custom worker num, better logging, better config

src/scgenerator/__init__.py

@@ -4,3 +4,4 @@ from .math import abs2, argclosest, span
 from .physics import fiber, materials, pulse, simulate, units
 from .physics.simulate import RK4IP, new_simulation, resume_simulations
 from .plotting import plot_avg, plot_results_1D, plot_results_2D, plot_spectrogram
+from .spectra import Pulse

src/scgenerator/cli/cli.py

@@ -2,15 +2,19 @@ import argparse
 import os
 import random
 from pathlib import Path
+from collections import ChainMap
 
-from scgenerator import io
+from ray.worker import get
-from scgenerator.physics.simulate import (
+
+from .. import io, env, const
+from ..logger import get_logger
+from ..physics.simulate import (
     SequencialSimulations,
     resume_simulations,
     run_simulation_sequence,
 )
-from scgenerator.physics.fiber import dispersion_coefficients
+from ..physics.fiber import dispersion_coefficients
-
+from pprint import pprint
 
 try:
     import ray
@@ -18,29 +22,26 @@ except ImportError:
     ray = None
 
 
+def set_env_variables(cmd_line_args: dict[str, str]):
+    cm = ChainMap(cmd_line_args, os.environ)
+    for env_key in const.global_config:
+        k = env_key.replace(const.ENVIRON_KEY_BASE, "").lower()
+        v = cm.get(k)
+        if v is not None:
+            os.environ[env_key] = str(v)
+
+
 def create_parser():
     parser = argparse.ArgumentParser(description="scgenerator command", prog="scgenerator")
-
     subparsers = parser.add_subparsers(help="sub-command help")
 
+    for key, args in const.global_config.items():
+        names = ["--" + key.replace(const.ENVIRON_KEY_BASE, "").replace("_", "-").lower()]
+        if "short_name" in args:
+            names.append(args["short_name"])
         parser.add_argument(
-        "--id",
+            *names, **{k: v for k, v in args.items() if k not in {"short_name", "type"}}
-        type=int,
-        default=random.randint(0, 1e18),
-        help="Unique id of the session. Only useful when running several processes at the same time.",
         )
-    parser.add_argument(
-        "--start-ray",
-        action="store_true",
-        help="initialize ray (ray must be installed)",
-    )
-
-    parser.add_argument(
-        "--no-ray",
-        action="store_true",
-        help="force not to use ray",
-    )
-    parser.add_argument("--output-name", "-o", help="path to the final output folder", default=None)
 
     run_parser = subparsers.add_parser("run", help="run a simulation from a config file")
     run_parser.add_argument("configs", help="path(s) to the toml configuration file(s)", nargs="+")
@@ -71,15 +72,19 @@ def create_parser():
 def main():
     parser = create_parser()
     args = parser.parse_args()
+
+    set_env_variables({k: v for k, v in vars(args).items() if v is not None})
+
     args.func(args)
 
-    print(f"coef hits : {dispersion_coefficients.hits}, misses : {dispersion_coefficients.misses}")
+    logger = get_logger(__name__)
+    logger.info(f"dispersion cache : {dispersion_coefficients.cache_info()}")
 
 
 def run_sim(args):
 
     method = prep_ray(args)
-    run_simulation_sequence(*args.configs, method=method, final_name=args.output_name)
+    run_simulation_sequence(*args.configs, method=method)
 
 
 def merge(args):
@@ -91,19 +96,20 @@ def merge(args):
 
 
 def prep_ray(args):
+    logger = get_logger(__name__)
     if ray:
-        if args.start_ray:
+        if env.get(const.START_RAY):
             init_str = ray.init()
-        elif not args.no_ray:
+        elif not env.get(const.NO_RAY):
             try:
                 init_str = ray.init(
                     address="auto",
                     _redis_password=os.environ.get("redis_password", "caco1234"),
                 )
-                print(init_str)
+                logger.info(init_str)
             except ConnectionError as e:
-                print(e)
+                logger.error(e)
-    return SequencialSimulations if args.no_ray else None
+    return SequencialSimulations if env.get(const.NO_RAY) else None
 
 
 def resume_sim(args):
@@ -111,9 +117,7 @@ def resume_sim(args):
     method = prep_ray(args)
     sim = resume_simulations(Path(args.sim_dir), method=method)
     sim.run()
-    run_simulation_sequence(
+    run_simulation_sequence(*args.configs, method=method, prev_sim_dir=sim.sim_dir)
-        *args.configs, method=method, prev_sim_dir=sim.sim_dir, final_name=args.output_name
-    )
 
 
 if __name__ == "__main__":

src/scgenerator/const.py

@@ -1,6 +1,9 @@
 __version__ = "0.1.0"
 
