libgunshotmatch 0.7.3__tar.gz → 0.8.0__tar.gz

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: libgunshotmatch
-Version: 0.7.3
+Version: 0.8.0
 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/v0.7.3
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.8.0
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/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/v0.7.3
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.8.0
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/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 = "0.7.3"
+__version__: str = "0.8.0"
 __email__: str = "dominic@davis-foster.co.uk"

libgunshotmatch-0.8.0/libgunshotmatch/comparison/__init__.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python3
+#
+#  __init__.py
+"""
+Comparison between projects and unknowns.
+
+The two submodules, :mod:`~.comparison.projects` and :mod:`~.comparison.unknowns`,
+provide identical APIs with different internals to handle reference projects (containing two or more repeats)
+and unknown samples (from a single datafile).
+
+.. versionadded:: 0.8.0
+"""
+#
+#  Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy
+#  of this software and associated documentation files (the "Software"), to deal
+#  in the Software without restriction, including without limitation the rights
+#  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+#  copies of the Software, and to permit persons to whom the Software is
+#  furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+#  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+#  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+#  DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+#  OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
+#  OR OTHER DEALINGS IN THE SOFTWARE.
+#
+
+# stdlib
+from typing import List, Sequence, Tuple
+
+# 3rd party
+from pyms.DPA.Alignment import Alignment  # type: ignore[import]
+from pyms.DPA.PairwiseAlignment import PairwiseAlignment, align_with_tree  # type: ignore[import]
+
+# this package
+from libgunshotmatch.project import Project
+
+# this package
+from . import projects, unknowns
+from ._utils import _PaddedPeakList
+
+__all__ = ("align_projects", "get_padded_peak_lists")
+
+# Aliases to prevent clashes with argument names
+_projects_mod = projects
+_unknowns_mod = unknowns
+
+
+def align_projects(projects: Sequence[Project] = (), unknowns: Sequence[Project] = ()) -> Alignment:
+	"""
+	Align multiple projects and/or unknowns.
+
+	:param projects:
+	:param unknowns:
+	"""
+
+	project_alignments = map(_projects_mod.filter_alignment_to_consolidate, projects)
+	unknown_alignments = map(_unknowns_mod.filter_alignment_to_consolidate, unknowns)
+
+	pwa = PairwiseAlignment([*project_alignments, *unknown_alignments], D=2.5, gap=0.3)
+	return align_with_tree(pwa)
+
+
+def get_padded_peak_lists(
+		alignment: Alignment,
+		projects: Sequence[Project] = (),
+		unknowns: Sequence[Project] = (),
+		) -> Tuple[List[_PaddedPeakList], List[_PaddedPeakList]]:
+	"""
+	Pad the consolidated peak lists in each project/unknown, from the given between-project alignment.
+
+	:param alignment:
+	:param projects:
+	:param unknowns:
+	"""
+
+	data = alignment.get_peak_alignment(require_all_expr=False, minutes=False)
+
+	projects_padded_cp = [_projects_mod.get_padded_peak_list(p, data) for p in projects]
+	unknowns_padded_cp = [_unknowns_mod.get_padded_peak_list(p, data) for p in unknowns]
+	return projects_padded_cp, unknowns_padded_cp

libgunshotmatch-0.8.0/libgunshotmatch/comparison/_utils.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+#
+#  _utils.py
+"""
+Utility functions.
+"""
+#
+#  Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy
+#  of this software and associated documentation files (the "Software"), to deal
+#  in the Software without restriction, including without limitation the rights
+#  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+#  copies of the Software, and to permit persons to whom the Software is
+#  furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+#  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+#  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+#  DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+#  OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
+#  OR OTHER DEALINGS IN THE SOFTWARE.
+#
+
+# stdlib
+from typing import List, MutableSequence, Optional
+
+# 3rd party
+import numpy
+
+# this package
+from libgunshotmatch import project
+from libgunshotmatch.consolidate import ConsolidatedPeak
+
+_PaddedPeakList = MutableSequence[Optional[ConsolidatedPeak]]
+
+
+def _get_padded_peak_list(project: project.Project, rts: List[float]) -> _PaddedPeakList:
+
+	assert project.consolidated_peaks is not None
+
+	padded_cp_list: _PaddedPeakList = []
+
+	for cp in project.consolidated_peaks:
+		if rts:
+			top_rt = rts.pop(0)
+			while numpy.isnan(top_rt):
+				padded_cp_list.append(None)
+				if rts:
+					top_rt = rts.pop(0)
+				else:
+					break
+		padded_cp_list.append(cp)
+
+	return padded_cp_list

