chore(deps): update dependency numpy to v2

CHANGELOG.md

@@ -2,22 +2,6 @@
 
 All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
 
-## [1.6.0](https://gitea.deepak.science:2222/physics/deepdog/compare/1.5.0...1.6.0) (2025-02-27)
-
-
-### Features
-
-* Adds ability to parse bayesruns without timestamps ([46f6b6c](https://gitea.deepak.science:2222/physics/deepdog/commit/46f6b6cdf15c67aedf0c871d201b8db320bccbdf))
-* allows negative log magnitude strings in models ([c8435b4](https://gitea.deepak.science:2222/physics/deepdog/commit/c8435b4b2a6e4b89030f53b5734eb743e2003fb7))
-
-## [1.5.0](https://gitea.deepak.science:2222/physics/deepdog/compare/1.4.0...1.5.0) (2024-12-30)
-
-
-### Features
-
-* add configurable max number of dipoles to write ([a1b59cd](https://gitea.deepak.science:2222/physics/deepdog/commit/a1b59cd18b30359328a09210d9393f211aab30c2))
-* add configurable max number of dipoles to write ([53f8993](https://gitea.deepak.science:2222/physics/deepdog/commit/53f8993f2b155228fff5cbee84f10c62eb149a1f))
-
 ## [1.4.0](https://gitea.deepak.science:2222/physics/deepdog/compare/1.3.0...1.4.0) (2024-09-04)
 
 

deepdog/direct_monte_carlo/direct_mc.py

@@ -284,47 +284,31 @@ class DirectMonteCarloRun:
 
 					pool_results = sum(result[0] for result in raw_pool_results)
 
-					_logger.debug(f"Pool results: {pool_results}")
-
 					if self.config.write_successes_to_file:
-
-						_logger.info("Writing dipole results")
-
 						cycle_success_configs = numpy.concatenate(
 							[result[1] for result in raw_pool_results]
 						)
-
-						dipole_count = numpy.array(cycle_success_configs).shape[1]
-
-						max_number_dipoles_to_write = self.config.target_success * 5
-						_logger.debug(
-							f"Limiting to {max_number_dipoles_to_write=}, have {len(cycle_success_configs)}"
-						)
-
 						if len(cycle_success_configs):
+
 							sorted_by_freq = numpy.array(
 								[
 									pdme.subspace_simulation.sort_array_of_dipoles_by_frequency(
 										dipole_config
 									)
-									for dipole_config in cycle_success_configs[
-										:max_number_dipoles_to_write
-									]
+									for dipole_config in cycle_success_configs
 								]
 							)
+							dipole_count = numpy.array(cycle_success_configs).shape[1]
+
+							number_dipoles_to_write = self.config.target_success * 5
+							_logger.info(
+								f"Limiting to {number_dipoles_to_write=}, have {dipole_count}"
+							)
 
 							for n in range(dipole_count):
-
-								dipole_filename = (
-									f"{self.config.tag}_{step_count}_dipole_{n}.csv"
-								)
-								_logger.debug(
-									f"Writing {min(len(cycle_success_configs), max_number_dipoles_to_write)} to {dipole_filename}"
-								)
-
 								numpy.savetxt(
-									dipole_filename,
-									sorted_by_freq[:, n],
+									f"{self.config.tag}_{step_count}_dipole_{n}.csv",
+									sorted_by_freq[::number_dipoles_to_write, n],
 									delimiter=",",
 								)
 						else:
@@ -332,6 +316,8 @@ class DirectMonteCarloRun:
 								"Instructed to write results, but none obtained"
 							)
 
+					_logger.debug(f"Pool results: {pool_results}")
+
 					total_success += pool_results
 					total_count += count_per_step
 					_logger.debug(

deepdog/results/__init__.py

@@ -19,11 +19,6 @@ FILENAME_REGEX = re.compile(
 	r"(?P<timestamp>\d{8}-\d{6})-(?P<filename_slug>.*)\.realdata\.fast_filter\.bayesrun\.csv"
 )
 
-# probably a better way but who cares
-NO_TIMESTAMP_FILENAME_REGEX = re.compile(
-	r"(?P<filename_slug>.*)\.realdata\.fast_filter\.bayesrun\.csv"
-)
-
 
 SUBSET_SIM_FILENAME_REGEX = re.compile(
 	r"(?P<filename_slug>.*)-(?:no_adaptive_steps_)?(?P<num_ss_runs>\d+)-nc_(?P<n_c>\d+)-ns_(?P<n_s>\d+)-mmax_(?P<mmax>\d+)\.multi\.subsetsim\.csv"
@@ -51,23 +46,15 @@ class GeneralOutput:
 	results: typing.Sequence[GeneralModelResult]
 
