Fixed resuming

src/scgenerator/cli/cli.py

@@ -52,6 +52,12 @@ def create_parser():
         "data_dir",
         help="path to the directory where the initial_config.toml and the data is stored",
     )
+    resume_parser.add_argument(
+        "configs",
+        nargs="*",
+        default=[],
+        help="list of subsequent config files (excluding the resumed one)",
+    )
     resume_parser.set_defaults(func=resume_sim)
 
     merge_parser = subparsers.add_parser("merge", help="merge simulation results")
@@ -99,9 +105,11 @@ def prep_ray(args):
 
 
 def resume_sim(args):
+
     method = prep_ray(args)
-    sim = resume_simulations(args.data_dir, args.id, method=method)
+    sim = resume_simulations(args.data_dir, method=method)
     sim.run()
+    run_simulation_sequence(*args.configs, method=method, prev_data_folder=sim.data_folder)
 
 
 if __name__ == "__main__":

src/scgenerator/data/submit_job_template.txt

@@ -50,5 +50,5 @@ done
 ##############################################################################################
 
 #### call your code below
-scgenerator run {configs_list}
+scgenerator {command} {configs_list}
 exit

src/scgenerator/initialize.py

@@ -175,7 +175,7 @@ def validate_config_sequence(*configs: os.PathLike) -> Dict[str, Any]:
     Parameters
     ----------
     configs : os.PathLike
-        sequence of paths to toml config files
+        sequence of paths to toml config files. The first element may be a folder containing data intead
 
     Returns
     -------
@@ -184,6 +184,8 @@ def validate_config_sequence(*configs: os.PathLike) -> Dict[str, Any]:
     """
     previous = None
     for config in configs:
+        if (p := Path(config)).is_dir():
+            config = p / "initial_config.toml"
         dico = io.load_toml(config)
         previous = override_config(dico, previous)
         validate(previous)

src/scgenerator/physics/simulate.py

@@ -710,8 +710,13 @@ class RaySimulations(Simulations, priority=2):
         self.p_bars.print()
 
 
-def run_simulation_sequence(*config_files: os.PathLike, method=None, final_name: str = None):
+def run_simulation_sequence(
-    prev = None
+    *config_files: os.PathLike,
+    method=None,
+    final_name: str = None,
+    prev_data_folder: os.PathLike = None,
+):
+    prev = prev_data_folder
     for config_file in config_files:
         sim = new_simulation(config_file, prev, method)
         sim.run()
@@ -738,10 +743,9 @@ def new_simulation(
     return _new_simulations(param_seq, task_id, method)
 
 
-def resume_simulations(
+def resume_simulations(data_folder: str, method: Type[Simulations] = None) -> Simulations:
-    data_folder: str, task_id: int = 0, method: Type[Simulations] = None
-) -> Simulations:
 
+    task_id = np.random.randint(1e9, 1e12)
     config = io.load_toml(os.path.join(data_folder, "initial_config.toml"))
     io.set_data_folder(task_id, data_folder)
     param_seq = initialize.RecoveryParamSequence(config, task_id)

src/scgenerator/scripts/slurm_submit.py

@@ -34,6 +34,9 @@ def create_parser():
         default=f"source {os.path.expanduser('~/anaconda3/etc/profile.d/conda.sh')} && conda activate sc",
         help="commands to run to setup the environement (default : activate the sc environment with conda)",
     )
+    parser.add_argument(
+        "--command", default="run", choices=["run", "resume"], help="command to run"
+    )
     return parser
 
 
@@ -47,6 +50,9 @@ def copy_starting_files():
 
 
 def main():
+
+    command_map = dict(run="Propagate", resume="Resuming")
+
     parser = create_parser()
     template = Paths.gets("submit_job_template")
     args = parser.parse_args()
@@ -69,13 +75,13 @@ def main():
     )
     job_name = f"supercontinuum {final_config['name']}"
     submit_sh = template.format(
-        job_name=job_name, configs_list=" ".join(args.configs), **vars(args)
+        job_name=job_name, configs_list=" ".join(f'"{c}"' for c in args.configs), **vars(args)
     )
     with open(file_name, "w") as file:
         file.write(submit_sh)
     subprocess.run(["sbatch", "--test-only", file_name])
     submit = input(
-        f"Propagate {sim_num} pulses from configs {args.configs} with {args.cpus_per_node} cpus"
+        f"{command_map[args.command]} {sim_num} pulses from configs {args.configs} with {args.cpus_per_node} cpus"
         + f" per node on {args.nodes} nodes for {format_time(args.time)} ? (y/[n])\n"
     )
     if submit.lower() in ["y", "yes"]:

src/scgenerator/spectra.py

@@ -32,7 +32,7 @@ class Spectrum(np.ndarray):
 class Pulse(Sequence):
     def __init__(self, path: str, ensure_2d=True):
         self.logger = get_logger(__name__)
-        self.path = path
+        self.path = str(path)
         self.__ensure_2d = ensure_2d
 
         if not os.path.isdir(self.path):