From 7a8e5ac75acf4c23ae51f6f473a139420e91a84e Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Fri, 11 Sep 2020 00:23:58 +0000 Subject: [PATCH] remove last .rst file from docs (#1185) --- doc/api.md | 39 +++++++++++++++++++++++++++++++++++++++ doc/api.rst | 37 ------------------------------------- doc/index.md | 4 ++-- setup.py | 2 +- 4 files changed, 42 insertions(+), 40 deletions(-) create mode 100644 doc/api.md delete mode 100644 doc/api.rst diff --git a/doc/api.md b/doc/api.md new file mode 100644 index 0000000000..f14ef10271 --- /dev/null +++ b/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: +``` diff --git a/doc/api.rst b/doc/api.rst deleted file mode 100644 index 46ec84d16f..0000000000 --- a/doc/api.rst +++ /dev/null @@ -1,37 +0,0 @@ -======================= -``sourmash`` Python API -======================= - -The primary programmatic way of interacting with ``sourmash`` is via -its Python API. Please also see `examples of using the API `_. - -.. contents:: - :depth: 2 - -``MinHash``: basic MinHash sketch functionality -=============================================== - -.. autoclass:: sourmash.MinHash - :members: - - .. automethod:: __init__ - - -``SourmashSignature``: save and load MinHash sketches in JSON -============================================================= - -.. automodule:: sourmash.signature - :members: - -``SBT``: save and load Sequence Bloom Trees in JSON -============================================================= - -.. automodule:: sourmash.sbt - :members: GraphFactory, Node, NodePos, SBT, Leaf - :undoc-members: - -``sourmash.fig``: make plots and figures -============================================ - -.. automodule:: sourmash.fig - :members: diff --git a/doc/index.md b/doc/index.md index 31fb4e830f..9ccc05ea7f 100644 --- a/doc/index.md +++ b/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. diff --git a/setup.py b/setup.py index 3ef2026809..8f343139a3 100644 --- a/setup.py +++ b/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'],