From 12a5ef901fc4226e84dcb11ba5f2d5ce50efcb66 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 16:52:12 -0800
Subject: [PATCH 01/19] Udpated build options, added additional versions of
 Python

---
 .github/workflows/build_tests.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index bb2d178..2d912f2 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -10,7 +10,9 @@ on:
   pull_request:
     branches:
     - '**'
-
+  schedule:
+    - cron: '0 0 1 * *'
+    
 jobs:
 
   build:
@@ -18,9 +20,9 @@ jobs:
     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: 3.9
     - name: Install dependencies
       run: |
         python --version
@@ -32,7 +34,7 @@ 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
@@ -67,7 +69,7 @@ jobs:
     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
@@ -103,7 +105,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - uses: actions/checkout@v2
@@ -151,7 +153,7 @@ jobs:
     - name: Set up Python 
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
     - uses: actions/checkout@v2
     - name: Install coverage
       run: |

From 9aac2ecec8b42d37ff65d53dbb0af1b87bd97c7f Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 16:54:48 -0800
Subject: [PATCH 02/19] minor update

---
 .github/workflows/build_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index 2d912f2..3dc8601 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -69,7 +69,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, 3.10, 3.11]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-latest]
     steps:
     - uses: actions/checkout@v2
@@ -107,7 +107,7 @@ jobs:
     - name: Set up Python 
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
     - uses: actions/checkout@v2
     - name: Install coverage
       run: |

From 8e65fb6b0287276eca019bfbd9600b685a162b5f Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 17:00:20 -0800
Subject: [PATCH 03/19] revert to older versions of python

---
 .github/workflows/build_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index 3dc8601..e1fb17f 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -69,7 +69,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.7', '3.8', '3.9']
         os: [ubuntu-latest]
     steps:
     - uses: actions/checkout@v2

From 5bad82ff55c55b6be5fc44766d38c86d26207f7b Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 17:19:22 -0800
Subject: [PATCH 04/19] updated versions on actions

---
 .github/workflows/build_tests.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index e1fb17f..fc53d27 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -49,11 +49,11 @@ jobs:
   #      os: [ubuntu-latest]    
   #  steps:
   #  - name: Set up Python 
-  #    uses: actions/setup-python@v2
+  #    uses: actions/setup-python@v4
   #    with:
   #      python-version: ${{ matrix.python-version }}
   #  - name: Download wheel
-  #    uses: actions/download-artifact@v2
+  #    uses: actions/download-artifact@v3
   #    with:
   #      name: wheel
   #  - name: Install chama
@@ -95,7 +95,7 @@ jobs:
       env:
         COVERAGE_FILE: .coverage.${{ 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 }}
@@ -116,7 +116,7 @@ jobs:
         pip install coveralls
         python setup.py develop
     - 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
@@ -135,12 +135,12 @@ 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
@@ -151,7 +151,7 @@ jobs:
     continue-on-error: true
     steps:
     - name: Set up Python 
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
     - uses: actions/checkout@v2
@@ -162,7 +162,7 @@ jobs:
         pip install -r requirements.txt
         python setup.py develop
     - 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

From 4c95be152fe8751d2383c0e21d1d75637ebed09e Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 17:30:19 -0800
Subject: [PATCH 05/19] Test pandas to <2.0

---
 requirements.txt | 2 +-
 setup.py         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 676de91..c1e2935 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 # Required
 pyomo
-pandas
+pandas<2.0
 numpy
 scipy
 
diff --git a/setup.py b/setup.py
index cfc1aef..0833e3b 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@
 MAINTAINER_EMAIL = 'kaklise@sandia.gov'
 LICENSE = 'Revised BSD'
 URL = 'https://github.com/sandialabs/chama'
-DEPENDENCIES = ['pyomo', 'pandas', 'numpy', 'scipy']
+DEPENDENCIES = ['pyomo', 'pandas<2.0', 'numpy', 'scipy']
 
 # use README file as the long description
 file_dir = os.path.abspath(os.path.dirname(__file__))

From c4616caeba5fa08d64ade627c9a9151132546252 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 18:33:53 -0800
Subject: [PATCH 06/19] updated to solution with the same objective

---
 documentation/optimization.rst | 2 +-
 examples/plume_example.py      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/documentation/optimization.rst b/documentation/optimization.rst
index 502806f..af7f3c9 100644
--- a/documentation/optimization.rst
+++ b/documentation/optimization.rst
@@ -326,7 +326,7 @@ by the sensor placement (listed as 'scenario-time').
     ...                          use_sensor_cost=True)
 	
     >>> print(results['Sensors'])
-    ['A', 'B', 'D']
+    ['A', 'B', 'C']
     >>> print(results['Objective'])
     11.0
     >>> print(round(results['FractionDetected'],2))
diff --git a/examples/plume_example.py b/examples/plume_example.py
index 6251ca4..c150177 100644
--- a/examples/plume_example.py
+++ b/examples/plume_example.py
@@ -94,4 +94,4 @@
 
 # Simple test to ensure results don't change
 assert results['Objective'] == 99.0
-assert results['Sensors'] == ['Sensor384', 'Sensor551', 'Sensor575', 'Sensor731', 'Sensor797']
\ No newline at end of file
+assert results['Sensors'] == ['Sensor384', 'Sensor551', 'Sensor575', 'Sensor681', 'Sensor751']