 
+from typing import Any
+
+
 def pbar_format(worker_id: int):
     if worker_id == 0:
         return dict(
@@ -17,12 +20,45 @@ def pbar_format(worker_id: int):
 
 
 ENVIRON_KEY_BASE = "SCGENERATOR_"
-PBAR_POLICY = ENVIRON_KEY_BASE + "PBAR_POLICY"
-LOG_POLICY = ENVIRON_KEY_BASE + "LOG_POLICY"
 TMP_FOLDER_KEY_BASE = ENVIRON_KEY_BASE + "SC_TMP_"
 PREFIX_KEY_BASE = ENVIRON_KEY_BASE + "PREFIX_"
 PARAM_SEPARATOR = " "
 
+PBAR_POLICY = ENVIRON_KEY_BASE + "PBAR_POLICY"
+LOG_FILE_LEVEL = ENVIRON_KEY_BASE + "LOG_FILE_LEVEL"
+LOG_PRINT_LEVEL = ENVIRON_KEY_BASE + "LOG_PRINT_LEVEL"
+START_RAY = ENVIRON_KEY_BASE + "START_RAY"
+NO_RAY = ENVIRON_KEY_BASE + "NO_RAY"
+OUTPUT_PATH = ENVIRON_KEY_BASE + "OUTPUT_PATH"
+
+
+global_config: dict[str, dict[str, Any]] = {
+    LOG_FILE_LEVEL: dict(
+        help="minimum lvl of message to be saved in the log file",
+        choices=["critical", "error", "warning", "info", "debug"],
+        default=None,
+        type=str,
+    ),
+    LOG_PRINT_LEVEL: dict(
+        help="minimum lvl of message to be printed to the standard output",
+        choices=["critical", "error", "warning", "info", "debug"],
+        default="error",
+        type=str,
+    ),
+    PBAR_POLICY: dict(
+        help="what to do with progress pars (print them, make them a txt file or nothing), default is print",
+        choices=["print", "file", "both", "none"],
+        default=None,
+        type=str,
+    ),
+    START_RAY: dict(action="store_true", help="initialize ray (ray must be installed)", type=bool),
+    NO_RAY: dict(action="store_true", help="force not to use ray", type=bool),
+    OUTPUT_PATH: dict(
+        short_name="-o", help="path to the final output folder", default=None, type=str
+    ),
+}
+
+
 SPEC1_FN = "spectrum_{}.npy"
 SPECN_FN = "spectra_{}.npy"
 Z_FN = "z.npy"

src/scgenerator/data/gas.toml

@@ -38,6 +38,14 @@ b = 3.978e-5
 a = 0.425
 b = 5.105e-5
 
+[air]
+a = 0.1358
+b = 3.64e-5
+
+[vacuum]
+a = 0
+b = 0
+
 [air.sellmeier]
 B = [57921050000.0, 1679170000.0]
 C = [238018500000000.0, 57362000000000.0]
@@ -45,6 +53,11 @@ P0 = 101325
 T0 = 288.15
 kind = 2
 
+[air.kerr]
+P0 = 101325
+T0 = 293.15
+n2 = 3.01e-23
+
 [nitrogen.sellmeier]
 B = [32431570000.0]
 C = [144000000000000.0]
@@ -181,3 +194,16 @@ P0 = 30400.0
 T0 = 273.15
 n2 = 5.8e-23
 source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
+
+[vacuum.sellmeier]
+B = []
+C = []
+P0 = 101325
+T0 = 273.15
+kind = 1
+
+[vacuum.kerr]
+P0 = 30400.0
+T0 = 273.15
+n2 = 0
+source = "none"

src/scgenerator/env.py

@@ -1,7 +1,14 @@
 import os
-from typing import Dict, Literal, Optional, Set
+from typing import Any, Dict, Literal, Optional, Set
 
