April 2024 post, Closes #73 (#75)

* april post init * update april post * build future and drafts * add renv profiles * renv profile packs * add readme workflow * add readme figs * add readme figs * move child doc * Apply suggestions from @maelle Co-authored-by: Maëlle Salmon <maelle.salmon@yahoo.se> * update post * update post * small grammar * better readme aux * updage workflow name * run readme weekly --------- Co-authored-by: Maëlle Salmon <maelle.salmon@yahoo.se>
drmowinckels · Apr 1, 2024 · 8073a4a · 8073a4a
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diff --git a/.Rprofile b/.Rprofile
@@ -1,4 +1,4 @@
-# source("renv/activate.R")
+source("renv/activate.R")
 # in .Rprofile of the website project
 if (file.exists("~/.Rprofile")) {
   base::sys.source("~/.Rprofile", envir = environment())

diff --git a/.github/workflows/build-site.yaml b/.github/workflows/build-site.yaml
@@ -7,7 +7,7 @@ on:
     branches:
       - main
 
-name: Build site
+name: Update website
 
 jobs:
   build:
@@ -44,7 +44,10 @@ jobs:
           if [[ '${{github.ref}}' == 'refs/heads/main' ]]; then
             hugo -e production
           else
-            hugo -b https://${{ github.head_ref }}--drmowinckels.netlify.app/
+            hugo \
+              --buildDrafts \
+              --buildFuture \
+              -b https://${{ github.head_ref }}--drmowinckels.netlify.app/
           fi
 
       - name: Deploy production 🚀

diff --git a/.github/workflows/render-readme.yml b/.github/workflows/render-readme.yml
@@ -0,0 +1,27 @@
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * WED'
+
+name: render-rmarkdown
+
+jobs:
+  render-rmarkdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RENV_PROFILE: readme
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-renv@v2
+      - name: Render README
+        run:  Rscript -e 'rmarkdown::render("README.Rmd", "github_document")'
+      - name: Commit results
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git commit README.md README_files/ \
+            -m 'Re-build README.Rmd' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,7 +10,14 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.0
 Imports: 
-    blogdown,
+    blogdown
+Config/renv/profiles/readme/dependencies: 
+    knitr, 
+    rmarkdown
+Config/renv/profiles/aboutme/dependencies: 
+    ggplot2, 
+    knitr, 
+    rmarkdown,
     dplyr,
     ggplot2,
     glue,
@@ -20,3 +27,4 @@ Imports:
     stringr,
     tidyr,
     vitae
+
diff --git a/README-files/plot-1.png b/README-files/plot-1.png
diff --git a/README.Rmd b/README.Rmd
@@ -0,0 +1,124 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "README-files/",
+  fig.retina = 3,
+  out.width = "100%"
+)
+```
+
+<center>
+![](assets/img/logo.png){width=50%}
+</center>
+
+# DrMowinckels website repo!
+
+Welcome to the repository for my website. 
+This repository contains the code for my content.
+
+
+```{r, echo = FALSE}
+posts <- list.files("content/blog", 
+           "^index.md",
+           recursive = TRUE, 
+           full.names = TRUE)
+posts <- lapply(posts, readLines)
+
+find_key <- function(x, key){
+  j <- lapply(x, function(x){
+    k <- grep(sprintf("^%s:", key), 
+            x, value = TRUE)
+    k <- gsub(sprintf("^%s: |'", key), "", k)
+    k[1] 
+  })
+  unlist(j)
+}
+
+postdf <- data.frame(
+  n = seq_along(posts),
+  draft = find_key(posts, "draft") |> 
+    grepl(pattern = "true", x = _),
+  date = as.Date(find_key(posts, "date")),
+  slug = find_key(posts, "slug") |> 
+    gsub('\\"', "", x = _),
+  title = find_key(posts, "title")
+) |> 
+  subset(subset = !draft)
+postdf$link <-  sprintf("[%s](https://drmowinckels.io/blog/%s)", 
+                  postdf$title,
+                  postdf$slug)
+
+today    <- Sys.Date()
+min_date <- min(postdf$date)
+last_post <- as.numeric(max(postdf$date) - today)
+
+postavg <- nrow(postdf)/as.numeric(today - min_date) * 30
+postavg <- sprintf("%0.2f", postavg)
+
+postbtw <- as.numeric(today - min_date) / nrow(postdf)
+postbtw <- sprintf("%s", round(postbtw, digits = 0))
+
+```
+
+## Some stats 
+
+🎉 DrMowinckels has **`r nrow(postdf)`** posts since **`r min_date`**!
+
+📅 That's a post roughly every **`r postbtw`** days, or about **`r postavg`** posts per month, since `r min_date`.
+
+
+✍️ The last post was published **`r last_post`** days ago (`r tail(postdf, 1)$link`).
+
+😉 I'll post as often as I am able, and hope people find it interesting. I'd love your feedback in the comments!
+
+
+```{r 'plot', echo = FALSE,  fig.width=10, fig.height=2.5}
+library(lattice)
+
+postdf$ones <- 1
+
+# Assuming postdf is loaded and has a 'date' column
+xyplot(ones ~ date, data = postdf,
+       type = 'p',
+       pch = "|",  
+       cex = 5,   
+       col = "cyan3",
+       xlab = "",
+       ylab = "",
+       main = "Published posts",
+       scales = list(x = list(cex = 1.4), y = list(draw = FALSE)),
+       strip = FALSE,  # Removes strip labels
+       axis.line = list(col = "transparent"),
+       layout = c(1, 1),  # Single panel
+       par.settings = list(
+         strip.border = list(col = "transparent"), #making the border transparent
+         axis.line = list(col = "transparent") #making the axes transparent
+       )
+      )
+
+```
+
+<details><summary>📂 Click to expand a full list of posts</summary>
+
+```{r posts-table, results='asis', echo = FALSE}
+data.frame(
+  Date = rev(postdf$date),
+  Title = rev(postdf$link)
+) |> 
+  knitr::kable()
+```
+</details>
+
+---
+
+_The automatically rendered readme was inspired by [Matt Dray](https://www.rostrum.blog/2021/04/14/gha-readme/) and [Piping Hot Data](https://github.com/shannonpileggi/pipinghotdata_distill/blob/master/README.Rmd)._
+
+
+_Updated `r Sys.time()`_
diff --git a/README.md b/README.md
@@ -1,20 +1,74 @@
-### Hi there 👋
 
