Merge branch 'test'

Author: mckeea

.github/runners/Dockerfile.llm-doc-annotator

@@ -0,0 +1,19 @@
+FROM python:3.11-slim
+
+# Set working directory
+WORKDIR /app
+
+# Install required system packages
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        build-essential \
+        curl \
+        git \
+        && rm -rf /var/lib/apt/lists/*
+
+# Install Python dependencies
+RUN pip install --no-cache-dir \
+    google-generativeai==0.8.5 \
+    tiktoken==0.9.0 \
+    PyYAML==6.0.2 \
+    json5

.github/runners/Dockerfile.quarto-doc-builder

@@ -0,0 +1,55 @@
+FROM debian:bookworm-slim
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    curl \
+    sudo \
+    git \
+    bash \
+    rsync \
+    ca-certificates \
+    python3 \
+    python3-pip \
+    fonts-dejavu \
+    coreutils \
+    procps \
+    chromium \
+    libreoffice-core \
+    libreoffice-writer \
+    libreoffice-java-common \
+    default-jre-headless
+
+
+# Install Quarto CLI
+RUN arch=$(dpkg --print-architecture) && \
+    case "$arch" in \
+      amd64)  deb=quarto-1.7.30-linux-amd64.deb ;; \
+      arm64)  deb=quarto-1.7.30-linux-arm64.deb ;; \
+      *)      echo "Unsupported architecture: $arch" && exit 1 ;; \
+    esac && \
+    wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.7.30/$deb && \
+    dpkg -i $deb && \
+    rm $deb
+
+# Install Node.js (for GitHub Actions written in Node)
+RUN curl -fsSL https://deb.nodesource.com/setup_18.x | bash - && \
+    apt-get install -y nodejs
+
+# Clean up apt, pip, Python, and docs
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    python3 -m pip cache purge && \
+    find /usr/local/lib/python3.*/ -name '__pycache__' -exec rm -r {} + && \
+    find /usr/local/lib/python3.*/ -name '*.pyc' -delete && \
+    rm -rf /root/.cache/pip /root/.cache/fontconfig && \
+    rm -rf $HF_HOME/hub/tmp-* $HF_HOME/hub/*.lock $HF_HOME/hub/models--*/blobs &&\
+    rm -rf /usr/share/doc /usr/share/man /usr/share/locale /var/cache/* /tmp/* /var/tmp/*
+
+
+# Entrypoint script
+COPY entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+ENTRYPOINT ["/entrypoint.sh"]

.github/scripts/generate_intros_and_keywords.py

@@ -1,13 +1,14 @@
 from pathlib import Path
 import json
-import time
 import re
 import google.generativeai as genai
 import tiktoken
 import yaml
-from io import StringIO
 import os
 from pathlib import Path
+import sys
+import json5
+import hashlib
 
 # Configuration
 API_KEY = os.getenv("GEMINI_API_KEY")
@@ -18,13 +19,18 @@
 
 SCRIPT_DIR = Path(__file__).resolve().parent
 INPUT_DIR = (SCRIPT_DIR / "../../DOCS").resolve()
+ROOT_DIR = (SCRIPT_DIR / "../../").resolve()
+CACHE_DIR = (SCRIPT_DIR / "../../.llm_cache").resolve()
+CACHE_DIR.mkdir(exist_ok=True)
+BLACKLISTED_DIRS = {"templates", "includes", "theme"}
 
-PROMPT = """You are an AI assistant helping to enrich a Quarto Markdown (.qmd) technical document prepared for the European Environment Agency (EEA).
+PROMPT = """You are an AI assistant helping to enrich technical documents for the Copernicus Land Monitoring Service (CLMS).
 
 Your tasks:
-1. Read and understand the entire attached document.
+1. Read and understand the entire attached document. Ignore yml metadata and focus on the main content.
 2. Generate a professional, engaging **Introduction** (max 1 paragraph) that clearly explains the document’s purpose, scope, and technical focus.
 3. Extract exactly 10 **precise and conceptually meaningful keywords or key phrases** that reflect the core scientific or technical content of the document.
+4. Use British English spelling and terminology.
 
