Improv/remove top level config

setup.py

@@ -3,18 +3,16 @@
 
 from simulator.utils.setup.documentation import DocCommand
 
-
 if __name__ == "__main__":
     setup(
         name="simulation_generator",
-        version="1.0.0",
+        version="1.0.1",
         packages=find_packages(exclude=("tests", "tests.*")),
         url="",
         license="",
         author="avcaron",
         author_email="",
         description="",
-        data_files=[(".", ["config.py", "config.json"])],
         scripts=list(
             filter(lambda s: "init" not in s, glob.glob("scripts/*.py"))
         ),

simulator/default.py

@@ -0,0 +1,7 @@
+import typing
+import pathlib
+
+SINGULARITY_PATH: typing.Final[pathlib.PurePath] = pathlib.PurePath()
+SINGULARITY_NAME: typing.Final[str] = "voxsim_singularity_latest.sif"
+SINGULARITY: typing.Final[pathlib.PurePath] = SINGULARITY_PATH / SINGULARITY_NAME
+SINGULARITY_EXEC: typing.Final[str] = "singularity"

simulator/runner/__init__.py

@@ -1 +1,2 @@
+from .config import SingularityConfig
 from .simulation_runner import SimulationRunner

simulator/runner/config.py

@@ -0,0 +1,10 @@
+import dataclasses
+import pathlib
+
+import simulator.default as default
+
+
+@dataclasses.dataclass
+class SingularityConfig:
+    singularity: pathlib.PurePath = default.SINGULARITY
+    singularity_exec: str = default.SINGULARITY_EXEC

simulator/runner/legacy.py

@@ -10,21 +10,21 @@
 from numpy import ones_like, sum
 import nrrd
 
-from config import get_config
+from .config import SingularityConfig
 from ..exceptions import SimulationRunnerException
 from ..utils.logging import RTLogging
 
-
 logger = logging.getLogger(basename(__file__).split(".")[0])
 
 
 class SimulationRunner:
+
     def __init__(
         self,
         base_naming,
         geometry_infos,
         simulation_infos=None,
-        singularity_conf=get_config(),
+        singularity_conf=SingularityConfig(),
         output_nifti=False,
     ):
         self._geometry_path = geometry_infos["file_path"]
@@ -40,17 +40,10 @@ def __init__(
             self._compartment_ids = simulation_infos["compartment_ids"]
 
         singularity_conf = (
-            singularity_conf if singularity_conf else get_config()
-        )
-        self._singularity = path.join(
-            singularity_conf["singularity_path"],
-            singularity_conf["singularity_name"],
-        )
-        self._singularity_exec = (
-            singularity_conf["singularity_exec"]
-            if "singularity_exec" in singularity_conf
-            else "singularity"
+            singularity_conf if singularity_conf else SingularityConfig()
         )
+        self._singularity = singularity_conf.singularity
+        self._singularity_exec = singularity_conf.singularity_exec
 
         self._run_simulation = True if simulation_infos else False
         self._extension = "nii.gz" if output_nifti else "nrrd"

simulator/runner/simulation_runner.py

@@ -5,15 +5,15 @@
 from os.path import basename
 from subprocess import PIPE, Popen
 
-from config import get_config
+from .config import SingularityConfig
 from .datastore import Datastore
 from ..utils.logging import RTLogging
 
-
 logger = logging.getLogger(basename(__file__).split(".")[0])
 
 
 class AsyncRunner:
+
     def __init__(self):
         self._event_loop = new_event_loop()
 
@@ -49,16 +49,11 @@ async def _run_async(self, command, log_file, log_tag):
 class SimulationRunner(AsyncRunner):
     _apps = {"phantom": "launch_voxsim", "diffusion mri": "launch_mitk"}
 
-    def __init__(self, singularity_conf=get_config()):
-        self._singularity = path.join(
-            singularity_conf["singularity_path"],
-            singularity_conf["singularity_name"],
-        )
+    def __init__(self, singularity_conf=SingularityConfig()):
+        self._singularity = singularity_conf.singularity
         super().__init__()
 
-        self._singularity_exec = "singularity"
-        if "singularity_exec" in singularity_conf:
-            self._singularity_exec = singularity_conf["singularity_exec"]
+        self._singularity_exec = singularity_conf.singularity_exec
 
     def _bind_singularity(self, step, paths, arguments):
         return "{} run -B {} --app {} {} {}".format(