V0.9 GITHUB

doc/Makefile

@@ -17,4 +17,6 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	pip install ../.
+	python generate_doc.py
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/api.rst

@@ -3,10 +3,22 @@ LENAPY API
 ==========
 
 .. automodule:: lenapy
-   :members:
-   
+    :show-inheritance:
+
 .. automodule:: lenapy.readers
-   :members:
+    :show-inheritance:
+
+.. automodule:: lenapy.utils
+    :show-inheritance:
+
+.. automodule:: lenapy.writers
+    :show-inheritance:
+
+Lenapy constants
+^^^^^^^^^^^^^^^^
+
+.. automodule:: lenapy.constants
+    :noindex:
 
 .. raw:: latex
 

doc/conf.py

@@ -7,6 +7,7 @@
 import sys, os
 import datetime
 sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('../lenapy'))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
@@ -31,11 +32,12 @@
 
 # autosummaries from source-files : use .. autosummary::
 autosummary_generate = True
-# autodoc dont show __init__ docstring
+# Inherit docstrings from parent classes
+autodoc_inherit_docstrings = True
+# autodoc don't show __init__ docstring
 autoclass_content = "both"
-# sort class members
+# sort class members by their order in the source
 autodoc_member_order = 'bysource'
-# autodoc_member_order = "groupwise"
 
 # show all members of a class in the Methods and Attributes sections automatically
 numpydoc_show_class_members = True
@@ -74,7 +76,6 @@
     "numpy": ("http://docs.scipy.org/doc/numpy/", None),
     "scipy": ("http://docs.scipy.org/doc/scipy/reference", None),
     "matplotlib": ("http://matplotlib.org", None),
-    "sphinx": ("http://www.sphinx-doc.org/en/stable/", None),
     "xarray": ("https://docs.xarray.dev/en/stable/", None),
 }
 

doc/generate_doc.py

@@ -0,0 +1,59 @@
+import os
+import importlib
+import inspect
+import sys
+
+
+def list_classes_and_functions(package_name):
+    results = {}
+    package = importlib.import_module(package_name)
+    package_path = package.__path__[0]
+
+    def walk_package(package_path, package_name):
+        for root, _, files in os.walk(package_path):
+            for file in files:
+                if file.endswith(".py") and file != "__init__.py":
+                    module_path = os.path.join(root, file)
+                    relative_module_path = os.path.relpath(module_path, package_path)
+                    module_name = os.path.splitext(relative_module_path.replace(os.sep, "."))[0]
+                    full_module_name = f"{package_name}.{module_name}"
+
+                    try:
+                        module = importlib.import_module(full_module_name)
+                        results[full_module_name] = {"classes": {}, "functions": []}
+
+                        for name, obj in inspect.getmembers(module):
+                            if inspect.isclass(obj) and obj.__module__ == full_module_name:
+                                class_methods = [method_name for method_name, method_obj in inspect.getmembers(obj)
+                                                 if inspect.isfunction(method_obj)]
+                                results[full_module_name]["classes"][name] = class_methods
+                            elif inspect.isfunction(obj) and obj.__module__ == full_module_name:
+                                results[full_module_name]["functions"].append(name)
+                    except ImportError as e:
+                        print(f"Failed to import module {full_module_name}: {e}", file=sys.stderr)
+
+    walk_package(package_path, package_name)
+    return results
+
+
+def write_results_to_file(results, output_file):
+    with open(output_file, 'w') as f:
+        f.write('.. autosummary::\n   :toctree:\n   :recursive:\n   :nosignatures:\n\n')
+
+        for module, members in results.items():
+            for cls, methods in members["classes"].items():
+                for method in methods:
+                    if method == "__init__":
+                        f.write(f"    {module}.{cls}\n")
+                        f.write(f"    {module}.{cls}.{method}\n")
+                    elif method == "__repr__":
+                        f.write(f"    {module}.{cls}\n")
+                    else:
+                        f.write(f"    {module}.{cls}.{method}\n")
+            for func in members["functions"]:
+                f.write(f"    {module}.{func}\n")
+
+
+result = list_classes_and_functions('lenapy')
+write_results_to_file(result, os.path.join(os.getcwd(), 'functions_classes.rst'))
+

doc/index.rst

@@ -11,6 +11,7 @@ Welcome to lenapy's documentation!
 * lenapy_ocean: encapsulation of the GSW library containing the main ocean thermodynamic calculation routines (TEOS10)
 * lenapy_geo: current operations on gridded data (longitude/latitude/depth)
 * lenapy_time: common operations on time series (filtering, climatology, regressions, etc.)
+* lenapy_harmo: operations related to spherical harmonics decomposition and their projections on latitude/longitude grids
 
 This library is based on the principle of class extension, i.e. functions can be applied directly to Datasets or DataArrays, by adding the extension of the module concerned and the name of the method. Ex: ds.lntime.filter(...), ds.lngeo.mean(...), de.lnocean.gohc, etc.
 

doc/make.bat

@@ -25,6 +25,8 @@ if errorlevel 9009 (
 
 if "%1" == "" goto help
 
+pip install .
+python generate_doc_data.py
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 goto end