fix the doc build

Author: tgnassou

.gitignore

@@ -127,3 +127,7 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+docs/source/auto_examples/
+docs/source/gen_modules/
+.DS_Store

docs/Makefile

@@ -49,7 +49,7 @@ help:
 
 .PHONY: clean
 clean:
-	rm -rf $(BUILDDIR)/*
+	rm -rf $(BUILDDIR)/* source/gen_modules source/auto_examples
 
 .PHONY: html
 html:

docs/source/_templates/class.rst

@@ -0,0 +1,12 @@
+{{ fullname | escape | underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :special-members: __contains__,__getitem__,__iter__,__len__,__add__,__sub__,__mul__,__div__,__neg__
+   :members:
+
+.. _sphx_glr_backreferences_{{ fullname }}:
+
+.. minigallery:: {{ fullname }}
+    :add-heading:

docs/source/_templates/function.rst

@@ -0,0 +1,10 @@
+{{ fullname | escape | underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}
+
+.. _sphx_glr_backreferences_{{ fullname }}:
+
+.. minigallery:: {{ fullname }}
+    :add-heading:

docs/source/_templates/module.rst

@@ -1,3 +1,6 @@
+.. Please when editing this file make sure to keep it matching the
+   docs in ../configuration.rst:reference_to_examples
+
 {{ fullname }}
 {{ underline }}
 
@@ -13,11 +16,10 @@
 
    .. autofunction:: {{ item }}
 
-   .. include:: backreferences/{{fullname}}.{{item}}.examples
-
-   .. raw:: html
+   .. _sphx_glr_backref_{{fullname}}.{{item}}:
 
-	       <div class="sphx-glr-clear"></div>
+   .. minigallery:: {{fullname}}.{{item}}
+       :add-heading:
 
    {%- endfor %}
    {% endif %}
@@ -33,11 +35,10 @@
    .. autoclass:: {{ item }}
       :members:
 
-   .. include:: backreferences/{{fullname}}.{{item}}.examples
+   .. _sphx_glr_backref_{{fullname}}.{{item}}:
 
-   .. raw:: html
-
-	       <div class="sphx-glr-clear"></div>
+   .. minigallery:: {{fullname}}.{{item}}
+       :add-heading:
 
    {%- endfor %}
    {% endif %}
@@ -54,4 +55,4 @@
       {{ item }}
    {%- endfor %}
    {% endif %}
-   {% endblock %}
+   {% endblock %}

docs/source/_templates/versions.html

@@ -4,23 +4,52 @@
 API and modules
 ===============
 
-.. currentmodule:: skada
+.. currentmodule:: skada.datasets
 
+.. automodule:: skada.datasets
+   :no-members:
+   :no-inherited-members:
 
-:py:mod:`skada`:
+:py:mod:`skada.datasets`:
 
-   .. autosummary::
-      :toctree: gen_modules/
-      :template: module.rst
+.. autosummary::
+   :toctree: gen_modules/
+   :template: function.rst
+
+   make_shifted_blobs
+   make_shifted_datasets
+   make_dataset_from_moons_distribution
+   make_variable_frequency_dataset
+
+.. currentmodule:: skada.da
+
+.. automodule:: skada.da
+   :no-members:
+   :no-inherited-members:
+
+:py:mod:`skada.da`:
+
+.. autosummary::
+   :toctree: gen_modules/
+   :template: class.rst
+
+   ReweightDensity
+   GaussianReweightDensity
+   ClassifierReweightDensity
+   SubspaceAlignment
+   TransferComponentAnalysis
+
+.. currentmodule:: skada.deepda
 
-      da
-      deepda
+.. automodule:: skada.deepda
+   :no-members:
+   :no-inherited-members:
 
-   
+:py:mod:`skada.deepda`:
 
 .. autosummary::
-   :toctree: ../modules/generated/
-   :template: module.rst
+   :toctree: gen_modules/
+   :template: class.rst
 
