fix refs

pysal · Oct 30, 2024 · 025d8a3 · 025d8a3
1 parent d8db216
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diff --git a/.gitignore b/.gitignore
@@ -95,3 +95,6 @@ ENV/
 .vscode
 
 nlcd_2011.tif
+
+docs/generated/
+docs/apidocs/
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 </p>
 
 [![Continuous Integration](https://github.com/pysal/tobler/actions/workflows/unittests.yml/badge.svg)](https://github.com/pysal/tobler/actions/workflows/unittests.yml)
-[![codecov](https://codecov.io/gh/pysal/tobler/branch/master/graph/badge.svg?token=XO4SilfBEb)](https://codecov.io/gh/pysal/tobler)![PyPI - Python Version](https://img.shields.io/pypi/pyversions/tobler)
+[![codecov](https://codecov.io/gh/pysal/tobler/branch/main/graph/badge.svg?token=XO4SilfBEb)](https://codecov.io/gh/pysal/tobler)![PyPI - Python Version](https://img.shields.io/pypi/pyversions/tobler)
 ![PyPI](https://img.shields.io/pypi/v/tobler)
 ![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/tobler)
 ![GitHub commits since latest release (branch)](https://img.shields.io/github/commits-since/pysal/tobler/latest)
@@ -62,7 +62,7 @@ If you have any suggestion, feature request, or bug report, please open a new [i
 
 ## License
 
-The project is licensed under the [BSD license](https://github.com/pysal/tobler/blob/master/LICENSE.txt).
+The project is licensed under the [BSD license](https://github.com/pysal/tobler/blob/main/LICENSE.txt).
 
 ## Funding
 

diff --git a/ci/311.yml b/ci/311.yml
@@ -35,4 +35,10 @@ dependencies:
   - numpydoc
   - nbsphinx
   - joblib
-  - astropy
+  - astropy
+  - nbsphinx_link
+  - myst-parser
+  - autodoc2
+  - nbsphinx_link
+  - pip:
+    - nbsphinx_link>=1.3.1 # not on conda yet
diff --git a/docs/_static/references.bib b/docs/_static/references.bib
diff --git a/docs/conf.py b/docs/conf.py
@@ -118,6 +118,12 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+# Bib Variables
+bibtex_default_style = 'alpha'
+bibtex_reference_style ="author_year"
+bibtex_bibfiles = ["_static/references.bib"]
+
+
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -132,7 +138,7 @@
 # Path should be relative to the ``_static`` files directory.
 # html_logo = "_static/images/CGS_logo.jpg"
 # html_logo = "_static/images/CGS_logo_green.png"
-html_logo = "figs/tobler.svg"
+html_logo = "figs/tobler_long.svg"
 html_favicon = "figs/tobler.ico"
 
 
@@ -302,7 +308,3 @@
                         'cluster', 'of', 'or', 'if', 'using', 'otherwise', 'required',
                         'from'}
 
-# Bib Variables
-bibtex_default_style = 'plain'
-bibtex_reference_style ="author_year"
-bibtex_bibfiles = ['references.bib']
diff --git a/docs/myst.md b/docs/myst.md
diff --git a/docs/myst_summary.md b/docs/myst_summary.md
diff --git a/docs/references.rst b/docs/references.rst
@@ -3,5 +3,5 @@
 References
 ==========
 
-.. bibliography:: references.bib
+.. bibliography:: _static/references.bib
    :all:
diff --git a/tobler/area_weighted/__init__.py b/tobler/area_weighted/__init__.py
@@ -1,4 +1,6 @@
-from .area_interpolate import _area_interpolate_binning as area_interpolate
+from .area_interpolate import area_interpolate
 from .area_interpolate import _area_tables_binning
 from .area_join import area_join
 from .area_interpolate_dask import area_interpolate_dask
+
+__all__ = [area_interpolate, area_join, area_interpolate_dask]
diff --git a/tobler/area_weighted/area_interpolate.py b/tobler/area_weighted/area_interpolate.py
@@ -12,6 +12,7 @@
 
 from tobler.util.util import _check_crs, _inf_check, _nan_check
 
+__all__ = ['area_interpolate']
 
 def _chunk_dfs(geoms_to_chunk, geoms_full, n_jobs):
     chunk_size = geoms_to_chunk.shape[0] // n_jobs + 1
@@ -203,7 +204,7 @@ def _area_tables_binning(source_df, target_df, spatial_index):
     return table
 
