From fa134a563acb2e46a27c32c434d4b290d042f650 Mon Sep 17 00:00:00 2001
From: korevaarzer <zanne.korevaar@tno.nl>
Date: Mon, 22 Dec 2025 10:21:31 +0100
Subject: [PATCH 1/4] Run ruff formatter in src directory

---
 src/geoloop/axisym/AxisymetricEL.py        |  1 -
 src/geoloop/bin/Flowdatamain.py            |  4 +-
 src/geoloop/bin/Plotmain.py                | 20 ++++++--
 src/geoloop/bin/Runbatch.py                |  3 +-
 src/geoloop/bin/Runmain.py                 | 11 +++-
 src/geoloop/bin/SingleRunSim.py            | 14 +++--
 src/geoloop/cli/batch.py                   | 17 +++----
 src/geoloop/cli/main.py                    | 59 ++++++++++++++++------
 src/geoloop/configuration.py               | 45 ++++++++++-------
 src/geoloop/geoloopcore/soilproperties.py  |  1 -
 src/geoloop/lithology/process_lithology.py | 32 +++++++-----
 src/geoloop/loadflowdata/flow_data.py      | 11 +++-
 src/geoloop/loadflowdata/loadprofile.py    |  4 +-
 src/geoloop/plotting/create_plots.py       | 13 +++--
 src/geoloop/utils/RunManager.py            | 14 ++---
 src/geoloop/utils/helpers.py               | 12 +++--
 16 files changed, 170 insertions(+), 91 deletions(-)

diff --git a/src/geoloop/axisym/AxisymetricEL.py b/src/geoloop/axisym/AxisymetricEL.py
index 4ce1672..5fab084 100644
--- a/src/geoloop/axisym/AxisymetricEL.py
+++ b/src/geoloop/axisym/AxisymetricEL.py
@@ -750,4 +750,3 @@ def thomas_heatloop(
 
     res2 = result.reshape(len(time), grid.nx, grid.ny, grid.nz)
     return res2
-
diff --git a/src/geoloop/bin/Flowdatamain.py b/src/geoloop/bin/Flowdatamain.py
index d533bf5..b9f5b9a 100644
--- a/src/geoloop/bin/Flowdatamain.py
+++ b/src/geoloop/bin/Flowdatamain.py
@@ -34,7 +34,7 @@ def main_flow_data(config_path: str | Path):
     flow = FlowData.from_config(config)
 
     # 2. Simulation time setup (1 hour step)
-    dt = 3600.0           # seconds
+    dt = 3600.0  # seconds
     tmax = 8760.0 * 3600  # one year in seconds
     Nt = int(np.ceil(tmax / dt))
 
@@ -54,7 +54,7 @@ def main_flow_data(config_path: str | Path):
     ax1.set_title("Instantaneous Flow Rate")
 
     # Cumulative flow (kg)
-    Qcum = np.cumsum(Q_flow) * dt   # dt is seconds → sum(kg/s * s) = kg
+    Qcum = np.cumsum(Q_flow) * dt  # dt is seconds → sum(kg/s * s) = kg
     ax2.set_xlabel(r"$t$ [hours]")
     ax2.set_ylabel(r"Cumulative flow [kg]")
     ax2.plot(hours, Qcum)
diff --git a/src/geoloop/bin/Plotmain.py b/src/geoloop/bin/Plotmain.py
index 35b4c62..13ce00f 100644
--- a/src/geoloop/bin/Plotmain.py
+++ b/src/geoloop/bin/Plotmain.py
@@ -4,7 +4,13 @@ import time
 
 import pandas as pd
 
-from geoloop.configuration import load_single_config, load_nested_config, PlotInputConfig, SingleRunConfig, LithologyConfig
+from geoloop.configuration import (
+    load_single_config,
+    load_nested_config,
+    PlotInputConfig,
+    SingleRunConfig,
+    LithologyConfig,
+)
 from geoloop.bin.SingleRunSim import SingleRun
 from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
 from geoloop.plotting.create_plots import PlotResults
@@ -82,7 +88,13 @@ def main_plotmain(config_path: str | Path) -> None:
                         run_name = plotinput.run_names[i]
                         runjson = run_name + ".json"
                         keysneeded = []
-                        keysoptional = ["litho_k_param", "loadprofile", "borefield", "variables_config", "flow_data"]
+                        keysoptional = [
+                            "litho_k_param",
+                            "loadprofile",
+                            "borefield",
+                            "variables_config",
+                            "flow_data",
+                        ]
                         config_sim = load_nested_config(
                             runjson, keysneeded, keysoptional
                         )
@@ -94,7 +106,9 @@ def main_plotmain(config_path: str | Path) -> None:
                             # in a single run always set the base case to True
                             run_config.litho_k_param["basecase"] = True
                             lithology_to_k = (
-                                ProcessLithologyToThermalConductivity.from_config(LithologyConfig(**run_config.litho_k_param))
+                                ProcessLithologyToThermalConductivity.from_config(
+                                    LithologyConfig(**run_config.litho_k_param)
+                                )
                             )
                             lithology_to_k.create_multi_thermcon_profiles()
                             run_config.lithology_to_k = lithology_to_k
diff --git a/src/geoloop/bin/Runbatch.py b/src/geoloop/bin/Runbatch.py
index a8b642a..e6e2787 100644
--- a/src/geoloop/bin/Runbatch.py
+++ b/src/geoloop/bin/Runbatch.py
@@ -15,9 +15,10 @@ command_dict = {
     "Plotmain": main_plotmain,
     "Loadprofile": main_load_profile,
     "Lithology": main_lithology,
-    "FlowData": main_flow_data
+    "FlowData": main_flow_data,
 }
 
+
 def run_batch_from_json(config_file: str) -> None:
     """
     Execute internal registered command functions defined in a JSON batch file.
diff --git a/src/geoloop/bin/Runmain.py b/src/geoloop/bin/Runmain.py
index 8281ca9..7385827 100644
--- a/src/geoloop/bin/Runmain.py
+++ b/src/geoloop/bin/Runmain.py
@@ -2,7 +2,12 @@ import sys
 import time
 from pathlib import Path
 
-from geoloop.configuration import load_nested_config, SingleRunConfig, LithologyConfig, StochasticRunConfig
+from geoloop.configuration import (
+    load_nested_config,
+    SingleRunConfig,
+    LithologyConfig,
+    StochasticRunConfig,
+)
 from geoloop.utils.helpers import save_MCrun_results
 from geoloop.utils.RunManager import run_models
 from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
@@ -45,7 +50,9 @@ def main_runmain(config_file_path: str | Path) -> None:
     # Optional lithology-based thermal conductivity sample generation
     config.lithology_to_k = None
     if config.litho_k_param:
-        lithology_to_k = ProcessLithologyToThermalConductivity.from_config(LithologyConfig(**config.litho_k_param))
+        lithology_to_k = ProcessLithologyToThermalConductivity.from_config(
+            LithologyConfig(**config.litho_k_param)
+        )
         lithology_to_k.create_multi_thermcon_profiles()
         config.lithology_to_k = lithology_to_k
 
diff --git a/src/geoloop/bin/SingleRunSim.py b/src/geoloop/bin/SingleRunSim.py
index 7745369..3b1e0e1 100644
--- a/src/geoloop/bin/SingleRunSim.py
+++ b/src/geoloop/bin/SingleRunSim.py
@@ -177,8 +177,6 @@ def Jfunc(
     return -retval[-1]
 
