Merge branch 'main' of https://github.com/eco4cast/neon4cast-ci

eco4cast · Jan 9, 2024 · 1341288 · 1341288
2 parents a2bb56c + f11351c
commit 1341288
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diff --git a/.github/workflows/combined.yaml b/.github/workflows/combined.yaml
@@ -1,8 +1,8 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  schedule:
-    - cron: '0 5 * * *'
+  #schedule:
+  #  - cron: '0 5 * * *'
   workflow_dispatch:
 
 name: submissions-score-dashboard-catalog

diff --git a/.github/workflows/drivers_stage1.yaml b/.github/workflows/drivers_stage1.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   schedule:
-    - cron: '0 23 * * *'
+    - cron: '0 5 * * *'
   workflow_dispatch:
 
 
@@ -29,16 +29,10 @@ jobs:
       - name: Update GEFS
         shell: Rscript {0}
         run: |
-          source("drivers/download_stage1_psuedo.R")
+          source("drivers/download_stage1.R")
 
       - name: Generate stage 2
         shell: Rscript {0}
         run: |
           source("drivers/generate_stage2.R")
 
-
-      - name: Update Stage3
-        shell: Rscript {0}
-        run: |
-          source("drivers/update_stage3.R")
-
diff --git a/.github/workflows/drivers_stage3.yaml b/.github/workflows/drivers_stage3.yaml
@@ -1,8 +1,8 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  #schedule:
-  #  - cron: '0 13 * * *'
+  schedule:
+    - cron: '0 23 * * *'
   workflow_dispatch:
 
 name: gefs_osn_stage3
@@ -25,6 +25,11 @@ jobs:
           install.packages("remotes")
           remotes::install_github("eco4cast/gefs4cast")
 
+      - name: Download Pseudo
+        shell: Rscript {0}
+        run: |
+          source("drivers/download_psuedo.R")
+
       - name: Update Stage3
         shell: Rscript {0}
         run: |

diff --git a/catalog/forecasts/Aquatics/Daily_Chlorophyll_a/collection.json b/catalog/forecasts/Aquatics/Daily_Chlorophyll_a/collection.json
@@ -183,7 +183,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-01-18T00:00:00Z"
+          "2024-02-08T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Aquatics/Daily_Dissolved_oxygen/collection.json b/catalog/forecasts/Aquatics/Daily_Dissolved_oxygen/collection.json
@@ -120,6 +120,11 @@
       "type": "application/json",
       "href": "../../models/model_items/tg_bag_mlp.json"
     },
+    {
+      "rel": "item",
+      "type": "application/json",
+      "href": "../../models/model_items/neon4cast_example.json"
+    },
     {
       "rel": "parent",
       "type": "application/json",
@@ -163,7 +168,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-11-07T00:00:00Z"
+          "2024-11-28T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Aquatics/Daily_Water_temperature/collection.json b/catalog/forecasts/Aquatics/Daily_Water_temperature/collection.json
@@ -190,6 +190,16 @@
       "type": "application/json",
       "href": "../../models/model_items/tg_auto_adam.json"
     },
+    {
+      "rel": "item",
+      "type": "application/json",
+      "href": "../../models/model_items/precip_mod.json"
+    },
+    {
+      "rel": "item",
+      "type": "application/json",
+      "href": "../../models/model_items/neon4cast_example.json"
+    },
     {
       "rel": "parent",
       "type": "application/json",
@@ -233,7 +243,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-11-07T00:00:00Z"
+          "2024-11-28T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Aquatics/collection.json b/catalog/forecasts/Aquatics/collection.json
@@ -68,7 +68,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-12-02T00:00:00Z"
+          "2024-12-23T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Beetles/Weekly_beetle_community_abundance/collection.json b/catalog/forecasts/Beetles/Weekly_beetle_community_abundance/collection.json
@@ -128,7 +128,7 @@
       "interval": [
         [
           "2023-01-02T00:00:00Z",
-          "2024-12-02T00:00:00Z"
+          "2024-12-23T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Beetles/Weekly_beetle_community_richness/collection.json b/catalog/forecasts/Beetles/Weekly_beetle_community_richness/collection.json
@@ -128,7 +128,7 @@
       "interval": [
         [
           "2023-01-02T00:00:00Z",
-          "2024-12-02T00:00:00Z"
+          "2024-12-23T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Beetles/collection.json b/catalog/forecasts/Beetles/collection.json
@@ -63,7 +63,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-12-02T00:00:00Z"
+          "2024-12-23T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Phenology/Daily_Green_chromatic_coordinate/collection.json b/catalog/forecasts/Phenology/Daily_Green_chromatic_coordinate/collection.json
@@ -95,6 +95,11 @@
       "type": "application/json",
       "href": "../../models/model_items/tg_randfor.json"
     },
+    {
+      "rel": "item",
+      "type": "application/json",
+      "href": "../../models/model_items/PEG.json"
+    },
     {
       "rel": "parent",
       "type": "application/json",
@@ -138,7 +143,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-01-18T00:00:00Z"
+          "2024-02-08T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Phenology/Daily_Red_chromatic_coordinate/collection.json b/catalog/forecasts/Phenology/Daily_Red_chromatic_coordinate/collection.json
@@ -110,6 +110,11 @@
       "type": "application/json",
       "href": "../../models/model_items/tg_auto_adam.json"
     },
+    {
+      "rel": "item",
+      "type": "application/json",
+      "href": "../../models/model_items/PEG.json"
+    },
     {
       "rel": "parent",
       "type": "application/json",
@@ -153,7 +158,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-01-18T00:00:00Z"
+          "2024-02-08T00:00:00Z"
         ]
       ]
     }

