Update plot code for bitrot

.github/workflows/expl_heuristic.yml

@@ -1,30 +1,46 @@
 name: expl_heuristic # Kotaro Yama
 
+# dropped the Docker container use (DLW April 2025)
+
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+
+defaults:
+  run:
+    shell: bash -l {0}
 
 jobs:
   build:
-
+    name: expl_heuristic
     runs-on: ubuntu-latest
-    container:
-        image: dlwoodruff/c2fcondatest:latest
-        env:
-          PATH: /opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-
+    timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test_env
+          python-version: 3.12
+          auto-activate-base: false
+
+      - name: Install Boost
+        run: sudo apt-get update && sudo apt-get install -y libboost-all-dev
+      - name: Install Eigen
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
 
       - name: make C++
         run: |
           cd cell2fire/Cell2FireC
           make
+      - name: install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install flake8
       - name: setup the program
         run: |
-          python setup.py develop
+          pip install -e .
 
       - name: Lint with flake8
         run: |
@@ -36,18 +52,11 @@ jobs:
         run: |
           cd cell2fire
           python main.py --input-instance-folder ../data/Sub40x40/ --output-folder ../Results/Sub40_n5cv1 --ignitions --sim-years 1 --nsims 5 --grids --finalGrid --weather rows --nweathers 129 --Fire-Period-Length 1.0 --output-messages --ROS-CV 1.0 --seed 123 --IgnitionRad 0 --stats --spreadPlots --heuristic -1
+      - name: Install pytest
+        run: pip install pytest
 
       - name: run tests
         run: |
           cd tests
-          pytest expl_heuristic.py --cov=../cell2fire --cov=./ --cov-report=xml
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
-        with:
-          file: ./tests/coverage.xml
-          flags: unittests
-          ###env_vars: OS,PYTHON
-          name: codecov-umbrella
-          fail_ci_if_error: false
+          pytest expl_heuristic.py
 

.github/workflows/fullstat_allplot.yml

@@ -1,53 +1,62 @@
 name: fullstat_allplot # Kotaro Yama
+# dropped the Docker container use (DLW April 2025)
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+
+defaults:
+  run:
+    shell: bash -l {0}
 
 jobs:
   build:
-
+    name: fullStatAllPlot
     runs-on: ubuntu-latest
-    container:
-        image: dlwoodruff/c2fcondatest:latest
-        env:
-          PATH: /opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-
+    timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test_env
+          python-version: 3.12
+          auto-activate-base: false
+
+      - name: Install Boost
+        run: sudo apt-get update && sudo apt-get install -y libboost-all-dev
+      - name: Install Eigen
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
 
       - name: make C++
         run: |
           cd cell2fire/Cell2FireC
           make
+      - name: install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install flake8
       - name: setup the program
         run: |
-          python setup.py develop
+          pip install -e .
 
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
       - name: create input data
         run: |
            cd cell2fire
            python main.py --input-instance-folder ../data/dogrib/ --output-folder ../results/dogrib_n100cv05 --ignitions --sim-years 1 --nsims 3 --grids --finalGrid --weather rows --nweathers 1 --Fire-Period-Length 1.0 --output-messages --ROS-CV 0.5 --seed 123 --IgnitionRad 0 --stats --allPlots
+      - name: Install pytest
+        run: pip install pytest
 
       - name: run tests
         run: |
           cd tests
-          pytest fullstat_allplot.py --cov=../cell2fire --cov=./ --cov-report=xml
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
-        with:
-          file: ./tests/coverage.xml
-          flags: unittests
-          ###env_vars: OS,PYTHON
-          name: codecov-umbrella
-          fail_ci_if_error: false
+          pytest fullstat_allplot.py
 

.github/workflows/sub20x20.yml

@@ -1,30 +1,45 @@
 name: sub20x20  # Test2_zonghan
+# dropped the Docker container use (DLW April 2025)
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+
+defaults:
+  run:
+    shell: bash -l {0}
 
 jobs:
   build:
-
+    name: sub20x20
     runs-on: ubuntu-latest
-    container:
-        image: dlwoodruff/c2fcondatest:latest
-        env:
-          PATH: /opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-
+    timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test_env
+          python-version: 3.12
+          auto-activate-base: false
+
+      - name: Install Boost
+        run: sudo apt-get update && sudo apt-get install -y libboost-all-dev
+      - name: Install Eigen
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
 
       - name: make C++
         run: |
           cd cell2fire/Cell2FireC
           make
+      - name: install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install flake8
       - name: setup the program
         run: |
-          python setup.py develop
+          pip install -e .
 
