libgunshotmatch 0.11.0__tar.gz → 0.11.2__tar.gz

{libgunshotmatch-0.11.0 → libgunshotmatch-0.11.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: libgunshotmatch
-Version: 0.11.0
+Version: 0.11.2
 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/v0.11.2
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.11.0 → libgunshotmatch-0.11.2}/README.rst

@@ -91,7 +91,7 @@ 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/v0.11.2
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.11.0 → libgunshotmatch-0.11.2}/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 = "0.11.2"
 __email__: str = "dominic@davis-foster.co.uk"

{libgunshotmatch-0.11.0 → libgunshotmatch-0.11.2}/libgunshotmatch/comparison/projects.py

@@ -52,15 +52,18 @@ def filter_alignment_to_consolidate(project: Project) -> Alignment:
 
 	# Sort expr_code and peakpos into order from datafile_data
 	desired_order = list(project.datafile_data)[::-1]
-	sort_map = [desired_order.index(code) for code in project.alignment.expr_code]
+	sort_map = [project.alignment.expr_code.index(code) for code in desired_order]
 	expr_code = [project.alignment.expr_code[idx] for idx in sort_map]
 	peakpos = [project.alignment.peakpos[idx] for idx in sort_map]
+	assert desired_order == expr_code
 
-	consolidated_peak_retention_times = [cp.rt_list for cp in project.consolidated_peaks]
+	consolidated_peak_retention_times = []
+	for cp in project.consolidated_peaks:
+		consolidated_peak_retention_times.append([None if numpy.isnan(rt) else rt for rt in cp.rt_list])
 
 	aligned_peaks_surviving_consolidate = []
 	for aligned_peaks in zip(*peakpos):
-		aprt = [p.rt for p in reversed(aligned_peaks)]
+		aprt = [None if p is None else p.rt for p in reversed(aligned_peaks)]
 		if aprt in consolidated_peak_retention_times:
 			aligned_peaks_surviving_consolidate.append(aligned_peaks)
 

{libgunshotmatch-0.11.0 → libgunshotmatch-0.11.2}/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-0.11.0 → libgunshotmatch-0.11.2}/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-0.11.0 → libgunshotmatch-0.11.2}/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-0.11.0 → libgunshotmatch-0.11.2}/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 → libgunshotmatch-0.11.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "whey"
 
 [project]
 name = "libgunshotmatch"
-version = "0.11.0"
+version = "0.11.2"
 description = "Base library for GunShotMatch."
 readme = "README.rst"
 keywords = []