Chris Black infotroph

Self-assessment ideas: R package testing + GitHub Actions

If you're new to either GitHub Actions or to CI testing of R packages, here are some exercises that can help you get a sense what's involved so that you can write a well-informed proposal. These are not mandatory, and we won't ask to see the results.

Set up simple GitHub Actions checks on an R package

Pick any R package on GitHub and fork it to your own account. It doesn’t matter who wrote the package or what it does, as long as it doesn’t yet have any Actions configured. If you prefer, you could make a new dummy package instead of forking one.
Add a GitHub Actions workflow that performs package checks on every push. Verify that the build passes reliably.

Adding GitHub Actions to PEcAn: Background info for GSoC 2020 applicants

Chris Black (@infotroph), 2020-02-29

Context

PEcAn is mostly developed by scientists who are skilled at programming but whose main job is not to write software, but rather to answer questions about the world. Therefore when someone has written code that helped them answer a question, we want it to be as easy as possible for them to contribute it to PEcAn without spending undue time worrying about configuring their development toolchain.

So your Git repository is getting ungainly large. What's causing it? Are the problem files still being updated, or are they the deleted ghosts of old binaries?

git cat-file --batch-check --batch-all-objects --unordered \
  | sort --numeric-sort --key=3 \
  | tail -n10 \
  | xargs -L1 sh -c \
    'pth=`git describe --always $0`; \
 printf "%s %s %s %s\n" $0 $1 $2 $pth'

	#!/bin/bash

	launchdir=$(dirname "$1")
	logfile="$launchdir"/slurm_submit_log.txt

	if [[ -z ${SLURM_ARRAY_TASK_ID} ]]; then
	echo "SLURM_ARRAY_TASK_ID not set. Exiting." >> "$logfile"
	exit 1
	fi


	* build a new local postgis image that wraps mdillon/postgis but invokes `postgres -c log_statement=all` at run
	(see ckb-notes/postgis_logging/)
	```
	docker build -t pecan/postgis:9.5_log -<<EOF
	FROM mdillon/postgis:9.5
	CMD ["postgres", "-c", "log_statement=all"]
	EOF
	```
	* modify actions files to use pecan/postgis:9.5_log instead of mdillon/postgis:9.5

	package v1.7.2 develop proposed_v1.8.0 notes
	PEcAn.all 1.7.2 1.7.2.9000 1.8.0 Only package whose version is strictly tied to the release
	PEcAn.allometry 1.7.2 1.7.2 1.7.3 cleanup only
	PEcAn.assim.batch 1.7.2 1.7.2.9000 1.8.0 breaking changes in gpeval and mcmc.GP, many fns moved from emulator
	PEcAn.BASGRA 1.7.2 1.7.2 1.8.0 adds Yasso support
	PEcAn.benchmark 1.7.2 1.7.2 1.7.3 cleanup only
	PEcAn.BIOCRO 1.7.2 1.7.2 1.7.3 cleanup only
	PEcAn.CABLE 1.7.2 1.7.2 1.7.3 cleanup only
	PEcAn.CLM45 1.7.2 1.7.2 1.7.3 cleanup only
	PEcAn.DALEC 1.7.2 1.7.2 1.7.3 cleanup only

	* built a local ARM tidyverse image (I did this in a tempdir)
	- Dockerfile:
	```
	FROM rocker/r-ver:4.2.1

	ENV S6_VERSION=v2.1.0.2
	ENV RSTUDIO_VERSION=daily
	ENV DEFAULT_USER=rstudio
	ENV PANDOC_VERSION=default
	ENV PATH=/usr/lib/rstudio-server/bin:$PATH

	# in R:

	rng_7 <- function(n) {
	sample(0:6, size = n, replace = TRUE)
	}

	scale_rng <- function(m, n) {
	range <- n - m
	n_digits <- ceiling(log10(range) / log10(7))
	exponents <- seq(from = n_digits - 1, to = 0)

	> tribble(~"X0.0 cm", ~"X1.5 cm", 1, 2) %>%
	+ pivot_longer(
	+ cols = everything(),
	+ names_pattern = "X([\\d.]+) cm",
	+ names_ptypes = list(name=double()))
	Error: Lossy cast from `x` <character> to `to` <double>.
	Locations: 1
	Run `rlang::last_error()` to see where the error occurred.

	0> git init
	Initialized empty Git repository in /Users/chrisb/git_test/.git/
	0> echo "some\ncontent" >> foo.txt
	0> git add .
	0> git commit -m 'first'
	[master (root-commit) 3e1a325] first
	1 file changed, 2 insertions(+)
	create mode 100644 foo.txt
	0> git diff-index HEAD
	0> touch foo.txt