       - name: Lint with flake8
         run: |
@@ -36,18 +51,11 @@ jobs:
         run: |
            cd cell2fire
            python main.py --input-instance-folder ../data/Sub20x20/ --output-folder ../results/Sub20x20 --ignitions --sim-years 1 --nsims 5 --finalGrid --weather rows --nweathers 1 --Fire-Period-Length 1.0 --output-messages --ROS-CV 0.0 --seed 123 --stats --allPlots --IgnitionRad 5 --grids --combine
-
+
+      - name: Install pytest
+        run: pip install pytest
       - name: run tests
         run: |
           cd tests
-          pytest test_20x20.py --cov=../cell2fire --cov=./ --cov-report=xml
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
-        with:
-          file: ./tests/coverage.xml
-          flags: unittests
-          ###env_vars: OS,PYTHON
-          name: codecov-umbrella
-          fail_ci_if_error: false
+          pytest test_20x20.py
 

.github/workflows/testReadme1.yml

@@ -1,30 +1,45 @@
 name: Test First Readme Example
+# dropped the Docker container use (DLW April 2025)
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+
+defaults:
+  run:
+    shell: bash -l {0}
 
 jobs:
   build:
-
+    name: readme1
     runs-on: ubuntu-latest
-    container:
-        image: dlwoodruff/c2fcondatest:latest
-        env:
-          PATH: /opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-
+    timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test_env
+          python-version: 3.12
+          auto-activate-base: false
+
+      - name: Install Boost
+        run: sudo apt-get update && sudo apt-get install -y libboost-all-dev
+      - name: Install Eigen
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
 
       - name: make C++
         run: |
           cd cell2fire/Cell2FireC
           make
+      - name: install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install flake8
       - name: setup the program
         run: |
-          python setup.py develop
+          pip install -e .
 
       - name: Lint with flake8
         run: |
@@ -36,18 +51,12 @@ jobs:
         run: |
            cd cell2fire
            python main.py --input-instance-folder ../data/Sub40x40/ --output-folder ../results/Sub40x40 --ignitions --sim-years 1 --nsims 5 --finalGrid --weather rows --nweathers 1 --Fire-Period-Length 1.0 --output-messages --ROS-CV 0.0 --seed 123 --stats --allPlots --IgnitionRad 5 --grids --combine
+      - name: Install pytest
+        run: pip install pytest
 
       - name: run tests
         run: |
           cd tests
-          pytest test_doccmd1.py --cov=../cell2fire --cov=./ --cov-report=xml
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
-        with:
-          file: ./tests/coverage.xml
-          flags: unittests
-          ###env_vars: OS,PYTHON
-          name: codecov-umbrella
-          fail_ci_if_error: false
+          pytest test_doccmd1.py
+
 

.github/workflows/test_datagenerator.yml

@@ -2,48 +2,56 @@ name: test_datagenerator
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+
+defaults:
+  run:
+    shell: bash -l {0}
 
 jobs:
   build:
-
+    name: test_datagenerator
     runs-on: ubuntu-latest
-    container:
-        image: dlwoodruff/c2fcondatest:latest
-        env:
-          PATH: /opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-
+    timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test_env
+          python-version: 3.12
+          auto-activate-base: false
+
+      - name: Install Boost
+        run: sudo apt-get update && sudo apt-get install -y libboost-all-dev
+      - name: Install Eigen
+        run: sudo apt-get update && sudo apt-get install -y libeigen3-dev
 
       - name: make C++
         run: |
           cd cell2fire/Cell2FireC
           make
+      - name: install dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install flake8
       - name: setup the program
         run: |
-          python setup.py develop
+          pip install -e .
 
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Install pytest
+        run: pip install pytest
 
       - name: run tests
         run: |
           cd tests
-          pytest test_datagenentor.py --cov=../cell2fire --cov=./ --cov-report=xml
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
-        with:
-          file: ./tests/coverage.xml
-          flags: unittests
-          ###env_vars: OS,PYTHON
-          name: codecov-umbrella
-          fail_ci_if_error: false
+          pytest test_datagenentor.py
+