From e38eaf99f7976516a8278ed1eb17cf06364174be Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Fri, 17 Oct 2025 09:14:25 -0600
Subject: [PATCH 01/19] use pathlib instead of makedirs to handle intermediate
 directory creation

---
 bird/calibration/param_nn.py                 | 5 +++--
 bird/preprocess/json_gen/generate_designs.py | 5 +++--
 bird/utilities/folderManagement.py           | 8 --------
 tests/meshing/test_block_cyl_mesh.py         | 2 +-
 tests/meshing/test_block_rect_mesh.py        | 2 +-
 5 files changed, 8 insertions(+), 14 deletions(-)

diff --git a/bird/calibration/param_nn.py b/bird/calibration/param_nn.py
index c0cc8255..5847fdb0 100644
--- a/bird/calibration/param_nn.py
+++ b/bird/calibration/param_nn.py
@@ -1,6 +1,7 @@
 import argparse
 import os
 import time
+from pathlib import Path
 
 import joblib
 import numpy as np
@@ -306,8 +307,8 @@ def load(self, weight_file):
         self.model.load_weights(weight_file)
 
     def prepareLog(self):
-        os.makedirs(self.model_folder, exist_ok=True)
-        os.makedirs(self.log_loss_folder, exist_ok=True)
+        Path(self.model_folder).mkdir(parents=True, exist_ok=True)
+        Path(self.log_loss_folder).mkdir(parents=True, exist_ok=True)
         try:
             os.remove(os.path.join(self.log_loss_folder, "log.csv"))
         except FileNotFoundError as err:
diff --git a/bird/preprocess/json_gen/generate_designs.py b/bird/preprocess/json_gen/generate_designs.py
index cdf06514..862de36a 100644
--- a/bird/preprocess/json_gen/generate_designs.py
+++ b/bird/preprocess/json_gen/generate_designs.py
@@ -1,6 +1,7 @@
 import os
 import pickle
 import shutil
+from pathlib import Path
 
 import numpy as np
 
@@ -174,7 +175,7 @@ def generate_small_reactor_cases(
         shutil.rmtree(study_folder)
     except:
         pass
-    os.makedirs(study_folder)
+    Path(study_folder).mkdir(parents=True, exist_ok=True)
     for sim_id in config_dict:
         sim_folder = id2simfolder(sim_id)
         shutil.copytree(
@@ -292,7 +293,7 @@ def generate_scaledup_reactor_cases(
         shutil.rmtree(study_folder)
     except:
         pass
-    os.makedirs(study_folder)
+    Path(study_folder).mkdir(parents=True, exist_ok=True)
     for sim_id in config_dict:
         sim_folder = id2simfolder(sim_id)
         shutil.copytree(
diff --git a/bird/utilities/folderManagement.py b/bird/utilities/folderManagement.py
index 3c31efa1..1147900b 100644
--- a/bird/utilities/folderManagement.py
+++ b/bird/utilities/folderManagement.py
@@ -4,14 +4,6 @@
 from bird import logger
 
 
-def makeRecursiveFolder(path):
-    folder_list = path.split("/")
-    localFolder = ""
-    for folder in folder_list:
-        localFolder = os.path.join(localFolder, folder)
-        os.makedirs(localFolder, exist_ok=True)
-
-
 def getManyFolders(rootFolder, prefix="flat_donut"):
     # Read Time
     fold_tmp = os.listdir(rootFolder)
diff --git a/tests/meshing/test_block_cyl_mesh.py b/tests/meshing/test_block_cyl_mesh.py
index c5d181a1..c9924ef9 100644
--- a/tests/meshing/test_block_cyl_mesh.py
+++ b/tests/meshing/test_block_cyl_mesh.py
@@ -13,7 +13,7 @@
 
 
 def base_mesh(input_file, topo_file, output_folder):
-    os.makedirs(output_folder, exist_ok=True)
+    Path(output_folder).mkdir(parents=True, exist_ok=True)
     geomDict = assemble_geom(input_file, topo_file)
     meshDict = assemble_mesh(input_file, geomDict)
     writeBlockMeshDict(output_folder, geomDict, meshDict)
diff --git a/tests/meshing/test_block_rect_mesh.py b/tests/meshing/test_block_rect_mesh.py
index 32e7c855..f651161f 100644
--- a/tests/meshing/test_block_rect_mesh.py
+++ b/tests/meshing/test_block_rect_mesh.py
@@ -13,7 +13,7 @@
 
 
 def base_mesh(input_file, output_folder):
-    os.makedirs(output_folder, exist_ok=True)
+    Path(output_folder).mkdir(parents=True, exist_ok=True)
     geomDict = assemble_geom(input_file)
     meshDict = assemble_mesh(input_file)
     writeBlockMeshDict(output_folder, geomDict, meshDict)

From 387de5ae0274cc360a5b600c1509aeafc8edcba3 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Fri, 17 Oct 2025 10:47:16 -0600
Subject: [PATCH 02/19] remove folderManagement and path appends

---
 bird/utilities/folderManagement.py            | 28 -------------
 papers/co2_model/validation/compareToExp.py   |  4 +-
 papers/sparger/process_geom/compare_qoi.py    | 13 +++---
 papers/sparger/process_geom/plot_cond.py      | 38 +++++++++++++----
 .../process_geom/plot_cond_multiFold.py       | 13 +++---
 papers/sparger/process_geom/plot_qoi.py       | 42 ++++++++++++++-----
 .../process_geom/plot_qoi_multiFold.py        | 15 +++----
 7 files changed, 80 insertions(+), 73 deletions(-)
 delete mode 100644 bird/utilities/folderManagement.py

diff --git a/bird/utilities/folderManagement.py b/bird/utilities/folderManagement.py
deleted file mode 100644
index 1147900b..00000000
--- a/bird/utilities/folderManagement.py
+++ /dev/null
@@ -1,28 +0,0 @@
-import os
-import re
-
-from bird import logger
-
-
-def getManyFolders(rootFolder, prefix="flat_donut"):
-    # Read Time
-    fold_tmp = os.listdir(rootFolder)
-    fold_num = []
-    # remove non floats
-    for i, entry in reversed(list(enumerate(fold_tmp))):
-        if not entry.startswith(prefix) or entry.endswith("N2"):
-            a = fold_tmp.pop(i)
-            # print('removed ', a)
-    for entry in fold_tmp:
-        num = re.findall(r"\d+", entry)
-        if len(num) > 1:
-            msg = f"Cannot find num of folder {entry}."
-            msg += "\nDo not trust the spearman stat"
-            logger.warning(msg)
-        else:
-            fold_num.append(int(num[0]))
-
-    sortedFold = [
-        x for _, x in sorted(zip(fold_num, fold_tmp), key=lambda pair: pair[0])
-    ]
-    return sortedFold
diff --git a/papers/co2_model/validation/compareToExp.py b/papers/co2_model/validation/compareToExp.py
index 5291917a..6f6964c3 100644
--- a/papers/co2_model/validation/compareToExp.py
+++ b/papers/co2_model/validation/compareToExp.py
@@ -1,11 +1,11 @@
 import argparse
 import os
 import sys
+from pathlib import Path
 
 import numpy as np
 from prettyPlot.plotting import plt, pretty_labels, pretty_legend
 
-from bird.utilities.folderManagement import *
 from bird.utilities.ofio import *
 
 parser = argparse.ArgumentParser(description="Case folder")
@@ -50,7 +50,7 @@
 
 figureFolder = "Figures"
 figureFolder = os.path.join(figureFolder, args.figureFolder)
-makeRecursiveFolder(figureFolder)
+Path(figureFolder).mkdir(exist_ok=True, parents=True)
 
 conv17 = np.load(os.path.join(args.caseFolder17, "convergence_gh.npz"))
 conv19 = np.load(os.path.join(args.caseFolder19, "convergence_gh.npz"))
diff --git a/papers/sparger/process_geom/compare_qoi.py b/papers/sparger/process_geom/compare_qoi.py
index f526e344..e0e607b9 100644
--- a/papers/sparger/process_geom/compare_qoi.py
+++ b/papers/sparger/process_geom/compare_qoi.py
@@ -1,17 +1,14 @@
 import argparse
-import sys
-
-import numpy as np
-
-sys.path.append("../utilities")
 import os
 import pickle
+import sys
+from pathlib import Path
 
