Improve a bit the index of the API (#355)

* Change API

* Update docs/src/api.rst

Co-authored-by: Joseph Paillard <[email protected]>

* remove not necessary class from init

* fix import

* fix reference for bibliography, example, template

* Apply suggestions from code review

Co-authored-by: Joseph Paillard <[email protected]>

* fix doc

---------

Co-authored-by: Joseph Paillard <[email protected]>

Author: lionelkusch

docs/src/api.rst

@@ -4,19 +4,37 @@
 API
 =================
 
-Estimators
-==========
-
 .. currentmodule:: hidimstat
 
-Functions
-=========
+Base Classes
+============
+
+.. autosummary::
+   :toctree: ./generated/api/base/
+   :template: class.rst
+
+   base_variable_importance.BaseVariableImportance
+   base_perturbation.BasePerturbation
+
+Feature Importance Classes
+==========================
+
+.. autosummary::
+   :toctree: ./generated/api/class/
+   :template: class.rst
+   
+   LOCO
+   CFI
+   PFI
+   D0CRT
+
+Feature Importance functions
+============================
 
 .. autosummary::
-   :toctree: ./generated/api/function/
+   :toctree: ./generated/api/class/
    :template: function.rst
 
-   quantile_aggregation
    clustered_inference
    clustered_inference_pvalue
    desparsified_lasso
@@ -25,18 +43,22 @@ Functions
    ensemble_clustered_inference
    ensemble_clustered_inference_pvalue
    model_x_knockoff
-   reid
 
-Classes
-=======
+Samplers
+========
 
 .. autosummary::
    :toctree: ./generated/api/class/
    :template: class.rst
-   
-   BaseVariableImportance
-   BasePerturbation
-   LOCO
-   CFI
-   PFI
-   D0CRT
+
+   conditional_sampling.ConditionalSampler
+
+Helper Functions
+================
+
+.. autosummary::
+   :toctree: ./generated/api/helper_functions/
+   :template: function.rst
+
+   quantile_aggregation
+   reid

docs/tools/_templates/class.rst

@@ -10,7 +10,7 @@
    .. automethod:: __init__
    {% endblock %}
 
-.. include:: {{module}}.{{objname}}.examples
+.. include:: ../../gallery/backreference/{{module}}.{{objname}}.examples
 
 .. raw:: html
 

docs/tools/_templates/function.rst

@@ -5,4 +5,4 @@
 
 .. autofunction:: {{ objname }}
 
-.. include:: {{module}}.{{objname}}.examples
+.. include:: ../../gallery/backreference/{{module}}.{{objname}}.examples

docs/tools/conf.py

@@ -50,7 +50,7 @@
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ["./_templates"]
+templates_path = ["../tools/_templates"]
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
@@ -69,7 +69,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["./_static"]
+html_static_path = ["../tools/_static"]
 html_logo = "./_static/logo.png"
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
@@ -99,7 +99,7 @@
 source_suffix = [".rst", ".md"]
 
 # sphinxcontrib-bibtex
-bibtex_bibfiles = ["./references.bib"]
+bibtex_bibfiles = ["../tools/references.bib"]
 bibtex_style = "unsrt"
 bibtex_reference_style = "author_year"
 bibtex_footbibliography_header = ""

src/hidimstat/__init__.py

@@ -1,5 +1,3 @@
-from .base_variable_importance import BaseVariableImportance
-from .base_perturbation import BasePerturbation
 from .ensemble_clustered_inference import (
     clustered_inference,
     clustered_inference_pvalue,

test/test_conditional_feature_importance.py

@@ -8,7 +8,8 @@
 from sklearn.model_selection import train_test_split
 from sklearn.metrics import root_mean_squared_error
 
-from hidimstat import CFI, BasePerturbation
+from hidimstat import CFI
+from hidimstat.base_perturbation import BasePerturbation
 from hidimstat._utils.exception import InternalError
 
 

test/test_leave_one_covariate_out.py

@@ -7,7 +7,8 @@
 from sklearn.model_selection import train_test_split
 from hidimstat._utils.scenario import multivariate_simulation
 
-from hidimstat import LOCO, BasePerturbation
+from hidimstat import LOCO
+from hidimstat.base_perturbation import BasePerturbation
 
 
 def test_loco():