Switch to using pyproject.toml

.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 black isort codespell
+
       - 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
@@ -94,7 +94,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install --upgrade pip
-          pip install nrel-bird
+          pip install nrel-bird[post]
           pip install pytest
       - name: Test
         run: pytest .

.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 sphinx sphinx-rtd-theme
 
       - 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
 ```
 

bird/meshing/stirred_tank_mesh_templates/base_tank/tank_par.yaml

@@ -1,23 +1,23 @@
 geometry:
-    Dt:        0.26		# Tank diameter  [m]
-    Da:        0.0866667	# Impleller tip Diameter  [m]
-    H:         0.39		# Height of the reactor  [m]
-    nimpellers:	1
-    C: 		[0.0866667]	# height of the center of impellers [m]
-    W:		0.026		# impeller blade width [m]
-    L:		0.013		# impeller blade length (beyond the hub) [m]
-    Lin:	0.013		# impeller blade length (inside the hub)
-    J:		0.026		# Baffle width
-    Wh:		0.0026		# Hub height (Width)
-    polyrad:	0.00866667	# Stem radius (R_shaft)
-    Z0:		0.0		# bottom of reactor
-    nbaffles:	6		# number of baffles and impeller fins
+    Dt:        0.26             # Tank diameter  [m]
+    Da:        0.0866667        # Impleller tip Diameter  [m]
+    H:         0.39             # Height of the reactor  [m]
+    nimpellers: 1
+    C:         [0.0866667]     # height of the center of impellers [m]
+    W:          0.026           # impeller blade width [m]
+    L:          0.013           # impeller blade length (beyond the hub) [m]
+    Lin:        0.013           # impeller blade length (inside the hub)
+    J:          0.026           # Baffle width
+    Wh:         0.0026          # Hub height (Width)
+    polyrad:    0.00866667      # Stem radius (R_shaft)
+    Z0:         0.0             # bottom of reactor
+    nbaffles:   6               # number of baffles and impeller fins
 
 mesh:
-    nr:		120		# mesh points per unit radial length
-    nz:		240		# mesh points per unit axial length
-    Npoly:	4		# mesh points in the polygon at the axis
-    Na:		6		# mesh points in the azimuthal direction
+    nr:         120             # mesh points per unit radial length
+    nz:         240             # mesh points per unit axial length
+    Npoly:      4               # mesh points in the polygon at the axis
+    Na:         6               # mesh points in the azimuthal direction
 
 
 

bird/version.py

@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.15"
+__version__ = "0.0.16"

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 +1,83 @@
+[build-system]
+requires = ["setuptools >= 64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nrel-bird"
+version = "0.0.16"
+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",
+    "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]
+packages = ["bird", "bird.meshing", "bird.preprocess", "bird.postprocess", "bird.calibration", "bird.utilities"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+bird = [
+    "*.json",
+    "*.yaml",
+    "*.csv",
+    "data_conditional_mean",
+]
+

tests/preprocess/test_stl_patch.py

@@ -5,20 +5,22 @@
 from bird import BIRD_PRE_PATCH_TEMP_DIR
 from bird.meshing._mesh_tools import parseJsonFile
 from bird.preprocess.stl_patch.stl_bc import write_boundaries
-from bird.utilities.stl_plotting import plotSTL, pretty_labels
+from bird.utilities.stl_plotting import plotSTL, plt, pretty_labels
 
 
-def test_spider_sparger():
+def test_spider_sparger(verbose=False):
     input_dict = parseJsonFile(
         os.path.join(BIRD_PRE_PATCH_TEMP_DIR, "spider_spg/inlets_outlets.json")
     )
     write_boundaries(input_dict)
     # plot
     axes = plotSTL("inlets.stl")
     pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
+    if verbose:
+        plt.show()
 
 
-def test_loop_reactor():
+def test_loop_reactor(verbose=False):
     input_dict = parseJsonFile(
         os.path.join(
             BIRD_PRE_PATCH_TEMP_DIR, "loop_reactor_expl/inlets_outlets.json"
@@ -28,9 +30,14 @@ def test_loop_reactor():
     # plot
     axes = plotSTL("inlets.stl")
     pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
+    # plot
+    axes = plotSTL("outlets.stl")
+    pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
+    if verbose:
+        plt.show()
 
 
-def test_loop_reactor_branch():
+def test_loop_reactor_branch(verbose=False):
     input_dict = parseJsonFile(
         os.path.join(
             BIRD_PRE_PATCH_TEMP_DIR, "loop_reactor_branch/inlets_outlets.json"
@@ -40,7 +47,14 @@ def test_loop_reactor_branch():
     # plot
     axes = plotSTL("inlets.stl")
     pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
+    # plot
+    axes = plotSTL("outlets.stl")
+    pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
+    if verbose:
+        plt.show()
 
 
 if __name__ == "__main__":
-    test_spider_sparger()
+    test_spider_sparger(verbose=True)
+    test_loop_reactor(verbose=True)
+    test_loop_reactor_branch(verbose=True)