-from folderManagement import *
-from ofio import *
+import numpy as np
 from prettyPlot.plotting import plt, pretty_labels, pretty_legend
 
 from bird.utilities.label_plot import label_conv
+from bird.utilities.ofio import *
 
 parser = argparse.ArgumentParser(description="Compare Qoi")
 parser.add_argument(
@@ -88,7 +85,7 @@
 dataFiles = args.dataFiles
 mode = args.mode
 
-makeRecursiveFolder(figureFolder)
+Path(figureFolder).mkdir(parents=True, exist_ok=True)
 data_structs = [np.load(dataFile) for dataFile in dataFiles]
 
 symbol_list = ["o", "s", "^"]
diff --git a/papers/sparger/process_geom/plot_cond.py b/papers/sparger/process_geom/plot_cond.py
index 04bf9c0a..91f6cda0 100644
--- a/papers/sparger/process_geom/plot_cond.py
+++ b/papers/sparger/process_geom/plot_cond.py
@@ -1,17 +1,39 @@
 import argparse
-import sys
-
-import numpy as np
-
-sys.path.append("../utilities")
 import os
 import pickle
+import sys
+from pathlib import Path
 
-from folderManagement import *
-from ofio import *
+import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
 from bird.utilities.label_plot import label_conv
+from bird.utilities.ofio import *
+
+
+def getManyFolders(rootFolder, prefix="flat_donut"):
+    # Read Time
+    fold_tmp = os.listdir(rootFolder)
+    fold_num = []
+    # remove non floats
+    for i, entry in reversed(list(enumerate(fold_tmp))):
+        if not entry.startswith(prefix) or entry.endswith("N2"):
+            a = fold_tmp.pop(i)
+            # print('removed ', a)
+    for entry in fold_tmp:
+        num = re.findall(r"\d+", entry)
+        if len(num) > 1:
+            msg = f"Cannot find num of folder {entry}."
+            msg += "\nDo not trust the spearman stat"
+            logger.warning(msg)
+        else:
+            fold_num.append(int(num[0]))
+
+    sortedFold = [
+        x for _, x in sorted(zip(fold_num, fold_tmp), key=lambda pair: pair[0])
+    ]
+    return sortedFold
+
 
 parser = argparse.ArgumentParser(description="Plot cond qoi")
 parser.add_argument(
@@ -96,7 +118,7 @@
 args = parser.parse_args()
 figureFolder = "Figures"
 figureFolder = os.path.join(figureFolder, args.figureFolder, "cond")
-makeRecursiveFolder(figureFolder)
+Path(figureFolder).mkdir(parents=True, exist_ok=True)
 field_names = args.field_list
 param_file = args.paramFile
 study_folder = args.studyFolder
diff --git a/papers/sparger/process_geom/plot_cond_multiFold.py b/papers/sparger/process_geom/plot_cond_multiFold.py
index b2ef5582..01ec82dc 100644
--- a/papers/sparger/process_geom/plot_cond_multiFold.py
+++ b/papers/sparger/process_geom/plot_cond_multiFold.py
@@ -1,17 +1,14 @@
 import argparse
-import sys
-
-import numpy as np
-
-sys.path.append("../utilities")
 import os
 import pickle
+import sys
+from pathlib import Path
 
-from folderManagement import *
-from ofio import *
+import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
 from bird.utilities.label_plot import label_conv
+from bird.utilities.ofio import *
 
 parser = argparse.ArgumentParser(description="Plot cond qoi")
 parser.add_argument(
@@ -80,7 +77,7 @@
 args = parser.parse_args()
 figureFolder = "Figures"
 figureFolder = os.path.join(figureFolder, args.figureFolder, "cond")
-makeRecursiveFolder(figureFolder)
+Path(figureFolder).mkdir(exist_ok=True, parents=True)
 field_names = args.field_list
 param_name = args.param_name
 param_vals = args.param_value
diff --git a/papers/sparger/process_geom/plot_qoi.py b/papers/sparger/process_geom/plot_qoi.py
index 76227422..0a5a9d54 100644
--- a/papers/sparger/process_geom/plot_qoi.py
+++ b/papers/sparger/process_geom/plot_qoi.py
@@ -1,17 +1,39 @@
 import argparse
-import sys
-
-import numpy as np
-
-sys.path.append("../utilities")
 import os
 import pickle
+import sys
+from pathlib import Path
 
-from folderManagement import *
-from ofio import *
+import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
 from bird.utilities.label_plot import label_conv
+from bird.utilities.ofio import *
+
+
+def getManyFolders(rootFolder, prefix="flat_donut"):
+    # Read Time
+    fold_tmp = os.listdir(rootFolder)
+    fold_num = []
+    # remove non floats
+    for i, entry in reversed(list(enumerate(fold_tmp))):
+        if not entry.startswith(prefix) or entry.endswith("N2"):
+            a = fold_tmp.pop(i)
+            # print('removed ', a)
+    for entry in fold_tmp:
+        num = re.findall(r"\d+", entry)
+        if len(num) > 1:
+            msg = f"Cannot find num of folder {entry}."
+            msg += "\nDo not trust the spearman stat"
+            logger.warning(msg)
+        else:
+            fold_num.append(int(num[0]))
+
+    sortedFold = [
+        x for _, x in sorted(zip(fold_num, fold_tmp), key=lambda pair: pair[0])
+    ]
+    return sortedFold
+
 
 parser = argparse.ArgumentParser(description="Plot Qoi")
 parser.add_argument(
@@ -124,9 +146,9 @@
 )
 
 
-makeRecursiveFolder(figure_qoi_folder)
-makeRecursiveFolder(figure_qoiNP_folder)
-makeRecursiveFolder(figure_qoiConv_folder)
+Path(figure_qoi_folder).mkdir(exist_ok=True, parents=True)
+Path(figure_qoiNP_folder).mkdir(exist_ok=True, parents=True)
+Path(figure_qoiConv_folder).mkdir(exist_ok=True, parents=True)
 var_names = args.var_list
 vmin = args.vmin
 vmax = args.vmax
diff --git a/papers/sparger/process_geom/plot_qoi_multiFold.py b/papers/sparger/process_geom/plot_qoi_multiFold.py
index 587ea49b..c3ad48ff 100644
--- a/papers/sparger/process_geom/plot_qoi_multiFold.py
+++ b/papers/sparger/process_geom/plot_qoi_multiFold.py
@@ -1,17 +1,14 @@
 import argparse
-import sys
-
-import numpy as np
-
-sys.path.append("../utilities")
 import os
 import pickle
+import sys
+from pathlib import Path
 
-from folderManagement import *
-from ofio import *
+import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
 from bird.utilities.label_plot import label_conv
+from bird.utilities.ofio import *
 
 parser = argparse.ArgumentParser(description="Plot Qoi")
 parser.add_argument(
@@ -82,8 +79,8 @@
 figure_qoiConv_Folder = os.path.join(
     figureFolder, args.figureFolder, "qoi_conv"
 )
-makeRecursiveFolder(figure_qoi_Folder)
-makeRecursiveFolder(figure_qoiConv_Folder)
+Path(figure_qoi_Folder).mkdir(parents=True, exist_ok=True)
+Path(figure_qoiConv_Folder).mkdir(parents=True, exist_ok=True)
 var_names = args.var_list
 param_name = args.param_name
 param_vals = args.param_value

From a45d4ff50830c7bba7935f7d0bae0dc4d622b573 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Fri, 17 Oct 2025 10:52:40 -0600
Subject: [PATCH 03/19] print bird on warning

---
 bird/logging_config.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/bird/logging_config.py b/bird/logging_config.py
index 0df52260..5e246367 100644
--- a/bird/logging_config.py
+++ b/bird/logging_config.py
@@ -6,9 +6,7 @@ class ConditionalFormatter(logging.Formatter):
     def format(self, record):
         """Change how to log if it is an INFO or a WARNING/ERROR"""
         if record.levelno >= logging.WARNING:
-            self._style._fmt = (
-                "%(asctime)s [%(levelname)s] %(name)s: %(message)s"
-            )
+            self._style._fmt = "%(asctime)s [%(levelname)s] bird: %(message)s"
         else:
             self._style._fmt = "%(asctime)s [%(levelname)s] bird: %(message)s"
         return super().format(record)

From 7ff751576685c45357cab5743172977801b6a593 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 10:23:29 -0600
Subject: [PATCH 04/19] remove value error warning

