theislab · MUCDK · Jan 19, 2025 · Jan 7, 2025 · Jan 7, 2025 · Jan 18, 2025
diff --git a/docs/Makefile b/docs/Makefile
@@ -22,3 +22,4 @@ help:
 clean:
 	@rm -rf $(BUILDDIR)/*
 	@rm -rf $(SOURCEDIR)/genapi/
+	@rm -rf $(SOURCEDIR)/**/genapi/
diff --git a/docs/developer.rst b/docs/developer.rst
diff --git a/docs/developer/backends.rst b/docs/developer/backends.rst
@@ -0,0 +1,13 @@
+Backends
+~~~~~~~~
+.. module:: moscot.backends
+.. currentmodule:: moscot
+.. autosummary::
+    :toctree: genapi
+
+    backends.ott.SinkhornSolver
+    backends.ott.GWSolver
+    backends.ott.OTTOutput
+    backends.ott.GraphOTTOutput
+    backends.utils.get_solver
+    backends.utils.get_available_backends
diff --git a/docs/developer/base.rst b/docs/developer/base.rst
@@ -0,0 +1,35 @@
+Base
+~~~~
+.. module:: moscot.base
+.. currentmodule:: moscot.base
+.. autosummary::
+    :toctree: genapi
+
+    problems.BaseProblem
+    problems.OTProblem
+    problems.BirthDeathProblem
+    problems.BaseCompoundProblem
+    problems.CompoundProblem
+    cost.BaseCost
+    problems.AnalysisMixin
+    problems.BirthDeathMixin
+    problems.birth_death.beta
+    problems.birth_death.delta
+
+.. module:: moscot.solvers
+.. currentmodule:: moscot.base
+.. autosummary::
+    :toctree: genapi
+
+    solver.BaseSolver
+    solver.OTSolver
+
+.. autosummary::
+    :toctree: genapi
+
+    output.BaseDiscreteSolverOutput
+    output.MatrixSolverOutput
+    solver.BaseSolver
+    solver.OTSolver
+    output.BaseDiscreteSolverOutput
+    output.MatrixSolverOutput
diff --git a/docs/developer/costs.rst b/docs/developer/costs.rst
@@ -0,0 +1,12 @@
+Costs
+~~~~~
+.. module:: moscot.costs
+.. currentmodule:: moscot
+.. autosummary::
+    :toctree: genapi
+
+    costs.BarcodeDistance
+    costs.LeafDistance
+    costs.get_cost
+    costs.get_available_costs
+    costs.register_cost
diff --git a/docs/developer/index.rst b/docs/developer/index.rst
@@ -0,0 +1,12 @@
+Developer API
+#############
+
+.. module:: moscot.dev
+
+.. toctree::
+    :maxdepth: 2
+
+    backends
+    costs
+    base
+    utils
diff --git a/docs/developer/utils.rst b/docs/developer/utils.rst
@@ -0,0 +1,21 @@
+Utils
+~~~~~
+.. module:: moscot.utils
+.. currentmodule:: moscot.utils
+.. autosummary::
+    :toctree: genapi
+
+    subset_policy.SubsetPolicy
+    subset_policy.OrderedPolicy
+    subset_policy.StarPolicy
+    subset_policy.ExternalStarPolicy
+    subset_policy.SequentialPolicy
+    subset_policy.TriangularPolicy
+    subset_policy.ExplicitPolicy
+    data.transcription_factors
+    data.proliferation_markers
+    data.apoptosis_markers
+    tagged_array.TaggedArray
+    tagged_array.Tag
+    tagged_array.DistributionCollection
+    tagged_array.DistributionContainer
diff --git a/docs/index.rst b/docs/index.rst
@@ -52,7 +52,7 @@ Important resources
         Learn how to install :mod:`moscot`.
 
     .. grid-item-card:: User API
-        :link: user
+        :link: user/index
         :link-type: doc
 
         Find a detailed documentation of :mod:`moscot`.
@@ -85,8 +85,8 @@ Important resources
 
     installation
     user_guide
-    user
-    developer
+    user/index
+    developer/index
     contributing
     notebooks/tutorials/index
     notebooks/examples/index

diff --git a/docs/user.rst b/docs/user.rst
diff --git a/docs/user/datasets.rst b/docs/user/datasets.rst
@@ -0,0 +1,18 @@
+Datasets
+~~~~~~~~
+.. module:: moscot.datasets
+.. currentmodule:: moscot
+.. autosummary::
+    :toctree: genapi
+
+    datasets.bone_marrow
+    datasets.c_elegans
+    datasets.drosophila
+    datasets.hspc
+    datasets.mosta
+    datasets.pancreas_multiome
+    datasets.sciplex
+    datasets.sim_align
+    datasets.simulate_data
+    datasets.tedsim
+    datasets.zebrafish
diff --git a/docs/user/index.rst b/docs/user/index.rst
@@ -0,0 +1,15 @@
+User API
+########
+
+.. module:: moscot.user
+
+Import :mod:`moscot` as::
+
+    import moscot as mt
+
+.. toctree::
+    :maxdepth: 2
+
+    problems
+    plotting
+    datasets
diff --git a/docs/user/plotting.rst b/docs/user/plotting.rst
@@ -0,0 +1,11 @@
+Plotting
+~~~~~~~~
+.. module:: moscot.plotting
+.. currentmodule:: moscot
+.. autosummary::
+    :toctree: genapi
+
+    plotting.cell_transition
+    plotting.sankey
+    plotting.push
+    plotting.pull
diff --git a/docs/user/problems.rst b/docs/user/problems.rst
@@ -0,0 +1,24 @@
+Biological Problems
+~~~~~~~~~~~~~~~~~~~
+.. module:: moscot.problems
+.. currentmodule:: moscot.problems
+.. autosummary::
+    :toctree: genapi
+
+    time.TemporalProblem
+    time.LineageProblem
+    space.AlignmentProblem
+    space.MappingProblem
+    spatiotemporal.SpatioTemporalProblem
+    cross_modality.TranslationProblem
+
+Generic Problems
+~~~~~~~~~~~~~~~~
+.. module:: moscot.generic
+.. currentmodule:: moscot.problems
+.. autosummary::
+    :toctree: genapi
+
+    generic.SinkhornProblem
+    generic.GWProblem
+    generic.FGWProblem
diff --git a/src/moscot/base/problems/birth_death.py b/src/moscot/base/problems/birth_death.py
@@ -188,7 +188,7 @@ def estimate_marginals(
 
         Examples
         --------
-        - See :doc:`../notebooks/examples/problems/800_score_genes_for_marginals`
+        - See :doc:`../../notebooks/examples/problems/800_score_genes_for_marginals`
             on examples how to use :meth:`~moscot.problems.time.TemporalProblem.score_genes_for_marginals`.
 
         """  # noqa: D205