From fdc03affc4e6104f515bb55dbebbf7c950b9ac8e Mon Sep 17 00:00:00 2001
From: Chris Schnaufer <schnaufer@email.arizona.edu>
Date: Mon, 1 Mar 2021 12:59:26 -0700
Subject: [PATCH 1/3] Removing incorrect files

---
 .github/workflows/docker_test_check_rgb.sh | 67 ---------------------
 .github/workflows/testing_docker.yaml      | 69 ----------------------
 2 files changed, 136 deletions(-)
 delete mode 100755 .github/workflows/docker_test_check_rgb.sh
 delete mode 100644 .github/workflows/testing_docker.yaml

diff --git a/.github/workflows/docker_test_check_rgb.sh b/.github/workflows/docker_test_check_rgb.sh
deleted file mode 100755
index ebeabc3..0000000
--- a/.github/workflows/docker_test_check_rgb.sh
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env bash
-
-# Checking the results of running the docker commands
-
-# Define expected results
-EXPECTED_FILES=("result.json")
-EXPECTED_CANOPYCOVER_VALUES=(99.8 20.9)
-
-# What folder are we looking in for outputs
-if [[ ! "${1}" == "" ]]; then
-  TARGET_FOLDER="${1}"
-else
-  TARGET_FOLDER="./outputs"
-fi
-
-# What our target file to read is
-if [[ ! "${2}" == "" ]]; then
-  CHECK_FILE="${2}"
-else
-  CHECK_FILE="canopycover.csv"
-fi
-EXPECTED_FILES+=("${CHECK_FILE}")
-
-# Check if expected files are found
-for i in $(seq 0 $(( ${#EXPECTED_FILES[@]} - 1 )))
-do
-  if [[ ! -f "${TARGET_FOLDER}/${EXPECTED_FILES[$i]}" ]]; then
-    echo "Expected file ${EXPECTED_FILES[$i]} is missing"
-    exit 10
-  fi
-done
-
-# Check the results of the canopy cover calculation
-RESULT_VALUES=(`gawk '
-BEGIN {
-    FPAT = "([^,]+)|(\"[^\"]+\")"
-}
-{
-  if ($1 != "local_datetime") { # Skipping the header line
-    printf("%s\n", $2)
-  }
-}
-END {
-}
-' "${TARGET_FOLDER}/${CHECK_FILE}"`)
-
-echo "Result counts: ${#EXPECTED_CANOPYCOVER_VALUES[@]} vs ${#RESULT_VALUES[@]}"
-if [[ ${#EXPECTED_CANOPYCOVER_VALUES[@]} != ${#RESULT_VALUES[@]} ]]; then
-  echo "Number of results found in file (${#RESULT_VALUES[@]}) don't match expected count (${#EXPECTED_CANOPYCOVER_VALUES[@]})"
-  if [[ ${#RESULT_VALUES[@]} > 0 ]]; then
-    for i in $(seq 0 $(( ${#RESULT_VALUES[@]} - 1 )))
-    do
-      echo "${i}: ${RESULT_VALUES[$i]}"
-    done
-  fi
-  exit 20
-fi
-
-for i in $(seq 0 $(( ${#EXPECTED_CANOPYCOVER_VALUES[@]} - 1 )))
-do
-  if [[ "${EXPECTED_CANOPYCOVER_VALUES[$i]}" == "${RESULT_VALUES[$i]}" ]]; then
-    echo "Values for index ${i} match: '${RESULT_VALUES[$i]}' '${EXPECTED_CANOPYCOVER_VALUES[$i]}'"
-  else
-    echo "Result value for index ${i}: '${RESULT_VALUES[$i]}' doesn't match expected: '${EXPECTED_CANOPYCOVER_VALUES[$i]}'"
-    exit 30
-  fi
-done
diff --git a/.github/workflows/testing_docker.yaml b/.github/workflows/testing_docker.yaml
deleted file mode 100644
index 0e3c590..0000000
--- a/.github/workflows/testing_docker.yaml
+++ /dev/null
@@ -1,69 +0,0 @@
-name: Testing Docker image
-on:
-  push:
-    branches:
-      - master
-      - develop
-  pull_request:
-    branches:
-      - master
-      - develop
-    tags:
-      - v*
-  schedule:
-    # Every 01:00 Sunday re-run the test on the main branch
-    - cron: '0 1 * * 0'
-  workflow_dispatch:
-
-jobs:
-  docker_testing:
-    runs-on: ubuntu-latest
-    name: Running Docker testing
-    steps:
-      - name: Fetch source code
-        uses: actions/checkout@v2
-      - name: Create folders
-        run: |
-             mkdir ./inputs && chmod 777 ./inputs
-             mkdir ./outputs && chmod 777 ./outputs
-      - name: List folder contents
-        run: |
-             echo "Current folder" && ls -la
-             echo "test_data" && ls -l ./test_data
-      - name: Copy testing data files
-        run: |
-             cp "${PWD}/test_data"/* "${PWD}/inputs/"
-             echo "inputs" && ls -l ./inputs
-      - name: Folder contents
-        run: |
-             echo "Current folder" && ls -l
-             echo "Inputs folder" && ls -l ./inputs
-             echo "Outputs folder" && ls -l ./outputs
-      - name: Build docker image
-        run: docker build -t canopycover_test:latest ./
-      - name: Compress docker image
-        run: docker save canopycover_test:latest | gzip -7 -c - > canopycover_test_image.tar.gz
-      - name: Upload docker image
-        uses: actions/upload-artifact@v2
-        with:
-          name: canopycover_test_image
-          path: canopycover_test_image.tar.gz
-      - name: Run docker test
-        run: docker run --rm -v "${PWD}/inputs:/inputs" -v "${PWD}/outputs:/outputs" canopycover_test:latest --working_space /outputs --metadata /inputs/meta.yaml /inputs/rgb_17_7_W.tif /inputs/mask_1.tif
-      - name: Output folder contents
-        run: echo "Outputs folder" && ls -l ./outputs
-      - name: Check outputs
-        run: |
-             cat outputs/canopycover.csv
-             chmod +x "./.github/workflows/docker_test_check_rgb.sh"
-             "./.github/workflows/docker_test_check_rgb.sh"
-
-  artifact_cleanup:
-    runs-on: ubuntu-latest
-    needs: [docker_testing]
-    name: Cleanup artifacts upon success
-    steps:
-      - name: Remove docker artifact
-        uses: geekyeggo/delete-artifact@v1
-        with:
-          name: canopycover_test_image

From 8db7e09e040f4f1539c72490e9e217d8f52f369b Mon Sep 17 00:00:00 2001
From: Chris Schnaufer <schnaufer@email.arizona.edu>
Date: Mon, 1 Mar 2021 13:00:33 -0700
Subject: [PATCH 2/3] Fixing wrong repo changes

---
 .github/workflows/docker_test_check_rgb.sh | 67 +++++++++++++++++++++
 .github/workflows/testing_docker.yaml      | 69 ++++++++++++++++++++++
 2 files changed, 136 insertions(+)
 create mode 100755 .github/workflows/docker_test_check_rgb.sh
 create mode 100644 .github/workflows/testing_docker.yaml

diff --git a/.github/workflows/docker_test_check_rgb.sh b/.github/workflows/docker_test_check_rgb.sh
new file mode 100755
index 0000000..ebeabc3
--- /dev/null
+++ b/.github/workflows/docker_test_check_rgb.sh
@@ -0,0 +1,67 @@
+#!/usr/bin/env bash
+
+# Checking the results of running the docker commands
+
+# Define expected results
+EXPECTED_FILES=("result.json")
+EXPECTED_CANOPYCOVER_VALUES=(99.8 20.9)
+
+# What folder are we looking in for outputs
+if [[ ! "${1}" == "" ]]; then
+  TARGET_FOLDER="${1}"
+else
+  TARGET_FOLDER="./outputs"
+fi
+
+# What our target file to read is
+if [[ ! "${2}" == "" ]]; then
+  CHECK_FILE="${2}"
+else
+  CHECK_FILE="canopycover.csv"
+fi
+EXPECTED_FILES+=("${CHECK_FILE}")
+
+# Check if expected files are found
+for i in $(seq 0 $(( ${#EXPECTED_FILES[@]} - 1 )))
+do
+  if [[ ! -f "${TARGET_FOLDER}/${EXPECTED_FILES[$i]}" ]]; then
+    echo "Expected file ${EXPECTED_FILES[$i]} is missing"
+    exit 10
+  fi
+done
+
+# Check the results of the canopy cover calculation
+RESULT_VALUES=(`gawk '
+BEGIN {
+    FPAT = "([^,]+)|(\"[^\"]+\")"
+}
+{
+  if ($1 != "local_datetime") { # Skipping the header line
+    printf("%s\n", $2)
+  }
+}
+END {
+}
+' "${TARGET_FOLDER}/${CHECK_FILE}"`)
+
+echo "Result counts: ${#EXPECTED_CANOPYCOVER_VALUES[@]} vs ${#RESULT_VALUES[@]}"
+if [[ ${#EXPECTED_CANOPYCOVER_VALUES[@]} != ${#RESULT_VALUES[@]} ]]; then
+  echo "Number of results found in file (${#RESULT_VALUES[@]}) don't match expected count (${#EXPECTED_CANOPYCOVER_VALUES[@]})"
+  if [[ ${#RESULT_VALUES[@]} > 0 ]]; then
+    for i in $(seq 0 $(( ${#RESULT_VALUES[@]} - 1 )))
+    do
+      echo "${i}: ${RESULT_VALUES[$i]}"
+    done
+  fi
+  exit 20
+fi
+
+for i in $(seq 0 $(( ${#EXPECTED_CANOPYCOVER_VALUES[@]} - 1 )))
+do
+  if [[ "${EXPECTED_CANOPYCOVER_VALUES[$i]}" == "${RESULT_VALUES[$i]}" ]]; then
+    echo "Values for index ${i} match: '${RESULT_VALUES[$i]}' '${EXPECTED_CANOPYCOVER_VALUES[$i]}'"
+  else
+    echo "Result value for index ${i}: '${RESULT_VALUES[$i]}' doesn't match expected: '${EXPECTED_CANOPYCOVER_VALUES[$i]}'"
+    exit 30
+  fi
+done
diff --git a/.github/workflows/testing_docker.yaml b/.github/workflows/testing_docker.yaml
new file mode 100644
index 0000000..0e3c590
--- /dev/null
+++ b/.github/workflows/testing_docker.yaml
@@ -0,0 +1,69 @@
+name: Testing Docker image
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+    tags:
+      - v*
+  schedule:
+    # Every 01:00 Sunday re-run the test on the main branch
+    - cron: '0 1 * * 0'
+  workflow_dispatch:
+
+jobs:
+  docker_testing:
+    runs-on: ubuntu-latest
+    name: Running Docker testing
