add api file

docs/source/API.rst

@@ -1,2 +1,76 @@
+.. automodule:: stream2
+
 API
-===
+===
+
+Import stream2 as::
+
+   import stream2 as st2
+
+Configuration for SIMBA
+~~~~~~~~~~~~~~~~~~~~~~~
+.. autosummary::
+   :toctree: _autosummary
+
+   settings.set_figure_params
+   settings.set_workdir
+
+
+Reading
+~~~~~~~
+
+.. autosummary::
+   :toctree: _autosummary
+
+   read_csv
+   read_h5ad
+   read_10X_output
+   read_mtx
+
+
+See more at `anndata <https://anndata.readthedocs.io/en/latest/api.html#reading>`_
+
+Preprocessing
+~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: _autosummary
+
+   pp.log_transform
+   pp.normalize
+   pp.cal_qc_rna
+   pp.filter_genes
+   pp.pca
+   pp.select_variable_genes   
+
+Tools
+~~~~~
+
+.. autosummary::
+   :toctree: _autosummary
+
+   tl.dimension_reduction
+   tl.seed_graph
+   tl.learn_graph
+   tl.infer_pseudotime
+   tl.add_path
+   tl.del_path
+   tl.get_weights
+   tl.extend_leaves
+   tl.refit_graph
+   tl.project_graph
+
+
+Plotting
+~~~~~~~~
+
+.. autosummary::
+   :toctree: _autosummary
+
+   pl.pca_variance_ratio
+   pl.variable_genes
+   pl.violin
+   pl.graph
+   pl.dimension_reduction
+   pl.stream_sc
+   pl.stream