Feedback&refactoring (#96)

* fix links

* add privacy folder

* update tutorials

* cleanup

* update tutorials

* bugfixing

* drop sdv

* TimeSeriesTabularVAE

* observation_times

* drop ctimegan

* update PBC

* improve docs

* improve time series docs

* cleanup

* improve docs

* add docs template with UML

* cleanup

* cleanup

Author: bcebere

README.md

@@ -54,7 +54,7 @@ $ pip install .
 ```python
 from synthcity.plugins import Plugins
 
-Plugins(categories=["generic"]).list()
+Plugins(categories=["generic", "privacy"]).list()
 ```
 
 * Load and train a tabular generator
@@ -113,7 +113,7 @@ Benchmarks.print(score)
 ```python
 from synthcity.plugins import Plugins
 
-Plugins(categories=["generic", "survival_analysis"]).list()
+Plugins(categories=["generic", "privacy", "survival_analysis"]).list()
 ```
 
 * Generate new data
@@ -144,7 +144,7 @@ syn_model.generate(count=10)
 ```python
 from synthcity.plugins import Plugins
 
-Plugins(categories=["generic", "time_series"]).list()
+Plugins(categories=["generic", "privacy", "time_series"]).list()
 ```
 
 * Generate new data
@@ -158,7 +158,7 @@ from synthcity.utils.datasets.time_series.google_stocks import GoogleStocksDatal
 static_data, temporal_data, horizons, outcome = GoogleStocksDataloader().load()
 data = TimeSeriesDataLoader(
     temporal_data=temporal_data,
-    temporal_horizons=horizons,
+    observation_times=horizons,
     static_data=static_data,
     outcome=outcome,
 )
@@ -201,12 +201,12 @@ assert syn_model.name() == reloaded.name()
 
 ## 📓 Tutorials
 
- - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Vr2PJswgfFYBkJCm3hhVkuH-9dXnHeYV?usp=sharing) [ Tutorial 0: Getting started with tabular data](https://github.com/vanderschaarlab/synthcity/blob/use_cases/tutorials/tutorial0_basic_examples.ipynb)
-  - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1rTTvV4FT-Ut-rIHoBPXQimiBlZ7zCv59?usp=sharing) [ Tutorial 1: Writing a new plugin](https://github.com/vanderschaarlab/synthcity/blob/use_cases/tutorials/tutorial1_add_a_new_plugin.ipynb)
-   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1FXpnQ9bpHzEgJgD-9pf_PPN4D80ENilE?usp=sharing) [ Tutorial 2: Benchmarking models](https://github.com/vanderschaarlab/synthcity/blob/use_cases/tutorials/tutorial2_benchmarks.ipynb)
-   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Wa2CPsbXzbKMPC5fSBhKl00Gi7QqVkse?usp=sharing) [ Tutorial 3: Generating Survival Analysis data](https://github.com/vanderschaarlab/synthcity/blob/use_cases/tutorials/tutorial3_survival_analysis.ipynb)
-   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1jN36GCAKEkjzDlczmQfR7Wbh3yF3cIz5?usp=sharing) [ Tutorial 4: Generating Time Series](https://github.com/vanderschaarlab/synthcity/blob/use_cases/tutorials/tutorial4_time_series.ipynb)
-   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Nf8d3Y6sXr1uco8MsJA4wb33iFvReL59?usp=sharing) [ Tutorial 5: Generating Data with Differential Privacy Guarantees](https://github.com/vanderschaarlab/synthcity/blob/use_cases/tutorials/tutorial5_differential_privacy.ipynb)
+ - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Vr2PJswgfFYBkJCm3hhVkuH-9dXnHeYV?usp=sharing) [ Tutorial 0: Getting started with tabular data](https://github.com/vanderschaarlab/synthcity/blob/main/tutorials/tutorial0_basic_examples.ipynb)
+  - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1rTTvV4FT-Ut-rIHoBPXQimiBlZ7zCv59?usp=sharing) [ Tutorial 1: Writing a new plugin](https://github.com/vanderschaarlab/synthcity/blob/main/tutorials/tutorial1_add_a_new_plugin.ipynb)
+   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1FXpnQ9bpHzEgJgD-9pf_PPN4D80ENilE?usp=sharing) [ Tutorial 2: Benchmarking models](https://github.com/vanderschaarlab/synthcity/blob/main/tutorials/tutorial2_benchmarks.ipynb)
+   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Wa2CPsbXzbKMPC5fSBhKl00Gi7QqVkse?usp=sharing) [ Tutorial 3: Generating Survival Analysis data](https://github.com/vanderschaarlab/synthcity/blob/main/tutorials/tutorial3_survival_analysis.ipynb)
+   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1jN36GCAKEkjzDlczmQfR7Wbh3yF3cIz5?usp=sharing) [ Tutorial 4: Generating Time Series](https://github.com/vanderschaarlab/synthcity/blob/main/tutorials/tutorial4_time_series.ipynb)
+   - [![Test In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Nf8d3Y6sXr1uco8MsJA4wb33iFvReL59?usp=sharing) [ Tutorial 5: Generating Data with Differential Privacy Guarantees](https://github.com/vanderschaarlab/synthcity/blob/main/tutorials/tutorial5_differential_privacy.ipynb)
 
