Update Sphinx config

.gitignore

@@ -35,4 +35,7 @@ Dockerfile-*linux*[^.template]
 
 # Units (pint) files
 units.cpython-*.pyc
-bindings/python/triplestore/__pycache__
+bindings/python/triplestore/__pycache__
+
+# Documentation
+pydoc/autoapi/

bindings/python/dlite-entity-python.i

@@ -1,6 +1,6 @@
 /* -*- Python -*-  (not really, but good for syntax highlighting) */
 
-/* Python-spesific extensions to dlite-entity.i */
+/* Python-specific extensions to dlite-entity.i */
 %pythoncode %{
 import sys
 import json
@@ -115,18 +115,19 @@ def standardise(v, prop, asdict=False):
         return conv(v)
 
 
-def get_instance(id: "str", metaid: "str"=None, check_storages: "bool"=True) -> "Instance":
+def get_instance(id: "str", metaid: "str" = None, check_storages: "bool" = True) -> "Instance":
     """Return instance with given id.
 
     Arguments:
-        id: Id of instance to return.
+        id: ID of instance to return.
         metaid: If given, dlite will try to convert the instance to a new
-            instance of `metaid`.
+            instance of ``metaid``.
         check_storages: Whether to check for the instance in storages listed
             in dlite.storage_path if the instance is not already in memory.
 
     Returns:
-        DLite instance.
+        DLite Instance.
+
     """
     if isinstance(id, dlite.Instance):
         inst = id

bindings/python/dlite-entity.i

@@ -122,16 +122,23 @@ struct _DLiteDimension {
 %feature("docstring", "\
 Creates a new property.
 
+```python
 Property(name, type, dims=None, unit=None, description=None)
-    Creates a new property with the provided attributes.
+```
 
+Creates a new property with the provided attributes.
+
+```python
 Property(seq)
-    Creates a new property from sequence of 6 strings, corresponding to
-    `name`, `type`, `dims`, `unit` and `description`.  Valid
-    values for `dims` are:
-      - '' or '[]': no dimensions
-      - '<dim1>, <dim2>': list of dimension names
-      - '[<dim1>, <dim2>]': list of dimension names
+```
+
+Creates a new property from sequence of 6 strings, corresponding to
+``name``, ``type``, ``dims``, ``unit`` and ``description``.
+Valid values for ``dims`` are:
+
+- ``''`` or ``'[]'``: No dimensions.
+- ``'<dim1>, <dim2>'``: List of dimension names.
+- ``'[<dim1>, <dim2>]'``: List of dimension names.
 
 ") _DLiteProperty;
 %rename(Property) _DLiteProperty;
@@ -608,15 +615,22 @@ Call signatures:
     dlite_swig_set_property_by_index($self, i, obj);
   }
 
-  %feature("docstring",
-           "Return property `name` as a string.\n"
-           "\n"
-           "`width`  Minimum field width. Unused if 0, auto if -1.\n"
-           "`prec`   Precision. Auto if -1, unused if -2.\n"
-           "`flags`  Or'ed sum of formatting flags:\n"
-           "    0  default (json)\n"
-           "    1  raw unquoted output\n"
-           "    2  quoted output")
+  %feature("docstring", "\
+Return property ``name`` as a string.
+
+Parameters:
+    width: Minimum field width. Unused if 0, auto if -1.
+    prec: Precision. Auto if -1, unused if -2.
+    flags: Or'ed sum of formatting flags:
+
+        - ``0``: Default (json).
+        - ``1``: Raw unquoted output.
+        - ``2``: Quoted output.
+
+Returns:
+    Property as a string.
+
+")
      get_property_as_string;
   %newobject get_property_as_string;
   char *get_property_as_string(const char *name,

bindings/python/dlite-misc-python.i

@@ -8,12 +8,14 @@ import dlite
 class err():
     """Context manager for temporary turning off or redirecting errors.
 
-    By default errors are skipped within the err context.  But if
-    `filename` is provided, the error messages are written to that file.
-    Special file names includes
-      - None or empty: no output is written
-      - <stderr>: write errors to stderr (default)
-      - <stdout>: write errors to stdout
+    By default errors are skipped within the err context. But if
+    ``filename`` is provided, the error messages are written to that file.
+    Special file names includes:
+
+    - ``None`` or empty: No output is written.
+    - ``<stderr>``: Write errors to stderr (default).
+    - ``<stdout>``: Write errors to stdout.
+
     """
     def __init__(self, filename=None):
         self.filename = filename

bindings/python/dlite-misc.i

@@ -41,22 +41,24 @@ const char *dlite_get_license(void);
 
 %feature("docstring", "\
 Returns an UUID, depending on:
-  - If `id` is NULL or empty, generates a new random version 4 UUID.
-  - If `id` is not a valid UUID string, generates a new version 5 sha1-based
-    UUID from `id` using the DNS namespace.
-  - Otherwise return `id` (which already must be a valid UUID).
+
+- If ``id`` is NULL or empty, generates a new random version 4 UUID.
+- If ``id`` is not a valid UUID string, generates a new version 5 sha1-based
+  UUID from ``id`` using the DNS namespace.
+
+Otherwise return ``id`` (which already must be a valid UUID).
 ") dlite_get_uuid;
 %cstring_bounded_output(char *buff36, DLITE_UUID_LENGTH+1);
 void dlite_get_uuid(char *buff36, const char *id=NULL);
 
 %feature("docstring", "\
-Returns the generated UUID version number if `id` had been passed to
-get_uuid() or zero if `id` is already a valid UUID.
+Returns the generated UUID version number if ``id`` had been passed to
+get_uuid() or zero if ``id`` is already a valid UUID.
 ") get_uuid_version;
 posstatus_t get_uuid_version(const char *id=NULL);
 
