clabtoolkit 0.3.3__tar.gz → 0.3.4__tar.gz

{clabtoolkit-0.3.3 → clabtoolkit-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clabtoolkit
-Version: 0.3.3
+Version: 0.3.4
 Summary: A comprehensive toolkit for neuroimaging data processing and analysis
 Author-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
 Maintainer-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>

{clabtoolkit-0.3.3 → clabtoolkit-0.3.4}/clabtoolkit/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Yasser Alemán-Gómez"""
 __email__ = "yasseraleman@protonmail.com"
-__version__ = "0.3.3"
+__version__ = "0.3.4"

{clabtoolkit-0.3.3 → clabtoolkit-0.3.4}/clabtoolkit/parcellationtools.py

@@ -802,7 +802,7 @@ class Parcellation:
         if fill:
 
             # Refilling the unlabeled voxels according to a supplied mask
-            self.data = cltseg.region_growing(self.data, bool_mask)
+            self.data = cltimg.region_growing(self.data, bool_mask)
 
         if hasattr(self, "index") and hasattr(self, "name") and hasattr(self, "color"):
             self.adjust_values()

{clabtoolkit-0.3.3 → clabtoolkit-0.3.4}/clabtoolkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clabtoolkit
-Version: 0.3.3
+Version: 0.3.4
 Summary: A comprehensive toolkit for neuroimaging data processing and analysis
 Author-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
 Maintainer-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>

clabtoolkit-0.3.4/docs/source/conf.py

@@ -0,0 +1,213 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../'))
+
+# Mock imports for ReadTheDocs build - comprehensive list
+autodoc_mock_imports = [
+    # 3D Visualization
+    'pyvista',
+    'vtk', 
+    'fury',
+    'trame',
+    'trame_client',
+    'trame_server',
+    'trame_vtk',
+    'trame_vuetify',
+    'trame_common',
+    'trame.app',
+    'trame.widgets',
+    'trame.html',
+    
+    # Neuroimaging
+    'dipy',
+    'dipy.io',
+    'dipy.io.streamline',
+    'dipy.io.stateful_tractogram',
+    'dipy.segment',
+    'dipy.segment.clustering',
+    'dipy.tracking',
+    'dipy.tracking.streamline',
+    'nilearn',
+    'nilearn.plotting',
+    'nilearn.maskers',
+    'pydicom',
+    'nibabel',
+    'nibabel.streamlines',
+    'nibabel.orientations',
+    'nibabel.processing',
+    
+    # Image Processing
+    'skimage',
+    'skimage.measure',
+    'skimage.morphology',
+    'skimage.filters',
+    'cv2',
+    
+    # Scientific Computing - additional submodules
+    'scipy.sparse',
+    'scipy.ndimage',
+    'scipy.spatial',
+    'scipy.interpolate',
+    'scipy.optimize',
+    
+    # Plotting and UI
+    'matplotlib',
+    'matplotlib.pyplot',
+    'matplotlib.patches',
+    'matplotlib.colors',
+    'matplotlib.figure',
+    'matplotlib.axes',
+    'seaborn',
+    'plotly',
+    'rich',
+    'rich.progress',
+    'rich.console',
+    'rich.panel',
+    'colorama',
+    'screeninfo',
+    
+    # Interactive Computing
+    'ipython',
+    'IPython',
+    'IPython.display',
+    'jupyter',
+    'ipywidgets',
+    
+    # GUI and System
+    'tkinter',
+    'pygame',
+    
+    # Data Processing
+    'h5py',
+    'openpyxl',
+    'lxml',
+    'beautifulsoup4',
+    'bs4',
+    
+    # Parallel and Performance
+    'joblib',
+    'numba',
+    'cupy',
+    'dask',
+    
+    # Machine Learning
+    'sklearn',
+    'scikit-learn',
+    'torch',
+    'tensorflow',
+    
+    # Network Analysis
+    'networkx',
+    'igraph',
+    
+    # Statistical Analysis
+    'statsmodels',
+    'pingouin',
+    'patsy',
+    
+    # Misc utilities
+    'tqdm',
+    'click',
+    'typer',
+    'pydantic',
+    'marshmallow',
+    'requests',
+    'urllib3',
+    'certifi',
+    'fsspec',
+    'pooch',
+    'duecredit'
+]
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'clabtoolkit'
+copyright = '2024, Yasser Alemán-Gómez'
+author = 'Yasser Alemán-Gómez'
+release = '0.3.3'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.autosummary',
+    'myst_parser',
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+
+# Autodoc settings
+autodoc_default_options = {
+    'members': True,
+    'member-order': 'bysource',
+    'special-members': '__init__',
+    'undoc-members': True,
+    'show-inheritance': True,
+    'exclude-members': '__weakref__'
+}
+
+# Show more detailed autodoc information
+autodoc_member_order = 'bysource'
+autodoc_typehints = 'description'
+autodoc_typehints_description_target = 'documented'
+
+# Additional autodoc settings for better documentation generation
+autodoc_preserve_defaults = True
+autodoc_class_signature = 'mixed'
+
+# Ensure modules can be imported even with missing dependencies
+import warnings
+warnings.filterwarnings("ignore", category=UserWarning)
+warnings.filterwarnings("ignore", category=DeprecationWarning)
+
+# Add clabtoolkit to the Python path
+sys.path.insert(0, os.path.abspath('../../clabtoolkit'))
+
+# Intersphinx mapping
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'pandas': ('https://pandas.pydata.org/docs/', None),
+    'nibabel': ('https://nipy.org/nibabel/', None),
+}
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+#html_theme = 'alabaster'  # Built-in theme, no extra install needed
+
+html_static_path = ['_static']
+
+html_theme_options = {
+    'canonical_url': '',
+    'analytics_id': '',
+    'logo_only': False,
+    'display_version': True,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+    'vcs_pageview_mode': '',
+    'style_nav_header_background': '#2980B9',
+    'collapse_navigation': False,
+    'sticky_navigation': True,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': False
+}

