From c66ac33c8ba454ebc6a3c75a66c826dc3bd34611 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Mon, 14 Jul 2025 15:34:48 +0800
Subject: [PATCH 01/17] DOC add plantuml C4 diagram

---
 .github/workflows/emscripten.yml |  2 +-
 .github/workflows/static.yml     |  2 +-
 .github/workflows/test.yml       |  2 +-
 .github/workflows/wheel.yml      |  4 +-
 .readthedocs.yml                 |  3 ++
 README.rst                       | 18 ++++----
 doc/conf.py                      |  4 +-
 doc/diagram.puml                 | 73 ++++++++++++++++++++++++++++++++
 doc/index.rst                    |  6 ++-
 pixi.lock                        | 17 +++++++-
 pyproject.toml                   |  2 +-
 tests/test_narx.py               |  2 +-
 12 files changed, 116 insertions(+), 19 deletions(-)
 create mode 100644 doc/diagram.puml

diff --git a/.github/workflows/emscripten.yml b/.github/workflows/emscripten.yml
index 759c057..ea761c4 100644
--- a/.github/workflows/emscripten.yml
+++ b/.github/workflows/emscripten.yml
@@ -9,7 +9,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Build WASM wheel
-        uses: pypa/cibuildwheel@v3.0.0
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_PLATFORM: pyodide
       - name: Upload package
diff --git a/.github/workflows/static.yml b/.github/workflows/static.yml
index 49765ec..f8b0fa4 100644
--- a/.github/workflows/static.yml
+++ b/.github/workflows/static.yml
@@ -9,7 +9,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.8.11
         with:
           environments: static
           cache: true
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index bdd930c..61c518b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -16,7 +16,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.8.11
         with:
           environments: >-
             dev
diff --git a/.github/workflows/wheel.yml b/.github/workflows/wheel.yml
index 7a6a74c..90e9fdf 100644
--- a/.github/workflows/wheel.yml
+++ b/.github/workflows/wheel.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.10
+      - uses: prefix-dev/setup-pixi@v0.8.11
         with:
           environments: dev
           cache: true
@@ -33,7 +33,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels
-        uses: pypa/cibuildwheel@v3.0.0
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_SKIP: "*_i686 *_ppc64le *_s390x *_universal2 *-musllinux_*"
           CIBW_PROJECT_REQUIRES_PYTHON: ">=3.10"
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 91913f3..44a22f3 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,6 +3,9 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
+  
+  apt_packages:
+    - plantuml
 
 sphinx:
    configuration: doc/conf.py
diff --git a/README.rst b/README.rst
index a14365f..1f27038 100644
--- a/README.rst
+++ b/README.rst
@@ -1,4 +1,4 @@
-FastCan: A Fast Canonical-Correlation-Based Greedy Search Algorithm
+fastcan: A fast canonical-correlation-based greedy search algorithm
 ===================================================================
 |conda| |Codecov| |CI| |Doc| |PythonVersion| |PyPi| |ruff| |pixi|
 
@@ -26,7 +26,7 @@ FastCan: A Fast Canonical-Correlation-Based Greedy Search Algorithm
 .. |pixi| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json&style=flat-square
    :target: https://pixi.sh
 
-FastCan is a greedy search algorithm that supports:
+fastcan is a greedy search algorithm that supports:
 
 #. Feature selection
 
@@ -54,7 +54,7 @@ Check `Home Page <https://fastcan.readthedocs.io/en/latest/>`_ for more informat
 Installation
 ------------
 
-Install **FastCan** via PyPi:
+Install **fastcan** via PyPi:
 
 * Run ``pip install fastcan``
 
@@ -90,21 +90,21 @@ array([0.34617598, 0.95815008])
 
 NARX Time Series Modelling
 --------------------------
-FastCan can be used for system identification.
+fastcan can be used for system identification.
 In particular, we provide a submodule `fastcan.narx` to build Nonlinear AutoRegressive eXogenous (NARX) models.
 For more information, check our `Home Page <https://fastcan.readthedocs.io/en/latest/>`_.
 
 
 Support Free-Threaded Wheels
 ----------------------------
-FastCan has support for free-threaded (also known as nogil) CPython 3.13.
+fastcan has support for free-threaded (also known as nogil) CPython 3.13.
 For more information about free-threaded CPython, check `how to install a free-threaded CPython <https://py-free-threading.github.io/installing_cpython/>`_.
 