 
-
-
 class SingleRunResult:
     """
     Container class holding the results of a single BHE simulation run.
@@ -840,7 +838,13 @@ def main_single_run_sim(config_file_path: Path | str) -> None:
 
     # Load configuration
     keysneeded = []
-    keysoptional = ["litho_k_param", "loadprofile", "borefield", "flow_data", "variables_config"]
+    keysoptional = [
+        "litho_k_param",
+        "loadprofile",
+        "borefield",
+        "flow_data",
+        "variables_config",
+    ]
     config_dict = load_nested_config(config_file_path, keysneeded, keysoptional)
 
     config = SingleRunConfig(**config_dict)  # validated Pydantic object
@@ -850,7 +854,9 @@ def main_single_run_sim(config_file_path: Path | str) -> None:
     if config.litho_k_param:
         # in a single run always set the base case to True
         config.litho_k_param["basecase"] = True
-        lithology_to_k = ProcessLithologyToThermalConductivity.from_config(LithologyConfig(**config.litho_k_param))
+        lithology_to_k = ProcessLithologyToThermalConductivity.from_config(
+            LithologyConfig(**config.litho_k_param)
+        )
         lithology_to_k.create_multi_thermcon_profiles()
         config.lithology_to_k = lithology_to_k
 
diff --git a/src/geoloop/cli/batch.py b/src/geoloop/cli/batch.py
index 222cc85..ebacbdf 100644
--- a/src/geoloop/cli/batch.py
+++ b/src/geoloop/cli/batch.py
@@ -8,9 +8,7 @@ batch_app = typer.Typer(help="Batch processing commands for geoloop.")
 
 
 @batch_app.command("run")
-def batch_run(
-    batchfile: Path = typer.Argument(..., help="Path to batch JSON file.")
-):
+def batch_run(batchfile: Path = typer.Argument(..., help="Path to batch JSON file.")):
     """Run a batch JSON file."""
     run_batch_from_json(str(batchfile))
 
@@ -21,7 +19,9 @@ def batch_create(
     stochastic_run: list[str] = typer.Option([], help="Runmain config files."),
     single_run: list[str] = typer.Option([], help="SingleRunSim config files."),
     process_lithology: list[str] = typer.Option([], help="Lithology config files."),
-    calculate_loadprofile: list[str] = typer.Option([], help="Loadprofile config files."),
+    calculate_loadprofile: list[str] = typer.Option(
+        [], help="Loadprofile config files."
+    ),
     calculate_flowdata: list[str] = typer.Option([], help="FlowData config files."),
     plot: list[str] = typer.Option([], help="Plotmain config files."),
 ):
@@ -72,7 +72,7 @@ def batch_wizard():
         typer.echo("\nSelect command to add:")
         choice = typer.prompt(
             "Options: stochastic-run, single-run, process-lithology, calculate-loadprofile, calculate-flowdata, plot, done",
-            type=str
+            type=str,
         )
 
         if choice.lower() == "done":
@@ -84,7 +84,7 @@ def batch_wizard():
             "process-lithology": "Lithology",
             "calculate-loadprofile": "Loadprofile",
             "calculate-flowdata": "FlowData",
-            "plot": "Plotmain"
+            "plot": "Plotmain",
         }
 
         if choice.lower() not in valid:
@@ -93,10 +93,7 @@ def batch_wizard():
 
         filepath = typer.prompt("Enter path to the config JSON file:")
 
-        commands.append({
-            "command": valid[choice.lower()],
-            "args": filepath
-        })
+        commands.append({"command": valid[choice.lower()], "args": filepath})
 
         typer.secho("Command added!\n", fg=typer.colors.GREEN)
 
diff --git a/src/geoloop/cli/main.py b/src/geoloop/cli/main.py
index 7395eeb..c6a43c6 100644
--- a/src/geoloop/cli/main.py
+++ b/src/geoloop/cli/main.py
@@ -16,8 +16,12 @@ simulation.add_typer(batch_app, name="batch")
 
 
 @simulation.command(name="batch-run")
-def batch_run(config_file_path: str = typer.Argument(...,
-                                                          help="Path to the Json file with a sequence of the command scripts and configuration arguments")) -> None:
+def batch_run(
+    config_file_path: str = typer.Argument(
+        ...,
+        help="Path to the Json file with a sequence of the command scripts and configuration arguments",
+    ),
+) -> None:
     """
     Run a batch of scripts, in sequence, for BHE simulation.
     """
@@ -25,55 +29,78 @@ def batch_run(config_file_path: str = typer.Argument(...,
 
 
 @simulation.command(name="single-run")
-def single_run(config_file_path: str = typer.Argument(...,
-                                                          help="Path to the Json file with the main model configuration parameters")) -> None:
+def single_run(
+    config_file_path: str = typer.Argument(
+        ..., help="Path to the Json file with the main model configuration parameters"
+    ),
+) -> None:
     """
     Run main script for a single BHE simulation.
     """
     main_single_run_sim(config_file_path)
 
+
 @simulation.command(name="stochastic-run")
-def stochastic_run(config_file_path: str = typer.Argument(...,
-                                                          help="Path to the Json file with the main model configuration parameters")) -> None:
+def stochastic_run(
+    config_file_path: str = typer.Argument(
+        ..., help="Path to the Json file with the main model configuration parameters"
+    ),
+) -> None:
     """
     Run main script for a stochastic BHE simulation.
     """
     main_runmain(config_file_path)
 
+
 @simulation.command(name="process-lithology")
-def process_lithology(config_file_path: str = typer.Argument(...,
-                                                          help="Path to the Json file with the subsurface model configuration parameters")) -> None:
+def process_lithology(
+    config_file_path: str = typer.Argument(
+        ...,
+        help="Path to the Json file with the subsurface model configuration parameters",
+    ),
+) -> None:
     """
     Run main script for calculating and plotting subsurface thermal properties.
     """
     main_lithology(config_file_path)
 
+
 @simulation.command(name="calculate-loadprofile")
-def calculate_loadprofile(config_file_path: str = typer.Argument(...,
-                                                          help="Path to the Json file with the subsurface model configuration parameters")) -> None:
+def calculate_loadprofile(
+    config_file_path: str = typer.Argument(
+        ...,
+        help="Path to the Json file with the subsurface model configuration parameters",
+    ),
+) -> None:
     """
     Run main script for calculating a time-profile of heat load.
     """
     main_load_profile(config_file_path)
 
+
 @simulation.command(name="calculate-flowdata")
-def calculate_flowdata(config_file_path: str = typer.Argument(...,
-                                                          help="Path to the Json file with the flow data configuration parameters")) -> None:
+def calculate_flowdata(
+    config_file_path: str = typer.Argument(
+        ..., help="Path to the Json file with the flow data configuration parameters"
+    ),
+) -> None:
     """
     Run main script for calculating a time-profile of flow rate.
     """
     main_flow_data(config_file_path)
 
+
 @simulation.command(name="plot")
-def plot_results(config_file_path: str = typer.Argument(...,
-                                                          help="Path to the Json file with the plotting configuration parameters")) -> None:
+def plot_results(
+    config_file_path: str = typer.Argument(
+        ..., help="Path to the Json file with the plotting configuration parameters"
+    ),
+) -> None:
     """
     Run main script for plotting the simulation results.
     """
     main_plotmain(config_file_path)
 
