Merge pull request #31 from AgPipeline/develop

Merging Actions fixes to main branch - no review

.github/workflows/docker_test_check.sh

@@ -37,7 +37,7 @@ BEGIN {
 }
 {
   if ($1 != "species") { # Skipping the header line
-    printf("(%s %s %s %s %s %s %s %s %s %s %s)\n", $9, $10, $11, $12, $13, $14, $15, $16, $17, $18, $19)
+    printf("(%s %s %s %s %s %s %s %s %s %s %s)\n", $7, $8, $9, $10, $11, $12, $13, $14, $15, $16, $17)
   }
 }
 END {

.github/workflows/testing_checks.yaml

@@ -51,6 +51,9 @@ jobs:
         uses: actions/checkout@v2
       - name: Finding files
         run: find . -type f -name "*.py" > action_test_files.txt
+      - name: Update apt databases
+        shell: bash
+        run: 'sudo apt-get update'
       - name: Install system requirements
         shell: bash
         run: 'sudo apt-get install -y python3-gdal gdal-bin libgdal-dev gcc g++ python3.8-dev'

algorithm_rgb.py

@@ -35,12 +35,6 @@
 VARIABLE_LABELS = 'excess_greenness_index, green_leaf_index, cive, normalized_difference_index(pxarray), ' \
                 'excess_red, exgr, combined_indices_1, combined_indices_2, vegetative_index, ngrdi, percent_green'
 
-# Optional override for the generation of a BETYdb compatible csv file
-WRITE_BETYDB_CSV = True
-
-# Optional override for the generation of a TERRA REF Geostreams compatible csv file
-WRITE_GEOSTREAMS_CSV = True
-
 
 # Entry point for plot-level RBG algorithm
 

test_data/rgb_plot.csv

@@ -1,2 +1,2 @@
-species,site,timestamp,lat,lon,citation_author,citation_year,citation_title,excess greenness index excess_greenness_index ([-510:510]), green leaf index  green_leaf_index ( [-1:1]), cive  cive ( [-255:255]), normalized difference index  normalized_difference_index(pxarray) ( [-127:129]), excess red  excess_red ( [-255:255]), exgr  exgr ( [-255:332]), combined indices 1  combined_indices_1 ( [-1000:1000]), combined indices 2  combined_indices_2 ( [-1000:1000]), vegetative index  vegetative_index ( [-255:255]), normalized green-red difference  ngrdi ( [-255:255]), percent green  percent_green ( [0:100])
-Sorghum bicolor,,2018-10-11,33.074547045002895,-111.97502671168866,"Clairessa Brown","2020","Woebbecke, D.M. et al",14,0.02,16.2,-1.53,56.5,-42.5,30.2,12.8,1.02,-0.02,0.34
+species,site,timestamp,citation_author,citation_year,citation_title,excess greenness index excess_greenness_index ([-510:510]), green leaf index  green_leaf_index ( [-1:1]), cive  cive ( [-255:255]), normalized difference index  normalized_difference_index(pxarray) ( [-127:129]), excess red  excess_red ( [-255:255]), exgr  exgr ( [-255:332]), combined indices 1  combined_indices_1 ( [-1000:1000]), combined indices 2  combined_indices_2 ( [-1000:1000]), vegetative index  vegetative_index ( [-255:255]), normalized green-red difference  ngrdi ( [-255:255]), percent green  percent_green ( [0:100])
+Sorghum bicolor,,2018-10-11,"Clairessa Brown","2020","Woebbecke, D.M. et al",14,0.02,16.2,-1.53,56.5,-42.5,30.2,12.8,1.02,-0.02,0.34