-- Pronouns: She/Her
-- How to reach me: 
-  - mastodon: [@DrMowinckels@fosstodon.org](https://fosstodon.org/web/@Drmowinckels)
-  - website:  [DrMowinckels](https://drmowinckels.io/)
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+<center>
+<img src="assets/img/logo.png" style="width:50.0%" />
+</center>
 
-I'm part of the [R-Ladies](https://rladies.org/) global team, where I particularly focus on the website development and maintenance, as well as the YouTube channel. 
-I am a Certified [Sorftware Carpentry](https://software-carpentry.org/) Instructor, where I am able to teach git, bash and R lessons, and a Certified [Posit Tidyverse instructor](https://education.rstudio.com/trainers/people/mowinckel+athanasia/).
+# DrMowinckels website repo!
 
-I work as a staff scientist at [the Center for Lifespan Changes in Brain and Cognition](www.oslobrains.no) at the University of Oslo.
+Welcome to the repository for my website. This repository contains the
+code for my content.
 
-- 🌱 I’m currently learning
-  - javascript
-  - make
-
+## Some stats
 
-This repository contains the source code for my website [drmowinckels.io/](https://drmowinckels.io/).
+🎉 DrMowinckels has **31** posts since **2018-03-08**!
 
-[![Netlify Status](https://api.netlify.com/api/v1/badges/50e45b32-809c-429b-8fa9-16fd1fb67ee3/deploy-status)](https://app.netlify.com/sites/drmowinckels/deploys)
+📅 That’s a post roughly every **71** days, or about **0.42** posts per
+month, since 2018-03-08.
+
+✍️ The last post was published **5** days ago ([Too much git
+cleaning](https://drmowinckels.io/blog/2024/git-clean-woes)).
+
+😉 I’ll post as often as I am able, and hope people find it interesting.
+I’d love your feedback in the comments!
+
+<img src="README-files/plot-1.png" width="100%" />
+
+<details>
+<summary>
+📂 Click to expand a full list of posts
+</summary>
+
+| Date       | Title                                                                                                                                                                                    |
+|:-----------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| 2024-04-01 | [Too much git cleaning](https://drmowinckels.io/blog/2024/git-clean-woes)                                                                                                                |
+| 2024-03-01 | [Setting up a Freesurfer LMM through R](https://drmowinckels.io/blog/freesurfer-lmm-r)                                                                                                   |
+| 2024-02-01 | [Teaching you - teaching me](https://drmowinckels.io/blog/teaching-unlocks)                                                                                                              |
+| 2024-01-01 | [New year, New blog](https://drmowinckels.io/blog/newyear-newblog)                                                                                                                       |
+| 2023-11-03 | [Reorganising Hugo Content and Aliasing](https://drmowinckels.io/blog/reorganising-hugo)                                                                                                 |
+| 2023-09-26 | [Posit::conf 2023](https://drmowinckels.io/blog/positconf-2023)                                                                                                                          |
+| 2022-12-01 | [Advent of R Functions](https://drmowinckels.io/blog/advent-of-r-functions)                                                                                                              |
+| 2022-11-07 | [Lets Get Applying](https://drmowinckels.io/blog/lets-get-applying)                                                                                                                      |
+| 2021-12-17 | [Rmarkdown Child Templates](https://drmowinckels.io/blog/rmarkdown-child-templates)                                                                                                      |
+| 2021-12-04 | [Adding giscus to your blogdown site](https://drmowinckels.io/blog/adding-giscus-to-your-blogdown-site)                                                                                  |
+| 2021-03-23 | [Using GitHub Actions to Build your Hugo Website](https://drmowinckels.io/blog/using-github-actions-to-build-your-hugo-website)                                                          |
+| 2021-03-14 | [New {ggseg} with Geom!](https://drmowinckels.io/blog/new-ggseg-with-geom)                                                                                                               |
