use pyproject.toml

.github/workflows/build_docs.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install sphinx sphinx_rtd_theme
+          pip install .[docs] --no-deps
 
       - name: Build documentation
         run: |

.github/workflows/ci.yml

@@ -36,9 +36,9 @@ jobs:
           python-version: ${{matrix.python-version}}
       - name: Install dependencies
         run: |
-          pip install black
-          pip install isort
-          pip install codespell
+          pip install --upgrade pip
+          pip install .[format] --no-deps
+
       - name: Formatting and sorting import
         run: |
           source .github/linters/formatting.sh
@@ -63,8 +63,8 @@ jobs:
       - name: Install dependencies
         run: |
           pip install --upgrade pip
-          pip install .
-          pip install pytest
+          pip install .[test,post]
+
       - name: Test preprocess
         run: |
           pytest tests/preprocess

.github/workflows/deploy_docs.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install sphinx sphinx_rtd_theme
+          pip install .[docs] --no-deps
 
       - name: Build documentation
         run: |

README.md

@@ -17,14 +17,20 @@ conda create --name bird python=3.10
 conda activate bird
 git clone https://github.com/NREL/BioReactorDesign.git
 cd BioReactorDesign
-pip install -e .
+pip install -e .[all]
 ```
 
 ## Installation of python package for users
 
 ```bash
 conda create --name bird python=3.10
 conda activate bird
+pip install nrel-bird[post]
+```
+
+If you do not need the post processing tools, please replace the last line with 
+
+```bash
 pip install nrel-bird
 ```
 

docs/source/quickstart.rst

@@ -14,7 +14,7 @@ Installation of python package for developers
    conda activate bird
    git clone https://github.com/NREL/BioReactorDesign.git
    cd BioReactorDesign
-   pip install -e .
+   pip install -e .[all]
 
 .. _installation_users:
 

pyproject.toml

@@ -0,0 +1,84 @@
+[build-system]
+requires = ["setuptools >= 64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nrel-bird"
+version = "0.0.15"
+description = "Bio Reactor Design (BiRD): a toolbox to simulate and analyze different designs of bioreactors in OpenFOAM"
+readme = {file = "README.md", content-type = "text/markdown"}
+authors = [
+  {name = "Malik Hassanaly", email = "[email protected]"},
+  {name = "Federico Municchi", email = "[email protected]"},
+  {name = "Hariswaran Sitaraman", email = "[email protected]"},
+  {name = "Mohammad Rahimi", email = "[email protected]"},
+]
+license = {text = "BSD-3-Clause"}
+requires-python = ">= 3.9"
+classifiers=[
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Natural Language :: English",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "numpy",
+    "prettyPlot",
+    "ruamel_yaml",
+    "numpy-stl==2.17.0",
+    "scipy",
+]
+
+
+[project.optional-dependencies]
+post = [
+    "corner",
+    "jax",
+    "numpyro>=0.16.1"
+]
+format = [
+    "black",
+    "isort",
+    "codespell"
+]
+docs = [
+    "sphinx",
+    "sphinx_rtd_theme"
+]
+test = [
+    "pytest"
+]
+all = [
+    "corner",
+    "jax",
+    "numpyro>=0.16.1",
+    "black",
+    "isort",
+    "codespell",
+    "sphinx",
+    "sphinx_rtd_theme",
+    "pytest",
+]
+
+
+[project.urls]
+homepage = "https://github.com/NREL/BioReactorDesign"
+documentation = "https://nrel.github.io/BioReactorDesign/"
+repository = "https://github.com/NREL/BioReactorDesign"
+
+[tool.setuptools]
+package-dir = {bird = "bird"}
+packages = ["bird"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+"bird" = [
+    "*.json",
+    "*.yaml",
+    "*.csv",
+    "data_conditional_mean",
+]
+