name: Pytest CI Workflow
description: Run pytest with coverage and report upload to Gitea
inputs:
  ci-branch:
    description: 'Target branch where test reports will be committed'
    required: true

  module-dir:
    description: 'Directory (folder) containing the Python module to test'
    required: true

  gitea-domain:
    description: 'Domain name of your Gitea instance without protocol (e.g., gitea.psi.ch)'
    required: true

  repo-path:
    description: 'Relative path to the root of your repository'
    required: true

  ci-token:
    description: ' CI authentication token (used for pushing to Gitea)'
    required: true

  enable_pixi_post_link_scripts:
    description: 'Set to true to enable post-link scripts for Pixi'
    required: false
    default: 'false'

  apt_packages:
    description: "List of system packages to install via apt-get"
    required: false
    default: ""

  custom_shell_commands:
    description: "Additional shell commands to run"
    required: false
    default: ""

  custom_shell_commands_after:
    description: "Additional shell commands to run"
    required: false
    default: ""

  test-files:
    description: "Comma-separated list of test files or directories to run"
    required: false
    default: ""

  env:
    description: "Environment type: pixi (default), pip, conda, or custom"
    required: false
    default: "pixi"

  env-setup-cmd:
    description: "Custom setup command(s) to prepare the environment (only used if env=custom)"
    required: false
    default: ""

  session-wrapper:
    description: "Wrapper de session (ex: dbus-run-session --)"
    required: false
    default: ""

  test-run-cmd:
    description: "Wrapper command to run pytest (e.g. 'dbus-run-session -- bash -c', 'tmux new-session ...'). If empty, pytest is run directly."
    required: false
    default: "$CMD"


runs:
  using: "composite"
  steps:
    - name: Checkout code 
      uses: actions/checkout@v4 
      with: 
        fetch-depth: 1

    - name: Install optional apt packages
      if: inputs.apt_packages != ''
      run: |
        OUTPUT_DIR="outputs"
        LOG_FILE="${OUTPUT_DIR}/sudo-install.log"
        VERSIONS_FILE="${OUTPUT_DIR}/sudo-versions.log"
        mkdir -p "$OUTPUT_DIR"

        git clone -q https://gitea.psi.ch/tligui_y/test-ci.git ./temp-ci

        echo "⚙️ Starting APT package installation..." | tee -a "$LOG_FILE"
        echo "   Packages: ${{ inputs.apt_packages }}" | tee -a "$LOG_FILE"

        # Run install, capture everything into the log
        sudo DEBIAN_FRONTEND=noninteractive apt-get update &>> "$LOG_FILE"
        sudo DEBIAN_FRONTEND=noninteractive apt-get install -y ${{ inputs.apt_packages }} &>> "$LOG_FILE"
        EXIT_CODE=$?

        if [ $EXIT_CODE -eq 0 ]; then
          echo "✅ Packages installed successfully!" | tee -a "$LOG_FILE"

          echo "📋 Installed APT packages (full list):" >> "$VERSIONS_FILE"
          dpkg -l >> "$VERSIONS_FILE"

          echo "Exit Code: 0" >> "$LOG_FILE"
          echo "Exit Code: 0" >> "$VERSIONS_FILE"
        else
          echo "❌ Package installation failed" | tee -a "$LOG_FILE"
          echo "Exit Code: $EXIT_CODE" >> "$LOG_FILE"
          exit $EXIT_CODE
        fi
      shell: bash


    - name: Setup environment
      shell: bash
      run: |
        OUTPUT_DIR="outputs"
        LOG_FILE="${OUTPUT_DIR}/env-setup.log"
        VERSIONS_FILE="${OUTPUT_DIR}/env-versions.log"

        case "${{ inputs.env }}" in
          pixi)
            echo "🔧 Installing Pixi..." | tee -a $LOG_FILE
            if [ "${{ inputs.enable_pixi_post_link_scripts }}" == "true" ]; then
              pixi config set --local run-post-link-scripts insecure
            fi

            curl -fsSL https://pixi.sh/install.sh | bash >> $LOG_FILE 2>&1 || {
              echo "❌ Pixi download failed" | tee -a $LOG_FILE
              echo "Exit Code: 1" >> $LOG_FILE
              exit 1
            }

            echo "$HOME/.pixi/bin" >> $GITHUB_PATH
            export PATH="$HOME/.pixi/bin:$PATH"

            if [ ! -f "pixi.toml" ]; then
              echo "❌ Missing pixi.toml at repo root" | tee -a $LOG_FILE
              echo "Exit Code: 1" >> $LOG_FILE
              exit 1
            fi

