Update docs (#13)

vanderschaarlab · Aug 22, 2023 · 691eaee · 691eaee
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diff --git a/.gitignore b/.gitignore
@@ -64,6 +64,6 @@ tests/test_workspace
 src/datagnosis/plugins/archived/
 /data/*
 !data/Brazil_covid19/
-
+docs/generated/*
 # Temp
 .coveragerc
diff --git a/README.md b/README.md
@@ -102,7 +102,7 @@ For benchmarking of the below methods see https://github.com/seedatnabeel/D-CAT.
 | Method | Type| Description | Score | Reference |
 | --- | --- | --- | --- | --- |
 | Area Under the Margin (AUM) | Generic | Characterizes data examples based on the margin of a classifier – i.e. the difference between the logit values of the correct class and the next class. | Hard - low scores. | [AUM Paper](https://arxiv.org/abs/2001.10528) |
-| Cleanlab *(rename) | Generic |Confident learning estimates the joint distribution of noisy and true labels — characterizing data as easy and hard for mislabeling. | Hard - low scores | [Cleanlab Paper](https://arxiv.org/pdf/1911.00068.pdf) |
+| Confident Learning | Generic |Confident learning estimates the joint distribution of noisy and true labels — characterizing data as easy and hard for mislabeling. | Hard - low scores | [Confident Learning Paper](https://arxiv.org/pdf/1911.00068.pdf) |
 | Conf Agree | Generic | Agreement measures the agreement of predictions on the same example. | Hard - low scores | [ Conf Agree Paper](https://arxiv.org/pdf/1910.13427.pdf)|
 | Data IQ |Generic | Data-IQ computes the aleatoric uncertainty and confidence to characterize the data into easy, ambiguous and hard examples. | Hard - low confidence scores. High Aleatoric Uncertainty scores define ambiguous | [Data-IQ Paper](https://arxiv.org/abs/2210.13043) |
 | Data Maps | Generic |Data Maps focuses on measuring variability (epistemic uncertainty) and confidence to characterize the data into easy, ambiguous and hard examples.|Hard - low confidence scores. High Epistemic Uncertainty scores define ambiguous| [Data-Maps Paper](https://arxiv.org/abs/2009.10795)|

diff --git a/docs/source/_templates/module.rst_t b/docs/source/_templates/module.rst_t
@@ -0,0 +1,11 @@
+{%- if show_headings %}
+{{- [basename, "module"] | join(' ') | e | heading }}
+
+{% endif -%}
+.. uml:: {{ qualname }}
+    :classes:
+.. automodule:: {{ qualname }}
+
+{%- for option in automodule_options %}
+   :{{ option }}:
+{%- endfor %}
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -3,6 +3,9 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+# stdlib
+import subprocess
+
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
@@ -11,6 +14,28 @@
 author = "Rob Davis"
 release = "0.0.1"
 
+
+subprocess.run(
+    [
+        "sphinx-apidoc",
+        "--ext-autodoc",
+        "--ext-doctest",
+        "--ext-mathjax",
+        "--ext-viewcode",
+        "-e",
+        "-T",
+        "-M",
+        "-F",
+        "-P",
+        "-f",
+        "-o",
+        "generated",
+        "-t",
+        "_templates",
+        "../src/datagnosis/",
+    ]
+)
+
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 

diff --git a/docs/source/datagnosis.md b/docs/source/datagnosis.md
diff --git a/docs/source/datagnosis.plugins.core.md b/docs/source/datagnosis.plugins.core.md
diff --git a/docs/source/datagnosis.plugins.generic.md b/docs/source/datagnosis.plugins.generic.md
diff --git a/docs/source/datagnosis.plugins.images.md b/docs/source/datagnosis.plugins.images.md
diff --git a/docs/source/datagnosis.plugins.md b/docs/source/datagnosis.plugins.md
diff --git a/docs/source/datagnosis.utils.md b/docs/source/datagnosis.utils.md
diff --git a/docs/source/datahandlers.rst b/docs/source/datahandlers.rst
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -0,0 +1,12 @@
+Tutorials
+============
+
+Getting started
+-----------------
+.. toctree::
+    :glob:
+    :maxdepth: 2
+
+    Getting started with tabular data <Tutorials/tutorial_01_simple_tabular_example.ipynb>
+    Adding a new plugin <Tutorials/tutorial_02_images.ipynb>
+    Benchmarks <Tutorials/tutorial_03_tabular_COVID19_data.ipynb>
diff --git a/docs/source/generators.rst b/docs/source/generators.rst
@@ -0,0 +1,28 @@
+Generators
+============
+
+General purpose
+-----------------
+.. toctree::
+    :glob:
+    :maxdepth: 2
+
+    Area Under the Margin (AUM) <generated/synthcity.plugins.generic.plugin_aum.rst>
+    Conf Agree <generated/synthcity.plugins.generic.plugin_conf_agree.rst>
+    Confident Learning <generated/synthcity.plugins.generic.plugin_confident_learning.rst>
+    Data IQ <generated/synthcity.plugins.generic.plugin_data_iq.rst>
+    Data Maps <generated/synthcity.plugins.generic.plugin_data_maps.rst>
+    Error L2-Norm (EL2N) <generated/synthcity.plugins.generic.plugin_el2n.rst>
+    Forgetting <generated/synthcity.plugins.generic.plugin_forgetting.rst>
+    Gradient Normed (GraNd) <generated/synthcity.plugins.generic.plugin_grand.rst>
+    Large Loss <generated/synthcity.plugins.generic.plugin_large_loss.rst>
+    Prototypicality <generated/synthcity.plugins.generic.plugin_prototypicality.rst>
+    Variance of Gradients (VOG) <generated/synthcity.plugins.generic.plugin_vog.rst>
+
+Image specific
+-----------------
+.. toctree::
+    :glob:
+    :maxdepth: 2
+
+    Active Learning Guided by Local Sensitivity and Hardness (ALLSH) <generated/synthcity.plugins.privacy.plugin_allsh.rst>
diff --git a/docs/source/index.md b/docs/source/index.md