Fixing sphinx docs

.gitignore

@@ -1,7 +1,7 @@
 __pycache__/
 .ipynb_checkpoints/
 .DS_Store
-docs/_build
+build
 *.egg-info
 .coverage*
 .idea/*

.readthedocs.yml

@@ -0,0 +1,11 @@
+version: 2
+
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt
+    - requirements: requirements.txt
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py

docs/Makefile → Makefile

@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
+SOURCEDIR     = docs
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -b coverage
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -14,63 +14,43 @@
 import sys
 from datetime import date
 
-file_loc = os.path.split(__file__)[0]
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(file_loc), ".")))
+sys.path.insert(0, os.path.abspath(".."))
 
 import pycytominer
-import groundwork_sphinx_theme
 
 # -- Project information -----------------------------------------------------
+
 project = pycytominer.__about__.__project__
 author = pycytominer.__about__.__author__
 copyright = "Copyright 2019 - {date} {author}".format(
     date=date.today().year, author=author
 )
 
-# The short X.Y version
-version = pycytominer.__about__.__version__
 # The full version, including alpha/beta/rc tags
+version = pycytominer.__about__.__version__
 release = version
 
-
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    "autoapi.extension",
-    "sphinx.ext.napoleon",
-    "sphinx.ext.autodoc",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.coverage",
-]
-autoapi_dirs = ["../pycytominer"]
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["**test**"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-html_theme = "groundwork"
-
-html_theme_options = {
-    "sidebar_width": "240px",
-    "stickysidebar": True,
-    "stickysidebarscrollable": True,
-    "contribute": True,
-    "github_fork": "useblocks/groundwork",
-    "github_user": "useblocks",
-}
+html_theme = "alabaster"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/index.rst

@@ -1,19 +1,20 @@
 .. pycytominer documentation master file, created by
-   sphinx-quickstart on Fri Oct  9 09:56:26 2020.
+   sphinx-quickstart on Fri Feb 19 14:44:29 2021.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to pycytominer's documentation!
-=======================================
+Pycytominer
+===========
 
-Release v\ |version|
+Software for processing image-based profiling readouts.
 
 .. toctree::
    :maxdepth: 2
+   :caption: Contents:
 
-   pycytominer
-
-
+   install
+   tutorial
+   modules
 
 Indices and tables
 ==================

docs/install.rst

@@ -0,0 +1,10 @@
+Install
+=======
+
+We are actively developing pycytominer, and no official release yet exists.
+
+To install a demo version, use
+
+.. code-block:: bash
+
+   pip install git+https://github.com/cytomining/pycytominer@282966b24bb5c6ac5150fad9deba16156c83a826

docs/tutorial.rst

@@ -0,0 +1,4 @@
+Tutorials
+=========
+
+Tutorials coming soon.

docs/make.bat → make.bat

@@ -7,8 +7,8 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=.
-set BUILDDIR=_build
+set SOURCEDIR=docs
+set BUILDDIR=build
 
 if "%1" == "" goto help