Bump version to 3.9.0 (#247)

* Fix minor issue with tip boxes in import_export.ipynb and ontology_interface.ipynb

* Bump version to 3.9.0

docs/source/jupyter/cuds_api.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/master?filepath=docs%2Fsource%2Fjupyter%2Fcuds_api.ipynb \"Click to run the tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v3.9.0?filepath=docs%2Fsource%2Fjupyter%2Fcuds_api.ipynb \"Click to run the tutorial yourself!\")\n",
     "    \n",
     "</figure>\n",
     "\n",
@@ -88,7 +88,7 @@
     }
    },
    "source": [
-    "The first step is to install the city ontology. Use the tool pico for this. If you want to know more about ontology installation, check the documentation on the [pico ontology installation tool](https://simphony.readthedocs.io/en/latest/utils.html#pico-installs-cuds-ontologies), [YAML ontology installation files](https://simphony.readthedocs.io/en/latest/working_with_ontologies.html#osp-core-yaml-ontology-format), and [installing OWL ontologies](https://simphony.readthedocs.io/en/latest/working_with_ontologies.html#owl-ontologies-and-rdfs-vocabularies)."
+    "The first step is to install the city ontology. Use the tool pico for this. If you want to know more about ontology installation, check the documentation on the [pico ontology installation tool](https://simphony.readthedocs.io/en/v3.9.0/utils.html#pico-installs-cuds-ontologies), [YAML ontology installation files](https://simphony.readthedocs.io/en/v3.9.0/working_with_ontologies.html#osp-core-yaml-ontology-format), and [installing OWL ontologies](https://simphony.readthedocs.io/en/latest/working_with_ontologies.html#owl-ontologies-and-rdfs-vocabularies)."
    ]
   },
   {
@@ -552,7 +552,7 @@
     }
    },
    "source": [
-    "The existing ontology individuals and the relationships among them have been depicted below, using the utility `pretty_print` (see the [Utilities section](https://simphony.readthedocs.io/en/latest/utils.html?highlight=pretty_print)). Note that some attributes that were not specified were set automatically to the default values specified in the ontology."
+    "The existing ontology individuals and the relationships among them have been depicted below, using the utility `pretty_print` (see the [Utilities section](https://simphony.readthedocs.io/en/v3.9.0/utils.html?highlight=pretty_print)). Note that some attributes that were not specified were set automatically to the default values specified in the ontology."
    ]
   },
   {

docs/source/jupyter/import_export.ipynb

@@ -15,7 +15,7 @@
    "source": [
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "    \n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/master?filepath=docs%2Fsource%2Fjupyter%2Fimport_export.ipynb \"Click to run the tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v3.9.0?filepath=docs%2Fsource%2Fjupyter%2Fimport_export.ipynb \"Click to run the tutorial yourself!\")\n",
     "    \n",
     "</figure>\n",
     "\n",
@@ -33,8 +33,7 @@
     "The full API specifications of the import and export functions can be found in the\n",
     "[utilities API reference page](../api_ref.md#osp.core.utils.export_cuds).\n",
     "    \n",
-    "</div>\n",
-    "</div>\n"
+    "</div>"
    ]
   },
   {

docs/source/jupyter/ontology_interface.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/master?filepath=docs%2Fsource%2Fjupyter%2Fontology_interface.ipynb \"Click to run the tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v3.9.0?filepath=docs%2Fsource%2Fjupyter%2Fontology_interface.ipynb \"Click to run the tutorial yourself!\")\n",
     "    \n",
     "</figure>\n",
     "\n",
@@ -212,14 +212,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<div style=\"background: #D3D3D3\">\n",
-    "<div class=\"admonition important\" style=\"padding: 6px 12px\">\n",
+    "<div class=\"admonition important\">\n",
     "<div class=\"admonition-title\" style=\"font-weight: bold\"><div style=\"display: inline-block\">Tip</div></div>\n",
     "    \n",
     "The dot notation supports IPython autocompletion. For example, when working on a Jupyter notebook, once the namespace has been imported, it is possible to get suggestions for the entity names by writing <code class=\"pre\">`namespace.`</code> and pressing TAB.\n",
-    "\n",
-    "</div>\n",
-    "</div>\n",
+    "    \n",
     "</div>"
    ]
   },

docs/source/jupyter/wrapper_development.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "<figure style=\"display: table; text-align:center; margin-left: auto; margin-right:auto\">\n",
     "\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/master?filepath=docs%2Fsource%2Fjupyter%2Fwrapper_development.ipynb \"Click to run the tutorial yourself!\")\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/simphony/docs/v3.9.0?filepath=docs%2Fsource%2Fjupyter%2Fwrapper_development.ipynb \"Click to run the tutorial yourself!\")\n",
     "    \n",
     "</figure>\n",
     "\n",

docs/source/links.md

@@ -51,7 +51,10 @@ demonstrated under the project https://github.com/simphony/simphony-common.
 
 # Compatibility table
 
-The following table describes the compatibilities between of SimPhoNy docs and OSP-core.
+The following table describes the compatibilities between the SimPhoNy docs and
+OSP-core up to version 2.5.1 of the documentation. For later releases, the
+version number of the documentation matches the version number of the OSP-core
+release to which it applies.
 
 ```{eval-rst}
 

docs/source/utils.md

@@ -132,17 +132,17 @@ Each function is used in a similar way to its command-line counterpart.
   type, which can be either paths to `yml` ontology installation files or
   names of ontologies that can be installed via this shortcut. It is meant to
   clone the
-  [behavior of its command-line counterpart](https://simphony.readthedocs.io/en/latest/utils.html#pico-installs).
+  [behavior of its command-line counterpart](https://simphony.readthedocs.io/en/v3.9.0/utils.html#pico-installs).
 
 - `uninstall`: accepts _one or more_ positional arguments of string type,
   which must be names of already installed ontology packages. It also
-  clones the [behavior of its command-line counterpart](https://simphony.readthedocs.io/en/latest/utils.html#pico-uninstalls).
+  clones the [behavior of its command-line counterpart](https://simphony.readthedocs.io/en/v3.9.0/utils.html#pico-uninstalls).
 
 - `packages`: accepts no arguments and returns an [iterator](https://wiki.python.org/moin/Iterator)
   over the names of the installed packages.
 
 - `namespaces`: accepts no arguments and returns an iterator yielding one
-  [`OntologyNamespace` object](https://simphony.readthedocs.io/en/latest/api_ref.html#osp.core.ontology.namespace.OntologyNamespace) for each installed namespace.
+  [`OntologyNamespace` object](https://simphony.readthedocs.io/en/v3.9.0/api_ref.html#osp.core.ontology.namespace.OntologyNamespace) for each installed namespace.
 
 Usage examples: