Merge pull request #237 from doizuc/dev

Add Application Testing Workflow

Great. Thanks, Nils.

.github/actions/SetupEnvironment/action.yml

@@ -0,0 +1,38 @@
+name: SetupEnvironment
+description: 'Setup python environment with conda'
+
+runs:
+  using: "composite"
+
+  steps:
+    - name: 🐍 Setup Mambaforge
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-version: latest
+#        miniforge-variant: Mambaforge
+#        use-mamba: true  # mambaforge is now deprecated in favor of miniforge
+        activate-environment: hypercp
+
+    - name: 🔂 Cache Environment
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.CONDA }}/envs
+        key:
+          conda-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER }}
+      env:
+        # Increase this value to reset cache if environment.yml has not changed
+        CACHE_NUMBER: 0
+      id: cache
+
+    - name: 🔄 Update Environment
+      if: steps.cache.outputs.cache-hit != 'true'
+      shell: bash -el {0}
+      run: |
+        mamba env update -n hypercp -f environment.yml
+        mamba install --channel=conda-forge pyinstaller==6.6
+
+    - name: 📸 Capture Environment
+      shell: bash -el {0}
+      run: |
+        mamba info
+        mamba list

.github/workflows/ApplicationTesting.yml

@@ -0,0 +1,40 @@
+name: ApplicationTesting
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+  workflow_dispatch:
+
+jobs:
+
+  ApplicationTesting:
+    name: Application Tests
+
+    runs-on: ${{ matrix.os }}
+    defaults: # Required for conda environment activation
+      run:
+        shell: bash -el {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ 'ubuntu-latest', 'macos-latest', 'windows-latest' ]
+
+    steps:
+      - name: ⏬ Checkout repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.inputs.branch }}
+
+      - name: 🔧 Setup Environment
+        uses: ./.github/actions/SetupEnvironment
+
+      - name: 📑 Capture Environment
+        run: |
+          mamba info
+          mamba list
+
+      - name: 🧪 Run Tests
+        run: |
+          python run_Sample_Data.py

.github/workflows/Build.yml

@@ -24,59 +24,28 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
 
     steps:
-      - name: Get Branch Name
-        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
-        id: extract_branch
-
-      - name: Checkout Repository
+      - name: ⏬ Checkout repository
         uses: actions/checkout@v4
         with:
-          ref: ${{ steps.extract_branch.outputs.branch }}
-
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: hypercp
-          use-mamba: true
-
-      - name: Cache Environment
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.CONDA }}/envs
-          key:
-            conda-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER }}
-        env:
-          # Increase this value to reset cache if environment.yml has not changed
-          CACHE_NUMBER: 0
-        id: cache
-
-      - name: Update Environment
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: |
-          mamba env update -n hypercp -f environment.yml
-          mamba install --channel=conda-forge pyinstaller==6.6
+          ref: ${{ github.event.inputs.branch }}
 
-      - name: Capture Environment
-        run: |
-          mamba info
-          mamba list
+      - name: 🔧 Setup Environment
+        uses: ./.github/actions/SetupEnvironment
 
-      - name: Make Bundle
+      - name: 📑 Make Bundle
         run: |
           python make.py
           echo "BUNDLE_NAME=$(ls Bundled/dist | head -1 | xargs)" >> $GITHUB_ENV
 
-      - name: Zip Bundle
+      - name: 📥 Zip Bundle
         uses: thedoctor0/[email protected]
         with:
           type: 'zip'
           directory: 'Bundled/dist/'
           path: '${{ env.BUNDLE_NAME }}'
           filename: '${{ env.BUNDLE_NAME }}.zip'
 
-      - name: Upload Bundle
+      - name: ⏫️ Upload Bundle
         uses: actions/upload-artifact@v4
         with:
           name: ${{ env.BUNDLE_NAME }}

Main.py

@@ -620,7 +620,7 @@ def __init__(
         # Confirm that core data files are in place. Download if necessary.
         fpfZhang = os.path.join(CODE_HOME, "Data", "Zhang_rho_db.mat")
         if not os.path.exists(fpfZhang):
-            Utilities.downloadZhangDB(fpfZhang)
+            Utilities.downloadZhangDB(fpfZhang, force=True)
 
         # Create a default main config to be filled with cmd argument
         # to avoid reading the one generated with the GUI

Source/Utilities.py

@@ -33,11 +33,11 @@ class Utilities:
     """A catchall class for HyperCP utilities"""
 
     @staticmethod
-    def downloadZhangDB(fpfZhang):
+    def downloadZhangDB(fpfZhang, force=False):
         infoText = "  NEW INSTALLATION\nGlint database required.\nClick OK to download.\n\nWARNING: THIS IS A 2.5 GB DOWNLOAD.\n\n\
         If canceled, Zhang et al. (2017) glint correction will fail. If download fails, a link and instructions will be provided in the terminal."
-        YNReply = Utilities.YNWindow("Database Download", infoText)
-        if YNReply == QMessageBox.Ok:
+        YNReply = True if force else Utilities.YNWindow("Database Download", infoText) == QMessageBox.Ok
+        if YNReply:
 
             url = "https://oceancolor.gsfc.nasa.gov/fileshare/dirk_aurin/Zhang_rho_db.mat"
             download_session = requests.Session()
@@ -283,6 +283,10 @@ def YNWindow(winText,infoText):
 
     @staticmethod
     def writeLogFile(logText, mode='a'):
+        if not os.path.exists('Logs'):
+            import logging
+            logging.getLogger().warning('Made directory: Logs/')
+            os.mkdir('Logs')
         with open('Logs/' + os.environ["LOGFILE"], mode, encoding="utf-8") as logFile:
             logFile.write(logText + "\n")
 

run_Sample_Data.py

@@ -29,8 +29,8 @@
 
 ################################################### CUSTOM SET UP ###################################################
 # Batch options
-MULTI_TASK = True   # Multiple threads for HyperSAS (any level) or TriOS (only L1A and up)
-MULTI_LEVEL = False  # Process raw (L0) to Level-2 (L2)
+MULTI_TASK = False  # Multiple threads for HyperSAS (any level) or TriOS (only L1A and up)
+MULTI_LEVEL = True  # Process raw (L0) to Level-2 (L2)
 CLOBBER = True      # True overwrites existing files
 PROC_LEVEL = "L2"   # Process to this level: L1A, L1AQC, L1B, LBQC, L2 (ignored for MULTI_LEVEL)
 
@@ -51,8 +51,7 @@
 
 #################################
 ## PATH options
-PATH_OS = os.path.expanduser("~")
-PATH_HCP = os.path.join(PATH_OS,'GitRepos','HyperCP')  # Local path to HyperCP repository.
+PATH_HCP = os.path.dirname(os.path.abspath(__file__))  # Path to HyperCP repository on host
 # PATH_DATA = f"{PATH_OS}/Projects/HyperPACE/field_data/HyperSAS/{CRUISE}"  # Top level data directory containing RAW/ and ancillary file.
 PATH_DATA = os.path.join(PATH_HCP,'Data','Sample_Data',PLATFORM)
 ##################################