Merge branch 'main' into fix_extrapolate_water

noaa-ocs-modeling · Aug 13, 2024 · f66f9c4 · f66f9c4
2 parents 12fa952 + 2cd962e
commit f66f9c4
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Showing 79 changed files with 1,610 additions and 952 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: install Poetry
-        uses: abatilo/actions-poetry@v2.1.3
+        uses: abatilo/actions-poetry@v3
       - name: install Dunamai
         run: pip install dunamai
       - name: extract version from VCS

diff --git a/.github/workflows/quick_test.yml b/.github/workflows/quick_test.yml
@@ -15,12 +15,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: clone repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: install Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
       - name: load cached Python installation
         id: cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
@@ -40,19 +42,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: clone repository
-        uses: actions/checkout@v2
-      - name: install Python
-        uses: actions/setup-python@v2
-        # due to coupledmodeldriver dependency python 3.10 cannot be supported
-        with:
-          python-version: 3.9
-      - name: load cached Python installation
-        id: cache
-        uses: actions/cache@v2
+        uses: actions/checkout@v4
+      - name: conda virtual environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          path: ${{ env.pythonLocation }}
-          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+          init-shell: bash
+          environment-name: ci-env
+          create-args: >-
+            python=3.9
+            libnetcdf
+            hdf5
+            udunits2
       - name: install dependencies
         run: pip install ".[testing]"
+        shell: micromamba-shell {0}
+      - name: rebuild netcdf from source
+        run: pip install --upgrade --force-reinstall --no-deps --no-cache-dir netcdf4 --no-binary netcdf4
+        shell: micromamba-shell {0}
       - name: run tests
         run: pytest --numprocesses auto
+        shell: micromamba-shell {0}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -18,12 +18,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: clone repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: install Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
       - name: load cached Python installation
         id: cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
@@ -44,51 +46,60 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest, macos-latest ]
-        # due to coupledmodeldriver dependency python 3.10 cannot be supported
-        python-version: [ '3.8', '3.9' ]
+        python-version: [ '3.9', '3.10', '3.11' ]
     steps:
       - name: clone repository
-        uses: actions/checkout@v2
-      - name: install Python
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v4
+      - name: conda virtual environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: load cached Python installation
-        id: cache
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.pythonLocation }}
-          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+          init-shell: bash
+          environment-name: ci-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+            libnetcdf
+            hdf5
+            udunits2
       - name: install dependencies
         run: pip install ".[testing]"
+        shell: micromamba-shell {0}
+      - name: rebuild netcdf from source
+        run: pip install --upgrade --force-reinstall --no-deps --no-cache-dir netcdf4 --no-binary netcdf4
+        shell: micromamba-shell {0}
       - name: run tests
         run: pytest --numprocesses auto
+        shell: micromamba-shell {0}
   test_with_coverage:
     needs: [ lint, test ]
     name: test with coverage
     runs-on: ubuntu-latest
     steps:
       - name: clone repository
-        uses: actions/checkout@v2
-      - name: install Python
-        uses: actions/setup-python@v2
-        # due to coupledmodeldriver dependency python 3.10 cannot be supported
-        with:
-          python-version: 3.9
-      - name: load cached Python installation
-        id: cache
-        uses: actions/cache@v2
+        uses: actions/checkout@v4
+      - name: conda virtual environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          path: ${{ env.pythonLocation }}
-          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+          init-shell: bash
+          environment-name: ci-env
+          create-args: >-
+            python=3.9
+            libnetcdf
+            hdf5
+            udunits2
       - name: install dependencies
         run: pip install ".[testing]"
+        shell: micromamba-shell {0}
+      - name: rebuild netcdf from source
+        run: pip install --upgrade --force-reinstall --no-deps --no-cache-dir netcdf4 --no-binary netcdf4
+        shell: micromamba-shell {0}
       - name: run tests with coverage
         run: pytest --numprocesses auto --cov . --cov-report xml:coverage.xml
+        shell: micromamba-shell {0}
       - name: show coverage report
         run: coverage report
+        shell: micromamba-shell {0}
       - name: upload coverage to Codecov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: coverage.xml

diff --git a/ensembleperturbation/client/perturb_tracks.py b/ensembleperturbation/client/perturb_tracks.py
@@ -106,7 +106,7 @@ def main():
     else:
         for forcing in arguments['forcings']:
             if isinstance(forcing, BestTrackForcingJSON):
-                storm = forcing.adcircpy_forcing.nhc_code
+                storm = forcing.pyschism_forcing.nhc_code
                 break
         else:
             raise ValueError('no best track forcing specified')

diff --git a/ensembleperturbation/client/plot_results.py b/ensembleperturbation/client/plot_results.py
@@ -6,7 +6,6 @@
 from matplotlib import pyplot
 import pandas
 from pandas import DataFrame
-import tables
 
 
 def main():
@@ -23,8 +22,6 @@ def main():
     )
     output_dataframe: DataFrame = pandas.read_hdf(combined_results_filename, key='zeta_max')
 
-    combined_results = tables.open_file(combined_results_filename)
-
     # just get standard deviation of the outputs
     output_standard_deviation = output_dataframe.std(axis=1, skipna=True)
 

diff --git a/ensembleperturbation/parsing/adcirc.py b/ensembleperturbation/parsing/adcirc.py
@@ -758,6 +758,20 @@ def combine_outputs(
                 if elevation_selection is not None:
                     elevation_subset = subset
 
+                if 'element' in file_data:
+                    # keep only elements where all nodes are present
+                    elements = file_data['element'].values
+                    element_mask = numpy.isin(elements, file_data['node'].values).all(axis=1)
+                    elements = elements[element_mask]
+                    # map nodes in element table to local numbering system (start at 0)
+                    node_mapper = numpy.zeros(file_data['node'].max().values + 1, dtype=int)
+                    node_index = numpy.arange(len(file_data['node']))
+                    node_mapper[file_data['node'].values] = node_index
+                    elements = node_mapper[elements]
+                    # update element table in dataset
+                    ele_da = DataArray(data=elements, dims=['nele', 'nvertex'])
+                    file_data = file_data.drop('element').assign_coords({'element': ele_da})
+
             output_data[basename] = file_data
 
     for basename, file_data in output_data.items():
@@ -832,7 +846,7 @@ def subset_dataset(
             elements = node_mapper[elements]
             # update element table in dataset
             ele_da = DataArray(data=elements, dims=['nele', 'nvertex'])
-            subset = subset.assign_coords({'element': ele_da})
+            subset = subset.drop('element').assign_coords({'element': ele_da})
         try:
             subset = subset.drop_sel(run='original')
         except: