Merge branch 'master' into yan-1070

ICRAR · Aug 15, 2022 · 76c56bc · 76c56bc
2 parents 2aa51ce + 66dd9be
commit 76c56bc
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diff --git a/.github/workflows/create-palettes.yml b/.github/workflows/create-palettes.yml
@@ -35,8 +35,8 @@ jobs:
 
       - name: Create palettes
         run: |
-          python3 tools/xml2palette/xml2palette.py -i ./ -t daliuge -o $OUTPUT_FILENAME.palette -p
-          python3 tools/xml2palette/xml2palette.py -i ./ -t template -o $OUTPUT_FILENAME-template.palette -p
+          python3 tools/xml2palette/xml2palette.py -t daliuge -r ./ $OUTPUT_FILENAME.palette
+          python3 tools/xml2palette/xml2palette.py -t template -r ./ $OUTPUT_FILENAME-template.palette
 
       - name: Commit palettes to EAGLE
         env:

diff --git a/daliuge-engine/dlg/apps/pyfunc.py b/daliuge-engine/dlg/apps/pyfunc.py
@@ -433,10 +433,16 @@ def optionalEval(x):
         # the correct UIDs
         logger.debug(f"Parameters found: {self.parameters}")
         posargs = self.arguments.args[:self.fn_npos]
+        keyargs = self.arguments.args[self.fn_npos:]
         kwargs = {}
         pargs = []
         # Initialize pargs dictionary and update with provided argument values
         pargsDict = collections.OrderedDict(zip(posargs,[None]*len(posargs)))
+        if self.arguments.defaults:
+            keyargsDict = dict(zip(keyargs, self.arguments.defaults[self.fn_npos:]))
+        else:
+            keyargsDict = {}
+        logger.debug("Initial keyargs dictionary: %s", keyargsDict)
         if "applicationArgs" in self.parameters:
             appArgs = self.parameters["applicationArgs"]  # we'll pop the identified ones
             _dum = [appArgs.pop(k) for k in self.func_def_keywords if k in appArgs]
@@ -465,16 +471,13 @@ def optionalEval(x):
                 inputs_dict,
                 posargs,
                 pargsDict,
-                appArgs,
+                keyargsDict,
                 check_len=check_len,
                 mode="inputs"))
         else:
             for i in range(min(len(inputs),self.fn_nargs)):
                 kwargs.update({self.arguments.args[i]: list(inputs.values())[i]})
 
-        logger.debug(f"Updating funcargs with input ports {kwargs}")
-        funcargs.update(kwargs)
-
         if ('outputs' in self.parameters and
             droputils.check_ports_dict(self.parameters['outputs'])):
             check_len = min(len(outputs),self.fn_nargs+
@@ -491,9 +494,12 @@ def optionalEval(x):
                 outputs_dict,
                 posargs,
                 pargsDict,
-                appArgs,
+                keyargsDict,
                 check_len=check_len,
                 mode="outputs"))
+        logger.debug(f"Updating funcargs with input ports {kwargs}")
+        funcargs.update(kwargs)
+
 
         # Try to get values for still missing positional arguments from Application Args
         if "applicationArgs" in self.parameters:

diff --git a/daliuge-engine/dlg/apps/scp.py b/daliuge-engine/dlg/apps/scp.py
@@ -41,8 +41,7 @@
 
 ##
 # @brief ScpApp
-# @details A BarrierAppDROP that copies the content of its single input onto its
-# single output via SSH's scp protocol.
+# @details A BarrierAppDROP that copies the content of its single input onto its single output via SSH's scp protocol.
 # @par EAGLE_START
 # @param category PythonApp
 # @param tag daliuge

diff --git a/docs/development/app_development/eagle_app_integration.rst b/docs/development/app_development/eagle_app_integration.rst
@@ -24,19 +24,30 @@ The xml2palette.py script is located in the tools directory within the DALiuGE r
 
 The xml2palette.py script can be run using this command line:
 
-.. code-block:: none
+.. code-block::
 
-  python3 xml2palette.py -i <path_to_input_directory> -t <tag> -o <path_output_file>
+  python3 xml2palette.py [-h] [-m MODULE] [-t TAG] [-c] [-r] [-s] [-v] idir ofile
 
+  positional arguments:
+    idir                  input directory path or file name
+    ofile                 output file name
 
-If no tag is specified, all components found in the input directory will part of the output file. If, however, a tag is specified, then only those components with a matching tag will be part of the output. Tags can be added to the Doxygen comments for a component using:
+  optional arguments:
+    -h, --help            show this help message and exit
+    -m MODULE, --module MODULE
+                          Module load path name
+    -t TAG, --tag TAG     filter components with matching tag
+    -c                    C mode, if not set Python will be used
+    -r, --recursive       Traverse sub-directories
+    -s, --parse_all       Try to parse non DAliuGE compliant functions and methods
+    -v, --verbose         increase output verbosity
+
+  If no tag is specified, all components found in the input directory will part of the output file. If, however, a tag is specified, then only those components with a matching tag will be part of the output. Tags can be added to the Doxygen comments for a component using:
 
 .. code-block:: python
 
   # @param tag <tag_name>
 
-There are also two optional arguments for xml2palette. Allow missing "EAGLE start" (-s) which allows xml2palette.py to run on code without any eagle-specific doxygen comments. Finally (-m) restricts xml2palette.py to produce a palette that only contains methods from within the specified module.
-
 Component Doxygen Markup Guide
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 In order to support the direct usage of newly written application components in the EAGLE editor, the |daliuge| system supports a custom set of Doxygen directives and tools. When writing an application component, developers can add specific custom `Doxygen <https://www.doxygen.nl/>`_ comments to the source code. These comments describe the component and can be used to automatically generate a JSON DALiuGE component description which in turn can be used in the *EAGLE*. A few basic rules to remember: