libgunshotmatch 0.6.0__py3-none-any.whl → 0.7.1__py3-none-any.whl

libgunshotmatch/__init__.py

@@ -29,5 +29,5 @@ Base library for GunShotMatch.
 __author__: str = "Dominic Davis-Foster"
 __copyright__: str = "2020-2023 Dominic Davis-Foster"
 __license__: str = "MIT License"
-__version__: str = "0.6.0"
+__version__: str = "0.7.1"
 __email__: str = "dominic@davis-foster.co.uk"

libgunshotmatch/consolidate/__init__.py

@@ -476,7 +476,7 @@ class ConsolidatedPeak:
 		return cls(
 				rt_list=d["rt_list"],
 				area_list=d["area_list"],
-				ms_list=d["ms_list"],
+				ms_list=[MassSpectrum.from_dict(msd) for msd in d["ms_list"]],
 				meta=d["meta"],
 				ms_comparison=d["ms_comparison"],
 				hits=hits,

libgunshotmatch/peak.py

@@ -422,15 +422,20 @@ def write_alignment(
 			)
 
 	rt_alignment = alignment.get_peak_alignment(require_all_expr=require_all_datafiles)
-	rt_alignment.to_json(output_dir_p / f"{project_name}_alignment_rt.json")
+	rt_alignment_filename = output_dir_p / f"{project_name}_alignment_rt.json"
+	rt_alignment_filename.write_clean(rt_alignment)
 
 	area_alignment = alignment.get_area_alignment(require_all_expr=require_all_datafiles)
-	area_alignment.to_json(output_dir_p / f"{project_name}_alignment_area.json")
+	area_alignment_filename = output_dir_p / f"{project_name}_alignment_area.json"
+	area_alignment_filename.write_clean(area_alignment)
 
 	ms_alignment = alignment.get_ms_alignment(require_all_expr=require_all_datafiles)
 	# ms_alignment.to_json(output_dir_p / 'alignment_ms.json')
-	with (output_dir_p / f"{project_name}_alignment_ms.json").open('w') as fp:
-		sdjson.dump(ms_alignment.to_dict(), fp)
+	alignment_ms_filename = (output_dir_p / f"{project_name}_alignment_ms.json")
+	alignment_ms_filename.dump_json(
+			ms_alignment.to_dict(),
+			json_library=sdjson,  # type: ignore
+			)
 
 
 def filter_aligned_peaks(

libgunshotmatch/utils.py

@@ -28,7 +28,7 @@ Utility functions.
 
 # stdlib
 from decimal import Decimal
-from typing import Any, Iterable, List, Optional, Sequence, Type, TypeVar, Union
+from typing import TYPE_CHECKING, Any, Iterable, List, Optional, Sequence, Tuple, Type, TypeVar, Union
 
 # 3rd party
 import numpy
@@ -37,7 +37,11 @@ from mathematical.utils import rounders
 from pyms.Spectrum import MassSpectrum  # type: ignore[import]
 from scipy.stats import truncnorm  # type: ignore[import]
 
-__all__ = ("round_rt", "get_truncated_normal", "ms_comparison")
+if TYPE_CHECKING:
+	# this package
+	from libgunshotmatch.project import Project
+
+__all__ = ("round_rt", "get_truncated_normal", "ms_comparison", "get_rt_range")
 
 
 def round_rt(rt: Union[str, float, Decimal]) -> Decimal:
@@ -136,3 +140,29 @@ def _to_list(l: Iterable[str]) -> List[str]:
 	"""
 
 	return list(l)
+
+
+def get_rt_range(project: "Project") -> Tuple[float, float]:
+	"""
+	Returns the minimum and maximum retention times (in minutes) across the repeats.
+
+	:param project:
+
+	:rtype:
+
+	,, versionadded:: 0.7.0
+	"""
+
+	# Get RT extremes from intensity matrix
+	min_rts, max_rts = [], []
+	for repeat in project.datafile_data.values():
+		im = repeat.datafile.intensity_matrix
+		assert im is not None
+		times = im.time_list
+		min_rts.append(times[0])
+		max_rts.append(times[-1])
+
+	min_rt = min(min_rts) / 60
+	max_rt = max(max_rts) / 60
+
+	return min_rt, max_rt

