libgunshotmatch 0.4.0__tar.gz → 0.5.0__tar.gz

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: libgunshotmatch
-Version: 0.4.0
+Version: 0.5.0
 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/v0.4.0
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.5.0
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/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/v0.4.0
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.5.0
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/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 = "0.4.0"
+__version__: str = "0.5.0"
 __email__: str = "dominic@davis-foster.co.uk"

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/libgunshotmatch/consolidate/__init__.py

@@ -548,13 +548,15 @@ def match_counter(
 	aligned_peaks = []
 	consolidated_peaks = []
 
-	for n in peak_numbers:
+	for idx, peak_no in enumerate(peak_numbers):
+		# idx relates to the position in the QualifiedPeak lists for each repeat.
+		# peak_no correlates to the ``peak_number`` attribute of the QualifiedPeak objects
 		row: List[Optional[QualifiedPeak]] = []
 		# for experiment in project.alignment.expr_code:
 		for experiment in qualified_peaks:
 			assert experiment is not None
 			for peak in experiment:
-				if peak.peak_number == n:
+				if peak.peak_number == peak_no:
 					row.append(peak)
 					break
 			else:
@@ -648,8 +650,8 @@ def match_counter(
 				area_data,
 				ms_data,
 				hits=hits_data,
-				ms_comparison=ms_comp_data.loc[n],
-				meta={"peak_number": n}
+				ms_comparison=ms_comp_data.loc[peak_no],
+				meta={"peak_number": idx}  # The position of the peaks in the QualifiedPeak lists
 				)
 
 		# consolidated_peak.hits = hits_data  # [:n_hits]

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/libgunshotmatch/datafile.py

@@ -472,6 +472,7 @@ class Repeat:
 		datafile = Datafile.from_dict(d["datafile"])
 
 		peaks = PeakList(peak_from_dict(peak) for peak in d["peaks"])
+		peaks.datafile_name = datafile.name
 
 		qualified_peaks_as_list = d["qualified_peaks"]
 		if qualified_peaks_as_list is None:

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/libgunshotmatch/method/__init__.py

@@ -148,7 +148,8 @@ class IntensityMatrixMethod(MethodBase):
 	#: The range of masses to which the GC-MS data should be limited to.
 	crop_mass_range: Optional[Tuple[int, int]] = attr.field(default=(50, 500), converter=convert_crop_mass_range)
 
-	#: Whether to perform Savitzky-Golay smoothing.
+	# Whether to perform Savitzky-Golay smoothing.
+	#: Settings for Savitzky-Golay smoothing.
 	savitzky_golay: SavitzkyGolayMethod = attr.field(
 			default=SavitzkyGolayMethod(),
 			converter=_convert_sg_method,

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/libgunshotmatch/peak.py

@@ -438,7 +438,7 @@ def filter_aligned_peaks(
 	Filter aligned peaks by minimum average peak area, and to the top ``n`` largest peaks.
 
 	:param alignment:
-	:param top_n_peaks: Filter to the largest ``n`` peaks.
+	:param top_n_peaks: Filter to the largest ``n`` peaks. If ``0`` all peaks are included.
 	:param min_peak_area: Exclude aligned peaks with an average peak area below this threshold.
 
 	:returns: :class:`pandas.DataFrame` giving the retention times of the aligned peaks.
@@ -458,17 +458,22 @@ def filter_aligned_peaks(
 	area_alignment = area_alignment.sort_values(by="mean")
 
 	########
-
-	print(f"Filtering to the largest {top_n_peaks} peaks with an average peak area above {min_peak_area}")
-
 	# Get indices of largest n peaks based on `ident_top_peaks`
 	top_peaks_indices = []
-	# print("tail of area_alignment=", area_alignment.tail(top_n_peaks))
 
-	# Limit to the largest `ident_top_peaks` peaks
-	for peak_no, areas in area_alignment.tail(top_n_peaks).iterrows():
-		# Ignore peak if average peak area is less then min_peak_area
-		if areas["mean"] >= min_peak_area:
+	if top_n_peaks:
+		print(f"Filtering to the largest {top_n_peaks} peaks with an average peak area above {min_peak_area}")
+
+		# print("tail of area_alignment=", area_alignment.tail(top_n_peaks))
+
+		# Limit to the largest `ident_top_peaks` peaks
+		for peak_no, areas in area_alignment.tail(top_n_peaks).iterrows():
+			# Ignore peak if average peak area is less then min_peak_area
+			if areas["mean"] >= min_peak_area:
+				top_peaks_indices.append(peak_no)
+
+	else:
+		for peak_no, _ in area_alignment.iterrows():
 			top_peaks_indices.append(peak_no)
 
 	# Remove peaks from rt_alignment if they are not in top_peaks_indices,

{libgunshotmatch-0.4.0 → libgunshotmatch-0.5.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "whey"
 
 [project]
 name = "libgunshotmatch"
-version = "0.4.0"
+version = "0.5.0"
 description = "Base library for GunShotMatch."
 readme = "README.rst"
 keywords = []