 
 ## 🔑 Methods
@@ -238,7 +238,7 @@ assert syn_model.name() == reloaded.name()
 |--- | --- | --- |
 |**nflow**| Normalizing Flows are generative models which produce tractable distributions where both sampling and density evaluation can be efficient and exact.| [Neural Spline Flows](https://arxiv.org/abs/1906.04032) |
 
-### Survival analysis methods
+### Static Survival analysis methods
 
 | Method | Description | Reference |
 |--- | --- | --- |
@@ -247,7 +247,7 @@ assert syn_model.name() == reloaded.name()
 |**survae** | SurvivalGAN version using VAE | --- |
 |**survival_nflow** | SurvivalGAN version using normalizing flows | --- |
 
-### Time Series methods
+### Time-Series and Time-Series Survival Analysis methods
 
 | Method | Description | Reference |
 |--- | --- | --- |

docs/README.md

@@ -40,7 +40,7 @@ $ pip install .
 ```python
 from synthcity.plugins import Plugins
 
-Plugins(categories=["generic"]).list()
+Plugins(categories=["generic", "privacy"]).list()
 ```
 
 * Load and train a generator
@@ -63,19 +63,6 @@ syn_model.fit(X)
 syn_model.generate(count = 10)
 ```
 
-* Generate new synthetic data under some constraints
-
-```python
-# Constraint: target <= 100
-from synthcity.plugins.core.constraints import Constraints
-
-constraints = Constraints(rules=[("target", "<=", 100)])
-
-generated = syn_model.generate(count=10, constraints=constraints)
-
-assert (generated["target"] <= 100).any()
-```
-
 * Benchmark the quality of the plugins
 
 ```python
@@ -105,14 +92,14 @@ score = Benchmarks.evaluate(
 Benchmarks.print(score)
 ```
 
-### Survival analysis
+### Static Survival analysis
 
 * List the available generators
 
 ```python
 from synthcity.plugins import Plugins
 
-Plugins(categories=["survival_analysis"]).list()
+Plugins(categories=["generic", "privacy", "survival_analysis"]).list()
 ```
 
 * Generate new data
@@ -136,14 +123,14 @@ syn_model.fit(data)
 syn_model.generate(count=10)
 ```
 
-### Time series
+### Time-Series & Time-Series Survival Analysis
 
 * List the available generators
 
 ```python
 from synthcity.plugins import Plugins
 
-Plugins(categories=["time_series"]).list()
+Plugins(categories=["generic", "privacy", "time_series"]).list()
 ```
 