{libgunshotmatch-0.6.0.dist-info → libgunshotmatch-0.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: libgunshotmatch
-Version: 0.6.0
+Version: 0.7.1
 Summary: Base library for GunShotMatch.
 Author-email: Dominic Davis-Foster <dominic@davis-foster.co.uk>
 License: MIT
@@ -135,7 +135,7 @@ libgunshotmatch
 .. |language| image:: https://img.shields.io/github/languages/top/GunShotMatch/libgunshotmatch
 	:alt: GitHub top language
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.6.0
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.7.1
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.6.0.dist-info → libgunshotmatch-0.7.1.dist-info}/RECORD

@@ -1,18 +1,18 @@
-libgunshotmatch/consolidate/__init__.py,sha256=bFfxfF4MH9LMUCK4q2Js2z11ZR28qeJDpRU9a5KOHyA,22793
+libgunshotmatch/consolidate/__init__.py,sha256=gOqPqFcoSkVob8hKOpcNobK84yADyCwB3UNBPJM3vAc,22834
 libgunshotmatch/consolidate/_fields.py,sha256=7gPIQaFaFySLZFrIuSMjwS84WEBHxZhCNhpXATlYjVw,2691
 libgunshotmatch/consolidate/_spectra.py,sha256=7q_xVPN_oASayLdyMDjwaBLG4maIybHCqkGhiMIO940,2343
 libgunshotmatch/method/__init__.py,sha256=k0Hs3c5Q13CENQHGtHVeDW2jQtR6UtiB1IVf_77lCT4,9432
 libgunshotmatch/method/_fields.py,sha256=GQNw9GdGhy9c_-0U_31eJDTXr1sG5_t5Lh0Z_nzE0RE,5025
-libgunshotmatch/__init__.py,sha256=0k-zbcVbpZIBMq4pzDOYJWmwZjs0XoWxjx-Xdj825Cc,1433
+libgunshotmatch/__init__.py,sha256=7QhxNRtPqOz7VBUPCKPF9uaMe4uR0nnuoshgiINneig,1433
 libgunshotmatch/datafile.py,sha256=sKCatM0F3fmceHQYObwgYr3EX9whKA0U2lOj-xqLt4c,16276
 libgunshotmatch/gzip_util.py,sha256=vVGZLAhW1WmENt2kDXMY68UR72MHvsCBPaB-xCyVYbg,2250
-libgunshotmatch/peak.py,sha256=KUg3FHZzi6Zhd3fMGwWiM_52WfSlqNiBuXTDycxjLgk,16605
+libgunshotmatch/peak.py,sha256=pn8eYS8dfBOCjCRr-rciU3v9k1EREvH6jYqQibdjdok,16777
 libgunshotmatch/project.py,sha256=t4YLCTKA1YYeRMiaXNz1-k21wYTtidN9FJM4aN9-rbw,6474
 libgunshotmatch/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 libgunshotmatch/search.py,sha256=qjIXuTo3OqvC_zSLdwZkEDHfza064iYCTZzGeAZoW5s,3137
-libgunshotmatch/utils.py,sha256=L5jf4kf-1bD9tOolUz97V2eyHkfT7pwAerZ_IKJsFpU,4251
-libgunshotmatch-0.6.0.dist-info/LICENSE,sha256=bFtJt-lyVJHV-88FeFa_r3BEOsmpna5qG2KOl9JUNfU,1064
-libgunshotmatch-0.6.0.dist-info/METADATA,sha256=QLB4AOTeadNfDxmPpWEqt_FJN-3gqm91GRsmCXo8rgs,6392
-libgunshotmatch-0.6.0.dist-info/WHEEL,sha256=3vSnEhs48RUlSXcCXKCl4DOHs_qqaP2dU3IGkMqN2oI,84
-libgunshotmatch-0.6.0.dist-info/entry_points.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-libgunshotmatch-0.6.0.dist-info/RECORD,,
+libgunshotmatch/utils.py,sha256=H-Ikm6oEGCgRoPvuCo3H5p1iKz3B9PuUqcpcH-rhgYA,4917
+libgunshotmatch-0.7.1.dist-info/LICENSE,sha256=bFtJt-lyVJHV-88FeFa_r3BEOsmpna5qG2KOl9JUNfU,1064
+libgunshotmatch-0.7.1.dist-info/METADATA,sha256=rvRV47dgFsu7xqyZQ6OukhBY9icHJ7KpqD3QvjXwVEc,6392
+libgunshotmatch-0.7.1.dist-info/WHEEL,sha256=3vSnEhs48RUlSXcCXKCl4DOHs_qqaP2dU3IGkMqN2oI,84
+libgunshotmatch-0.7.1.dist-info/entry_points.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+libgunshotmatch-0.7.1.dist-info/RECORD,,