Merge branch 'master' into pydantic2

.github/pull_request_template.md

@@ -2,7 +2,7 @@
 
 
 ## Type of change
-- [ ] Bug fix
+- [ ] Bug fix & code cleanup
 - [ ] New feature
 - [ ] Documentation update
 - [ ] Test update

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);