Repair the documentation (#1298)

* update deps fro docs

* add yaml

* missing dep

* add more reqs

* maybe like this?

* some more adjustments

* some more adjustments

* some more adjustments

* include API in TOC

* include API in TOC

* include API in TOC

* TOC fixes

* try this

* try this

* looking good now

* remove unneded dep

Author: cdiener

.readthedocs.yaml

@@ -0,0 +1,31 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: documentation_builder/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: documentation_builder/requirements.txt
+   - method: pip
+     path: .

documentation_builder/conf.py

@@ -36,7 +36,11 @@
     "nbsphinx",
 ]
 # Document Python Code
-autoapi_dirs = [SRC_PATH]
+autoapi_dirs = [join(SRC_PATH, "cobra")]
+autoapi_add_toctree_entry = False
+
+# Enable typehints
+autodoc_typehints = "signature"
 
 # Napoleon settings
 napoleon_numpy_docstring = True
@@ -46,7 +50,7 @@
 
 # General information about the project.
 project = "cobra"
-copyright = "2016-2019, The cobrapy core team"
+copyright = "2016-2022, The cobrapy core team"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

documentation_builder/index.rst

@@ -2,14 +2,14 @@ Documentation for COBRApy
 =========================
 
 For installation instructions, please see `INSTALL.rst
-<https://github.com/opencobra/cobrapy/blob/stable/INSTALL.rst>`_.
+<https://github.com/opencobra/cobrapy/blob/devel/INSTALL.rst>`_.
 
 Many of the examples below are viewable as IPython notebooks, which can
 be viewed at `nbviewer
 <http://nbviewer.ipython.org/github/opencobra/cobrapy/tree/stable/documentation_builder/>`_.
 
 .. toctree::
-    :numbered:
+    :numbered: 3
     :maxdepth: 2
 
     getting_started
@@ -29,7 +29,7 @@ be viewed at `nbviewer
     dfba
     pymatbridge
     faq
-    _autogen/modules
+    API </autoapi/cobra/index.rst>
 
 
 Indices and tables

documentation_builder/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx~=2.2
+Sphinx~=5.3
 sphinxcontrib-napoleon
 sphinx-autoapi
 nbsphinx>=0.2.4

release-notes/next-release.md

@@ -4,6 +4,8 @@
 
 ## Fixes
 
+Fix automatic building of the documentation.
+
 ## Other
 
 ## Deprecated features