 
-def _area_interpolate_binning(
+def area_interpolate(
     source_df,
     target_df,
     extensive_variables=None,
@@ -221,36 +222,47 @@ def _area_interpolate_binning(
     Parameters
     ----------
     source_df : geopandas.GeoDataFrame
+
     target_df : geopandas.GeoDataFrame
+
     extensive_variables : list
         [Optional. Default=None] Columns in dataframes for extensive variables
+
     intensive_variables : list
         [Optional. Default=None] Columns in dataframes for intensive variables
+
     table : scipy.sparse.csr_matrix
         [Optional. Default=None] Area allocation source-target correspondence
         table. If not provided, it will be built from `source_df` and
         `target_df` using `tobler.area_interpolate._area_tables_binning`
+
     allocate_total : boolean
         [Optional. Default=True] True if total value of source area should be
         allocated. False if denominator is area of i. Note that the two cases
         would be identical when the area of the source polygon is exhausted by
         intersections. See Notes for more details.
+
     spatial_index : str
         [Optional. Default="auto"] Spatial index to use to build the
         allocation of area from source to target tables. It currently support
         the following values:
-            - "source": build the spatial index on `source_df`
-            - "target": build the spatial index on `target_df`
-            - "auto": attempts to guess the most efficient alternative.
-              Currently, this option uses the largest table to build the
-              index, and performs a `bulk_query` on the shorter table.
+
+        - "source": build the spatial index on `source_df`
+        - "target": build the spatial index on `target_df`
+        - "auto": attempts to guess the most efficient alternative.
+        
+        Currently, this option uses the largest table to build the
+        index, and performs a `bulk_query` on the shorter table.
         This argument is ignored if n_jobs>1 (or n_jobs=-1).
+
     n_jobs : int
         [Optional. Default=1] Number of processes to run in parallel to
         generate the area allocation. If -1, this is set to the number of CPUs
         available. If `table` is passed, this is ignored.
+
     categorical_variables : list
         [Optional. Default=None] Columns in dataframes for categorical variables
+
     categorical_frequency : Boolean
         [Optional. Default=True] If True, `estimates` returns the frequency of each
         value in a categorical variable in every polygon of `target_df` (proportion of
@@ -278,18 +290,16 @@ def _area_interpolate_binning(
     an extensive attribute, then setting allocate_total=False will use the
     following weights:
 
-    .. math::
-     v_j = \\sum_i v_i w_{i,j}
+    $$v_j = \\sum_i v_i w_{i,j}$$
 
-     w_{i,j} = a_{i,j} / a_i
+    $$w_{i,j} = a_{i,j} / a_i$$
 
     where a_i is the total area of source polygon i.
     For an intensive variable, the estimate at target polygon j is:
 
-    .. math::
-     v_j = \\sum_i v_i w_{i,j}
+    $$v_j = \\sum_i v_i w_{i,j}$$
 
-     w_{i,j} = a_{i,j} / \\sum_k a_{k,j}
+    $$w_{i,j} = a_{i,j} / \\sum_k a_{k,j}$$
 
     For categorical variables, the estimate returns ratio of presence of each
     unique category.

diff --git a/tobler/area_weighted/area_interpolate_dask.py b/tobler/area_weighted/area_interpolate_dask.py
@@ -2,11 +2,13 @@
 Area Weighted Interpolation, out-of-core and parallel through Dask
 """
 
-import pandas
 import geopandas
 import numpy as np
-from .area_interpolate import _area_interpolate_binning as area_interpolate
+import pandas
+
+from .area_interpolate import area_interpolate
 
