Merge pull request #53 from USEPA/new_release_0-3-8

New release 0 3 8

.github/workflows/documentation_test.yml

@@ -4,6 +4,9 @@ on:
   pull_request:
     branches:
       [main]
+  push:
+    branches:
+      [main, dev]
 
 # Allows you to run this workflow manually from the Actions tab
 #workflow_dispatch:
@@ -20,16 +23,20 @@ jobs:
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v2
+      - uses: r-lib/actions/setup-pandoc@v2
       - uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
       - name: Install dependencies
         run: |
           pip install -r requirements.txt
-          pip install sphinx sphinx_rtd_theme
+          pip install -r requirements_dev.txt
       - name: Sphinx build
         run: |
           #sphinx-build docs/source _build
           cd docs
           make html
+          make doctest
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1
         with:

.github/workflows/test.yml

@@ -18,11 +18,11 @@ jobs:
       REPO_NAME: ${{ github.event.repository.name }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
-        include:
-          - os: windows-latest
-            python-version: "3.9"
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        #exclude:
+        #  - os: windows-latest
+        #    python-version: "3.7"
 
     steps:
       - uses: actions/checkout@v3
@@ -37,13 +37,32 @@ jobs:
           python -VV
           python -m pip install --upgrade pip
           pip install pytest
+
+      #Dropped win3.7
+      #pip install pipwin
+      #pipwin install gdal
+      #pipwin install fiona
 
-      # fiona doesn't have wheels for windows
-      - if: matrix.os == 'windows-latest'
+      - if: ${{ (matrix.os == 'windows-latest') && (matrix.python-version == 3.8) }}
+        run: |
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.1.10.1/GDAL-3.6.2-cp38-cp38-win_amd64.whl
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.1.10.1/Fiona-1.8.22-cp38-cp38-win_amd64.whl
+          
+      - if: ${{ (matrix.os == 'windows-latest') && (matrix.python-version == 3.9) }}
         run: |
           pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/GDAL-3.7.1-cp39-cp39-win_amd64.whl
           pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/Fiona-1.9.4.post1-cp39-cp39-win_amd64.whl
       
+      - if: ${{ (matrix.os == 'windows-latest') && (matrix.python-version == 3.10) }}
+        run: |
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/GDAL-3.7.1-cp310-cp310-win_amd64.whl
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/Fiona-1.9.4.post1-cp310-cp310-win_amd64.whl    
+      
+      - if: ${{ (matrix.os == 'windows-latest') && (matrix.python-version == 3.11) }}
+        run: |
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/GDAL-3.7.1-cp311-cp311-win_amd64.whl
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/Fiona-1.9.4.post1-cp311-cp311-win_amd64.whl    
+      
       - name: Install package and dependencies
         run: |
           python -m pip install --no-deps .

.github/workflows/test_r.yaml

@@ -0,0 +1,68 @@
+name: R-test
+
+on:
+  push:
+    branches:
+      [main, dev]
+  pull_request:
+    branches:
+      [main]
+  schedule:
+    - cron: '11 1 1 * *'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  R-test:
+    name: python ${{ matrix.python-version }}, ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    env:
+      REPO_NAME: ${{ github.event.repository.name }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        include:
+          - os: windows-latest
+            python-version: "3.9"
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Update pip and install testing pkgs
+        run: |
+          python -VV
+          python -m pip install --upgrade pip
+          pip install pytest
+      
+      # fiona doesn't have wheels for windows
+      - if: matrix.os == 'windows-latest'
+        run: |
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/GDAL-3.7.1-cp39-cp39-win_amd64.whl
+          pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/Fiona-1.9.4.post1-cp39-cp39-win_amd64.whl
+      
+      - name: Install package and dependencies
+        run: |
+          python -m pip install --no-deps .
+          pip install -r requirements.txt
+      
+      - name: Run pip env using R reticulate
+        run: |
+          install.packages("reticulate")
+          reticulate::import("harmonize_wq")
+        shell: Rscript {0}
+
+      - name: Run pytest
+        run: pytest -v harmonize_wq

README.md

@@ -1,5 +1,5 @@
 # harmonize-wq
-Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats
+Standardize, clean, and wrangle Water Quality Portal data into more analytic-ready formats
 
 US EPA’s [Water Quality Portal (WQP)](https://www.waterqualitydata.us/) aggregates water quality, biological, and physical data provided by many organizations and has become an essential resource with tools to query and retrieval data using [python](https://github.com/USGS-python/dataretrieval) or [R](https://github.com/USGS-R/dataRetrieval). Given the variety of data and variety of data originators, using the data in analysis often requires data cleaning to ensure it meets the required quality standards and data wrangling to get it in a more analytic-ready format.  Recognizing the definition of analysis-ready varies depending on the analysis, the harmonixe_wq package is intended to be a flexible water quality specific framework to help:
 - Identify differences in data units (including speciation and basis)