Merging with main

.github/linters/.codespellrc

@@ -1,3 +1,3 @@
 [codespell]
-skip = None, .git,OFsolvers,tutorial_cases,experimental_cases,build,_build,__pycache__,data_conditional_mean,Figures,assets
+skip = None, .git,OFsolvers,*.pdf, tutorial_cases,experimental_cases,build,_build,__pycache__,data_conditional_mean,Figures,assets,htmlcov
 ignore-words = .github/linters/.codespell-ignore-words

.github/workflows/build_docs.yml

@@ -11,7 +11,10 @@ jobs:
 
   build_docs:
     runs-on: ubuntu-latest
-
+    defaults:
+      run:
+        shell: bash -l {0}
+        working-directory: ${{github.workspace}}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -21,11 +24,24 @@ jobs:
         with:
           python-version: '3.10'
           cache: 'pip'
-
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: strict
+          cache-downloads: true
+          cache-env: true
+
       - name: Install dependencies
         run: |
+          micromamba install --yes -n test-env -c conda-forge paraview
           python -m pip install --upgrade pip
-          pip install sphinx sphinx_rtd_theme
+          pip install -e . 
+          pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints
 
       - name: Build documentation
         run: |

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
       - '*.rst'
       - 'README*'
       - 'LICENSE'
-      - 'assets/*'
+      - 'docs/**'
 
    pull_request:
      branches: [main]
@@ -17,7 +17,7 @@ on:
       - '*.rst'
       - 'README*'
       - 'LICENSE'
-      - 'assets/*'
+      - 'docs/**'
 
 jobs:
   Lint:
@@ -30,6 +30,7 @@ jobs:
         os: ['ubuntu-latest']
     defaults:
       run:
+        shell: bash -l {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
@@ -52,30 +53,39 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.13']
         os: ['ubuntu-latest', 'macos-latest']
     defaults:
       run:
+        shell: bash -l {0}
         working-directory: ${{github.workspace}}
+
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{matrix.python-version}}
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: strict
+          cache-downloads: true
+          cache-env: true
+
       - name: Install dependencies
         run: |
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
-          pip install .
+          pip install . 
           pip install pytest
-      - name: Test preprocess
-        run: |
-          pytest tests/preprocess
-      - name: Test mesh
-        run: |
-          pytest tests/meshing
-      - name: Test postprocessing
-        run: |
-          pytest tests/postprocess
+
+      - name: Test
+        run: pytest .
 
   Test-pypi-Bird:
     name: Test-pypi-BiRD (${{ matrix.python-version }}, ${{ matrix.os }})
@@ -87,17 +97,32 @@ jobs:
         os: ['ubuntu-latest']
     defaults:
       run:
+        shell: bash -l {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{matrix.python-version}}
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: strict
+          cache-downloads: true
+          cache-env: true
+
       - name: Install dependencies
         run: |
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install nrel-bird
           pip install pytest
+
       - name: Test
         run: pytest .
 
@@ -111,6 +136,7 @@ jobs:
         os: ['ubuntu-22.04']
     defaults:
       run:
+        shell: bash -l {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
@@ -120,10 +146,24 @@ jobs:
       - uses: gerlero/setup-openfoam@v1
         with:
           openfoam-version: 9
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: strict
+          cache-downloads: true
+          cache-env: true
+
       - name: Install dependencies
         run: |
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install .
+
       - name: Compile solver
         run: |
           cd OFsolvers/birdmultiphaseEulerFoam
@@ -176,4 +216,9 @@ jobs:
           cd tutorial_cases/airlift_40m
           bash run.sh
           cd ../../
+      - name: Run flat panel reactor tutorial
+        run: |
+          cd tutorial_cases/FlatPanel_250L_ASU
+          bash run.sh
+          cd ../../
 

.github/workflows/codecov.yml

@@ -0,0 +1,62 @@
+name: CodeCov
+
+on:
+  push:
+     branches: [ main ]
+     paths-ignore:
+      - '*.md'
+      - '*.rst'
+      - 'README*'
+      - 'LICENSE'
+      - 'docs/**'
+
+jobs:
+  codecov:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+        working-directory: ${{github.workspace}}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+          cache: 'pip'
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: strict
+          cache-downloads: true
+          cache-env: true
+
+      - name: Install dependencies
+        run: |
+          micromamba install --yes -n test-env -c conda-forge paraview
+          pip install --upgrade pip
+          pip install pytest
+          pip install pytest-cov
+          pip install -e .
+
+      - name: Generate coverage report
+        run: |
+          pytest --cov=./ --cov-report=xml:coverage.xml          
+      - name: Upload coverage to Codecov
+
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          verbose: true

