Merge branch 'main' into main-pr

HopkinsIDD · Jun 15, 2024 · 7140b95 · 7140b95
2 parents ebfa093 + f4a5639
commit 7140b95
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Showing 8 changed files with 288,590 additions and 106 deletions.
diff --git a/.github/workflows/after-validate-submission.yaml b/.github/workflows/after-validate-submission.yaml
@@ -69,7 +69,7 @@ jobs:
            Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubVis")'
       - name: Install hubUtils
         run: |
-           Rscript -e 'remotes::install_github("kjsato/hubUtils@enhancement/v3-utils", upgrade = "never")'
+           Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubUtils")'
       - name: Install hubEnsembles
         run: |
            Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubEnsembles")'

diff --git a/.github/workflows/validate-submission.yaml b/.github/workflows/validate-submission.yaml
@@ -33,19 +33,10 @@ jobs:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ hashFiles('DESCRIPTION') }}
           restore-keys: ${{ runner.os }}-r-
-      - name: Install hubUtils from specific branch
-        run: |
-          Rscript -e 'install.packages("remotes")'
-          Rscript -e 'remotes::install_github("kjsato/hubUtils@enhancement/v3-utils", upgrade = "never")'
-      - name: Install hubAdmin from specific branch
-        run: |
-          Rscript -e 'remotes::install_github("kjsato/hubAdmin@feature/sample-support", upgrade = "never")'
-      - name: Install hubData from specific branch
-        run: |
-          Rscript -e 'remotes::install_github("kjsato/hubData@feature/handle-samples", upgrade = "never")'
       - name: Install HubValidations
         run: |
-          remotes::install_github("kjsato/hubValidations@patch4conversion_origin_date", upgrade = "never")
+          install.packages("remotes")
+          remotes::install_github("Infectious-Disease-Modeling-Hubs/hubValidations", upgrade = "always")
         shell: Rscript {0}
 
       - name: Run validations

diff --git a/hub-config/admin.json b/hub-config/admin.json
@@ -1,16 +1,12 @@
 {
-    "schema_version": "https://raw.githubusercontent.com/kjsato/schemas/br-v3.0.0/v3.0.0/admin-schema.json",
-    "name": "US RSV Forecast Hub",
-    "maintainer": "Johns Hopkins University, Infectious Disease Dynamics Group",
+    "schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/admin-schema.json",
+    "name": "Simple Forecast Hub",
+    "maintainer": "Consortium of Infectious Disease Modeling Hubs",
     "contact": {
         "name": "K. Sato",
         "email": "[email protected]"
     },
-    "repository": {
-        "host": "github",
-        "owner": "kjsato",
-        "name": "rsv-forecast-hub"
-    },
+    "repository_url": "https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate",
     "file_format": ["csv", "parquet"],
     "timezone": "US/Eastern"
 }
diff --git a/hub-config/tasks.json b/hub-config/tasks.json
@@ -1,8 +1,7 @@
 {
-    "schema_version": "https://raw.githubusercontent.com/kjsato/schemas/br-v3.0.0/v3.0.0/tasks-schema.json",
+    "schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json",
     "rounds": [
 	{
-            "round_name": "retrospective round",
             "round_id_from_variable": true,
             "round_id": "origin_date",
             "model_tasks": [
@@ -11,7 +10,6 @@
                     "origin_date": {
                         "required": null,
                         "optional": [
-                            "2023-10-18", "2023-10-22", "2023-10-29", 
                             "2023-11-12", "2023-11-19", "2023-11-26", "2023-12-03",
                             "2023-12-10", "2023-12-17", "2023-12-24", "2023-12-31",
                             "2024-01-07", "2024-01-14", "2024-01-21", "2024-01-28",
@@ -149,7 +147,6 @@
                  "origin_date": {
                      "required": null,
                      "optional": [
-                         "2023-10-18", "2023-10-22", "2023-10-29", 
                          "2023-11-12", "2023-11-19", "2023-11-26", "2023-12-03",
                          "2023-12-10", "2023-12-17", "2023-12-24", "2023-12-31",
                          "2024-01-07", "2024-01-14", "2024-01-21", "2024-01-28",
@@ -233,15 +230,13 @@
                 },
                 "output_type": {
                     "sample":{
-                        "output_type_id_params":{
-                            "is_required": true,
-                            "type": "integer",
-                            "min_samples_per_task": 100,
-                            "max_samples_per_task": 100
+                        "output_type_id":{
+                            "required": null,
+                            "optional":[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]
                         },
                         "value":{
-                            "type":"integer",
-                            "minimum":0
+                        "type":"double",
+                        "minimum":0
                         }
                     }
                 },
@@ -276,7 +271,7 @@
        	"submissions_due": {
             "relative_to": "origin_date",
             "start": -6,
-            "end": 252
+            "end": 100
         }
     }
     ]

diff --git a/model-output/CU-RSV_SVIRS/2024-05-12-CU-RSV_SVIRS.parquet b/model-output/CU-RSV_SVIRS/2024-05-12-CU-RSV_SVIRS.parquet
diff --git a/scripts/retro_ensemble.R b/scripts/retro_ensemble.R