zkamvar

#!/usr/bin/env bash 

wd=$(pwd)
# Clone the hub and the dashboard
git clone https://github.com/reichlab/flu-metrocast.git
git clone https://github.com/reichlab/metrocast-dashboard.git

# Temporarily place the ptc/data and predevals/data branches as
# sub-directories of the dashboard. This allows us to quickly 
# preview the changes using the site builder 

zkamvar

#!/usr/bin/env bash
set -eo pipefail
#
# PURPOSE:
#   This script demonstrates the dashboard workflow process as it
#   exists **independent of GitHub workflows**. This script is not
#   concerned about where data are stored or when they are updated.
#
# RATIONALE:
#   Building a dashboard website requires three tools:

zkamvar

#!/usr/bin/env bash

if ! type gh > /dev/null; then
  echo "github CLI (gh) must be installed"
  exit 1
fi

action=${1}
if [ -z "$action" ]; then
  echo "Replace a tagged action with a commit hash"

zkamvar

On 2025-01-17, the hubverse development team released the v5 schemas.

This release contains the following changes:

• Added explicit checks of round_id format through a regex pattern check to the round.round_id property when round.round_id_from_variable is false. This provides upfront validation of the expected format of manually-supplied round IDs (i.e. those not sourced from a task ID) (hubverse-org/schemas#112).
• BREAKING CHANGE: Restricted the target_metadata.target_keys object to contain only a single key value pair (if not null). This means that target keys can now only consist of a single value from a single task ID (hubverse-org/schemas#117).
• BREAKING CHANGE The target_variable and target_outcome properties are removed from the standard Task IDs that can be validated against the schema (hubverse-org/schemas#117).

zkamvar

# NOTE: this is a WIP. It does not yet work. 

library(hubAdmin)
library(hubUtils)
library(glue)
tasks <- read_config(".", "tasks")

transform_to_v4 <- function(this_output_type,  kind = 1, task = 1, round = 1) {
  if (kind == "sample") {
    class(this_output_type) <- "output_type_item"

zkamvar

library(gert)
library(tinkr) # pak::pak("ropensci/tinkr#119")
library(xml2)
here::i_am("2024-11-05-update-contributing.R")

#' Update the CONTRIBUTING.md for a given hubverse package
#' 
#' This function will update some of the steps in the CONTRIBUTING to add a link to the 
#' PR checklist, update the usethis code example, and clarify that the development version
#' will have "development version" as the header for the NEWS

zkamvar

#!/usr/bin/env bash
# 
# This will search GitHub for hubs that use quantiles, CDF, or PMF output
# types and check if they use "optional" in their hub-config/tasks.json
# files.
echo "======== SEARCHING GITHUB ============"
curl -L \
  -H "Accept: application/vnd.github+json" \
  -H "Authorization: Bearer $(gh auth token)" \
  -H "X-GitHub-Api-Version: 2022-11-28" \

zkamvar

Last month, I opened a discussion to formalize R package release process guidelines and it has been approved by the core devs of the Hubverse development team. The most visible change is how you will install hubverse packages. You should no longer use remotes::install_github().

To install ALL hubverse packages, you can use:

install.packages("hubverse", repos = c("https://hubverse-org.r-universe.dev", "https://cran.r-project.org"))

Timeline

zkamvar

#' Produce a list of all GitHub contributors to a project
#'
#' If you want a way to give thanks to specific people who have contributed to a project
#' since a given release, this will extract the GitHub user names from a given package's 
#' NEWS file. This assumes that 1) the package has a `NEWS.md` file and 2) the package 
#' uses level 1 headers and semantic versioning for each version in the news file. 
#' 
#' @param package the name of a package
#' @param since a version number (must match a version recorded in the NEWS)
#' @return a character vector with GitHub user names

zkamvar

library("gh")
library("base64enc")

# get a file from a repository
get_repo_file <- function(org = "carpentries", lesson = "sandpaper-docs", file = "CONTRIBUTING.md", ...) {
  gh("GET /repos/{org}/{lesson}/contents/{file}", 
    .params = list(
      org = org,
      lesson = lesson,
      file = file