libgunshotmatch-0.8.0/libgunshotmatch/comparison/projects.py

@@ -0,0 +1,90 @@
+#!/usr/bin/env python3
+#
+#  project.py
+"""
+Comparison between projects.
+"""
+#
+#  Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy
+#  of this software and associated documentation files (the "Software"), to deal
+#  in the Software without restriction, including without limitation the rights
+#  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+#  copies of the Software, and to permit persons to whom the Software is
+#  furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+#  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+#  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+#  DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+#  OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
+#  OR OTHER DEALINGS IN THE SOFTWARE.
+#
+
+# 3rd party
+import numpy
+import pandas  # type: ignore[import]
+from pyms.DPA.Alignment import Alignment  # type: ignore[import]
+
+# this package
+from libgunshotmatch.project import Project
+from libgunshotmatch.utils import create_alignment
+
+# this package
+from ._utils import _get_padded_peak_list, _PaddedPeakList
+
+__all__ = ("filter_alignment_to_consolidate", "get_padded_peak_list")
+
+
+def filter_alignment_to_consolidate(project: Project) -> Alignment:
+	"""
+	Filter peaks from a project's ``alignment`` to only those which survived the ``consolidate`` process.
+
+	:param project:
+	"""
+
+	assert project.consolidated_peaks is not None
+
+	# 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]
+	expr_code = [project.alignment.expr_code[idx] for idx in sort_map]
+	peakpos = [project.alignment.peakpos[idx] for idx in sort_map]
+
+	consolidated_peak_retention_times = [cp.rt_list for cp in project.consolidated_peaks]
+
+	aligned_peaks_surviving_consolidate = []
+	for aligned_peaks in zip(*peakpos):
+		aprt = [p.rt for p in reversed(aligned_peaks)]
+		if aprt in consolidated_peak_retention_times:
+			aligned_peaks_surviving_consolidate.append(aligned_peaks)
+
+	alignment_surviving_consolidate = list(zip(*aligned_peaks_surviving_consolidate))
+
+	# Sanity check
+	for c_expr_peaks, expr_peaks in zip(alignment_surviving_consolidate, peakpos):
+		for peak in c_expr_peaks:
+			assert peak in expr_peaks
+
+	# Create new Alignment object
+	return create_alignment(alignment_surviving_consolidate, expr_code)
+
+
+def get_padded_peak_list(project: Project, alignment_rts: pandas.DataFrame) -> _PaddedPeakList:
+	"""
+	Returns a list of consolidated peaks for the project, based on the between-project alignment.
+
+	:param project:
+	:param alignment_rts: Pandas DataFrame giving retention times for the peak alignment.
+		The output of :meth:`~pyms.DPA.Alignment.Alignment.get_peak_alignment`.
+
+	"""
+
+	rts = [numpy.mean(row[1:]) for row in alignment_rts[list(project.datafile_data)].itertuples()]
+
+	return _get_padded_peak_list(project, rts)

libgunshotmatch-0.8.0/libgunshotmatch/comparison/unknowns.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python3
+#
+#  unknown.py
+"""
+Comparison between project(s) and unknowns.
+"""
+#
+#  Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy
+#  of this software and associated documentation files (the "Software"), to deal
+#  in the Software without restriction, including without limitation the rights
+#  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+#  copies of the Software, and to permit persons to whom the Software is
+#  furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+#  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+#  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+#  DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+#  OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
+#  OR OTHER DEALINGS IN THE SOFTWARE.
+#
+
+# 3rd party
+import pandas  # type: ignore[import]
+from pyms.DPA.Alignment import Alignment  # type: ignore[import]
+
+# this package
+from libgunshotmatch.project import Project
+from libgunshotmatch.utils import create_alignment
+
+# this package
+from ._utils import _get_padded_peak_list, _PaddedPeakList
+
+__all__ = ("filter_alignment_to_consolidate", "get_padded_peak_list")
+
+
+def filter_alignment_to_consolidate(unknown: Project) -> Alignment:
+	"""
+	Filter peaks from an unknown's ``alignment`` to only those which survived the ``consolidate`` process.
+
+	:param project:
+	"""
+
+	assert unknown.consolidated_peaks is not None
+
+	cp_rts = [cp.rt for cp in unknown.consolidated_peaks]
+
+	aligned_peaks = [peak for peak in unknown.alignment.peakpos[0] if peak.rt in cp_rts]
+
+	# Sanity check
+	for c_expr_peaks, expr_peaks in zip([aligned_peaks], unknown.alignment.peakpos):
+		for peak in c_expr_peaks:
+			assert peak in expr_peaks
+
+	# Create new Alignment object
+	return create_alignment([aligned_peaks], [unknown.name])
+
+
+def get_padded_peak_list(unknown: Project, alignment_rts: pandas.DataFrame) -> _PaddedPeakList:
+	"""
+	Returns a list of consolidated peaks for the unknown sample, based on the between-project alignment.
+
+	:param unknown:
+	:param alignment_rts: Pandas DataFrame giving retention times for the peak alignment.
+		The output of :meth:`~pyms.DPA.Alignment.Alignment.get_peak_alignment`.
+	"""
+
+	rts = list(alignment_rts[unknown.name])
+
+	return _get_padded_peak_list(unknown, rts)

