diff --git a/docs/source/conf.py b/docs/source/conf.py
index cdc8bd2e..11874848 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -57,6 +57,7 @@
     "sphinx_click.ext",
     "sphinx_tabs.tabs",
     "sphinx_copybutton",
+    "myst_parser",
 ]
 
 intersphinx_mapping = {
@@ -77,7 +78,10 @@
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-source_suffix = ".rst"
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
 
 # source_parsers = {'.md': MarkdownParser}
 
diff --git a/docs/source/dev/README.rst b/docs/source/dev/README.rst
index 957e2f2f..68e2ee84 100644
--- a/docs/source/dev/README.rst
+++ b/docs/source/dev/README.rst
@@ -29,7 +29,7 @@ learn how to `create a branch <https://docs.github.com/en/pull-requests/collabor
 and `request a review <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/requesting-a-pull-request-review>`_.
 
 If you are not sure where or how to start contributing to COMPASS, consider reaching out to the
-current developer(s): **Paul Pinchuk** ["ppinchuk@nlr.gov"] or **Guilherme Pimenta Castelao** ["gpimenta@nlr.gov"].
+current developer(s): **Paul Pinchuk** ["ppinchuk@nlr.gov"] or **Guilherme Castelao** ["gpimenta@nlr.gov"].
 
 When you are ready to contribute to COMPASS, clone a copy of the COMPASS repository from GitHub, check out your
 own branch, and make the appropriate changes locally. Ensure that your new code adheres to all of the guidelines
@@ -121,6 +121,7 @@ Use the following import conventions::
    import numpy as np
    import pandas as pd
 
+Note that ``ruff`` will monitor and enforce some style rules such as ordering of imports.
 
 Test coverage
 -------------
@@ -132,13 +133,13 @@ You can run python COMPASS tests locally using ``pixi``:
 
 .. code-block:: shell
 
-    pixi r -e ptest tests-p
+    pixi run -e ptest tests-p
 
 To speed up testing, the tests can be run in parallel using ``-n auto``:
 
 .. code-block:: shell
 
-    pixi r -e ptest tests-p -n auto
+    pixi run -e ptest tests-p -n auto
 
 Tests for a module should ideally cover all code in that module,
 i.e., statement coverage should be at 100%, though this alone does not ensure that
diff --git a/examples/parse_existing_docs/README.md b/examples/parse_existing_docs/README.md
index 98813816..f039d14a 100644
--- a/examples/parse_existing_docs/README.md
+++ b/examples/parse_existing_docs/README.md
@@ -2,9 +2,9 @@
 
 This directory contains examples/tutorials to help you parse local documents using ``COMPASS``.
 
-- [`Parsing via CLI`](./CLI): Example showing how to parse local documents via the CLI
+- {doc}`Parsing via CLI <./CLI/README>`: Example showing how to parse local documents via the CLI
   using a typical ``COMPASS`` configuration file.
-- [`Parsing via Code`](./code): Tutorial using the ``COMPASS`` Python API to write code that
+- {doc}`Parsing via Code <./code/README>`: Tutorial using the ``COMPASS`` Python API to write code that
   parses a local PDF file.
 
