mirror of
https://github.com/msberends/AMR.git
synced 2026-06-29 17:36:20 +02:00
272 lines
12 KiB
YAML
272 lines
12 KiB
YAML
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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on:
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push:
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branches: "main"
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name: Update TODO Tracker
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jobs:
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update-todo:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0 # full history required for git blame
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- name: Generate TODO report
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env:
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GH_TOKEN: ${{ secrets.GH_REPO_SCOPE }}
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run: |
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set -euo pipefail
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export TZ=Europe/Amsterdam
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REPO="msberends/AMR"
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REPO_URL="https://github.com/$REPO/blob/main"
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NOW=$(date +%s)
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LAST_UPDATED=$(date +"%e %B %Y %H:%M:%S %Z" | sed 's/^ *//')
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STALE_DAYS=180
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# ── helper: human-readable age ──────────────────────────────
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format_age() {
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local d=$1
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if [ "$d" -lt 0 ] 2>/dev/null; then echo "unknown"; return; fi
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local y=$((d / 365)) m=$(( (d % 365) / 30 ))
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if [ "$y" -gt 0 ] && [ "$m" -gt 0 ]; then echo "${y}y ${m}m"
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elif [ "$y" -gt 0 ]; then echo "${y}y"
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elif [ "$m" -gt 0 ]; then echo "${m}m"
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else echo "${d}d"
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fi
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}
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export -f format_age
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# ── step 1: find all markers ────────────────────────────────
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grep -rn \
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--include='*.R' --include='*.Rmd' --include='*.yaml' \
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--include='*.yml' --include='*.md' --include='*.css' \
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--include='*.js' \
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--exclude='todo-tracker.yml' --exclude='todo.md' \
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-E '\b(TODO|FIXME|HACK|XXX)\b' . > /tmp/raw.txt || true
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if [ ! -s /tmp/raw.txt ]; then
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echo -e "## \`TODO\` Report\n\n**Last Updated: ${LAST_UPDATED}**\n\nNo markers found." > todo.md
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exit 0
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fi
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# ── step 2: enrich with git blame & extract issue refs ──────
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> /tmp/enriched.tsv
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> /tmp/issues_seen.txt
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while IFS= read -r match; do
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clean=$(printf '%s\n' "$match" | sed 's|^\./||')
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file=$(printf '%s\n' "$clean" | cut -d: -f1)
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lineno=$(printf '%s\n' "$clean" | cut -d: -f2)
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text=$(printf '%s\n' "$clean" | cut -d: -f3-)
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# determine marker type (first match wins, TODO is default)
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marker="TODO"
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for m in FIXME HACK XXX; do
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if printf '%s\n' "$text" | grep -qw "$m"; then marker="$m"; break; fi
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done
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# git blame timestamp
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blame_ts=$(git blame -L "${lineno},${lineno}" --porcelain -- "$file" 2>/dev/null \
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| awk '/^author-time/{print $2}' || echo "0")
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blame_ts=${blame_ts:-0}
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if [ "$blame_ts" -gt 0 ] 2>/dev/null; then
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age_days=$(( (NOW - blame_ts) / 86400 ))
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else
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age_days=-1
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fi
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# extract issue references (#NNN)
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issues=$(printf '%s\n' "$text" | grep -oE '#[0-9]+' | sed 's/#//' | tr '\n' ',' | sed 's/,$//' || true)
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if [ -n "$issues" ]; then
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for inum in $(echo "$issues" | tr ',' ' '); do
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echo "$inum" >> /tmp/issues_seen.txt
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done
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fi
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printf '%s\t%s\t%s\t%s\t%s\t%s\n' \
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"$file" "$lineno" "$marker" "$age_days" "$issues" "$text" >> /tmp/enriched.tsv
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done < /tmp/raw.txt
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# ── step 3: query GitHub API for referenced issues ──────────
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> /tmp/issue_info.tsv
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if [ -s /tmp/issues_seen.txt ]; then
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sort -un /tmp/issues_seen.txt | while read -r inum; do
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info=$(gh api "/repos/$REPO/issues/$inum" \
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--jq '"\(.state)\t\(.title)"' 2>/dev/null \
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|| echo "unknown (could not fetch)")
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printf '%s\t%s\n' "$inum" "$info" >> /tmp/issue_info.tsv
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done
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fi
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# ── step 4: build the report ────────────────────────────────
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{
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# ── header ──
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echo "## \`TODO\` Report"
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echo ""
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echo "**Last Updated: ${LAST_UPDATED}**"
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echo ""
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echo "_This overview is automatically updated on each push to \`main\`. It scans for \`TODO\`, \`FIXME\`, \`HACK\`, and \`XXX\` markers across the codebase._"
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echo ""
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# ── summary table ──
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total=$(wc -l < /tmp/enriched.tsv | tr -d ' ')
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files_affected=$(awk -F'\t' '{print $1}' /tmp/enriched.tsv | sort -u | wc -l | tr -d ' ')
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todo_n=$(awk -F'\t' '$3=="TODO"' /tmp/enriched.tsv | wc -l | tr -d ' ')
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fixme_n=$(awk -F'\t' '$3=="FIXME"' /tmp/enriched.tsv | wc -l | tr -d ' ')
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hack_n=$(awk -F'\t' '$3=="HACK"' /tmp/enriched.tsv | wc -l | tr -d ' ')