From 6392aea6f0b9d8b2829f548c3a8ce8e09beb98c5 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 18:37:03 -0800
Subject: [PATCH 07/19] added back in additional python versions

---
 .github/workflows/build_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index fc53d27..9b1db49 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -69,7 +69,7 @@ jobs:
     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

From ab4636e61eae71f12242fe91c442e09196809e4f Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 18:54:51 -0800
Subject: [PATCH 08/19] remove dependency on nose

---
 .github/workflows/build_tests.yml | 5 ++++-
 documentation/developers.rst      | 4 ++--
 documentation/installation.rst    | 2 +-
 requirements.txt                  | 2 +-
 4 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index 9b1db49..be660d9 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -91,7 +91,10 @@ jobs:
       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${{ matrix.python-version }} --source=chama --omit="*/tests/*" -m nose -v --nologcapture --with-doctest --doctest-extension=.rst --traverse-namespace documentation/*.rst chama
+        coverage run --context=${{ 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
diff --git a/documentation/developers.rst b/documentation/developers.rst
index 58f6608..48a2613 100644
--- a/documentation/developers.rst
+++ b/documentation/developers.rst
@@ -24,9 +24,9 @@ The latest stable version is hosted on PyPI at https://pypi.python.org/pypi/cham
 **Testing:**
 Automated testing is run using TravisCI at https://travis-ci.org/sandialabs/chama.
 Test coverage statistics are collected using Coveralls at https://coveralls.io/github/sandialabs/chama.
-Tests can be run locally using nosetests::
+Tests can be run locally using pytest::
   
-	nosetests -v --with-coverage --cover-package=chama chama
+	pytest chama
 
 **Documentation:**
 Documentation is built using Read the Docs and hosted at https://chama.readthedocs.io.
diff --git a/documentation/installation.rst b/documentation/installation.rst
index ca27b7b..c497159 100644
--- a/documentation/installation.rst
+++ b/documentation/installation.rst
@@ -39,7 +39,7 @@ Optional Python package dependencies include:
 
 * Matplotlib [Hunt07]_: Used to produce graphics, 
   http://matplotlib.org.
-* nose: Used to run software tests, http://nose.readthedocs.io.
+* pytest: Used to run software tests, https://docs.pytest.org/.
 
 Required Pyomo supported MIP solver:
 
diff --git a/requirements.txt b/requirements.txt
index c1e2935..bb75005 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,5 +5,5 @@ numpy
 scipy
 
 # Optional
-nose
+pytest
 matplotlib

From 86c7c1a19295626357806e840d1c63c9c708b807 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Fri, 17 Nov 2023 19:08:48 -0800
Subject: [PATCH 09/19] ensure matplotlib is optional by removing plt colormap
 from input args

---
 chama/graphics.py | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/chama/graphics.py b/chama/graphics.py
index e9e416a..478cc50 100644
--- a/chama/graphics.py
+++ b/chama/graphics.py
@@ -19,7 +19,7 @@
     from matplotlib.collections import PatchCollection
     from matplotlib.animation import FuncAnimation
 except:
-    pass
+    plt = None
     
 from scipy.spatial import ConvexHull  
 import numpy as np
@@ -27,7 +27,7 @@
 
 
 def signal_convexhull(signal, scenarios, threshold, timesteps=None,  
-                      colormap=plt.cm.viridis, 
+                      colormap=None, 
                       x_range=(None, None), y_range=(None, None),
                       z_range=(None, None)):
     """
@@ -54,6 +54,11 @@ 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'
@@ -104,7 +109,7 @@ 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 +152,11 @@ 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'
@@ -318,7 +327,10 @@ 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')
+        
     fig, ax = plt.subplots()
     # ln, = plt.plot([],[],animated=True)
 
@@ -371,7 +383,9 @@ 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')
 

From 9a288a97a58384ebc75772339f30d502aaa958b2 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Sat, 18 Nov 2023 10:45:25 -0800
Subject: [PATCH 10/19] Remove deprecated pandas lookup

---
 chama/impact.py  | 11 +++++++----
 requirements.txt |  2 +-
 setup.py         |  2 +-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/chama/impact.py b/chama/impact.py
index 4e99640..8072b23 100644
--- a/chama/impact.py
+++ b/chama/impact.py
@@ -153,10 +153,13 @@ def detection_time_to_impact(detection_time, impact_data):
     impact_data.interpolate(inplace=True)
     
     det_damage = detection_time.copy()
-    det_damage['T'] = impact_data.lookup(detection_time['T'],
-                                         detection_time['Scenario'])
-    det_damage.rename(columns={'T': 'Impact'}, inplace=True)
-
+    times = detection_time['T']
+    scenarios = detection_time['Scenario']
+    impact_vals = impact_data.to_numpy()[impact_data.index.get_indexer(times), 
+                                         impact_data.columns.get_indexer(scenarios)]
+    det_damage['Impact'] = impact_vals
+    del det_damage['T']
+    
     return det_damage
 
 
diff --git a/requirements.txt b/requirements.txt
index bb75005..e4fb280 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 # Required
 pyomo
-pandas<2.0
+pandas
 numpy
 scipy
 
diff --git a/setup.py b/setup.py
index 0833e3b..cfc1aef 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@
 MAINTAINER_EMAIL = 'kaklise@sandia.gov'
 LICENSE = 'Revised BSD'
 URL = 'https://github.com/sandialabs/chama'
-DEPENDENCIES = ['pyomo', 'pandas<2.0', 'numpy', 'scipy']
+DEPENDENCIES = ['pyomo', 'pandas', 'numpy', 'scipy']
 
