rename brd to bird

Author: malihass

Diff for: .github/workflows/ci.yml

@@ -1,8 +1,8 @@
-name: brd-CI
+name: bird-CI
 
 on:
    push:
-     branches: [main, reorg]
+     branches: [main, reorg, rename]
      paths-ignore:
       - '*.md'
       - 'README*'

Diff for: .gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# output
+.DS_Store

Diff for: README.md

@@ -2,8 +2,8 @@
 
 from prettyPlot.plotting import plt, pretty_labels
 
-# from brd import BRD_COND_MEAN_DATA_DIR
-from brd.postProcess.conditional_mean import (
+# from bird import BIRD_COND_MEAN_DATA_DIR
+from bird.postProcess.conditional_mean import (
     compute_cond_mean,
     save_cond,
     sequencePlot,
@@ -22,7 +22,7 @@ def main():
         metavar="",
         required=True,
         help="caseFolder to analyze",
-        default="brd/postProcess/data_conditional_mean",
+        default="bird/postProcess/data_conditional_mean",
     )
 
     parser.add_argument(

Diff for: applications/compute_conditional_mean.py

@@ -2,7 +2,7 @@
 
 from prettyPlot.plotting import plt
 
-from brd.postProcess.early_pred import (
+from bird.postProcess.early_pred import (
     bayes_fit,
     fit_and_ext,
     multi_data_load,
@@ -12,7 +12,7 @@
 
 
 def main():
-    from brd import BRD_EARLY_PRED_DATA_DIR
+    from bird import BIRD_EARLY_PRED_DATA_DIR
 
     parser = argparse.ArgumentParser(description="Early prediction")
     parser.add_argument(
@@ -22,7 +22,7 @@ def main():
         metavar="",
         required=True,
         help="Data folder containing multiple QOI time histories",
-        default=BRD_EARLY_PRED_DATA_DIR,
+        default=BIRD_EARLY_PRED_DATA_DIR,
     )
     parser.add_argument(
         "-func",

Diff for: applications/early_prediction.py

@@ -4,8 +4,8 @@
 
 import numpy as np
 
-from brd import BRD_BLOCK_CYL_MESH_TEMP_DIR
-from brd.meshing.block_cyl_mesh import (
+from bird import BIRD_BLOCK_CYL_MESH_TEMP_DIR
+from bird.meshing.block_cyl_mesh import (
     assemble_geom,
     assemble_mesh,
     writeBlockMeshDict,

Diff for: applications/write_block_cyl_mesh.py

@@ -4,8 +4,8 @@
 
 import numpy as np
 
-from brd import BRD_STIR_TANK_MESH_TEMP_DIR
-from brd.meshing.stir_tank_mesh import (
+from bird import BIRD_STIR_TANK_MESH_TEMP_DIR
+from bird.meshing.stir_tank_mesh import (
     get_reactor_geom,
     write_blocks,
     write_edges,
@@ -34,7 +34,7 @@ def main():
         required=True,
         help="YAML file containing geometry details of reactor",
         default=os.path.join(
-            BRD_STIR_TANK_MESH_TEMP_DIR, "base_tank", "tank_par.yaml"
+            BIRD_STIR_TANK_MESH_TEMP_DIR, "base_tank", "tank_par.yaml"
         ),
     )
     args = parser.parse_args()

Diff for: applications/write_stir_tank_mesh.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from brd.meshing.stl_mesh_tools import makeSpider, saveSTL
+from bird.meshing.stl_mesh_tools import makeSpider, saveSTL
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Generate Spider Sparger STL")
@@ -61,7 +61,7 @@
 
     if args.verbose:
         # plot
-        from brd.utilities.stl_plotting import plotSTL, plt, pretty_labels
+        from bird.utilities.stl_plotting import plotSTL, plt, pretty_labels
 
         axes = plotSTL("spg.stl")
         pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)

Diff for: applications/write_stl_mesh.py

@@ -0,0 +1,24 @@
+"""Bio reactor design"""
+
+import os
+
+from bird.version import __version__
+
+BIRD_DIR = os.path.dirname(os.path.realpath(__file__))
+BIRD_MESH_DIR = os.path.join(BIRD_DIR, "meshing")
+BIRD_POST_DIR = os.path.join(BIRD_DIR, "postProcess")
+BIRD_BLOCK_CYL_MESH_TEMP_DIR = os.path.join(
+    BIRD_MESH_DIR, "block_cyl_mesh_templates"
+)
+BIRD_BLOCK_CYL_CASE_TEMP_DIR = os.path.join(
+    BIRD_MESH_DIR, "block_cyl_case_templates"
+)
+BIRD_STIR_TANK_MESH_TEMP_DIR = os.path.join(
+    BIRD_MESH_DIR, "stir_tank_mesh_templates"
+)
+BIRD_STIR_TANK_CASE_TEMP_DIR = os.path.join(
+    BIRD_MESH_DIR, "stir_tank_case_templates"
+)
+BIRD_EARLY_PRED_DATA_DIR = os.path.join(BIRD_POST_DIR, "data_early")
+# BIRD_COND_MEAN_DATA_DIR = os.path.join(BIRD_POST_DIR, "data_conditional_mean")
+BIRD_INV_DIR = os.path.join(BIRD_DIR, "inverse_modeling")

Diff for: bird/__init__.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from brd.meshing._mesh_tools import *
+from bird.meshing._mesh_tools import *
 
 
 def assemble_geom(input_file, topo_file):

Diff for: brd/meshing/_mesh_tools.py renamed to bird/meshing/_mesh_tools.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from brd.meshing._stir_tank_reactor import StirTankReactor
+from bird.meshing._stir_tank_reactor import StirTankReactor
 
 
 def get_reactor_geom(yamlfile):

Diff for: brd/meshing/_stir_tank_reactor.py renamed to bird/meshing/_stir_tank_reactor.py

@@ -9,7 +9,7 @@
 
 from ofio import *
 
-from brd.utilities.bubble_col_util import *
+from bird.utilities.bubble_col_util import *
 
 parser = argparse.ArgumentParser(
     description="Compute means QoI of OpenFOAM fields"

Diff for: brd/meshing/block_cyl_cases_templates/case/system/blockMeshDict renamed to bird/meshing/block_cyl_cases_templates/case/system/blockMeshDict

@@ -3,9 +3,9 @@
 
 from prettyPlot.plotting import plt
 
-from brd.utilities.bubble_col_util import *
-from brd.utilities.mathtools import *
-from brd.utilities.ofio import *
+from bird.utilities.bubble_col_util import *
+from bird.utilities.mathtools import *
+from bird.utilities.ofio import *
 
 
 def compute_cond_mean(