 Keyword guidance:
 - Do **not** use general terms like \"Urban Atlas\", \"metadata\", \"documentation\", \"nomenclature\", or \"report\".
@@ -38,6 +44,8 @@
   \"introduction\": \"...\",
   \"keywords\": [\"keyword1\", \"keyword2\", ..., \"keyword10\"]
 }
+
+Avoid trailing commas in the JSON output.
 """
 
 # Setup Gemini
@@ -48,15 +56,15 @@
 
 
 # Function to update YAML frontmatter using PyYAML
-def update_yaml_header(content: str, description: str, keywords_list: list):
-    lines = content.splitlines()
+def update_qmd_file(doc_path, description: str, keywords_list: list):
+    lines = doc_path.read_text(encoding="utf-8").splitlines()
     if lines[0].strip() != "---":
-        return content
+        return
 
     try:
         end_idx = lines[1:].index("---") + 1
     except ValueError:
-        return content
+        return
 
     yaml_block = "\n".join(lines[1:end_idx])
     yaml_data = yaml.safe_load(yaml_block) or {}
@@ -65,16 +73,17 @@ def update_yaml_header(content: str, description: str, keywords_list: list):
 
     new_yaml_block = yaml.dump(yaml_data, sort_keys=False, allow_unicode=True).strip()
     new_lines = ["---"] + new_yaml_block.splitlines() + ["---"] + lines[end_idx + 1 :]
-    return "\n".join(new_lines)
+
+    doc_path.write_text("\n".join(new_lines), encoding="utf-8")
 
 
 # Function to process one document with Gemini
 def process_document_with_llm(doc_path: Path):
-    print("Processing ", doc_path)
     global total_tokens_sent
 
     file_contents = doc_path.read_text(encoding="utf-8")
     input_tokens = len(encoding.encode(file_contents))
+    print(f"[LLM] Processing: {doc_path} ({input_tokens} input tokens)")
     if total_tokens_sent + input_tokens > TOKEN_LIMIT_PER_MINUTE:
         print(
             f"[SKIPPED] {doc_path} would exceed token budget. Estimated at {input_tokens} tokens."
@@ -106,27 +115,71 @@ def process_document_with_llm(doc_path: Path):
         raw_text = re.sub(r"\s*```$", "", raw_text)
 
     try:
-        parsed_output = json.loads(raw_text)
-        introduction = parsed_output["introduction"]
-        keywords_list = parsed_output["keywords"]
-        keywords = ", ".join(keywords_list)
+        parsed_output = json5.loads(raw_text)
+        return {
+            "introduction": parsed_output["introduction"],
+            "keywords": parsed_output["keywords"],
+        }
     except (json.JSONDecodeError, KeyError) as e:
         print(f"[ERROR] Invalid response for {doc_path}:", raw_text)
-        return
+        return None
 
-    updated_content = update_yaml_header(file_contents, introduction, keywords_list)
-    output_file = doc_path.with_name(doc_path.stem + ".qmd")
-    output_file.write_text(updated_content, encoding="utf-8")
 
-    print("Estimated input tokens:", input_tokens)
+# Function to read paths of modified documents (.qmd) from a file. The file is provided by github actions as an input.
+def read_paths_from_filename():
+    input_file = sys.argv[1]
+    try:
+        with open(input_file, "r") as f:
+            return [line.strip() for line in f if line.strip()]
+    except FileNotFoundError:
+        raise FileNotFoundError(f"File not found: {input_file}")
+    except Exception as e:
+        raise RuntimeError(f"Error reading file: {e}")
 