+| 2020-12-31 | [New Years Wishes](https://drmowinckels.io/blog/new-year-s-wishes)                                                                                                                       |
+| 2020-12-25 | [R-Package Advent Calendar 2020](https://drmowinckels.io/blog/r-package-advent-calendar)                                                                                                 |
+| 2020-06-24 | [The Linear Regression Family in R](https://drmowinckels.io/blog/the-linear-regression-family-in-r)                                                                                      |
+| 2020-05-25 | [Changing your Blogdown Workflow](https://drmowinckels.io/blog/changing-you-blogdown-workflow)                                                                                           |
+| 2020-04-30 | [Using Freesurfer annotation files to plot in R](https://drmowinckels.io/blog/using-freesurfer-annotation-files-to-plot-in-r)                                                            |
+| 2019-12-11 | [Do you wanna build a snowman?](https://drmowinckels.io/blog/do-you-wanna-build-a-snowman)                                                                                               |
+| 2019-12-06 | [ggseg3d - creating interactive brain segmentation plots with plotly](https://drmowinckels.io/blog/ggseg3d-creating-interactive-brain-segmentation-plots-with-plotly)                    |
+| 2019-11-16 | [Plotting GAMM interactions with ggplot2](https://drmowinckels.io/blog/plotting-gamm-interactions-with-ggplot2)                                                                          |
+| 2019-07-17 | [“R for Psychologists - part II”](https://drmowinckels.io/blog/r-for-psychologists-part-ii)                                                                                              |
+| 2019-02-02 | [Building tidy tools - a quick recap of RStudio::conf 2019 workshop & teeny demonstration](https://drmowinckels.io/blog/building-tidy-tools-a-quick-recap-of-rstudio-conf-2019-workshop) |
+| 2019-01-19 | [Why RStudio::conf is the best conference experience I have had](https://drmowinckels.io/blog/why-rstudio-conf-is-the-best-conference-experience-i-have-had)                             |
+| 2018-12-13 | [Christmas tree in ggplot](https://drmowinckels.io/blog/christmas-tree-in-ggplot)                                                                                                        |
+| 2018-11-09 | [R for psychologists - just dive into it!](https://drmowinckels.io/blog/r-just-dive-into-it)                                                                                             |
+| 2018-10-01 | [Get the brain animated!](https://drmowinckels.io/blog/get-the-brain-animated)                                                                                                           |
+| 2018-08-30 | [Introducing the ggseg R-package for brain segmentations](https://drmowinckels.io/blog/introducing-the-ggseg-r-package-for-brain-segmentations)                                          |
+| 2018-05-25 | [Circular plots in R and adding images](https://drmowinckels.io/blog/circluar-plots-in-r-and-adding-images)                                                                              |
+| 2018-05-07 | [Adding external images to plots](https://drmowinckels.io/blog/adding-external-images-to-plots)                                                                                          |
+| 2018-04-05 | [GAMM random effects](https://drmowinckels.io/blog/gamm-random-effects)                                                                                                                  |
+| 2018-03-08 | [GAMM spaghetti plots in R with ggplot](https://drmowinckels.io/blog/gamm-spaghetti-plots-in-r-with-ggplot)                                                                              |
+
+</details>
+
+------------------------------------------------------------------------
+
+*The automatically rendered readme was inspired by [Matt
+Dray](https://www.rostrum.blog/2021/04/14/gha-readme/) and [Piping Hot
+Data](https://github.com/shannonpileggi/pipinghotdata_distill/blob/master/README.Rmd).*
+
+*Updated 2024-03-27 00:57:01.937857*
diff --git a/content/blog/2021/12-17-rmarkdown-child-templates/index.md b/content/blog/2021/12-17-rmarkdown-child-templates/index.md
@@ -221,4 +221,4 @@ Now, we can copy and paste that code chunk for all three species, and have a nea
 You can have a look at the documents in the github repo of this post, and hopefully it will make some sense.
 
 -   [Main document](https://github.com/Athanasiamo/DrMowinckels/tree/master/content/blog/2021-12-17-rmarkdown-child-templates/main-document.Rmd)
--   [Child document](https://github.com/Athanasiamo/DrMowinckels/tree/master/content/blog/2021-12-17-rmarkdown-child-templates/species-child.Rmd)
+-   [Child document](https://github.com/Athanasiamo/DrMowinckels/tree/master/static/blog/2021-12-17-rmarkdown-child-templates/species-child.Rmd)
diff --git a/content/blog/2021/12-17-rmarkdown-child-templates/species-child.knit.md~ b/content/blog/2021/12-17-rmarkdown-child-templates/species-child.knit.md~
diff --git a/content/blog/2024/04-01_git_clean/confused-kitten.png b/content/blog/2024/04-01_git_clean/confused-kitten.png
diff --git a/content/blog/2024/04-01_git_clean/index.Rmd b/content/blog/2024/04-01_git_clean/index.Rmd
@@ -0,0 +1,72 @@
+---
+title: Too much git cleaning
+author: Dr. Mowinckel
+date: '2024-04-01'
+image: 'confused-kitten.png'
+tags:
+  - git
+  - fail
+  - rstudio
+  - r
+slug: "2024/git-clean-woes"
+summary: |
+  Version control is great, but sometimes it can trip you up!
+  In this post I recount my rather stupid mistake of using `git clean` when I shouldn't have, 
+  and how I got out of it.
+---
+
+```{r, include=FALSE}
+options(max.print = 40)
+```
+
+I have a type of love-hate relationship with git.
+While I love the idea of version control, I often find myself in a situation where I have to clean up my git history.
+Maybe I have committed a file that I shouldn't have, or I have made a mistake in my commit message, or I went down a path that just didn't work out.
+In these cases, I find myself using `git clean` or `git checkout` quite a bit.
+In the worst case, I'll even do a `git reset --hard` to go back to a previous commit.
+What all these do, is enable me to go back in time and start over.
+`reset` will let you go back in time even after committing, and deciding that the commit is not what you wanted.
+The other two help more if you haven't committed yet, but have made changes that you want to get rid of.
+
+I have found that the more I use these commands, the more I get used to them.
+But that doesn't mean that I actually do them correctly. 
+I have had my fair share of mistakes, where I have lost work that I didn't want to lose.
+I had one when preparing my [previous post](/blog/2024/freesurfer-lmm-r/)!
+
+I was working on the {neuromat} package, and I had made some changes to the code that just wasn't what i was after.
+I decided I wanted to ditch the changes, and go back to what I had before.
+
+`git clean -f`
+
+`git clean -f` removes any untracked files, poof, gone are they. 
+And one of the main things I had done was rename and create new files and re-arrange my code.
+So, that quickly deleted all of that work. 
+Which I kind of wanted, it just went further back in time than I expected.
+
+To my horror... I had forgotten to commit the changes I wanted to keep.
+The majority of the good things I had done, went away with the stuff I didn't like. 
+I felt... defeated.
+
+I had to start over, and redo the work I had done.
+[Maëlle Salmon](https://masalmon.eu/) to the rescue!
+I had a chat with her, mostly ranting about how stupid I was, and she suggested I could try to just "undo" in any of my open documents.
+In this instance, I was using RStudio IDE, which is my go-to IDE for R work, especially R package dev work (lookout for a future post on my IDE preferences).
+"Undo" here meant hitting `ctrl`+ `z`.
+In my fury over my git mistakes, I forgot that such a simple solution could exist!
+
+Presto, I could just "undo" myself back to the state I wanted to be in.
+Ok, so I did lose some things that I had done, but they were rather small and easy to fix.
+
+Both for the mistake, and not thinking of the fairly simple solution.
+
+Thankfully, other more experienced and advanced developers than me also make such mistakes.
+
+{{< toot user="Patricia" server="social.vivaldi.net" toot="112094753393319808" >}}
+
+It's always nice to know that you're not alone in your mistakes.
+
+And trust that the awesome [Julia Evans](https://fosstodon.org/@b0rk@jvns.ca) of course has [a zine](https://wizardzines.com/comics/losing-your-work/) for this!
+And if she has a zine for it, I know I'm in good company.
+
+And if you, like me (and so many others), need help on your git journey, Maëlle also has an amazing R package to help you practice!
+Read her [Instroduction to {saperlipopette}](https://masalmon.eu/2024/01/18/saperlipopette-package-practice-git/) to get started!