Apply black formatting

Fixes #57

.github/workflows/test.yml

@@ -10,9 +10,9 @@ jobs:
   pre-commit:
       runs-on: ubuntu-latest
       steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - uses: pre-commit/action@v3.0.1
@@ -23,17 +23,17 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -e ".[dev]"
+        pip install -e . --group dev
 
     # - name: Run mypy
     #   run: |

.readthedocs.yml

@@ -1,15 +1,16 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.13"
-
+  commands:
-sphinx:
+    - pip install cmake
-  configuration: docs/source/conf.py
+    - pip install -r docs/requirements.txt
-
+    - pip install -e .
-python:
+    - cmake --workflow --preset documentation-workflow
-  install:
+    # Copy built documentation to Read the Docs output directory
-    - requirements: docs/requirements.txt
+    - mkdir -p $READTHEDOCS_OUTPUT/html
-    - method: pip
+    - cp -r build/html/* $READTHEDOCS_OUTPUT/html/
-      path: .
+    - cp -r build/markdown/* $READTHEDOCS_OUTPUT/html/
+    - cp -r build/rst/* $READTHEDOCS_OUTPUT/html/

CHANGELOG.rst

@@ -1,6 +1,30 @@
 Changelog
 =========
 
+0.7.0
+-----
+
+- Add :confval:`llms_txt_uri_template` configuration option to control the link behavior in :confval:`llms_txt_filename`.
+  `#48 <https://github.com/jdillard/sphinx-llms-txt/pull/48>`_
+
+0.6.0
+-----
+
+- Improve _sources directory handling
+  `#47 <https://github.com/jdillard/sphinx-llms-txt/pull/47>`_
+
+0.5.3
+-----
+
+- Make sphinx a required dependency since there are imports from Sphinx
+  `#44 <https://github.com/jdillard/sphinx-llms-txt/pull/44>`_
+
+0.5.2
+-----
+
+- Remove support for singlehtml
+  `#40 <https://github.com/jdillard/sphinx-llms-txt/pull/40>`_
+
 0.5.1
 -----
 

CMakeLists.txt

@@ -0,0 +1,8 @@
+cmake_minimum_required(VERSION 3.15)
+project(SphinxLLMsTxt VERSION 1.0.0 LANGUAGES NONE)
+
+# Add CMake module path
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+
+# Add documentation
+add_subdirectory(docs)

CMakePresets.json

@@ -0,0 +1,53 @@
+{
+  "version": 6,
+  "configurePresets": [
+    {
+      "name": "documentation",
+      "displayName": "Documentation Build",
+      "description": "Configure project with documentation environment setup",
+      "binaryDir": "${sourceDir}/build"
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "html",
+      "displayName": "Build HTML Documentation",
+      "configurePreset": "documentation",
+      "targets": ["html"]
+    },
+    {
+      "name": "markdown",
+      "displayName": "Build Markdown Documentation",
+      "configurePreset": "documentation",
+      "targets": ["markdown"]
+    },
+    {
+      "name": "rst",
+      "displayName": "Build reStructuredText Documentation",
+      "configurePreset": "documentation",
+      "targets": ["rst"]
+    },
+    {
+      "name": "docs-parallel",
+      "displayName": "Build HTML and Markdown in parallel",
+      "configurePreset": "documentation",
+      "targets": ["html", "markdown", "rst"]
+    }
+  ],
+  "workflowPresets": [
+    {
+      "name": "documentation-workflow",
+      "displayName": "Documentation Build Workflow",
+      "steps": [
+        {
+          "type": "configure",
+          "name": "documentation"
+        },
+        {
+          "type": "build",
+          "name": "docs-parallel"
+        }
+      ]
+    }
+  ]
+}

cmake/SphinxUtils.cmake

@@ -0,0 +1,28 @@
+# Sphinx related utilities
+
+set(SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/source)
+set(SPHINX_BUILD ${CMAKE_BINARY_DIR})
+
+# Function to find Sphinx in the system
+function(setup_sphinx_environment)
+    # Find sphinx-build executable in system
+    find_program(SPHINX_EXECUTABLE
+        NAMES sphinx-build
+        DOC "Sphinx documentation generator"
+    )
+
+    if(NOT SPHINX_EXECUTABLE)
+        message(FATAL_ERROR "sphinx-build not found. Please install Sphinx.")
+    endif()
+
+    # Export to parent scope
+    set(SPHINX_EXECUTABLE "${SPHINX_EXECUTABLE}" PARENT_SCOPE)
+endfunction()
+
+# Function to add a Sphinx builder target
+function(add_sphinx_builder builder_name)
+    add_custom_target(${builder_name}
+        COMMAND ${SPHINX_EXECUTABLE} -b ${builder_name} ${SPHINX_SOURCE} ${SPHINX_BUILD}/${builder_name}
+        VERBATIM
+    )
+endfunction()

docs/CMakeLists.txt

@@ -0,0 +1,7 @@
+include(SphinxUtils)
+
+setup_sphinx_environment()
+
+add_sphinx_builder(html)
+add_sphinx_builder(markdown)
+add_sphinx_builder(rst)

docs/requirements.txt

@@ -3,4 +3,7 @@ esbonio
 sphinx-contributors
 sphinx
 sphinx-llms-txt
+sphinx-inline-tabs
 sphinxext-opengraph
+sphinx-markdown-builder
+sphinxcontrib-restbuilder

docs/source/advanced-configuration.rst

@@ -261,6 +261,99 @@ If you want to include absolute URLs for resources in your documentation, you ca
 
 When this option is set, all resolved paths in directives will be prefixed with this URL, creating absolute paths in the generated files.
 