-.. automodule:: skada
-   :members:
+   DeepCORAL
+   DeepJDOT

docs/source/all.rst

@@ -8,23 +8,15 @@
 import sys
 import os
 import re
+from numpydoc import numpydoc, docscrape  # noqa
 
-try:
-    import sphinx_gallery
-
-    sphinx_gallery.__version__
-
-
-except ImportError:
-    print("warning sphinx-gallery not installed")
-
+import sphinx_gallery  # noqa
+import sphinx_rtd_theme  # noqa
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath("."))
 sys.path.insert(0, os.path.abspath(".."))
-sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- General configuration ------------------------------------------------
@@ -35,23 +27,42 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named #'sphinx.ext.*') or your custom
 # ones.
+# extensions = [
+#     "sphinx.ext.autodoc",
+#     "sphinx.ext.autosummary",
+#     "sphinx.ext.doctest",
+#     "sphinx.ext.intersphinx",
+#     # "sphinx.ext.todo",
+#     "sphinx.ext.coverage",
+#     "sphinx.ext.mathjax",
+#     "sphinx.ext.ifconfig",
+#     "sphinx.ext.viewcode",
+#     # "sphinx.ext.napoleon",
+#     "sphinx_gallery.gen_gallery",
+#     'numpydoc',
+# ]
+
 extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
-    "sphinx.ext.doctest",
-    "sphinx.ext.intersphinx",
-    "sphinx.ext.todo",
-    "sphinx.ext.coverage",
-    "sphinx.ext.mathjax",
-    "sphinx.ext.ifconfig",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.napoleon",
-    "sphinx_gallery.gen_gallery",
+    'sphinx.ext.autodoc',
+    # 'sphinx.ext.napoleon',
+    'numpydoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx_gallery.gen_gallery',
+    'sphinx.ext.graphviz',
 ]
 
+# autodoc / autosummary
 autosummary_generate = True
+# autodoc_default_options = {'inherited-members': None}
+numpydoc_show_class_members = False 
 
-napoleon_numpy_docstring = True
+# napoleon_numpy_docstring = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -68,7 +79,7 @@
 master_doc = "index"
 
 # General information about the project.
-project = ""
+project = "SKADA"
 copyright = "2022, The SKADA team"
 author = "Théo Gnassounou, Rémi Flamary, Alexandre Gramfort"
 
@@ -101,7 +112,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns = ['build']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -120,6 +131,7 @@
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "default"
+highlight_language = 'python3'
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -165,6 +177,7 @@
 # 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 = []
 html_static_path = ["_static"]
 # html_css_files = ["css/custom.css"]
 
@@ -316,19 +329,19 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
-    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
-    "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
-    "matplotlib": ("http://matplotlib.org/", None),
-    "torch": ("https://pytorch.org/docs/stable/", None),
+    # "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+    # "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
+    # "matplotlib": ("http://matplotlib.org/", None),
+    # "torch": ("https://pytorch.org/docs/stable/", None),
 }
 
 sphinx_gallery_conf = {
-    "examples_dirs": ["../../examples", "../../examples/da"],
+    "examples_dirs": ["../../examples"],
     "gallery_dirs": "auto_examples",
     "nested_sections": False,
     "backreferences_dir": "gen_modules/backreferences",
     "inspect_global_variables": True,
-    "doc_module": ("ot", "numpy", "scipy", "pylab"),
+    "doc_module": ("skada", "ot", "numpy", "scipy", "pylab"),
     "matplotlib_animations": True,
     "reference_url": {"skada": None},
 }

docs/source/conf.py

@@ -4,5 +4,5 @@ Examples gallery
 This is a gallery of all the SKADA example files. 
 
 
-Domai Adaptation Examples
--------------------------
+Domain Adaptation Examples
+--------------------------

examples/README.txt

@@ -1,7 +1,7 @@
 """
-====================================================
 Plot dataset source domain and shifted target domain
 ====================================================
+
 This illustrates the :func:`~skada.datasets.make_dataset_from_moons_distribution`
 dataset generator. Each method consists of generating source data
 and shifted target data.