ReadTheDocs

AstraZeneca · Dec 15, 2021 · 72d3036 · 72d3036
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diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,9 @@
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = chemicalx
+SOURCEDIR     = source
+BUILDDIR      = build
+
+.PHONY: help Makefile
+
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)"
diff --git a/docs/index.html b/docs/index.html
@@ -0,0 +1,8 @@
+<!DOCTYPE html>
+
+<html>
+<head>
+  <title>Redirect</title>
+  <meta http-equiv="refresh" content="0; url=https://chemicalx.readthedocs.io" />
+</head>
+</html>
diff --git a/docs/requirements_1.txt b/docs/requirements_1.txt
@@ -0,0 +1,11 @@
+tqdm
+numpy
+sphinx==4.0.2
+sphinx_rtd_theme==0.5.2
+sklearn
+scipy
+pandas
+six
+nbsphinx
+nbsphinx_link
+jupyter-sphinx
diff --git a/docs/source/_static/css/custom.css b/docs/source/_static/css/custom.css
@@ -0,0 +1,195 @@
+.wy-side-nav-search .wy-dropdown > a img.logo, .wy-side-nav-search > a img.logo {
+}
+
+.wy-side-nav-search {
+  background: rgb(243,244,247);
+}
+
+.wy-side-nav-search > div.version {
+  color: black;
+}
+
+.wy-nav-content-wrap {
+  background: inherit;
+}
+
+.wy-side-nav-search input[type="text"] {
+  border: none;
+  box-shadow: none;
+  background: white;
+  border-radius: 0;
+  font-size: 100%;
+}
+
+.wy-menu-vertical li.current a,
+.wy-menu-vertical li.toctree-l1.current > a {
+  border: none;
+}
+
+.ethical-rtd > div.ethical-sidebar,
+.ethical-rtd > div.ethical-footer {
+  display: none !important;
+}
+
+h1 {
+  text-transform: uppercase;
+  font-family: inherit;
+  font-weight: 200;
+}
+
+h2,
+.rst-content .toctree-wrapper p.caption {
+  font-family: inherit;
+  font-weight: 200;
+}
+
+.rst-content a:visited {
+  color: #3091d1;
+}
+
+/* Begin code */
+.rst-content pre.literal-block,
+.rst-content div[class^="highlight"] {
+  border: none;
+}
+
+.rst-content pre.literal-block,
+.rst-content div[class^="highlight"] pre,
+.rst-content .linenodiv pre {
+  font-size: 80%;
+}
+
+.highlight {
+  background: #f6f8fa;
+  border-radius: 6px;
+}
+
+.highlight .kn,
+.highlight .k {
+  color: #d73a49;
+}
+
+.highlight .nn {
+  color: inherit;
+  font-weight: inherit;
+}
+
+.highlight .nc {
+  color: #e36209;
+  font-weight: inherit;
+}
+
+.highlight .fm,
+.highlight .nd,
+.highlight .nf,
+.highlight .nb {
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+}
+
+.highlight .bp,
+.highlight .n {
+  color: inherit;
+}
+
+.highlight .kc,
+.highlight .s1,
+.highlight .s2,
+.highlight .mi,
+.highlight .mf,
+.highlight .bp,
+.highlight .bn,
+.highlight .ow {
+  color: #005cc5;
+  font-weight: inherit;
+}
+
+.highlight .c1 {
+  color: #6a737d;
+}
+
+.rst-content code.xref {
+  padding: .2em .4em;
+  background: rgba(27,31,35,.05);
+  border-radius: 6px;
+  border: none;
+}
+/* End code */
+
+.rst-content dl:not(.docutils) dt,
+.rst-content dl:not(.docutils) dl dt {
+  background: rgb(243,244,247);
+}
+
+.rst-content dl:not(.docutils) dt.field-odd {
+  text-transform: uppercase;
+  background: inherit;
+  border: none;
+  padding: 6px 0;
+}
+
+.rst-content dl:not(.docutils) .property:first-child .pre {
+  text-transform: uppercase;
+  font-style: normal;
+}
+
+em.sig-param span.n:first-child, em.sig-param span.n:nth-child(2) {
+  color: black;
+  font-style: normal;
+}
+
+em.sig-param span.n:nth-child(3),
+em.sig-param span.n:nth-child(3) a {
+  color: inherit;
+  font-weight: normal;
+  font-style: normal;
+}
+
+em.sig-param span.default_value {
+  font-family: SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",Courier,monospace;
+  font-style: normal;
+  font-size: 90%;
+}
+
+.sig-paren {
+  padding: 0 4px;
+}
+
+.wy-table-responsive table td,
+.wy-table-responsive table th {
+  white-space: normal;
+}
+
+.wy-table-bordered-all,
+.rst-content table.docutils {
+  border: none;
+}
+
+.wy-table-bordered-all td,
+.rst-content table.docutils td {