 # use README file as the long description
 file_dir = os.path.abspath(os.path.dirname(__file__))

From fccc342316d47ec254af8ddfccfc29b4a7009c2b Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Sat, 18 Nov 2023 11:31:21 -0800
Subject: [PATCH 11/19] udpated build workflow

---
 .github/workflows/build_tests.yml | 33 +++++++++++++++++--------------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index be660d9..1a6beff 100644
--- a/.github/workflows/build_tests.yml
+++ b/.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
@@ -16,13 +16,17 @@ on:
 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@v4
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python --version
@@ -36,8 +40,8 @@ jobs:
     - name: Save wheel
       uses: actions/upload-artifact@v3
       with:
-        name: wheel
-        path: dist/chama*.whl
+        name: chama_${{ matrix.python-version }}_${{ matrix.os }}.whl
+        path: dist/chama*
 
   #test:
   #  name: Import test
@@ -45,7 +49,7 @@ jobs:
   #  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:
   #  - name: Set up Python 
@@ -65,7 +69,7 @@ jobs:
   #    run: |
   #      python -c "import chama"
 
-  linux:
+  create_coverage_reports:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -86,13 +90,12 @@ jobs:
         pip install -r requirements.txt
         conda install -y -c conda-forge glpk
         pip install coverage coveralls wntr
-        python setup.py develop
+        python -m pip install -e .
     - name: Run Tests
       run: |
         export PATH=/usr/share/miniconda/bin:$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/*" -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:
@@ -103,8 +106,8 @@ jobs:
         name: coverage
         path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
 
-  coverage:
-    needs: [ linux ]
+  combine_reports:
+    needs: [ create_coverage_reports ]
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 
@@ -148,8 +151,8 @@ jobs:
         name: coverage
         path: htmlcov
 
-  coveralls:
-    needs: [ linux ]
+  combine_reports_upload_coveralls:
+    needs: [ create_coverage_reports ]
     runs-on: ubuntu-latest
     continue-on-error: true
     steps:
@@ -163,7 +166,7 @@ jobs:
         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@v3
       with:

From 01ff73f3e4e948def74453bf6711f59850a61891 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Sat, 18 Nov 2023 12:10:21 -0800
Subject: [PATCH 12/19] Removed animation function, not compatible with
 GaussianPuff simulation, use static graphics options

---
 chama/graphics.py            | 230 +++++++++++++++++------------------
 chama/tests/test_graphics.py |   3 -
 2 files changed, 115 insertions(+), 118 deletions(-)

diff --git a/chama/graphics.py b/chama/graphics.py
index 478cc50..6da2a5c 100644
--- a/chama/graphics.py
+++ b/chama/graphics.py
@@ -7,21 +7,16 @@
 
     signal_convexhull
     signal_xsection
-    animate_puffs
     sensor_locations
 """
 from __future__ import print_function, division
 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.collections import PatchCollection
-    from matplotlib.animation import FuncAnimation
 except:
     plt = None
-    
-from scipy.spatial import ConvexHull  
+
+from scipy.spatial import ConvexHull
 import numpy as np
 from chama.sensors import Mobile
 
@@ -247,114 +242,6 @@ def contour_data(temp, threshold, log_flag):
     fig.show()
 
