Move to pyproject (#147)

* move to pyproj

* support py3.14

* rogue dep

* fix cov report folder

* deploy in nox

* remove fixformat in docs

* rename reg test

Author: malihass

.github/linters/formatting.sh

@@ -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/build_docs.yml

@@ -37,23 +37,27 @@ jobs:
       - 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 @@ jobs:
         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
@@ -120,14 +125,14 @@ jobs:
         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

.github/workflows/ci.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/codecov.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: |

.github/workflows/deploy_docs.yml

@@ -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)

README.md

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

bird/requirements.txt

@@ -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