            echo "📦 Installing dependencies from pixi.toml..." | tee -a $LOG_FILE
            pixi install >> $LOG_FILE 2>&1 || {
              echo "❌ Pixi project dependencies failed" | tee -a $LOG_FILE
              echo "Exit Code: 1" >> $LOG_FILE
              exit 1
            }

            echo "📋 Pixi environment details:" | tee -a $VERSIONS_FILE
            pixi list >> $VERSIONS_FILE 2>&1

            echo "✅ Pixi environment ready" | tee -a $LOG_FILE
            echo "Exit Code: 0" >> $LOG_FILE
            echo "Exit Code: 0" >> "$VERSIONS_FILE"
            ;;

          pip)
            echo "📦 Installing pip dependencies..." | tee -a $LOG_FILE
            python -m pip install --upgrade pip >> $LOG_FILE 2>&1
            if [ -f "requirements.txt" ]; then
              pip install -r requirements.txt >> $LOG_FILE 2>&1 || {
                echo "❌ Pip install failed" | tee -a $LOG_FILE
                echo "Exit Code: 1" >> $LOG_FILE
                exit 1
              }
              echo "📋 Pip environment details:" | tee -a $VERSIONS_FILE
              pip freeze >> $VERSIONS_FILE 2>&1

              echo "✅ Pip environment ready" | tee -a $LOG_FILE
              echo "Exit Code: 0" >> $LOG_FILE
              echo "Exit Code: 0" >> "$VERSIONS_FILE"
            else
              echo "⚠️ No requirements.txt found, skipping." | tee -a $LOG_FILE
              echo "Exit Code: 0" >> $LOG_FILE
            fi
            ;;

          conda)
            echo "📦 Setting up conda environment..." | tee -a $LOG_FILE
            if [ -f "environment.yml" ]; then
              conda env create -f environment.yml >> $LOG_FILE 2>&1 || {
                echo "❌ Conda env create failed" | tee -a $LOG_FILE
                echo "Exit Code: 1" >> $LOG_FILE
                exit 1
              }
              echo "📋 Conda environment details:" | tee -a $VERSIONS_FILE
              conda list >> $VERSIONS_FILE 2>&1

              echo "✅ Conda environment ready" | tee -a $LOG_FILE
              echo "Exit Code: 0" >> $LOG_FILE
              echo "Exit Code: 0" >> "$VERSIONS_FILE"
            else
              echo "⚠️ No environment.yml found, skipping." | tee -a $LOG_FILE
              echo "Exit Code: 0" >> $LOG_FILE
            fi
            ;;

          custom)
            echo "⚙️ Running custom environment setup..." | tee -a $LOG_FILE
            if [ -n "${{ inputs.env-setup-cmd }}" ]; then
              bash -c "${{ inputs.env-setup-cmd }}" >> $LOG_FILE 2>&1 || {
                echo "❌ Custom env setup failed" | tee -a $LOG_FILE
                echo "Exit Code: 1" >> $LOG_FILE
                exit 1
              }

              echo "📋 Custom environment details (uname + python + pip list):" | tee -a $VERSIONS_FILE
              uname -a >> $VERSIONS_FILE
              python --version >> $VERSIONS_FILE 2>&1 || true
              pip freeze >> $VERSIONS_FILE 2>&1 || true

              echo "✅ Custom environment ready" | tee -a $LOG_FILE
              echo "Exit Code: 0" >> $LOG_FILE
              echo "Exit Code: 0" >> "$VERSIONS_FILE"
            else
              echo "⚠️ No custom setup command provided." | tee -a $LOG_FILE
              echo "Exit Code: 0" >> $LOG_FILE
            fi
            ;;
        esac


    - name: Run custom shell commands before
      shell: bash
      run: |
        OUTPUT_DIR="outputs"
        LOG_FILE="${OUTPUT_DIR}/custom-shell-before.log"
        mkdir -p "$OUTPUT_DIR"

        if [ -z "$(echo "${{ inputs.custom_shell_commands }}" | xargs)" ]; then
          echo "💡 No custom shell commands found" | tee -a "$LOG_FILE"
          echo "Exit Code: 0" >> "$LOG_FILE"
          exit 0
        fi

        echo "📜 Executing custom shell commands..." | tee -a "$LOG_FILE"

        echo "Writing to file"

        export LOG_FILE="$LOG_FILE"
        {
          echo "set -e"
          echo 'trap "{ EXIT_CODE=\$?; if [ \$EXIT_CODE -eq 0 ]; then echo Exit Code: 0 >> \"$LOG_FILE\"; else echo Exit Code: 1 >> \"$LOG_FILE\"; fi; } 2>/dev/null" EXIT'
          echo "set -x"
          echo "${{ inputs.custom_shell_commands }}"
        } > custom_commands.sh

        echo "chmod to file"
        chmod +x custom_commands.sh

        echo "Execute file"
        ./custom_commands.sh >> "$LOG_FILE" 2>&1
        EXIT_CODE=$?