 
-def animate_puffs(puff, x_range=(None, None), y_range=(None, None)):
-    """
-    Plots the horizontal movement of puffs from a GaussianPuff simulation
-    over time. Each puff is represented as a circle centered at the puff
-    center location with radius equal to the standard deviation in the
-    horizontal direction (sigmaY).
-
-    Parameters
-    ------------------
-    puff: pandas DataFrame
-        The puff DataFrame created by a GaussianPuff object
-    x_range: tuple (xmin, xmax) (optional)
-        The x-axis limits for the plot
-    y_range: tuple (ymin, ymax) (optional)
-        The y-axis limits for the plot
-    """
-
-    def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
-        """
-        Make a scatter plot of circles. 
-        Similar to plt.scatter, but the size of circles are in data scale.
-
-        Parameters
-        ----------
-        x, y : scalar or array_like, shape (n, )
-            Input data
-        s : scalar or array_like, shape (n, ) 
-            Radius of circles.
-        c : color or sequence of color, optional, default : 'b'
-            `c` can be a single color format string, or a sequence of color
-            specifications of length `N`, or a sequence of `N` numbers to be
-            mapped to colors using the `cmap` and `norm` specified via kwargs.
-            Note that `c` should not be a single numeric RGB or RGBA sequence 
-            because that is indistinguishable from an array of values
-            to be colormapped. (If you insist, use `color` instead.)  
-            `c` can be a 2-D array in which the rows are RGB or RGBA, however. 
-        vmin, vmax : scalar, optional, default: None
-            `vmin` and `vmax` are used in conjunction with `norm` to normalize
-            luminance data.  If either are `None`, the min and max of the
-            color array is used.
-        kwargs : `~matplotlib.collections.Collection` properties
-            Eg. alpha, edgecolor(ec), facecolor(fc), linewidth(lw),
-            linestyle(ls), norm, cmap, transform, etc.
-
-        Returns
-        -------
-        paths : `~matplotlib.collections.PathCollection`
-        """
-
-        if np.isscalar(c):
-            kwargs.setdefault('color', c)
-            c = None
-
-        if 'fc' in kwargs:
-            kwargs.setdefault('facecolor', kwargs.pop('fc'))
-        if 'ec' in kwargs:
-            kwargs.setdefault('edgecolor', kwargs.pop('ec'))
-        if 'ls' in kwargs:
-            kwargs.setdefault('linestyle', kwargs.pop('ls'))
-        if 'lw' in kwargs:
-            kwargs.setdefault('linewidth', kwargs.pop('lw'))
-        # You can set `facecolor` with an array for each patch,
-        # while you can only set `facecolors` with a value for all.
-
-        zipped = np.broadcast(x, y, s)
-        patches = [Circle((x_, y_), s_)
-                   for x_, y_, s_ in zipped]
-        collection = PatchCollection(patches, **kwargs)
-        if c is not None:
-            c = np.broadcast_to(c, zipped.shape).ravel()
-            collection.set_array(c)
-            collection.set_clim(vmin, vmax)
-
-        ax = plt.gca()
-        ax.add_collection(collection)
-        ax.autoscale_view()
-        plt.draw_if_interactive()
-        if c is not None:
-            plt.sci(collection)
-        return collection
-    
-    if plt is None:
-        raise ImportError('matplotlib is required for graphics')
-        
-    fig, ax = plt.subplots()
-    # ln, = plt.plot([],[],animated=True)
-
-    def update(time):
-        plt.cla()
-        ax.set_xlim(x_range[0], x_range[1])
-        ax.set_ylim(y_range[0], y_range[1])
-        ax.set_title('T = %6.2f' % time)
-        ax.set_xlabel('X')
-        ax.set_ylabel('Y')
-
-        temp = puff.loc[puff['T'] == 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')
-
-    plt.show()
-
-
 def sensor_locations(sensors, x_range=(None, None), y_range=(None, None), 
                      z_range=(None, None), legend=False,
                      colors=None, markers=None):
@@ -415,3 +302,116 @@ def sensor_locations(sensors, x_range=(None, None), y_range=(None, None),
     if legend:
         ax.legend()
     fig.show()
+
+# Animation function is no longer working
+# Use convex hull or xsection on individual timesteps
+# def animate_puffs(puff, x_range=(None, None), y_range=(None, None)):
+#     """
+#     Plots the horizontal movement of puffs from a GaussianPuff simulation
+#     over time. Each puff is represented as a circle centered at the puff
+#     center location with radius equal to the standard deviation in the
+#     horizontal direction (sigmaY).
+
+#     Parameters
+#     ------------------
+#     puff: pandas DataFrame
+#         The puff DataFrame created by a GaussianPuff object
+#     x_range: tuple (xmin, xmax) (optional)
+#         The x-axis limits for the plot
+#     y_range: tuple (ymin, ymax) (optional)
+#         The y-axis limits for the plot
+#     """
+
+#     def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
+#         """
+#         Make a scatter plot of circles. 
+#         Similar to plt.scatter, but the size of circles are in data scale.
+
+#         Parameters
+#         ----------
+#         x, y : scalar or array_like, shape (n, )
+#             Input data
+#         s : scalar or array_like, shape (n, ) 
+#             Radius of circles.
+#         c : color or sequence of color, optional, default : 'b'
+#             `c` can be a single color format string, or a sequence of color
+#             specifications of length `N`, or a sequence of `N` numbers to be
+#             mapped to colors using the `cmap` and `norm` specified via kwargs.
+#             Note that `c` should not be a single numeric RGB or RGBA sequence 
+#             because that is indistinguishable from an array of values
+#             to be colormapped. (If you insist, use `color` instead.)  
+#             `c` can be a 2-D array in which the rows are RGB or RGBA, however. 
+#         vmin, vmax : scalar, optional, default: None
+#             `vmin` and `vmax` are used in conjunction with `norm` to normalize
+#             luminance data.  If either are `None`, the min and max of the
+#             color array is used.
+#         kwargs : `~matplotlib.collections.Collection` properties
+#             Eg. alpha, edgecolor(ec), facecolor(fc), linewidth(lw),
+#             linestyle(ls), norm, cmap, transform, etc.
+
+#         Returns
+#         -------
+#         paths : `~matplotlib.collections.PathCollection`
+#         """
+
+#         if np.isscalar(c):
+#             kwargs.setdefault('color', c)
+#             c = None
+
+#         if 'fc' in kwargs:
+#             kwargs.setdefault('facecolor', kwargs.pop('fc'))
+#         if 'ec' in kwargs:
+#             kwargs.setdefault('edgecolor', kwargs.pop('ec'))
+#         if 'ls' in kwargs:
+#             kwargs.setdefault('linestyle', kwargs.pop('ls'))
+#         if 'lw' in kwargs:
+#             kwargs.setdefault('linewidth', kwargs.pop('lw'))
+#         # You can set `facecolor` with an array for each patch,
+#         # while you can only set `facecolors` with a value for all.
+
+#         zipped = np.broadcast(x, y, s)
+#         patches = [Circle((x_, y_), s_)
+#                    for x_, y_, s_ in zipped]
+#         collection = PatchCollection(patches, **kwargs)
+#         if c is not None:
+#             c = np.broadcast_to(c, zipped.shape).ravel()
+#             collection.set_array(c)
+#             collection.set_clim(vmin, vmax)
+
+#         ax = plt.gca()
+#         ax.add_collection(collection)
+#         ax.autoscale_view()
+#         plt.draw_if_interactive()
+#         if c is not None:
+#             plt.sci(collection)
+#         return collection
+    
+#     if plt is None:
+#         raise ImportError('matplotlib is required for graphics')
+
+#     from matplotlib.patches import Circle, Ellipse, Rectangle
+#     from matplotlib.collections import PatchCollection
+#     from matplotlib.animation import FuncAnimation
+
+#     fig, ax = plt.subplots()
+#     # ln, = plt.plot([],[],animated=True)
+
+#     def update(time):
+#         plt.cla()
+#         ax.set_xlim(x_range[0], x_range[1])
+#         ax.set_ylim(y_range[0], y_range[1])
+#         ax.set_title('T = %6.2f' % time)
+#         ax.set_xlabel('X')
+#         ax.set_ylabel('Y')
+
+#         temp = puff.loc[puff['T'] == 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')
+
+#     plt.show()
\ No newline at end of file
diff --git a/chama/tests/test_graphics.py b/chama/tests/test_graphics.py
index abca0ca..93b6f53 100644
--- a/chama/tests/test_graphics.py
+++ b/chama/tests/test_graphics.py
@@ -58,9 +58,6 @@ def test_signal_xsection(self):
         
         self.assertTrue(isfile(filename))
 
-    def test_signal_animate(self):
-        pass
-
 
 class TestSensorGraphics(unittest.TestCase):
     

From 42847b5d365bac7f9122df01f5fd097969072628 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Sat, 18 Nov 2023 12:10:33 -0800
Subject: [PATCH 13/19] minor update

---
 documentation/installation.rst | 2 +-
 readthedocs.yml                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/documentation/installation.rst b/documentation/installation.rst
index c497159..b8cb540 100644
--- a/documentation/installation.rst
+++ b/documentation/installation.rst
@@ -5,7 +5,7 @@
 Installation
 ======================================
 
-Chama requires Python (tested on 3.7, 3.8, and 3.9) along with several Python package dependencies.  
+Chama requires Python (tested on 3.7-3.11) along with several Python package dependencies.  
 Information on installing and using Python can be found at 
 https://www.python.org/.  
 Python distributions, such as Anaconda, are recommended to manage the Python interface.  
diff --git a/readthedocs.yml b/readthedocs.yml
index 1e9ad4d..1060976 100644
--- a/readthedocs.yml
+++ b/readthedocs.yml
@@ -1,5 +1,5 @@
 conda:
     file: documentation/environment.yml
 python:
-    version: 3.8
+    version: 3.9
     setup_py_install: true
\ No newline at end of file

From d7f42d182911f544849333292c8582b75013f106 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Mon, 20 Nov 2023 07:40:39 -0800
Subject: [PATCH 14/19] Added animate_puffs back in with a test

---
 chama/graphics.py            | 251 +++++++++++++++++------------------
 chama/tests/test_graphics.py |  22 +++
 2 files changed, 145 insertions(+), 128 deletions(-)

diff --git a/chama/graphics.py b/chama/graphics.py
index 6da2a5c..26ac682 100644
--- a/chama/graphics.py
+++ b/chama/graphics.py
@@ -69,20 +69,15 @@ 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,
@@ -90,8 +85,8 @@ def signal_convexhull(signal, scenarios, threshold, timesteps=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)
@@ -242,6 +237,119 @@ def contour_data(temp, threshold, log_flag):
     fig.show()
 
