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2.1 Compile SV Data (as needed)

2.1 Compile SV Data (as needed) #7

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2.1 Compile SV Data (as needed)

2.1 Compile SV Data (as needed) #7

Workflow file for this run

.github/workflows/update_svData.yml at 9a6d7e8
### Overwrite FrEDI data with past data
name: 2.1 Compile SV Data (as needed)
on:
workflow_dispatch:
inputs:
run_sv:
type: choice
description: Update SV proportions
required: true
options:
- no
- yes
run_formats:
type: choice
description: Update SV formatting table
required: true
options:
- no
- yes
run_pop:
type: choice
description: Update SV population projections
required: true
options:
- no
- yes
branch_name:
type: string
description: Which FrEDI Package branch do you want to use?
jobs:
compile_data:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
name: Process Data
steps:
- name: Checkout
uses: actions/checkout@v3
- name: Send input status
run: |
echo "${{ inputs.run_sv }} ${{ inputs.run_formats }} ${{ inputs.run_pop }}"
- name: Setup R
uses: r-lib/actions/setup-r@v2
- name: Setup R package dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
cache: true
cache-version: 1
packages: |
any::tidyverse
any::ggpubr
any::openxlsx
any::devtools
- name: Install FrEDI
run: |
Rscript -e 'devtools::install_github(
repo = "https://github.com/USEPA/FrEDI",
ref = "${{ github.event.inputs.branch_name }}",
subdir = "FrEDI",
dependencies = FALSE,
upgrade = "never",
force = TRUE,
type = "source"
)'
- name: Configure SV data
if: |
${{ inputs.run_sv }} == 'true' ||
${{ inputs.run_pop }} == 'true' ||
${{ inputs.run_formats }} == 'true'
run: |
Rscript -e '
source("./scripts/update_svDataObjects.R")
fpath1 <- getwd()
sv0 <- ifelse("${{ inputs.run_sv }}" == "true",TRUE,FALSE)
pop0 <- ifelse("${{ inputs.run_pop }}" == "true",TRUE, FALSE)
format0 <- ifelse("${{ inputs.run_formats }}" == "true",TRUE,FALSE)
list1 <- update_svDataObjects(
fpath0 = fpath1,
sv = sv0,
pop = pop0,
format = format0,
save = TRUE,
return = TRUE
)
'
- name: Commit results
if: |
${{ inputs.run_sv }} == 'true' ||
${{ inputs.run_pop }} == 'true' ||
${{ inputs.run_formats }} == 'true'
run: |
git config --local core.autocrlf false
git config --local user.email "${{ github.actor }}@users.noreply.github.com"
git config --local user.name "${{ github.actor }}"
git add data/sv/**.rda
git pull origin ${{ github.head_ref }} --autostash --rebase -X ours
git commit -a -m "Updated SV FrEDI data objects"
git push