+.. _customizing_uri_links:
+
+Customizing URI Links in llms.txt
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+By default, the ``llms.txt`` file links to source files in the ``_sources`` directory when available, falling back to HTML pages when sources aren't available.
+You can customize this behavior using URI templates with :confval:`llms_txt_uri_template`:
+
+.. code-block:: python
+
+   # Default: Link to source files, if _sources exists
+   llms_txt_uri_template = "{base_url}_sources/{docname}{suffix}{sourcelink_suffix}"
+
+   # Default: Link to HTML pages instead, if _sources doesn't exist
+   llms_txt_uri_template = "{base_url}{docname}.html"
+
+   # Manual: Link to a custom markdown build
+   llms_txt_uri_template = "{base_url}{docname}.md"
+
+.. _available_template_variables:
+
+Available Template Variables
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Your URI template can use the following variables:
+
+- ``{base_url}`` - The base URL from ``html_baseurl`` configuration (includes trailing slash)
+- ``{docname}`` - The document name (e.g., ``index``, ``guide/intro``)
+- ``{suffix}`` - The source file suffix (e.g., ``.rst``, ``.md``) - may be empty if no source file exists
+- ``{sourcelink_suffix}`` - The suffix from ``html_sourcelink_suffix`` configuration (e.g., ``.txt``)
+
+.. tip::
+   Instead of using the default of linking to ``_sources``, you can generate Markdown and/or reStructuredText files from your documentation and link to those in ``llms.txt``.
+   See :ref:`cmake_workflow` for an example of building both HTML and Markdown and/or reStructuredText in parallel.
+   Note that ``_sources`` is still needed for ``llms-full.txt`` at this time.
+
+.. _cmake_workflow:
+
+CMake Workflow
+^^^^^^^^^^^^^^
+
+This project uses CMake to orchestrate documentation builds across multiple output formats, serving as a simple demo of the functionality.
+Building multiple formats allows you to compare what works best for your docs, as well as allows users to choose which format to feed to their LLM.
+This approach enables parallel builds and integrates well with CI/CD platforms like Read the Docs.
+
+Key Files
+~~~~~~~~~
+
+.. code-block:: text
+
+   .
+   ├── .readthedocs.yml
+   ├── CMakeLists.txt
+   ├── CMakePresets.json
+   ├── cmake/
+   │   └── SphinxUtils.cmake
+   └── docs/
+       └── CMakeLists.txt
+
+:ghfile:`.readthedocs.yml`
+   A Read The Docs config file that installs dependencies, then runs the full documentation workflow which builds all output formats in parallel, and copies them into a single deploy location.
+
+:ghfile:`CMakeLists.txt`
+   A CMake config file that sets up the project and includes the ``cmake/`` module path.
+
+:ghfile:`docs/CMakeLists.txt`
+   A CMake config file that includes the Sphinx utilities and defines the documentation-specific build targets.
+
+:ghfile:`cmake/SphinxUtils.cmake`
+   A CMake module that provides Sphinx related utilities.
+
+:ghfile:`CMakePresets.json`
+   Defines presets for configuring and building documentation:
+
+   - **Configure Presets:** Sets up the build directory.
+   - **Build Presets:** Defines Build formats individually and all in parallel.
+   - **Workflow Presets:** Runs the configure preset followed by the parallel build preset.
+
+Usage
+~~~~~
+
+To build documentation locally using CMake:
+
+.. code-block:: console
+
+   # Run the full workflow (configure + build all formats)
+   cmake --workflow --preset documentation-workflow
+
+   # Or configure and build separately
+   cmake --preset documentation
+   cmake --build --preset html        # Build HTML only
+   cmake --build --preset docs-parallel  # Build all formats
+
 .. _integration_examples:
 
 Integration Examples
@@ -285,6 +378,7 @@ Here's a complete example showing multiple :doc:`configuration-values`:
    This is a comprehensive documentation set for our project.
    It includes API references, usage examples, and tutorials.
    """
+   llms_txt_uri_template = "{base_url}{docname}.md"
 
    # Path handling
    html_baseurl = "https://docs.example.com/"

docs/source/conf.py

@@ -15,12 +15,21 @@ import subprocess
 project = "sphinx-llms-txt"
 copyright = "Jared Dillard"
 author = "Jared Dillard"
+
+llms_txt_uri_template = "{base_url}{docname}.md"
 llms_txt_code_files = ["+:../../sphinx_llms_txt/*.py"]
 llms_txt_summary = """
 A Sphinx extension that generates a summary llms.txt file,written in Markdown,
 and a single combined documentation llms-full.txt file, written in reStructuredText.
 """
 