 
-
 if __name__ == "__main__":
     simulation()
-
diff --git a/src/geoloop/configuration.py b/src/geoloop/configuration.py
index 62c7a1b..d3d286a 100644
--- a/src/geoloop/configuration.py
+++ b/src/geoloop/configuration.py
@@ -44,6 +44,7 @@ class LithologyConfig(BaseModel):
     n_samples : int
         Number of stochastic realizations to generate.
     """
+
     config_file_path: str | Path
     out_dir_lithology: str | Path
     input_dir_lithology: str | Path
@@ -80,7 +81,9 @@ class LithologyConfig(BaseModel):
             self.borehole_lithology_path = Path(self.borehole_lithology_path)
         if not self.borehole_lithology_path.is_absolute():
             self.borehole_lithology_path = (
-                base_dir_lithology / Path(self.input_dir_lithology) / self.borehole_lithology_path
+                base_dir_lithology
+                / Path(self.input_dir_lithology)
+                / self.borehole_lithology_path
             ).resolve()
 
         if not isinstance(self.out_dir_lithology, Path):
@@ -125,6 +128,7 @@ class LoadProfileConfig(BaseModel):
     lp_minQ : float or int, optional
         Minimum heat load constraint if type is FROMFILE.
     """
+
     config_file_path: str | Path
     lp_outdir: str | Path | None = None
     lp_inputdir: str | Path | None = None
@@ -263,6 +267,7 @@ class FlowDataConfig(BaseModel):
     fp_smoothing : str, optional
         Smoothing method applied to the flow profile, if type is FROMFILE.
     """
+
     config_file_path: str | Path
     fp_type: Literal["CONSTANT", "VARIABLE", "FROMFILE"]
     fp_outdir: str | Path | None = None
@@ -324,7 +329,6 @@ class FlowDataConfig(BaseModel):
                 )
         return self
 
-
     @model_validator(mode="after")
     def process_config_paths(self):
         """
@@ -359,7 +363,7 @@ class FlowDataConfig(BaseModel):
         return self
 
 
-class SingleRunConfig(BaseModel, extra='allow'):
+class SingleRunConfig(BaseModel, extra="allow"):
     """
     Configuration object for a single geothermal borehole simulation run.
 
@@ -467,6 +471,7 @@ class SingleRunConfig(BaseModel, extra='allow'):
     flow_data : dict, optional
         FlowData module configuration.
     """
+
     # Path to the configuration json
     config_file_path: Path = None
 
@@ -476,7 +481,7 @@ class SingleRunConfig(BaseModel, extra='allow'):
 
     # Borehole design
     # Required Parameters
-    type: Literal["UTUBE" , "COAXIAL"]
+    type: Literal["UTUBE", "COAXIAL"]
     H: float | int
     D: float | int
     r_b: float
@@ -485,13 +490,13 @@ class SingleRunConfig(BaseModel, extra='allow'):
     k_p: float
     k_g: float | list[float]
 
-    fluid_str: Literal['water', 'MEG', 'MPG', 'MEA', 'MMA']
+    fluid_str: Literal["water", "MEG", "MPG", "MEA", "MMA"]
     fluid_percent: float | int
     m_flow: float
     epsilon: float
 
     # Optional / Conditional for borehole
-    r_in: list[float]  | None = None
+    r_in: list[float] | None = None
     pos: list[list[float]] = None
     nInlets: int = None
 
@@ -662,7 +667,9 @@ class SingleRunConfig(BaseModel, extra='allow'):
 
         if not base_dir_path.is_absolute():
             if self.config_file_path is None:
-                raise ValueError("Cannot resolve relative base_dir: config_path not set")
+                raise ValueError(
+                    "Cannot resolve relative base_dir: config_path not set"
+                )
             elif isinstance(self.config_file_path, str):
                 self.config_file_path = Path(self.config_file_path)
             base_dir_path = self.config_file_path.parent / base_dir_path
@@ -705,6 +712,7 @@ class StochasticRunConfig(BaseModel):
     elif dist_name == "triangular":
         min, peak, max = dist[1], dist[2], dist[3]
     """
+
     n_samples: int | None = None
     k_s_scale: tuple[str, float, float] = None
     k_p: tuple[str, float, float] = None
@@ -776,14 +784,15 @@ class PlotInputConfig(BaseModel):
         Flag that determines whether to create crossplots and barplots.
         Only compatible with stochastic simulations
     newplot : bool
-        	Flag to plot the simulation(s) listed in run_names seperately or together.
-        	Only simulations with the same run_modes can be plot together
+                Flag to plot the simulation(s) listed in run_names seperately or together.
+                Only simulations with the same run_modes can be plot together
     crossplot_vars : list of str
-        	Variable input parameters and results to target in crossplots and tornado plots.
-        	Only used if plot_crossplot_barplot is true
+                Variable input parameters and results to target in crossplots and tornado plots.
+                Only used if plot_crossplot_barplot is true
     plot_temperature_field : bool
         Flag that determines whether to plot full 3D temperature fields. Only used if model_type is FINVOL.
     """
+
     config_file_path: Path = None
 
     base_dir: str | Path
@@ -826,7 +835,9 @@ class PlotInputConfig(BaseModel):
 
         if not base_dir_path.is_absolute():
             if self.config_file_path is None:
-                raise ValueError("Cannot resolve relative base_dir: config_path not set")
+                raise ValueError(
+                    "Cannot resolve relative base_dir: config_path not set"
+                )
             elif isinstance(self.config_file_path, str):
                 self.config_file_path = Path(self.config_file_path)
             base_dir_path = self.config_file_path.parent / base_dir_path
@@ -856,6 +867,7 @@ def load_json(path: str | Path) -> dict:
     with open(path) as f:
         return json.load(f)
 
+
 def load_single_config(main_config_path: str | Path) -> dict:
     """
     Load main JSON as dictionary.
@@ -879,10 +891,9 @@ def load_single_config(main_config_path: str | Path) -> dict:
 
     return config
 
+
 def load_nested_config(
-    main_config_path: str,
-    keys_needed: list[str] = [],
-    keys_optional: list[str] = []
+    main_config_path: str, keys_needed: list[str] = [], keys_optional: list[str] = []
 ) -> dict:
     """
     Load main JSON and inject referenced sub-configs as nested dictionaries.
@@ -928,8 +939,8 @@ def load_nested_config(
             try:
                 subconfig = load_json(subpath)
                 subconfig["config_file_path"] = subpath
-                config[key] = subconfig   # replace path with nested dict
+                config[key] = subconfig  # replace path with nested dict
             except FileNotFoundError:
                 print(f"Optional config file not found: {subpath}, skipping.")
 
-    return config
\ No newline at end of file
+    return config
diff --git a/src/geoloop/geoloopcore/soilproperties.py b/src/geoloop/geoloopcore/soilproperties.py
index 71d7042..82f69d7 100644
--- a/src/geoloop/geoloopcore/soilproperties.py
+++ b/src/geoloop/geoloopcore/soilproperties.py
@@ -5,7 +5,6 @@ from geoloop.geoloopcore.strat_interpolator import StratInterpolator, TgInterpol
 from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
 
 
-
 class SoilProperties:
     """
     Store soil thermal properties, including geotherm (temperature vs. depth)
diff --git a/src/geoloop/lithology/process_lithology.py b/src/geoloop/lithology/process_lithology.py
index a0ee552..470fdc6 100644
--- a/src/geoloop/lithology/process_lithology.py
+++ b/src/geoloop/lithology/process_lithology.py
@@ -370,7 +370,9 @@ class ProcessLithologyToThermalConductivity:
         return borehole_lithology_ab
 
     @classmethod
-    def from_config(cls, config: LithologyConfig) -> "ProcessLithologyToThermalConductivity":
+    def from_config(
+        cls, config: LithologyConfig
+    ) -> "ProcessLithologyToThermalConductivity":
         """
         Create a ProcessLithologyToThermalConductivity instance from a configuration dict.
 
