changes from pr review

config/egfr.yaml

@@ -33,6 +33,7 @@ algorithms:
           - 0.1
         mu:
           - 0.008
+        dummy_mode: ["file"]
   -
     name: omicsintegrator2
     params:

input/README.md

@@ -11,9 +11,9 @@ All other columns specify additional node attributes such as prizes.
 Any nodes that are listed in a node file but are not present in one or more edges in the edge file will be removed.
 For example:
 ```
-NODEID	prize	sources	targets	active
-A	1.0		True	True
-B	3.3	True		True
+NODEID	prize	sources	targets	dummy
+A	1.0		True	True    True
+B	3.3	True	True	
 C	2.5		True	True
 D	1.9	True	True	True
 ```
@@ -26,23 +26,6 @@ There are 4 dummy mode possibilities:
  4. file -> custom nodes - connect the dummy node to a specific list of nodes provided in a file
 To support the `file` dummy node logic as part of OmicsIntegrator1, you can either add a seperate `dummy.txt` file (and add this to the `node_files` argument in `config.yaml `) or add a `dummy` column node attribute to a file that contains `NODEID`, `prize`, `source`, etc. 
 
-If adding a seperate `dummy.txt` file:
-Make a file with the name `dummy.txt` and list the dummy nodes, each seperated by a new line. Example:
-```
-A
-B
-C
-```
-
-If adding the `dummy` column node attribute, then add the dummy column and specify boolean values for the `dummy` attribute:
-```
-NODEID	prize	sources	targets	dummy
-A	1.0		True	True    True
-B	3.3	True	True	
-C	2.5		True	True
-D	1.9	True	True	True
-```
-
 A secondary format provides only a list of node identifiers and uses the filename as the node attribute, as in the example `sources.txt`.
 This format may be deprecated.
 

spras/omicsintegrator1.py

@@ -135,10 +135,11 @@ def run(edges=None, prizes=None, dummy_nodes=None, dummy_mode=None, mu_squared=N
         #   4. file -> custom nodes - connect the dummy node to a specific list of nodes provided in a file
 
         # add dummy node file to the volume if dummy_mode is not None and it is 'file'
-        if dummy_mode is not None and dummy_mode == 'file':
-                # needs to use dummy node file that was put in the dataset
-                bind_path, dummy_file = prepare_volume(dummy_nodes, work_dir)
-                volumes.append(bind_path)
+        if dummy_mode == 'file':
+            if dummy_nodes is None:
+                raise ValueError("dummy_nodes file is required when dummy_mode is set to 'file'")
+            bind_path, dummy_file = prepare_volume(dummy_nodes, work_dir)
+            volumes.append(bind_path)
 
         out_dir = Path(output_file).parent
         # Omics Integrator 1 requires that the output directory exist