+# This doesn't seem to be supported
+# rst_file_suffix = ".html.rst"
+
+extlinks = {
+    "ghfile": ("https://github.com/jdillard/sphinx-llms-txt/blob/main/%s", "%s")
+}
+
 # check if the current commit is tagged as a release (vX.Y.Z)
 try:
     GIT_TAG_OUTPUT = subprocess.check_output(["git", "tag", "--points-at", "HEAD"])
@@ -49,6 +58,9 @@ extensions = [
     "sphinx.ext.intersphinx",
     "sphinx_contributors",
     "sphinx_llms_txt",
+    "sphinxcontrib.restbuilder",
+    "sphinx_inline_tabs",
+    "sphinx.ext.extlinks",
 ]
 
 # The language for content autogenerated by Sphinx. Refer to documentation
@@ -88,7 +100,7 @@ html_theme_options = {
     "source_directory": "docs/source/",
 }
 
-html_baseurl = "https://sphinx-llms-txt.readthedocs.org/"
+html_baseurl = "https://sphinx-llms-txt.readthedocs.org/en/latest/"
 
 
 # -- Options for HTMLHelp output ---------------------------------------------

docs/source/configuration-values.rst

@@ -58,6 +58,15 @@ Project Configuration Values
 
    .. versionadded:: 0.2.0
 
+.. confval:: llms_txt_uri_template
+
+   - **Type**: string or ``None``
+   - **Default**: ``None``
+   - **Description**: Template string for generating URIs in ``llms.txt``.
+     See :ref:`customizing_uri_links`.
+
+   .. versionadded:: 0.7.0
+
 .. confval:: llms_txt_directives
 
    - **Type**: list of strings

docs/source/contributing.rst

@@ -19,7 +19,7 @@ Local development
 
    .. code-block:: console
 
-      pip install -e ".[dev]"
+      pip install -e . --group dev
 
 #. Install pre-commit Git hook scripts:
 

docs/source/getting-started.rst

@@ -4,17 +4,19 @@ Getting Started
 Installation
 ------------
 
-Directly install via ``pip`` by using:
+Directly install by using:
 
-.. code-block:: bash
+.. tab:: via pip
 
-    pip install sphinx-llms-txt
+   .. code-block:: bash
 
-Or with ``conda`` via ``conda-forge``:
+      pip install sphinx-llms-txt
 
-.. code::
+.. tab:: via conda:
 
-   conda install -c conda-forge sphinx-llms-txt
+   .. code-block:: bash
+
+      conda install -c conda-forge sphinx-llms-txt
 
 Usage
 -----
@@ -32,7 +34,45 @@ After the HTML finishes building, **sphinx-llms-txt** will output the location o
     sphinx-llms-txt: Created /path/to/_build/html/llms-full.txt with 45 sources and 6879 lines
     sphinx-llms-txt: created /path/to/_build/html/llms.txt
 
+Choosing an Output Format
+-------------------------
 
-.. tip:: Make sure to confirm the accuracy of the output files after installs and upgrades.
+By default, **sphinx-llms-txt** requires no additional configuration and links to raw reStructuredText source files in :confval:`_sources/ <sphinx:html_copy_source>`.
+For optimal LLM support, you can use `sphinx-markdown-builder`_ and/or `sphinxcontrib-restbuilder`_, set up in parallel builds using :ref:`CMake <cmake_workflow>`.
+
+.. list-table:: Output Format Comparison
+   :header-rows: 1
+   :widths: 18 27 27 27
+
+   * -
+     - Default (no config)
+     - Markdown (CMake)
+     - RST (CMake)
+   * - **Format**
+     - Raw RST source
+     - Rendered Markdown
+     - Rendered RST
+   * - **LLM Readability**
+     - Good - preserves structure for simple syntax
+     - Excellent - native LLM format
+     - Good - Can provide more structured content
+   * - **Key Advantage**
+     - Zero setup required
+     - More compact (less input tokens)
+     - Can preserve Sphinx semantics
+   * - **Key Disadvantage**
+     - Raw directives (e.g., autodoc) won't be parsed
+     - Loses structure from complex directives
+     - Can lose structure from complex directives
+   * - **llms-full.txt support**
+     - Suported with above caveats
+     - Pending `support <https://github.com/liran-funaro/sphinx-markdown-builder/pull/37>`__
+     - Pending `support <https://github.com/sphinx-contrib/restbuilder/pull/35>`__
+
+
+See :ref:`cmake_workflow` for an example of building HTML, Markdown, and RST in parallel.
+Use :confval:`llms_txt_uri_template` to configure links to point to your preferred format.
+
+.. _sphinx-markdown-builder: https://pypi.org/project/sphinx-markdown-builder/
+.. _sphinxcontrib-restbuilder: https://pypi.org/project/sphinxcontrib-restbuilder/
 
-See :doc:`advanced-configuration` for more information about how to use **sphinx-llms-txt**.

docs/source/index.rst

@@ -13,16 +13,16 @@ You can see this Sphinx project's `llms.txt`_ and `llms-full.txt`_ files as a si
 Highlights
 ----------
 
-1. **Content Collection**: Quickly gathers content from _sources, without needing a separate build
+**Zero Configuration**
-2. **Directive Processing**: Resolves ``include`` directives by automatically incorporating their content
+   Add the extension to your ``conf.py`` and you're done.
-3. **Path Resolution**: Transforms relative paths in directives to full paths
+   The extension automatically collects your documentation and generates both ``llms.txt`` and ``llms-full.txt`` during your normal Sphinx build.
-4. **Output Generation**: Creates two optional files:
 
-   - ``llms.txt``: A concise summary of your documentation, in Markdown
+**Intelligent Content Processing**
-   - ``llms-full.txt``: A comprehensive version with all documentation content, in reStructuredText
+   Automatically resolves ``include`` directives, transforms relative paths, and handles your documentation structure without manual intervention.
 
