Merge pull request #152 from ArnauMiro/149-update_docs

149 update docs

Author: bef-18

Diff for: docs/source/_ext/module_alias.py

@@ -0,0 +1,107 @@
+# This extension will rewrite the modules vmmath and inp_out (at the moment) with their alias
+import os
+import re
+
+def modify_rst_before_build(app, config):
+    rst_dir = os.path.join(app.confdir, 'api')
+    
+    # Mapping of actual module names to desired documentation names
+    module_aliases = {
+        'pyLOM.vmmath': 'pyLOM.math',
+        'pyLOM.inp_out': 'pyLOM.io'
+    }
+
+    try:
+        for filename in os.listdir(rst_dir):
+            if filename.endswith('.rst'):
+                filepath = os.path.join(rst_dir, filename)
+                
+                # Check if this file needs to be renamed
+                for original, alias in module_aliases.items():
+                    if filename == f"{original}.rst":
+                        # Rename the file
+                        new_filepath = os.path.join(rst_dir, f"{alias}.rst")
+                        os.rename(filepath, new_filepath)
+                        filepath = new_filepath
+                        break
+                
+                with open(filepath, 'r') as f:
+                    content = f.read()
+                
+                # Replace module names in the content
+                for original, alias in module_aliases.items():
+                    # Replace module name in automodule directive
+                    content = re.sub(
+                        rf'(.. automodule:: ){original}(\n)',
+                        fr'\1{alias}\2',
+                        content
+                    )
+                    
+                    # Replace all occurrences of the original module name
+                    content = content.replace(original, alias)
+                    
+                    # Replace module name in headings and other references
+                    content = content.replace(
+                        f"{original.split('.')[-1]}",
+                        f"{alias.split('.')[-1]}"
+                    )
+                    content = content.replace(
+                        f"module {original}", 
+                        f"module {alias}"
+                    )
+                
+                with open(filepath, 'w') as f:
+                    f.write(content)
+                
+    except Exception as e:
+        print(f"Error modifying RST files: {e}")
+
+def modify_html_files(app, exception):
+    if exception is not None:
+        return
+
+    # Mapping of actual module names to desired documentation names
+    module_aliases = {
+        'pyLOM.vmmath': 'pyLOM.math',
+        'pyLOM.inp_out': 'pyLOM.io'
+    }
+
+    # Directory where HTML files are generated
+    html_dir = os.path.join(app.outdir)
+
+    try:
+        for root, dirs, files in os.walk(html_dir):
+            for filename in files:
+                if filename.endswith('.html'):
+                    filepath = os.path.join(root, filename)
+                    
+                    with open(filepath, 'r', encoding='utf-8') as f:
+                        content = f.read()
+                    
+                    modified = False
+                    
+                    # Replace module names in the content
+                    for original, alias in module_aliases.items():
+                        if original in content:
+                            content = content.replace(original, alias)
+                            modified = True
+                    
+                    # Write back if modified
+                    if modified:
+                        with open(filepath, 'w', encoding='utf-8') as f:
+                            f.write(content)
+    except Exception as e:
+        print(f"Error modifying HTML files: {e}")
+
+def setup(app):
+    # Connect to the config-inited event to modify RST files before build
+    app.connect('config-inited', modify_rst_before_build)
+    
+    # Connect to the build-finished event to modify HTML files
+    app.connect('build-finished', modify_html_files)
+    
+    return {
+        'version': '0.1',
+        'parallel_read_safe': True,
+        'parallel_write_safe': True,
+    }

Diff for: docs/source/api/pyLOM.inp_out.rst renamed to docs/source/api/pyLOM.io.rst

@@ -4,7 +4,7 @@ pyLOM.inp\_out
 Module contents
 ---------------
 
-.. automodule:: pyLOM.inp_out
+.. automodule:: pyLOM.io
    :members:
    :undoc-members:
    :show-inheritance:

Diff for: docs/source/api/pyLOM.vmmath.rst renamed to docs/source/api/pyLOM.math.rst

@@ -1,10 +1,10 @@
-pyLOM.vmmath
+pyLOM.math
 ============
 
 Module contents
 ---------------
 
-.. automodule:: pyLOM.vmmath
+.. automodule:: pyLOM.math
    :members:
    :undoc-members:
    :show-inheritance:

Diff for: docs/source/api/pyLOM.rst

@@ -14,9 +14,9 @@ Subpackages
    pyLOM.NN
    pyLOM.POD
    pyLOM.SPOD
-   pyLOM.inp_out
+   pyLOM.io
    pyLOM.utils
-   pyLOM.vmmath
+   pyLOM.math
 
 Module contents
 ---------------

Diff for: docs/source/conf.py

@@ -2,27 +2,28 @@
 import os
 import sys
 sys.path.insert(0, os.path.abspath('../..'))
-# import pyLOM
+sys.path.insert(0, os.path.abspath('_ext'))
+import pyLOM
 # -- Project information -----------------------------------------------------
 project = 'pyLOM'
 copyright = '2023-2025'
 author = 'pyLOM developers'
-# TODO: ask to add pyLOM.__version__  to avoid this hardcoded variable
-version = '2.1.0' # pyLOM.__version__ is not defined
+version = pyLOM.__version__
 
 # -- General configuration ---------------------------------------------------
 extensions = [
     'sphinx.ext.duration',
     'sphinx.ext.doctest',
     'sphinx.ext.autodoc',
+    'module_alias',
     'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
     'sphinx.ext.intersphinx',
     'sphinx_copybutton',
     'sphinx.ext.mathjax',
     'sphinx_design',
-    'nbsphinx'
+    'nbsphinx',
 ]
 
 # Set the default syntax highlighter

Diff for: docs/source/installation/installation_pypi.rst

@@ -21,7 +21,7 @@ A GPU-supported version of the tool can be installed directly from PyPI using th
 Note that the ``cuda12x`` can be exchanged by:
 
 - ``cuda``: Triggers the non-compiled version of ``cupy`` so that it builds specifically for your system.
-- ``rocm-4-0``: Deploys a version of ``cupy`` tailored for AMD GPUs using ROCM.
+- ``rocm-4-0``: in order to deploy a version of ``cupy`` tailored for AMD GPUs using ROCM. ROCM is still experimental. Please be aware that the CUDA/ROCM version should match the ones in your system.
 
 Optional Modules
 ----------------

Diff for: docs/source/notebook_examples/NN/KAN_training.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# How to train an MLP using the Pipeline"
+    "# How to train an KAN using the Pipeline"
    ]
   },
   {