---
 bird/postprocess/early_pred.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bird/postprocess/early_pred.py b/bird/postprocess/early_pred.py
index d96edf26..2ce81e1a 100644
--- a/bird/postprocess/early_pred.py
+++ b/bird/postprocess/early_pred.py
@@ -102,7 +102,9 @@ def multi_data_load(data_root, tmax=600, data_files=None, color_files=None):
         A = np.loadtxt(filename)
         data_dict[datf] = {}
         data_dict[datf]["t"] = A[:, 0]
-        data_dict[datf]["y"] = A[:, 5] / (A[:, 4] * 16 / 44 + A[:, 5])
+        data_dict[datf]["y"] = A[:, 5] / np.clip(
+            (A[:, 4] * 16 / 44 + A[:, 5]), a_min=1e-12, a_max=None
+        )
         # chop data before increase and right after t=10s
         increase_ind_arr = np.argwhere(np.diff(data_dict[datf]["y"]) > 0)
         increase_ind = increase_ind_arr[

From 5c0143090227096929dac3af6f94c42a6907643b Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 10:25:00 -0600
Subject: [PATCH 05/19] remove more bird utilities

---
 applications/write_stl_patch.py               |  4 ++--
 bird/utilities/stl_plotting.py                | 24 +++++++++++++++----
 papers/sparger/process_geom/compare_qoi.py    |  3 ++-
 .../sparger/process_geom}/label_plot.py       |  0
 papers/sparger/process_geom/plot_cond.py      |  3 ++-
 .../process_geom/plot_cond_multiFold.py       |  3 ++-
 papers/sparger/process_geom/plot_qoi.py       |  3 ++-
 .../process_geom/plot_qoi_multiFold.py        |  3 ++-
 tests/preprocess/test_stl_patch.py            |  8 +++----
 9 files changed, 36 insertions(+), 15 deletions(-)
 rename {bird/utilities => papers/sparger/process_geom}/label_plot.py (100%)

diff --git a/applications/write_stl_patch.py b/applications/write_stl_patch.py
index fe7d9f24..655156a2 100644
--- a/applications/write_stl_patch.py
+++ b/applications/write_stl_patch.py
@@ -32,8 +32,8 @@
 
     if args.verbose:
         # plot
-        from bird.utilities.stl_plotting import plotSTL, plt, pretty_labels
+        from bird.utilities.stl_plotting import plot_stl, plt, pretty_labels
 
-        axes = plotSTL("inlets.stl")
+        axes = plot_stl("inlets.stl")
         pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
         plt.show()
diff --git a/bird/utilities/stl_plotting.py b/bird/utilities/stl_plotting.py
index 19fdaabb..e6b8b835 100644
--- a/bird/utilities/stl_plotting.py
+++ b/bird/utilities/stl_plotting.py
@@ -1,10 +1,25 @@
+import matplotlib
 import numpy as np
+from mpl_toolkits import mplot3d
 from prettyPlot.plotting import plt, pretty_labels, pretty_legend
+from stl import mesh
 
 
-def plotSTL(stl_file):
-    from mpl_toolkits import mplot3d
-    from stl import mesh
+def plot_stl(stl_file: str) -> matplotlib.axes.Axes:
+    """
+    Plot a 2D STL file with matplotlib
+    This is useful to check boundary condition definition with STL
+
+    Parameters
+    ----------
+    stl_file: str
+        Name of the STL file to display
+
+    Returns
+    ----------
+    axes: matplotlib.axes.Axes
+        Axes of the plot created
+    """
 
     # Create a new plot
     figure = plt.figure()
@@ -25,7 +40,8 @@ def plotSTL(stl_file):
     max_z = np.amax(your_mesh.points[:, 2])
 
     amp = np.array([max_x - min_x, max_y - min_y, max_z - min_z])
-    # 2D view
+
+    # Rotate so we have a 2D view
     if abs(amp[0]) < 1e-12:
         axes.view_init(0, 90)
     elif abs(amp[1]) < 1e-12:
diff --git a/papers/sparger/process_geom/compare_qoi.py b/papers/sparger/process_geom/compare_qoi.py
index e0e607b9..0f5d3012 100644
--- a/papers/sparger/process_geom/compare_qoi.py
+++ b/papers/sparger/process_geom/compare_qoi.py
@@ -7,9 +7,10 @@
 import numpy as np
 from prettyPlot.plotting import plt, pretty_labels, pretty_legend
 
-from bird.utilities.label_plot import label_conv
 from bird.utilities.ofio import *
 
+from .label_plot import label_conv
+
 parser = argparse.ArgumentParser(description="Compare Qoi")
 parser.add_argument(
     "-df",
diff --git a/bird/utilities/label_plot.py b/papers/sparger/process_geom/label_plot.py
similarity index 100%
rename from bird/utilities/label_plot.py
rename to papers/sparger/process_geom/label_plot.py
diff --git a/papers/sparger/process_geom/plot_cond.py b/papers/sparger/process_geom/plot_cond.py
index 91f6cda0..6bebeb5d 100644
--- a/papers/sparger/process_geom/plot_cond.py
+++ b/papers/sparger/process_geom/plot_cond.py
@@ -7,9 +7,10 @@
 import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
-from bird.utilities.label_plot import label_conv
 from bird.utilities.ofio import *
 
+from .label_plot import label_conv
+
 
 def getManyFolders(rootFolder, prefix="flat_donut"):
     # Read Time
diff --git a/papers/sparger/process_geom/plot_cond_multiFold.py b/papers/sparger/process_geom/plot_cond_multiFold.py
index 01ec82dc..a571a62f 100644
--- a/papers/sparger/process_geom/plot_cond_multiFold.py
+++ b/papers/sparger/process_geom/plot_cond_multiFold.py
@@ -7,9 +7,10 @@
 import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
-from bird.utilities.label_plot import label_conv
 from bird.utilities.ofio import *
 
+from .label_plot import label_conv
+
 parser = argparse.ArgumentParser(description="Plot cond qoi")
 parser.add_argument(
     "-sf",
diff --git a/papers/sparger/process_geom/plot_qoi.py b/papers/sparger/process_geom/plot_qoi.py
index 0a5a9d54..81e4ec4f 100644
--- a/papers/sparger/process_geom/plot_qoi.py
+++ b/papers/sparger/process_geom/plot_qoi.py
@@ -7,9 +7,10 @@
 import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
-from bird.utilities.label_plot import label_conv
 from bird.utilities.ofio import *
 
+from .label_plot import label_conv
+
 
 def getManyFolders(rootFolder, prefix="flat_donut"):
     # Read Time
diff --git a/papers/sparger/process_geom/plot_qoi_multiFold.py b/papers/sparger/process_geom/plot_qoi_multiFold.py
index c3ad48ff..6f2e2547 100644
--- a/papers/sparger/process_geom/plot_qoi_multiFold.py
+++ b/papers/sparger/process_geom/plot_qoi_multiFold.py
@@ -7,9 +7,10 @@
 import numpy as np
 from prettyPlot.plotting import plt, pretty_labels
 
-from bird.utilities.label_plot import label_conv
 from bird.utilities.ofio import *
 
+from .label_plot import label_conv
+
 parser = argparse.ArgumentParser(description="Plot Qoi")
 parser.add_argument(
     "-sf",
diff --git a/tests/preprocess/test_stl_patch.py b/tests/preprocess/test_stl_patch.py
index ea339480..f76c2309 100644
--- a/tests/preprocess/test_stl_patch.py
+++ b/tests/preprocess/test_stl_patch.py
@@ -7,7 +7,7 @@
 
 from bird.preprocess.stl_patch.stl_bc import write_boundaries
 from bird.utilities.parser import parse_json
-from bird.utilities.stl_plotting import plotSTL
+from bird.utilities.stl_plotting import plot_stl
 
 
 def test_spider_sparger():
@@ -28,7 +28,7 @@ def test_spider_sparger():
     # Output to temporary directory and delete when done
     with tempfile.TemporaryDirectory() as tmpdirname:
         write_boundaries(input_dict, output_folder=tmpdirname)
-        axes = plotSTL(os.path.join(tmpdirname, "inlets.stl"))
+        axes = plot_stl(os.path.join(tmpdirname, "inlets.stl"))
         pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
 