-from .const import ENVIRON_KEY_BASE, LOG_POLICY, PBAR_POLICY, TMP_FOLDER_KEY_BASE
+from .const import (
+    ENVIRON_KEY_BASE,
+    LOG_FILE_LEVEL,
+    LOG_PRINT_LEVEL,
+    PBAR_POLICY,
+    TMP_FOLDER_KEY_BASE,
+    global_config,
+)
 
 
 def data_folder(task_id: int) -> Optional[str]:
@@ -10,6 +17,14 @@ def data_folder(task_id: int) -> Optional[str]:
     return tmp
 
 
+def get(key: str) -> Any:
+    str_value = os.environ.get(key)
+    try:
+        return global_config[key]["type"](str_value)
+    except (ValueError, KeyError):
+        return None
+
+
 def all_environ() -> Dict[str, str]:
     """returns a dictionary of all environment variables set by any instance of scgenerator"""
     d = dict(filter(lambda el: el[0].startswith(ENVIRON_KEY_BASE), os.environ.items()))
@@ -17,7 +32,7 @@ def all_environ() -> Dict[str, str]:
 
 
 def pbar_policy() -> Set[Literal["print", "file"]]:
-    policy = os.getenv(PBAR_POLICY)
+    policy = get(PBAR_POLICY)
     if policy == "print" or policy is None:
         return {"print"}
     elif policy == "file":
@@ -28,13 +43,23 @@ def pbar_policy() -> Set[Literal["print", "file"]]:
         return set()
 
 
-def log_policy() -> Set[Literal["print", "file"]]:
+def log_file_level() -> Set[Literal["critical", "error", "warning", "info", "debug"]]:
-    policy = os.getenv(LOG_POLICY)
+    policy = get(LOG_FILE_LEVEL)
-    if policy == "print" or policy is None:
+    try:
-        return {"print"}
+        policy = policy.lower()
-    elif policy == "file":
+        if policy in {"critical", "error", "warning", "info", "debug"}:
-        return {"file"}
+            return policy
-    elif policy == "both":
+    except AttributeError:
-        return {"file", "print"}
+        pass
-    else:
+    return None
-        return set()
+
+
+def log_print_level() -> Set[Literal["critical", "error", "warning", "info", "debug"]]:
+    policy = get(LOG_PRINT_LEVEL)
+    try:
+        policy = policy.lower()
+        if policy in {"critical", "error", "warning", "info", "debug"}:
+            return policy
+    except AttributeError:
+        pass
+    return None

src/scgenerator/initialize.py

@@ -212,7 +212,6 @@ class Config(BareConfig):
         for param in [
             "behaviors",
             "z_num",
-            "frep",
             "tolerated_error",
             "parallel",
             "repeat",

src/scgenerator/logger.py

@@ -1,37 +1,16 @@
 import logging
 
-from .env import log_policy
+from .env import log_file_level, log_print_level
-
-# class DebugOnlyFileHandler(logging.FileHandler):
-#     def __init__(
-#         self, filename, mode: str, encoding: Optional[str] = None, delay: bool = False
-#     ) -> None:
-#         super().__init__(filename, mode=mode, encoding=encoding, delay=delay)
-#         self.setLevel(logging.DEBUG)
-
-#     def emit(self, record: logging.LogRecord) -> None:
-#         if not record.levelno == logging.DEBUG:
-#             return
-#         return super().emit(record)
 
 
-DEFAULT_LEVEL = logging.INFO
+lvl_map: dict[str, int] = dict(
-
-lvl_map = dict(
     debug=logging.DEBUG,
     info=logging.INFO,
     warning=logging.WARNING,
     error=logging.ERROR,
-    fatal=logging.FATAL,
     critical=logging.CRITICAL,
 )
 
-loggers = []
-
-
-def _set_debug():
-    DEFAULT_LEVEL = logging.DEBUG
-
 
 def get_logger(name=None):
     """returns a logging.Logger instance. This function is there because if scgenerator
@@ -50,21 +29,10 @@ def get_logger(name=None):
     """
     name = __name__ if name is None else name
     logger = logging.getLogger(name)
-    if name not in loggers:
-        loggers.append(logger)
     return configure_logger(logger)
 