-5. **Content Filtering**: Allows you to exclude specific pages or sections
+**Customizable When Needed**
-6. **Source Code**: Allows you to include specific source code files
+   Filter content, include source code files, or integrate with alternative output formats like Markdown for even better LLM compatibility.
+   See :doc:`getting-started` for output format options and :doc:`configuration-values` for all settings.
 
 .. toctree::
    :maxdepth: 2

pyproject.toml

@@ -26,13 +26,16 @@ classifiers = [
 license = {text = "MIT"}
 readme = "README.md"
 dynamic = ["version"]
+dependencies = [
+    "sphinx",
+]
 
 [project.urls]
 download = "https://pypi.org/project/sphinx-llms-txt/"
 source = "https://github.com/jdillard/sphinx-llms-txt"
 changelog = "https://github.com/jdillard/sphinx-llms-txt/blob/master/CHANGELOG.rst"
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "pytest>=7.0.0",
     "black",
@@ -40,12 +43,13 @@ dev = [
     "mypy",
     "isort",
     "pre-commit",
-    "sphinx",
 ]
 test = [
     "pytest>=7.0.0",
 ]
 
+[tool.setuptools]
+  packages = ["sphinx_llms_txt"]
 
 [tool.setuptools.dynamic]
 version = {attr = "sphinx_llms_txt.__version__"}

sphinx_llms_txt/__init__.py

@@ -21,7 +21,7 @@ from .manager import LLMSFullManager
 from .processor import DocumentProcessor
 from .writer import FileWriter
 
-__version__ = "0.5.1"
+__version__ = "0.7.0"
 
 # Export classes needed by tests
 __all__ = [
@@ -85,6 +85,7 @@ def build_finished(app: Sphinx, exception):
         config = {
             "llms_txt_file": app.config.llms_txt_file,
             "llms_txt_filename": app.config.llms_txt_filename,
+            "llms_txt_uri_template": app.config.llms_txt_uri_template,
             "llms_txt_title": app.config.llms_txt_title,
             "llms_txt_summary": summary,
             "llms_txt_full_file": app.config.llms_txt_full_file,
@@ -115,6 +116,7 @@ def setup(app: Sphinx) -> Dict[str, Any]:
 
     app.add_config_value("llms_txt_file", True, "env")
     app.add_config_value("llms_txt_filename", "llms.txt", "env")
+    app.add_config_value("llms_txt_uri_template", None, "env")
     app.add_config_value("llms_txt_full_file", True, "env")
     app.add_config_value("llms_txt_full_filename", "llms-full.txt", "env")
     app.add_config_value("llms_txt_full_max_size", None, "env")
@@ -129,7 +131,7 @@ def setup(app: Sphinx) -> Dict[str, Any]:
     def builder_inited(app):
         """Used to limit what builders are allowed to run the extension."""
 
-        allowed_builders = ["html", "singlehtml", "dirhtml"]
+        allowed_builders = ["html", "dirhtml"]
         if hasattr(app, "builder") and app.builder.name in allowed_builders:
             # Reset manager and root paragraph for each build
             global _manager, _root_first_paragraph

sphinx_llms_txt/manager.py

@@ -197,7 +197,6 @@ class LLMSFullManager:
         possible_sources = [
             Path(outdir) / "_sources",
             Path(outdir) / "html" / "_sources",
-            Path(outdir) / "singlehtml" / "_sources",
         ]
 
         for path in possible_sources:
@@ -205,25 +204,43 @@ class LLMSFullManager:
                 sources_dir = path
                 break
 
-        if not sources_dir:
+        # Get the correct page order (with or without source suffixes)
-            logger.warning(
-                "Could not find _sources directory, skipping llms-full creation"
-            )
-            return
-
-        # Get the correct page order with source suffixes
         page_order = self.collector.get_page_order(sources_dir)
 
         if not page_order:
-            logger.warning(
+            logger.warning("Could not determine page order, skipping file generation")
-                "Could not determine page order, skipping llms-full creation"
-            )
             return
 
