chore: bump spras (#45)

tristan-f-r · web-flow · commit f9f919ca2380 · 2025-09-06T16:38:23.000-07:00
diff --git a/configs/dmmm.yaml b/configs/dmmm.yaml
@@ -10,13 +10,10 @@ container_registry:
 reconstruction_settings:
   locations:
     reconstruction_dir: "output"
-    run: true
 
 analysis:
   summary:
     include: false
-  graphspace:
-    include: false
   cytoscape:
     include: false
   ml:
diff --git a/configs/pra.yaml b/configs/pra.yaml
@@ -11,13 +11,10 @@ container_registry:
 reconstruction_settings:
   locations:
     reconstruction_dir: "output"
-    run: true
 
 analysis:
   summary:
     include: false
-  graphspace:
-    include: false
   cytoscape:
     include: false
   ml:
diff --git a/pyproject.toml b/pyproject.toml
@@ -13,7 +13,7 @@ dependencies = [
 [dependency-groups]
 dev = [
     "pre-commit>=4.2.0",
-    "snakemake>=9.6.0",
+    "snakemake==9.9.0",
 ]
 
 [tool.ruff]
diff --git a/run_snakemake.sh b/run_snakemake.sh
@@ -13,8 +13,8 @@ set -o nounset
 cd "$(dirname "$0")"
 
 main() {
-    uv tool run snakemake --cores 1 -d datasets/yeast-osmotic-stress -s datasets/yeast-osmotic-stress/Snakefile
-    uv tool run snakemake --cores 1 -d datasets/hiv -s datasets/hiv/Snakefile
+    uv run snakemake --cores 1 -d datasets/yeast-osmotic-stress -s datasets/yeast-osmotic-stress/Snakefile
+    uv run snakemake --cores 1 -d datasets/hiv -s datasets/hiv/Snakefile
 }
 
 main "$@"
diff --git a/spras b/spras
@@ -1 +1 @@
-Subproject commit 892b364dd176716ba8ac03e1fa979bfc1da2a758
+Subproject commit fad9fbf782ae0bd1e0cf660b7ef2a2d61df41cf5
diff --git a/uv.lock b/uv.lock

Original file line number	Diff line number	Diff line change
`@@ -13,7 +13,7 @@ dependencies = [`
`13`	`13`	`[dependency-groups]`
`14`	`14`	`dev = [`
`15`	`15`	`"pre-commit>=4.2.0",`
`16`		`- "snakemake>=9.6.0",`
	`16`	`+ "snakemake==9.9.0",`
`17`	`17`	`]`
`18`	`18`
`19`	`19`	`[tool.ruff]`
Original file line number	Diff line number	Diff line change
`@@ -13,8 +13,8 @@ set -o nounset`
`13`	`13`	`cd "$(dirname "$0")"`
`14`	`14`
`15`	`15`	`main() {`
`16`		`- uv tool run snakemake --cores 1 -d datasets/yeast-osmotic-stress -s datasets/yeast-osmotic-stress/Snakefile`
`17`		`- uv tool run snakemake --cores 1 -d datasets/hiv -s datasets/hiv/Snakefile`
	`16`	`+ uv run snakemake --cores 1 -d datasets/yeast-osmotic-stress -s datasets/yeast-osmotic-stress/Snakefile`
	`17`	`+ uv run snakemake --cores 1 -d datasets/hiv -s datasets/hiv/Snakefile`
`18`	`18`	`}`
`19`	`19`
`20`	`20`	`main "$@"`