        echo "Finished file"

        if [ $EXIT_CODE -eq 0 ]; then
          echo "✅ Custom shell executed successfully" | tee -a "$LOG_FILE"
          echo "Exit Code: 0" >> "$LOG_FILE"
        else
          echo "❌ Custom shell execution failed" | tee -a "$LOG_FILE"
          exit 1
        fi

    - name: Run tests and generate reports
      shell: bash
      run: |
        OUTPUT_DIR="outputs"
        LOG_FILE="${OUTPUT_DIR}/test-ci.log"

        export LOG_FILE

        echo "⚡ Running tests and generating reports..." | tee -a "$LOG_FILE"
        cp temp-ci/conftest.py ./

        if [ -n "${{ inputs.test-files }}" ]; then
          TEST_PATH="${{ inputs.test-files }}"
        else
          TEST_PATH="."
        fi

        PYTEST_ARGS="--continue-on-collection-errors \
          --cov=${{ inputs.module-dir }} \
          --json-report \
          --json-report-file=markdown/pytest-report.json \
          --capture=no \
          --log-file=outputs/pytest-output.log"

        CMD="pytest -s $TEST_PATH $PYTEST_ARGS"
        case "${{ inputs.env }}" in
          pixi)   CMD="pixi run $CMD" ;;
          conda)  CMD="conda run -n myenv $CMD" ;;
          pip|custom) ;;  
        esac

        exec >>"$LOG_FILE" 2>&1

        echo "⚡ Running tests and generating reports..."

        cat > custom_cmd.sh <<'EOS'
        ${{ inputs.test-run-cmd }}
        EOS

        chmod +x custom_cmd.sh
        export CMD
        ./custom_cmd.sh 2>&1

        echo "▶️ END"

        awk '/=+ test session starts =+/{flag=1} /-+ JSON report -+/{flag=0} flag' outputs/pytest-output.log > outputs/raw-test-output.log
        awk '/=+ short test summary info =+/,/=+.* in .*s =+/' outputs/pytest-output.log > outputs/short-test-output.log

        set -e

        echo "" >> $LOG_FILE
        echo "📋 Short test summary:" >> "$LOG_FILE"
        if [ -s outputs/short-test-output.log ]; then
          cat outputs/short-test-output.log >> "$LOG_FILE"
        else
          echo "✅ All tests passed, nothing to report." >> "$LOG_FILE"
        fi

        echo "print pytest"
        cat outputs/pytest-output.log

        mkdir -p markdown

        echo "" >> $LOG_FILE
        echo "📈 Generating coverage summary..." >> $LOG_FILE

        # Combine all .coverage.* into one
        pixi run coverage combine > /dev/null 2>> outputs/coverage-error.log

        # Generate markdown report once
        pixi run coverage report --skip-covered --skip-empty --format=markdown > markdown/coverage-summary.md 2>> outputs/coverage-error.log && {
          echo "✅ Coverage summary generated" >> $LOG_FILE
        } || {
          echo "❌ Coverage summary generation failed" >> $LOG_FILE
          echo "🪵 Extracting coverage error:" >> $LOG_FILE
          cat outputs/coverage-error.log >> $LOG_FILE
          echo "Exit Code: 1" >> $LOG_FILE
          exit 1
        }

        if [ -f markdown/runtime_params.log ]; then
          echo "✅ [INFO] File 'runtime_params.log' found in project root."
          ls -lh markdown/runtime_params.log
          echo "Content of runtime_params.log:"
          cat runtime_params.log
        else
          echo "❌ [WARNING] File 'runtime_params.log' NOT FOUND in project root: $(pwd)"
          echo "Files in current directory:"
          ls -lh
        fi


        echo "" >> $LOG_FILE
        echo "📊 Generating tests markdown summary..." >> $LOG_FILE

