Merge pull request #272 from EC-USGS/v1.0.0

Release 1.0.0
EC-USGS · Dec 18, 2023 · f773869 · f773869
2 parents 8503ca7 + f883c8d
commit f773869
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diff --git a/.flake8 b/.flake8
@@ -5,44 +5,10 @@ exclude =
     build
     dist
     examples
-    # autotest
 ignore =
     # https://flake8.pycqa.org/en/latest/user/error-codes.html
-    # F401 # 'module' imported but unused
-    # https://pycodestyle.readthedocs.io/en/latest/intro.html#error-codes
-    # continuation line under-indented for hanging indent
-    E121,
-    # continuation line missing indentation or outdented
-    E122,
-    # continuation line over-indented for hanging indent
-    E126,
-    # continuation line over-indented for visual indent
-    E127,
-    # continuation line under-indented for visual indent
-    E128,
-    # whitespace before
-    E203,
-    # multiple spaces before operator
-    E221,
-    # multiple spaces after operator
-    E222,
-    # missing whitespace around arithmetic operator
-    E226,
-    # E231 # missing whitespace after ','
-    # E241 # multiple spaces after ','
-    # E402 # module level import not at top of file
-    # E501 # line too long (> 79 characters)
-    # E502 # backslash is redundant between brackets
-    # E722 # do not use bare 'except'
-    # ambiguous variable name
-    E741,
-    # W291 # trailing whitespace
-    # W292 # no newline at end of file
-    #     W293 # blank line contains whitespace
-    # blank line at end of file
-    W391,
     # line break before binary operator
     W503,
-    # line break after binary operator
-    W504,
+    # space before colon
+    E203,
 statistics = True
diff --git a/.github/scripts/symlink_gfortran_mac.sh b/.github/scripts/symlink_gfortran_mac.sh
@@ -2,7 +2,7 @@
 
 # get full gfortran version string
 # assumes installed via brew as by
-# https://github.com/awvwgk/setup-fortran
+# https://github.com/fortran-lang/setup-fortran
 #
 # sed not head for first line, avoid ruby broken pipe issues
 # (https://stackoverflow.com/a/2845541/6514033)

diff --git a/.github/scripts/update_version.py b/.github/scripts/update_version.py
@@ -29,7 +29,11 @@ def get_authors():
 
 
 def update_version_py(timestamp: datetime, version: Version):
-    lines = open(_version_py_path, "r").readlines() if _version_py_path.exists() else []
+    lines = (
+        open(_version_py_path, "r").readlines()
+        if _version_py_path.exists()
+        else []
+    )
     authors = get_authors()
     with open(_version_py_path, "w") as f:
         f.write(
@@ -39,13 +43,18 @@ def update_version_py(timestamp: datetime, version: Version):
         f.write(f'__version__ = "{version}"\n')
         f.writelines(
             [
-                f"__pakname__ = \"{_project_name}\"\n",
+                f'__pakname__ = "{_project_name}"\n',
                 "\n",
                 "author_dict = {\n",
-            ] + [f"    \"{a['given-names']} {a['family-names']}\": \"{a['email']}\",\n" for a in authors] + [
+            ]
+            + [
+                f"    \"{a['given-names']} {a['family-names']}\": \"{a['email']}\",\n"
+                for a in authors
+            ]
+            + [
                 "}\n",
-                "__author__ = \", \".join(author_dict.keys())\n",
-                "__author_email__ = \", \".join(s for _, s in author_dict.items())\n",
+                '__author__ = ", ".join(author_dict.keys())\n',
+                '__author_email__ = ", ".join(s for _, s in author_dict.items())\n',
             ]
         )
         f.close()

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -9,6 +9,14 @@ on:
       - "*"
       - "!v[0-9]+.[0-9]+.[0-9]+*"
 
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        type: boolean
+        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+        required: false
+        default: false
+
 jobs:
 
   pyws_setup:
@@ -101,7 +109,7 @@ jobs:
           pylint --jobs=2 --errors-only --exit-zero ./pywatershed ./autotest
 
   test:
-    name: ${{ matrix.os}} py${{ matrix.python-version }}
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -112,9 +120,14 @@ jobs:
         os: [ "ubuntu-latest", "macos-latest", "windows-latest" ]
         python-version: ["3.9", "3.10"]
     steps:
+
       - name: Checkout repo
         uses: actions/checkout@v3
 
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
@@ -134,11 +147,11 @@ jobs:
           if [[ "$MF6_REMOTE" != "$req_remote" ]]; then exit 1; fi
 
       - name: Setup gfortran
-        uses: awvwgk/setup-fortran@main
+        uses: fortran-lang/setup-fortran@v1
         with:
           compiler: gcc
           version: 11
-      
+
       - name: Link gfortran dylibs on Mac
         if: runner.os == 'macOS'
         run: .github/scripts/symlink_gfortran_mac.sh
@@ -174,39 +187,87 @@ jobs:
           pip -V
           pip list
 
-      - name: Run available domains with PRMS and convert csv output to NetCDF
-        working-directory: test_data/scripts
+      - name: hru_1 - generate and manage test data domain, run PRMS and convert csv output to NetCDF
+        working-directory: autotest
+        run: |
+          python generate_test_data.py \
+            -n=auto --domain=hru_1 --remove_prms_csvs --remove_prms_output_dirs
+
+      - name: hru_1 - list netcdf input files
+        working-directory: test_data
+        run: |
+          find hru_1/output/ -name '*.nc'
+
+      - name: hru_1 - pywatershed tests
+        working-directory: autotest
+        run: pytest
+          -vv
+          -n=auto
+          --domain_yaml=../test_data/hru_1/hru_1.yaml
+          --durations=0
+          --cov=pywatershed
+          --cov-report=xml
+          --junitxml=pytest_hru_1.xml
+
+
+      - name: drb_2yr - generate and manage test data
+        working-directory: autotest
+        run: |
+          python generate_test_data.py \
+            -n=auto --domain=drb_2yr --remove_prms_csvs --remove_prms_output_dirs
+
+      - name: drb_2yr - list netcdf input files
+        working-directory: test_data
+        run: |
+          find drb_2yr/output/ -name '*.nc'
+
+      - name: drb_2yr - pywatershed tests
+        working-directory: autotest
+        run: pytest
+          -vv
+          -n=auto
+          --domain_yaml=../test_data/drb_2yr/drb_2yr.yaml
+          --durations=0
+          --cov=pywatershed
+          --cov-report=xml
+          --junitxml=pytest_drb_2yr.xml
+
+      - name: ucb_2yr - generate and manage test data
+        working-directory: autotest
         run: |
-          pytest -v -n=auto --durations=0 test_run_domains.py
-          pytest -v -n=auto --durations=0 test_nc_domains.py
+          python generate_test_data.py \
+            -n=auto --domain=ucb_2yr --remove_prms_csvs --remove_prms_output_dirs
 
-      - name: List all NetCDF files in test_data directory
+      - name: ucb_2yr - list netcdf input files
         working-directory: test_data
         run: |
-          find . -name "*.nc"
+          find ucb_2yr/output/ -name '*.nc'
 
-      - name: Run tests
+      - name: ucb_2yr - pywatershed tests
         working-directory: autotest
         run: pytest
-          -v
+          -vv
           -n=auto
+          --domain_yaml=../test_data/ucb_2yr/ucb_2yr.yaml
           --durations=0
-          --all_domains
           --cov=pywatershed
           --cov-report=xml
-          --junitxml=pytest.xml
+          --junitxml=pytest_ucb_2yr.xml
 
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: Test results for ${{ runner.os }}-${{ matrix.python-version }}
-          path: ./autotest/pytest.xml
+          path: |
+            ./autotest/pytest_hru_1.xml
+            ./autotest/pytest_drb_2yr.xml
+            ./autotest/pytest_ucb_2yr.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3
         with:
-          file: ./autotest/coverage.xml
+          file: ./autotest/coverage.xml  # should be just the ucb result
           # flags: unittests
           env_vars: RUNNER_OS,PYTHON_VERSION
           # name: codecov-umbrella

diff --git a/.github/workflows/ci_examples.yaml b/.github/workflows/ci_examples.yaml
@@ -31,8 +31,11 @@ jobs:
       - name: Checkout repo
         uses: actions/[email protected]
 