{clabtoolkit-0.3.3 → clabtoolkit-0.3.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "clabtoolkit"
-version = "0.3.3"
+version = "0.3.4"
 description = "A comprehensive toolkit for neuroimaging data processing and analysis"
 authors = [
     {name = "Yasser Alemán-Gómez", email = "yasseraleman@protonmail.com"}

clabtoolkit-0.3.3/docs/source/conf.py

@@ -1,78 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-import os
-import sys
-sys.path.insert(0, os.path.abspath('../../'))
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
-project = 'clabtoolkit'
-copyright = '2024, Yasser Alemán-Gómez'
-author = 'Yasser Alemán-Gómez'
-release = '0.3.1'
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.autosummary',
-    'myst_parser',
-]
-
-templates_path = ['_templates']
-exclude_patterns = []
-
-# Napoleon settings
-napoleon_google_docstring = True
-napoleon_numpy_docstring = True
-napoleon_include_init_with_doc = False
-napoleon_include_private_with_doc = False
-
-# Autodoc settings
-autodoc_default_options = {
-    'members': True,
-    'member-order': 'bysource',
-    'special-members': '__init__',
-    'undoc-members': True,
-    'exclude-members': '__weakref__'
-}
-
-# Intersphinx mapping
-intersphinx_mapping = {
-    'python': ('https://docs.python.org/3/', None),
-    'numpy': ('https://numpy.org/doc/stable/', None),
-    'pandas': ('https://pandas.pydata.org/docs/', None),
-    'nibabel': ('https://nipy.org/nibabel/', None),
-}
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = 'sphinx_rtd_theme'
-#html_theme = 'alabaster'  # Built-in theme, no extra install needed
-
-html_static_path = ['_static']
-
-html_theme_options = {
-    'canonical_url': '',
-    'analytics_id': '',
-    'logo_only': False,
-    'display_version': True,
-    'prev_next_buttons_location': 'bottom',
-    'style_external_links': False,
-    'vcs_pageview_mode': '',
-    'style_nav_header_background': '#2980B9',
-    'collapse_navigation': False,
-    'sticky_navigation': True,
-    'navigation_depth': 4,
-    'includehidden': True,
-    'titles_only': False
-}