feat: visjs (#48)

* chore: fix up config, bump cores

* chore: bump web dependencies

* feat: use visjs

Author: tristan-f-r

.github/workflows/publish.yml

@@ -59,7 +59,7 @@ jobs:
         run: snakemake --cores 4 --configfile configs/dmmm.yaml --show-failed-logs -s spras/Snakefile
       - name: Run Snakemake workflow for PRAs
         shell: bash --login {0}
-        run: snakemake --cores 1 --configfile configs/pra.yaml --show-failed-logs -s spras/Snakefile
+        run: snakemake --cores 4 --configfile configs/pra.yaml --show-failed-logs -s spras/Snakefile
       - name: Setup PNPM
         uses: pnpm/action-setup@v4
         with:

configs/dmmm.yaml

@@ -58,21 +58,21 @@ datasets:
     edge_files: ["network1.txt"]
     other_files: []
     data_dir: "datasets/yeast-osmotic-stress/processed"
-  - label: dmmm_alopecia_areata
+  - label: dmmmalopecia_areata
     data_dir: datasets/diseases
     edge_files:
       - raw/string_interactome.txt
     node_files:
       - prize_files/alopecia_areata_prizes.txt
     other_files: []
-  - label: dmmm_diabetes_mellitus
+  - label: dmmmdiabetes_mellitus
     data_dir: datasets/diseases
     edge_files:
       - raw/string_interactome.txt
     node_files:
       - prize_files/diabetes_mellitus_prizes.txt
     other_files: []
-  - label: dmmm_cellline_fadu
+  - label: dmmmcellline_fadu
     data_dir: datasets/depmap
     edge_files: ["../../databases/irefindex/phosphosite-irefindex13.0-uniprot.txt"]
     node_files: ["processed/FADU_cell_line_prizes_input_nonzero.txt"]
@@ -81,12 +81,12 @@ gold_standards:
   - label: gs0
     node_files: ['GS_files/Alopecia_areata_GS.txt']
     data_dir: "datasets/diseases"
-    dataset_labels: ["dmmm_alopecia_areata"]
+    dataset_labels: ["dmmmalopecia_areata"]
   - label: gs1
     node_files: ['GS_files/Diabetes_mellitus_GS.txt']
     data_dir: "datasets/diseases"
-    dataset_labels: ["dmmm_diabetes_mellitus"]
+    dataset_labels: ["dmmmdiabetes_mellitus"]
   - label: gs_fadu
     node_files: ["processed/FADU_gold_standard.txt"]
     data_dir: datasets/depmap
-    dataset_labels: ["dmmm_cellline_fadu"]
+    dataset_labels: ["dmmmcellline_fadu"]

web/package.json

@@ -10,11 +10,14 @@
     "astro": "astro"
   },
   "dependencies": {
-    "@fontsource-variable/noto-sans": "^5.2.7",
-    "astro": "^5.9.4",
-    "cytoscape": "^3.32.0",
-    "dayjs": "^1.11.13",
+    "@fontsource-variable/noto-sans": "^5.2.10",
+    "astro": "^5.16.6",
+    "dayjs": "^1.11.19",
     "medium-zoom": "^1.1.0",
-    "sass": "^1.89.2"
+    "sass": "^1.97.1"
+  },
+  "devDependencies": {
+    "vis-data": "^8.0.3",
+    "vis-network": "^10.0.2"
   }
 }