 * Generate new data
@@ -157,7 +144,7 @@ from synthcity.utils.datasets.time_series.google_stocks import GoogleStocksDatal
 static_data, temporal_data, horizons, outcome = GoogleStocksDataloader().load()
 data = TimeSeriesDataLoader(
     temporal_data=temporal_data,
-    temporal_horizons=horizons,
+    observation_times=horizons,
     static_data=static_data,
     outcome=outcome,
 )

docs/_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 %}

docs/advanced.rst

@@ -8,6 +8,7 @@ Core components
     :glob:
     :maxdepth: 2
 
+    Plugin <generated/synthcity.plugins.core.plugin.rst>
     Dataloader <generated/synthcity.plugins.core.dataloader.rst>
     Constraints <generated/synthcity.plugins.core.constraints.rst>
     Distribution <generated/synthcity.plugins.core.distribution.rst>

docs/conf.py

@@ -41,6 +41,7 @@
         "-f",
         "-o",
         "generated",
+        "-t", "_templates",
         "../src/synthcity/",
     ]
 )
@@ -81,8 +82,12 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "m2r2",
-    "sphinxemoji.sphinxemoji",
+    #"sphinxemoji.sphinxemoji",
     "nbsphinx",
+    "sphinx_diagrams",
+    'IPython.sphinxext.ipython_console_highlighting',
+    'sphinx.ext.graphviz','sphinx.ext.inheritance_diagram',
+    "sphinx_pyreverse",
 ]
 
 autodoc_default_options = {
@@ -111,7 +116,7 @@
 # a list of builtin themes.
 #
 html_theme = "sphinx_rtd_theme"
-sphinxemoji_style = "twemoji"
+#sphinxemoji_style = "twemoji"
 
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -126,9 +131,6 @@
 .. only:: html
     .. role:: raw-html(raw)
         :format: html
-    .. nbinfo::
-        :raw-html:`<a href="https://colab.research.google.com/github/DTUWindEnergy/PyWake/blob/master/{{ docname }}"><img alt="Open and run in Colab (interactive)" src="https://colab.research.google.com/assets/colab-badge.svg" style="vertical-align:text-bottom"></a>
-        <a href="https://gitlab.windenergy.dtu.dk/TOPFARM/PyWake/-/tree/master/{{ docname }}"><img alt="Edit on Gitlab" src="https://img.shields.io/badge/Edit%20on-Gitlab-blue?style=flat&logo=gitlab" style="vertical-align:text-bottom"></a>`
 """
 
 autodoc_mock_imports = [

docs/examples.rst

@@ -20,12 +20,9 @@ General-purpose generators
     :glob:
     :maxdepth: 2
 
-    AdsGAN <tutorials/plugins/generic/plugin_adsgan.ipynb>
     Bayesian Network <tutorials/plugins/generic/plugin_bayesian_network.ipynb>
     CTGAN <tutorials/plugins/generic/plugin_ctgan.ipynb>
     Normalizing Flows <tutorials/plugins/generic/plugin_nflow.ipynb>
-    PATEGAN <tutorials/plugins/generic/plugin_pategan.ipynb>
-    PrivBayes <tutorials/plugins/generic/plugin_privbayes.ipynb>
     TVAE <tutorials/plugins/generic/plugin_tvae.ipynb>
 
 
@@ -45,11 +42,11 @@ Privacy-related generators
     :glob:
     :maxdepth: 2
 
-    DECAF <tutorials/plugins/fairness/plugin_decaf.ipynb>
-    DP-GAN <tutorials/plugins/generic/plugin_dpgan.ipynb>
-    AdsGAN <tutorials/plugins/generic/plugin_adsgan.ipynb>
-    PATEGAN <tutorials/plugins/generic/plugin_pategan.ipynb>
-    PrivBayes <tutorials/plugins/generic/plugin_privbayes.ipynb>
+    DECAF <tutorials/plugins/privacy/plugin_decaf.ipynb>
+    DP-GAN <tutorials/plugins/privacy/plugin_dpgan.ipynb>
+    AdsGAN <tutorials/plugins/privacy/plugin_adsgan.ipynb>
+    PATEGAN <tutorials/plugins/privacy/plugin_pategan.ipynb>
+    PrivBayes <tutorials/plugins/privacy/plugin_privbayes.ipynb>
 
