From 0c4b2d000fef3e0ec379a3c064ba6ed9379362f1 Mon Sep 17 00:00:00 2001
From: "Tristan F.-R." <pub.tristanf@gmail.com>
Date: Tue, 1 Jul 2025 12:32:11 -0700
Subject: [PATCH 1/3] fix: re-add yeast

---
 configs/dmmm.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/configs/dmmm.yaml b/configs/dmmm.yaml
index 9d0fec3..3a78106 100644
--- a/configs/dmmm.yaml
+++ b/configs/dmmm.yaml
@@ -54,3 +54,9 @@ datasets:
     edge_files: ["phosphosite-irefindex13.0-uniprot.txt"]
     other_files: []
     data_dir: "datasets/hiv/processed"
+  - label: dmmmyeast
+    node_files: ["prizes1_dummies.txt"]
+    edge_files: ["network1.txt"]
+    # Placeholder
+    other_files: []
+    data_dir: "datasets/yeast-osmotic-stress/processed"

From 87b1775f0c7ee5899d51abe4480d2c96230b938b Mon Sep 17 00:00:00 2001
From: "Tristan F.-R." <pub.tristanf@gmail.com>
Date: Tue, 1 Jul 2025 21:10:41 +0000
Subject: [PATCH 2/3] docs: mention old configs

---
 configs/dmmm.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/configs/dmmm.yaml b/configs/dmmm.yaml
index 3a78106..b9d9932 100644
--- a/configs/dmmm.yaml
+++ b/configs/dmmm.yaml
@@ -43,6 +43,8 @@ algorithms:
         g: [0]
 
 datasets:
+  # TODO: use old paramaters for datasets
+  # HIV: https://github.com/Reed-CompBio/spras-benchmarking/blob/0293ae4dc0be59502fac06b42cfd9796a4b4413e/hiv-benchmarking/spras-config/config.yaml
   - label: dmmmhiv060
     node_files: ["processed_prize_060.txt"]
     edge_files: ["phosphosite-irefindex13.0-uniprot.txt"]
@@ -54,6 +56,7 @@ datasets:
     edge_files: ["phosphosite-irefindex13.0-uniprot.txt"]
     other_files: []
     data_dir: "datasets/hiv/processed"
+  # Yeast: https://github.com/tristan-f-r/spras-benchmarking/blob/9477d85871024a5e3a4b0b8b9be7e78c0d0ee961/yeast-osmotic-stress/config.yaml
   - label: dmmmyeast
     node_files: ["prizes1_dummies.txt"]
     edge_files: ["network1.txt"]

From c0a0cafcbfac9e6efedf072256b4543dee170313 Mon Sep 17 00:00:00 2001
From: "Tristan F.-R." <pub.tristanf@gmail.com>
Date: Tue, 1 Jul 2025 21:47:51 +0000
Subject: [PATCH 3/3] docs: remove inconsistent placeholder cmt

---
 configs/dmmm.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/configs/dmmm.yaml b/configs/dmmm.yaml
index b9d9932..4ff108e 100644
--- a/configs/dmmm.yaml
+++ b/configs/dmmm.yaml
@@ -48,7 +48,6 @@ datasets:
   - label: dmmmhiv060
     node_files: ["processed_prize_060.txt"]
     edge_files: ["phosphosite-irefindex13.0-uniprot.txt"]
-    # Placeholder
     other_files: []
     data_dir: "datasets/hiv/processed"
   - label: dmmmhiv05
@@ -60,6 +59,5 @@ datasets:
   - label: dmmmyeast
     node_files: ["prizes1_dummies.txt"]
     edge_files: ["network1.txt"]
-    # Placeholder
     other_files: []
     data_dir: "datasets/yeast-osmotic-stress/processed"