Merge pull request #146 from liuzhenqi77/improvements

Various improvements again

.github/workflows/docs.yml

@@ -3,7 +3,7 @@ name: netneurotools-docs
 on: 
   workflow_dispatch:
   push:
-      branches:
+    branches:
       - main
 
 permissions:

.github/workflows/tests-basic.yml

@@ -34,7 +34,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
@@ -49,7 +49,7 @@ jobs:
       - name: Install netneurotools
         run: |
           python -m pip install --upgrade pip
-          python -m pip install '.[test]'
+          python -m pip install '.[test,numba]'
       - name: Print netneurotools version
         run: python -c "import netneurotools; print(netneurotools.__version__)" 
       - name: Run tests

.github/workflows/tests-plotting-pyvista.yml

@@ -7,11 +7,13 @@ on:
       - main
     paths:
       - 'netneurotools/plotting/pyvista_plotters.py'
+      - 'netneurotools/plotting/tests/test_pyvista.py'
   pull_request:
     branches:
       - main
     paths:
       - 'netneurotools/plotting/pyvista_plotters.py'
+      - 'netneurotools/plotting/tests/test_pyvista.py'
 
 jobs:
   run_pyvista_tests:

docs/api.rst

@@ -25,7 +25,6 @@ To download templates
    :template: function.rst
    :toctree: generated/
 
-
    fetch_fsaverage
    fetch_fsaverage_curated
    fetch_hcp_standards
@@ -45,7 +44,7 @@ To download atlases
     fetch_schaefer2018
     fetch_mmpall
     fetch_pauli2018
-    fetch_ye2020
+    fetch_tian2020msa
     fetch_voneconomo
 
 To download project-related data
@@ -188,7 +187,8 @@ Brain network metrics
    diffusion_efficiency
    resource_efficiency_bin
    flow_graph
-   assortativity
+   assortativity_und
+   assortativity_dir
    matching_ind_und
    rich_feeder_peripheral
 
@@ -207,14 +207,11 @@ Statistical network metrics
    :toctree: generated/
 
    network_pearsonr
-   network_pearsonr_numba
    network_pearsonr_pairwise
    effective_resistance
    network_polarisation
    network_variance
-   network_variance_numba
    network_covariance
-   network_covariance_numba
 
 
 .. _ref_modularity:
@@ -295,31 +292,69 @@ Regressions
 
 .. currentmodule:: netneurotools.spatial
 
-Calculating spatial statistics
+To calculate spatial statistics
 
 .. autosummary::
    :template: function.rst
    :toctree: generated/
 
    morans_i
    local_morans_i
+   gearys_c
+   local_gearys_c
+   lees_i
+   local_lees_i
 
 
 .. _ref_interface:
 
-:mod:`netneurotools.interface` - Interface for external tools
--------------------------------------------------------------
+:mod:`netneurotools.interface` - Interface with external data and tools
+-----------------------------------------------------------------------
 
 .. automodule:: netneurotools.interface
    :no-members:
    :no-inherited-members:
 
 .. currentmodule:: netneurotools.interface
 
+To parcellate surface data
+
 .. autosummary::
    :template: function.rst
    :toctree: generated/
 
+   vertices_to_parcels
+   parcels_to_vertices
+
+To work with CIFTI files
+
+.. autosummary::
+   :template: function.rst
+   :toctree: generated/
+
+   describe_cifti
+   extract_cifti_volume
+   extract_cifti_surface
+   extract_cifti_labels
+   extract_cifti_surface_labels
+   deconstruct_cifti
+
+To work with FreeSurfer files
+
+.. autosummary::
+   :template: function.rst
+   :toctree: generated/
+
+   extract_annot_labels
+
+To work with GIFTI files
+
+.. autosummary::
+   :template: function.rst
+   :toctree: generated/
+
+   extract_gifti_labels
+
 
 .. _ref_experimental:
 

docs/conf.py

@@ -112,7 +112,7 @@
     'python': ('https://docs.python.org/3', None),
     'matplotlib': ('https://matplotlib.org/stable', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy', None),
     'sklearn': ('https://scikit-learn.org/stable', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
     'pyvista': ('https://docs.pyvista.org/', None),

netneurotools/__init__.py

@@ -2,6 +2,13 @@
 from . import _version
 __version__ = _version.get_versions()['version']
 
+try:
+    from numba import njit
+    has_numba = True
+except ImportError:
+    has_numba = False
+
 __all__ = [
-    '__version__'
+    '__version__',
+    has_numba
 ]

netneurotools/datasets/__init__.py

@@ -13,7 +13,7 @@
     # cortical
     fetch_cammoun2012, fetch_schaefer2018, fetch_mmpall,
     # subcortical
-    fetch_pauli2018, fetch_ye2020,
+    fetch_pauli2018, fetch_tian2020msa,
     # annotation
     fetch_voneconomo
 )
@@ -46,7 +46,7 @@
     'fetch_conte69', 'fetch_yerkes19',
     # fetch_atlas
     'fetch_cammoun2012', 'fetch_schaefer2018', 'fetch_mmpall',
-    'fetch_pauli2018', 'fetch_ye2020',
+    'fetch_pauli2018', 'fetch_tian2020msa',
     'fetch_voneconomo',
     # fetch_project
     'fetch_vazquez_rodriguez2019', 'fetch_mirchi2018',

netneurotools/datasets/fetch_atlas.py

@@ -328,8 +328,8 @@ def fetch_pauli2018(force=False, data_dir=None, verbose=1):
     return Bunch(**data)
 
 
-def fetch_ye2020():
-    """Fetch Ye et al., 2020 subcortical parcellation."""
+def fetch_tian2020msa():
+    """Fetch Tian et al., 2020 subcortical parcellation."""
     pass
 
 

netneurotools/datasets/tests/test_datasets_utils.py

@@ -28,7 +28,7 @@ def test_get_dataset_info(dset, expected):
         utils._get_dataset_info('notvalid')
 
 
-def test_get_data_dir(tmpdir):
+def test_get_data_dir(tmp_path):
     """Test getting data directory."""
-    data_dir = utils._get_data_dir(tmpdir)
+    data_dir = utils._get_data_dir(tmp_path)
     assert os.path.isdir(data_dir)