Oct mid 24 (#71)

* fix help generation as last merge excluded fixes

* \r return character no longer catered for in output impacting help

* added desc to support bug fix floating number  parameters

* molecules @ property retrieval bug from last commit

* refactor broke @ molecules, reinstated identifiers and and removed output text formatting of synonyms

* support openad bmfm demo

* version update

* formatting black

---------

Co-authored-by: Phil Downey <phildowney@pd-work-mac.local>

Author: PhillipDowney

openad/app/magic/openad_magic.py

@@ -71,7 +71,6 @@ def openad(self, line, cell=None, local_ns=None):
             result = strip_leading_blanks(result)
             result = result.replace("<br>", "\n")
 
-        # MAJOR-RELEASE-TODO: display function should never return data
         return result
 
     @needs_local_scope
@@ -98,8 +97,8 @@ def openadd(self, line, cell=None, local_ns=None):
         # MAJOR-RELEASE-TODO: data function should never display
         if isinstance(result, Styler):
             result = result.data
-        if isinstance(result, str):
-            display(Markdown(result))
+        # if isinstance(result, str):
+        #    display(Markdown(result))
         return result
 
 

openad/app/main.py

@@ -652,6 +652,10 @@ def default(self, line):
             # print("------------------------------")
             y = self.current_statement_defs.parseString(convert(inp), parseAll=True)
             x = lang_parse(self, y)
+            if GLOBAL_SETTINGS["grammar_refresh"]:
+                create_statements(self)
+                GLOBAL_SETTINGS["grammar_refresh"] = False
+
             self.prompt = refresh_prompt(self.settings)
             MEMORY.before_command()
         except Exception as err1:  # pylint: disable=broad-exception-caught # error could be unknown

openad/app/main_lib.py

@@ -259,16 +259,12 @@ def lang_parse(cmd_pointer, parser):
     elif parser.getName() == "show_molecules":
         return show_molecules(cmd_pointer, parser)
     elif parser.getName() == "save_molecules_DEPRECATED":
-        # MAJOR-RELEASE-TODO: Remove this, this is deprecated functionality
         return save_molecules_DEPRECATED(cmd_pointer, parser)
     elif parser.getName() == "load_molecules_DEPRECATED":
-        # MAJOR-RELEASE-TODO: Remove this, this is deprecated functionality
         return load_molecules_DEPRECATED(cmd_pointer, parser)
     elif parser.getName() == "merge_molecules_DEPRECATED":
-        # MAJOR-RELEASE-TODO: Remove this, this is deprecated functionality
         return merge_molecules_DEPRECATED(cmd_pointer, parser)
     elif parser.getName() == "list_molecule_sets_DEPRECATED":
-        # MAJOR-RELEASE-TODO: Remove this, this is deprecated functionality
         return display_molsets_DEPRECATED(cmd_pointer, parser)
     elif parser.getName() == "enrich_mws_with_analysis":
         return enrich_mws_with_analysis(cmd_pointer, parser)

openad/app/metadata.json

@@ -1,7 +1,7 @@
 {
 	"banner": "OPENAD",
 	"title": "Welcome to the Open Accelerated Discovery CLI",
-	"version": "0.6.1",
+	"version": "0.6.2",
 	"commands": {
 		"intro": "If this is your first time, let us help you getting started.",
 		"? toolkits": "Learn about the toolkits.",
@@ -10,4 +10,4 @@
 		"? <soft>...</soft>": "List commands containing \"...\"",
 		"docs": "Read the docs in your browser."
 	}
-}
+}

openad/core/grammar.py

@@ -159,8 +159,8 @@ def field_list_act(toks):
 grammar_help = []  # Help text
 
 
-# Add molecule grammar
-smol_grammar_add(statements=statements, grammar_help=grammar_help)
+# Add molecule grammar (moved to refresh zone)
+# smol_grammar_add(statements=statements, grammar_help=grammar_help)
 
 # Add protein grammar
 mmol_grammar_add(statements=statements, grammar_help=grammar_help)
@@ -993,8 +993,10 @@ def create_statements(cmd_pointer):
         temp_help = []
 
         service_grammar_add(statements=cmd_pointer.current_statements, help=temp_help, service_catalog=service_catalog)
+        smol_grammar_add(statements=cmd_pointer.current_statements, grammar_help=temp_help)
 
         # cmd_pointer.current_statements.extend(service_statements)
+
         cmd_pointer.current_help.help_model_services.clear()
         cmd_pointer.current_help.help_model_services.extend(temp_help)
         cmd_pointer.current_help.reset_help()