@@ -386,21 +388,23 @@ class ProcessLithologyToThermalConductivity:
         """
 
         borehole_path = config.borehole_lithology_path
-        borehole_df = pd.read_excel(borehole_path, sheet_name=config.borehole_lithology_sheetname)
+        borehole_df = pd.read_excel(
+            borehole_path, sheet_name=config.borehole_lithology_sheetname
+        )
 
         return cls(
-            borehole_df = borehole_df,
-            Tg = config.Tg,
-            Tgrad = config.Tgrad,
-            z_Tg = config.z_Tg,
-            phi_scale = config.phi_scale,
-            lithology_scale = config.lithology_scale,
-            lithology_error = config.lithology_error,
-            nsamples = config.n_samples,
-            basecase = config.basecase,
-            out_dir = config.out_dir_lithology,
-            out_table = config.out_table,
-            read_from_table = config.read_from_table,
+            borehole_df=borehole_df,
+            Tg=config.Tg,
+            Tgrad=config.Tgrad,
+            z_Tg=config.z_Tg,
+            phi_scale=config.phi_scale,
+            lithology_scale=config.lithology_scale,
+            lithology_error=config.lithology_error,
+            nsamples=config.n_samples,
+            basecase=config.basecase,
+            out_dir=config.out_dir_lithology,
+            out_table=config.out_table,
+            read_from_table=config.read_from_table,
         )
 
     def create_single_thermcon_profile(
diff --git a/src/geoloop/loadflowdata/flow_data.py b/src/geoloop/loadflowdata/flow_data.py
index 5ae7c29..9ecf082 100644
--- a/src/geoloop/loadflowdata/flow_data.py
+++ b/src/geoloop/loadflowdata/flow_data.py
@@ -135,10 +135,17 @@ class FlowData:
             Initialized FlowData object.
         """
         if config.fp_type == "CONSTANT":
-            return cls(config.fp_type, peak_flow=config.fp_peak, outdir=config.fp_outdir)
+            return cls(
+                config.fp_type, peak_flow=config.fp_peak, outdir=config.fp_outdir
+            )
 
         elif config.fp_type == "VARIABLE":
-            return cls(config.fp_type, base_flow=config.fp_base, peak_flow=config.fp_peak, outdir=config.fp_outdir)
+            return cls(
+                config.fp_type,
+                base_flow=config.fp_base,
+                peak_flow=config.fp_peak,
+                outdir=config.fp_outdir,
+            )
 
         elif config.fp_type == "FROMFILE":
             return cls(
diff --git a/src/geoloop/loadflowdata/loadprofile.py b/src/geoloop/loadflowdata/loadprofile.py
index 98643f0..9b7f823 100644
--- a/src/geoloop/loadflowdata/loadprofile.py
+++ b/src/geoloop/loadflowdata/loadprofile.py
@@ -303,7 +303,7 @@ class LoadProfile:
                 base=config.lp_base,
                 peak=config.lp_peak,
                 minscaleflow=config.lp_minscaleflow,
-                outdir=config.lp_outdir
+                outdir=config.lp_outdir,
             )
 
         elif config.lp_type == LoadProfile.FROMFILE:
@@ -318,7 +318,7 @@ class LoadProfile:
                 minQ=config.lp_minQ,
                 minscaleflow=config.lp_minscaleflow,
                 inputcolumn=inputcolumn,
-                smoothing=smoothing
+                smoothing=smoothing,
             )
 
         else:
diff --git a/src/geoloop/plotting/create_plots.py b/src/geoloop/plotting/create_plots.py
index af83f61..c9eda99 100644
--- a/src/geoloop/plotting/create_plots.py
+++ b/src/geoloop/plotting/create_plots.py
@@ -821,9 +821,16 @@ class PlotResults:
                     plt.gca().set_aspect("equal", adjustable="box")
                     gt.utilities._format_axes(ax)
 
-                    levels = np.linspace(np.nanmin(temperature), np.nanmax(temperature), 10)
-                    cs = plt.contourf(X, Y, temperature.reshape((N_xy, N_xy)),
-                                      levels=levels, cmap='viridis')
+                    levels = np.linspace(
+                        np.nanmin(temperature), np.nanmax(temperature), 10
+                    )
+                    cs = plt.contourf(
+                        X,
+                        Y,
+                        temperature.reshape((N_xy, N_xy)),
+                        levels=levels,
+                        cmap="viridis",
+                    )
                     cbar = fig.colorbar(cs)
 
                     # Borehole wall outline
diff --git a/src/geoloop/utils/RunManager.py b/src/geoloop/utils/RunManager.py
index 3eb4317..53557b4 100644
--- a/src/geoloop/utils/RunManager.py
+++ b/src/geoloop/utils/RunManager.py
@@ -47,24 +47,18 @@ def sample_parameter_space(config: SingleRunConfig) -> tuple[dict, list[str]]:
     varying_parameters = []
 
     for param_name in variable_param_names:
-
         dist = getattr(variables_config, param_name)
 
         if isinstance(dist, tuple):
-
             dist_name = dist[0].lower()
             varying_parameters.append(param_name)
 
             if dist_name == "normal":
                 mean, std_dev = dist[1], dist[2]
-                samples = norm(loc=mean, scale=std_dev).rvs(
-                    size=n_samples
-                )
+                samples = norm(loc=mean, scale=std_dev).rvs(size=n_samples)
             elif dist_name == "uniform":
                 min, max = dist[1], dist[2]
-                samples = uniform(loc=min, scale=max - min).rvs(
-                    size=n_samples
-                )
+                samples = uniform(loc=min, scale=max - min).rvs(size=n_samples)
 
             elif dist_name == "lognormal":
                 mu, sigma = dist[1], dist[2]
@@ -88,7 +82,9 @@ def sample_parameter_space(config: SingleRunConfig) -> tuple[dict, list[str]]:
 
     # broadcast locked (non-varying) parameters
     for param_name in locked_param_names:
-        sample_space[param_name] = [getattr(config, param_name) for _ in range(n_samples)]
+        sample_space[param_name] = [
+            getattr(config, param_name) for _ in range(n_samples)
+        ]
 
     return sample_space, varying_parameters
 
diff --git a/src/geoloop/utils/helpers.py b/src/geoloop/utils/helpers.py
index c245381..6fc93ec 100644
--- a/src/geoloop/utils/helpers.py
+++ b/src/geoloop/utils/helpers.py
@@ -8,7 +8,9 @@ import xarray as xr
 from geoloop.configuration import SingleRunConfig, StochasticRunConfig
 
 
-def get_param_names(config: SingleRunConfig | StochasticRunConfig | None = None) -> tuple[list[str], list[str]]:
+def get_param_names(
+    config: SingleRunConfig | StochasticRunConfig | None = None,
+) -> tuple[list[str], list[str]]:
     """
     Identify locked and variable parameter names from a configuration dictionary for Monte Carlo simulations.
 