+__all__ = ['area_interpolate_dask']
 
 def area_interpolate_dask(
     source_dgdf,

diff --git a/tobler/area_weighted/area_join.py b/tobler/area_weighted/area_join.py
@@ -4,6 +4,8 @@
 
 __author__ = "Martin Fleischmann <[email protected]>"
 
+__all__ = ["area_join"]
+
 
 def area_join(source_df, target_df, variables):
     """
@@ -22,7 +24,7 @@ def area_join(source_df, target_df, variables):
     -------
     joined : geopandas.GeoDataFrame
          target_df GeoDataFrame with joined variables as additional columns
-    
+
     """
     if not pd.api.types.is_list_like(variables):
         variables = [variables]

diff --git a/tobler/dasymetric/__init__.py b/tobler/dasymetric/__init__.py
@@ -1,2 +1,4 @@
 from .masked_area_interpolate import masked_area_interpolate
-from .raster_tools import extract_raster_features, _fast_append_profile_in_gdf
+from .raster_tools import extract_raster_features, _fast_append_profile_in_gdf
+
+__all__ = ["masked_area_interpolate"]
diff --git a/tobler/dasymetric/masked_area_interpolate.py b/tobler/dasymetric/masked_area_interpolate.py
@@ -5,6 +5,8 @@
 from ..area_weighted import area_interpolate
 from .raster_tools import extract_raster_features
 
+__all__ = ["masked_area_interpolate"]
+
 
 def masked_area_interpolate(
     source_df,

diff --git a/tobler/dasymetric/raster_tools.py b/tobler/dasymetric/raster_tools.py
@@ -19,6 +19,8 @@
 
 GPD_10 = Version(gpd.__version__) >= Version("1.0.0dev")
 
+__all__ = ["extract_raster_features"]
+
 
 def _chunk_dfs(geoms_to_chunk, n_jobs):
     chunk_size = geoms_to_chunk.shape[0] // n_jobs + 1

diff --git a/tobler/model/__init__.py b/tobler/model/__init__.py
@@ -1 +1,3 @@
 from .glm import glm
+
+__all__ = ['glm']
diff --git a/tobler/model/glm.py b/tobler/model/glm.py
@@ -1,10 +1,13 @@
 """Model-based methods for areal interpolation."""
 
+import numpy as np
 import statsmodels.formula.api as smf
 from statsmodels.genmod.families import Gaussian, NegativeBinomial, Poisson
-from ..util.util import _check_presence_of_crs
+
 from ..dasymetric import _fast_append_profile_in_gdf
-import numpy as np
+from ..util.util import _check_presence_of_crs
+
+__all__ = ["glm"]
 
 
 def glm(

diff --git a/tobler/pycno/__init__.py b/tobler/pycno/__init__.py
@@ -1 +1,3 @@
 from .pycno import pycno_interpolate
+
+__all__ = ['pycno_interpolate']
diff --git a/tobler/pycno/pycno.py b/tobler/pycno/pycno.py
@@ -1,7 +1,6 @@
 """Pycnophylactic Interpolation (contributed by @danlewis85)."""
 # https://github.com/danlewis85/pycno/
 
-import geopandas as gpd
 import numpy as np
 import pandas as pd
 import rasterio
@@ -24,6 +23,8 @@
 from pandas import DataFrame
 from rasterio.features import rasterize
 
+__all__ = ["pycno_interpolate"]
+
 
 def pycno(
     gdf, value_field, cellsize, r=0.2, handle_null=True, converge=3, verbose=True

diff --git a/tobler/util/__init__.py b/tobler/util/__init__.py
@@ -1 +1,3 @@
-from .util import *
+from .util import *
+
+__all__ = ['h3fy', 'circumradius']
diff --git a/tobler/util/util.py b/tobler/util/util.py
@@ -11,6 +11,8 @@
 
 GPD_10 = Version(geopandas.__version__) >= Version("1.0.0dev")
 
+__all__ = ["h3fy", "circumradius"]
+
 
 def circumradius(resolution):
     """Find the circumradius of an h3 hexagon at given resolution.

diff --git a/tools/changelog_0.3.0.md b/tools/changelog_0.3.0.md