publish_bioconda

#!/usr/bin/env bash

# Submit a PR to https://github.com/bioconda/bioconda-recipes
# in order to update Nextclade on 'bioconda' channel of 'conda'.
#
# Dependencies:
#  mkdir -p "${HOME}/bin"
#  export PATH="${HOME}/bin:${PATH}"
#  curl -fsSL "https://github.com/cli/cli/releases/download/v2.42.1/gh_2.42.1_linux_amd64.tar.gz" | tar xz -C "${HOME}/bin" --strip-components=2 gh_2.42.1_linux_amd64/bin/gh
#  curl -fsSL "https://github.com/TomWright/dasel/releases/download/v2.5.0/dasel_linux_amd64" -o "${HOME}/bin/dasel" && chmod +x "${HOME}/bin/dasel"
#  curl -fsSL "https://github.com/jqlang/jq/releases/download/jq-1.7.1/jq-linux-amd64" -o ${HOME}/bin/jq && chmod +x ${HOME}/bin/jq
#
# Requires git user name and email to be set. For example:
#  git config user.email "${{ secrets.GIT_USER_EMAIL }}"
#  git config user.name "${{ secrets.GIT_USER_NAME }}"

set -euxo pipefail
trap 'exit' INT

# Directory where this script resides
THIS_DIR="$(
  cd "$(dirname "${BASH_SOURCE[0]}")"
  pwd
)"

#: "${GITHUB_TOKEN:? Env var \$GITHUB_TOKEN is required.}"

export artifacts_dir="${THIS_DIR}/../artifacts"

artifacts=(
  'nextclade-aarch64-apple-darwin'
  'nextclade-aarch64-unknown-linux-gnu'
  'nextclade-x86_64-apple-darwin'
  'nextclade-x86_64-unknown-linux-gnu'
)

mkdir -p "${artifacts_dir}"

function download_artifact() {
  name=${1:?}
  curl -fsSL -o "${artifacts_dir}/${name}" "https://github.com/nextstrain/nextclade/releases/latest/download/${name}"
}
export -f download_artifact

# Download executables
parallel --jobs="${#artifacts[@]}" download_artifact ::: "${artifacts[@]}"

chmod +x "${artifacts_dir}"/*

# Setup git identity
gh auth setup-git >/dev/null

# Get the version string and validate it
version="$("${artifacts_dir}/nextclade-x86_64-unknown-linux-gnu" --version | awk '{ print $2 }')"
if [ "$("${THIS_DIR}/semver" validate "${version}")" != "valid" ]; then
  echo "The version emitted by 'nextclade --version' is invalid: ${version}. Refusing to proceed." >&2
  exit 1
fi

## Clone upstream repo (https://github.com/bioconda/bioconda-recipes)
git clone --quiet --origin upstream --single-branch --branch master "https://github.com/bioconda/bioconda-recipes"

pushd bioconda-recipes >/dev/null

version_old=$(sed -n 's|.*version = "\(.*\)".*|\1|p' "recipes/nextclade/meta.yaml")

## Add Nextstrain fork (https://github.com/nextstrain/bioconda-recipes) as a remote
git remote add nextstrain "https://github.com/nextstrain/bioconda-recipes" >/dev/null

# Update master branch of the fork
git push nextstrain upstream/master:master

# Delete branch if already exists locally
git branch --delete --force "bump/nextclade-${version}" || true

# Delete branch if already exists in the fork
git push nextstrain --delete "bump/nextclade-${version}" || true

# Create a new branch
git switch --quiet --create "bump/nextclade-${version}"

## Bump the version
"${THIS_DIR}/update-bioconda.py" "nextclade" "${version}" "${artifacts_dir}" "recipes/nextclade/meta.yaml"

# Print the diff
git --no-pager diff --unified=0 --no-prefix --no-commit-id --word-diff

# Stage and commit the changes
git add "recipes/nextclade/meta.yaml"
git commit --quiet -m "Update nextclade to ${version}"

# Push to the fork
git push --quiet --set-upstream nextstrain "bump/nextclade-${version}"

# Revert any other changes so that they don't get committed accidentally
git add -A
git reset --quiet --hard HEAD
git clean --quiet -dfx

home=$(tail -n +3 recipes/nextclade/meta.yaml | dasel select -r yaml -w json -s ".about.home" | jq -r)
summary=$(tail -n +3 recipes/nextclade/meta.yaml | dasel select -r yaml -w json -s ".about.summary" | jq -r)
maintainers_gh_handles=$(tail -n +3 recipes/nextclade/meta.yaml | dasel select -r yaml -w json -s ".extra.recipe-maintainers" | jq -r '[ .[] | "@" + . ] | join(", ")')

# Create PR body. This is what goes to the first message.
function pr_body() {
  cat <<~~
Update [nextclade](https://bioconda.github.io/recipes/nextclade/README.html): ${version_old} → ${version}.

<img src=https://img.shields.io/conda/dn/bioconda/nextclade.svg />

<table>
<tr>
	<td>Home</td>
	<td><a href="${home}">${home}</a></td>
</tr>
<tr>
	<td>Summary</td>
	<td>${summary}</td>
</tr>
<tr>
	<td>Recipe maintainers</td>
	<td>${maintainers_gh_handles}</td>
</tr>
</table>

@BiocondaBot please add label

@BiocondaBot please fetch artifacts

Note: this pull request is submitted [automatically](https://github.com/nextstrain/nextclade/blob/master/.github/workflows/bioconda.yml), triggered by [a release](https://github.com/nextstrain/nextclade/releases) in [nextstrain/nextclade](https://github.com/nextstrain/nextclade) repo. If you want to get in touch, please ping recipe maintainers and/or someone from [\`@nextstrain/core\`](https://github.com/orgs/nextstrain/teams/core/members) team.

~~
}

# Submit the PR, reading message body from stdin
function submit_pr() {
  pr_body | gh pr create \
    --title "Update nextclade to ${version}" \
    --body-file - \
    --repo "bioconda/bioconda-recipes"
}

# Get PR number from the output of gh command
function get_pr_number() {
  # The message from gh command typically ends with a URL to the PR and PR number is the last component of the path.
  # Split the string on '/' and take the last component.
  echo "${1##*/}"
}

# Close PR given its number
function close_pr() {
  gh pr close "${1:?}" --delete-branch --repo "bioconda/bioconda-recipes"
}

# Comment on PR given its number and a message from stdin
function comment_on_pr() {
  gh pr comment "${1:?}" --body-file -
}

if ! result=$(submit_pr 2>&1); then
  echo "${result}" >&2
  if [[ "${result}" == *"already exists"* ]]; then
    # Failed because PR already exists. Close and resubmit.
    pr_number=$(get_pr_number "${result}")
    close_pr "${pr_number}"
    submit_pr
  else
    exit 1
  fi
else
  echo "${result}"
  pr_number=$(get_pr_number "${result}")
  echo "@BiocondaBot please add label" | comment_on_pr "${pr_number}"
fi

popd >/dev/null

rm -rf bioconda-recipes