] fst NEWS --- NEWS.md | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..20c64ca --- /dev/null +++ b/NEWS.md @@ -0,0 +1,8 @@ +# v0.0.0.9000 + +Initial workshop delivered at CSEE 2023, coauthored with @icrichmond + +https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop + + +**Full Changelog**: https://github.com/robitalec/reproducible-workflows-workshop/commits/v0.0.0.9000 \ No newline at end of file