 
@@ -51,7 +51,7 @@ def test_loop_reactor():
     # Output to temporary directory and delete when done
     with tempfile.TemporaryDirectory() as tmpdirname:
         write_boundaries(input_dict, output_folder=tmpdirname)
-        axes = plotSTL(os.path.join(tmpdirname, "inlets.stl"))
+        axes = plot_stl(os.path.join(tmpdirname, "inlets.stl"))
         pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
 
 
@@ -73,7 +73,7 @@ def test_loop_reactor_branch():
     # Output to temporary directory and delete when done
     with tempfile.TemporaryDirectory() as tmpdirname:
         write_boundaries(input_dict, output_folder=tmpdirname)
-        axes = plotSTL(os.path.join(tmpdirname, "inlets.stl"))
+        axes = plot_stl(os.path.join(tmpdirname, "inlets.stl"))
         pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
 
 

From 33a92d9a55df87fdbb19db98988442c1482d8670 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 10:25:27 -0600
Subject: [PATCH 06/19] move bissection to mathtools

---
 bird/meshing/_mesh_tools.py | 66 +++++++++++--------------------------
 bird/utilities/mathtools.py | 60 +++++++++++++++++++++++++++++++++
 bird/version.py             |  2 +-
 3 files changed, 80 insertions(+), 48 deletions(-)

diff --git a/bird/meshing/_mesh_tools.py b/bird/meshing/_mesh_tools.py
index 0fef1067..bc4955a1 100644
--- a/bird/meshing/_mesh_tools.py
+++ b/bird/meshing/_mesh_tools.py
@@ -1,6 +1,7 @@
 import numpy as np
 
 from bird import logger
+from bird.utilities.mathtools import bissection
 
 
 def make_walls_from_topo(topo_dict: dict) -> dict:
@@ -70,8 +71,8 @@ def make_bound_from_topo(topo_dict):
     }
 
 
-def stretch_fun(G, N1):
-    result = (1.0 - G) / (G * (1 - np.power(G, 1.0 / N1)))
+def stretch_fun(G, N):
+    result = (1.0 - G) / (G * (1 - np.power(G, 1.0 / N)))
     return result
 
 
@@ -80,29 +81,6 @@ def stretch_fun(G, N1):
 #    return result
 
 
-def bissection(val, stretch_fun, N1):
-    Gmin = 0.00001
-    Gmax = 1000000
-    resultmin = stretch_fun(Gmin, N1) - val
-    resultmax = stretch_fun(Gmax, N1) - val
-    if resultmin * resultmax > 0:
-        error_msg = "Initial bounds of grading do not encompass the solution"
-        logger.error(error_msg)
-        raise ValueError(error_msg)
-
-    for i in range(1000):
-        Gmid = 0.5 * (Gmax + Gmin)
-        resultmid = stretch_fun(Gmid, N1) - val
-        if resultmid * resultmax < 0:
-            Gmin = Gmid
-            resultmin = resultmid
-        else:
-            Gmax = Gmid
-            resultmax = resultmid
-
-    return Gmid
-
-
 def is_wall(l_wall: list[int], r_wall: list[int], ir: int, il: int) -> int:
     """
     Is the present block a wall (not meshed)
@@ -223,9 +201,8 @@ def verticalCoarsening(
                 raise ValueError(error_msg)
 
             if ratio_dir[ind] == "+":
-                gradVert[ind] = 1.0 / bissection(
-                    length / deltaE, stretch_fun, NVert[ind]
-                )
+                nl_func = lambda x: stretch_fun(x, NVert[ind])
+                gradVert[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 iterate = False
                 origNVert = NVert[ind]
                 while gradVert[ind] < 1 and NVert[ind] > 1:
@@ -233,9 +210,8 @@ def verticalCoarsening(
                     NVert[ind] = max(
                         int(round(min(0.99 * NVert[ind], NVert[ind] - 1))), 1
                     )
-                    gradVert[ind] = 1.0 / bissection(
-                        length / deltaE, stretch_fun, NVert[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NVert[ind])
+                    gradVert[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
@@ -245,9 +221,8 @@ def verticalCoarsening(
 
             elif ratio_dir[ind] == "-":
                 deltaE = block_cell_minus_length[ind - 1]
-                gradVert[ind] = bissection(
-                    length / deltaE, stretch_fun, NVert[ind]
-                )
+                nl_func = lambda x: stretch_fun(x, NVert[ind])
+                gradVert[ind] = bissection(length / deltaE, nl_func)
 
                 iterate = False
                 origNVert = NVert[ind]
@@ -256,9 +231,8 @@ def verticalCoarsening(
                     NVert[ind] = max(
                         int(round(min(0.99 * NVert[ind], NVert[ind] - 1))), 1
                     )
-                    gradVert[ind] = bissection(
-                        length / deltaE, stretch_fun, NVert[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NVert[ind])
+                    gradVert[ind] = bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NVert[{ind}] from {origNVert} to {NVert[ind]}"
@@ -337,9 +311,8 @@ def radialCoarsening(
                 raise ValueError(error_msg)
 
             if ratio_dir[ind] == "+":
-                gradR[ind] = 1.0 / bissection(
-                    length / deltaE, stretch_fun, NR[ind]
-                )
+                nl_func = lambda x: stretch_fun(x, NR[ind])
+                gradR[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 iterate = False
                 origNR = NR[ind]
                 while gradR[ind] < 1 and NR[ind] > 1:
@@ -347,9 +320,8 @@ def radialCoarsening(
                     NR[ind] = max(
                         int(round(min(0.99 * NR[ind], NR[ind] - 1))), 1
                     )
-                    gradR[ind] = 1.0 / bissection(
-                        length / deltaE, stretch_fun, NR[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NR[ind])
+                    gradR[ind] = 1.0 / bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NR[{ind}] from {origNR} to {NR[ind]}"
@@ -359,15 +331,15 @@ def radialCoarsening(
 
             elif ratio_dir[ind] == "-":
                 deltaE = block_cell_minus_length[ind - 1]
-                gradR[ind] = bissection(length / deltaE, stretch_fun, NR[ind])
+                nl_func = lambda x: stretch_fun(x, NR[ind])
+                gradR[ind] = bissection(length / deltaE, nl_func)
                 iterate = False
                 origNR = NR[ind]
                 while gradR[ind] > 1 and NR[ind] > 1:
                     iterate = True
                     NR[ind] = max(int(round(min(0.99 * NR[ind], -1))), 1)
-                    gradR[ind] = bissection(
-                        length / deltaE, stretch_fun, NR[ind]
-                    )
+                    nl_func = lambda x: stretch_fun(x, NR[ind])
+                    gradR[ind] = bissection(length / deltaE, nl_func)
                 if iterate:
                     logger.warning(
                         f"reduced NR[{ind}] from {origNR} to {NR[ind]}"
diff --git a/bird/utilities/mathtools.py b/bird/utilities/mathtools.py
index 159d8b88..27e97307 100644
--- a/bird/utilities/mathtools.py
+++ b/bird/utilities/mathtools.py
@@ -1,3 +1,5 @@
+from typing import Callable
+
 import numpy as np
 
 from bird import logger
@@ -90,3 +92,61 @@ def conditional_average(
     y_cond = weightVal / (weight)
 
     return x_cond, y_cond
+
+
+def bissection(
+    func_val: float,
+    nonlin_fun: Callable,
+    num_iter: int = 1000,
+    x_min: float = 1e-6,
+    x_max: float = 1e6,
+):
+    """
+    Solve a 1D non linear equation with a bissection method
+    This is useful for adjusting the mesh grading so that mesh size varies smoothly
+
+    Parameters
+    ----------
+    func_val:
+        Target value for the non linear function
+    nonlin_fun:
+        Non linear function
+    num_iter: int
+        Number of bissection iterations
+        Defaults to 1000
+    x_min : float
+        Lower bound of the search interval
+        Defaults to 1e-6
+    x_max : float
+        Upper bound of the search interval
+        Defaults to 1e6
+
+
+    Returns
+    ----------
+    x_mid: float
+        The argument that achieves the desired function value
+    """
+
+    # Make sure residual sign changes over the search interval
+    residual_min = nonlin_fun(x_min) - func_val
+    residual_max = nonlin_fun(x_max) - func_val
+    if residual_min * residual_max > 0:
+        error_msg = "No guaranteed bissection solution"
+        error_msg += (
+            "\nSearch interval [{x_min:.4g}, {x_max:.4g}] may be too narrow"
+        )
+        raise ValueError(error_msg)
+
+    # Do the bissection search
+    for i in range(num_iter):
+        x_mid = 0.5 * (x_max + x_min)
+        residual_mid = nonlin_fun(x_mid) - func_val
+        if residual_mid * residual_max < 0:
+            x_min = x_mid
+            residual_min = residual_mid
+        else:
+            x_max = x_mid
+            residual_max = residual_mid
+
+    return x_mid
diff --git a/bird/version.py b/bird/version.py
index 68c45d06..460ec86b 100644
--- a/bird/version.py
+++ b/bird/version.py
@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.45"
+__version__ = "0.0.47"

