Code cleanup (#591)

# Description
Reverting some bad code and formatting that was unfortunately
introduced.

## Type of change
- [x] Bug fix
- [ ] New feature
- [ ] Documentation update
- [ ] Test update

## Checklist for the reviewer
This checklist should be used as a help for the reviewer.

- [ ] Is the change limited to one issue?
- [ ] Does this PR close the issue?
- [ ] Is the code easy to read and understand?
- [ ] Do all new feature have an accompanying new test?
- [ ] Has the documentation been updated as necessary?

bindings/python/dlite-entity-python.i

@@ -93,7 +93,7 @@ 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:
@@ -105,7 +105,6 @@ def get_instance(id: "str", metaid: "str" = None, check_storages: "bool" = True)
 
     Returns:
         DLite Instance.
-
     """
     if isinstance(id, Instance):
         inst = id

bindings/python/dlite-entity.i

@@ -622,22 +622,21 @@ Call signatures:
   }
 
   %feature("docstring", "\
-Return property ``name`` as a string.
+Return property `name` as a string.
 
-Parameters:
+Arguments:
     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.
+        - `0`: Default (json).
+        - `1`: Raw unquoted output.
+        - `2`: Quoted output.
 
 Returns:
     Property as a string.
 
-")
-     get_property_as_string;
+") get_property_as_string;
   %newobject get_property_as_string;
   char *get_property_as_string(const char *name,
                                int width=0, int prec=-2, int flags=0) {

bindings/python/dlite-misc-python.i

@@ -8,12 +8,12 @@ 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.
+    `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.
+    - "None" or empty: No output is written.
+    - "<stderr>": Write errors to stderr (default).
+    - "<stdout>": Write errors to stdout.
 
     """
     def __init__(self, filename=None):

bindings/python/dlite-misc.i

@@ -42,23 +42,23 @@ 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.
+- 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).
+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;
@@ -68,7 +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));
@@ -83,15 +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
 
@@ -111,11 +111,11 @@ 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);
 
@@ -150,9 +150,9 @@ void dlite_err_set_stream(FILE *);
 %feature("docstring", "\
 Set error log file. Special values includes:
 
-- ``None`` or empty: Turn off error output.
-- ``<stderr>``: Standard error.
-- ``<stdout>``: Standard output.
+- `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;

bindings/python/dlite-python.i

@@ -592,6 +592,7 @@ obj_t *dlite_swig_get_scalar(DLiteType type, size_t size, void *data)
       case 4: value = *((float32_t *)data); break;
       case 8: value = *((float64_t *)data); break;
 #ifdef HAVE_FLOAT80_T
+      // TODO: check for overflow
       case 10: value = *((float80_t *)data); break;
 #endif
 #ifdef HAVE_FLOAT96_T

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. */
@@ -71,7 +71,7 @@ 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
@@ -80,14 +80,8 @@ location : string
     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
-    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).
-
+    ``key=value`` pairs. See the documentation of the individual drivers to
+    see which options they support.
 ") _DLiteStorage;
 %rename(Storage) _DLiteStorage;
 
@@ -138,7 +132,7 @@ struct _DLiteStorage {
 
   %feature("docstring",
            "Returns a list of UUIDs of all instances in the storage whos "
-           "metadata matches ``pattern``. If ``pattern`` is None, all UUIDs "
+           "metadata 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);

bindings/python/factory.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 """A module that makes it easy to add dlite functionality to existing classes.
 