 
-# def set_level_all(lvl):
+def configure_logger(logger: logging.Logger):
-#     _default_lvl =
-#     logging.basicConfig(level=lvl_map[lvl])
-#     for logger in loggers:
-#         logger.setLevel(lvl_map[lvl])
-#         for handler in logger.handlers:
-#             handler.setLevel(lvl_map[lvl])
-
-
-def configure_logger(logger):
     """configures a logging.Logger obj
 
     Parameters
@@ -81,17 +49,20 @@ def configure_logger(logger):
     """
     if not hasattr(logger, "already_configured"):
 
-        if "file" in log_policy():
+        print_lvl = lvl_map.get(log_print_level())
+        file_lvl = lvl_map.get(log_file_level())
+
+        if file_lvl is not None:
             formatter = logging.Formatter("{levelname}: {name}: {message}", style="{")
             file_handler1 = logging.FileHandler("scgenerator.log", "a+")
             file_handler1.setFormatter(formatter)
-            file_handler1.setLevel(logging.DEBUG)
+            file_handler1.setLevel(file_lvl)
             logger.addHandler(file_handler1)
-        if "print" in log_policy():
+        if print_lvl is not None:
             stream_handler = logging.StreamHandler()
-            stream_handler.setLevel(logging.INFO)
+            stream_handler.setLevel(print_lvl)
             logger.addHandler(stream_handler)
-        logger.setLevel(logging.DEBUG)
 
+        logger.setLevel(min(print_lvl, file_lvl))
         logger.already_configured = True
     return logger

src/scgenerator/math.py

@@ -91,7 +91,7 @@ def u_nm(n, m):
 
 
 @np_cache
-def nfft_matrix(t: np.ndarray, f: np.ndarray) -> np.ndarray:
+def ndft_matrix(t: np.ndarray, f: np.ndarray) -> np.ndarray:
     """creates the nfft matrix
 
     Parameters
@@ -111,7 +111,7 @@ def nfft_matrix(t: np.ndarray, f: np.ndarray) -> np.ndarray:
 
 
 @np_cache
-def infft_matrix(t: np.ndarray, f: np.ndarray) -> np.ndarray:
+def indft_matrix(t: np.ndarray, f: np.ndarray) -> np.ndarray:
     """creates the nfft matrix
 
     Parameters
@@ -126,10 +126,10 @@ def infft_matrix(t: np.ndarray, f: np.ndarray) -> np.ndarray:
     np.ndarray, shape = (m, n)
         multiply ~X(f) by this matrix to get x(t)
     """
-    return np.linalg.pinv(nfft_matrix(t, f))
+    return np.linalg.pinv(ndft_matrix(t, f))
 
 
-def nfft(t: np.ndarray, s: np.ndarray, f: np.ndarray) -> np.ndarray:
+def ndft(t: np.ndarray, s: np.ndarray, f: np.ndarray) -> np.ndarray:
     """computes the Fourier transform of an uneven signal
 
     Parameters
@@ -146,10 +146,10 @@ def nfft(t: np.ndarray, s: np.ndarray, f: np.ndarray) -> np.ndarray:
     np.ndarray, shape = (m, )
         amplitude at each frequency
     """
-    return nfft_matrix(t, f) @ s
+    return ndft_matrix(t, f) @ s
 
 
-def infft(f: np.ndarray, a: np.ndarray, t: np.ndarray) -> np.ndarray:
+def indft(f: np.ndarray, a: np.ndarray, t: np.ndarray) -> np.ndarray:
     """computes the inverse Fourier transform of an uneven spectrum
 
     Parameters
@@ -166,7 +166,7 @@ def infft(f: np.ndarray, a: np.ndarray, t: np.ndarray) -> np.ndarray:
     np.ndarray, shape = (m, )
         amplitude at each point of t
     """
-    return infft_matrix(t, f) @ a
+    return indft_matrix(t, f) @ a
 
 
 def make_uniform_2D(values, x_axis, y_axis, n=1024, method="linear"):

src/scgenerator/physics/fiber.py

@@ -130,7 +130,7 @@ def n_eff_marcatili(lambda_, n_gas_2, core_radius, he_mode=(1, 1)):
     lambda_ : ndarray, shape (n, )
         wavelengths array (m)
     n_gas_2 : ndarray, shape (n, )
-        refractive index of the gas as function of lambda_
+        square of the refractive index of the gas as function of lambda_
     core_radius : float
         inner radius of the capillary (m)
     he_mode : tuple, shape (2, ), optional
@@ -455,7 +455,6 @@ def HCPCF_dispersion(
         Temperature of the material
     pressure : float
         constant pressure
-        FIXME tupple : a pressure gradient from pressure[0] to pressure[1] is computed
 
