Docs: Fix some warnings from Sphinx (#1211)

* Fix some warnings from Sphinx

* Correct headings to avoid duplicate object description warning

* Add typedef and name to error codes matching  style of PluginErrCodes

* Add correct directive

Author: nameloCmaS

bindings/python/dlite-entity.i

@@ -105,10 +105,6 @@ Arguments:
     name: Dimension name.
     description: Dimension description.
 
-Attributes:
-    name: Dimension name.
-    description: Dimension description.
-
 ") _DLiteDimension;
 %rename(Dimension) _DLiteDimension;
 struct _DLiteDimension {
@@ -151,16 +147,6 @@ Arguments:
          be a valid unit label defined by EMMO or a custom ontology.
     description: Optional: A human description of the property.
 
-Attributes:
-    name: Property name.
-    size: Number of bytes needed to represent a single instance of `type`
-        in memory.
-    ref: Value of the `ref` argument.
-    ndims: Number of dimensions of the property. A scalar has `ndims=0`.
-    unit: The unit of the property.
-    description: Property description.
-    dims: Deprecated alias for shape.
-
 ") _DLiteProperty;
 %rename(Property) _DLiteProperty;
 struct _DLiteProperty {
@@ -300,7 +286,7 @@ methods:
 
 For details, see the documentation of the individual class methods.
 
-Attributes:
+Arguments:
     uuid: The UUID of the instance.
     uri: The URI of the instance.
 

bindings/python/dlite-misc-python.i

@@ -32,9 +32,6 @@ class errctl():
             - "<stderr>": Write errors to stderr (default).
             - "<stdout>": Write errors to stdout.
 
-    Attributes:
-        filename: Filename to redirect errors to.
-
     """
     def __init__(self, hide=(), show=(), filename="<stderr>"):
         allcodes = [-i for i in range(1, _dlite._get_number_of_errors())]

bindings/python/python-protocol-plugins/zip.py

@@ -20,6 +20,7 @@ def open(self, location, options=None):
             location: A URL or path to a zip file.
                 If `location` is a URL, a local cache is created and reused.
             options: The following options are supported:
+
                 - timeout: Number of seconds before timing out when downloading
                   an URL.
                 - nocache: If true and path is a URL, the zip file will be

doc/Doxyfile.in

@@ -393,7 +393,7 @@ INLINE_SIMPLE_STRUCTS  = NO
 # types are typedef'ed and only the typedef is referenced, never the tag name.
 # The default value is: NO.
 
-TYPEDEF_HIDES_STRUCT   = NO
+TYPEDEF_HIDES_STRUCT   = YES
 
 # The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
 # cache is used to resolve symbols given their name and scope. Since this can be
@@ -833,6 +833,7 @@ EXCLUDE_SYMLINKS       = NO
 # exclude all test directories for example use the pattern */test/*
 
 EXCLUDE_PATTERNS       = */tests/test_* \
+                         */tests/* \
                          */old/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
@@ -930,8 +931,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-#USE_MDFILE_AS_MAINPAGE = @dlite_SOURCE_DIR@/README.md
-USE_MDFILE_AS_MAINPAGE = @CMAKE_CURRENT_BINARY_DIR@/README.md
+USE_MDFILE_AS_MAINPAGE = 
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1157,15 +1157,6 @@ HTML_COLORSTYLE_SAT    = 100
 
 HTML_COLORSTYLE_GAMMA  = 80
 
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting this
-# to YES can help to show when doxygen was last run and thus if the
-# documentation is up to date.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_TIMESTAMP         = NO
-
 # If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
 # documentation will contain a main index with vertical navigation menus that
 # are dynamically created via Javascript. If disabled, the navigation index will
@@ -1730,14 +1721,6 @@ LATEX_HIDE_INDICES     = NO
 
 LATEX_BIB_STYLE        = plain
 
-# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
-# page will contain the date and time when the page was generated. Setting this
-# to NO can help when comparing the output of multiple runs.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_TIMESTAMP        = NO
-
 #---------------------------------------------------------------------------
 # Configuration options related to the RTF output
 #---------------------------------------------------------------------------

doc/contributors_guide/tips_and_tricks.md

@@ -171,7 +171,7 @@ to rerun valgrind on that issue, you can run
 
 Both of the above commands will write the output to `<BUILD_DIR>/Testing/Temporary/MemoryChecker.<#>.log`, where `<#>` is the test number.
 
-```note
+```{note}
 The first time you run `make memcheck`, a supression file will be created, suppressing issues that does not comes from DLite.
 Generating a suppression file may take long time, but it will only be generated once unless you manually add more suppressions to one of the `cmake/valgrind-*.supp` files.
 ```

doc/getting_started/tutorial.md

@@ -384,7 +384,7 @@ You can use the method `person.set_quantity` to set a property with a quantity o
 
 ```
 
-```note
+```{note}
 If you need in your program to use a specific units registry, use the function
 [`pint.set_application_registry()`]
 ```

doc/index.rst

@@ -11,7 +11,6 @@ DLite
 
    getting_started/index
    user_guide/index
-   api_reference/index
    contributors_guide/index
    license
 

doc/respirator.py

@@ -24,7 +24,7 @@ def __init__(self,
                  output_path: Union[str,Path],
                  template_path: Union[str, Path],
                  index_file = 'index.xml',
-                 filename_filter=".*\.h"):
+                 filename_filter=r".*\.h"):
         """
         initialize class
         """

doc/user_guide/search_paths.md

@@ -47,7 +47,7 @@ Appending to DLite path variables
 The `dlite` Python module defines the path variables listed in the table above.
 A Python script or application can configure new datamodels and plugins by appending to these variables.
 
-:::{example}
+:::{hint}
 Adding the sub-directory `datamodels` to the search path for datamodels, can be done with:
 
 ```python

src/utils/fileutils.h

@@ -16,10 +16,10 @@
  */
 
 /** Error codes */
-enum {
+typedef enum {
  fu_PathError=5870,
  fu_OpenDirectoryError,
-};
+} FUErrCodes;
 
 
 #if defined(__unix__) || (defined(__APPLE__) && defined(__MACH__))