libgunshotmatch 0.11.0__py3-none-any.whl → 0.11.1__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 = "0.11.0"
+__version__: str = "0.11.1"
 __email__: str = "dominic@davis-foster.co.uk"

libgunshotmatch/consolidate/__init__.py

@@ -477,10 +477,17 @@ class ConsolidatedPeak:
 		for hit in d["hits"]:
 			hits.append(ConsolidatedSearchResult.from_dict(hit))
 
+		ms_list: MutableSequence[Optional[MassSpectrum]] = []
+		for msd in d["ms_list"]:
+			if msd is None:
+				ms_list.append(None)
+			else:
+				ms_list.append(MassSpectrum.from_dict(msd))
+
 		return cls(
 				rt_list=d["rt_list"],
 				area_list=d["area_list"],
-				ms_list=[MassSpectrum.from_dict(msd) for msd in d["ms_list"]],
+				ms_list=ms_list,
 				meta=d["meta"],
 				ms_comparison=d["ms_comparison"],
 				hits=hits,

libgunshotmatch/peak.py

@@ -241,6 +241,10 @@ class PeakList(List[Peak]):
 
 		peaks_as_pure_list: List[Dict[str, Any]] = []
 		for peak in self:
+			if peak is None:
+				peaks_as_pure_list.append(None)
+				continue
+
 			try:
 				ion_areas = peak.ion_areas
 			except ValueError:

libgunshotmatch/project.py

@@ -28,7 +28,7 @@ Represents a collection of repeat analyses.
 
 # stdlib
 import os
-from typing import Any, Dict, List, Mapping, Optional, Type
+from typing import Any, Dict, List, Mapping, MutableSequence, Optional, Type
 
 # 3rd party
 import attr
@@ -131,14 +131,15 @@ class Project:
 		"""
 
 		alignment_as_dict = d["alignment"]
-		alignment_peaks: List[List[Peak]] = []
+		alignment_peaks: List[MutableSequence[Optional[Peak]]] = []
 		for row in alignment_as_dict["peaks"]:
 			alignment_peaks.append([])
 			for peak in row:
 				# print(peak)
-				peak_obj = peak_from_dict(peak)
-
-				alignment_peaks[-1].append(peak_obj)
+				if peak is None:
+					alignment_peaks[-1].append(None)
+				else:
+					alignment_peaks[-1].append(peak_from_dict(peak))
 
 		alignment = create_alignment(
 				alignment_peaks,

libgunshotmatch/utils.py

@@ -171,7 +171,11 @@ def get_rt_range(project: "Project") -> Tuple[float, float]:
 	return min_rt, max_rt
 
 
-def create_alignment(peakpos: Sequence[Sequence[Peak]], expr_code: List[str], similarity: float = 0) -> Alignment:
+def create_alignment(
+		peakpos: Sequence[Sequence[Optional[Peak]]],
+		expr_code: List[str],
+		similarity: float = 0,
+		) -> Alignment:
 	"""
 	Create a new :class:`pyms.DPA.Alignment.Alignment` object.
 
@@ -185,7 +189,7 @@ def create_alignment(peakpos: Sequence[Sequence[Peak]], expr_code: List[str], si
 	"""
 
 	alignment = Alignment(None)
-	alignment.peakpos = [list(p) for p in peakpos]
+	alignment.peakpos = [list(p) for p in peakpos]  # type: ignore[arg-type]
 	alignment.peakalgt = numpy.transpose(alignment.peakpos).tolist()  # type: ignore[arg-type]
 	alignment.expr_code = expr_code
 	alignment.similarity = similarity

{libgunshotmatch-0.11.0.dist-info → libgunshotmatch-0.11.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: libgunshotmatch
-Version: 0.11.0
+Version: 0.11.1
 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/v0.11.0
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.11.1
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.11.0.dist-info → libgunshotmatch-0.11.1.dist-info}/RECORD