.github/workflows/deploy_docs.yml

@@ -11,6 +11,10 @@ jobs:
 
   build_deploy_docs:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+        working-directory: ${{github.workspace}}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
@@ -22,11 +26,24 @@ jobs:
         with:
           python-version: '3.10'
           cache: 'pip'
-
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: strict
+          cache-downloads: true
+          cache-env: true
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install sphinx sphinx_rtd_theme
+          micromamba install --yes -n test-env -c conda-forge paraview
+          pip install --upgrade pip
+          pip install -e .
+          pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints
 
       - name: Build documentation
         run: |

.gitignore

@@ -136,3 +136,4 @@ dmypy.json
 *.stl
 
 *.swp
+.vim

README.md

@@ -1,4 +1,4 @@
-# <ins>Bi</ins>o <ins>R</ins>eactor <ins>D</ins>esign (BiRD) [![bird-CI](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml/badge.svg)](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml) [![bird-pyversion](https://img.shields.io/pypi/pyversions/NREL-bird.svg)](https://pypi.org/project/NREL-bird/)  [![bird-pypi](https://badge.fury.io/py/nrel-bird.svg)](https://badge.fury.io/py/nrel-bird)
+# <ins>Bi</ins>o <ins>R</ins>eactor <ins>D</ins>esign (BiRD) [![bird-CI](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml/badge.svg)](https://github.com/NREL/BioReactorDesign/actions/workflows/ci.yml) [![bird-pyversion](https://img.shields.io/pypi/pyversions/NREL-bird.svg)](https://pypi.org/project/NREL-bird/) [![coverage](https://codecov.io/gh/NREL/BioReactorDesign/graph/badge.svg)](https://app.codecov.io/gh/nrel/bioreactordesign)  [![bird-pypi](https://badge.fury.io/py/nrel-bird.svg)](https://badge.fury.io/py/nrel-bird)
 
 ## Quick start
 1. Follow the steps to install the python package (see `Installation of python package for developers` or `Installation of python package for users` below)
@@ -13,7 +13,7 @@ bash run.sh
 ## Installation of python package for developers
 
 ```bash
-conda create --name bird python=3.10
+conda create -c conda-forge --name bird python=3.10 paraview
 conda activate bird
 git clone https://github.com/NREL/BioReactorDesign.git
 cd BioReactorDesign
@@ -23,11 +23,13 @@ pip install -e .
 ## Installation of python package for users
 
 ```bash
-conda create --name bird python=3.10
+conda create -c conda-forge --name bird python=3.10 paraview
 conda activate bird
-pip install nrel-bird
+pip install nrel-bird=={version}
 ```
 
+We highly recommend that you specify the version explicitly as the library is still rapidly changing.
+
 ## Installation of BiRD OpenFOAM solver (for developers and users)
 
 1. Activate your OpenFOAM-9 environment (`source <OpenFOAM-9 installation directory>/etc/<your-shell>rc`)
@@ -43,17 +45,20 @@ See the [nrel.github.io/BioReactorDesign](https://nrel.github.io/BioReactorDesig
 
 Software record [SWR 24-35](https://www.osti.gov/biblio/2319227)
 
-To cite BioReactorDesign use these articles on [CO2 interphase mass transfer (open access)](https://arxiv.org/pdf/2404.19636) on [aerobic bioreactors](https://www.sciencedirect.com/science/article/pii/S0263876218304337) 
-and on [butanediol synthesis](https://www.sciencedirect.com/science/article/pii/S0263876223004689)
+To cite BiRD, please use these articles on [CO2 interphase mass transfer](https://doi.org/10.1016/j.cherd.2025.01.034) (open access [link](https://arxiv.org/pdf/2404.19636) ) on [aerobic bioreactors](https://doi.org/10.1016/j.cherd.2018.08.033) and on [butanediol synthesis](https://doi.org/10.1016/j.cherd.2023.07.031)
+
+
 ```
-@article{hassanaly2024inverse,
-  title={Bayesian calibration of bubble size dynamics applied to \ce{CO2} gas fermenters},
-  author={Hassanaly, Malik and Parra-Alvarez, John M. and Rahimi, Mohammad J. and Sitaraman, Hariswaran},
-  journal={Under Review},
-  year={2024},
+@article{hassanaly2025bayesian,
+  title={Bayesian calibration of bubble size dynamics applied to CO2 gas fermenters},
+  author={Hassanaly, Malik and Parra-Alvarez, John M and Rahimi, Mohammad J and Municchi, Federico and Sitaraman, Hariswaran},
+  journal={Chemical Engineering Research and Design},
+  volume={215},
+  pages={312--328},
+  year={2025},
+  publisher={Elsevier}
 }
 
-
 @article{rahimi2018computational,
   title={Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas--liquid mass transfer, oxygen uptake, and dynamic oxygen distribution},
   author={Rahimi, Mohammad J and Sitaraman, Hariswaran and Humbird, David and Stickel, Jonathan J},