 
-def _parse_string_output_filename(
-	filename: str,
-) -> typing.Tuple[typing.Optional[str], str]:
-	if match := FILENAME_REGEX.match(filename):
-		groups = match.groupdict()
-		return (groups["timestamp"], groups["filename_slug"])
-	elif match := NO_TIMESTAMP_FILENAME_REGEX.match(filename):
-		groups = match.groupdict()
-		return (None, groups["filename_slug"])
-	else:
-		raise ValueError(f"Could not parse {filename} as a bayesrun output filename")
-
-
 def _parse_output_filename(file: pathlib.Path) -> BayesrunOutputFilename:
 	filename = file.name
-	timestamp, slug = _parse_string_output_filename(filename)
-	return BayesrunOutputFilename(timestamp=timestamp, filename_slug=slug, path=file)
+	match = FILENAME_REGEX.match(filename)
+	if not match:
+		raise ValueError(f"{filename} was not a valid bayesrun output")
+	groups = match.groupdict()
+	return BayesrunOutputFilename(
+		timestamp=groups["timestamp"], filename_slug=groups["filename_slug"], path=file
+	)
 
 
 def _parse_ss_output_filename(file: pathlib.Path) -> BayesrunOutputFilename:

deepdog/results/read_csv.py

@@ -8,8 +8,6 @@ MODEL_REGEXES = [
 		r"geom_(?P<xmin>-?\d+)_(?P<xmax>-?\d+)_(?P<ymin>-?\d+)_(?P<ymax>-?\d+)_(?P<zmin>-?\d+)_(?P<zmax>-?\d+)-orientation_(?P<orientation>free|fixedxy|fixedz)-dipole_count_(?P<avg_filled>\d+)_(?P<field_name>\w*)",
 		r"geom_(?P<xmin>-?\d+)_(?P<xmax>-?\d+)_(?P<ymin>-?\d+)_(?P<ymax>-?\d+)_(?P<zmin>-?\d+)_(?P<zmax>-?\d+)-magnitude_(?P<log_magnitude>\d*\.?\d+)-orientation_(?P<orientation>free|fixedxy|fixedz)-dipole_count_(?P<avg_filled>\d+)_(?P<field_name>\w*)",
 		r"geom_(?P<xmin>-?\d*\.?\d+)_(?P<xmax>-?\d*\.?\d+)_(?P<ymin>-?\d*\.?\d+)_(?P<ymax>-?\d*\.?\d+)_(?P<zmin>-?\d*\.?\d+)_(?P<zmax>-?\d*\.?\d+)-magnitude_(?P<log_magnitude>\d*\.?\d+)-orientation_(?P<orientation>free|fixedxy|fixedz)-dipole_count_(?P<avg_filled>\d+)_(?P<field_name>\w*)",
-		r"geom_(?P<xmin>-?\d+)_(?P<xmax>-?\d+)_(?P<ymin>-?\d+)_(?P<ymax>-?\d+)_(?P<zmin>-?\d+)_(?P<zmax>-?\d+)-magnitude_(?P<log_magnitude>-?\d*\.?\d+)-orientation_(?P<orientation>free|fixedxy|fixedz)-dipole_count_(?P<avg_filled>\d+)_(?P<field_name>\w*)",
-		r"geom_(?P<xmin>-?\d*\.?\d+)_(?P<xmax>-?\d*\.?\d+)_(?P<ymin>-?\d*\.?\d+)_(?P<ymax>-?\d*\.?\d+)_(?P<zmin>-?\d*\.?\d+)_(?P<zmax>-?\d*\.?\d+)-magnitude_(?P<log_magnitude>-?\d*\.?\d+)-orientation_(?P<orientation>free|fixedxy|fixedz)-dipole_count_(?P<avg_filled>\d+)_(?P<field_name>\w*)",
 	]
 ]
 

pyproject.toml

@@ -1,13 +1,13 @@
 [tool.poetry]
 name = "deepdog"
-version = "1.6.0"
+version = "1.4.0"
 description = ""
 authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
 
 [tool.poetry.dependencies]
 python = ">=3.8.1,<3.10"
 pdme = "^1.5.0"
-numpy = "1.22.3"
+numpy = "2.1.3"
 scipy = "1.10"
 tqdm = "^4.66.2"
 

tests/results/test_column_results.py

@@ -48,28 +48,6 @@ def test_parse_groupdict_with_magnitude():
 	assert parsed == expected
 
 
-def test_parse_groupdict_with_negative_magnitude():
-	example_column_name = "geom_-20_20_-10_10_0_5-magnitude_-3.5-orientation_free-dipole_count_100_success"
-
-	parsed = deepdog.results.read_csv._parse_bayesrun_column(example_column_name)
-	assert parsed is not None
-	expected = deepdog.results.read_csv.BayesrunColumnParsed(
-		{
-			"xmin": "-20",
-			"xmax": "20",
-			"ymin": "-10",
-			"ymax": "10",
-			"zmin": "0",
-			"zmax": "5",
-			"orientation": "free",
-			"avg_filled": "100",
-			"log_magnitude": "-3.5",
-			"field_name": "success",
-		}
-	)
-	assert parsed == expected
-
-
 # def test_parse_no_match_column_name():
 # 	parsed = deepdog.results.parse_bayesrun_column("There's nothing here")
 # 	assert parsed is None

tests/results/test_parse_filename.py

@@ -1,19 +0,0 @@
-import deepdog.results
-import pytest
-
-
-def test_parse_bayesrun_filename():
-	valid1 = "20250226-204120-dot1-dot1-2-0.realdata.fast_filter.bayesrun.csv"
-
-	timestamp, slug = deepdog.results._parse_string_output_filename(valid1)
-	assert timestamp == "20250226-204120"
-	assert slug == "dot1-dot1-2-0"
-
-	valid2 = "dot1-dot1-2-0.realdata.fast_filter.bayesrun.csv"
-
-	timestamp, slug = deepdog.results._parse_string_output_filename(valid2)
-	assert timestamp is None
-	assert slug == "dot1-dot1-2-0"
-
-	with pytest.raises(ValueError):
-		deepdog.results._parse_string_output_filename("not_a_valid_filename")