 
+def animate_puffs(puff, 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
+    center location with radius equal to the standard deviation in the
+    horizontal direction (sigmaY).
+
+    Parameters
+    ------------------
+    puff: pandas DataFrame
+        The puff DataFrame created by a GaussianPuff object
+    repeat : bool, optional
+        If True, the animation will repeat
+    """
+
+    def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
+        """
+        Make a scatter plot of circles. 
+        Similar to plt.scatter, but the size of circles are in data scale.
+
+        Parameters
+        ----------
+        x, y : scalar or array_like, shape (n, )
+            Input data
+        s : scalar or array_like, shape (n, ) 
+            Radius of circles.
+        c : color or sequence of color, optional, default : 'b'
+            `c` can be a single color format string, or a sequence of color
+            specifications of length `N`, or a sequence of `N` numbers to be
+            mapped to colors using the `cmap` and `norm` specified via kwargs.
+            Note that `c` should not be a single numeric RGB or RGBA sequence 
+            because that is indistinguishable from an array of values
+            to be colormapped. (If you insist, use `color` instead.)  
+            `c` can be a 2-D array in which the rows are RGB or RGBA, however. 
+        vmin, vmax : scalar, optional, default: None
+            `vmin` and `vmax` are used in conjunction with `norm` to normalize
+            luminance data.  If either are `None`, the min and max of the
+            color array is used.
+        kwargs : `~matplotlib.collections.Collection` properties
+            Eg. alpha, edgecolor(ec), facecolor(fc), linewidth(lw),
+            linestyle(ls), norm, cmap, transform, etc.
+
+        Returns
+        -------
+        paths : `~matplotlib.collections.PathCollection`
+        """
+
+        if np.isscalar(c):
+            kwargs.setdefault('color', c)
+            c = None
+
+        if 'fc' in kwargs:
+            kwargs.setdefault('facecolor', kwargs.pop('fc'))
+        if 'ec' in kwargs:
+            kwargs.setdefault('edgecolor', kwargs.pop('ec'))
+        if 'ls' in kwargs:
+            kwargs.setdefault('linestyle', kwargs.pop('ls'))
+        if 'lw' in kwargs:
+            kwargs.setdefault('linewidth', kwargs.pop('lw'))
+        # You can set `facecolor` with an array for each patch,
+        # while you can only set `facecolors` with a value for all.
+
+        zipped = np.broadcast(x, y, s)
+        patches = [Circle((x_, y_), s_)
+                    for x_, y_, s_ in zipped]
+        collection = PatchCollection(patches, **kwargs)
+        if c is not None:
+            c = np.broadcast_to(c, zipped.shape).ravel()
+            collection.set_array(c)
+            collection.set_clim(vmin, vmax)
+
+        ax = plt.gca()
+        ax.add_collection(collection)
+        ax.autoscale_view()
+        plt.draw_if_interactive()
+        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
+    x_range = (puff['X'].min() - buffer, puff['X'].max() + buffer)
+    y_range = (puff['Y'].min() - buffer, puff['Y'].max() + buffer)
+        
+    from matplotlib.patches import Circle, Ellipse, Rectangle
+    from matplotlib.collections import PatchCollection
+    from matplotlib.animation import FuncAnimation, FFMpegWriter
+
+    fig, ax = plt.subplots()
+    # ln, = plt.plot([],[],animated=True)
+
+    def update(time):
+        plt.cla()
+        ax.set_xlim(x_range[0], x_range[1])
+        ax.set_ylim(y_range[0], y_range[1])
+        ax.set_title('T = %6.2f' % time)
+        ax.set_xlabel('X')
+        ax.set_ylabel('Y')
+
+        temp = puff.loc[puff['T'] == time]
+        out = circles(temp['X'], temp['Y'], temp['sigmaY'], alpha=0.5,
+                      edgecolor='none')
+        return out
+    
+    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), 
                      z_range=(None, None), legend=False,
                      colors=None, markers=None):
@@ -302,116 +410,3 @@ def sensor_locations(sensors, x_range=(None, None), y_range=(None, None),
     if legend:
         ax.legend()
     fig.show()
-
-# Animation function is no longer working
-# Use convex hull or xsection on individual timesteps
-# def animate_puffs(puff, x_range=(None, None), y_range=(None, None)):
-#     """
-#     Plots the horizontal movement of puffs from a GaussianPuff simulation
-#     over time. Each puff is represented as a circle centered at the puff
-#     center location with radius equal to the standard deviation in the
-#     horizontal direction (sigmaY).
-
-#     Parameters
-#     ------------------
-#     puff: pandas DataFrame
-#         The puff DataFrame created by a GaussianPuff object
-#     x_range: tuple (xmin, xmax) (optional)
-#         The x-axis limits for the plot
-#     y_range: tuple (ymin, ymax) (optional)
-#         The y-axis limits for the plot
-#     """
-
-#     def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
-#         """
-#         Make a scatter plot of circles. 
-#         Similar to plt.scatter, but the size of circles are in data scale.
-
-#         Parameters
-#         ----------
-#         x, y : scalar or array_like, shape (n, )
-#             Input data
-#         s : scalar or array_like, shape (n, ) 
-#             Radius of circles.
-#         c : color or sequence of color, optional, default : 'b'
-#             `c` can be a single color format string, or a sequence of color
-#             specifications of length `N`, or a sequence of `N` numbers to be
-#             mapped to colors using the `cmap` and `norm` specified via kwargs.
-#             Note that `c` should not be a single numeric RGB or RGBA sequence 
-#             because that is indistinguishable from an array of values
-#             to be colormapped. (If you insist, use `color` instead.)  
-#             `c` can be a 2-D array in which the rows are RGB or RGBA, however. 
-#         vmin, vmax : scalar, optional, default: None
-#             `vmin` and `vmax` are used in conjunction with `norm` to normalize
-#             luminance data.  If either are `None`, the min and max of the
-#             color array is used.
-#         kwargs : `~matplotlib.collections.Collection` properties
-#             Eg. alpha, edgecolor(ec), facecolor(fc), linewidth(lw),
-#             linestyle(ls), norm, cmap, transform, etc.
-
-#         Returns
-#         -------
-#         paths : `~matplotlib.collections.PathCollection`
-#         """
-
-#         if np.isscalar(c):
-#             kwargs.setdefault('color', c)
-#             c = None
-
-#         if 'fc' in kwargs:
-#             kwargs.setdefault('facecolor', kwargs.pop('fc'))
-#         if 'ec' in kwargs:
-#             kwargs.setdefault('edgecolor', kwargs.pop('ec'))
-#         if 'ls' in kwargs:
-#             kwargs.setdefault('linestyle', kwargs.pop('ls'))
-#         if 'lw' in kwargs:
-#             kwargs.setdefault('linewidth', kwargs.pop('lw'))
-#         # You can set `facecolor` with an array for each patch,
-#         # while you can only set `facecolors` with a value for all.
-
-#         zipped = np.broadcast(x, y, s)
-#         patches = [Circle((x_, y_), s_)
-#                    for x_, y_, s_ in zipped]
-#         collection = PatchCollection(patches, **kwargs)
-#         if c is not None:
-#             c = np.broadcast_to(c, zipped.shape).ravel()
-#             collection.set_array(c)
-#             collection.set_clim(vmin, vmax)
-
-#         ax = plt.gca()
-#         ax.add_collection(collection)
-#         ax.autoscale_view()
-#         plt.draw_if_interactive()
-#         if c is not None:
-#             plt.sci(collection)
-#         return collection
-    
-#     if plt is None:
-#         raise ImportError('matplotlib is required for graphics')
-
-#     from matplotlib.patches import Circle, Ellipse, Rectangle
-#     from matplotlib.collections import PatchCollection
-#     from matplotlib.animation import FuncAnimation
-
-#     fig, ax = plt.subplots()
-#     # ln, = plt.plot([],[],animated=True)
-
-#     def update(time):
-#         plt.cla()
-#         ax.set_xlim(x_range[0], x_range[1])
-#         ax.set_ylim(y_range[0], y_range[1])
-#         ax.set_title('T = %6.2f' % time)
-#         ax.set_xlabel('X')
-#         ax.set_ylabel('Y')
-
-#         temp = puff.loc[puff['T'] == 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')
-
-#     plt.show()
\ No newline at end of file
diff --git a/chama/tests/test_graphics.py b/chama/tests/test_graphics.py
index 93b6f53..dd0acb0 100644
--- a/chama/tests/test_graphics.py
+++ b/chama/tests/test_graphics.py
@@ -28,7 +28,12 @@ def setUpClass(self):
     