     Returns
     -------
@@ -692,15 +691,7 @@ def compute_dispersion(params: BareParams):
             )
 
         else:
-            # Load material info
+            material_dico = toml.loads(io.Paths.gets("gas"))[params.gas_name]
-            gas_name = params.gas_name
-
-            if gas_name == "vacuum":
-                material_dico = None
-            else:
-                material_dico = toml.loads(io.Paths.gets("gas"))[gas_name]
-
-            # compute dispersion
             if params.dynamic_dispersion:
                 return dynamic_HCPCF_dispersion(
                     lambda_,
@@ -716,9 +707,6 @@ def compute_dispersion(params: BareParams):
                     params.interp_degree,
                 )
             else:
-
-                # actually compute the dispersion
-
                 beta2 = HCPCF_dispersion(
                     lambda_,
                     material_dico,
@@ -730,10 +718,14 @@ def compute_dispersion(params: BareParams):
                 )
 
                 if material_dico is not None:
-                    A_eff = 1.5 * params.core_radius ** 2
+
+                    A_eff = 1.5 * params.core_radius ** 2 if params.A_eff is None else params.A_eff
+                    if params.n2 is None:
                         n2 = mat.non_linear_refractive_index(
                             material_dico, params.pressure, params.temperature
                         )
+                    else:
+                        n2 = params.n2
                     gamma = gamma_parameter(n2, params.w0, A_eff)
                 else:
                     gamma = None

src/scgenerator/physics/materials.py

@@ -39,7 +39,7 @@ def number_density_van_der_waals(
         ValueError : Since the Van der Waals equation is a cubic one, there could be more than one real, positive solution
     """
 
-    logger = get_logger
+    logger = get_logger(__name__)
 
     if pressure == 0:
         return 0
@@ -73,7 +73,7 @@ def number_density_van_der_waals(
         s = f"Van der Waals eq with parameters P={pressure}, T={temperature}, a={a}, b={b}"
         s += f", There is more than one possible number density : {roots}."
         s += f", {np.min(roots)} was returned"
-        logger.info(s)
+        logger.warning(s)
     return np.min(roots)
 
 
@@ -90,6 +90,8 @@ def sellmeier(lambda_, material_dico, pressure=None, temperature=None):
     ----------
         an array n(lambda_)^2 - 1
     """
+    logger = get_logger(__name__)
+
     WL_THRESHOLD = 8.285e-6
     temp_l = lambda_[lambda_ < WL_THRESHOLD]
     kind = 1
@@ -101,7 +103,6 @@ def sellmeier(lambda_, material_dico, pressure=None, temperature=None):
     t0 = material_dico["sellmeier"].get("t0", 273.15)
     kind = material_dico["sellmeier"].get("kind", 1)
 
-    # Sellmeier equation
     chi = np.zeros_like(lambda_)  # = n^2 - 1
     if kind == 1:
         for b, c in zip(B, C):
@@ -120,6 +121,7 @@ def sellmeier(lambda_, material_dico, pressure=None, temperature=None):
     if pressure is not None:
         chi *= pressure / P0
 
+    logger.debug(f"computed chi between {np.min(chi):.2e} and {np.max(chi):.2e}")
     return chi
 
 

src/scgenerator/physics/simulate.py

@@ -3,11 +3,10 @@ import os
 from datetime import datetime
 from pathlib import Path
 from typing import Dict, List, Tuple, Type
-from typing_extensions import runtime
 
 import numpy as np
 
-from .. import env, initialize, io, utils
+from .. import const, env, initialize, io, utils
 from ..errors import IncompleteDataFolderError
 from ..logger import get_logger
 from . import pulse
@@ -290,7 +289,6 @@ class SequentialRK4IP(RK4IP):
         save_data=False,
         job_identifier="",
         task_id=0,
-        n_percent=10,
     ):
         self.pbars = pbars
         super().__init__(
@@ -298,7 +296,6 @@ class SequentialRK4IP(RK4IP):
             save_data=save_data,
             job_identifier=job_identifier,
             task_id=task_id,
-            n_percent=n_percent,
         )
 