@@ -2,21 +2,21 @@ libgunshotmatch/comparison/__init__.py,sha256=g-KDfzG-oyRf2aeXlMaJJ3aWfQtQkr5-bG
 libgunshotmatch/comparison/_utils.py,sha256=aZ6fnFM4M_vTsKq5t79V4tfven1eVdG4EUCuYFuXMVs,1895
 libgunshotmatch/comparison/projects.py,sha256=Dq294cDndmQI2FnIcVXwleCQF0mF2m8U5wWnO5_aD9A,3356
 libgunshotmatch/comparison/unknowns.py,sha256=kvJJDtfpMp-c3hjCOz7YtvuuDR0YksWmyUuaSBC_5Jg,2710
-libgunshotmatch/consolidate/__init__.py,sha256=ezF2MwUykNSzB5s3X8HiPohTef_kS4gXtRBKG1p6zwc,24567
+libgunshotmatch/consolidate/__init__.py,sha256=qjY5meI2TMCpMGwzLSo4NZ4HbhH8VJoR1t9ev4ObBmA,24706
 libgunshotmatch/consolidate/_fields.py,sha256=0kfPXJ0EG7GhdFiNzvcmd6W4i1x6Y0s2Y58z3RltPiA,2759
 libgunshotmatch/consolidate/_spectra.py,sha256=24aDoPwGWEyIFCH-fwRa4nifNMPqUyd-qTogk3BMeLY,2319
 libgunshotmatch/method/__init__.py,sha256=TP_3rvv3WEbV6Y5E_QWd2lcORPFnbXV4YRKGwXDa4ds,9423
 libgunshotmatch/method/_fields.py,sha256=HBFl0XmHBaAOHYdABs2NRbjtngGEw7kY0xP6D2Fl7h4,4941
-libgunshotmatch/__init__.py,sha256=OXM6TubGh5_DlwFy9SnXURf9fzbaz9cy-gNRZIAhimw,1434
+libgunshotmatch/__init__.py,sha256=RYV-3nDk5ruAuFXDnZuk5LbiFM_503YfSuKwtGTdddk,1434
 libgunshotmatch/datafile.py,sha256=4C4BiR95PBfIUbiUKQzVfh57tgZu_l6rLS8bIgrgPUs,16246
 libgunshotmatch/gzip_util.py,sha256=PcfT4QC4TM0KI3uCGetRpjChbTXTGmNEJBr7BghO3i8,2414
-libgunshotmatch/peak.py,sha256=qe3-y0EsA37W2qMlMVruEOFRRxSG7NVWDcd8TvjZaqY,17546
-libgunshotmatch/project.py,sha256=ch8v8egvcULjYk7_40KywgM-_j3mf2tvRTzAsIC6Kp0,6904
+libgunshotmatch/peak.py,sha256=jIbuOTj_FWTeb46pZtzSwnGsMK_c71Dd9_T9Gj2DxNk,17616
+libgunshotmatch/project.py,sha256=498xoKkDSFDsFodwoRwwEfRL-FOX_hnzyDLLgPNxWr0,6987
 libgunshotmatch/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 libgunshotmatch/search.py,sha256=GMP7_DMnXFq3TG8AT1WARIn4ObCfOGfTDakpGeKzJYw,3123
-libgunshotmatch/utils.py,sha256=8wrdSk1ZWIgIu6eN9QEDF23goxN7z2VszxcDYZZ8ov0,5729
-libgunshotmatch-0.11.0.dist-info/LICENSE,sha256=bFtJt-lyVJHV-88FeFa_r3BEOsmpna5qG2KOl9JUNfU,1064
-libgunshotmatch-0.11.0.dist-info/METADATA,sha256=8TbC-eZngXagQbCQ_G5iStuzriCjYSvGD5umtsxjkAo,6394
-libgunshotmatch-0.11.0.dist-info/WHEEL,sha256=pUf8gZsdmDXXTtqZfolZFpfoEwFoEdADIuUvQVl5qAY,83
-libgunshotmatch-0.11.0.dist-info/entry_points.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-libgunshotmatch-0.11.0.dist-info/RECORD,,
+libgunshotmatch/utils.py,sha256=7WVJPd9wNBFFoAFqh2J6Lsu7BGrGksW32ZqpH7ZIL_I,5776
+libgunshotmatch-0.11.1.dist-info/LICENSE,sha256=bFtJt-lyVJHV-88FeFa_r3BEOsmpna5qG2KOl9JUNfU,1064
+libgunshotmatch-0.11.1.dist-info/METADATA,sha256=X6IRaQ7QLl3ugK51lSmpa205f0Ds1QmbVICEaFucBtw,6394
+libgunshotmatch-0.11.1.dist-info/WHEEL,sha256=pUf8gZsdmDXXTtqZfolZFpfoEwFoEdADIuUvQVl5qAY,83
+libgunshotmatch-0.11.1.dist-info/entry_points.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+libgunshotmatch-0.11.1.dist-info/RECORD,,