From d4dfa4c97d37e08285224a50133625c969170a26 Mon Sep 17 00:00:00 2001
From: Luchesar ILIEV <luchesar.iliev@gmail.com>
Date: Tue, 17 Sep 2024 18:22:46 +0300
Subject: [PATCH 1/2] docs: add decorated functions list

---
 .gitignore                    |  1 +
 scripts/gen-decorated-docs.py | 33 +++++++++++++++++++++++++++++++++
 src/ramanchada2/__init__.py   |  2 ++
 tox.ini                       | 17 ++++++++++++++---
 4 files changed, 50 insertions(+), 3 deletions(-)
 create mode 100644 scripts/gen-decorated-docs.py

diff --git a/.gitignore b/.gitignore
index e8f94558..b93c8e53 100644
--- a/.gitignore
+++ b/.gitignore
@@ -83,6 +83,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+spectrum_functions.md
 
 # PyBuilder
 .pybuilder/
diff --git a/scripts/gen-decorated-docs.py b/scripts/gen-decorated-docs.py
new file mode 100644
index 00000000..ba5c16cf
--- /dev/null
+++ b/scripts/gen-decorated-docs.py
@@ -0,0 +1,33 @@
+import inspect
+
+import ramanchada2 as rc2
+
+
+# Get all methods or functions with decorators
+def get_decorated_functions(cls):
+    decorated_functions = []
+    for name, method in inspect.getmembers(cls, predicate=inspect.isfunction):
+
+        if hasattr(method, "__wrapped__"):
+
+            doc = method.__doc__  # Get the docstring (None if not available)
+            decorated_functions.append((name, "" if doc is None else doc))
+    return decorated_functions
+
+
+def generate_decorated_function_docs_markdown(cls, filename="spectrum_functions.md"):
+    """
+    Generates a markdown file that lists decorated functions and their docstrings.
+    """
+    with open(filename, "w") as f:
+        f.write(f"# Decorated Functions in {cls.__name__}\n\n")
+
+        decorated_funcs_with_docs = get_decorated_functions(cls)
+
+        for func_name, doc in decorated_funcs_with_docs:
+            f.write(f"### Function: `{func_name}`\n\n")
+            f.write(f"**Docstring:** {doc if doc else 'No docstring available'}\n\n")
+            f.write("---\n\n")
+
+
+generate_decorated_function_docs_markdown(rc2.spectrum.Spectrum)
diff --git a/src/ramanchada2/__init__.py b/src/ramanchada2/__init__.py
index 0b427bf8..eecb76ce 100644
--- a/src/ramanchada2/__init__.py
+++ b/src/ramanchada2/__init__.py
@@ -82,6 +82,8 @@
 [h5pyd]: https://github.com/HDFGroup/h5pyd
 [ramanchada]: https://github.com/h2020charisma/ramanchada
 [NeXus]: https://www.nexusformat.org/
+
+.. include:: ../../../../../../spectrum_functions.md
 """
 
 from __future__ import annotations
diff --git a/tox.ini b/tox.ini
index 9cd3c1b2..cb9713cd 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,11 +1,11 @@
 [tox]
-env_list = clean, py311, mypy, flake8, docs
+env_list = clean, py311, mypy, black, usort, flake8, docs
 
 [gh-actions]
 python =
     3.9: py39
     3.10: py310
-    3.11: py311, mypy, flake8, docs
+    3.11: py311, mypy, black, usort, flake8, docs
     3.12: py312
 
 [flake8]
@@ -42,15 +42,26 @@ base_python = python3.11
 deps = mypy
 commands = mypy src tests
 
+[testenv:black]
+base_python = python3.11
+deps=black
+commands = black scripts
+
+[testenv:usort]
+base_python = python3.11
+deps=usort
+commands = usort format scripts
+
 [testenv:flake8]
 base_python = python3.11
 deps = flake8
-commands = flake8 src tests
+commands = flake8 scripts src tests
 
 [testenv:docs]
 base_python = python3.11
 deps = pdoc
 commands =
+    python scripts/gen-decorated-docs.py
     pdoc ramanchada2 -o {toxinidir}/docs/_build --no-browser --search --math --docformat google --show-source
 
 [testenv:ipynb]

From b71e7c04586c1bb2dd9d6b7fb66a63f0b7e6ebeb Mon Sep 17 00:00:00 2001
From: Luchesar ILIEV <luchesar.iliev@gmail.com>
Date: Tue, 17 Sep 2024 18:25:36 +0300
Subject: [PATCH 2/2] docs: remove default pdoc options

---
 tox.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tox.ini b/tox.ini
index cb9713cd..9c25d0cd 100644
--- a/tox.ini
+++ b/tox.ini
@@ -62,7 +62,7 @@ base_python = python3.11
 deps = pdoc
 commands =
     python scripts/gen-decorated-docs.py
-    pdoc ramanchada2 -o {toxinidir}/docs/_build --no-browser --search --math --docformat google --show-source
+    pdoc ramanchada2 -o {toxinidir}/docs/_build --math --docformat google
 
 [testenv:ipynb]
 deps = jupyter