Fix ovo init when new OVO_HOME is set

Author: David Prihoda

ovo/__init__.py

@@ -81,24 +81,24 @@ def get_scheduler(scheduler_key: str) -> Scheduler:
     # Additional imports at the bottom to avoid circular dependencies
     from ovo.core.logic import design_logic, descriptor_logic, job_logic, project_logic, import_export_logic
 
-except OVONotInitializedError:
+except OVONotInitializedError as e:
     if ("init" in sys.argv and "home" in sys.argv) or "-h" in sys.argv or "--help" in sys.argv:
         # Ignore initialization error if we are initializing the home dir
         pass
     else:
-        message = "\n[green]OVO_HOME[/green] env variable not set.\n"
-
-        if shell_config_path := get_shell_config_path():
-            with open(shell_config_path, "r") as f:
-                contents = f.read()
-            if "OVO_HOME" in contents:
-                message += (
-                    f"\nLooks like you have already initialized OVO and added [green]OVO_HOME[/green] "
-                    f"to your {os.path.basename(shell_config_path)}, please run:\n" + get_source_command()
-                )
-            else:
-                message += (
-                    "\nPlease initialize OVO using [bold]ovo init home[/bold] or set [green]OVO_HOME[/green] env var."
-                )
+        if os.getenv("OVO_HOME"):
+            message = str(e)
+        else:
+            message = (
+                "\nPlease initialize OVO using [bold]ovo init home[/bold] or set [green]OVO_HOME[/green] env var."
+            )
+            if shell_config_path := get_shell_config_path():
+                with open(shell_config_path, "r") as f:
+                    contents = f.read()
+                if "OVO_HOME" in contents:
+                    message = (
+                        f"\n[green]OVO_HOME[/green] env variable not set.\nLooks like you have already initialized OVO and added [green]OVO_HOME[/green] "
+                        f"to your {os.path.basename(shell_config_path)}, please run:\n" + get_source_command()
+                    )
         console.print(Panel.fit(message, title="⚠️  OVO not initialized", border_style="red"))
         sys.exit(2)

ovo/app/pages/rfdiffusion/binder_design.py

@@ -100,7 +100,7 @@ def intro_step():
 - Percentage of individual amino acids
 - Charge at pH 7.4 and 5.5, isoelectric point
 - Aromaticity
-- Sequence entropy, highlighting repetitive sequences
+- Sequence entropy, highlighting sequences with compositionally biased regions
 - And more; computed using BioPython ProteinAnalysis<sup>[4]</sup>
 
 #### Rosetta descriptors<sup>[2]</sup>

ovo/app/pages/rfdiffusion/scaffold_design.py

@@ -86,7 +86,7 @@ def intro_step():
 
 - Percentage of individual amino acids
 - Charge at pH 7.4 and 5.5, isoelectric point
-- Sequence entropy, highlighting repetitive sequences
+- Sequence entropy, highlighting sequences with compositionally biased regions
 - Aromaticity
 - And more; computed using BioPython ProteinAnalysis<sup>[6]</sup>
 

ovo/cli/init.py

@@ -120,7 +120,8 @@ def home(
 All paths can be customized later in the [bold]config.yml[/bold] file.
 """)
         home_dir = yes or Prompt.ask(
-            prompt="Enter path, or press [bold]Enter[/bold] to select the default", default=DEFAULT_OVO_HOME
+            prompt="Enter path, or press [bold]Enter[/bold] to select the default",
+            default=os.getenv("OVO_HOME", DEFAULT_OVO_HOME), # Use OVO_HOME env var if set already
         )
 
     home_dir = os.path.abspath(os.path.expanduser(home_dir))

ovo/core/configuration.py

@@ -273,12 +273,14 @@ def load_config(home_dir: str) -> OVOConfig:
     if not os.path.exists(home_dir) or not os.path.exists(config_path):
         # Config dir does not exist yet, print error and exit
         if home_dir != DEFAULT_OVO_HOME:
+            # Custom OVO_HOME set but invalid
             if not os.path.exists(home_dir):
-                raise OVOCliError(f"OVO_HOME directory does not exist: {home_dir}")
+                raise OVONotInitializedError(f"OVO_HOME directory set but is not accessible: {home_dir}")
             else:
-                raise OVOCliError(f"OVO config file not found in OVO_HOME: {home_dir}")
+                raise OVONotInitializedError(f"OVO config file not found in OVO_HOME: {home_dir}")
         else:
-            raise OVONotInitializedError()
+            # Default OVO_HOME, raise not initialized error
+            raise OVONotInitializedError("OVO not initialized")
 
     console.print(f"[bold]OVO home[/bold] [green]{home_dir}[/green]")
 

ovo/core/database/descriptors_proteinqc.py

@@ -454,7 +454,7 @@
 
 ENTROPY = NumericGlobalDescriptor(
     name="Sequence entropy",
-    description="Diversity/orderedness of amino acids in a protein sequence; high values = more variety, low values = more repetition. For each overlapping 21-residue window (if sequence is longer than 21), the binary Shannon entropy of the amino acid composition is calculated and averaged to produce a single metric for the sequence. A sequence of identical amino acids has entropy 0, while a sequence with a uniform distribution of all 20 amino acids in each segment reaches log2(20) ~ 4.32.",
+    description="Diversity/orderedness of amino acids in a protein sequence; high values = more variety, low values = more compositional bias. For each overlapping 21-residue window (if sequence is longer than 21), the binary Shannon entropy of the amino acid composition is calculated and averaged to produce a single metric for the sequence. A sequence of identical amino acids has entropy 0, while a sequence with a uniform distribution of all 20 amino acids in each segment reaches log2(20) ~ 4.32.",
     tool="Sequence composition",
     key="proteinqc|seq_composition|avg_entropy",
     comparison="higher_is_better",