Sphinx (#16)

* adding Sphinx to Poetry * Adding sphinx_rtd_theme via Poetry * updated docs files for src structure and updated requirements.txt and yaml for RTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
choderalab · May 1, 2024 · 4472149 · 4472149
1 parent e16b507
commit 4472149
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diff --git a/docs/api.rst b/docs/api.rst
@@ -4,4 +4,7 @@ API Documentation
 .. autosummary::
    :toctree: autosummary
 
-   missense_kinase_toolkit.canvas
+   missense_kinase_toolkit.cbioportal
+   missense_kinase_toolkit.klifs
+   missense_kinase_toolkit.pfam
+   missense_kinase_toolkit.scrapers
diff --git a/docs/conf.py b/docs/conf.py
@@ -15,7 +15,7 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath("../src"))
 
 import missense_kinase_toolkit
 
@@ -76,7 +76,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -2,3 +2,12 @@ Getting Started
 ===============
 
 This page details how to get started with missense-kinase-toolkit.
+
+Installation
+++++++++++++
+
+We have used `poetry` as our default package manager for this project. Once you have cloned the repository and have either installed `poetry` locally or in your environment of interest, you can install the package by running the following command in the root directory of the repository using the provided `poetry.lock` file and the following command
+
+.. code-block:: bash
+
+    poetry run missense-kinase-toolkit --build
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,4 @@
+numpy
+matplotlib
+sphinx
+sphinx_rtd_theme
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -33,6 +33,8 @@ beautifulsoup4 = "^4.12.3"
 [tool.poetry.group.dev.dependencies]
 black = "^24.3.0"
 flake8 = "^7.0.0"
+sphinx = "^7.3.7"
+sphinx-rtd-theme = "^2.0.0"
 
 
 [tool.poetry.group.test.dependencies]

diff --git a/readthedocs.yml b/readthedocs.yml
@@ -1,7 +1,6 @@
 # .readthedocs.yaml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-# taken from https://education.molssi.org/python-package-best-practices/10-documentation.html#read-the-docs
 
 # Required
 version: 2
@@ -30,4 +29,4 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
     install:
-    - requirements: docs/requirements.yaml
+    - requirements: docs/requirements.txt