 Support WASM Wheels
 -------------------
-FastCan is compiled to WebAssembly (WASM) wheels using `pyodide <https://github.com/pyodide/pyodide>`_, and they are available on the assets of GitHub releases.
+fastcan is compiled to WebAssembly (WASM) wheels using `pyodide <https://github.com/pyodide/pyodide>`_, and they are available on the assets of GitHub releases.
 You can try it in a `REPL <https://pyodide.org/en/stable/console.html>`_ directly in a browser.
-The WASM wheels of FastCan can be installed by
+The WASM wheels of fastcan can be installed by
 
 >>> import micropip # doctest: +SKIP
 >>> await micropip.install('URL of the wasm wheel (end with _wasm32.whl)') # doctest: +SKIP
@@ -112,13 +112,13 @@ The WASM wheels of FastCan can be installed by
 📝 **Note:** Due to the Cross-Origin Resource Sharing (CORS) block in web browsers,
 you may need `Allow CORS: Access-Control-Allow-Origin Chrome extension <https://chrome.google.com/webstore/detail/allow-cors-access-control/lhobafahddgcelffkeicbaginigeejlf>`_.
 
-📝 **Note:** The nightly wasm wheel of FastCan's dependency (i.e. scikit-learn) can be found in `Scientific Python Nightly Wheels <https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/>`_.
+📝 **Note:** The nightly wasm wheel of fastcan's dependency (i.e. scikit-learn) can be found in `Scientific Python Nightly Wheels <https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/>`_.
 
 
 Citation
 --------
 
-FastCan is a Python implementation of the following papers.
+fastcan is a Python implementation of the following papers.
 
 If you use the `h-correlation` method in your work please cite the following reference:
 
diff --git a/doc/conf.py b/doc/conf.py
index bc47a1b..078549f 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -41,8 +41,10 @@
     # Link to other project's documentation (see mapping below)
     "sphinx.ext.intersphinx",
     "sphinx_gallery.gen_gallery",
-    # for dropdown directive
+    # For dropdown directive
     "sphinx_design",
+    # For PlantUML diagrams
+    "sphinxcontrib.plantuml",
 ]
 