-## Class customisations
-
-In order to handle special cases, the following methods may be defined/overridden in
-the class that is to be extended:
+Class customisations
+--------------------
+In order to handle special cases, the following methods may be
+defined/overridden in the class that is to be extended:
 
 ```python
 _dlite_get_<name>(self, name)
@@ -46,10 +46,11 @@ def __init__(cls, name, bases, attr) -> None:
 class BaseExtension(metaclass=MetaExtension):
     """Base class for extension.
 
-    Except for ``dlite_id``, all arguments are passed further to the ``__init__()``
-    function of the class we are inheriting from. If ``instanceid`` is given, the id of
-    the underlying dlite instance will be set to it.
+    Except for `dlite_id`, all arguments are passed further to the `__init__()`
+    function of the class we are inheriting from.
 
+    If `instanceid` is given, the id of the underlying dlite instance
+    will be set to it.
     """
 
     def __init__(self, *args, instanceid: str = None, **kwargs) -> None:
@@ -59,11 +60,12 @@ def __init__(self, *args, instanceid: str = None, **kwargs) -> None:
     def _dlite_init(self, instanceid: str = None) -> None:
         """Initialise the underlying DLite Instance.
 
-        If ``id`` is given, the id of the underlying DLite Instance will be set to it.
-
-        Parameters:
-            instanceid: A DLite ID (UUID) to use for the underlying DLite Instance.
+        If `id` is given, the id of the underlying DLite Instance will be
+        set to it.
 
+        Arguments:
+            instanceid: A DLite ID (UUID) to use for the underlying DLite
+                Instance.
         """
         dims = self._dlite_infer_dimensions()
         self.dlite_inst = Instance.from_metaid(
@@ -74,12 +76,11 @@ def _dlite_init(self, instanceid: str = None) -> None:
     def _dlite_get(self, name: str) -> "Any":
         """Returns the value of property `name` from the wrapped object.
 
-        Parameters:
+        Arguments:
             name: The property to retrieve.
 
         Returns:
             The property value.
-
         """
         if hasattr(self, f"_dlite_get_{name}"):
             return getattr(self, f"_dlite_get_{name}")()
@@ -92,10 +93,9 @@ def _dlite_get(self, name: str) -> "Any":
     def _dlite_set(self, name: str, value: "Any") -> None:
         """Sets value of property ``name`` in the wrapped object.
 
-        Parameters:
+        Arguments:
             name: The property to set a value for.
             value: The value to set for the property.
-
         """
         if hasattr(self, f"_dlite_set_{name}"):
             getattr(self, f"_dlite_set_{name}")(value)
@@ -154,9 +154,11 @@ def _dlite_assign_properties(self) -> None:
     def _dlite__new__(cls, inst=None):
         """Class method returning a new uninitialised instance of the class
         that is extended.
-        This method simply returns ``cls.__new__(cls)``. Override
-        this method if the extended class already defines a __new__()
-        method.
+
+        This method simply returns `cls.__new__(cls)`.
+
+        Override this method if the extended class already defines a
+        `__new__()` method.
         """
         return cls.__new__(cls)
 
@@ -179,15 +181,16 @@ def dlite_load(self, *args) -> None:
 
 
 def instancefactory(theclass: type, inst: Instance) -> "Any":
-    """Returns an extended instance of ``theclass`` initiated from dlite
+    """Returns an extended instance of `theclass` initiated from dlite
     instance ``inst``.
 
-    Parameters:
-        theclass: The class to instantiate an object from using ``inst``.
-        inst: A DLite Instance to use as source for a ``theclass`` instance object.
+    Arguments:
+        theclass: The class to instantiate an object from using `inst`.
+        inst: A DLite Instance to use as source for a `theclass` instance
+            object.
 
     Returns:
-        A ``theclass`` instance object based on the DLite Instance ``inst``.
+        A `theclass` instance object based on the DLite Instance `inst`.
 
     """
     cls = classfactory(theclass, meta=inst.meta)
@@ -208,30 +211,26 @@ def objectfactory(
     id: "Optional[str]" = None,
     instanceid: "Optional[str]" = None,
 ) -> "Any":
-    """Returns an extended copy of ``obj``.
-
-    If ``deepcopy`` is ``True``, a deep copy is returned, otherwise a shallow copy is
-    returned. By default, the returned object will have the same class as ``obj``.
-    If ``cls`` is provided, the class of the returned object will be set to ``cls``
-    (typically a subclass of ``obj.__class__``).
+    """Returns an extended copy of `obj`.
 
-    The ``url``, ``storage``, and ``id`` arguments are passed to ``classfactory()``.
+    The `url`, `storage`, and `id` arguments are passed to `classfactory()`.
 
-    Parameters:
+    Arguments:
         obj: A Python object.
         meta: A DLite Metadata Instance.
-        deepcopy: Whether or not to perform a deep or shallow copy of ``obj``.
-        cls: A class to use for the new object. If this is not supplied, the new object
-            will be the same class as the original.
-        url: URL referring to the metadata. Should be of the form
-            ``driver://location?options#id``. Only used if ``cls`` is not specified.
-        storage: Storage from which to load meta data. Only used if ``cls`` is not
-            specified.
-        id: A unique ID referring to the meta data if ``storage`` is provided.
+        deepcopy: Whether to perform a deep copy.  Otherwise a shallow copy
+            is performed.
+        cls: A class to use for the new object. If this is not supplied,
+            the new object will be of the same class as the original.
+        url: If given and `meta` is not given, load metadata from this URL.
+            It should be of the form `driver://location?options#id`.
+        storage: If given and `meta` and `url` are not given, load metadata
+            from this storage.
+        id: A unique ID referring to the metadata if `storage` is provided.
         instanceid: A DLite ID (UUID) to use for the underlying DLite Instance.
 
     Returns:
-        A new, extended copy of the Python object ``obj``.
+        A new, extended copy of the Python object `obj`.
 
     """
     cls = cls if cls is not None else classfactory(
@@ -255,18 +254,19 @@ def classfactory(
     id: "Optional[str]" = None,
 ) -> type:
     """Factory function that returns a new class that inherits from both
-    ``theclass`` and ``BaseExtension``.
+    `theclass` and `BaseExtension`.
 
-    Parameters:
+    Arguments:
         theclass: The class to extend.
         meta: Metadata instance.
-        url: URL referring to the metadata. Should be of the form
-            ``driver://location?options#id``.
-        storage: Storage to load meta from.
-        id: A unique ID referring to the metadata if ``storage`` is provided.
+        url: If given and `meta` is not given, load metadata from this URL.
+            It should be of the form `driver://location?options#id`.
+        storage: If given and `meta` and `url` are not given, load metadata
+            from this storage.
+        id: A unique ID referring to the metadata if `storage` is provided.
 
     Returns:
-        A new class based on ``theclass`` and ``BaseExtensions``.
+        A new class based on `theclass` and `BaseExtensions`.
 
     """
     if meta is None: