Merge branch 'main' of https://github.com/USEPA/WNTR into swntr

.github/workflows/build_tests.yml

@@ -21,9 +21,9 @@ jobs:
         os: [windows-latest, macOS-13, ubuntu-latest]
       fail-fast: false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -37,7 +37,7 @@ jobs:
         python setup.py bdist_wheel
         ls dist/*
     - name: Save wheel
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: wntr_${{ matrix.python-version }}_${{ matrix.os }}.whl
         path: dist/wntr*
@@ -52,11 +52,11 @@ jobs:
       fail-fast: false
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Download wheel
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: wntr_${{ matrix.python-version }}_${{ matrix.os }}.whl
     - name: Install wntr
@@ -76,9 +76,9 @@ jobs:
         os: [windows-latest, macOS-13, ubuntu-latest]
       fail-fast: false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -94,33 +94,35 @@ jobs:
         coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=wntr --omit="*/tests/*","*/sim/network_isolation/network_isolation.py","*/sim/aml/evaluator.py" --append -m pytest --doctest-glob="*.rst" documentation
       env:
         COVERAGE_FILE: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
-
     - name: Save coverage
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: coverage
+        name: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
         path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
+        include-hidden-files: true
 
   combine_reports:
     needs: [ pytest_coverage ]
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.11
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Install coverage
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
         python -m pip install -e .
-    # pip install coveralls
+        pip install coveralls
     - name: Download coverage artifacts from test matrix
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
-        name: coverage
+        pattern: .coverage.*.ubuntu-latest # coverage from other OS cause problems
     - name: Setup coverage and combine reports
+      run: coverage combine .coverage.*.ubuntu-latest
+    - name: Create coverage report
       run: |
         echo "[paths]" > .coveragerc
         echo "source = " >> .coveragerc
@@ -129,55 +131,21 @@ jobs:
         echo "    D:\\a\\WNTR\\WNTR\\wntr" >> .coveragerc
         echo "    /home/runner/work/WNTR/WNTR/wntr" >> .coveragerc
         echo "    /Users/runner/work/WNTR/WNTR/wntr" >> .coveragerc
-        coverage combine
-    - name: Create coverage report
-      run: |
+        echo "    ${{ github.workspace }}/wntr" >> .coveragerc
         coverage report
         coverage json --pretty-print
         coverage html --show-contexts
     - name: Save coverage JSON
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: coverage
+        name: coverage-json
         path: coverage.json
     - name: Save coverage html
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: coverage
+        name: coverage-html
         path: htmlcov
-
-  combine_reports_upload_coveralls:
-    needs: [ pytest_coverage ]
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-    - name: Set up Python 
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.11
-    - uses: actions/checkout@v2
-    - name: Install coverage
-      run: |
-        python -m pip install --upgrade pip
-        pip install coveralls
-        pip install -r requirements.txt
-        python -m pip install -e .
-    - name: Download coverage artifacts from test matrix
-      uses: actions/download-artifact@v2
-      with:
-        name: coverage
-    - name: Setup coverage and combine reports
-      run: |
-        echo "[paths]" > .coveragerc
-        echo "source = " >> .coveragerc
-        echo "    wntr/" >> .coveragerc
-        echo "    wntr\\" >> .coveragerc
-        echo "    D:\\a\\WNTR\\WNTR\\wntr" >> .coveragerc
-        echo "    /home/runner/work/WNTR/WNTR/wntr" >> .coveragerc
-        echo "    /Users/runner/work/WNTR/WNTR/wntr" >> .coveragerc
-        coverage combine
     - name: Push to coveralls
-      run: |
-        coveralls --service=github
+      run: coveralls --service=github --rcfile=.coveragerc
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -10,48 +10,72 @@ on:
 jobs:
 
   wheels:
+    name: Build distribution 📦 on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-2019, macOS-13, ubuntu-20.04] 
+        os: [windows-latest, macOS-13, macos-13, ubuntu-latest] 
     steps:
-    - uses: actions/checkout@v3
+    - name: Harden Runner
+      uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
+      with:
+        egress-policy: audit
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
     - name: Build wheels
-      uses: pypa/cibuildwheel@v2.11.1
+      uses: pypa/cibuildwheel@79b0dd328794e1180a7268444d46cdf12e1abd01 # v2.21.0
       env:
         CIBW_ENVIRONMENT: BUILD_WNTR_EXTENSIONS='true'
-        CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-*
+        CIBW_BUILD: cp38-* cp39-* cp310-* cp311-* cp312-*
         CIBW_SKIP: "*-win32 *-manylinux_i686 pp* *-musllinux*"
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
       with:
+        name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
         path: ./wheelhouse/*.whl
 
