dlaehnemann

I find the release-please manual for setting up GitHub Actions a bit unclear, even though it describes how to configure your repository so it can open and approve pull requests. It also mentions, that you will need a personal access token with the correct permissions, if you want your regular GitHub Actions CI tests to run on the resulting pull requests. However, it doesn't specify which exact permissions you need to set for your personal access token and how to get the workflow to see the token as a repository secret. So I am documenting two basic options for setting up release-please with GitHub Actions here, because I am sure to forget this quickly (and it took me a lot of attempts and then some systematic testing to to figure this out).

Option 1: release-please with GITHUB_TOKEN (automatic pull requests, no CI

dlaehnemann

The manual for the release-please GitHub Action describes how to configure your repository so it can open and approve pull requests. It also mentions, that you will need a personal access token with the correct permissions, if you want your regular GitHub Actions CI tests to run on the resulting pull requests. However, it doesn't specify which exact permissions you need to set for your personal access token and how to get the workflow to see the token as a repository secret. So I am documenting this here, because I am sure to forget this quickly (and it took me several attempts to figure this out).

fine-grained personal access token

Follow the [GitHub documentation for creating a fine-grained personal access token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-acc

dlaehnemann

{
  "$schema": "https://vega.github.io/schema/vega-lite/v5.json",
  "params": [
    {
      "name": "orientation",
      "bind": {"input": "checkbox"}
    },
    {
      "name": "strand",
      "value": "true",

dlaehnemann

library("tidyverse")
library("httr")

try_fields <- function(case_hash) {
  print(str_c("Now on case with hash:", case_hash, sep=" ") )
  # all fields that can contain a tumor purity value
  fields = c(
    "files.cases.samples.portions.slides.percent_tumor_cells",
    "files.cases.samples.portions.slides.percent_tumor_nuclei",
    "samples.portions.slides.percent_tumor_cells",

dlaehnemann

dlaehnemann

Whenever I want to create pull requests to a repo that I don't have write access to, I:

1. Fork the original repo to my account.
2. Clone the original repo to my local machine.
3. Add my fork as an additional remote and make it the push default.
4. Make changes in a new branch locally.
5. Push this branch to my fork.
6. Create a pull request from there.

dlaehnemann

I try to use conda for as many software installations in data analysis as possible, as this will ususally guarantee that I can use up to date versions of that software.

This now includes R, and as I mostly use R through Rstudio Desktop, I checked how I can use a custom R installation with Rstudio Desktop. As described in the Rstudio docs, you just have to set the environment variable RSTUDIO_WHICH_R to the R binary of your wanted installation. For this environment variable to be set when launching Rstudio from Ubuntu's application launcher, you have to make the respective environment setting in the rstudio.desktop file.

As a reminder for me, and maybe as info for others, the general setup is:

1. Install Rstudio: https://www.rstudio.com/products/rstudio/download/#download
2. Install (Mini-)conda: https://conda.io/miniconda.html

dlaehnemann

dlaehnemann

dlaehnemann