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/consolidate/__init__.py

@@ -246,6 +246,9 @@ class ConsolidatedPeak:
 	:param hits: Optional list of possible identities for this peak.
 	:param ms_comparison: Mapping or Pandas :class:`~pandas.Series` giving pairwise mass spectral comparison scores.
 	:param meta: Optional dictionary for storing e.g. peak number or whether the peak should be hidden.
+
+	.. latex:clearpage::
+	.. autosummary-widths:: 3/10
 	"""
 
 	#: List of retention times of the aligned peaks.
@@ -456,7 +459,7 @@ class ConsolidatedPeak:
 
 	def __len__(self) -> int:
 		"""
-		How many instances of the peak make up this :~.ConsolidatedPeak`.
+		How many instances of the peak make up this :class:`~.ConsolidatedPeak`.
 		"""
 
 		return numpy.count_nonzero(~numpy.isnan(self.rt_list))
@@ -692,7 +695,7 @@ class ConsolidatedPeakFilter:
 
 	min_appearances: int = Integer.field(default=-1)
 	"""
-	Number of times the hit must appear across individual the aligned peaks.
+	Number of times the hit must appear across the individual aligned peaks.
 
 	Consolidated peaks where the most common hit appears fewer times than this will be excluded.
 
@@ -708,6 +711,10 @@ class ConsolidatedPeakFilter:
 		Construct a :class:`~.ConsolidatedPeakFilter` from a :class:`~.ConsolidateMethod`.
 
 		:param method:
+
+		:rtype:
+
+		.. latex:clearpage::
 		"""
 
 		return cls(

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/datafile.py

@@ -49,7 +49,7 @@ from libgunshotmatch import gzip_util
 from libgunshotmatch.method import SavitzkyGolayMethod
 from libgunshotmatch.peak import PeakList, QualifiedPeak, _to_peak_list, peak_from_dict
 
-__all__ = ["Datafile", "FileType", "Repeat", "get_info_from_gcms_data", "GCMSDataInfo"]
+__all__ = ("Datafile", "FileType", "Repeat", "get_info_from_gcms_data", "GCMSDataInfo")
 
 
 class FileType(IntEnum):
@@ -189,6 +189,7 @@ class Datafile:
 		:param crop_mass_range: The range of masses to which the GC-MS data should be limited to.
 
 		"""
+
 		intensity_matrix = build_intensity_matrix_i(gcms_data)
 
 		# Show the m/z of the maximum and minimum bins
@@ -321,9 +322,7 @@ class Datafile:
 
 	def export(self, output_dir: PathLike) -> str:
 		"""
-		Export as a ``.gsmd`` file.
-
-		:returns: The output filename.
+		Export as a ``.gsmd`` file and return the output filename.
 		"""
 
 		export_filename = os.path.join(output_dir, f"{self.name}.gsmd")
@@ -344,7 +343,7 @@ class Datafile:
 
 class GCMSDataInfo(NamedTuple):
 	"""
-	Represents information about a :class:`pyms.GCMS.Class.GCMS_data` object returned by :func:`get_info_from_gcms_data`.
+	Represents information about a :class:`~pyms.GCMS.Class.GCMS_data` object returned by :func:`get_info_from_gcms_data`.
 	"""
 
 	#: The minimum and maximum retention times.
@@ -501,9 +500,7 @@ class Repeat:
 
 	def export(self, output_dir: PathLike) -> str:
 		"""
-		Export as a ``.gsmr`` file.
-
-		:returns: The output filename.
+		Export as a ``.gsmr`` file and return the output filename.
 
 		.. versionadded:: 0.4.0
 		"""

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/gzip_util.py

@@ -35,7 +35,7 @@ import sdjson
 from domdf_python_tools.paths import PathPlus
 from domdf_python_tools.typing import PathLike
 
-__all__ = ["read_gzip_json", "write_gzip_json"]
+__all__ = ("read_gzip_json", "write_gzip_json")
 
 JSONOutput = Union[str, int, float, bool, None, Dict[str, Any], List[Any]]
 JSONInput = Union[JSONOutput, Tuple[Any, ...], OrderedDict]

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/method/__init__.py

@@ -53,7 +53,7 @@ from libgunshotmatch.method._fields import (
 		)
 from libgunshotmatch.utils import _fix_init_annotations, _to_list
 