         # Apply exclusion filter if configured
         page_order = self.collector.filter_excluded_pages(page_order)
 
-        # Determine output file name and location
+        # If no sources directory, only generate llms.txt and return early
+        if not sources_dir:
+            # Generate llms.txt if requested
+            if self.config.get("llms_txt_file"):
+                filtered_page_order = self._filter_ignored_pages(page_order)
+                self.writer.write_verbose_info_to_file(
+                    filtered_page_order,
+                    self.collector.page_titles,
+                    0,  # No line count since no llms-full.txt
+                    sources_dir,
+                )
+
+            # Only warn if user explicitly wants llms-full.txt
+            if self.config.get("llms_txt_full_file"):
+                # Check if html_copy_source is False
+                if self.app and not self.app.config.html_copy_source:
+                    logger.warning(
+                        "Could not find _sources directory, skipping llms-full.txt."
+                        "Set html_copy_source = True in conf.py to enable."
+                    )
+                else:
+                    logger.warning(
+                        "Could not find _sources directory, skipping llms-full.txt"
+                    )
+            return
+
+        # Determine output file name and location for llms-full.txt
         output_filename = self.config.get("llms_txt_full_filename")
         output_path = Path(outdir) / output_filename
 
@@ -507,6 +524,7 @@ class LLMSFullManager:
                         filtered_page_order,
                         self.collector.page_titles,
                         total_line_count,
+                        sources_dir,
                     )
                 return
             elif action == "note":
@@ -520,6 +538,7 @@ class LLMSFullManager:
                         filtered_page_order,
                         self.collector.page_titles,
                         total_line_count,
+                        sources_dir,
                     )
                 return
             elif action == "keep":
@@ -538,7 +557,10 @@ class LLMSFullManager:
         if success and self.config.get("llms_txt_file"):
             filtered_page_order = self._filter_ignored_pages(page_order)
             self.writer.write_verbose_info_to_file(
-                filtered_page_order, self.collector.page_titles, total_line_count
+                filtered_page_order,
+                self.collector.page_titles,
+                total_line_count,
+                sources_dir,
             )
 
     def _read_source_file(self, file_path: Path, docname: str) -> Tuple[str, int]:

sphinx_llms_txt/processor.py

@@ -128,8 +128,11 @@ class DocumentProcessor:
         Returns:
             Processed content with directive paths properly resolved
         """
+        # Get code block ranges to skip directives inside them
+        code_block_ranges = self._get_code_block_ranges(content)
+
         # Get the configured path directives to process
-        default_path_directives = ["image", "figure"]
+        default_path_directives = ["image", "figure", "literalinclude"]
         custom_path_directives = self.config.get("llms_txt_directives")
         path_directives = set(default_path_directives + custom_path_directives)
 
@@ -143,6 +146,11 @@ class DocumentProcessor:
         is_test = "pytest" in str(source_path) and "subdir" in str(source_path)
 
         def replace_directive_path(match, base_url=base_url, is_test=is_test):
+            # Check if this directive is within a code block
+            if self._is_in_code_block(match.start(), code_block_ranges):
+                # This directive is inside a code block, don't process it
+                return match.group(0)
+
             prefix = match.group(1)  # The entire directive prefix including whitespace
             path = match.group(3).strip()  # The path argument
 
@@ -276,6 +284,71 @@ class DocumentProcessor:
 
         return possible_paths
 
+    def _get_code_block_ranges(self, content: str) -> List[Tuple[int, int]]:
+        """Find all code block ranges in the content.
+
+        Args:
+            content: The source content to analyze
+
+        Returns:
+            List of (start, end) tuples representing code block character
+            ranges
+        """
+        code_block_ranges = []
+
+        # Match code block as well as `code` and `sourcecode` aliases
+        code_block_pattern = re.compile(
+            r"^(\s*)\.\.\s+(code-block|code|sourcecode)::\s*\S*\s*$", re.MULTILINE
+        )
+
+        for match in code_block_pattern.finditer(content):
+            start_pos = match.start()
+            indent = match.group(1)
+            indent_len = len(indent)
+
+            # Find the end of the code block by looking for the next line
+            # that is not indented more than the directive
+            block_start = match.end()
+            pos = block_start
+
+            # Skip any blank lines immediately after the directive
+            while pos < len(content) and content[pos] in "\n":
+                pos += 1
+
+            # Find where the code block ends
+            lines = content[pos:].split("\n")
+            block_end = pos
+            for line in lines:
+                if line.strip():  # Non-empty line
+                    # Check indentation level
+                    line_indent = len(line) - len(line.lstrip())
+                    if line_indent <= indent_len:
+                        # The block ends when we find a line that is indented
+                        # less than the directive itself
+                        break
+                block_end += len(line) + 1  # +1 for the newline
+
+            code_block_ranges.append((start_pos, block_end))
+
+        return code_block_ranges
+
+    def _is_in_code_block(
+        self, match_start: int, code_block_ranges: List[Tuple[int, int]]
+    ) -> bool:
+        """Check if a match position is within a code block.
+
+        Args:
+            match_start: The starting position of the match
+            code_block_ranges: List of (start, end) tuples for code blocks
+
+        Returns:
+            True if the match is within a code block, False otherwise
+        """
+        for block_start, block_end in code_block_ranges:
+            if block_start <= match_start < block_end:
+                return True
+        return False
+
     def _process_includes(self, content: str, source_path: Path) -> str:
         """Process include directives in content.
 