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xxx_n=$(awk -F'\t' '$3=="XXX"' /tmp/enriched.tsv | wc -l | tr -d ' ')
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stale_n=$(awk -F'\t' -v s="$STALE_DAYS" '$4 > s' /tmp/enriched.tsv | wc -l | tr -d ' ')
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linked_n=$(awk -F'\t' '$5 != ""' /tmp/enriched.tsv | wc -l | tr -d ' ')
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unlinked_n=$(awk -F'\t' '$5 == ""' /tmp/enriched.tsv | wc -l | tr -d ' ')
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# oldest marker
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oldest_line=$(awk -F'\t' '$4 >= 0' /tmp/enriched.tsv | sort -t$'\t' -k4 -rn | head -1)
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oldest_days=$(echo "$oldest_line" | cut -f4)
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oldest_file=$(echo "$oldest_line" | cut -f1)
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oldest_lineno=$(echo "$oldest_line" | cut -f2)
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oldest_age=$(format_age "$oldest_days")
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echo "### Summary"
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echo ""
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echo "| Metric | Value |"
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echo "|:---|---:|"
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echo "| Total markers | **${total}** |"
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[ "$todo_n" -gt 0 ] && echo "| \`TODO\` | ${todo_n} |"
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[ "$fixme_n" -gt 0 ] && echo "| \`FIXME\` | ${fixme_n} |"
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[ "$hack_n" -gt 0 ] && echo "| \`HACK\` | ${hack_n} |"
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[ "$xxx_n" -gt 0 ] && echo "| \`XXX\` | ${xxx_n} |"
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echo "| Files affected | ${files_affected} |"
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echo "| Stale (> 6 months) | ${stale_n} |"
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echo "| Oldest marker | ${oldest_age}, \`${oldest_file}\` L${oldest_lineno} |"
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echo "| Linked to issues | ${linked_n} |"
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echo "| Unlinked (no issue ref) | ${unlinked_n} |"
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echo ""
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# ── by referenced issue ──
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if [ -s /tmp/issue_info.tsv ]; then
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echo "### By Referenced Issue"
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echo ""
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has_closed=false
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while IFS=$'\t' read -r inum state title; do
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count=$(awk -F'\t' -v n="$inum" '$5 ~ "(^|,)"n"(,|$)"' /tmp/enriched.tsv | wc -l | tr -d ' ')
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[ "$state" = "closed" ] && has_closed=true
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state_icon=""
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[ "$state" = "closed" ] && state_icon=" :warning:"
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echo "<details><summary><b>#${inum}</b> (${state}): <i>${title}</i> — ${count} marker(s)${state_icon}</summary>"
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echo ""
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awk -F'\t' -v n="$inum" '$5 ~ "(^|,)"n"(,|$)"' /tmp/enriched.tsv \
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| while IFS=$'\t' read -r f l m d refs txt; do
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age_str=$(format_age "$d")
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flag=""
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[ "$d" -gt "$STALE_DAYS" ] 2>/dev/null && flag=" :warning:"
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# re-read the actual source line and trim leading/trailing whitespace
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src_text=$(sed -n "${l}p" "$f" 2>/dev/null | sed 's/^[[:space:]]*//;s/[[:space:]]*$//' || true)
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echo "- [\`${f}\` L${l}](${REPO_URL}/${f}#L${l}) (${age_str} ago)${flag}"
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[ -n "$src_text" ] && echo " \`${src_text}\`"
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done
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echo ""
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echo "</details>"
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echo ""
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done < /tmp/issue_info.tsv
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if [ "$has_closed" = true ]; then
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echo "> **Warning:** some markers reference closed issues and may be stale."
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echo ""
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fi
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fi
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# ── by file ──
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echo "### By File"
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echo ""
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prev_file=""
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prev_lineno=-99
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while IFS=$'\t' read -r file lineno marker age_days issues text; do
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if [ "$file" != "$prev_file" ]; then
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# close previous code block
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if [ -n "$prev_file" ]; then
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echo '```'
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echo ""
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fi
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file_count=$(awk -F'\t' -v f="$file" '$1==f' /tmp/enriched.tsv | wc -l | tr -d ' ')
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echo "#### [\`${file}\`](${REPO_URL}/${file}) — ${file_count} marker(s)"
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echo '```r'
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prev_lineno=-99
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fi
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# blank line between non-sequential lines (visual grouping)
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if [ "$file" = "$prev_file" ] && [ $((lineno - prev_lineno)) -gt 1 ]; then
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echo ""
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fi
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age_str=$(format_age "$age_days")
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flag=""
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[ "$age_days" -gt "$STALE_DAYS" ] 2>/dev/null && flag=" !!"
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# re-read the actual source line to avoid TSV round-trip corruption
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src_line=$(sed -n "${lineno}p" "$file" 2>/dev/null | sed 's/[[:space:]]*$//' || true)
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printf 'L%s: %s ◁ %s ago%s\n' "$lineno" "$src_line" "$age_str" "$flag"
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prev_file="$file"
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prev_lineno="$lineno"
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done < <(sort -t$'\t' -k1,1 -k2,2n /tmp/enriched.tsv)
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# close final code block
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if [ -n "$prev_file" ]; then
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echo '```'
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fi
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} > todo.md
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- name: Update GitHub issue
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uses: peter-evans/create-or-update-comment@v4
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with:
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token: ${{ secrets.GH_REPO_SCOPE }}
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issue-number: 231
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comment-id: 3253439219
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body-file: todo.md
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edit-mode: replace
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