From e9b6b43feb8edd450ad7788ba6e7d04f6a970a27 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 10:33:44 -0600
Subject: [PATCH 07/19] consistency func/fun

---
 bird/utilities/mathtools.py | 12 ++++++------
 bird/version.py             |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/bird/utilities/mathtools.py b/bird/utilities/mathtools.py
index 27e97307..4cf528ea 100644
--- a/bird/utilities/mathtools.py
+++ b/bird/utilities/mathtools.py
@@ -95,19 +95,19 @@ def conditional_average(
 
 
 def bissection(
-    func_val: float,
+    fun_val: float,
     nonlin_fun: Callable,
     num_iter: int = 1000,
     x_min: float = 1e-6,
     x_max: float = 1e6,
-):
+) -> float:
     """
     Solve a 1D non linear equation with a bissection method
     This is useful for adjusting the mesh grading so that mesh size varies smoothly
 
     Parameters
     ----------
-    func_val:
+    fun_val:
         Target value for the non linear function
     nonlin_fun:
         Non linear function
@@ -129,8 +129,8 @@ def bissection(
     """
 
     # Make sure residual sign changes over the search interval
-    residual_min = nonlin_fun(x_min) - func_val
-    residual_max = nonlin_fun(x_max) - func_val
+    residual_min = nonlin_fun(x_min) - fun_val
+    residual_max = nonlin_fun(x_max) - fun_val
     if residual_min * residual_max > 0:
         error_msg = "No guaranteed bissection solution"
         error_msg += (
@@ -141,7 +141,7 @@ def bissection(
     # Do the bissection search
     for i in range(num_iter):
         x_mid = 0.5 * (x_max + x_min)
-        residual_mid = nonlin_fun(x_mid) - func_val
+        residual_mid = nonlin_fun(x_mid) - fun_val
         if residual_mid * residual_max < 0:
             x_min = x_mid
             residual_min = residual_mid
diff --git a/bird/version.py b/bird/version.py
index 460ec86b..24558041 100644
--- a/bird/version.py
+++ b/bird/version.py
@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.47"
+__version__ = "0.0.48"

From ef7a482374988372316f9f056954f61658e3370e Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 12:09:39 -0600
Subject: [PATCH 08/19] test size group read and make sure bubble size groups
 are correctly read from phaseProperties

---
 bird/utilities/ofio.py          | 126 +++++++++++++++++++++++---------
 tests/io/test_read_foam_dict.py |  37 ++++++++++
 tests/io/test_read_ndf.py       |  26 +++++++
 3 files changed, 156 insertions(+), 33 deletions(-)
 create mode 100644 tests/io/test_read_ndf.py

diff --git a/bird/utilities/ofio.py b/bird/utilities/ofio.py
index 776c1204..a1e51b3c 100644
--- a/bird/utilities/ofio.py
+++ b/bird/utilities/ofio.py
@@ -479,47 +479,92 @@ def read_field(
     return field, field_dict
 
 
-def readSizeGroups(file):
-    sizeGroup = {}
-    f = open(file, "r")
-    lines = f.readlines()
-    f.close()
-    begin = None
-    for iline, line in enumerate(lines):
-        if "sizeGroups" in line:
-            begin = iline + 2
-        if not begin is None and ");" in line:
-            end = iline - 1
-            break
-    for line in lines[begin : end + 1]:
-        tmp = line.split("{")
-        name = tmp[0].strip()
-        size = tmp[1].split(";")[0].split()[1]
-        sizeGroup[name] = float(size)
-    # Sort by size
-    sizeGroup = dict(sorted(sizeGroup.items(), key=lambda item: item[1]))
-    binGroup = {}
-    groups = list(sizeGroup.keys())
-    for igroup, group in enumerate(groups):
+def read_size_groups(case_folder: str) -> dict:
+    """
+    Get the bubble size groups represented by the number density fields (fX.gas)
+
+    Parameters
+    ----------
+    case_folder: str
+        Path to case folder
+
+    Returns
+    ----------
+    ndf_groups: dict
+        Dictionary describing the number density fields
+        Key is the name of the number density field (fX)
+        Value is a dictionary with keys 'diam' and 'bin_size'
+        corresponding to the bubble diameter and the bin size in m
+    """
+
+    phaseProperties_file = os.path.join(
+        case_folder, "constant", "phaseProperties"
+    )
+    phaseProperties = read_openfoam_dict(phaseProperties_file)
+
+    # Make sure that population balance is used
+    try:
+        assert phaseProperties["populationBalances"] == ["bubbles"]
+        assert phaseProperties["gas"]["diameterModel"] == "velocityGroup"
+        assert (
+            phaseProperties["gas"]["velocityGroupCoeffs"]["populationBalance"]
+            == "bubbles"
+        )
+    except AssertionError:
+        logger.warning(
+            "Reading size groups for a case where population balance is not used"
+        )
+
+    size_grouptmp = phaseProperties["gas"]["velocityGroupCoeffs"]["sizeGroups"]
+    logger.debug(f"Found {len(size_grouptmp)} number density fields")
+
+    # Associate number density field to size
+    size_group = {}
+    for name in size_grouptmp:
+        size_group[name] = float(size_grouptmp[name]["dSph"])
+
+    # Sort by size in ascending order
+    size_group = dict(sorted(size_group.items(), key=lambda item: item[1]))
+
+    # Get the bin size
+    bin_size_group = {}
+    group_names = list(size_group.keys())
+    logger.warning(
+        "The bin sizes definition make assumption of uniformity and need to be revisited if used"
+    )
+    for igroup, name in enumerate(group_names):
         if igroup == 0:
             bin_size = (
-                sizeGroup[groups[igroup + 1]] - sizeGroup[groups[igroup]]
+                size_group[group_names[igroup + 1]]
+                - size_group[group_names[igroup]]
             )
-        elif igroup == len(groups) - 1:
+        elif igroup == len(group_names) - 1:
             bin_size = (
-                sizeGroup[groups[igroup]] - sizeGroup[groups[igroup - 1]]
+                size_group[group_names[igroup]]
+                - size_group[group_names[igroup - 1]]
             )
         else:
             bin_size_p = (
-                sizeGroup[groups[igroup + 1]] - sizeGroup[groups[igroup]]
+                size_group[group_names[igroup + 1]]
+                - size_group[group_names[igroup]]
             )
             bin_size_m = (
-                sizeGroup[groups[igroup]] - sizeGroup[groups[igroup - 1]]
+                size_group[group_names[igroup]]
+                - size_group[group_names[igroup - 1]]
             )
             assert abs(bin_size_p - bin_size_m) < 1e-12
             bin_size = bin_size_m
-        binGroup[group] = bin_size
-    return sizeGroup, binGroup
+        bin_size_group[name] = bin_size
+
+    # Put size and bin size together
+    ndf_groups = {}
+    for name in group_names:
+        ndf_groups[name] = {
+            "diam": size_group[name],
+            "bin_size": bin_size_group[name],
+        }
+
+    return ndf_groups
 
 
 def get_case_times(
@@ -748,15 +793,30 @@ def parse_block(index: int) -> tuple:
                         index += 1
                     result[key] = dictlist
                 else:
-                    # Standard list
+                    # Standard list or dict-like list (e.g. sizeGroups)
                     lst = []
+                    dictlist = {}
+
                     while tokens[index] != ")":
-                        lst.append(tokens[index])
+                        label = tokens[index]
                         index += 1
-                    index += 1
+
+                        if index < len(tokens) and tokens[index] == "{":
+                            # Inline dict entry like: f1 { dSph 1e-3; value 0.0; }
+                            index += 1
+                            subdict, index = parse_block(index)
+                            dictlist[label] = subdict
+                        else:
+                            # Skip semicolons if present (e.g. in lists like species)
+                            if label != ";":
+                                lst.append(label)
+
+                    index += 1  # skip ')'
                     if index < len(tokens) and tokens[index] == ";":
                         index += 1
-                    result[key] = lst
+
+                    # Choose dictlist only if it has content; otherwise, use lst
+                    result[key] = dictlist if dictlist else lst
 