 For rendered versions of these guides, see the
diff --git a/pixi.lock b/pixi.lock
index f7a6fcf8..c39df66c 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -3258,12 +3258,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py313h3dea7bd_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.8-py313h683a580_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/minizip-4.0.10-h05a5f5f_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mistune-3.2.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/multidict-6.7.0-py313h3dea7bd_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/muparser-2.3.5-h5888daf_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.6-hc388f54_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.6-pyhcf101f3_1.conda
@@ -3747,12 +3749,14 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/maturin-1.11.5-py310h26217a3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/minizip-4.0.10-he2fa2e2_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mistune-3.2.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/multidict-6.7.0-py313hd3a54cf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/muparser-2.3.5-h5ad3122_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.6-hc388f54_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.6-pyhcf101f3_1.conda
@@ -4198,12 +4202,14 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/osx-64/matplotlib-base-3.10.8-py313h4ad75b8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-64/minizip-4.0.10-hfb7a1ec_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mistune-3.2.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-64/multidict-6.7.0-py313h5d7b66b_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-64/muparser-2.3.5-hb996559_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.6-hc388f54_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.6-pyhcf101f3_1.conda
@@ -4644,12 +4650,14 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/matplotlib-base-3.10.8-py313h58042b9_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/minizip-4.0.10-hff1a8ea_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mistune-3.2.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/multidict-6.7.0-py313h92dd972_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/muparser-2.3.5-h11e0b38_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.6-hc388f54_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.6-pyhcf101f3_1.conda
@@ -5080,6 +5088,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/win-64/markupsafe-3.0.3-py313hd650c13_0.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/matplotlib-base-3.10.8-py313he1ded55_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/minizip-4.0.10-h9fa1bad_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mistune-3.2.0-pyhcf101f3_0.conda
@@ -5087,6 +5096,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/win-64/multidict-6.7.0-py313hd650c13_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/muparser-2.3.5-he0c23c2_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.6-hc388f54_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.6-pyhcf101f3_1.conda
@@ -5479,9 +5489,11 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py313h3dea7bd_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.8-py313h683a580_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/multidict-6.7.0-py313h3dea7bd_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nltk-3.9.2-pyhcf101f3_1.conda
@@ -5838,9 +5850,11 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/maturin-1.11.5-py310h26217a3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/multidict-6.7.0-py313hd3a54cf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.5-ha32ae93_3.conda
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       - conda: https://conda.anaconda.org/conda-forge/noarch/nltk-3.9.2-pyhcf101f3_1.conda
@@ -6159,9 +6173,11 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/osx-64/markupsafe-3.0.3-py313h0f4d31d_0.conda
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       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
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       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-64/ncurses-6.5-h0622a9a_3.conda
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       - conda: https://conda.anaconda.org/conda-forge/noarch/nltk-3.9.2-pyhcf101f3_1.conda
@@ -6474,9 +6490,11 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/multidict-6.7.0-py313h92dd972_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nltk-3.9.2-pyhcf101f3_1.conda
@@ -6782,10 +6800,12 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/win-64/markupsafe-3.0.3-py313hd650c13_0.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/matplotlib-base-3.10.8-py313he1ded55_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/mkl-2025.3.0-hac47afa_455.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/multidict-6.7.0-py313hd650c13_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nltk-3.9.2-pyhcf101f3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/numpy-2.4.1-py313hce7ae62_0.conda
@@ -16700,8 +16720,8 @@ packages:
   timestamp: 1736252433366
 - pypi: ./
   name: infra-compass
-  version: 0.15.3.dev10+gef29098
-  sha256: eb5dc5c0df2360c67414fd36615a23a5a5030398e4650f89474f88f163f3783f
+  version: 0.15.3.dev18+gf162d3b
+  sha256: 8b71867bb1c51d3ead52967606d6654e8c7199b431dfce4a05cebbebc42d16bc
   requires_dist:
   - beautifulsoup4>=4.12.3,<5
   - click>=8.1.7,<9
@@ -16740,6 +16760,7 @@ packages:
   - sphinx-copybutton>=0.5 ; extra == 'doc'
   - sphinx-tabs>=3.4 ; extra == 'doc'
   - sphinxcontrib-mermaid>=1.2.3,<2 ; extra == 'doc'
+  - myst-parser>=5.0.0,<6 ; extra == 'doc'
   - anthropic>=0.40.0,<0.41 ; extra == 'anthropic'
   - botocore>=1.35.72,<2 ; extra == 'anthropic'
   - boto3>=1.35.71,<2 ; extra == 'anthropic'
@@ -23529,6 +23550,18 @@ packages:
   version: 3.0.0
   sha256: 684fec138b463d1fc6fa88fd2967e25b3af0629eb0b5e6f3bbc017e64e2f68c6
   requires_python: '>=3.10'
+- conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda
+  sha256: 123cc004e2946879708cdb6a9eff24acbbb054990d6131bb94bca7a374ebebfc
+  md5: 1997a083ef0b4c9331f9191564be275e
+  depends:
+  - markdown-it-py >=2.0.0,<5.0.0
+  - python >=3.10
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/mdit-py-plugins?source=hash-mapping
+  size: 43805
+  timestamp: 1754946862113
 - pypi: https://files.pythonhosted.org/packages/b3/38/89ba8ad64ae25be8de66a6d463314cf1eb366222074cfda9ee839c56a4b4/mdurl-0.1.2-py3-none-any.whl
   name: mdurl
   version: 0.1.2
@@ -23832,6 +23865,23 @@ packages:
   purls: []
   size: 148557
   timestamp: 1747117340968
+- conda: https://conda.anaconda.org/conda-forge/noarch/myst-parser-5.0.0-pyhd8ed1ab_0.conda
+  sha256: f352d594d968acd31052c5f894ae70718be56481ffa9c304fdfcbe78ddf66eb1
+  md5: a65e2c3c764766f0b28a3ac5052502a6
+  depends:
+  - docutils >=0.20,<0.23
+  - jinja2
+  - markdown-it-py >=4.0.0,<4.1.0
+  - mdit-py-plugins >=0.5,<0.6
+  - python >=3.11
+  - pyyaml
+  - sphinx >=8,<10
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/myst-parser?source=hash-mapping
+  size: 73535
+  timestamp: 1768942892170
 - conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
   sha256: 1b66960ee06874ddceeebe375d5f17fb5f393d025a09e15b830ad0c4fffb585b
   md5: 00f5b8dafa842e0c27c1cd7296aa4875
diff --git a/pyproject.toml b/pyproject.toml
index 205ea817..8325bab7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -79,6 +79,7 @@ doc = [
   "sphinx-copybutton>=0.5",
   "sphinx-tabs>=3.4",
   "sphinxcontrib-mermaid>=1.2.3,<2",
+  "myst-parser>=5.0.0,<6",
 ]
 anthropic = [
   "anthropic>=0.40.0,<0.41",
@@ -248,6 +249,7 @@ sphinx-click = ">=6.1.0,<7"
 sphinx-copybutton = ">=0.5.2,<0.6"
 sphinx-tabs = ">=3.4.1,<4"
 sphinxcontrib-mermaid = ">=1.2.3,<2"
+myst-parser = ">=5.0.0,<6"
 
 [tool.pixi.feature.python-anthropic.dependencies]
 anthropic = ">=0.40.0,<0.41"