@@ -286,11 +359,18 @@ class DocumentProcessor:
         Returns:
             Processed content with include directives replaced with included content
         """
+        code_block_ranges = self._get_code_block_ranges(content)
+
         # Find all include directives using regex
         include_pattern = build_directive_pattern(["include"])
 
         # Function to replace each include with content
         def replace_include(match):
+            # Check if this include is within a code block
+            if self._is_in_code_block(match.start(), code_block_ranges):
+                # This include is inside a code block, don't process it
+                return match.group(0)
+
             include_path = match.group(3)
             directive_part = match.group(
                 1

sphinx_llms_txt/writer.py

@@ -19,6 +19,42 @@ class FileWriter:
         self.outdir = outdir
         self.app = app
 
+    def _resolve_uri_template(self, sources_dir: Path = None) -> str:
+        """Resolve which URI template to use based on configuration and sources_dir.
+
+        Args:
+            sources_dir: Path to _sources directory (None if not found)
+
+        Returns:
+            The template string to use for generating URIs
+        """
+        # If custom template exists
+        custom_template = self.config.get("llms_txt_uri_template")
+
+        if custom_template:
+            # Validate user's template by checking for valid variable names
+            try:
+                # Try formatting with test valid values to validate syntax
+                test_values = {
+                    "base_url": "http://example.com/",
+                    "docname": "test",
+                    "suffix": ".rst",
+                    "sourcelink_suffix": ".txt",
+                }
+                custom_template.format(**test_values)
+                return custom_template
+            except (KeyError, ValueError) as e:
+                logger.warning(
+                    f"sphinx-llms-txt: Invalid llms_txt_uri_template: {e}. "
+                    f"Falling back to default."
+                )
+
+        # Else, use one of the default templates
+        if sources_dir:
+            return "{base_url}_sources/{docname}{suffix}{sourcelink_suffix}"
+        else:
+            return "{base_url}{docname}.html"
+
     def write_combined_file(
         self, content_parts: List[str], output_path: Path, total_line_count: int
     ) -> bool:
@@ -50,6 +86,7 @@ class FileWriter:
         page_order: Union[List[str], List[Tuple[str, str]]],
         page_titles: Dict[str, str],
         total_line_count: int = 0,
+        sources_dir: Path = None,
     ) -> bool:
         """Write summary information to the llms.txt file.
 
@@ -57,6 +94,7 @@ class FileWriter:
             page_order: Ordered list of document names or (docname, suffix) tuples
             page_titles: Dictionary mapping docnames to titles
             total_line_count: Total number of lines in the combined content
+            sources_dir: Path to _sources directory (None if not found)
 
         Returns:
             True if successful, False otherwise
@@ -102,14 +140,37 @@ class FileWriter:
                 if not base_url.endswith("/"):
                     base_url += "/"
 
+                # Get sourcelink suffix from Sphinx config
+                sourcelink_suffix = ""
+                if self.app and hasattr(self.app.config, "html_sourcelink_suffix"):
+                    sourcelink_suffix = self.app.config.html_sourcelink_suffix
+                    # Handle empty string case specially
+                    if sourcelink_suffix == "":
+                        sourcelink_suffix = ""  # Keep it empty
+                    elif not sourcelink_suffix.startswith("."):
+                        sourcelink_suffix = "." + sourcelink_suffix
+
+                # Resolve which template to use
+                uri_template = self._resolve_uri_template(sources_dir)
+
                 for item in page_order:
                     # Handle both old format (str) and new format (tuple)
                     if isinstance(item, tuple):
-                        docname, _ = item
+                        docname, suffix = item
                     else:
                         docname = item
+                        suffix = None
+
                     title = page_titles.get(docname, docname)
-                    f.write(f"- [{title}]({base_url}{docname}.html)\n")
+
+                    uri = uri_template.format(
+                        base_url=base_url,
+                        docname=docname,
+                        suffix=suffix or "",
+                        sourcelink_suffix=sourcelink_suffix,
+                    )
+
+                    f.write(f"- [{title}]({uri})\n")
 
             logger.info(f"sphinx-llms-txt: created {output_path}")
             return True

tests/test_llms_txt.py

@@ -198,6 +198,31 @@ def test_process_includes(tmp_path):
     assert processed_content == expected_content
 
