Merge pull request #687 from CGATOxford/{IS}_fix_rtd

RTD fixes ahead of new documentation

Author: IanSudbery

.readthedocs.yml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: doc/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: doc/requirements.txt

doc/conf.py

@@ -12,9 +12,23 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+from mock import Mock as MagicMock
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+            return MagicMock()
+
+MOCK_MODULES = [ 'numpy',
+                 'pandas', 
+                 'pysam', 
+                 'regex', "umi_tools._dedup_umi", 
+                 "umi_tools.whitelist_methods"]
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
 from recommonmark.parser import CommonMarkParser
 

doc/index.rst

@@ -3,7 +3,7 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-.. image:: https://images1-focus-opensocial.googleusercontent.com/gadgets/proxy?url=https://cloud.githubusercontent.com/assets/6096414/19521726/a4dea98e-960c-11e6-806a-a18ff04a391e.png&container=focus&resize_w=550
+.. image:: https://cloud.githubusercontent.com/assets/6096414/19521726/a4dea98e-960c-11e6-806a-a18ff04a391e.png
 
 Tools for dealing with Unique Molecular Identifiers
 ====================================================

doc/requirements.txt

@@ -1,10 +1,7 @@
-setuptools>=1.1
-numpy>=1.7
-pandas>=0.12.0
-pysam>=0.9
 future
-six
-regex
-scipy
-matplotlib
+mock
 sphinx-markdown-tables
+commonmark
+recommonmark
+sphinx-rtd-theme
+