 
-# Process all .qmd files
-BLACKLISTED_DIRS = {"templates", "includes", "theme"}
+# Cache-related functions
+def file_hash(path):
+    return hashlib.sha256(path.read_bytes()).hexdigest()
+
+
+def get_cache_path(qmd_path):
+    safe_path = "__".join(qmd_path.parts)
+    return CACHE_DIR / f"{safe_path}.json"
+
+
+def load_cached_result(cache_path):
+    if cache_path.exists():
+        with cache_path.open() as f:
+            return json.load(f)
+    return {}
+
+
+def save_cached_result(cache_path, data):
+    with cache_path.open("w") as f:
+        json.dump(data, f, indent=2)
+
+
+if __name__ == "__main__":
+    modified_paths = set(Path(p) for p in read_paths_from_filename())
+
+    for full_doc_path in INPUT_DIR.rglob("*.qmd"):
+        doc_path = full_doc_path.relative_to(ROOT_DIR)
+        if any(part in BLACKLISTED_DIRS for part in doc_path.parts):
+            continue
+
+        cache_path = get_cache_path(doc_path)
+        current_hash = file_hash(doc_path)
+        cache = load_cached_result(cache_path)
+
+        if doc_path in modified_paths or cache.get("hash") != current_hash:
+            result = process_document_with_llm(doc_path)
+            cache = {
+                "hash": current_hash,
+                "intro": result["introduction"],
+                "keywords": result["keywords"],
+            }
+            save_cached_result(cache_path, cache)
 
-for doc_path in INPUT_DIR.rglob("*.qmd"):
-    if any(part in BLACKLISTED_DIRS for part in doc_path.parts):
-        continue
-    process_document_with_llm(doc_path)
+        update_qmd_file(doc_path, cache["intro"], cache["keywords"])
 
-print("Total tokens sent:", total_tokens_sent)
+    print("Total tokens sent:", total_tokens_sent)

.github/scripts/generate_keywords.py

@@ -19,7 +19,40 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
         with:
-          fetch-depth: 0
+          fetch-depth: 2
+
+      - name: Mark repo as safe for Git
+        run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+
+      - name: Show commit history
+        run: git log --oneline -n 5
+
+      - name: Get changed .qmd files on current branch
+        run: |
+          (git diff --name-only HEAD^ HEAD | grep -E '\.qmd$' || true) > modified_docs_list.txt
+          echo "Modified .qmd files:"
+          cat modified_docs_list.txt
+
+      - name: Generate intros and keywords
+        uses: addnab/docker-run-action@v3
+        with:
+          image: mckeea/llm-doc-annotator:latest
+          options: -e GEMINI_API_KEY=${{ secrets.GEMINI_API_KEY }} -v ${{ github.workspace }}:/app
+          run: python .github/scripts/generate_intros_and_keywords.py modified_docs_list.txt
+
+      - name: Commit updated LLM cache
+        run: |
+          git config user.name "GitHub Actions"
+          git config user.email "actions@github.com"
+
+          git add .llm_cache
+
+          if git diff --cached --quiet; then
+            echo "No changes to commit."
+          else
+            git commit -m "Update LLM cache [skip ci]"
+            git push origin HEAD
+          fi
 
       - name: Generate intros and keywords
         uses: addnab/docker-run-action@v3

.github/workflows/deploy-docs.yml

@@ -0,0 +1,16 @@
+{
+  "hash": "6c2405be4e8491221a1444f66040b7dfa982e079673ff790b6d64a756a545499",
+  "intro": "This document outlines the IT architecture principles and implementation guidelines for the Copernicus Land Monitoring Service (CLMS), managed by the European Environment Agency (EEA). It establishes a framework for developing consistent, scalable, and secure IT solutions within the CLMS programme. Emphasising key aspects like modularity, reproducibility, transparency, maintainability, observability, security and resilience, these guidelines ensure that all IT solutions are coherent, adaptable, and efficiently operated, contributing to the overarching goals of the CLMS.",
+  "keywords": [
+    "IT solution reproducibility",
+    "REST API service",
+    "Continuous Integration and Continuous Deployment",
+    "Client specific software modularity",
+    "Infrastructure-as-a-code",
+    "Role-based access control",
+    "Disaster recovery plan",
+    "IT solution cloud agnosticism",
+    "Source code inline documentation",
+    "Automated metric monitoring"
+  ]
+}