 
+def test_process_includes_in_code_block(tmp_path):
+    """Test that an `include` within a `code-block` is not processed."""
+    # Create a processor
+    config = {"llms_txt_directives": []}
+    processor = DocumentProcessor(config)
+
+    # Create a source file that uses include syntax within a `code-block`
+    source_content = (
+        "Normal paragraph.\n\n"
+        ".. code-block:: rst\n\n"
+        "   .. include:: foo.txt\n\n"
+        "Another normal paragraph."
+    )
+    source_file = tmp_path / "source.txt"
+    with open(source_file, "w", encoding="utf-8") as f:
+        f.write(source_content)
+
+    # Run the include directive processor
+    processed_content = processor._process_includes(source_content, source_file)
+
+    # Check that the include directive was not processed
+    expected_content = source_content
+    assert processed_content == expected_content
+
+
 def test_process_includes_with_relative_paths(tmp_path):
     """Test that include directives with relative paths are processed correctly."""
     # Create a processor
@@ -794,6 +819,7 @@ def test_summary_default_uses_first_paragraph():
             llms_txt_summary = None  # Not configured
             llms_txt_file = True
             llms_txt_filename = "llms.txt"
+            llms_txt_uri_template = None
             llms_txt_title = None
             llms_txt_full_file = True
             llms_txt_full_filename = "llms-full.txt"
@@ -1031,3 +1057,128 @@ def test_code_files_ignored_patterns(tmp_path, caplog):
     assert (
         "Code file pattern 'docs/**/*.rst' ignored." in captured_warnings[0]
     ), f"Warning message should contain expected text. Got: {captured_warnings[0]}"
+
+
+def test_llms_txt_generated_without_sources_dir(tmp_path):
+    """Test that llms.txt is generated even when _sources directory doesn't exist."""
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Create manager
+    manager = LLMSFullManager()
+
+    # Set config to enable llms.txt
+    config = {
+        "llms_txt_file": True,
+        "llms_txt_filename": "llms.txt",
+        "llms_txt_full_file": True,
+        "llms_txt_full_filename": "llms-full.txt",
+        "llms_txt_exclude": [],
+        "llms_txt_directives": [],
+    }
+    manager.set_config(config)
+
+    # Create directories (but no _sources)
+    outdir = tmp_path / "build"
+    srcdir = tmp_path / "source"
+    outdir.mkdir()
+    srcdir.mkdir()
+
+    # Mock env with documents
+    class MockEnv:
+        all_docs = {"index": None, "about": None}
+        titles = {
+            "index": type("TitleNode", (), {"astext": lambda self: "Home"})(),
+            "about": type("TitleNode", (), {"astext": lambda self: "About"})(),
+        }
+        toctree_includes = {"index": ["about"]}
+
+    manager.set_env(MockEnv())
+    manager.set_master_doc("index")
+
+    # Update page titles directly in the collector
+    manager.update_page_title("index", "Home")
+    manager.update_page_title("about", "About")
+
+    # Call combine_sources - should generate llms.txt even without _sources
+    manager.combine_sources(str(outdir), str(srcdir))
+
+    # Verify llms.txt was created
+    llms_txt = outdir / "llms.txt"
+    assert llms_txt.exists(), "llms.txt should be generated even without _sources"
+
+    # Verify llms-full.txt was NOT created (since no _sources)
+    llms_full_txt = outdir / "llms-full.txt"
+    assert (
+        not llms_full_txt.exists()
+    ), "llms-full.txt should not be generated without _sources"
+
+    # Read llms.txt and verify it has content
+    with open(llms_txt, "r", encoding="utf-8") as f:
+        content = f.read()
+
+    # Should contain page titles and links
+    assert "Home" in content
+    assert "About" in content
+    assert "index.html" in content
+    assert "about.html" in content
+
+
+def test_llms_txt_no_warning_when_full_file_disabled(tmp_path, caplog):
+    """
+    Test that no warning is logged when llms_txt_full_file=False and
+    _sources doesn't exist.
+    """
+    from unittest.mock import patch
+
+    from sphinx_llms_txt.manager import LLMSFullManager
+
+    # Create manager
+    manager = LLMSFullManager()
+
+    # Set config with llms_txt_full_file=False
+    config = {
+        "llms_txt_file": True,
+        "llms_txt_filename": "llms.txt",
+        "llms_txt_full_file": False,  # User doesn't want llms-full.txt
+        "llms_txt_full_filename": "llms-full.txt",
+        "llms_txt_exclude": [],
+        "llms_txt_directives": [],
+    }
+    manager.set_config(config)
+
+    # Create directories (but no _sources)
+    outdir = tmp_path / "build"
+    srcdir = tmp_path / "source"
+    outdir.mkdir()
+    srcdir.mkdir()
+
+    # Mock env with documents
+    class MockEnv:
+        all_docs = {"index": None}
+        titles = {"index": type("TitleNode", (), {"astext": lambda self: "Home"})()}
+        toctree_includes = {"index": []}
+
+    manager.set_env(MockEnv())
+    manager.set_master_doc("index")
+    manager.update_page_title("index", "Home")
+
+    # Capture warnings
+    captured_warnings = []
+
+    def capture_warning(message, *args, **kwargs):
+        if "_sources" in str(message):
+            captured_warnings.append(message)
+
+    with patch("sphinx_llms_txt.manager.logger.warning", side_effect=capture_warning):
+        # Call combine_sources
+        manager.combine_sources(str(outdir), str(srcdir))
+
+    # Verify NO warning was logged since llms_txt_full_file=False
+    assert (
+        len(captured_warnings) == 0
+    ), "No warning should be logged when llms_txt_full_file=False"
+
+    # Verify llms.txt was still created
+    llms_txt = outdir / "llms.txt"
+    assert llms_txt.exists()