 # List of patterns, relative to source directory, that match files and
diff --git a/doc/diagram.puml b/doc/diagram.puml
new file mode 100644
index 0000000..54924a3
--- /dev/null
+++ b/doc/diagram.puml
@@ -0,0 +1,73 @@
+@startuml fastcan
+skinparam backgroundColor transparent
+!include https://raw.githubusercontent.com/plantuml-stdlib/C4-PlantUML/master/C4_Component.puml
+!include <logos/numpy>
+!include <logos/python>
+!include <logos/c>
+
+
+AddContainerTag("module", $legendText="module")
+AddContainerTag("db", $legendText="input/output", $sprite="numpy", $bgColor="gray", $fontColor="white", $borderColor="gray")
+AddComponentTag("python", $legendText="Python code", $sprite="python")
+AddComponentTag("cython", $legendText="Cython code", $sprite="c", $bgColor="gold", $fontColor="brown", $borderColor="gold")
+UpdateContainerBoundaryStyle($type="module", $legendText="module boundary")
+
+
+Container_Boundary(fastcan, "fastcan", $descr="A library for fast feature engineering and data preprocessing"){
+    Component(cancorr_fast, "cancorr_fast", $tags="cython", $descr="Fast canonical correlation based forward search")
+    Component(FastCan, "FastCan", $tags="python", $descr="Feature selector")
+    Component(minibatch, "minibatch", $tags="python", $descr="Prunes samples in batch-wise")
+    Component(refine, "refine", $tags="python", $descr="Refines selection of FastCan")
+
+
+    Rel(FastCan, cancorr_fast, "Sends features to", "arrays")
+    Rel(minibatch, cancorr_fast, "Sends samples to", "arrays")
+    Rel(FastCan, refine, "Sends selected features to", "arrays")
+    Rel(refine, cancorr_fast, "Sends features to", "arrays")
+}
+
+Container_Boundary(narx, "narx", $descr="A submodule for NARX modelling"){
+    Component(make_narx, "make_narx", $tags="python", $descr="Builder for NARX model instances")
+    Component(narx_fast, "narx_fast", $tags="cython", $descr="Fast computation of gradient and prediction for NARX models")
+    Component(NARX, "NARX", $tags="python", $descr="NARX model")
+    Component(time_shift, "time_shift", $tags="python", $descr="Transforming time-series to time-shifted features")
+    Component(poly, "poly", $tags="python", $descr="Nonlinearises features with polynomial basis functions")
+    ' Component(tp2fd, "tp2fd", $tags="python", $descr="Converts time_shift ids and poly ids to feat ids and delay ids")
+    Component(print_narx, "print_narx", $tags="python", $descr="Prints NARX model summary")
+
+    Rel(NARX, print_narx, "Sends NARX model to", "NARX model")
+    ' Rel(make_narx, poly, "Makes polynomial features using", "unique id numbers")
+    Rel(make_narx, time_shift, "Sends time series to", "arrays")
+    ' Rel(make_narx, tp2fd, "Sends time_shift ids and poly ids to", "unique id numbers")
+    Rel(time_shift, poly, "Sends time-shifted features to", "arrays")
+    Rel(poly, FastCan, "Sends polynomial features to", "arrays")
+    ' Rel(tp2fd, NARX, "Sends feat ids and delay ids to", "unique id numbers")
+    Rel(NARX, narx_fast, "Sends initial conditions of inputs, prediction and gradients to", "fit, predict")
+
+}
+
+Person(person, "User", $descr="A data scientist or developer using NumPy, SciPy, and scikit-learn")
+ContainerDb(output, "fastcan output", $tags="db", $techn="indices", $descr="Selected indices of features or samples")
+ContainerDb(input, "fastcan input", $tags="db", $techn="arrays, allow multi-output", $descr="Input data")
+ContainerDb(narx_output, "narx output", $tags="db", $techn="arrays", $descr="Prediction and gradients of NARX model")
+ContainerDb(narx_input, "narx input", $tags="db", $techn="arrays, allow nan, allow multi-output", $descr="Time-series data")
+
+Rel(input, FastCan, "Sends features to", "arrays")
+Rel(input, minibatch, "Sends samples to", "arrays")
+Rel(narx_input, make_narx, "Sends time series to", "arrays")
+Rel(narx_input, NARX, "Sends time series to", "arrays")
+
+Rel(cancorr_fast, output, "Sends selected indices to", "indices")
+Rel(output, refine, "Sends selected indices to", "indices")
+Rel(narx_fast, narx_output, "Sends prediction and gradients to", "arrays")
+Rel(output, NARX, "Sends selected polynomial features to", "indices")
+
+Rel(person, input, "Processes arrays using", "NumPy, scikit-learn pipeline")
+Rel(person, narx_input, "Processes time series using", "NumPy, scikit-learn pipeline")
+
+Container(optimizer, "SciPy Optimiser", "module", $tags="module", $descr="Minimises objective functions using prediction errors and gradients")
+Rel(narx_output, optimizer, "Sends prediction and gradients to", "arrays")
+Rel(optimizer, NARX, "Updates coefficients for", "arrays")
+
+SHOW_LEGEND()
+@enduml
\ No newline at end of file
diff --git a/doc/index.rst b/doc/index.rst
index 071cafd..06fde70 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -9,7 +9,11 @@
 
 .. include:: ../README.rst
 
+Architecture Diagram
+--------------------
 
+.. uml:: diagram.puml
+   :align: center
 
 API Reference
 -------------
@@ -49,7 +53,7 @@ Useful Links
 API Compatibility
 -----------------
 
-The API of this package is align with scikit-learn.
+The API of this library is align with scikit-learn.
 