+  border: none;
+}
+
+.wy-table-odd td,
+.wy-table-striped tr:nth-child(2n-1) td,
+.rst-content table.docutils:not(.field-list) tr:nth-child(2n-1) td {
+  background: rgb(243,244,247);
+}
+
+.wy-table td,
+.rst-content table.docutils td,
+.rst-content table.field-list td,
+.wy-table th,
+.rst-content table.docutils th,
+.rst-content table.field-list th {
+  padding: 14px;
+}
+
+table.colwidths-given tr td p,
+table.colwidths-given tr th p {
+  text-align: center;
+}
+
+table.colwidths-given tr td:first-child p,
+table.colwidths-given tr th:first-child p {
+  text-align: left;
+}
diff --git a/docs/source/_static/img/chemicalx.jpg b/docs/source/_static/img/chemicalx.jpg
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,65 @@
+import datetime
+import doctest
+import os
+import sys
+
+import sphinx_rtd_theme
+
+import chemicalx
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "jupyter_sphinx",
+]
+
+source_suffix = ".rst"
+master_doc = "index"
+
+author = "Benedek Rozemberczki & Charles Tapley Hoyt & Benjamin Gyori"
+project = "chemicalx"
+copyright = "{}, {}".format(datetime.datetime.now().year, author)
+
+# version = chemicalx.__version__
+# release = chemicalx.__version__
+
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+doctest_default_flags = doctest.NORMALIZE_WHITESPACE
+intersphinx_mapping = {"python": ("https://docs.python.org/", None)}
+
+html_theme_options = {
+    "collapse_navigation": False,
+    "display_version": True,
+    "logo_only": True,
+}
+
+html_logo = "_static/img/chemicalx.jpg"
+html_static_path = ["_static"]
+html_context = {"css_files": ["_static/css/custom.css"]}
+rst_context = {"chemicalx": chemicalx}
+
+add_module_names = False
+
+
+def setup(app):
+    def skip(app, what, name, obj, skip, options):
+        members = [
+            "__init__",
+            "__repr__",
+            "__weakref__",
+            "__dict__",
+            "__module__",
+        ]
+        return True if name in members else skip
+
+    app.connect("autodoc-skip-member", skip)
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,24 @@
+:github_url: https://github.com/AstraZeneca/chemicalx
+
+ChemicalX Documentation
+===============================
+
+
+
+.. toctree::
+   :glob:
+   :maxdepth: 2
+   :caption: Package Reference
+
+   modules/root
+
+
+.. toctree::
+   :glob:
+   :maxdepth: 2
+   :caption: Notes
+
+   notes/installation
+   notes/introduction
+   notes/resources
+
diff --git a/docs/source/modules/root.rst b/docs/source/modules/root.rst
@@ -0,0 +1,14 @@
+Rexmex
+==================
+
+.. contents:: Contents
+    :local:
+
+
+Score Cards
+--------------------
+
+.. automodule:: chemicalx.models
+    :members:
+    :undoc-members:
+
diff --git a/docs/source/notes/installation.rst b/docs/source/notes/installation.rst
@@ -0,0 +1,3 @@
+Installation
+============
+
diff --git a/docs/source/notes/introduction.rst b/docs/source/notes/introduction.rst
@@ -0,0 +1,17 @@
+Introduction by example
+=======================
+
+Overview
+=======================
+--------------------------------------------------------------------------------
+
+We shortly overview the fundamental concepts and features of **ChemicalX** through simple examples. These are the following:
+
+.. contents::
+    :local:
+
+Design philosophy
+-----------------
+
+
+
diff --git a/docs/source/notes/resources.rst b/docs/source/notes/resources.rst
@@ -0,0 +1,21 @@
+External resources
+==================
+
+Models
+--------------------
+
+* Name Name, Name Name, Name Name: **Title* `Paper <>`_
+* Name Name, Name Name, Name Name: **Title* `Paper <>`_
+
+Datasets
+--------------------
+
+* Name Name, Name Name, Name Name: **Title* `Paper <>`_
+* Name Name, Name Name, Name Name: **Title* `Paper <>`_
+
+
+Related Software
+--------------------
+
+* Name Name, Name Name, Name Name: **Title* `Paper <>`_
+* Name Name, Name Name, Name Name: **Title* `Paper <>`_