        pixi run python temp-ci/json_to_md.py \
        --input "markdown/pytest-report.json" \
        --output "markdown/TEST-REPORT.md" \
        --log_long "outputs/raw-test-output.log" \
        --log_short "outputs/short-test-output.log" \
        --params "markdown/runtime_params.json" \
        >> "outputs/md-report.log" 2>&1 && {
          echo "✅ Tests markdown generated" >> $LOG_FILE
        } || {
            echo "❌ Tests markdown generation failed" >> $LOG_FILE
            echo "🪵 Extracting markdown generation error:" >> $LOG_FILE
            cat outputs/md-report.log >> $LOG_FILE
            echo "Exit Code: 1" >> $LOG_FILE
            exit 1
        }

        echo "" >> $LOG_FILE
        echo "🌳 Generating JSON tree view..." >> $LOG_FILE
        pixi run python temp-ci/json_to_tree.py \
          "markdown/pytest-report.json" \
          >> "outputs/json-tree-gen.log" 2>&1 && {
          echo "✅ JSON tree view generated" >> $LOG_FILE
        } || {
          echo "❌ JSON tree generation failed" >> $LOG_FILE
          echo "🪵 Extracting json file error:" >> $LOG_FILE
          cat outputs/json-tree-gen.log >> $LOG_FILE
          echo "Exit Code: 1" >> $LOG_FILE
          exit 1
        }

        rm -rf ./temp-test-ci 
        echo "Exit Code: 0" >> $LOG_FILE

    - name: Run custom shell commands after 
      if: inputs.custom_shell_commands_after != ''
      shell: bash
      run: |
        OUTPUT_DIR="outputs"
        LOG_FILE="${OUTPUT_DIR}/custom-shell_after.log"

        mkdir -p "$OUTPUT_DIR"

        echo "📜 Executing custom shell commands..."
        echo "${{ inputs.custom_shell_commands_after }}" >> custom_commands_bis.sh
        chmod +x custom_commands_bis.sh

        # bash -e ./custom_commands_bis.sh >> $LOG_FILE 2>&1

        ./custom_commands_bis.sh >> $LOG_FILE 2>&1

        cat $LOG_FILE

        echo "✅ Custom shell executed" >> $LOG_FILE
        echo "Exit Code: 0" >> $LOG_FILE

    - name: Commit and push reports
      shell: bash
      run: |
        echo "📤 Committing test reports..."
        git config user.name "ci-bot"
        git config user.email "ci-bot@example.com"
        git add markdown/
        git commit -m "CI: update test report and coverage files" || echo "⚠️ Nothing to commit"

        echo "🚀 Pushing to branch '${{ inputs.ci-branch }}'..."
        git push https://ci-token:${{ inputs.ci-token }}@${{ inputs.gitea-domain }}/${{ inputs.repo-path }}.git HEAD:${{ inputs.ci-branch }} > push.log 2>&1 || {
          echo "❌ Push failed"
          cat push.log
          exit 1
        }
        echo "✅ Reports pushed"

    - name: Clone Gitea Wiki
      shell: bash
      env:
        CI_TOKEN: ${{ inputs.ci-token }}
      run: |
        REPO_NAME="${{ github.repository }}"
        DOMAIN="${{ inputs.gitea-domain }}"
        WIKI_REPO="https://ci-token:${CI_TOKEN}@${DOMAIN}/${REPO_NAME}.wiki.git"

        OUTPUT_DIR="outputs"
        LOG_FILE="${OUTPUT_DIR}/wiki-clone.log"

        mkdir -p "$OUTPUT_DIR"

        echo "📚 Cloning wiki repo: $WIKI_REPO" >> $LOG_FILE

        git clone "$WIKI_REPO" wiki >> wiki_clone.log 2>&1 && {
          echo "✅ Wiki cloned to ./wiki" >> $LOG_FILE
        } || {
          echo "❌ Wiki clone failed" >> $LOG_FILE
          cat wiki_clone.log >> $LOG_FILE
          echo "Exit Code: 1" >> $LOG_FILE
          exit 1
        }