         gauss_plume = chama.simulation.GaussianPlume(self.grid, self.source, 
                                                      self.atm)
+        gauss_puff = chama.simulation.GaussianPuff(self.grid, self.source, 
+                                                   self.atm, tpuff=0.5,
+                                                   tend=30)
         self.signal = gauss_plume.conc
+        self.puff = gauss_puff.puff
+        
         
     @classmethod
     def tearDownClass(self):
@@ -58,6 +63,23 @@ def test_signal_xsection(self):
         
         self.assertTrue(isfile(filename))
 
+    def test_puff_animation(self):
+        filename = abspath(join(testdir, 'plot_puff_animation.gif'))
+        if isfile(filename):
+            os.remove(filename)
+        
+        anim = chama.graphics.animate_puffs(self.puff)
+        
+        from matplotlib.animation import FuncAnimation, writers
+        try: 
+            writer = writers.list()[0]
+            anim.save(filename, writer=writer)
+            self.assertTrue(isfile(filename))
+        except:
+            pass
+        
+        self.assertTrue(isinstance(anim, FuncAnimation))
+
 
 class TestSensorGraphics(unittest.TestCase):
     

From 12cb2cca5221db097747fa519988443187cce35f Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Mon, 20 Nov 2023 08:23:29 -0800
Subject: [PATCH 15/19] cleanup

---
 .github/workflows/build_tests.yml | 62 +++++++++++++++----------------
 chama/graphics.py                 | 12 +++---
 2 files changed, 37 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index 1a6beff..c7d8bbd 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -43,33 +43,33 @@ jobs:
         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', '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: 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"
+  install:
+    name: Import test
+    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: 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"
 
-  create_coverage_reports:
+  pytest_coverage:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -106,8 +106,8 @@ jobs:
         name: coverage
         path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
 
-  combine_reports:
-    needs: [ create_coverage_reports ]
+  coverage_reports:
+    needs: [ pytest_coverage ]
     runs-on: ubuntu-latest
     steps:
     - name: Set up Python 
@@ -120,7 +120,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install -r requirements.txt
         pip install coveralls
-        python setup.py develop
+        python -m pip install -e .
     - name: Download coverage artifacts from test matrix
       uses: actions/download-artifact@v3
       with:
@@ -151,8 +151,8 @@ jobs:
         name: coverage
         path: htmlcov
 
-  combine_reports_upload_coveralls:
-    needs: [ create_coverage_reports ]
+  coveralls:
+    needs: [ pytest_coverage ]
     runs-on: ubuntu-latest
     continue-on-error: true
     steps:
diff --git a/chama/graphics.py b/chama/graphics.py
index 26ac682..03cddba 100644
--- a/chama/graphics.py
+++ b/chama/graphics.py
@@ -13,6 +13,9 @@
 try:
     import matplotlib.pyplot as plt
     from matplotlib import ticker
+    from matplotlib.patches import Circle
+    from matplotlib.collections import PatchCollection
+    from matplotlib.animation import FuncAnimation
 except:
     plt = None
 
@@ -21,8 +24,8 @@
 from chama.sensors import Mobile
 
 
-def signal_convexhull(signal, scenarios, threshold, timesteps=None,  
-                      colormap=None, 
+def signal_convexhull(signal, scenarios, threshold, timesteps=None,
+                      colormap=None,
                       x_range=(None, None), y_range=(None, None),
                       z_range=(None, None)):
     """
@@ -318,13 +321,10 @@ def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
     
     if plt is None:
         raise ImportError('matplotlib is required for graphics')
+        
     buffer = puff['sigmaY'].max() + puff['sigmaY'].max()/5
     x_range = (puff['X'].min() - buffer, puff['X'].max() + buffer)
     y_range = (puff['Y'].min() - buffer, puff['Y'].max() + buffer)
-        
-    from matplotlib.patches import Circle, Ellipse, Rectangle
-    from matplotlib.collections import PatchCollection
-    from matplotlib.animation import FuncAnimation, FFMpegWriter
 
     fig, ax = plt.subplots()
     # ln, = plt.plot([],[],animated=True)

