[MRG] Replace last .rst file from docs

doc/api.md

@@ -0,0 +1,39 @@
+# `sourmash` Python API
+
+The primary programmatic way of interacting with `sourmash` is via
+its Python API.  Please also see [examples of using the API](api-example.md).
+
+```{contents}
+   :depth: 2
+```
+
+## `MinHash`: basic MinHash sketch functionality
+
+```{eval-rst}
+.. autoclass:: sourmash.MinHash
+   :members:
+
+   .. automethod:: __init__
+```
+
+## `SourmashSignature`: save and load MinHash sketches in JSON
+
+```{eval-rst}
+.. automodule:: sourmash.signature
+   :members:
+```
+
+## `SBT`: save and load Sequence Bloom Trees in JSON
+
+```{eval-rst}
+.. automodule:: sourmash.sbt
+   :members: GraphFactory, Node, NodePos, SBT, Leaf
+   :undoc-members:
+```
+
+# `sourmash.fig`: make plots and figures
+
+```{eval-rst}
+.. automodule:: sourmash.fig
+   :members:
+```

doc/index.md

@@ -28,7 +28,7 @@ background information on how and why MinHash works.
 ----
 
 To use sourmash, you must be comfortable with the UNIX command line;
-programmers may find the [Python library and API](api.rst) useful as well.
+programmers may find the [Python library and API](api.md) useful as well.
 
 If you use sourmash, please cite us!
 
@@ -62,7 +62,7 @@ be stored, searched, explored, and taxonomically annotated.
 
 * `sourmash` also has a simple Python API for interacting with signatures,
   including support for online updating and querying of signatures
-  (see [the API docs](api.rst)).
+  (see [the API docs](api.md)).
 
 * `sourmash` relies on an underlying Rust core for performance.
 

setup.py

@@ -78,7 +78,7 @@ def build_native(spec):
     "extras_require": {
         'test' : ['pytest', 'pytest-cov', 'recommonmark', 'hypothesis'],
         'demo' : ['jupyter', 'jupyter_client', 'ipython'],
-        'doc' : ['sphinx', 'myst-parser[sphinx]', 'alabaster',
+        'doc' : ['sphinx', 'myst-parser[sphinx]>=0.12.2', 'alabaster',
                  "sphinxcontrib-napoleon", "nbsphinx",
                  "ipython"],
         '10x': ['bam2fasta==1.0.4'],