+    steps:
+      - name: Fetch source code
+        uses: actions/checkout@v2
+      - name: Create folders
+        run: |
+             mkdir ./inputs && chmod 777 ./inputs
+             mkdir ./outputs && chmod 777 ./outputs
+      - name: List folder contents
+        run: |
+             echo "Current folder" && ls -la
+             echo "test_data" && ls -l ./test_data
+      - name: Copy testing data files
+        run: |
+             cp "${PWD}/test_data"/* "${PWD}/inputs/"
+             echo "inputs" && ls -l ./inputs
+      - name: Folder contents
+        run: |
+             echo "Current folder" && ls -l
+             echo "Inputs folder" && ls -l ./inputs
+             echo "Outputs folder" && ls -l ./outputs
+      - name: Build docker image
+        run: docker build -t canopycover_test:latest ./
+      - name: Compress docker image
+        run: docker save canopycover_test:latest | gzip -7 -c - > canopycover_test_image.tar.gz
+      - name: Upload docker image
+        uses: actions/upload-artifact@v2
+        with:
+          name: canopycover_test_image
+          path: canopycover_test_image.tar.gz
+      - name: Run docker test
+        run: docker run --rm -v "${PWD}/inputs:/inputs" -v "${PWD}/outputs:/outputs" canopycover_test:latest --working_space /outputs --metadata /inputs/meta.yaml /inputs/rgb_17_7_W.tif /inputs/mask_1.tif
+      - name: Output folder contents
+        run: echo "Outputs folder" && ls -l ./outputs
+      - name: Check outputs
+        run: |
+             cat outputs/canopycover.csv
+             chmod +x "./.github/workflows/docker_test_check_rgb.sh"
+             "./.github/workflows/docker_test_check_rgb.sh"
+
+  artifact_cleanup:
+    runs-on: ubuntu-latest
+    needs: [docker_testing]
+    name: Cleanup artifacts upon success
+    steps:
+      - name: Remove docker artifact
+        uses: geekyeggo/delete-artifact@v1
+        with:
+          name: canopycover_test_image

From e2de0307d1fd11bc07908c8827a4f1e92020603a Mon Sep 17 00:00:00 2001
From: Chris Schnaufer <schnaufer@email.arizona.edu>
Date: Fri, 19 Mar 2021 12:14:49 -0700
Subject: [PATCH 3/3] Fixing Actions YAML branch names

---
 .github/workflows/testing_checks.yaml | 4 ++--
 .github/workflows/testing_docker.yaml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testing_checks.yaml b/.github/workflows/testing_checks.yaml
index 4bed72f..dd730aa 100644
--- a/.github/workflows/testing_checks.yaml
+++ b/.github/workflows/testing_checks.yaml
@@ -2,11 +2,11 @@ name: Enforcing tests
 on:
   push:
     branches:
-      - master
+      - main
       - develop
   pull_request:
     branches:
-      - master
+      - main
       - develop
     tags:
       - v*
diff --git a/.github/workflows/testing_docker.yaml b/.github/workflows/testing_docker.yaml
index 0e3c590..5df4583 100644
--- a/.github/workflows/testing_docker.yaml
+++ b/.github/workflows/testing_docker.yaml
@@ -2,11 +2,11 @@ name: Testing Docker image
 on:
   push:
     branches:
-      - master
+      - main
       - develop
   pull_request:
     branches:
-      - master
+      - main
       - develop
     tags:
       - v*