 .. |sklearn| image:: images/scikit-learn-logo-notext.png
    :width: 100pt
diff --git a/pixi.lock b/pixi.lock
index cd85c91..29cd125 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -562,6 +562,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/3c/dd/018ce05c532a22007ac58d4f45232514cd9d6dd0ee1dc374e309db830983/sphinx_basic_ng-1.0.0b2-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c6/43/65c0acbd8cc6f50195a3a1fc195c404988b15c67090e73c7a41a9f57d6bd/sphinx_design-0.6.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/77/c7/52b48aec16b26c52aba854d03a3a31e0681150301dac1bea2243645a69e7/sphinx_gallery-0.19.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/4d/e0/91ee50f1a020e2ed48d370a054f94b012ba0d757214a420ac43c9327f818/sphinxcontrib-plantuml-0.30.tar.gz
       - pypi: https://files.pythonhosted.org/packages/5d/85/9ebeae2f76e9e77b952f4b274c27238156eae7979c5421fba91a28f4970d/sphinxcontrib_applehelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/35/7a/987e583882f985fe4d7323774889ec58049171828b58c2217e7f79cdf44e/sphinxcontrib_devhelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0a/7b/18a8c0bcec9182c05a0b3ec2a776bba4ead82750a55ff798e8d406dae604/sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl
@@ -840,6 +841,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/c6/43/65c0acbd8cc6f50195a3a1fc195c404988b15c67090e73c7a41a9f57d6bd/sphinx_design-0.6.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/77/c7/52b48aec16b26c52aba854d03a3a31e0681150301dac1bea2243645a69e7/sphinx_gallery-0.19.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/4d/e0/91ee50f1a020e2ed48d370a054f94b012ba0d757214a420ac43c9327f818/sphinxcontrib-plantuml-0.30.tar.gz
       - pypi: https://files.pythonhosted.org/packages/5d/85/9ebeae2f76e9e77b952f4b274c27238156eae7979c5421fba91a28f4970d/sphinxcontrib_applehelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/35/7a/987e583882f985fe4d7323774889ec58049171828b58c2217e7f79cdf44e/sphinxcontrib_devhelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0a/7b/18a8c0bcec9182c05a0b3ec2a776bba4ead82750a55ff798e8d406dae604/sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl
@@ -1090,6 +1092,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/c6/43/65c0acbd8cc6f50195a3a1fc195c404988b15c67090e73c7a41a9f57d6bd/sphinx_design-0.6.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/77/c7/52b48aec16b26c52aba854d03a3a31e0681150301dac1bea2243645a69e7/sphinx_gallery-0.19.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/4d/e0/91ee50f1a020e2ed48d370a054f94b012ba0d757214a420ac43c9327f818/sphinxcontrib-plantuml-0.30.tar.gz
       - pypi: https://files.pythonhosted.org/packages/5d/85/9ebeae2f76e9e77b952f4b274c27238156eae7979c5421fba91a28f4970d/sphinxcontrib_applehelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/35/7a/987e583882f985fe4d7323774889ec58049171828b58c2217e7f79cdf44e/sphinxcontrib_devhelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0a/7b/18a8c0bcec9182c05a0b3ec2a776bba4ead82750a55ff798e8d406dae604/sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl
@@ -1340,6 +1343,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/c6/43/65c0acbd8cc6f50195a3a1fc195c404988b15c67090e73c7a41a9f57d6bd/sphinx_design-0.6.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/77/c7/52b48aec16b26c52aba854d03a3a31e0681150301dac1bea2243645a69e7/sphinx_gallery-0.19.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/4d/e0/91ee50f1a020e2ed48d370a054f94b012ba0d757214a420ac43c9327f818/sphinxcontrib-plantuml-0.30.tar.gz
       - pypi: https://files.pythonhosted.org/packages/5d/85/9ebeae2f76e9e77b952f4b274c27238156eae7979c5421fba91a28f4970d/sphinxcontrib_applehelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/35/7a/987e583882f985fe4d7323774889ec58049171828b58c2217e7f79cdf44e/sphinxcontrib_devhelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0a/7b/18a8c0bcec9182c05a0b3ec2a776bba4ead82750a55ff798e8d406dae604/sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl
@@ -1580,6 +1584,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/c6/43/65c0acbd8cc6f50195a3a1fc195c404988b15c67090e73c7a41a9f57d6bd/sphinx_design-0.6.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/77/c7/52b48aec16b26c52aba854d03a3a31e0681150301dac1bea2243645a69e7/sphinx_gallery-0.19.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/4d/e0/91ee50f1a020e2ed48d370a054f94b012ba0d757214a420ac43c9327f818/sphinxcontrib-plantuml-0.30.tar.gz
       - pypi: https://files.pythonhosted.org/packages/5d/85/9ebeae2f76e9e77b952f4b274c27238156eae7979c5421fba91a28f4970d/sphinxcontrib_applehelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/35/7a/987e583882f985fe4d7323774889ec58049171828b58c2217e7f79cdf44e/sphinxcontrib_devhelp-2.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0a/7b/18a8c0bcec9182c05a0b3ec2a776bba4ead82750a55ff798e8d406dae604/sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl
@@ -3605,13 +3610,14 @@ packages:
 - pypi: ./
   name: fastcan
   version: 0.4.0
-  sha256: 327259867342e372de54fcbb50da07c104703821040da6cbff3f125c846a1374
+  sha256: d6ce8adf0fa75fd949496cb6cb7602278dae2a1029b5ff4803901e07ff4a7b47
   requires_dist:
   - scikit-learn>=1.7.0
   - furo ; extra == 'docs'
   - matplotlib ; extra == 'docs'
   - sphinx-gallery ; extra == 'docs'
   - sphinx-design ; extra == 'docs'
+  - sphinxcontrib-plantuml ; extra == 'docs'
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
@@ -11639,6 +11645,15 @@ packages:
   - flake8 ; extra == 'test'
   - mypy ; extra == 'test'
   requires_python: '>=3.5'
+- pypi: https://files.pythonhosted.org/packages/4d/e0/91ee50f1a020e2ed48d370a054f94b012ba0d757214a420ac43c9327f818/sphinxcontrib-plantuml-0.30.tar.gz
+  name: sphinxcontrib-plantuml
+  version: '0.30'
+  sha256: 2a1266ca43bddf44640ae44107003df4490de2b3c3154a0d627cfb63e9a169bf
+  requires_dist:
+  - sphinx>=1.6
+  - pytest ; extra == 'test'
+  - pillow ; extra == 'test'
+  - flake8 ; extra == 'test'
 - pypi: https://files.pythonhosted.org/packages/27/83/859ecdd180cacc13b1f7e857abf8582a64552ea7a061057a6c716e790fce/sphinxcontrib_qthelp-2.0.0-py3-none-any.whl
   name: sphinxcontrib-qthelp
   version: 2.0.0
diff --git a/pyproject.toml b/pyproject.toml
index 36b2cf3..faffea4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,7 @@ download = "https://pypi.org/project/fastcan/#files"
 tracker = "https://github.com/scikit-learn-contrib/fastcan/issues"
 