     def step_saved(self):
@@ -314,7 +311,6 @@ class MutliProcRK4IP(RK4IP):
         save_data=False,
         job_identifier="",
         task_id=0,
-        n_percent=10,
     ):
         self.worker_id = worker_id
         self.p_queue = p_queue
@@ -323,7 +319,6 @@ class MutliProcRK4IP(RK4IP):
             save_data=save_data,
             job_identifier=job_identifier,
             task_id=task_id,
-            n_percent=n_percent,
         )
 
     def step_saved(self):
@@ -512,6 +507,9 @@ class MultiProcSimulations(Simulations, priority=1):
 
     def __init__(self, param_seq: initialize.ParamSequence, task_id):
         super().__init__(param_seq, task_id=task_id)
+        if param_seq.config.worker_num is not None:
+            self.sim_jobs_per_node = param_seq.config.worker_num
+        else:
             self.sim_jobs_per_node = max(1, os.cpu_count() // 2)
         self.queue = multiprocessing.JoinableQueue(self.sim_jobs_per_node)
         self.progress_queue = multiprocessing.Queue()
@@ -656,6 +654,8 @@ class RaySimulations(Simulations, priority=2):
 
     @property
     def sim_jobs_total(self):
+        if self.param_seq.config.worker_num is not None:
+            return self.param_seq.config.worker_num
         tot_cpus = sum([node.get("Resources", {}).get("CPU", 0) for node in ray.nodes()])
         tot_cpus = min(tot_cpus, self.max_concurrent_jobs)
         return int(min(self.param_seq.num_sim, tot_cpus))
@@ -664,7 +664,6 @@ class RaySimulations(Simulations, priority=2):
 def run_simulation_sequence(
     *config_files: os.PathLike,
     method=None,
-    final_name: str = None,
     prev_sim_dir: os.PathLike = None,
 ):
     prev = prev_sim_dir
@@ -674,6 +673,7 @@ def run_simulation_sequence(
         prev = sim.sim_dir
     path_trees = io.build_path_trees(sim.sim_dir)
 
+    final_name = env.get(const.OUTPUT_PATH)
     if final_name is None:
         final_name = path_trees[0][-1][0].parent.name + " merged"
 
@@ -687,6 +687,7 @@ def new_simulation(
 ) -> Simulations:
 
     config_dict = io.load_toml(config_file)
+    logger = get_logger(__name__)
 
     if prev_sim_dir is not None:
         config_dict["prev_sim_dir"] = str(prev_sim_dir)
@@ -698,7 +699,7 @@ def new_simulation(
     else:
         param_seq = initialize.ContinuationParamSequence(prev_sim_dir, config_dict)
 
-    print(f"{param_seq.name=}")
+    logger.info(f"running {param_seq.name}")
 
     return Simulations.new(param_seq, task_id, method)
 

src/scgenerator/plotting.py

@@ -422,7 +422,7 @@ def plot_spectrogram(
     values = spec[ind_t][:, ind_f]
     if f_range[2].type == "WL":
         values = np.apply_along_axis(
-            units.to_WL, 1, values, params.frep, units.m(f_range[2].inv(new_f))
+            units.to_WL, 1, values, params.repetition_rate, units.m(f_range[2].inv(new_f))
         )
         values = np.apply_along_axis(make_uniform_1D, 1, values, new_f)
 
@@ -528,7 +528,7 @@ def plot_results_2D(
     # make uniform if converting to wavelength
     if plt_range.unit.type == "WL":
         if is_spectrum:
-            values = np.apply_along_axis(units.to_WL, 1, values, params.frep, x_axis)
+            values = np.apply_along_axis(units.to_WL, 1, values, params.repetition_rate, x_axis)
         values = np.array(
             [make_uniform_1D(v, x_axis, n=len(x_axis), method="linear") for v in values]
         )
@@ -648,7 +648,7 @@ def plot_results_1D(
     # make uniform if converting to wavelength
     if plt_range.unit.type == "WL":
         if is_spectrum:
-            values = units.to_WL(values, params.frep, units.m.inv(params.w[ind]))
+            values = units.to_WL(values, params.repetition_rate, units.m.inv(params.w[ind]))
 