@@ -246,9 +248,11 @@ def save_singlerun_results(config: SingleRunConfig, result: Any, outpath: Path)
 
     # Create dictionary of input parameters
     param_dict = {
-        key: ([getattr(config, key)]
-        if isinstance(getattr(config, key), np.ndarray)
-        else getattr(config, key))
+        key: (
+            [getattr(config, key)]
+            if isinstance(getattr(config, key), np.ndarray)
+            else getattr(config, key)
+        )
         for key in param_names
     }
 
-- 
GitLab


From abc1d35863b787071299b76ae0b0a2d0bb917733 Mon Sep 17 00:00:00 2001
From: korevaarzer <zanne.korevaar@tno.nl>
Date: Mon, 22 Dec 2025 10:24:56 +0100
Subject: [PATCH 2/4] Run ruff linter in src directory (linting errors
 remaining)

---
 src/geoloop/axisym/AxisymetricEL.py        |  1 -
 src/geoloop/bin/Flowdatamain.py            |  2 +-
 src/geoloop/bin/Lithologymain.py           |  5 +++--
 src/geoloop/bin/Loadprofilemain.py         |  2 +-
 src/geoloop/bin/Plotmain.py                | 10 +++++-----
 src/geoloop/bin/Runbatch.py                |  2 +-
 src/geoloop/bin/Runmain.py                 |  6 +++---
 src/geoloop/bin/SingleRunSim.py            |  4 ++--
 src/geoloop/cli/batch.py                   |  1 +
 src/geoloop/cli/main.py                    |  7 +++----
 src/geoloop/configuration.py               |  4 ++--
 src/geoloop/geoloopcore/getloaddata.py     |  2 +-
 src/geoloop/lithology/process_lithology.py |  2 +-
 src/geoloop/plotting/create_plots.py       |  2 +-
 src/geoloop/utils/RunManager.py            |  4 ++--
 15 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/src/geoloop/axisym/AxisymetricEL.py b/src/geoloop/axisym/AxisymetricEL.py
index 5fab084..e5412b6 100644
--- a/src/geoloop/axisym/AxisymetricEL.py
+++ b/src/geoloop/axisym/AxisymetricEL.py
@@ -1,6 +1,5 @@
 import matplotlib.pyplot as plt
 import numpy as np
-import pandas as pd
 
 
 def check_asarray(rmin: float | np.ndarray, nr: int) -> np.ndarray:
diff --git a/src/geoloop/bin/Flowdatamain.py b/src/geoloop/bin/Flowdatamain.py
index b9f5b9a..cfa81ff 100644
--- a/src/geoloop/bin/Flowdatamain.py
+++ b/src/geoloop/bin/Flowdatamain.py
@@ -4,7 +4,7 @@ from pathlib import Path
 import matplotlib.pyplot as plt
 import numpy as np
 
-from geoloop.configuration import load_single_config, FlowDataConfig
+from geoloop.configuration import FlowDataConfig, load_single_config
 from geoloop.loadflowdata.flow_data import FlowData
 
 
diff --git a/src/geoloop/bin/Lithologymain.py b/src/geoloop/bin/Lithologymain.py
index cf36fa3..28a6680 100644
--- a/src/geoloop/bin/Lithologymain.py
+++ b/src/geoloop/bin/Lithologymain.py
@@ -1,11 +1,12 @@
+from pathlib import Path
+
 import numpy as np
 import xarray as xr
-from pathlib import Path
 
+from geoloop.configuration import LithologyConfig, load_single_config
 from geoloop.geoloopcore.strat_interpolator import StratInterpolator
 from geoloop.lithology.plot_lithology import plot_lithology_and_thermcon
 from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
-from geoloop.configuration import load_single_config, LithologyConfig
 
 
 def main_lithology(config_path: str | Path) -> None:
diff --git a/src/geoloop/bin/Loadprofilemain.py b/src/geoloop/bin/Loadprofilemain.py
index b0f7c95..dfd4a37 100644
--- a/src/geoloop/bin/Loadprofilemain.py
+++ b/src/geoloop/bin/Loadprofilemain.py
@@ -3,7 +3,7 @@ from pathlib import Path
 import matplotlib.pyplot as plt
 import numpy as np
 
-from geoloop.configuration import load_single_config, LoadProfileConfig
+from geoloop.configuration import LoadProfileConfig, load_single_config
 from geoloop.loadflowdata.loadprofile import LoadProfile
 
 
diff --git a/src/geoloop/bin/Plotmain.py b/src/geoloop/bin/Plotmain.py
index 13ce00f..e6bc013 100644
--- a/src/geoloop/bin/Plotmain.py
+++ b/src/geoloop/bin/Plotmain.py
@@ -1,17 +1,17 @@
-from pathlib import Path
 import sys
 import time
+from pathlib import Path
 
 import pandas as pd
 
+from geoloop.bin.SingleRunSim import SingleRun
 from geoloop.configuration import (
-    load_single_config,
-    load_nested_config,
+    LithologyConfig,
     PlotInputConfig,
     SingleRunConfig,
-    LithologyConfig,
+    load_nested_config,
+    load_single_config,
 )
-from geoloop.bin.SingleRunSim import SingleRun
 from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
 from geoloop.plotting.create_plots import PlotResults
 from geoloop.plotting.load_data import DataSelection, DataTotal, PlotInput
diff --git a/src/geoloop/bin/Runbatch.py b/src/geoloop/bin/Runbatch.py
index e6e2787..3496387 100644
--- a/src/geoloop/bin/Runbatch.py
+++ b/src/geoloop/bin/Runbatch.py
@@ -2,12 +2,12 @@ import json
 import sys
 from pathlib import Path
 
+from geoloop.bin.Flowdatamain import main_flow_data
 from geoloop.bin.Lithologymain import main_lithology
 from geoloop.bin.Loadprofilemain import main_load_profile
 from geoloop.bin.Plotmain import main_plotmain
 from geoloop.bin.Runmain import main_runmain
 from geoloop.bin.SingleRunSim import main_single_run_sim
-from geoloop.bin.Flowdatamain import main_flow_data
 
 command_dict = {
     "SingleRunSim": main_single_run_sim,
diff --git a/src/geoloop/bin/Runmain.py b/src/geoloop/bin/Runmain.py
index 7385827..ee0b4e2 100644
--- a/src/geoloop/bin/Runmain.py
+++ b/src/geoloop/bin/Runmain.py
@@ -3,14 +3,14 @@ import time
 from pathlib import Path
 
 from geoloop.configuration import (
-    load_nested_config,
-    SingleRunConfig,
     LithologyConfig,
+    SingleRunConfig,
     StochasticRunConfig,
+    load_nested_config,
 )
+from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
 from geoloop.utils.helpers import save_MCrun_results
 from geoloop.utils.RunManager import run_models
-from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
 
 
 def main_runmain(config_file_path: str | Path) -> None:
diff --git a/src/geoloop/bin/SingleRunSim.py b/src/geoloop/bin/SingleRunSim.py
index 3b1e0e1..a230387 100644
--- a/src/geoloop/bin/SingleRunSim.py
+++ b/src/geoloop/bin/SingleRunSim.py
@@ -9,8 +9,7 @@ import xarray as xr
 from numpy.typing import NDArray
 from scipy.optimize import minimize
 