 Domain adaptation generators
 ------------------------------

docs/generators.rst

@@ -7,12 +7,9 @@ General purpose
     :glob:
     :maxdepth: 2
 
-    AdsGAN <generated/synthcity.plugins.generic.plugin_adsgan.rst>
     Bayesian Network <generated/synthcity.plugins.generic.plugin_bayesian_network.rst>
     CTGAN <generated/synthcity.plugins.generic.plugin_ctgan.rst>
     Normalizing Flows <generated/synthcity.plugins.generic.plugin_nflow.rst>
-    PATEGAN <generated/synthcity.plugins.generic.plugin_pategan.rst>
-    PrivBayes <generated/synthcity.plugins.generic.plugin_privbayes.rst>
     RTVAE <generated/synthcity.plugins.generic.plugin_rtvae.rst>
     TVAE <generated/synthcity.plugins.generic.plugin_tvae.rst>
 
@@ -22,22 +19,22 @@ Privacy-focused
     :glob:
     :maxdepth: 2
 
-    AdsGAN <generated/synthcity.plugins.generic.plugin_adsgan.rst>
-    PATEGAN <generated/synthcity.plugins.generic.plugin_pategan.rst>
-    PrivBayes <generated/synthcity.plugins.generic.plugin_privbayes.rst>
-    DP-GAN <generated/synthcity.plugins.generic.plugin_dpgan.rst>
-    DECAF <generated/synthcity.plugins.fairness.plugin_decaf.rst>
+    AdsGAN <generated/synthcity.plugins.privacy.plugin_adsgan.rst>
+    PATEGAN <generated/synthcity.plugins.privacy.plugin_pategan.rst>
+    PrivBayes <generated/synthcity.plugins.privacy.plugin_privbayes.rst>
+    DP-GAN <generated/synthcity.plugins.privacy.plugin_dpgan.rst>
+    DECAF <generated/synthcity.plugins.privacy.plugin_decaf.rst>
 
 Domain adaptation
------------------
+-------------------
 .. toctree::
     :glob:
     :maxdepth: 2
 
     RadialGAN <generated/synthcity.plugins.domain_adaptation.plugin_radialgan.rst>
 
-Survival Analysis
------------------
+Static Survival Analysis
+--------------------------
 .. toctree::
     :glob:
     :maxdepth: 2
@@ -47,8 +44,8 @@ Survival Analysis
     SurVAE <generated/synthcity.plugins.survival_analysis.plugin_survae.rst>
     Surival NFlows <generated/synthcity.plugins.survival_analysis.plugin_survival_nflow.rst>
 
-Time-series
------------------
+Time-series & Time-Series Survival Analysis
+----------------------------------------------
 .. toctree::
     :glob:
     :maxdepth: 2

docs/index.rst

@@ -20,6 +20,14 @@ Examples
 
     examples.rst
 
+Dataloaders
+============
+.. toctree::
+    :glob:
+    :maxdepth: 3
+
+    Dataloaders <generated/synthcity.plugins.core.dataloader.rst>
+
 Generators
 ==========
 .. toctree::

docs/metrics.rst

@@ -1,5 +1,5 @@
-Metrics
-============
+Metrics and benchmarks
+=======================
 .. toctree::
     :glob:
     :maxdepth: 2
@@ -11,3 +11,4 @@ Metrics
     Privacy Metrics <generated/synthcity.metrics.eval_privacy.rst>
     Attacks <generated/synthcity.metrics.eval_attacks.rst>
     Weighted metrics <generated/synthcity.metrics.weighted_metrics.rst>
+    Benchmarks <generated/synthcity.benchmark.rst>

docs/requirements.txt

@@ -13,6 +13,8 @@ Pillow==9.3.0
 seaborn
 sphinx==4.3.1
 sphinx-autopackagesummary
+sphinx-pyreverse
+sphinx_diagrams
 sphinx_gallery==0.10.1
 sphinx_rtd_theme==1.0.0
 sphinxcontrib-napoleon