Update pathway_counts.csv #67

	name: When stats change, knit stats.Rmd
	## stat data files = _data/edit_counts.csv and _data/pathway_counts.csv

	on:
	workflow_dispatch:
	push:
	branches:
	- main
	paths:
	- _data/*_counts.csv

	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	update-stats:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	ref: main

	- name: Setup R
	uses: r-lib/actions/setup-r@v2

	- name: Install packages
	run: \|
	sudo apt-get update
	sudo apt-get install libcurl4-openssl-dev libmagick++-dev
	Rscript -e 'install.packages(c("knitr","scales","plyr","dplyr","magrittr","magick","remotes","stringr","ggplot2"))'

	- name: Install BiocManager
	run: \|
	remotes::install_cran("BiocManager")
	shell: Rscript {0}

	- name: BiocManager installations
	run: \|
	BiocManager::install("RColorBrewer", ask = FALSE)
	BiocManager::install("rWikiPathways", ask = FALSE)
	shell: Rscript {0}

	- name: Knit stats.Rmd
	run: Rscript -e 'knitr::knit("_rmd/stats.Rmd", "stats.md")'

	- name: Commit report
	run: \|
	git config --global user.name 'GitHub Action'
	git config --global user.email '[email protected]'
	git add .
	if git diff --exit-code --staged; then
	echo "No changes"
	else
	git pull
	git commit -m 'Update stats .md and files'
	git push
	fi

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