             # key followed by scalar
             elif index < len(tokens):
diff --git a/tests/io/test_read_foam_dict.py b/tests/io/test_read_foam_dict.py
index b8051d24..fe5989a1 100644
--- a/tests/io/test_read_foam_dict.py
+++ b/tests/io/test_read_foam_dict.py
@@ -41,6 +41,41 @@ def test_read_phaseProperties():
     )
 
 
+def test_read_ndf():
+    """
+    Test for reading content of `constant/phaseProperties` with population balance
+    """
+    const_folder = os.path.join(
+        Path(__file__).parent,
+        "..",
+        "..",
+        "bird",
+        "postprocess",
+        "data_conditional_mean",
+        "constant",
+    )
+    # Read non uniform field
+    foam_dict = read_openfoam_dict(
+        filename=os.path.join(const_folder, "phaseProperties")
+    )
+
+    assert foam_dict["phases"] == ["gas", "liquid"]
+    assert foam_dict["populationBalances"] == ["bubbles"]
+    assert foam_dict["gas"]["diameterModel"] == "velocityGroup"
+    assert len(foam_dict["gas"]["velocityGroupCoeffs"]["sizeGroups"]) == 21
+    assert (
+        abs(
+            float(
+                foam_dict["gas"]["velocityGroupCoeffs"]["sizeGroups"]["f4"][
+                    "dSph"
+                ]
+            )
+            - 2.5e-3
+        )
+        < 1e-12
+    )
+
+
 def test_read_thermophysicalProperties():
     """
     Test for reading content of `constant/thermophysicalProperties`
@@ -58,6 +93,7 @@ def test_read_thermophysicalProperties():
         filename=os.path.join(const_folder, "thermophysicalProperties.gas")
     )
 
+    print(foam_dict)
     assert foam_dict["species"] == ["H2", "CO2", "N2"]
     assert (
         foam_dict["CO2"]["thermodynamics"]["highCpCoeffs"][0] == "3.85746029"
@@ -108,6 +144,7 @@ def test_read_controlDict():
 
 
 if __name__ == "__main__":
+    test_read_thermophysicalProperties()
     test_read_phaseProperties()
     test_read_thermophysicalProperties()
     test_read_momentumTransport()
diff --git a/tests/io/test_read_ndf.py b/tests/io/test_read_ndf.py
new file mode 100644
index 00000000..2ea0b069
--- /dev/null
+++ b/tests/io/test_read_ndf.py
@@ -0,0 +1,26 @@
+import os
+from pathlib import Path
+
+import numpy as np
+
+from bird.utilities.ofio import read_size_groups
+
+
+def test_read_size_groups():
+    """
+    Test for getting size group info
+    """
+    case_folder = os.path.join(
+        Path(__file__).parent,
+        "..",
+        "..",
+        "bird",
+        "postprocess",
+        "data_conditional_mean",
+    )
+    ndf_groups = read_size_groups(case_folder)
+
+    assert len(ndf_groups) == 21
+    assert abs(ndf_groups["f4"]["diam"] - 2.5e-3) < 1e-12
+    assert abs(ndf_groups["f20"]["diam"] - 10.5e-3) < 1e-12
+    # Place holder for bin size

From 15d89983c272ce37f37cff848f7d726edfa3804e Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 12:10:56 -0600
Subject: [PATCH 09/19] update version

---
 bird/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bird/version.py b/bird/version.py
index 24558041..a0013d91 100644
--- a/bird/version.py
+++ b/bird/version.py
@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.48"
+__version__ = "0.0.49"

From 123c91b36bf8f2b1f0815fee2659efca5e840abc Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 12:19:16 -0600
Subject: [PATCH 10/19] add a retry in case conda fails

---
 .github/workflows/ci.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 03f0bc95..b9bb1f0b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -76,6 +76,10 @@ jobs:
 
       - name: Install dependencies
         run: |
+          conda config --set remote_read_timeout_secs 60
+          conda config --set remote_connect_timeout_secs 30
+          conda config --set retry_max 10
+          conda config --set retry_wait_seconds 10
           conda install -y -c conda-forge paraview
           pip install --upgrade pip
           pip install .
@@ -112,6 +116,10 @@ jobs:
 
       - name: Install dependencies
         run: |
+          conda config --set remote_read_timeout_secs 60
+          conda config --set remote_connect_timeout_secs 30
+          conda config --set retry_max 10
+          conda config --set retry_wait_seconds 10
           conda install -y -c conda-forge paraview
           pip install --upgrade pip
           pip install nrel-bird
@@ -151,6 +159,10 @@ jobs:
 
       - name: Install dependencies
         run: |
+          conda config --set remote_read_timeout_secs 60
+          conda config --set remote_connect_timeout_secs 30
+          conda config --set retry_max 10
+          conda config --set retry_wait_seconds 10
           conda install -y -c conda-forge paraview
           pip install --upgrade pip
           pip install .

From e13e9737c971ddf860709e97f6bdabdc56824588 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 12:23:40 -0600
Subject: [PATCH 11/19] add a retry in case conda fails

---
 .github/workflows/ci.yml | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b9bb1f0b..2dc955e1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -73,13 +73,14 @@ jobs:
           python-version: ${{matrix.python-version}}
           channels: conda-forge
           channel-priority: strict
-
-      - name: Install dependencies
         run: |
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
-          conda config --set retry_max 10
+          conda config --set remote_max_retries 10
           conda config --set retry_wait_seconds 10
+
+      - name: Install dependencies
+        run: |
           conda install -y -c conda-forge paraview
           pip install --upgrade pip
           pip install .
@@ -113,13 +114,14 @@ jobs:
           python-version: ${{matrix.python-version}}
           channels: conda-forge
           channel-priority: strict
-
-      - name: Install dependencies
         run: |
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
-          conda config --set retry_max 10
+          conda config --set remote_max_retries 10
           conda config --set retry_wait_seconds 10
+
+      - name: Install dependencies
+        run: |
           conda install -y -c conda-forge paraview
           pip install --upgrade pip
           pip install nrel-bird
@@ -156,13 +158,14 @@ jobs:
           python-version: ${{matrix.python-version}}
           channels: conda-forge
           channel-priority: strict
-
-      - name: Install dependencies
         run: |
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
-          conda config --set retry_max 10
+          conda config --set remote_max_retries 10
           conda config --set retry_wait_seconds 10
+
+      - name: Install dependencies
+        run: |
           conda install -y -c conda-forge paraview
           pip install --upgrade pip
           pip install .

From cb7e6ad397a26660572dd99d4a860ac19aa338bd Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 12:28:48 -0600
Subject: [PATCH 12/19] add a retry in case conda fails

---
 .github/workflows/ci.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2dc955e1..a389767b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -73,6 +73,8 @@ jobs:
           python-version: ${{matrix.python-version}}
           channels: conda-forge
           channel-priority: strict
+
+      - name: Configure conda retries
         run: |
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
@@ -114,6 +116,8 @@ jobs:
           python-version: ${{matrix.python-version}}
           channels: conda-forge
           channel-priority: strict
+
+      - name: Configure conda retries
         run: |
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
@@ -158,6 +162,8 @@ jobs:
           python-version: ${{matrix.python-version}}
           channels: conda-forge
           channel-priority: strict
+
+      - name: Configure conda retries
         run: |
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30

From d64b53470f29744bffe3a6fc7dc90a07bc883eb8 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 12:33:09 -0600
Subject: [PATCH 13/19] add a retry in case conda fails

---
 .github/workflows/ci.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a389767b..1d95b6ad 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -79,7 +79,6 @@ jobs:
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
           conda config --set remote_max_retries 10
-          conda config --set retry_wait_seconds 10
 
       - name: Install dependencies
         run: |
@@ -122,7 +121,6 @@ jobs:
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
           conda config --set remote_max_retries 10
-          conda config --set retry_wait_seconds 10
 
       - name: Install dependencies
         run: |
@@ -168,7 +166,6 @@ jobs:
           conda config --set remote_read_timeout_secs 60
           conda config --set remote_connect_timeout_secs 30
           conda config --set remote_max_retries 10
-          conda config --set retry_wait_seconds 10
 
