Oct24 (#65)

* merge and update for new llm

* updated sky yaml for ollama

* updates and bug fixes for release

* updates and bug fixes for release

* updates and bug fixes for release

* updates and bug fixes for release

* updates and bug fixes for release

---------

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

Author: PhillipDowney

README.md

@@ -52,6 +52,7 @@ The OpenAD client is accessible from a command line interface, Jupyter Notebook
 <div markdown="block">
 
 -   `%Openadd` has been added to the magic commands for commands that return data.
+-   New Macro Molecule viewer for visualising proteins
 -   Upgraded SkyPilot to 0.6.0
 -   Support for deploying in OpenShift AI/Open Data hub workbench or Podman/Docker image. [See the workbench repo](https://github.com/acceleratedscience/openad_workbench).
 -   Support for application API

docs/output/markdown/commands.md

@@ -830,7 +830,7 @@ Optional Parameters that can be specified in the `using` clause: <br>
 -   `availability_pricing_threshold=<int>` Maximum price in USD per g/ml of compounds. Default: no threshold. <br>
 -   `available_smiles='<smiles>.<smiles>.<smiles>'` List of molecules available as precursors, delimited with a period. <br>
 -   `exclude_smiles='<smiles>.<smiles>.<smiles>'` List of molecules to exlude from the set of precursors, delimited with a period. <br>
--   `exclude_substructures='<smiles>.<smiles>.<smiles>'` List of substructures to excludefrom the set of precursors, delimited with a period. <br>
+-   `exclude_substructures='<smiles>.<smiles>.<smiles>'` List of substructures to exclude from the set of precursors, delimited with a period. <br>
 -   `exclude_target_molecule=<boolean>` Excluded target molecule. The default is True <br>
 -   `fap=<float>` Every retrosynthetic step is evaluated with the FAP, and is only retained when forward confidence is greater than the FAP value. The default is 0.6. <br>
 -   `max_steps=<int>` The maximum number steps in the results. The default is 3. <br>

openad/app/main.py

@@ -643,7 +643,7 @@ def default(self, line):
                 # Brutal situation where someone hit clear sessions in another session
                 # , shut down abruptly so as not to kill registry file.
                 output_error(
-                    "Fatal error: the session registry is not avaiable, performing emergency shutdown" + str(e),
+                    "Fatal error: the session registry is not available, performing emergency shutdown" + str(e),
                     return_val=False,
                 )
                 self.do_exit("exit emergency")

openad/app/metadata.json

@@ -1,7 +1,7 @@
 {
 	"banner": "OPENAD",
 	"title": "Welcome to the Open Accelerated Discovery CLI",
-	"version": "0.4.4",
+	"version": "0.5.1",
 	"commands": {
 		"intro": "If this is your first time, let us help you getting started.",
 		"? toolkits": "Learn about the toolkits.",

openad/core/grammar.py

@@ -157,10 +157,21 @@ def _append_matches(match_list, inp, output, match_word=False):
         # Underline matching string
         if match_word:
             # Exact word match --> underline both single and plural instances.
-            command_str = re.sub(rf"(?<!<){inp}(s?)(?![^<>]*?>)", rf"<underline>{inp}\1</underline>", command_str)
+            command_str = re.sub(
+                rf"(?<!<){re.escape(inp)}(s?)(?![^<>]*?>)", rf"<underline>{re.escape(inp)}\1</underline>", command_str
+            )
         else:
             # String match --> only underline the matching string.
-            command_str = re.sub(rf"(?<!<){inp}(?![^<>]*?>)", rf"<underline>{inp}</underline>", command_str)
+
+            command_str = re.sub(
+                rf"(?<!<){re.escape(inp)}(?![^<>]*?>)", rf"<underline>{re.escape(inp)}</underline>", command_str
+            )
+        # Work around for escape character compensation in re
+        command_str = command_str.replace("\ ", " ")
+        command_str = command_str.replace("\[", "[")
+        command_str = command_str.replace("\]", "]")
+        command_str = command_str.replace("\<", "<")
+        command_str = command_str.replace("\>", ">")
 
         output.append(f"- <cmd>{command_str}</cmd>")
     return output