Updates to support Pandas 2.0 and test against additional versions of Python

.github/workflows/build_tests.yml

@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# This workflow will install Python dependencies, run tests and coverage
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: build
@@ -10,17 +10,23 @@ on:
   pull_request:
     branches:
     - '**'
-
+  schedule:
+    - cron: '0 0 1 * *'
+
 jobs:
 
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-latest]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python --version
@@ -32,42 +38,41 @@ jobs:
         python setup.py bdist_wheel
         ls dist/*
     - name: Save wheel
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
-        name: wheel
-        path: dist/chama*.whl
+        name: chama_${{ matrix.python-version }}_${{ matrix.os }}.whl
+        path: dist/chama*
 
-  #test:
-  #  name: Import test
-  #  needs: build
-  #  runs-on: ${{ matrix.os }}
-  #  strategy:
-  #    matrix:
-  #      python-version: [3.7, 3.8, 3.9]
-  #      os: [ubuntu-latest]    
-  #  steps:
-  #  - name: Set up Python 
-  #    uses: actions/setup-python@v2
-  #    with:
-  #      python-version: ${{ matrix.python-version }}
-  #  - name: Download wheel
-  #    uses: actions/download-artifact@v2
-  #    with:
-  #      name: wheel
-  #  - name: Install chama
-  #    run: |
-  #      python -m pip install --upgrade pip
-  #      pip install wheel
-  #      pip install --find-links=. chama
-  #  - name: Import test
-  #    run: |
-  #      python -c "import chama"
+  import:
+    needs: build
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-latest]
+    steps:
+    - name: Set up Python 
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Download wheel
+      uses: actions/download-artifact@v3
+      with:
+        name: chama_${{ matrix.python-version }}_${{ matrix.os }}.whl
+    - name: Install chama
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel pyomo pandas numpy scipy
+        pip install --no-index --pre --find-links=. chama
+    - name: Import chama
+      run: |
+        python -c "import chama"
 
-  linux:
+  pytest_coverage:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-latest]
     steps:
     - uses: actions/checkout@v2
@@ -84,37 +89,38 @@ jobs:
         pip install -r requirements.txt
         conda install -y -c conda-forge glpk
         pip install coverage coveralls wntr
-        python setup.py develop
-    - name: Run Tests
+        python -m pip install -e .
+    - name: Run tests and coverage
       run: |
         export PATH=/usr/share/miniconda/bin:$PATH
         coverage erase
-        coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=chama --omit="*/tests/*" -m nose -v --nologcapture --with-doctest --doctest-extension=.rst --traverse-namespace documentation/*.rst chama
+        coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=chama --omit="*/tests/*" -m pytest --doctest-modules --doctest-glob="*.rst" chama
+        coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=chama --omit="*/tests/*" --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@v3
       with:
         name: coverage
         path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
 
-  coverage:
-    needs: [ linux ]
+  coverage_reports:
+    needs: [ pytest_coverage ]
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - uses: actions/checkout@v2
     - name: Install coverage
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
         pip install coveralls
-        python setup.py develop
-    - name: Download coverage artifacts from test matrix
-      uses: actions/download-artifact@v2
+        python -m pip install -e .
+    - name: Download coverage artifacts
+      uses: actions/download-artifact@v3
       with:
         name: coverage
     - name: Setup coverage and combine reports
@@ -133,34 +139,34 @@ jobs:
         coverage json --pretty-print
         coverage html --show-contexts
     - name: Save coverage JSON
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: coverage
         path: coverage.json
     - name: Save coverage html
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: coverage
         path: htmlcov
 
   coveralls:
-    needs: [ linux ]
+    needs: [ pytest_coverage ]
     runs-on: ubuntu-latest
     continue-on-error: true
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - uses: actions/checkout@v2
     - name: Install coverage
       run: |
         python -m pip install --upgrade pip
         pip install coveralls
         pip install -r requirements.txt
-        python setup.py develop
+        python -m pip install -e .
     - name: Download coverage artifacts from test matrix
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: coverage
     - name: Setup coverage and combine reports

chama/__init__.py

@@ -4,7 +4,7 @@
 from chama import optimize
 from chama import graphics
 
-__version__ = '0.2.0'
+__version__ = '0.3.0'
 
 __copyright__ = """Copyright 2016 National Technology & Engineering 
     Solutions of Sandia, LLC (NTESS). Under the terms of Contract 

chama/graphics.py

@@ -14,20 +14,19 @@
 try:
     import matplotlib.pyplot as plt
     from matplotlib import ticker
-    from mpl_toolkits.mplot3d import Axes3D
-    from matplotlib.patches import Circle, Ellipse, Rectangle
+    from matplotlib.patches import Circle
     from matplotlib.collections import PatchCollection
     from matplotlib.animation import FuncAnimation
 except:
-    pass
-    
-from scipy.spatial import ConvexHull  
+    plt = None
+
+from scipy.spatial import ConvexHull
 import numpy as np
 from chama.sensors import Mobile
 