   source:
+    name: Make SDist artifact 📦
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - name: Harden Runner
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
-      - name: build the sdist
-        run: |
-          python -m pip install --upgrade build
-          python -m build --sdist
-      - uses: actions/upload-artifact@v3
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
         with:
+          name: cibw-sdist
           path: dist/*.tar.gz
 
   publish-to-pypi:
+    name: Publish Python 🐍 distribution 📦 to PyPI
     needs: [wheels, source]
     runs-on: ubuntu-latest
+    environment:
+      name: release
+    permissions:
+      id-token: write
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     steps:
-      - uses: actions/download-artifact@v3
+      - name: Harden Runner
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
+        with:
+          egress-policy: audit
+
+      - uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         with:
-          name: artifact
+          pattern: cibw-*
           path: dist
+          merge-multiple: true
 
-      - uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: pypa/gh-action-pypi-publish@0ab0b79471669eb3a4d647e625009c62f9f3b241 # release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_WNTR_API_TOKEN }}

documentation/gis.rst

@@ -114,12 +114,13 @@ For example, the junctions GeoDataFrame contains the following information:
     :skipif: gpd is None
 
     >>> print(wn_gis.junctions.head())
-       node_type  elevation  initial_quality                   geometry
-    10  Junction    216.408        5.000e-04  POINT (20.00000 70.00000)
-    11  Junction    216.408        5.000e-04  POINT (30.00000 70.00000)
-    12  Junction    213.360        5.000e-04  POINT (50.00000 70.00000)
-    13  Junction    211.836        5.000e-04  POINT (70.00000 70.00000)
-    21  Junction    213.360        5.000e-04  POINT (30.00000 40.00000)
+         node_type  elevation  initial_quality                   geometry
+    name                                                                 
+    10    Junction    216.408        5.000e-04  POINT (20.00000 70.00000)
+    11    Junction    216.408        5.000e-04  POINT (30.00000 70.00000)
+    12    Junction    213.360        5.000e-04  POINT (50.00000 70.00000)
+    13    Junction    211.836        5.000e-04  POINT (70.00000 70.00000)
+    21    Junction    213.360        5.000e-04  POINT (30.00000 40.00000)
 
 Each GeoDataFrame contains attributes and geometry:
 
@@ -335,21 +336,23 @@ and then translates the GeoDataFrames coordinates to EPSG:3857.
 
     >>> wn_gis = wntr.network.to_gis(wn, crs='EPSG:4326')
     >>> print(wn_gis.junctions.head())
-       node_type  elevation  initial_quality                   geometry
-    10  Junction    216.408        5.000e-04  POINT (20.00000 70.00000)
-    11  Junction    216.408        5.000e-04  POINT (30.00000 70.00000)
-    12  Junction    213.360        5.000e-04  POINT (50.00000 70.00000)
-    13  Junction    211.836        5.000e-04  POINT (70.00000 70.00000)
-    21  Junction    213.360        5.000e-04  POINT (30.00000 40.00000)
-
+         node_type  elevation  initial_quality                   geometry
+    name                                                                 
+    10    Junction    216.408        5.000e-04  POINT (20.00000 70.00000)
+    11    Junction    216.408        5.000e-04  POINT (30.00000 70.00000)
+    12    Junction    213.360        5.000e-04  POINT (50.00000 70.00000)
+    13    Junction    211.836        5.000e-04  POINT (70.00000 70.00000)
+    21    Junction    213.360        5.000e-04  POINT (30.00000 40.00000)
+
     >>> wn_gis.to_crs('EPSG:3857')
     >>> print(wn_gis.junctions.head())
-       node_type  elevation  initial_quality                          geometry
-    10  Junction    216.408        5.000e-04  POINT (2226389.816 11068715.659)
-    11  Junction    216.408        5.000e-04  POINT (3339584.724 11068715.659)
-    12  Junction    213.360        5.000e-04  POINT (5565974.540 11068715.659)
-    13  Junction    211.836        5.000e-04  POINT (7792364.356 11068715.659)
-    21  Junction    213.360        5.000e-04   POINT (3339584.724 4865942.280)
+         node_type  elevation  initial_quality                          geometry
+    name                                                                        
+    10    Junction    216.408        5.000e-04  POINT (2226389.816 11068715.659)
+    11    Junction    216.408        5.000e-04  POINT (3339584.724 11068715.659)
+    12    Junction    213.360        5.000e-04  POINT (5565974.540 11068715.659)
+    13    Junction    211.836        5.000e-04  POINT (7792364.356 11068715.659)
+    21    Junction    213.360        5.000e-04   POINT (3339584.724 4865942.280)
 