-      - name: Install gfortran
-        uses: modflowpy/install-gfortran-action@v1
+      - name: Setup gfortran
+        uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: gcc
+          version: 11
 
       - name: Download GIS files
         working-directory: examples

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -25,28 +25,41 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Setup gfortran
+        uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: gcc
+          version: 11
+
       - name: Install Dependencies via Micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment.yml
           cache-environment: true
           cache-downloads: true
           create-args: >-
-            python=3.9
+            python=3.10
             conda
       
       - name: Checkout MODFLOW 6
         uses: actions/checkout@v3
         with:
           repository: MODFLOW-USGS/modflow6
-          ref: master
+          ref: develop
           path: modflow6
 
       - name: Update flopy MODFLOW 6 classes
         working-directory: modflow6/autotest
         run: |
           python update_flopy.py
 
+      - name: Set environment variables
+        run: |
+          echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
+          echo "PYWS_FORTRAN=true" >> $GITHUB_ENV
+          echo 'SETUPTOOLS_ENABLE_FEATURES="legacy-editable"' >> $GITHUB_ENV
+          cat .mf6_ci_ref_remote  >> $GITHUB_ENV
+          
       - name: Install pywatershed
         run: |
           pip install .
@@ -56,27 +69,72 @@ jobs:
           pip -V
           pip list
 
-      - name: Run available domains with PRMS and convert csv output to NetCDF
-        working-directory: test_data/scripts
+      - name: hru_1 - generate and manage test data domain, run PRMS and convert csv output to NetCDF
+        working-directory: autotest
+        run: |
+          python generate_test_data.py \
+            -n=auto --domain=hru_1 --remove_prms_csvs --remove_prms_output_dirs
+
+      - name: hru_1 - list netcdf input files
+        working-directory: test_data
+        run: |
+          find hru_1/output/ -name '*.nc'
+
+      - name: hru_1 - pywatershed tests
+        working-directory: autotest
+        run: pytest
+          -vv
+          -n=auto
+          --domain_yaml=../test_data/hru_1/hru_1.yaml
+          --durations=0
+          --cov=pywatershed
+          --cov-report=xml
+          --junitxml=pytest_hru_1.xml
+
+
+      - name: drb_2yr - generate and manage test data
+        working-directory: autotest
+        run: |
+          python generate_test_data.py \
+            -n=auto --domain=drb_2yr --remove_prms_csvs --remove_prms_output_dirs
+
+      - name: drb_2yr - list netcdf input files
+        working-directory: test_data
+        run: |
+          find drb_2yr/output/ -name '*.nc'
+
+      - name: drb_2yr - pywatershed tests
+        working-directory: autotest
+        run: pytest
+          -vv
+          -n=auto
+          --domain_yaml=../test_data/drb_2yr/drb_2yr.yaml
+          --durations=0
+          --cov=pywatershed
+          --cov-report=xml
+          --junitxml=pytest_drb_2yr.xml
+
+      - name: ucb_2yr - generate and manage test data
+        working-directory: autotest
         run: |
-          pytest -v -n=auto --durations=0 test_run_domains.py
-          pytest -v -n=auto --durations=0 test_nc_domains.py
+          python generate_test_data.py \
+            -n=auto --domain=ucb_2yr --remove_prms_csvs --remove_prms_output_dirs
 
-      - name: List all NetCDF files in test_data directory
+      - name: ucb_2yr - list netcdf input files
         working-directory: test_data
         run: |
-          find . -name "*.nc"
+          find ucb_2yr/output/ -name '*.nc'
 
-      - name: Run tests
+      - name: ucb_2yr - pywatershed tests
         working-directory: autotest
         run: pytest
-          -v
+          -vv
           -n=auto
+          --domain_yaml=../test_data/ucb_2yr/ucb_2yr.yaml
           --durations=0
-          --all_domains
           --cov=pywatershed
           --cov-report=xml
-          --junitxml=pytest.xml
+          --junitxml=pytest_ucb_2yr.xml
 
       - name: Update version
         id: version