Move to pyproject

.github/workflows/build_docs.yml

@@ -41,7 +41,7 @@ jobs:
           micromamba install --yes -n test-env -c conda-forge paraview
           python -m pip install --upgrade pip
           pip install -e . 
-          pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints
+          pip install .[docs]
 
       - name: Build documentation
         run: |

.github/workflows/ci.yml

@@ -37,23 +37,27 @@
       - uses: actions/setup-python@v5
         with:
           python-version: ${{matrix.python-version}}
-      - name: Install dependencies
-        run: |
-          pip install black
-          pip install isort
-          pip install codespell
+          cache: 'pip'
+
+      - name: Cache Nox
+        uses: actions/cache@v4
+        with:
+          path: .nox
+          key: ${{ runner.os }}-lint-nox-${{ hashFiles('noxfile.py') }}
+
+      - name: Install nox
+        run: pip install nox
+
       - name: Formatting and sorting import
-        run: |
-          source .github/linters/formatting.sh
-          format . true
+        run: nox -s linter
 
-  Test-BiRD:
-    name: Test-BiRD (${{ matrix.python-version }}, ${{ matrix.os }})
+  Unit-Test-BiRD:
+    name: Unit-Test-BiRD (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.13']
+        python-version: ['3.10', '3.14']
         os: ['ubuntu-latest', 'macos-latest']
     defaults:
       run:
@@ -81,14 +85,15 @@
         run: |
           micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
-          pip install . 
-          pip install pytest
+          pip install --upgrade nox
+          pip install .[tests] 
 
       - name: Test
-        run: pytest .
+        run: nox -s tests -- no-reports
+
 
-  Test-pypi-Bird:
-    name: Test-pypi-BiRD (${{ matrix.python-version }}, ${{ matrix.os }})
+  Unit-Test-pypi-Bird:
+    name: Unit-Test-pypi-BiRD (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -120,105 +125,105 @@
         run: |
           micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
-          pip install nlr-bird
-          pip install pytest
+          pip install --upgrade nox
+          pip install nlr-bird[tests]
 
       - name: Test
-        run: pytest .
+        run: nox -s tests -- no-reports
 
-  Test-OF:
-    name: Test-OF (${{ matrix.python-version }}, ${{ matrix.os }})
+  Regression-Test-OF:
+    name: Regression-Test-OF (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         python-version: ['3.10']
         os: ['ubuntu-22.04']
     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}}
       - 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
           export WM_COMPILE_OPTION=Debug
           ./Allwmake
           cd ../../
       - name: Run deckwer17 PBE
         run: |
           cd experimental_cases/deckwer17
           bash run.sh 
           cd ../../
       - name: Run deckwer17 constantD
         run: |
           cd experimental_cases/deckwer17
           cp constant/phaseProperties_constantd constant/phaseProperties
           bash run.sh 
           cd ../../
       - name: Run deckwer19 PBE
         run: |
           cd experimental_cases/deckwer19
           bash run.sh 
           cd ../../
       - name: Run side sparger tutorial
         run: |
           cd tutorial_cases/side_sparger
           bash run.sh 
           cd ../../
       - name: Run bubble column tutorial
         run: |
           cd tutorial_cases/bubble_column_20L
           bash run.sh 
           cd ../../
       - name: Run stirred-tank tutorial
         run: |
           cd tutorial_cases/stirred_tank
           bash run.sh 
           cd ../../
       - name: Run reactive loop reactor tutorial
         run: |
           cd tutorial_cases/loop_reactor_reacting
           bash run.sh 
           cd ../../
       - name: Run mixing loop reactor tutorial
         run: |
           cd tutorial_cases/loop_reactor_mixing
           bash run.sh 
           cd ../../
       - name: Run airlift reactor tutorial
         run: |
           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

@@ -24,7 +24,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.13'
+          python-version: '3.14'
           cache: 'pip'
 
       - name: Set up micromamba
@@ -42,13 +42,13 @@ jobs:
         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 .
+          pip install --upgrade nox
+          pip install .[tests]
 
       - name: Generate coverage report
         run: |
-          pytest --cov=./ --cov-report=xml:coverage.xml          
+          pytest --cov=./ --cov-report=xml:coverage.xml
+
       - name: Upload coverage to Codecov
 
         uses: codecov/codecov-action@v5

.github/workflows/deploy_docs.yml

@@ -42,8 +42,7 @@ jobs:
         run: |
           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
+          pip install -e .[docs]
 
       - name: Build documentation
         run: |

README.md

@@ -1,4 +1,4 @@
-# <ins>Bi</ins>o <ins>R</ins>eactor <ins>D</ins>esign (BiRD) [![bird-CI](https://github.com/NatLabRockies/BioReactorDesign/actions/workflows/ci.yml/badge.svg)](https://github.com/NatLabRockies/BioReactorDesign/actions/workflows/ci.yml) [![bird-pyversion](https://img.shields.io/pypi/pyversions/NLR-bird.svg)](https://pypi.org/project/NLR-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/nlr-bird.svg)](https://badge.fury.io/py/nlr-bird)
+# <ins>Bi</ins>o <ins>R</ins>eactor <ins>D</ins>esign (BiRD) [![bird-CI](https://github.com/NatLabRockies/BioReactorDesign/actions/workflows/ci.yml/badge.svg)](https://github.com/NatLabRockies/BioReactorDesign/actions/workflows/ci.yml) [![bird-pyversion](https://img.shields.io/pypi/pyversions/NLR-bird.svg)](https://pypi.org/project/NLR-bird/) [![coverage](https://codecov.io/gh/NatlabRockies/BioReactorDesign/graph/badge.svg)](https://app.codecov.io/gh/nrel/bioreactordesign)  [![bird-pypi](https://badge.fury.io/py/nlr-bird.svg)](https://badge.fury.io/py/nlr-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)

bird/version.py

@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.52"
+__version__ = "0.0.53"

docs/source/contribute.rst

@@ -12,8 +12,8 @@ You can automatically enforce the formatting guidelines with
 
 .. code-block:: console
 
-   pip install black isort codespell
-   bash fixFormat.sh
+   pip install nox
+   nox -s lint -- write 
 