 Snap point geometries to the nearest point or line
 ----------------------------------------------------

requirements.txt

@@ -12,6 +12,7 @@ folium
 utm
 openpyxl
 geopandas<1.0
+fiona<1.10
 rtree
 pyswmm
 swmmio

wntr/gis/geospatial.py

@@ -64,8 +64,7 @@ def snap(A, B, tolerance):
     assert A.crs == B.crs
 
     # Modify B to include "indexB" as a separate column
-    B = B.reset_index()
-    B.rename(columns={'index':'indexB'}, inplace=True)
+    B = B.reset_index(names='indexB')
 
     # Define the coordinate reference system, based on B
     crs = B.crs
@@ -228,7 +227,7 @@ def intersect(A, B, B_value=None, include_background=False, background_value=0):
 
     n = intersects.groupby('_tmp_index_name')['geometry'].count()
     B_indices = intersects.groupby('_tmp_index_name')['index_right'].apply(list)
-    stats = pd.DataFrame(index=A.index, data={'intersections': B_indices,
+    stats = pd.DataFrame(index=A.index.copy(), data={'intersections': B_indices,
                                               'n': n,})
     stats['n'] = stats['n'].fillna(0)
     stats['n'] = stats['n'].apply(int)

wntr/gis/network.py

@@ -133,7 +133,6 @@ def _extract_geodataframe(df, crs=None, links_as_points=False):
                 # Set index
                 if len(df) > 0:
                     df.set_index('name', inplace=True)
-                    df.index.name = None
 
                 df = gpd.GeoDataFrame(df, crs=crs, geometry=geom)
             else:
@@ -300,7 +299,7 @@ def add_link_attributes(self, values, name):
                     self.pumps[name] = np.nan
                 self.pumps.loc[link_name, name] = value
 
-    def _read(self, files, index_col='index'):
+    def _read(self, files, index_col='name'):
 
         if 'junctions' in files.keys():
             data = gpd.read_file(files['junctions']).set_index(index_col)
@@ -321,7 +320,7 @@ def _read(self, files, index_col='index'):
             data = gpd.read_file(files['valves']).set_index(index_col)
             self.valves = pd.concat([self.valves, data])
 
-    def read_geojson(self, files, index_col='index'):
+    def read_geojson(self, files, index_col='name'):
         """
         Append information from GeoJSON files to a WaterNetworkGIS object
 
@@ -336,7 +335,7 @@ def read_geojson(self, files, index_col='index'):
         """
         self._read(files, index_col)
 
-    def read_shapefile(self, files, index_col='index'):
+    def read_shapefile(self, files, index_col='name'):
         """
         Append information from Esri Shapefiles to a WaterNetworkGIS object
 

wntr/network/io.py

@@ -486,7 +486,6 @@ def write_inpfile(wn, filename: str, units=None, version: float = 2.2,
 
     """
     if wn._inpfile is None:
-        logger.warning("Writing a minimal INP file without saved non-WNTR options (energy, etc.)")
         wn._inpfile = wntr.epanet.InpFile()
     if units is None:
         units = wn._options.hydraulic.inpfile_units
@@ -551,7 +550,7 @@ def write_geojson(wn, prefix: str, crs=None, pumps_as_points=True,
     wn_gis.write_geojson(prefix=prefix)
 
 
-def read_geojson(files, index_col='index', append=None):
+def read_geojson(files, index_col='name', append=None):
     """
     Create or append a WaterNetworkModel from GeoJSON files
 
@@ -612,7 +611,7 @@ def write_shapefile(wn, prefix: str, crs=None, pumps_as_points=True,
                        valves_as_points=valves_as_points)
     wn_gis.write_shapefile(prefix=prefix)
 
-def read_shapefile(files, index_col='index', append=None):
+def read_shapefile(files, index_col='name', append=None):
     """
 
     Create or append a WaterNetworkModel from Esri Shapefiles
@@ -635,7 +634,7 @@ def read_shapefile(files, index_col='index', append=None):
 
     """
     gis_data = WaterNetworkGIS()
-    gis_data.read_shapefile(files, index_col='index')
+    gis_data.read_shapefile(files,index_col=index_col)
     wn = gis_data._create_wn(append=append)
 
     return wn