 %feature("docstring", "\
-Returns a (metadata) uri by combining `name`, `version` and `namespace` as:
+Returns a (metadata) uri by combining ``name``, ``version`` and ``namespace`` as:
 
     namespace/version/name
 ") dlite_join_meta_uri;
@@ -66,7 +68,7 @@ char *dlite_join_meta_uri(const char *name, const char *version,
 
 
 %feature("docstring", "\
-Returns (name, version, namespace)-tuplet from valid metadata `uri`.
+Returns (name, version, namespace)-tuplet from valid metadata ``uri``.
 ") dlite_split_meta_uri;
 %cstring_output_allocate(char **name,      if (*$1) free(*$1));
 %cstring_output_allocate(char **version,   if (*$1) free(*$1));
@@ -81,15 +83,15 @@ Returns an url constructed from the arguments of the form:
 
     driver://location?options#fragment
 
-The `driver`, `options` and `fragment` arguments may be None.
+The ``driver``, ``options`` and ``fragment`` arguments may be None.
 ") dlite_join_url;
 %newobject dlite_join_url;
 char *dlite_join_url(const char *driver, const char *location,
                      const char *options=NULL, const char *fragment=NULL);
 
 %feature("docstring", "\
 Returns a (driver, location, options, fragment)-tuplet by splitting
-`url` of the form
+``url`` of the form
 
     driver://location?options#fragment
 
@@ -108,11 +110,12 @@ Match string 's' against glob pattern 'pattern' and return zero on
 match.
 
 Understands the following patterns:
-     *       any number of characters
-     ?       any single character
-     [a-z]   any single character in the range a-z
-     [^a-z]  any single character not in the range a-z
-     \x      match x
+
+- ``*``: Any number of characters.
+- ``?``: Any single character.
+- ``[a-z]``: Any single character in the range a-z.
+- ``[^a-z]``: Any single character not in the range a-z.
+- ``\\x``: Match x.
 ") globmatch;
 int globmatch(const char *pattern, const char *s);
 
@@ -145,10 +148,12 @@ Set error stream.
 void dlite_err_set_stream(FILE *);
 
 %feature("docstring", "\
-Set error log file.  Special values includes:
-  - None | "": turn off error output
-  - <stderr>:  standard error
-  - <stdout>:  standard output
+Set error log file. Special values includes:
+
+- ``None`` or empty: Turn off error output.
+- ``<stderr>``: Standard error.
+- ``<stdout>``: Standard output.
+
 All other values are treated as a filename that will be opened in append mode.
 ") dlite_err_set_file;
 void dlite_err_set_file(const char *filename);

bindings/python/dlite-storage.i

@@ -9,8 +9,8 @@
 
 /* Storage iterator */
 %feature("docstring", "\
-Iterates over instances in storage `s`.  If `pattern` is given, only
-instances whos metadata URI matches `pattern` are returned.
+Iterates over instances in storage ``s``.  If ``pattern`` is given, only
+instances whos metadata URI matches ``pattern`` are returned.
 ") StorageIterator;
 %inline %{
   struct StorageIterator {
@@ -57,7 +57,7 @@ Returns next instance or None if exhausted.") next;
 enum _DLiteIDFlag {
   dliteIDTranslateToUUID=0, /*!< Translate id's that are not a valid UUID to
                                  a (version 5) UUID (default). */
-  dliteIDRequireUUID=1,     /*!< Require that `id` is a valid UUID. */
+  dliteIDRequireUUID=1,     /*!< Require that ``id`` is a valid UUID. */
   dliteIDKeepID=2           /*!< Store data under the given id, even if it
                                  is not a valid UUID.  Not SOFT compatible,
                                  but may be useful for input files. */
@@ -71,21 +71,23 @@ Represents a data storage.
 Parameters
 ----------
 driver_or_url : string
-    Name of driver used to connect to the storage or, if `location` is not
+    Name of driver used to connect to the storage or, if ``location`` is not
     given, the URL to the storage:
 
         driver://location?options
 
 location : string
-    The location to the storage.  For file storages, this is the file name.
+    The location to the storage. For file storages, this is the file name.
 options : string
     Additional options passed to the driver as a list of semicolon-separated
-    ``key=value`` pairs.  Each driver may have their own options.  Some
+    ``key=value`` pairs. Each driver may have their own options. Some
     common options are:
-      - mode={'append','r','w'}: 'append': append to existing storage or
-        create a new one (hdf5,json).
-      - compact={'yes','no'}: Whether to store in a compact format (json).
-      - meta={'yes','no'}: Whether to format output as metadata (json).
+
+    - ``mode={'append','r','w'}``:
+      - 'append': Append to existing storage or create a new one (hdf5,json).
+    - ``compact={'yes','no'}``: Whether to store in a compact format (json).
+    - ``meta={'yes','no'}``: Whether to format output as metadata (json).
+
 ") _DLiteStorage;
 %rename(Storage) _DLiteStorage;
 
@@ -120,7 +122,7 @@ Returns name of driver for this storage.") get_driver;
 
   %feature("docstring", "\
 Returns a list of UUIDs of all instances in the storage whos metadata
-matches `pattern`.  If `pattern` is None, all UUIDs will be returned.
+matches ``pattern``. If ``pattern`` is None, all UUIDs will be returned.
 ") get_uuids;
   char **get_uuids(const char *pattern=NULL) {
     return dlite_storage_uuids($self, pattern);