 [project.optional-dependencies]
-docs = ["furo", "matplotlib", "sphinx_gallery", "sphinx-design"]
+docs = ["furo", "matplotlib", "sphinx_gallery", "sphinx-design", "sphinxcontrib-plantuml"]
 
 [build-system]
 requires = ["meson-python>=0.18.0", "Cython>=3.1.0", "scikit-learn>=1.7.0"]
diff --git a/tests/test_narx.py b/tests/test_narx.py
index c72af2d..f8f1b03 100644
--- a/tests/test_narx.py
+++ b/tests/test_narx.py
@@ -614,4 +614,4 @@ def test_auto_reg():
     )
     model.fit(X, y)
     y_pred = model.predict(X, y_init=y[: model.max_delay_])
-    assert r2_score(y, model.predict(X, y_init=y)) > 0.5
+    assert r2_score(y, y_pred) > 0.5

From a4a0a227ceaf87256d86955807a92028a1fff33a Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Mon, 14 Jul 2025 15:57:08 +0800
Subject: [PATCH 02/17] fix java error

---
 .readthedocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 44a22f3..bff92ad 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,6 +3,7 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
+    java: "openjdk-17"
   
   apt_packages:
     - plantuml

From 661f65daa01fc18118d76e69a23b0d5395b46829 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Mon, 14 Jul 2025 16:03:19 +0800
Subject: [PATCH 03/17] manually install java

---
 .readthedocs.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index bff92ad..086133e 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,7 +3,10 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
-    java: "openjdk-17"
+  # Java is required for PlantUML to generate C4 diagrams
+  commands:
+    - sudo apt-get update
+    - sudo apt-get install -y openjdk-17-jdk
   
   apt_packages:
     - plantuml

From 3fc4ae462e2567f6938148108cc9d7ba7befaec5 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Mon, 14 Jul 2025 16:12:17 +0800
Subject: [PATCH 04/17] apt install java

---
 .readthedocs.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 086133e..94aaeb3 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,13 +3,11 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
-  # Java is required for PlantUML to generate C4 diagrams
-  commands:
-    - sudo apt-get update
-    - sudo apt-get install -y openjdk-17-jdk
   
+  # Java is required for PlantUML to generate C4 diagrams
   apt_packages:
     - plantuml
+    - openjdk-17-jdk
 
 sphinx:
    configuration: doc/conf.py

From 568e16420a4f947a3783aca99eb77d352b2ab3c9 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Mon, 14 Jul 2025 16:22:13 +0800
Subject: [PATCH 05/17] add graphviz

---
 .readthedocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 94aaeb3..d08fb61 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -8,6 +8,7 @@ build:
   apt_packages:
     - plantuml
     - openjdk-17-jdk
+    - graphviz
 
 sphinx:
    configuration: doc/conf.py

From 4a29d0f738c4ddb9ad9bff9a323738714ffbc649 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Mon, 14 Jul 2025 16:55:58 +0800
Subject: [PATCH 06/17] use latext plantuml

---
 .readthedocs.yml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index d08fb61..618a035 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,12 +3,14 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
-  
-  # Java is required for PlantUML to generate C4 diagrams
-  apt_packages:
-    - plantuml
-    - openjdk-17-jdk
-    - graphviz
+  jobs:
+    post_install:
+      # Download the latest PlantUML jar
+      - wget https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar -P /tmp/
+      # Create an executable wrapper script for Sphinx
+      - echo '#!/bin/sh' > /usr/local/bin/plantuml
+      - echo 'java -jar /tmp/plantuml.jar "$@"' >> /usr/local/bin/plantuml
+      - chmod +x /usr/local/bin/plantuml
 
 sphinx:
    configuration: doc/conf.py

From 4ac036305c38cf44e28623d8d6250565be2d4926 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:10:01 +0800
Subject: [PATCH 07/17] update plantuml

---
 .readthedocs.yml | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 618a035..a98b76d 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,14 +3,8 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
-  jobs:
-    post_install:
-      # Download the latest PlantUML jar
-      - wget https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar -P /tmp/
-      # Create an executable wrapper script for Sphinx
-      - echo '#!/bin/sh' > /usr/local/bin/plantuml
-      - echo 'java -jar /tmp/plantuml.jar "$@"' >> /usr/local/bin/plantuml
-      - chmod +x /usr/local/bin/plantuml
+  apt_packages:
+    - plantuml=1:1.2021.14+ds-1
 
 sphinx:
    configuration: doc/conf.py

From ae63c334a3d7d3818c86df317a8506fa926bfef5 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:25:21 +0800
Subject: [PATCH 08/17] install lastest plantuml

---
 .readthedocs.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index a98b76d..768dd71 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,8 +3,12 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
-  apt_packages:
-    - plantuml=1:1.2021.14+ds-1
+  jobs:
+    # Install PlantUML
+    pre_install:
+      - curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
+      - printf '#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar "$@"' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+      - chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
 
 sphinx:
    configuration: doc/conf.py

From 242eb6ff90defb9f8f71aca248905724adbad44b Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:29:23 +0800
Subject: [PATCH 09/17] echo

---
 .readthedocs.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 768dd71..3770684 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -7,11 +7,12 @@ build:
     # Install PlantUML
     pre_install:
       - curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
-      - printf '#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar "$@"' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+      - echo -e '#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar "$@"' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
       - chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
 
 sphinx:
    configuration: doc/conf.py
+   fail_on_warning: true
 
 python:
   install:

From 86a573499cca2a1ee8692fecd90c75997f060f88 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:33:54 +0800
Subject: [PATCH 10/17] bug

---
 .readthedocs.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 3770684..b59302e 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -7,7 +7,8 @@ build:
     # Install PlantUML
     pre_install:
       - curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
-      - echo -e '#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar "$@"' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+      - echo '#!/bin/bash' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+      - echo 'exec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar "$@"' >> ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
       - chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
 
 sphinx:

From 74ce668587f43679f0b38bebf6a533aed10dc84e Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:36:06 +0800
Subject: [PATCH 11/17] debug

---
 .readthedocs.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index b59302e..0289a22 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -7,8 +7,12 @@ build:
     # Install PlantUML
     pre_install:
       - curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
-      - echo '#!/bin/bash' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
-      - echo 'exec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar "$@"' >> ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+      - |
+        (
+          echo '#!/bin/bash'
+          echo "exec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar \"\$@\""
+        ) > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+      - ls -l ${READTHEDOCS_VIRTUALENV_PATH}/bin/
       - chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
 
 sphinx:

From 18413a9c20756144ffcbbd34bf90d5a6b8ecd1d2 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:40:53 +0800
Subject: [PATCH 12/17] java