tests/test_uri_template.py

@@ -0,0 +1,175 @@
+"""Test URI template functionality for llms.txt links."""
+
+from sphinx_llms_txt import FileWriter
+
+
+def test_uri_template_with_sources_dir(tmp_path):
+    """Test that default template uses _sources links when sources_dir exists."""
+    build_dir = tmp_path / "build"
+    build_dir.mkdir()
+
+    # Create _sources directory to simulate its existence
+    sources_dir = build_dir / "_sources"
+    sources_dir.mkdir()
+
+    # Mock app with html_sourcelink_suffix
+    class MockApp:
+        class Config:
+            html_sourcelink_suffix = ".txt"
+
+        config = Config()
+
+    config = {
+        "llms_txt_file": True,
+        "llms_txt_filename": "llms.txt",
+        "llms_txt_uri_template": (
+            "{base_url}_sources/{docname}{suffix}{sourcelink_suffix}"
+        ),
+        "html_baseurl": "https://example.com",
+    }
+    writer = FileWriter(config, str(build_dir), MockApp())
+
+    page_titles = {
+        "index": "Home Page",
+        "about": "About Us",
+    }
+
+    # Page order with suffixes (simulating _sources files exist)
+    page_order = [("index", ".rst"), ("about", ".md")]
+
+    writer.write_verbose_info_to_file(page_order, page_titles, 0, sources_dir)
+
+    # Check that the file was created
+    verbose_file = build_dir / "llms.txt"
+    assert verbose_file.exists()
+
+    # Read the file content
+    with open(verbose_file, "r", encoding="utf-8") as f:
+        content = f.read()
+
+    # Should link to _sources files
+    assert "- [Home Page](https://example.com/_sources/index.rst.txt)" in content
+    assert "- [About Us](https://example.com/_sources/about.md.txt)" in content
+
+
+def test_uri_template_without_sources_dir(tmp_path):
+    """
+    Test that HTML template is used when sources_dir doesn't exist and no custom
+    template.
+    """
+    build_dir = tmp_path / "build"
+    build_dir.mkdir()
+
+    config = {
+        "llms_txt_file": True,
+        "llms_txt_filename": "llms.txt",
+        # No custom template set
+        "html_baseurl": "https://example.com",
+    }
+    writer = FileWriter(config, str(build_dir))
+
+    page_titles = {
+        "index": "Home Page",
+        "about": "About Us",
+    }
+
+    # Page order without suffixes (simulating no _sources)
+    page_order = [("index", None), ("about", None)]
+
+    # Pass None for sources_dir to simulate it doesn't exist
+    writer.write_verbose_info_to_file(page_order, page_titles, 0, None)
+
+    # Check that the file was created
+    verbose_file = build_dir / "llms.txt"
+    assert verbose_file.exists()
+
+    # Read the file content
+    with open(verbose_file, "r", encoding="utf-8") as f:
+        content = f.read()
+
+    # Should fallback to HTML links
+    assert "- [Home Page](https://example.com/index.html)" in content
+    assert "- [About Us](https://example.com/about.html)" in content
+
+
+def test_uri_template_custom(tmp_path):
+    """Test that custom URI template works correctly."""
+    build_dir = tmp_path / "build"
+    build_dir.mkdir()
+
+    sources_dir = build_dir / "_sources"
+    sources_dir.mkdir()
+
+    # Mock app with html_sourcelink_suffix
+    class MockApp:
+        class Config:
+            html_sourcelink_suffix = ".txt"
+
+        config = Config()
+
+    # Custom template that uses different path
+    config = {
+        "llms_txt_file": True,
+        "llms_txt_filename": "llms.txt",
+        "llms_txt_uri_template": "{base_url}raw/{docname}{suffix}",
+        "html_baseurl": "https://example.com/",
+    }
+    writer = FileWriter(config, str(build_dir), MockApp())
+
+    page_titles = {
+        "index": "Home Page",
+    }
+
+    page_order = [("index", ".rst")]
+
+    writer.write_verbose_info_to_file(page_order, page_titles, 0, sources_dir)
+
+    verbose_file = build_dir / "llms.txt"
+    with open(verbose_file, "r", encoding="utf-8") as f:
+        content = f.read()
+
+    # Should use custom template
+    assert "- [Home Page](https://example.com/raw/index.rst)" in content
+
+
+def test_uri_template_invalid_fallback(tmp_path):
+    """
+    Test that invalid template falls back to default sources template when
+    sources_dir exists.
+    """
+    build_dir = tmp_path / "build"
+    build_dir.mkdir()
+
+    sources_dir = build_dir / "_sources"
+    sources_dir.mkdir()
+
+    # Mock app with html_sourcelink_suffix
+    class MockApp:
+        class Config:
+            html_sourcelink_suffix = ".txt"
+
+        config = Config()
+
+    # Invalid template with typo in variable name
+    config = {
+        "llms_txt_file": True,
+        "llms_txt_filename": "llms.txt",
+        "llms_txt_uri_template": "{base_urll}/{docname}",
+        "html_baseurl": "https://example.com",
+    }
+    writer = FileWriter(config, str(build_dir), MockApp())
+
+    page_titles = {
+        "index": "Home Page",
+    }
+
+    page_order = [("index", ".rst")]
+
+    writer.write_verbose_info_to_file(page_order, page_titles, 0, sources_dir)
+
+    verbose_file = build_dir / "llms.txt"
+    with open(verbose_file, "r", encoding="utf-8") as f:
+        content = f.read()
+
+    # Should fallback to default sources template
+    assert "- [Home Page](https://example.com/_sources/index.rst.txt)" in content