Merge branch 'jhong/iss1429' of github.com:YosefLab/scvi-tools into j…

…hong/iss1429

.gitignore

@@ -68,7 +68,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/api/
+docs/api/reference/
 
 # PyBuilder
 target/

docs/api/datasets.rst → docs/api/datasets.md

@@ -1,21 +1,21 @@
-========
-Datasets
-========
+# Datasets
 
+Import scvi-tools as:
 
-Import scvi-tools as::
-
-   import scvi
-
+```
+import scvi
+```
 
+```{eval-rst}
 .. currentmodule:: scvi
 
+```
 
-Built in data
-~~~~~~~~~~~~~
+## Built in data
 
 Here we host some published datasets that are useful for benchmarking and testing models.
 
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :nosignatures:
@@ -37,3 +37,4 @@ Here we host some published datasets that are useful for benchmarking and testin
    data.retina
    data.prefrontalcortex_starmap
    data.frontalcortex_dropseq
+```

docs/api/developer.rst → docs/api/developer.md

@@ -1,24 +1,25 @@
-=========
-Developer
-=========
+# Developer
 
+Import scvi-tools as:
 
-Import scvi-tools as::
-
-   import scvi
-
+```
+import scvi
+```
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
-Data Registration
------------------
+## Data Registration
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 AnnDataFields delineate how scvi-tools refers to fields in AnnData objects. The AnnDataManager provides an interface
 for operating over a collection of AnnDataFields and an AnnData object.
 
-
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :nosignatures:
@@ -33,15 +34,17 @@ for operating over a collection of AnnDataFields and an AnnData object.
    data.fields.ProteinObsmField
    data.fields.LabelsWithUnlabeledObsField
 
+```
 
-Data Loaders
-------------
+## Data Loaders
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 DataLoaders for loading tensors from AnnData objects. DataSplitters for splitting data into train/test/val.
 
-
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :nosignatures:
@@ -53,15 +56,17 @@ DataLoaders for loading tensors from AnnData objects. DataSplitters for splittin
    dataloaders.SemiSupervisedDataLoader
    dataloaders.SemiSupervisedDataSplitter
 
+```
 
-Distributions
--------------
+## Distributions
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 Parameterizable probability distributions.
 
-
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :nosignatures:
@@ -71,14 +76,17 @@ Parameterizable probability distributions.
    distributions.ZeroInflatedNegativeBinomial
    distributions.JaxNegativeBinomialMeanDisp
 
+```
 
-Model (Base)
-------------
+## Model (Base)
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 These classes should be used to construct user-facing model classes.
 
+```{eval-rst}
 .. autosummary::
     :toctree: reference/
     :nosignatures:
@@ -92,14 +100,17 @@ These classes should be used to construct user-facing model classes.
     model.base.PyroSampleMixin
     model.base.PyroJitGuideWarmup
     model.base.DifferentialComputation
+```
 
-Module
-------
+## Module
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 Existing module classes with respective generative and inference procedures.
 
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :template: class_no_inherited.rst
@@ -117,14 +128,17 @@ Existing module classes with respective generative and inference procedures.
    module.VAEC
    module.AmortizedLDAPyroModule
 
+```
 
-External module
----------------
+## External module
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 Module classes in the external API with respective generative and inference procedures.
 
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :template: class_no_inherited.rst
@@ -135,14 +149,17 @@ Module classes in the external API with respective generative and inference proc
    external.stereoscope.RNADeconv
    external.stereoscope.SpatialDeconv
 
+```
 
-Module (Base)
--------------
+## Module (Base)
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 These classes should be used to construct module classes that define generative models and inference schemes.
 
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :template: class_no_inherited.rst
@@ -153,14 +170,17 @@ These classes should be used to construct module classes that define generative
    module.base.LossRecorder
    module.base.auto_move_data
 
+```
 
-Neural networks
----------------
+## Neural networks
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 Basic neural network building blocks.
 
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :template: class_no_inherited.rst
@@ -171,15 +191,18 @@ Basic neural network building blocks.
    nn.Decoder
    nn.one_hot
 
+```
 
-Train
------
+## Train
 
+```{eval-rst}
 .. currentmodule:: scvi
 
+```
 
 TrainingPlans define train/test/val optimization steps for modules.
 
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :template: class_no_inherited.rst
@@ -194,18 +217,22 @@ TrainingPlans define train/test/val optimization steps for modules.
    train.SaveBestState
    train.LoudEarlyStopping
 
+```
 
-Utilities
----------
+## Utilities
 
+```{eval-rst}
 .. currentmodule:: scvi
+```
 
 Utility functions used by scvi-tools.
 
+```{eval-rst}
 .. autosummary::
    :toctree: reference/
    :nosignatures:
 
    utils.track
    utils.setup_anndata_dsp
    utils.attrdict
+```

docs/api/index.md

@@ -0,0 +1,15 @@
+# API
+
+Import scvi-tools as:
+
+```
+import scvi
+```
+
+```{toctree}
+:maxdepth: 2
+
+user
+developer
+datasets
+```