chore: refactoring to help with getting dipole random generation going

tantri/cli/__init__.py

@@ -10,7 +10,7 @@ LOG_PATTERN = "%(asctime)s | %(levelname)-7s | %(name)s | %(message)s"
 def _set_up_logging(filename):
 	handlers = [logging.StreamHandler()]
 	if filename is not None:
-		handlers.append(logging.FileHandler(filename)) # type: ignore idk what the typing issue is
+		handlers.append(logging.FileHandler(filename))
 	logging.basicConfig(
 		level=logging.DEBUG,
 		format=LOG_PATTERN,
@@ -21,7 +21,9 @@ def _set_up_logging(filename):
 
 
 @click.group()
-@click.option("--log", help="Enable logging to stream only", is_flag=True, default=False)
+@click.option(
+	"--log", help="Enable logging to stream only", is_flag=True, default=False
+)
 @click.option("--log-file", help="A filename to use for logging (implies --log)")
 @click.version_option(tantri.get_version())
 def cli(log, log_file):
@@ -32,9 +34,17 @@ def cli(log, log_file):
 
 
 @cli.command()
-@click.option("--dipoles-file", default="dipoles.json", help="Filename containing json array of dipoles")
+@click.option(
-@click.option("--dots-file", default="dots.json", help="Filename containing json array of dots")
+	"--dipoles-file",
+	default="dipoles.json",
+	help="Filename containing json array of dipoles",
+)
+@click.option(
+	"--dots-file", default="dots.json", help="Filename containing json array of dots"
+)
 def hello(dipoles_file, dots_file):
 	_logger.info("in hello")
-	_logger.info(f"Received parameters [dipoles_file: {dipoles_file}] and [dots_file: {dots_file}]")
+	_logger.info(
+		f"Received parameters [dipoles_file: {dipoles_file}] and [dots_file: {dots_file}]"
+	)
 	click.echo("in hello")

tantri/cli/file_importer.py

@@ -16,7 +16,9 @@ def read_data_from_filename(filename: str):
 		with open(filename, "r") as file:
 			return json.load(file)
 	except Exception as e:
-		_logger.error(f"failed to read the file {filename}, raising and aborting", exc_info=e)
+		_logger.error(
+			f"failed to read the file {filename}, raising and aborting", exc_info=e
+		)
 
 
 def read_dots_json_file(filename: str) -> Sequence[tantri.dipoles.DotPosition]:
@@ -24,6 +26,6 @@ def read_dots_json_file(filename: str) -> Sequence[tantri.dipoles.DotPosition]:
 	return tantri.cli.input_files.rows_to_dots(data)
 
 
-def read_dipoles_json_file(filename: str) -> Sequence[tantri.dipoles.DotPosition]:
+def read_dipoles_json_file(filename: str) -> Sequence[tantri.dipoles.DipoleTO]:
 	data = read_data_from_filename(filename)
-	return tantri.cli.input_files.rows_to_dots(data)
+	return tantri.cli.input_files.rows_to_dipoles(data)

tantri/cli/input_files/__init__.py

@@ -1,8 +1,7 @@
 from tantri.cli.input_files.read_dots import rows_to_dots
-from tantri.cli.input_files.read_dipoles import rows_to_dipoles, DipoleTO
+from tantri.cli.input_files.read_dipoles import rows_to_dipoles
 
 __all__ = [
 	"rows_to_dots",
 	"rows_to_dipoles",
-	"DipoleTO",
 ]

tantri/cli/input_files/read_dipoles.py

@@ -1,27 +1,18 @@
-import numpy
 from typing import Sequence
-from dataclasses import dataclass
+from tantri.dipoles import DipoleTO
-
-
-# Lazily just separating this from tantri.dipoles.Dipole where there's additional cached stuff, this is just a thing
-# we can use as a DTO For dipole info.
-@dataclass
-class DipoleTO:
-	# assumed len 3
-	p: numpy.ndarray
-	s: numpy.ndarray
-
-	# should be 1/tau up to some pis
-	w: float
 
 
 def row_to_dipole(input_dict: dict) -> DipoleTO:
 	p = input_dict["p"]
 	if len(p) != 3:
-		raise ValueError(f"p parameter in input_dict [{input_dict}] does not have length 3")
+		raise ValueError(
+			f"p parameter in input_dict [{input_dict}] does not have length 3"
+		)
 	s = input_dict["s"]
 	if len(s) != 3:
-		raise ValueError(f"s parameter in input_dict [{input_dict}] does not have length 3")
+		raise ValueError(
+			f"s parameter in input_dict [{input_dict}] does not have length 3"
+		)
 	w = input_dict["w"]
 
 	return DipoleTO(p, s, w)

tantri/cli/input_files/read_dots.py

@@ -6,11 +6,15 @@ from typing import Sequence
 def row_to_dot(input_dict: dict) -> tantri.dipoles.DotPosition:
 	r = input_dict["r"]
 	if len(r) != 3:
-		raise ValueError(f"r parameter in input_dict [{input_dict}] does not have length 3")
+		raise ValueError(
+			f"r parameter in input_dict [{input_dict}] does not have length 3"
+		)
 	label = input_dict["label"]
 
 	return tantri.dipoles.DotPosition(numpy.array(r), label)
 
 
-def rows_to_dots(dot_dict_array: Sequence[dict]) -> Sequence[tantri.dipoles.DotPosition]:
+def rows_to_dots(
+	dot_dict_array: Sequence[dict],
+) -> Sequence[tantri.dipoles.DotPosition]:
 	return [row_to_dot(input_dict) for input_dict in dot_dict_array]

tantri/dipoles/__init__.py

@@ -3,6 +3,7 @@ import numpy
 import numpy.random
 import typing
 from enum import Enum
+from tantri.dipoles.types import DipoleTO
 
 import logging
 
@@ -126,4 +127,5 @@ class DipoleTimeSeries:
 __all__ = [
 	"Dipole",
 	"DipoleTimeSeries",
+	"DipoleTO",
 ]

tantri/dipoles/generation/__init__.py

@@ -0,0 +1,38 @@
+import numpy
+from typing import Sequence
+from dataclasses import dataclass
+from tantri.dipoles.types import DipoleTO
+
+
+# stuff for generating random dipoles from parameters
+
+
+# A description of the parameters needed to generate random dipoles
+@dataclass
+class DipoleGenerationConfig:
+	# assumed len 3
+	p: numpy.ndarray
+	s: numpy.ndarray
+
+	# should be 1/tau up to some pis
+	w: float
+
+
+def row_to_dipole(input_dict: dict) -> DipoleTO:
+	p = input_dict["p"]
+	if len(p) != 3:
+		raise ValueError(
+			f"p parameter in input_dict [{input_dict}] does not have length 3"
+		)
+	s = input_dict["s"]
+	if len(s) != 3:
+		raise ValueError(
+			f"s parameter in input_dict [{input_dict}] does not have length 3"
+		)
+	w = input_dict["w"]
+
+	return DipoleTO(p, s, w)
+
+
+def rows_to_dipoles(dot_dict_array: Sequence[dict]) -> Sequence[DipoleTO]:
+	return [row_to_dipole(input_dict) for input_dict in dot_dict_array]

tantri/dipoles/types.py

@@ -0,0 +1,14 @@
+import numpy
+from dataclasses import dataclass
+
+
+# Lazily just separating this from Dipole where there's additional cached stuff, this is just a thing
+# we can use as a DTO For dipole info.
+@dataclass
+class DipoleTO:
+	# assumed len 3
+	p: numpy.ndarray
+	s: numpy.ndarray
+
+	# should be 1/tau up to some pis
+	w: float