ready to merge

src/scgenerator/__init__.py

@@ -13,7 +13,7 @@ from .plotting import (
     get_extent,
 )
 from .spectra import Spectrum, SimulationSeries
-from ._utils import Paths, open_config, parameter
+from ._utils import Paths, _open_config, parameter, open_single_config
 from ._utils.parameter import Configuration, Parameters
 from ._utils.utils import PlotRange
 from ._utils.legacy import convert_sim_folder

src/scgenerator/_utils/__init__.py

@@ -103,12 +103,12 @@ def conform_toml_path(path: os.PathLike) -> str:
 
 
 def open_single_config(path: os.PathLike) -> dict[str, Any]:
-    d = open_config(path)
+    d = _open_config(path)
     f = d.pop("Fiber")[0]
     return d | f
 
 
-def open_config(path: os.PathLike):
+def _open_config(path: os.PathLike):
     """returns a dictionary parsed from the specified toml file
     This also handle having a 'INCLUDE' argument that will fill
     otherwise unspecified keys with what's in the INCLUDE file(s)"""
@@ -170,7 +170,7 @@ def load_config_sequence(path: os.PathLike) -> tuple[Path, list[dict[str, Any]]]
     Parameters
     ----------
     path : os.PathLike
-        path to the config toml file
+        path to the config toml file or a directory containing config files
 
     Returns
     -------
@@ -180,9 +180,15 @@ def load_config_sequence(path: os.PathLike) -> tuple[Path, list[dict[str, Any]]]
         one config per fiber
 
     """
-    loaded_config = open_config(path)
+    path = Path(path)
+    fiber_list: list[dict[str, Any]]
+    if path.name.lower().endswith(".toml"):
+        loaded_config = _open_config(path)
+        fiber_list = loaded_config.pop("Fiber")
+    else:
+        loaded_config = dict(name=path.name)
+        fiber_list = [_open_config(p) for p in sorted(path.glob("initial_config*.toml"))]
 
-    fiber_list: list[dict[str, Any]] = loaded_config.pop("Fiber")
     if len(fiber_list) == 0:
         raise ValueError(f"No fiber in config {path}")
     final_path = loaded_config.get("name")

src/scgenerator/_utils/legacy.py

@@ -1,3 +1,4 @@
+from genericpath import exists
 import os
 import sys
 from pathlib import Path
@@ -28,11 +29,13 @@ def load_config_sequence(path: os.PathLike) -> tuple[list[Path], list[dict[str,
 
 def convert_sim_folder(path: os.PathLike):
     path = Path(path).resolve()
+    new_root = path.parent / "sc_legagy_converter" / path.name
+    os.makedirs(new_root, exist_ok=True)
     config_paths, configs = load_config_sequence(path)
     master_config = dict(name=path.name, Fiber=configs)
-    with open(path / "initial_config.toml", "w") as f:
+    with open(new_root / "initial_config.toml", "w") as f:
         toml.dump(master_config, f, encoder=toml.TomlNumpyEncoder())
-    configuration = Configuration(path / "initial_config.toml", final_output_path=path)
+    configuration = Configuration(path, final_output_path=new_root)
     pbar = PBars(configuration.total_num_steps, "Converting")
 
     new_paths: dict[VariationDescriptor, Parameters] = dict(configuration)

src/scgenerator/_utils/parameter.py

@@ -480,7 +480,7 @@ class Parameters(_AbstractParameters):
 
     @classmethod
     def load(cls, path: os.PathLike) -> "Parameters":
-        return cls(**utils.open_config(path))
+        return cls(**utils._open_config(path))
 
     @classmethod
     def load_and_compute(cls, path: os.PathLike) -> "Parameters":
@@ -1011,7 +1011,7 @@ class Configuration:
         num = utils.find_last_spectrum_num(data_dir)
         if config_dict is None:
             try:
-                config_dict = utils.open_config(data_dir / PARAM_FN)
+                config_dict = utils._open_config(data_dir / PARAM_FN)
             except FileNotFoundError:
                 self.logger.warning(f"did not find {PARAM_FN!r} in {data_dir}")
                 return self.State.ABSENT, 0

src/scgenerator/physics/__init__.py

@@ -10,8 +10,7 @@ from scipy.optimize import minimize_scalar
 
 from .. import math
 from . import fiber, materials, units, pulse
-from .. import _utils
+from .._utils import cache, load_material_dico
-from .._utils import cache
 
 T = TypeVar("T")
 
@@ -62,7 +61,7 @@ def material_dispersion(
         )
         return disp
     else:
-        material_dico = utils.load_material_dico(material)
+        material_dico = load_material_dico(material)
         if ideal:
             n_gas_2 = materials.sellmeier(wavelengths, material_dico, pressure, temperature) + 1
         else:

src/scgenerator/physics/pulse.py

@@ -810,7 +810,8 @@ def find_lobe_limits(x_axis, values, debug="", already_sorted=True):
             )
             ax.legend()
             fig.savefig(out_path, bbox_inches="tight")
-        plt.close()
+        if fig is not None:
+            plt.close(fig)
 
     else:
         good_roots, left_lim, right_lim = _select_roots(d_spline, d_roots, dd_roots, fwhm_pos)

src/scgenerator/physics/simulate.py

@@ -219,6 +219,17 @@ class RK4IP:
         return self.stored_spectra
 
     def irun(self) -> Generator[tuple[int, int, np.ndarray], None, None]:
+        """run the simulation as a generator obj
+
+        Yields
+        -------
+        int
+            current simulation step
+        int
+            current number of spectra returned
+        np.ndarray
+            spectrum
+        """
 
         # Print introduction
         self.logger.debug(

src/scgenerator/scripts/__init__.py

@@ -12,7 +12,7 @@ from ..const import PARAM_FN, PARAM_SEPARATOR
 from ..physics import fiber, units
 from ..plotting import plot_setup
 from ..spectra import SimulationSeries
-from .._utils import auto_crop, open_config, save_toml, translate_parameters
+from .._utils import auto_crop, _open_config, save_toml, translate_parameters
 from .._utils.parameter import (
     Configuration,
     Parameters,
@@ -258,7 +258,7 @@ def finish_plot(fig, legend_axes, all_labels, params):
 
 def plot_helper(config_path: Path) -> Iterable[tuple[dict, list[str], Parameters]]:
     cc = cycler(color=[f"C{i}" for i in range(10)]) * cycler(ls=["-", "--"])
-    pseq = Configuration(open_config(config_path))
+    pseq = Configuration(_open_config(config_path))
     for style, (variables, params) in zip(cc, pseq):
         lbl = [pretty_format_value(name, value) for name, value in variables[1:-1]]
         yield style, lbl, params
@@ -267,7 +267,7 @@ def plot_helper(config_path: Path) -> Iterable[tuple[dict, list[str], Parameters
 def convert_params(params_file: os.PathLike):
     p = Path(params_file)
     if p.name == PARAM_FN:
-        d = open_config(params_file)
+        d = _open_config(params_file)
         d = translate_parameters(d)
         save_toml(params_file, d)
         print(f"converted {p}")