general cleanup

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "scgenerator"
-version = "0.3.8"
+version = "0.3.9"
 description = "Simulate nonlinear pulse propagation in optical fibers"
 readme = "README.md"
 authors = [{ name = "Benoit Sierro", email = "benoit.sierro@iap.unibe.ch" }]

src/scgenerator/io.py

@@ -13,6 +13,19 @@ from zipfile import ZipFile
 import numpy as np
 
 
+class TimedMessage:
+    def __init__(self, interval: float = 10.0):
+        self.interval = datetime.timedelta(seconds=interval)
+        self.next = datetime.datetime.now()
+
+    def ready(self) -> bool:
+        t = datetime.datetime.now()
+        if self.next <= t:
+            self.next = t + self.interval
+            return True
+        return False
+
+
 def data_file(path: str) -> Path:
     """returns a `Path` object pointing to the desired data file included in `scgenerator`"""
     return importlib.resources.path("scgenerator", "data") / path

src/scgenerator/parameter.py

@@ -492,8 +492,8 @@ class Parameters:
                 continue
             yield k, v
 
-    def copy(self, deep: bool = True, freeze: bool = False) -> Parameters:
-        """create a deep copy of self. if freeze is True, the returned copy is read-only"""
+    def copy(self, deep: bool = False, freeze: bool = False) -> Parameters:
+        """create a (deep) copy of self. if freeze is True, the returned copy is read-only"""
         if deep:
             params = Parameters(**deepcopy(self._param_dico))
         else:

src/scgenerator/solver.py

@@ -12,9 +12,12 @@ from typing import Any, Iterator, Sequence
 import numba
 import numpy as np
 
+from scgenerator.io import TimedMessage
+from scgenerator.logger import get_logger
 from scgenerator.math import abs2
 from scgenerator.operators import SpecOperator, VariableQuantity
-from scgenerator.utils import TimedMessage
+
+logger = get_logger(__name__)
 
 
 class SimulationResult:
@@ -229,10 +232,7 @@ def solve43(
                 continue
         else:
             rejected.append((h, error))
-            print(
-                f"{z = :.3f} rejected step {step_ind} with {h = :.2g}, {error = :.2g}",
-                file=sys.stderr,
-            )
+            logger.info(f"{z = :.3f} rejected step {step_ind} with {h = :.2g}, {error = :.2g}")
 
         h = h * next_h_factor
 
@@ -243,7 +243,7 @@ def solve43(
             store_next = False
 
         if msg.ready():
-            print(f"step {step_ind}, {z = :.3f}, {error = :g}, {h = :.3g}", file=sys.stderr)
+            logger.info(f"step {step_ind}, {z = :.3f}, {error = :g}, {h = :.3g}")
 
 
 def integrate(

src/scgenerator/spectra.py

@@ -207,11 +207,14 @@ class Propagation(Generic[ParamsOrNone]):
 
     def _load_slice(self, key: slice) -> Spectrum:
         _iter = range(len(self))[key]
-        out = np.zeros((len(_iter), self.parameters.t_num), dtype=complex)
         if self.parameters is not None:
-            out = Spectrum(out, self.parameters)
+            out = Spectrum(
+                np.zeros((len(_iter), self.parameters.t_num), dtype=complex), self.parameters
+            )
             for i in _iter:
                 out[i] = self.io.load_spectrum(i)
+        else:
+            out = np.array([self.io.load_spectrum(i) for i in _iter])
         return out
 
     def append(self, spectrum: np.ndarray):

src/scgenerator/utils.py

@@ -27,19 +27,6 @@ from scgenerator.logger import get_logger
 T_ = TypeVar("T_")
 
 
-class TimedMessage:
-    def __init__(self, interval: float = 10.0):
-        self.interval = datetime.timedelta(seconds=interval)
-        self.next = datetime.datetime.now()
-
-    def ready(self) -> bool:
-        t = datetime.datetime.now()
-        if self.next <= t:
-            self.next = t + self.interval
-            return True
-        return False
-
-
 def conform_variable_entry(d) -> list[dict[str, list]]:
     if isinstance(d, MutableMapping):
         d = [{k: v} for k, v in d.items()]