-from geoloop.configuration import load_nested_config, SingleRunConfig, LithologyConfig
-from geoloop.utils.helpers import save_singlerun_results
+from geoloop.configuration import LithologyConfig, SingleRunConfig, load_nested_config
 from geoloop.geoloopcore.b2g import B2G
 from geoloop.geoloopcore.b2g_ana import B2G_ana
 from geoloop.geoloopcore.boreholedesign import BoreholeDesign
@@ -23,6 +22,7 @@ from geoloop.geoloopcore.pygfield_ana import (
 from geoloop.geoloopcore.simulationparameters import SimulationParameters
 from geoloop.geoloopcore.soilproperties import SoilProperties
 from geoloop.lithology.process_lithology import ProcessLithologyToThermalConductivity
+from geoloop.utils.helpers import save_singlerun_results
 
 
 def optimize_forkeys(
diff --git a/src/geoloop/cli/batch.py b/src/geoloop/cli/batch.py
index ebacbdf..044b381 100644
--- a/src/geoloop/cli/batch.py
+++ b/src/geoloop/cli/batch.py
@@ -1,5 +1,6 @@
 import json
 from pathlib import Path
+
 import typer
 
 from geoloop.bin.Runbatch import run_batch_from_json
diff --git a/src/geoloop/cli/main.py b/src/geoloop/cli/main.py
index c6a43c6..80b0a1a 100644
--- a/src/geoloop/cli/main.py
+++ b/src/geoloop/cli/main.py
@@ -1,13 +1,12 @@
 import typer
 
-from geoloop.bin.SingleRunSim import main_single_run_sim
+from geoloop.bin.Flowdatamain import main_flow_data
 from geoloop.bin.Lithologymain import main_lithology
 from geoloop.bin.Loadprofilemain import main_load_profile
 from geoloop.bin.Plotmain import main_plotmain
-from geoloop.bin.Runmain import main_runmain
 from geoloop.bin.Runbatch import run_batch_from_json
-from geoloop.bin.Flowdatamain import main_flow_data
-
+from geoloop.bin.Runmain import main_runmain
+from geoloop.bin.SingleRunSim import main_single_run_sim
 from geoloop.cli.batch import batch_app
 
 # Set up the main app
diff --git a/src/geoloop/configuration.py b/src/geoloop/configuration.py
index d3d286a..fec5dd2 100644
--- a/src/geoloop/configuration.py
+++ b/src/geoloop/configuration.py
@@ -1,9 +1,9 @@
 import json
 from pathlib import Path
-from pydantic import BaseModel, model_validator
-
 from typing import Literal
 
+from pydantic import BaseModel, model_validator
+
 
 class LithologyConfig(BaseModel):
     """
diff --git a/src/geoloop/geoloopcore/getloaddata.py b/src/geoloop/geoloopcore/getloaddata.py
index f53e150..ec96aa3 100644
--- a/src/geoloop/geoloopcore/getloaddata.py
+++ b/src/geoloop/geoloopcore/getloaddata.py
@@ -1,6 +1,6 @@
 import numpy as np
 
-from geoloop.configuration import SingleRunConfig, LoadProfileConfig, FlowDataConfig
+from geoloop.configuration import FlowDataConfig, LoadProfileConfig, SingleRunConfig
 from geoloop.loadflowdata.flow_data import FlowData
 from geoloop.loadflowdata.loadprofile import LoadProfile
 
diff --git a/src/geoloop/lithology/process_lithology.py b/src/geoloop/lithology/process_lithology.py
index 470fdc6..c2779c3 100644
--- a/src/geoloop/lithology/process_lithology.py
+++ b/src/geoloop/lithology/process_lithology.py
@@ -5,9 +5,9 @@ import numpy as np
 import pandas as pd
 import xarray as xr
 
+from geoloop.configuration import LithologyConfig
 from geoloop.constants import lithology_properties_xlsx
 from geoloop.geoloopcore.strat_interpolator import TgInterpolator
-from geoloop.configuration import LithologyConfig
 
 # TODO: save the config paramters (error and scaling factors) in the thermcon h5 file that now only stores the results
 
diff --git a/src/geoloop/plotting/create_plots.py b/src/geoloop/plotting/create_plots.py
index c9eda99..bb7ad17 100644
--- a/src/geoloop/plotting/create_plots.py
+++ b/src/geoloop/plotting/create_plots.py
@@ -10,10 +10,10 @@ import seaborn as sns
 import xarray as xr
 from PIL import Image
 
-from geoloop.utils.helpers import get_param_names
 from geoloop.bin.SingleRunSim import SingleRun
 from geoloop.constants import format_dict, units_dict
 from geoloop.geoloopcore.strat_interpolator import StratInterpolator
+from geoloop.utils.helpers import get_param_names
 
 
 class PlotResults:
diff --git a/src/geoloop/utils/RunManager.py b/src/geoloop/utils/RunManager.py
index 53557b4..d218991 100644
--- a/src/geoloop/utils/RunManager.py
+++ b/src/geoloop/utils/RunManager.py
@@ -4,10 +4,10 @@ import numpy as np
 from scipy.stats import lognorm, norm, triang, uniform
 from tqdm import tqdm
 
-from geoloop.configuration import SingleRunConfig
-from geoloop.utils.helpers import get_param_names
 from geoloop.bin.SingleRunSim import SingleRun, optimize_forkeys
+from geoloop.configuration import SingleRunConfig
 from geoloop.geoloopcore.simulationparameters import SimulationParameters
+from geoloop.utils.helpers import get_param_names
 
 
 def sample_parameter_space(config: SingleRunConfig) -> tuple[dict, list[str]]:
-- 
GitLab


From 345c3dc270d615a0ab4f8eda00847a4cc32e554e Mon Sep 17 00:00:00 2001
From: korevaarzer <zanne.korevaar@tno.nl>
Date: Mon, 22 Dec 2025 10:25:38 +0100
Subject: [PATCH 3/4] Add package building dependencies to venv and dev
 dependencies group

---
 pyproject.toml |   6 +-
 uv.lock        | 330 +++++++++++++++++++++++++++++++++++++++++++++++--
 2 files changed, 324 insertions(+), 12 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b079eac..097470d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ dependencies = [
     "typer>=0.20.0",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "ruff>=0.14.6",
     "black",
@@ -47,6 +47,10 @@ dev = [
     "mike>=2.1.3,<3",
     "mkdocstrings>=0.30.1",
     "mkdocstrings-python>=1.18.2",
+    "build>=1.3.0",
+    "twine>=6.2.0",
+    "wheel>=0.45.1",
+    "setuptools>=80.9.0",
 ]
 
 [tool.setuptools.packages.find]
diff --git a/uv.lock b/uv.lock
index 64df28b..e4e9a41 100644
--- a/uv.lock
+++ b/uv.lock
@@ -60,6 +60,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/68/11/21331aed19145a952ad28fca2756a1433ee9308079bd03bd898e903a2e53/black-25.12.0-py3-none-any.whl", hash = "sha256:48ceb36c16dbc84062740049eef990bb2ce07598272e673c17d1a7720c71c828", size = 206191, upload-time = "2025-12-08T01:40:50.963Z" },
 ]
 
+[[package]]
+name = "build"
+version = "1.3.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "colorama", marker = "os_name == 'nt'" },
+    { name = "packaging" },
+    { name = "pyproject-hooks" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/25/1c/23e33405a7c9eac261dff640926b8b5adaed6a6eb3e1767d441ed611d0c0/build-1.3.0.tar.gz", hash = "sha256:698edd0ea270bde950f53aed21f3a0135672206f3911e0176261a31e0e07b397", size = 48544, upload-time = "2025-08-01T21:27:09.268Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/cb/8c/2b30c12155ad8de0cf641d76a8b396a16d2c36bc6d50b621a62b7c4567c1/build-1.3.0-py3-none-any.whl", hash = "sha256:7145f0b5061ba90a1500d60bd1b13ca0a8a4cebdd0cc16ed8adf1c0e739f43b4", size = 23382, upload-time = "2025-08-01T21:27:07.844Z" },
+]
+
 [[package]]
 name = "certifi"
 version = "2025.11.12"
@@ -69,6 +83,31 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/70/7d/9bc192684cea499815ff478dfcdc13835ddf401365057044fb721ec6bddb/certifi-2025.11.12-py3-none-any.whl", hash = "sha256:97de8790030bbd5c2d96b7ec782fc2f7820ef8dba6db909ccf95449f2d062d4b", size = 159438, upload-time = "2025-11-12T02:54:49.735Z" },
 ]
 