diff --git a/catalog/forecasts/Phenology/collection.json b/catalog/forecasts/Phenology/collection.json
@@ -63,7 +63,7 @@
       "interval": [
         [
           "2023-01-01T00:00:00Z",
-          "2024-12-02T00:00:00Z"
+          "2024-12-23T00:00:00Z"
         ]
       ]
     }

diff --git a/.../Beetles/abundance_weekly/collection.json → ...in_Net_ecosystem_exchange/collection.json b/.../Beetles/abundance_weekly/collection.json → ...in_Net_ecosystem_exchange/collection.json
@@ -1,6 +1,6 @@
 {
-  "id": "abundance_weekly",
-  "description": "This page includes all models for the abundance_weekly variable.",
+  "id": "30min_Net_ecosystem_exchange",
+  "description": "This page includes all models for the 30min_Net_ecosystem_exchange variable.",
   "stac_version": "1.0.0",
   "license": "CC0-1.0",
   "stac_extensions": [
@@ -13,67 +13,7 @@
     {
       "rel": "item",
       "type": "application/json",
-      "href": "../../models/model_items/tg_humidity_lm_all_sites.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_precip_lm_all_sites.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_temp_lm.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_humidity_lm.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_precip_lm.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_randfor.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_lasso.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_temp_lm_all_sites.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_arima.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_tbats.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_randfor_all_sites.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_ets.json"
-    },
-    {
-      "rel": "item",
-      "type": "application/json",
-      "href": "../../models/model_items/tg_lasso_all_sites.json"
+      "href": "../../models/model_items/climatology.json"
     },
     {
       "rel": "parent",
@@ -96,34 +36,29 @@
     },
     {
       "rel": "about",
-      "href": "www.neon4cast.org",
+      "href": "https://projects.ecoforecast.org/neon4cast-docs/",
       "type": "text/html",
       "title": "NEON Ecological Forecasting Challenge Documentation"
     },
     {
       "rel": "describedby",
-      "href": "www.neon4cast.org",
-      "title": "NEON Ecological Forecasting Challenge Documentation",
+      "href": "https://projects.ecoforecast.org/neon4cast-docs/",
+      "title": "NEON Forecast Challenge Dashboard",
       "type": "text/html"
     }
   ],
-  "title": "abundance_weekly",
+  "title": "30min_Net_ecosystem_exchange",
   "extent": {
     "spatial": {
       "bbox": [
-        [
-          -156.6194,
-          71.2824,
-          -66.7987,
-          71.2824
-        ]
+        [-156.6194, 17.9696, -66.8687, 71.2824]
       ]
     },
     "temporal": {
       "interval": [
         [
-          "2021-05-17T00:00:00Z",
-          "2024-10-28T00:00:00Z"
+          "2023-11-14T00:00:00Z",
+          "2024-01-09T00:00:00Z"
         ]
       ]
     }
@@ -192,13 +127,21 @@
   ],
   "assets": {
     "data": {
-      "href": "s3://anonymous@bio230014-bucket01/challenges/forecasts/parquet/project_id=neon4cast/duration=P1W/variable=abundance?endpoint_override=sdsc.osn.xsede.org",
+      "href": "\"s3://anonymous@bio230014-bucket01/challenges/forecasts/parquet/project_id=neon4cast/duration=PT30M/variable=nee?endpoint_override=sdsc.osn.xsede.org\"",
       "type": "application/x-parquet",
       "title": "Database Access",
       "roles": [
         "data"
       ],
-      "description": "Use `arrow` for remote access to the database. This R code will return results for the NEON Ecological Forecasting Aquatics theme.\n\n### R\n\n```{r}\n# Use code below\n\nall_results <- arrow::open_dataset(s3://anonymous@bio230014-bucket01/challenges/forecasts/parquet/project_id=neon4cast/duration=P1W/variable=abundance?endpoint_override=sdsc.osn.xsede.org)\ndf <- all_results |> dplyr::collect()\n\n```\n       \n\nYou can use dplyr operations before calling `dplyr::collect()` to `summarise`, `select` columns, and/or `filter` rows prior to pulling the data into a local `data.frame`. Reducing the data that is pulled locally will speed up the data download speed and reduce your memory usage.\n\n\n"
+      "description": "Use `arrow` for remote access to the database. This R code will return results for forecasts of the variable by the specific model .\n\n### R\n\n```{r}\n# Use code below\n\nall_results <- arrow::open_dataset(\"s3://anonymous@bio230014-bucket01/challenges/forecasts/parquet/project_id=neon4cast/duration=PT30M/variable=nee?endpoint_override=sdsc.osn.xsede.org\")\ndf <- all_results |> dplyr::collect()\n\n```\n       \n\nYou can use dplyr operations before calling `dplyr::collect()` to `summarise`, `select` columns, and/or `filter` rows prior to pulling the data into a local `data.frame`. Reducing the data that is pulled locally will speed up the data download speed and reduce your memory usage.\n\n\n"
+    },
+    "thumbnail": {
+      "href": "pending",
+      "type": "image/JPEG",
+      "roles": [
+        "thumbnail"
+      ],
+      "title": "pending"
     }
   }
 }
diff --git a/catalog/forecasts/Terrestrial/30min_latent_heat_flux/collection.json b/catalog/forecasts/Terrestrial/30min_latent_heat_flux/collection.json
@@ -58,7 +58,7 @@
       "interval": [
         [
           "2023-11-14T00:00:00Z",
-          "2023-12-24T00:00:00Z"
+          "2024-01-09T00:00:00Z"
         ]
       ]
     }