     # change the resolution
     if isinstance(spacing, float):
@@ -810,8 +810,8 @@ def plot_avg(
     values *= yscaling
     mean_values = np.mean(values, axis=0)
     if plt_range.unit.type == "WL" and renormalize:
-        values = np.apply_along_axis(units.to_WL, 1, values, params.frep, x_axis)
+        values = np.apply_along_axis(units.to_WL, 1, values, params.repetition_rate, x_axis)
-        mean_values = units.to_WL(mean_values, params.frep, x_axis)
+        mean_values = units.to_WL(mean_values, params.repetition_rate, x_axis)
 
     # change the resolution
     if isinstance(spacing, float):

src/scgenerator/scripts/slurm_submit.py

@@ -8,13 +8,9 @@ from pathlib import Path
 from typing import Tuple
 
 import numpy as np
-from toml import load
-
-from scgenerator.utils.parameter import BareConfig
 
 from ..initialize import validate_config_sequence
 from ..io import Paths, load_config
-from ..utils import count_variations
 
 
 def primes(n):
@@ -90,7 +86,7 @@ def create_parser():
         "--environment-setup",
         required=False,
         default=f"source {os.path.expanduser('~/anaconda3/etc/profile.d/conda.sh')} && conda activate sc && "
-        "export SCGENERATOR_PBAR_POLICY=file && export SCGENERATOR_LOG_POLICY=file",
+        "export SCGENERATOR_PBAR_POLICY=file && export SCGENERATOR_LOG_PRINT_LEVEL=none && export SCGENERATOR_LOG_FILE_LEVEL=info",
         help="commands to run to setup the environement (default : activate the sc environment with conda)",
     )
     parser.add_argument(

src/scgenerator/spectra.py

@@ -198,7 +198,7 @@ class Pulse(Sequence):
         spec = np.load(self.path / SPECN_FN.format(i))
         if self.__ensure_2d:
             spec = np.atleast_2d(spec)
-        spec = Spectrum(spec, self.wl, self.params.frep)
+        spec = Spectrum(spec, self.wl, self.params.repetition_rate)
         self.cache[i] = spec
         return spec
 

src/scgenerator/utils/__init__.py

@@ -187,7 +187,7 @@ def count_variations(config: BareConfig) -> int:
     """returns (sim_num, variable_params_num) where sim_num is the total number of simulations required and
     variable_params_num is the number of distinct parameters that will vary."""
     sim_num = np.prod([len(l) for l in config.variable.values()]) * config.repeat
-    return sim_num
+    return int(sim_num)
 
 
 def format_variable_list(l: List[Tuple[str, Any]]):

src/scgenerator/utils/parameter.py

@@ -339,7 +339,7 @@ class BareParams:
     peak_power: float = Parameter(positive(float, int))
     mean_power: float = Parameter(positive(float, int))
     energy: float = Parameter(positive(float, int))
-    soliton_num: float = Parameter(positive(float, int))
+    soliton_num: float = Parameter(non_negative(float, int))
     quantum_noise: bool = Parameter(boolean)
     shape: str = Parameter(literal("gaussian", "sech"))
     wavelength: float = Parameter(in_range_incl(100e-9, 3000e-9))
@@ -362,10 +362,10 @@ class BareParams:
     lower_wavelength_interp_limit: float = Parameter(in_range_incl(100e-9, 3000e-9))
     upper_wavelength_interp_limit: float = Parameter(in_range_incl(200e-9, 5000e-9))
     interp_degree: int = Parameter(positive(int))
-    frep: float = Parameter(positive(float, int))
     prev_sim_dir: str = Parameter(string)
     readjust_wavelength: bool = Parameter(boolean)
     recovery_last_stored: int = Parameter(non_negative(int))
+    worker_num: int = Parameter(positive(int))
 
     # computed
     field_0: np.ndarray = Parameter(type_checker(np.ndarray))

testing/long_tests/test_recovery_param_seq.py

@@ -12,7 +12,6 @@ class TestRecoveryParamSequence(unittest.TestCase):
     def setUp(self):
         shutil.copytree("/Users/benoitsierro/sc_tests/scgenerator_full anomalous55", TMP)
         self.conf = toml.load(TMP + "/initial_config.toml")
-        logger.DEFAULT_LEVEL = logger.logging.FATAL
         io.set_data_folder(55, TMP)
 
     def test_remaining_simulations_count(self):