 
 Tests

noxfile.py

@@ -0,0 +1,181 @@
+# noxfile.py
+
+import importlib
+import os
+import shutil
+
+import nox
+
+nox.options.sessions = []
+
+
+@nox.session(name="cleanup", python=False)
+def run_cleanup(session: nox.Session) -> None:
+    """Use os/shutil to remove some files/directories"""
+
+    if os.path.exists(".coverage"):
+        os.remove(".coverage")
+
+    if os.path.exists("reports"):
+        shutil.rmtree("reports")
+
+    folders = [".pytest_cache"]
+    for f in folders:
+        if os.path.exists(f):
+            shutil.rmtree(f)
+
+    # Recursively delete all __pycache__ folders and .pyc files
+    session.run(
+        "find",
+        ".",
+        "-type",
+        "d",
+        "-name",
+        "__pycache__",
+        "-exec",
+        "rm",
+        "-r",
+        "{}",
+        "+",
+        external=True,
+    )
+    session.run(
+        "find", ".", "-type", "f", "-name", "*.pyc", "-delete", external=True
+    )
+
+
+@nox.session(name="lint", python=False)
+@nox.session(name="linter", python=False)
+def run_lint(session: nox.Session) -> None:
+    """
+    Run black and isort with the github config file
+
+    """
+
+    session.run("pip", "install", "--upgrade", "--quiet", "black")
+    session.run("pip", "install", "--upgrade", "--quiet", "isort")
+
+    black_command = [
+        "black",
+        "--line-length",
+        "79",
+        "--target-version",
+        "py310",
+        ".",
+    ]
+    isort_command = [
+        "isort",
+        "--profile",
+        "black",
+        "--multi-line",
+        "3",
+        "--trailing-comma",
+        "--force-grid-wrap",
+        "0",
+        "--line-length",
+        "79",
+        "--use-parentheses",
+        ".",
+    ]
+
+    if not "write" in session.posargs:
+        black_command.insert(1, "--check")
+        isort_command.insert(1, "--check-only")
+        isort_command.insert(2, "--diff")
+
+    session.run(*black_command)
+    session.run(*isort_command)
+
+
+@nox.session(name="spell", python=False)
+@nox.session(name="codespell", python=False)
+def run_codespell(session: nox.Session) -> None:
+    """
+    Run codespell with the github config file
+
+    Use the optional 'write' argument to write the corrections directly into
+    the files. Otherwise, you will only see a summary of the found errors.
+
+    """
+
+    session.run("pip", "install", "--upgrade", "--quiet", "codespell")
+    command = ["codespell", "--config", ".github/linters/.codespellrc"]
+
+    if "write" in session.posargs:
+        command.append("-w")
+
+    session.run(*command)
+
+
+@nox.session(name="pypi", python=False)
+@nox.session(name="deploy", python=False)
+def run_deploy(session: nox.Session) -> None:
+    """
+    Deploy to pypi
+    """
+    session.run("pip", "install", "build")
+    session.run("pip", "install", "twine")
+    session.run("python", "-m", "build")
+    session.run(
+        "python",
+        "-m",
+        "twine",
+        "upload",
+        "--verbose",
+        "--repository",
+        "pypi",
+        "dist/*",
+    )
+
+
+@nox.session(name="tests", python=False)
+@nox.session(name="test", python=False)
+def run_pytest(session: nox.Session) -> None:
+    """
+    Run pytest and generate test/coverage reports
+
+    Use the optional 'parallel' argument to run the tests in parallel. As just
+    a flag, the number of workers will be determined automatically. Otherwise,
+    you can specify the number of workers using an int, e.g., parallel=4.
+
+    """
+
+    package = importlib.util.find_spec("bird")
+
+    if "no-reports" in session.posargs:
+        command = [
+            "pytest",
+            f"--cov=.",  # for editable or site-packages
+            "tests/",
+        ]
+    else:
+        command = [
+            "pytest",
+            "--cov=bird",
+            "--cov-report=html:reports/htmlcov",
+            "--cov-report=xml:reports/coverage.xml",
+            "--junitxml=reports/junit.xml",
+            "tests/",
+        ]
+
+    for arg in session.posargs:
+        if arg.startswith("parallel="):
+            command[1:1] = ["-n", arg.split("=")[-1]]
+        elif arg.startswith("parallel"):
+            command[1:1] = ["-n", "auto"]
+    session.run(*command)
+    run_cleanup(session)
+
+
+def run_pre_commit(session: nox.Session) -> None:
+    """
+    Run all linters/tests and make new badges
+
+    Order of sessions: flake8, codespell, pytest, genbade. Using 'format' for
+    linter, 'write' for codespell, and/or 'parallel' for pytest is permitted.
+
+    """
+
+    run_lint(session)
+    run_codespell(session)
+    run_pytest(session)