 
-def signal_convexhull(signal, scenarios, threshold, timesteps=None,  
-                      colormap=plt.cm.viridis, 
+def signal_convexhull(signal, scenarios, threshold, timesteps=None,
+                      colormap=None,
                       x_range=(None, None), y_range=(None, None),
                       z_range=(None, None)):
     """
@@ -54,6 +53,11 @@ def signal_convexhull(signal, scenarios, threshold, timesteps=None,
     z_range: tuple (optional)
         The z-axis limits for the plot
     """
+    if plt is None:
+        raise ImportError('matplotlib is required for graphics')
+    if colormap is None:
+        colormap = plt.get_cmap('viridis')
+
     t_col = 'T'
     x_col = 'X'
     y_col = 'Y'
@@ -69,29 +73,24 @@ def signal_convexhull(signal, scenarios, threshold, timesteps=None,
     for scenario in scenarios:
         i = 0
         for timestep in timesteps:
+            color = colormap(i)
+            i += 1 / float(len(timesteps))
+
+            signal_t = signal[signal[t_col] == timestep]
+            conc_filter = signal_t[scenario] > threshold
+
+            data = signal_t[[x_col, y_col, z_col]][conc_filter]
+            data = data.values
             try:
-                color = colormap(i)
-                i += 1 / float(len(timesteps))
-
-                signal_t = signal[signal[t_col] == timestep]
-                conc_filter = signal_t[scenario] > threshold
-
-                # plot points
-                # data = signal_t[[x_col,y_col,z_col,scenario]][conc_filter]
-                # data = data.as_matrix()
-                # ax.scatter(data[:,0], data[:,1], data[:,2], c=data[:,3],s=30)
-
-                data = signal_t[[x_col, y_col, z_col]][conc_filter]
-                data = data.as_matrix()
                 hull = ConvexHull(data)
                 ax.plot_trisurf(data[:, 0], data[:, 1], data[:, 2],
                                 triangles=hull.simplices,
                                 edgecolor='none', 
                                 shade=False,
                                 color=color)
             except:
-                pass
-
+                print('Convex Hull not created for scenario %s timestep %d' % (scenario, timestep))
+                      
     ax.set_xlabel(x_col)
     ax.set_ylabel(y_col)
     ax.set_zlabel(z_col)
@@ -104,7 +103,7 @@ def signal_convexhull(signal, scenarios, threshold, timesteps=None,
 
 def signal_xsection(signal, signal_name, threshold=None, timesteps=None, 
                     x_value=None, y_value=None, z_value=None, log_flag=False,
-                    colormap=plt.cm.viridis, alpha=0.7, N=5,
+                    colormap=None, alpha=0.7, N=5,
                     x_range=(None, None), y_range=(None, None), 
                     z_range=(None, None)):
     """
@@ -147,7 +146,11 @@ def signal_xsection(signal, signal_name, threshold=None, timesteps=None,
     z_range: tuple (optional)
         The z-axis limits for the plot
     """
-
+    if plt is None:
+        raise ImportError('matplotlib is required for graphics')
+    if colormap is None:
+        colormap = plt.get_cmap('viridis')
+
     t_col = 'T'
     x_col = 'X'
     y_col = 'Y'
@@ -238,7 +241,7 @@ def contour_data(temp, threshold, log_flag):
     fig.show()
 
 
-def animate_puffs(puff, x_range=(None, None), y_range=(None, None)):
+def animate_puffs(puff, x_range=(None, None), y_range=(None, None), repeat=True):
     """
     Plots the horizontal movement of puffs from a GaussianPuff simulation
     over time. Each puff is represented as a circle centered at the puff
@@ -253,6 +256,8 @@ def animate_puffs(puff, x_range=(None, None), y_range=(None, None)):
         The x-axis limits for the plot
     y_range: tuple (ymin, ymax) (optional)
         The y-axis limits for the plot
+    repeat : bool, optional
+        If True, the animation will repeat
     """
 
     def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
@@ -304,7 +309,7 @@ def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
 
         zipped = np.broadcast(x, y, s)
         patches = [Circle((x_, y_), s_)
-                   for x_, y_, s_ in zipped]
+                    for x_, y_, s_ in zipped]
         collection = PatchCollection(patches, **kwargs)
         if c is not None:
             c = np.broadcast_to(c, zipped.shape).ravel()
@@ -318,6 +323,17 @@ def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
         if c is not None:
             plt.sci(collection)
         return collection
+
+    if plt is None:
+        raise ImportError('matplotlib is required for graphics')
+
+    buffer = puff['sigmaY'].max() + puff['sigmaY'].max()/5
+    xmin = min([v for v in [puff['X'].min() - buffer, x_range[0]] if v is not None])
+    xmax = max([v for v in [puff['X'].max() + buffer, x_range[1]] if v is not None])
+    ymin = min([v for v in [puff['Y'].min() - buffer, y_range[0]] if v is not None])
+    ymax = max([v for v in [puff['Y'].max() + buffer, y_range[1]] if v is not None])
+    x_range = (xmin, xmax)
+    y_range = (ymin, ymax)
 
     fig, ax = plt.subplots()
     # ln, = plt.plot([],[],animated=True)
@@ -334,13 +350,13 @@ def update(time):
         out = circles(temp['X'], temp['Y'], temp['sigmaY'], alpha=0.5,
                       edgecolor='none')
         return out
-
-    ani = FuncAnimation(fig, update, frames=puff['T'].unique())
-
-    # Need a coder like ffmpeg installed in order to save
-    # ani.save('puff.mp4')
+
+    anim = FuncAnimation(fig, update, frames=puff['T'].unique(), interval=50, 
+                         blit=False, repeat=repeat)
 
     plt.show()
+
+    return anim
 
 
 def sensor_locations(sensors, x_range=(None, None), y_range=(None, None), 
@@ -371,7 +387,9 @@ def sensor_locations(sensors, x_range=(None, None), y_range=(None, None),
         sensor. The key:value pairs are {'sensor name' : String
         representing the marker to be passed to the plot function)
     """
-
+    if plt is None:
+        raise ImportError('matplotlib is required for graphics')
+
     fig = plt.figure()
     ax = fig.add_subplot(111, projection='3d')