+[[package]]
+name = "cffi"
+version = "2.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pycparser", marker = "implementation_name != 'PyPy'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/eb/56/b1ba7935a17738ae8453301356628e8147c79dbb825bcbc73dc7401f9846/cffi-2.0.0.tar.gz", hash = "sha256:44d1b5909021139fe36001ae048dbdde8214afa20200eda0f64c068cac5d5529", size = 523588, upload-time = "2025-09-08T23:24:04.541Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ff/df/a4f0fbd47331ceeba3d37c2e51e9dfc9722498becbeec2bd8bc856c9538a/cffi-2.0.0-cp312-cp312-manylinux1_i686.manylinux2014_i686.manylinux_2_17_i686.manylinux_2_5_i686.whl", hash = "sha256:21d1152871b019407d8ac3985f6775c079416c282e431a4da6afe7aefd2bccbe", size = 212529, upload-time = "2025-09-08T23:22:47.349Z" },
+    { url = "https://files.pythonhosted.org/packages/d5/72/12b5f8d3865bf0f87cf1404d8c374e7487dcf097a1c91c436e72e6badd83/cffi-2.0.0-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:b21e08af67b8a103c71a250401c78d5e0893beff75e28c53c98f4de42f774062", size = 220097, upload-time = "2025-09-08T23:22:48.677Z" },
+    { url = "https://files.pythonhosted.org/packages/c2/95/7a135d52a50dfa7c882ab0ac17e8dc11cec9d55d2c18dda414c051c5e69e/cffi-2.0.0-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl", hash = "sha256:1e3a615586f05fc4065a8b22b8152f0c1b00cdbc60596d187c2a74f9e3036e4e", size = 207983, upload-time = "2025-09-08T23:22:50.06Z" },
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+source = { registry = "https://pypi.org/simple" }
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 name = "et-xmlfile"
 version = "2.0.0"
@@ -278,9 +359,10 @@ dependencies = [
     { name = "xarray" },
 ]
 
-[package.optional-dependencies]
+[package.dev-dependencies]
 dev = [
     { name = "black" },
+    { name = "build" },
     { name = "flake8" },
     { name = "mike" },
     { name = "mkdocs" },
@@ -289,20 +371,16 @@ dev = [
     { name = "mkdocstrings-python" },
     { name = "pytest" },
     { name = "ruff" },
+    { name = "setuptools" },
+    { name = "twine" },
+    { name = "wheel" },
 ]
 
 [package.metadata]
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-    { name = "flake8", marker = "extra == 'dev'" },
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@@ -319,7 +395,23 @@ requires-dist = [
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     { name = "xarray", specifier = ">=2025.3.1" },
 ]
-provides-extras = ["dev"]
+
+[package.metadata.requires-dev]
+dev = [
+    { name = "black" },
+    { name = "build", specifier = ">=1.3.0" },
+    { name = "flake8" },
+    { name = "mike", specifier = ">=2.1.3,<3" },
+    { name = "mkdocs", specifier = ">=1.6.1" },
+    { name = "mkdocs-material", specifier = ">=9.6.23" },
+    { name = "mkdocstrings", specifier = ">=0.30.1" },
+    { name = "mkdocstrings-python", specifier = ">=1.18.2" },
+    { name = "pytest", specifier = ">=8.4.2" },
+    { name = "ruff", specifier = ">=0.14.6" },
+    { name = "setuptools", specifier = ">=80.9.0" },
+    { name = "twine", specifier = ">=6.2.0" },
+    { name = "wheel", specifier = ">=0.45.1" },
+]
 
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+dependencies = [
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     { url = "https://files.pythonhosted.org/packages/04/11/432f32f8097b03e3cd5fe57e88efb685d964e2e5178a48ed61e841f7fdce/pyyaml_env_tag-1.1-py3-none-any.whl", hash = "sha256:17109e1a528561e32f026364712fee1264bc2ea6715120891174ed1b980d2e04", size = 4722, upload-time = "2025-05-13T15:23:59.629Z" },
 ]
 
+[[package]]
+name = "readme-renderer"
+version = "44.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "docutils" },
+    { name = "nh3" },
+    { name = "pygments" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/5a/a9/104ec9234c8448c4379768221ea6df01260cd6c2ce13182d4eac531c8342/readme_renderer-44.0.tar.gz", hash = "sha256:8712034eabbfa6805cacf1402b4eeb2a73028f72d1166d6f5cb7f9c047c5d1e1", size = 32056, upload-time = "2024-07-08T15:00:57.805Z" }
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+    { url = "https://files.pythonhosted.org/packages/e1/67/921ec3024056483db83953ae8e48079ad62b92db7880013ca77632921dd0/readme_renderer-44.0-py3-none-any.whl", hash = "sha256:2fbca89b81a08526aadf1357a8c2ae889ec05fb03f5da67f9769c9a592166151", size = 13310, upload-time = "2024-07-08T15:00:56.577Z" },
+]
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 name = "requests"
 version = "2.32.5"
@@ -1179,6 +1415,27 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/1e/db/4254e3eabe8020b458f1a747140d32277ec7a271daf1d235b70dc0b4e6e3/requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6", size = 64738, upload-time = "2025-08-18T20:46:00.542Z" },
 ]
 
+[[package]]
+name = "requests-toolbelt"
+version = "1.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "requests" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/f3/61/d7545dafb7ac2230c70d38d31cbfe4cc64f7144dc41f6e4e4b78ecd9f5bb/requests-toolbelt-1.0.0.tar.gz", hash = "sha256:7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6", size = 206888, upload-time = "2023-05-01T04:11:33.229Z" }
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+]
+
+[[package]]
+name = "rfc3986"
+version = "2.0.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/85/40/1520d68bfa07ab5a6f065a186815fb6610c86fe957bc065754e47f7b0840/rfc3986-2.0.0.tar.gz", hash = "sha256:97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c", size = 49026, upload-time = "2022-01-10T00:52:30.832Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ff/9a/9afaade874b2fa6c752c36f1548f718b5b83af81ed9b76628329dab81c1b/rfc3986-2.0.0-py2.py3-none-any.whl", hash = "sha256:50b1502b60e289cb37883f3dfd34532b8873c7de9f49bb546641ce9cbd256ebd", size = 31326, upload-time = "2022-01-10T00:52:29.594Z" },
+]
+
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 name = "rich"
 version = "14.2.0"
@@ -1285,6 +1542,28 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/0b/68/4cc6d36beeaabb532d15ead8ed635fb34bf0b2c7ee02de3f79e9b1ba5ebc/secondarycoolantprops-1.3-py3-none-any.whl", hash = "sha256:10e10e276f946009f7c6730e17d5c92652db7ab256502d2ad1591664b4462d76", size = 13386, upload-time = "2025-01-21T20:04:16.001Z" },
 ]
 