       - name: Install dependencies
         run: |

From 79bbf48213c89d363daefed853619c0e8779f6b6 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 12:55:20 -0600
Subject: [PATCH 14/19] try with mamba instead

---
 .github/workflows/ci.yml | 59 +++++++++++++++++-----------------------
 1 file changed, 25 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1d95b6ad..14f066c1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -66,25 +66,22 @@ jobs:
         with:
           python-version: ${{matrix.python-version}}
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
-
-      - name: Configure conda retries
-        run: |
-          conda config --set remote_read_timeout_secs 60
-          conda config --set remote_connect_timeout_secs 30
-          conda config --set remote_max_retries 10
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
-          pip install .
+          pip install . 
           pip install pytest
 
       - name: Test
@@ -108,23 +105,20 @@ jobs:
         with:
           python-version: ${{matrix.python-version}}
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
-
-      - name: Configure conda retries
-        run: |
-          conda config --set remote_read_timeout_secs 60
-          conda config --set remote_connect_timeout_secs 30
-          conda config --set remote_max_retries 10
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install nrel-bird
           pip install pytest
@@ -153,23 +147,20 @@ jobs:
         with:
           openfoam-version: 9
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
-
-      - name: Configure conda retries
-        run: |
-          conda config --set remote_read_timeout_secs 60
-          conda config --set remote_connect_timeout_secs 30
-          conda config --set remote_max_retries 10
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install .
 

From caf77ab2815064131b463ee456253ed4f87edafb Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 13:02:23 -0600
Subject: [PATCH 15/19] switch everything to mamba

---
 .github/workflows/build_docs.yml  | 15 +++++++++------
 .github/workflows/codecov.yml     | 13 ++++++++-----
 .github/workflows/deploy_docs.yml | 15 +++++++++------
 3 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index 40f3315a..3497584c 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -25,19 +25,22 @@ jobs:
           python-version: '3.10'
           cache: 'pip'
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e . 
           pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints
 
       - name: Build documentation
diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
index 6defac05..28e9b622 100644
--- a/.github/workflows/codecov.yml
+++ b/.github/workflows/codecov.yml
@@ -27,17 +27,20 @@ jobs:
           python-version: '3.13'
           cache: 'pip'
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          micromamba install --yes -n test-env -c conda-forge paraview
           pip install --upgrade pip
           pip install pytest
           pip install pytest-cov
diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
index ef1ee504..3751c0dc 100644
--- a/.github/workflows/deploy_docs.yml
+++ b/.github/workflows/deploy_docs.yml
@@ -26,18 +26,21 @@ jobs:
         with:
           python-version: '3.10'
           cache: 'pip'
- 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: test-env
-          python-version: ${{matrix.python-version}}
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
           channels: conda-forge
           channel-priority: strict
+          cache-downloads: true
+          cache-env: true
 
       - name: Install dependencies
         run: |
-          conda install -y -c conda-forge paraview
+          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

From 744ee1a6664d507c05931c773ebe17130eda6e40 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 16:30:07 -0600
Subject: [PATCH 16/19] remove in file tests

---
 bird/meshing/block_cyl_mesh.py                   |  9 ---------
 bird/postprocess/early_pred.py                   | 10 ----------
 bird/postprocess/kla_utils.py                    |  4 ----
 bird/preprocess/dynamic_mixer/mixing_fvModels.py |  6 ------
 bird/preprocess/species_gen/setup_thermo_prop.py |  9 ---------
 bird/preprocess/stl_patch/stl_bc.py              | 11 -----------
 tests/io/test_case.py                            |  5 -----
 tests/io/test_read_foam_dict.py                  |  7 -------
 tests/io/test_read_foam_fields.py                |  3 ---
 tests/io/test_read_global_vars.py                |  3 ---
 tests/postprocess/test_cond_mean.py              |  3 ---
 tests/postprocess/test_post_quantities.py        |  7 -------
 tests/preprocess/test_stl_patch.py               |  6 ------
 13 files changed, 83 deletions(-)

diff --git a/bird/meshing/block_cyl_mesh.py b/bird/meshing/block_cyl_mesh.py
index 8dbf25c2..518ba23d 100644
--- a/bird/meshing/block_cyl_mesh.py
+++ b/bird/meshing/block_cyl_mesh.py
@@ -550,12 +550,3 @@ def writeBlockMeshDict(out_folder, geom_dict, mesh_dict):
 
     fw.close()
 
-
-def main(input_file, topo_file, output_folder):
-    geom_dict = assemble_geom(input_file, topo_file)
-    mesh_dict = assemble_mesh(input_file, geom_dict)
-    writeBlockMeshDict(output_folder, geom_dict, mesh_dict)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/bird/postprocess/early_pred.py b/bird/postprocess/early_pred.py
index 2ce81e1a..2e491048 100644
--- a/bird/postprocess/early_pred.py
+++ b/bird/postprocess/early_pred.py
@@ -266,13 +266,3 @@ def bayes_fit(data_dict, num_warmup=1000, num_samples=500):
 
     return data_dict
 
-
-if __name__ == "__main__":
-    from bird import BIRD_EARLY_PRED_DATA_DIR
-
-    data_dict, color_files = multi_data_load(BIRD_EARLY_PRED_DATA_DIR)
-    data_dict = fit_and_ext(data_dict)
-    plotAllEarly(data_dict, color_files=color_files, chop=True, extrap=True)
-    bayes_fit(data_dict)
-    plotAllEarly_uq(data_dict, color_files=color_files)
-    plt.show()
diff --git a/bird/postprocess/kla_utils.py b/bird/postprocess/kla_utils.py
index b08bfd65..c7a5af4d 100644
--- a/bird/postprocess/kla_utils.py
+++ b/bird/postprocess/kla_utils.py
@@ -371,7 +371,3 @@ def print_res_dict(res_dict: dict) -> None:
     logger.info(f"\tkla = {kla_nb*3600:.4g} +/- {kla_err_nb*3600:.4g} [h-1]")
     logger.info(f"\tcstar = {cs_nb:.4g} +/- {cs_err_nb:.4g} [mol/m3]")
 
-
-if __name__ == "__main__":
-    res_dict = compute_kla("data_kla/volume_avg.dat", time_ind=0, conc_ind=1)
-    print_res_dict(res_dict)
diff --git a/bird/preprocess/dynamic_mixer/mixing_fvModels.py b/bird/preprocess/dynamic_mixer/mixing_fvModels.py
index 80b0df2b..69cc48f4 100644
--- a/bird/preprocess/dynamic_mixer/mixing_fvModels.py
+++ b/bird/preprocess/dynamic_mixer/mixing_fvModels.py
@@ -55,9 +55,3 @@ def write_fvModel(input_dict, output_folder=".", force_sign=False):
 
     write_end(output_folder)
 
-
-if __name__ == "__main__":
-    input_dict = parse_json(
-        os.path.join("mixing_template", "loop_reactor_list", "mixers.json"),
-    )
-    write_fvModel(input_dict)
diff --git a/bird/preprocess/species_gen/setup_thermo_prop.py b/bird/preprocess/species_gen/setup_thermo_prop.py
index 95ff2138..31c68dc6 100644
--- a/bird/preprocess/species_gen/setup_thermo_prop.py
+++ b/bird/preprocess/species_gen/setup_thermo_prop.py
@@ -420,12 +420,3 @@ def write_species_properties(case_folder: str, phase: str = "gas") -> None:
     )
     write_openfoam_dict(thermo_properties_update, filename=filename)
 