        SHORT_SHA=$(git rev-parse --short HEAD)
        REPO_URL="https://${{ inputs.gitea-domain }}/${{ github.repository }}"
        RUN_LINK="${REPO_URL}/actions/runs/${GITHUB_RUN_NUMBER}"

        echo "🌳 Generating wiki reports..." >> $LOG_FILE

        TEST_FILE="run-${GITHUB_RUN_NUMBER}-TEST-commit-${SHORT_SHA}.md"
        COVERAGE_FILE="run-${GITHUB_RUN_NUMBER}-COVERAGE-commit-${SHORT_SHA}.md"

        echo "## Test Report" > "wiki/${TEST_FILE}"
        echo "[View CI Run ${GITHUB_RUN_NUMBER}](${RUN_LINK}) | [Commit ${SHORT_SHA}](${REPO_URL}/commit/${SHORT_SHA})" >> "wiki/${TEST_FILE}"
        cat markdown/TEST-REPORT.md >> "wiki/${TEST_FILE}"

        echo "## Coverage Report" > "wiki/${COVERAGE_FILE}"
        echo "[View CI Run ${GITHUB_RUN_NUMBER}](${RUN_LINK}) | [Commit ${SHORT_SHA}](${REPO_URL}/commit/${SHORT_SHA})" >> "wiki/${COVERAGE_FILE}"
        cat markdown/coverage-summary.md >> "wiki/${COVERAGE_FILE}"

        HOME_FILE="wiki/Home.md"
        TEMP_CONTENT=$(mktemp)

        {
          echo "# Test Reports History"
          echo ""
          echo "## Latest Run"
          echo "- [run ${GITHUB_RUN_NUMBER} TEST commit ${SHORT_SHA}](${TEST_FILE})"
          echo "- [run ${GITHUB_RUN_NUMBER} COVERAGE commit ${SHORT_SHA}](${COVERAGE_FILE})"
          echo ""
          echo "## Previous Runs"
          
          if [[ -f "${HOME_FILE}" && -s "${HOME_FILE}" ]]; then
            sed -n '/## Latest Run/{n;p;n;p}' "${HOME_FILE}"
            sed -n '/## Previous Runs/,$p' "${HOME_FILE}" | tail -n +2 | grep -v "^#" || true
          fi
        } > "${TEMP_CONTENT}" 2> reports.log 2>&1 && {
          echo "✅ Wiki report preparation succeeded" >> $LOG_FILE
        } || {
          echo "❌ Wiki report preparation failed" >> $LOG_FILE
          cat reports.log >> $LOG_FILE
          echo "Exit Code: 1" >> $LOG_FILE
          exit 1
        }

        mv "${TEMP_CONTENT}" "${HOME_FILE}"
        echo "Exit Code: 0" >> $LOG_FILE


    - name: Commit and push wiki
      shell: bash
      env:
        CI_TOKEN: ${{ inputs.ci-token }}
      run: |
        OUTPUT_DIR="$(pwd)/outputs"
        LOG_FILE="${OUTPUT_DIR}/commit-push-wiki.log"

        mkdir -p "$OUTPUT_DIR"

        echo "🚀 Pushing wiki changes..." >> $LOG_FILE
        cd wiki

        git config user.name "ci-bot"
        git config user.email "ci-bot@example.com"
        git add .

        if git commit -m "Update wiki with run ${GITHUB_RUN_NUMBER}"; then
          REPO_NAME="${{ github.repository }}"
          DOMAIN="${{ inputs.gitea-domain }}"
          WIKI_REPO="https://ci-token:${CI_TOKEN}@${DOMAIN}/${REPO_NAME}.wiki.git"
          git push "$WIKI_REPO" HEAD:main >> git.log 2>&1 || {
            echo "❌ Push failed: Unable to push wiki changes" >> $LOG_FILE
            cat git.log >> $LOG_FILE
            echo "Exit Code: 1" >> $LOG_FILE
            exit 1
          }
          echo "✅ Wiki updated successfully" >> $LOG_FILE
        else
          echo "⚠️ No changes to commit" >> $LOG_FILE
        fi
        echo "Exit Code: 0" >> $LOG_FILE

    - name: Log wiki report URLs
      shell: bash
      run: |
        OUTPUT_DIR="outputs"
        LOG_FILE=""$OUTPUT_DIR"/wiki-report-urls.log"

        mkdir -p "$OUTPUT_DIR"

        REPO_URL="https://${{ inputs.gitea-domain }}/${{ github.repository }}"
        SHORT_SHA=$(git rev-parse --short HEAD)
        echo "🔗 Wiki Test Report URL:" >> $LOG_FILE
        echo "  ${REPO_URL}/wiki/run-${GITHUB_RUN_NUMBER}-TEST-commit-${SHORT_SHA}.md" >> $LOG_FILE
        echo "🔗 Wiki Coverage Report URL:" >> $LOG_FILE
        echo "  ${REPO_URL}/wiki/run-${GITHUB_RUN_NUMBER}-COVERAGE-commit-${SHORT_SHA}.md" >> $LOG_FILE
        echo "Exit Code: 0" >> $LOG_FILE