+[[package]]
+name = "secretstorage"
+version = "3.5.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "cryptography" },
+    { name = "jeepney" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/1c/03/e834bcd866f2f8a49a85eaff47340affa3bfa391ee9912a952a1faa68c7b/secretstorage-3.5.0.tar.gz", hash = "sha256:f04b8e4689cbce351744d5537bf6b1329c6fc68f91fa666f60a380edddcd11be", size = 19884, upload-time = "2025-11-23T19:02:53.191Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/b7/46/f5af3402b579fd5e11573ce652019a67074317e18c1935cc0b4ba9b35552/secretstorage-3.5.0-py3-none-any.whl", hash = "sha256:0ce65888c0725fcb2c5bc0fdb8e5438eece02c523557ea40ce0703c266248137", size = 15554, upload-time = "2025-11-23T19:02:51.545Z" },
+]
+
+[[package]]
+name = "setuptools"
+version = "80.9.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/18/5d/3bf57dcd21979b887f014ea83c24ae194cfcd12b9e0fda66b957c69d1fca/setuptools-80.9.0.tar.gz", hash = "sha256:f36b47402ecde768dbfafc46e8e4207b4360c654f1f3bb84475f0a28628fb19c", size = 1319958, upload-time = "2025-05-27T00:56:51.443Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl", hash = "sha256:062d34222ad13e0cc312a4c02d73f059e86a4acbfbdea8f8f76b28c99f306922", size = 1201486, upload-time = "2025-05-27T00:56:49.664Z" },
+]
+
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 name = "shellingham"
 version = "1.5.4"
@@ -1315,6 +1594,26 @@ wheels = [
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 ]
 
+[[package]]
+name = "twine"
+version = "6.2.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "id" },
+    { name = "keyring", marker = "platform_machine != 'ppc64le' and platform_machine != 's390x'" },
+    { name = "packaging" },
+    { name = "readme-renderer" },
+    { name = "requests" },
+    { name = "requests-toolbelt" },
+    { name = "rfc3986" },
+    { name = "rich" },
+    { name = "urllib3" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/e0/a8/949edebe3a82774c1ec34f637f5dd82d1cf22c25e963b7d63771083bbee5/twine-6.2.0.tar.gz", hash = "sha256:e5ed0d2fd70c9959770dce51c8f39c8945c574e18173a7b81802dab51b4b75cf", size = 172262, upload-time = "2025-09-04T15:43:17.255Z" }
+wheels = [
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+]
+
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 name = "typer"
 version = "0.20.0"
@@ -1402,6 +1701,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/33/e8/e40370e6d74ddba47f002a32919d91310d6074130fe4e17dabcafc15cbf1/watchdog-6.0.0-py3-none-win_ia64.whl", hash = "sha256:a1914259fa9e1454315171103c6a30961236f508b9b623eae470268bbcc6a22f", size = 79067, upload-time = "2024-11-01T14:07:11.845Z" },
 ]
 
+[[package]]
+name = "wheel"
+version = "0.45.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/8a/98/2d9906746cdc6a6ef809ae6338005b3f21bb568bea3165cfc6a243fdc25c/wheel-0.45.1.tar.gz", hash = "sha256:661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729", size = 107545, upload-time = "2024-11-23T00:18:23.513Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/0b/2c/87f3254fd8ffd29e4c02732eee68a83a1d3c346ae39bc6822dcbcb697f2b/wheel-0.45.1-py3-none-any.whl", hash = "sha256:708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248", size = 72494, upload-time = "2024-11-23T00:18:21.207Z" },
+]
+
 [[package]]
 name = "xarray"
 version = "2025.12.0"
-- 
GitLab


From 902bd6377691c4160f2dfde9251a16833885d346 Mon Sep 17 00:00:00 2001
From: korevaarzer <zanne.korevaar@tno.nl>
Date: Mon, 22 Dec 2025 10:25:38 +0100
Subject: [PATCH 4/4] Add package building dependencies to venv and dev
 dependencies group

---
 .gitlab-ci.yml |   2 +-
 pyproject.toml |   6 +-
 uv.lock        | 330 +++++++++++++++++++++++++++++++++++++++++++++++--
 3 files changed, 325 insertions(+), 13 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 859bdd7..7dc3c64 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,7 +8,7 @@ Run tests:
   before_script:
     - pip install uv
     - uv venv
-    - uv sync --extra dev
+    - uv sync --group dev
     - uv pip install -e .
   script:
     - uv run pytest -vv
diff --git a/pyproject.toml b/pyproject.toml
index b079eac..097470d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ dependencies = [
     "typer>=0.20.0",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "ruff>=0.14.6",
     "black",
@@ -47,6 +47,10 @@ dev = [
     "mike>=2.1.3,<3",
     "mkdocstrings>=0.30.1",
     "mkdocstrings-python>=1.18.2",
+    "build>=1.3.0",
+    "twine>=6.2.0",
+    "wheel>=0.45.1",
+    "setuptools>=80.9.0",
 ]
 
 [tool.setuptools.packages.find]
diff --git a/uv.lock b/uv.lock
index 64df28b..e4e9a41 100644
--- a/uv.lock
+++ b/uv.lock
@@ -60,6 +60,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/68/11/21331aed19145a952ad28fca2756a1433ee9308079bd03bd898e903a2e53/black-25.12.0-py3-none-any.whl", hash = "sha256:48ceb36c16dbc84062740049eef990bb2ce07598272e673c17d1a7720c71c828", size = 206191, upload-time = "2025-12-08T01:40:50.963Z" },
 ]
 
+[[package]]
+name = "build"
+version = "1.3.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "colorama", marker = "os_name == 'nt'" },
+    { name = "packaging" },
+    { name = "pyproject-hooks" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/25/1c/23e33405a7c9eac261dff640926b8b5adaed6a6eb3e1767d441ed611d0c0/build-1.3.0.tar.gz", hash = "sha256:698edd0ea270bde950f53aed21f3a0135672206f3911e0176261a31e0e07b397", size = 48544, upload-time = "2025-08-01T21:27:09.268Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/cb/8c/2b30c12155ad8de0cf641d76a8b396a16d2c36bc6d50b621a62b7c4567c1/build-1.3.0-py3-none-any.whl", hash = "sha256:7145f0b5061ba90a1500d60bd1b13ca0a8a4cebdd0cc16ed8adf1c0e739f43b4", size = 23382, upload-time = "2025-08-01T21:27:07.844Z" },
+]
+
 [[package]]
 name = "certifi"
 version = "2025.11.12"
@@ -69,6 +83,31 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/70/7d/9bc192684cea499815ff478dfcdc13835ddf401365057044fb721ec6bddb/certifi-2025.11.12-py3-none-any.whl", hash = "sha256:97de8790030bbd5c2d96b7ec782fc2f7820ef8dba6db909ccf95449f2d062d4b", size = 159438, upload-time = "2025-11-12T02:54:49.735Z" },
 ]
 
+[[package]]
+name = "cffi"
+version = "2.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "pycparser", marker = "implementation_name != 'PyPy'" },
+]
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 version = "1.6.5"
@@ -198,6 +237,39 @@ wheels = [
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+source = { registry = "https://pypi.org/simple" }
+dependencies = [
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@@ -289,20 +371,16 @@ dev = [
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     { name = "pytest" },
     { name = "ruff" },
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+    { name = "twine" },
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 version = "1.5.4"
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+    { name = "keyring", marker = "platform_machine != 'ppc64le' and platform_machine != 's390x'" },
+    { name = "packaging" },
+    { name = "readme-renderer" },
+    { name = "requests" },
+    { name = "requests-toolbelt" },
+    { name = "rfc3986" },
+    { name = "rich" },
+    { name = "urllib3" },
+]
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+]
+
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 name = "xarray"
 version = "2025.12.0"
-- 
GitLab