---
 .readthedocs.yml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 0289a22..da7290c 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,16 +3,13 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
+  apt_packages:
+    - default-jre
   jobs:
     # Install PlantUML
     pre_install:
       - curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
-      - |
-        (
-          echo '#!/bin/bash'
-          echo "exec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar \"\$@\""
-        ) > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
-      - ls -l ${READTHEDOCS_VIRTUALENV_PATH}/bin/
+      - bash -c 'echo -e "#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar \"\$@\"" > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml'
       - chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
 
 sphinx:

From 6d90d790865ab55ec6f9b0d4dad28e6baded3583 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:42:30 +0800
Subject: [PATCH 13/17] double quotes

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index da7290c..bc3cb4c 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -9,7 +9,7 @@ build:
     # Install PlantUML
     pre_install:
       - curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
-      - bash -c 'echo -e "#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar \"\$@\"" > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml'
+      - bash -c "echo -e '#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar \"\$@\"' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml"
       - chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
 
 sphinx:

From 7ec0b417f6e85699a01957a1b735b486fd8a2829 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:52:26 +0800
Subject: [PATCH 14/17] script

---
 .readthedocs.yml           |  7 +------
 scripts/rtd_pre_install.sh | 17 +++++++++++++++++
 2 files changed, 18 insertions(+), 6 deletions(-)
 create mode 100644 scripts/rtd_pre_install.sh

diff --git a/.readthedocs.yml b/.readthedocs.yml
index bc3cb4c..113aedd 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,14 +3,9 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
-  apt_packages:
-    - default-jre
   jobs:
-    # Install PlantUML
     pre_install:
-      - curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
-      - bash -c "echo -e '#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar \"\$@\"' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml"
-      - chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+      - bash scripts/rtd_pre_install.sh
 
 sphinx:
    configuration: doc/conf.py
diff --git a/scripts/rtd_pre_install.sh b/scripts/rtd_pre_install.sh
new file mode 100644
index 0000000..690d170
--- /dev/null
+++ b/scripts/rtd_pre_install.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Stop and exit on error
+set -euox pipefail
+
+# Check for required tools
+java -version
+
+# This folder is on PATH and does not require sudo
+# Download latest plantuml.jar from github
+curl -o ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar -L https://github.com/plantuml/plantuml/releases/latest/download/plantuml.jar
+# Create an executable script for plantuml
+printf '#!/bin/bash\nexec java -Djava.awt.headless=true -jar ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml.jar "$@"' > ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+chmod +x ${READTHEDOCS_VIRTUALENV_PATH}/bin/plantuml
+
+# Check plantuml version
+plantuml -version

From 904074b2505982f466ebdc67b4ab9b62907b71f2 Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 09:53:37 +0800
Subject: [PATCH 15/17] add java

---
 .readthedocs.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 113aedd..eaa7702 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,6 +3,8 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.13"
+  apt_packages:
+    - default-jre
   jobs:
     pre_install:
       - bash scripts/rtd_pre_install.sh

From fea85d24c2baabe3f0774869224d6ff1dcd5c46e Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 10:00:41 +0800
Subject: [PATCH 16/17] add graphviz

---
 .readthedocs.yml           | 1 +
 scripts/rtd_pre_install.sh | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index eaa7702..a8bca69 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,6 +5,7 @@ build:
     python: "3.13"
   apt_packages:
     - default-jre
+    - graphviz
   jobs:
     pre_install:
       - bash scripts/rtd_pre_install.sh
diff --git a/scripts/rtd_pre_install.sh b/scripts/rtd_pre_install.sh
index 690d170..78fe7cc 100644
--- a/scripts/rtd_pre_install.sh
+++ b/scripts/rtd_pre_install.sh
@@ -5,6 +5,7 @@ set -euox pipefail
 
 # Check for required tools
 java -version
+dot -V
 
 # This folder is on PATH and does not require sudo
 # Download latest plantuml.jar from github

From d93f9b1da872c748dd4890c9ee6998b84e3c948c Mon Sep 17 00:00:00 2001
From: SIKAI ZHANG <34108862+MatthewSZhang@users.noreply.github.com>
Date: Tue, 15 Jul 2025 10:04:43 +0800
Subject: [PATCH 17/17] add comment

---
 .readthedocs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index a8bca69..eb05b26 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -4,8 +4,8 @@ build:
   tools:
     python: "3.13"
   apt_packages:
-    - default-jre
-    - graphviz
+    - default-jre # for plantuml
+    - graphviz # for plantuml
   jobs:
     pre_install:
       - bash scripts/rtd_pre_install.sh