-
-if __name__ == "__main__":
-    from bird import BIRD_DIR
-
-    case_folder = os.path.join(BIRD_DIR, "../experimental_cases/deckwer17")
-    write_species_properties(case_folder, phase="gas")
-    write_species_properties(case_folder, phase="liquid")
-    # fill_global_prop(os.path.join(BIRD_DIR,"../experimental_cases_new/disengagement/bubble_column_pbe_20L/"))
-    # fill_global_prop(os.path.join(BIRD_DIR, "../experimental_cases_new/deckwer17"))
diff --git a/bird/preprocess/stl_patch/stl_bc.py b/bird/preprocess/stl_patch/stl_bc.py
index 216c762c..855c09cb 100644
--- a/bird/preprocess/stl_patch/stl_bc.py
+++ b/bird/preprocess/stl_patch/stl_bc.py
@@ -47,14 +47,3 @@ def write_boundaries(input_dict, output_folder="."):
             boundary_mesh.save(
                 os.path.join(output_folder, f"{boundary_name}.stl")
             )
-
-
-if __name__ == "__main__":
-    input_dict = parse_json(
-        "bc_patch_mesh_template/loop_reactor_expl/inlets_outlets.json"
-    )
-    write_boundaries(input_dict)
-    input_dict = parse_json(
-        "bc_patch_mesh_template/loop_reactor_branch/inlets_outlets.json"
-    )
-    write_boundaries(input_dict)
diff --git a/tests/io/test_case.py b/tests/io/test_case.py
index 2d80f37f..b0b9c636 100644
--- a/tests/io/test_case.py
+++ b/tests/io/test_case.py
@@ -80,8 +80,3 @@ def test_mesh_vol():
 
     assert np.linalg.norm(volumes - volumes2) < 1e-12
 
-
-if __name__ == "__main__":
-    test_case_time()
-    test_mesh()
-    test_mesh_vol()
diff --git a/tests/io/test_read_foam_dict.py b/tests/io/test_read_foam_dict.py
index fe5989a1..b93f7e23 100644
--- a/tests/io/test_read_foam_dict.py
+++ b/tests/io/test_read_foam_dict.py
@@ -142,10 +142,3 @@ def test_read_controlDict():
     assert foam_dict["writeControl"] == "adjustableRunTime"
     assert foam_dict["maxCo"] == "0.5"
 
-
-if __name__ == "__main__":
-    test_read_thermophysicalProperties()
-    test_read_phaseProperties()
-    test_read_thermophysicalProperties()
-    test_read_momentumTransport()
-    test_read_controlDict()
diff --git a/tests/io/test_read_foam_fields.py b/tests/io/test_read_foam_fields.py
index 44afb59e..e75f1ce4 100644
--- a/tests/io/test_read_foam_fields.py
+++ b/tests/io/test_read_foam_fields.py
@@ -213,6 +213,3 @@ def test_read_mu_liquid():
         os.path.join(case_folder, "80", "thermo:mu.liquid"),
     )
 
-
-if __name__ == "__main__":
-    test_read_mu_liquid()
diff --git a/tests/io/test_read_global_vars.py b/tests/io/test_read_global_vars.py
index edc164c8..560e7bd4 100644
--- a/tests/io/test_read_global_vars.py
+++ b/tests/io/test_read_global_vars.py
@@ -105,6 +105,3 @@ def test_read_global_vars():
         < 1e-3
     )
 
-
-if __name__ == "__main__":
-    test_read_global_vars()
diff --git a/tests/postprocess/test_cond_mean.py b/tests/postprocess/test_cond_mean.py
index a3ec6785..f89e6c6f 100644
--- a/tests/postprocess/test_cond_mean.py
+++ b/tests/postprocess/test_cond_mean.py
@@ -44,6 +44,3 @@ def test_compute_cond():
         pretty_labels(plot_name, "y [m]", 14)
         plt.close()
 
-
-if __name__ == "__main__":
-    test_compute_cond()
diff --git a/tests/postprocess/test_post_quantities.py b/tests/postprocess/test_post_quantities.py
index 9ecde554..faf8e205 100644
--- a/tests/postprocess/test_post_quantities.py
+++ b/tests/postprocess/test_post_quantities.py
@@ -367,10 +367,3 @@ def test_fitted_kla():
     for time_folder in [str(entry) for entry in range(81, 91)]:
         shutil.rmtree(os.path.join(case_folder, time_folder))
 
-
-if __name__ == "__main__":
-    # test_compute_superficial_gas_velocity()
-    # test_compute_gh()
-    # test_ave_y_liq()
-    # test_ave_conc_liq()
-    test_fitted_kla()
diff --git a/tests/preprocess/test_stl_patch.py b/tests/preprocess/test_stl_patch.py
index f76c2309..bb5f9e90 100644
--- a/tests/preprocess/test_stl_patch.py
+++ b/tests/preprocess/test_stl_patch.py
@@ -76,9 +76,3 @@ def test_loop_reactor_branch():
         axes = plot_stl(os.path.join(tmpdirname, "inlets.stl"))
         pretty_labels("x", "y", zlabel="z", fontsize=14, ax=axes)
 
-
-if __name__ == "__main__":
-    from prettyPlot.plotting import plt
-
-    test_spider_sparger()
-    plt.show()

From 67a1ae68fd789dec7d00461f9e065f05d41814b5 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 16:30:21 -0600
Subject: [PATCH 17/19] report 95% confidence

---
 bird/postprocess/stats.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/bird/postprocess/stats.py b/bird/postprocess/stats.py
index 34565b47..e79f69b0 100644
--- a/bird/postprocess/stats.py
+++ b/bird/postprocess/stats.py
@@ -153,6 +153,10 @@ def calc_mean(
     """
     Compute mean and the uncertainty about the mean, from a time-series
 
+    Following Trenberth, "Some Effects of Finite Sample Size and Persistence on Meteorological Statistics. Part I: Autocorrelations", 1984
+    And Oliver et al., "Estimating uncertainties in statistics computed from direct numerical simulation", 2014
+
+
     Parameters
     ----------
     time_series: np.ndarray
@@ -167,7 +171,7 @@ def calc_mean(
     mean_val: float
         Mean value of the time_series
     unc_val: float
-        68% uncertainty (1 sigma) about the mean
+        95% uncertainty (1.96 sigma) about the mean
 
     """
 
@@ -181,4 +185,4 @@ def calc_mean(
     sigsq = np.var(time_series) * N / (N - T0)
     unc_val = np.sqrt(sigsq * T0 / N)
 
-    return mean_val, unc_val
+    return mean_val, unc_val * 1.96

From 6943225681b352c876cb33dd316d06424cc2fccb Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 16:30:52 -0600
Subject: [PATCH 18/19] cleanup public facing API doc

---
 docs/source/bird.postprocess.rst | 47 ++++++++++++++++----------------
 docs/source/bird.rst             |  8 ++++--
 2 files changed, 29 insertions(+), 26 deletions(-)

diff --git a/docs/source/bird.postprocess.rst b/docs/source/bird.postprocess.rst
index 9ac22476..8dfe4b94 100644
--- a/docs/source/bird.postprocess.rst
+++ b/docs/source/bird.postprocess.rst
@@ -1,29 +1,30 @@
 bird.postprocess package
 ========================
 
-bird.postprocess.conditional\_mean module
------------------------------------------
-
-.. automodule:: bird.postprocess.conditional_mean
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bird.postprocess.early\_pred module
------------------------------------
-
-.. automodule:: bird.postprocess.early_pred
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bird.postprocess.kla\_utils module
-----------------------------------
-
-.. automodule:: bird.postprocess.kla_utils
-   :members:
-   :undoc-members:
-   :show-inheritance:
+.. comment API for now
+   bird.postprocess.conditional\_mean module
+   -----------------------------------------
+   
+   .. automodule:: bird.postprocess.conditional_mean
+      :members:
+      :undoc-members:
+      :show-inheritance:
+   
+   bird.postprocess.early\_pred module
+   -----------------------------------
+   
+   .. automodule:: bird.postprocess.early_pred
+      :members:
+      :undoc-members:
+      :show-inheritance:
+   
+   bird.postprocess.kla\_utils module
+   ----------------------------------
+   
+   .. automodule:: bird.postprocess.kla_utils
+      :members:
+      :undoc-members:
+      :show-inheritance:
 
 bird.postprocess.post\_quantities module
 ----------------------------------------
diff --git a/docs/source/bird.rst b/docs/source/bird.rst
index e8fb4a96..9d4cc2d5 100644
--- a/docs/source/bird.rst
+++ b/docs/source/bird.rst
@@ -7,9 +7,11 @@ Subpackages
 .. toctree::
    :maxdepth: 1
 
-   bird.calibration
-   bird.meshing
+   .. comment API for now
+      bird.calibration
+      bird.meshing
+      bird.preprocess
+   
    bird.postprocess
-   bird.preprocess
    bird.utilities
 

From bcf48d8f362657d519ff7e963b585fa455e2cc04 Mon Sep 17 00:00:00 2001
From: Malik <malik.hassanaly@gmail.com>
Date: Sun, 19 Oct 2025 16:31:02 -0600
Subject: [PATCH 19/19] update v

---
 bird/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bird/version.py b/bird/version.py
index a0013d91..6825d034 100644
--- a/bird/version.py
+++ b/bird/version.py
@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.49"
+__version__ = "0.0.50"