From 9e79d36913f288ce5346365783997e5df2e65113 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Mon, 20 Nov 2023 08:41:26 -0800
Subject: [PATCH 16/19] minor update to build script

---
 .github/workflows/build_tests.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index c7d8bbd..07fcce6 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -43,8 +43,7 @@ jobs:
         name: chama_${{ matrix.python-version }}_${{ matrix.os }}.whl
         path: dist/chama*
 
-  install:
-    name: Import test
+  import:
     needs: build
     runs-on: ${{ matrix.os }}
     strategy:
@@ -59,7 +58,7 @@ jobs:
     - name: Download wheel
       uses: actions/download-artifact@v3
       with:
-        name: wheel
+        name: chama_${{ matrix.python-version }}_${{ matrix.os }}.whl
     - name: Install chama
       run: |
         python -m pip install --upgrade pip

From 940ba087f567cd274fa97f849219c1196fe89df8 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Mon, 20 Nov 2023 12:24:47 -0800
Subject: [PATCH 17/19] minor update

---
 .github/workflows/build_tests.yml | 11 +++++------
 chama/graphics.py                 |  1 +
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml
index 07fcce6..692b0b9 100644
--- a/.github/workflows/build_tests.yml
+++ b/.github/workflows/build_tests.yml
@@ -62,9 +62,9 @@ jobs:
     - name: Install chama
       run: |
         python -m pip install --upgrade pip
-        pip install wheel
-        pip install --find-links=. chama
-    - name: Import test
+        pip install wheel pyomo pandas numpy scipy
+        pip install --no-index --pre --find-links=. chama
+    - name: Import chama
       run: |
         python -c "import chama"
 
@@ -90,13 +90,12 @@ jobs:
         conda install -y -c conda-forge glpk
         pip install coverage coveralls wntr
         python -m pip install -e .
-    - name: Run Tests
+    - name: Run tests and coverage
       run: |
         export PATH=/usr/share/miniconda/bin:$PATH
         coverage erase
         coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=chama --omit="*/tests/*" -m pytest --doctest-modules --doctest-glob="*.rst" chama
         coverage run --context=${{ 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
@@ -120,7 +119,7 @@ jobs:
         pip install -r requirements.txt
         pip install coveralls
         python -m pip install -e .
-    - name: Download coverage artifacts from test matrix
+    - name: Download coverage artifacts
       uses: actions/download-artifact@v3
       with:
         name: coverage
diff --git a/chama/graphics.py b/chama/graphics.py
index 03cddba..0d79839 100644
--- a/chama/graphics.py
+++ b/chama/graphics.py
@@ -7,6 +7,7 @@
 
     signal_convexhull
     signal_xsection
+    animate_puffs
     sensor_locations
 """
 from __future__ import print_function, division

From 1e7769458f839c5a71b66e2db1aa547b0f87948d Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Mon, 20 Nov 2023 13:25:58 -0800
Subject: [PATCH 18/19] Added the x and y range input args back to puff
 animation

---
 chama/graphics.py            | 16 ++++++++++++----
 chama/tests/test_graphics.py |  4 +++-
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/chama/graphics.py b/chama/graphics.py
index 0d79839..0e2d530 100644
--- a/chama/graphics.py
+++ b/chama/graphics.py
@@ -241,7 +241,7 @@ def contour_data(temp, threshold, log_flag):
     fig.show()
 
 
-def animate_puffs(puff, repeat=True):
+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
@@ -252,6 +252,10 @@ def animate_puffs(puff, repeat=True):
     ------------------
     puff: pandas DataFrame
         The puff DataFrame created by a GaussianPuff object
+    x_range: tuple (xmin, xmax) (optional)
+        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
     """
@@ -322,10 +326,14 @@ def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
     
     if plt is None:
         raise ImportError('matplotlib is required for graphics')
-        
+    
     buffer = puff['sigmaY'].max() + puff['sigmaY'].max()/5
-    x_range = (puff['X'].min() - buffer, puff['X'].max() + buffer)
-    y_range = (puff['Y'].min() - buffer, puff['Y'].max() + buffer)
+    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)
diff --git a/chama/tests/test_graphics.py b/chama/tests/test_graphics.py
index dd0acb0..9530a7e 100644
--- a/chama/tests/test_graphics.py
+++ b/chama/tests/test_graphics.py
@@ -68,7 +68,9 @@ def test_puff_animation(self):
         if isfile(filename):
             os.remove(filename)
         
-        anim = chama.graphics.animate_puffs(self.puff)
+        anim = chama.graphics.animate_puffs(self.puff, 
+                                            x_range=(-60,None), 
+                                            y_range=(None,60))
         
         from matplotlib.animation import FuncAnimation, writers
         try: 

From bc2bbe6419ff615ceebe95a2f53e8d86424615d9 Mon Sep 17 00:00:00 2001
From: Katherine Klise <kaklise@sandia.gov>
Date: Mon, 20 Nov 2023 15:21:36 -0800
Subject: [PATCH 19/19] bump version number

---
 chama/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/chama/__init__.py b/chama/__init__.py
index eca15b2..baaf6fe 100644
--- a/chama/__init__.py
+++ b/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