-__all__ = [
+__all__ = (
 		"MethodBase",
 		"Method",
 		"IntensityMatrixMethod",
@@ -62,7 +62,7 @@ __all__ = [
 		"AlignmentMethod",
 		"ConsolidateMethod",
 		"SavitzkyGolayMethod",
-		]
+		)
 
 _MB = TypeVar("_MB", bound="MethodBase")
 
@@ -272,7 +272,7 @@ class ConsolidateMethod(MethodBase):
 
 def _submethod_field(submethod_type: Type[_MB]) -> _MB:
 	# Actually returns attr.Attribute, but mypy doesn't like it
-	return attr.field(default=attr.Factory(submethod_type), converter=submethod_type._coerce)
+	return attr.field(factory=submethod_type, converter=submethod_type._coerce)
 
 
 @_fix_init_annotations
@@ -280,6 +280,8 @@ def _submethod_field(submethod_type: Type[_MB]) -> _MB:
 class Method(MethodBase):
 	"""
 	Overall GunShotMatch method.
+
+	.. latex:vspace:: 4mm
 	"""
 
 	#: Method used for constructing an intensity matrix from a datafile.

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/method/_fields.py

@@ -33,7 +33,7 @@ from typing import Any, Generic, Iterable, Optional, Set, Tuple, Type, TypeVar,
 import attr
 from pyms.Utils.Time import time_str_secs  # type: ignore[import]
 
-__all__ = [
+__all__ = (
 		"Boolean",
 		"FieldType",
 		"Integer",
@@ -42,7 +42,7 @@ __all__ = [
 		"convert_crop_mass_range",
 		"convert_rt_range",
 		"default_base_peak_filter"
-		]
+		)
 
 _FT = TypeVar("_FT")
 

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/peak.py

@@ -46,7 +46,7 @@ from pyms.Peak.List.Function import sele_peaks_by_rt  # type: ignore[import]
 from pyms.Spectrum import MassSpectrum  # type: ignore[import]
 from pyms_nist_search import SearchResult
 
-__all__ = [
+__all__ = (
 		"PeakList",
 		"QualifiedPeak",
 		"QualifiedPeakList",
@@ -54,8 +54,8 @@ __all__ = [
 		"filter_aligned_peaks",
 		"filter_peaks",
 		"peak_from_dict",
-		"write_alignment"
-		]
+		"write_alignment",
+		)
 
 
 class QualifiedPeak(Peak):
@@ -217,6 +217,8 @@ class QualifiedPeak(Peak):
 class PeakList(List[Peak]):
 	"""
 	Represents a list of peaks.
+
+	.. autosummary-widths:: 35/100
 	"""
 
 	#: String identifier for the datafile the peaks were detected in.
@@ -362,6 +364,10 @@ def align_peaks(
 	:param gap_penalty: Gap parameter for pairwise alignments.
 	:param min_peaks: Minimum number of peaks required for the alignment position to survive filtering.
 		If set to ``-1`` the number of repeats in the project are used.
+
+	:rtype:
+
+	.. latex:clearpage::
 	"""
 
 	print("\nAligning\n")
@@ -434,7 +440,7 @@ def write_alignment(
 	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
+			json_library=sdjson,  # type: ignore[arg-type]
 			)
 
 
@@ -500,6 +506,10 @@ def peak_from_dict(d: Dict[str, Any]) -> Peak:
 	Construct a :class:`~pyms.Peak.Class.Peak` from a dictionary.
 
 	:param d:
+
+	:rtype:
+
+	.. latex:clearpage::
 	"""
 
 	peak_obj = Peak(d["rt"], MassSpectrum(**d["mass_spectrum"]), outlier=d["is_outlier"])

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/search.py

@@ -38,7 +38,7 @@ from pyms.Peak.Class import Peak  # type: ignore[import]
 from libgunshotmatch.peak import QualifiedPeak
 from libgunshotmatch.utils import round_rt
 
-__all__ = ["identify_peaks"]
+__all__ = ("identify_peaks", )
 
 
 def identify_peaks(

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/libgunshotmatch/utils.py

@@ -34,6 +34,8 @@ from typing import TYPE_CHECKING, Any, Iterable, List, Optional, Sequence, Tuple
 import numpy
 from chemistry_tools.spectrum_similarity import SpectrumSimilarity
 from mathematical.utils import rounders
+from pyms.DPA.Alignment import Alignment  # type: ignore[import]
+from pyms.Peak.Class import Peak  # type: ignore[import]
 from pyms.Spectrum import MassSpectrum  # type: ignore[import]
 from scipy.stats import truncnorm  # type: ignore[import]
 
@@ -41,7 +43,7 @@ if TYPE_CHECKING:
 	# this package
 	from libgunshotmatch.project import Project
 
-__all__ = ("round_rt", "get_truncated_normal", "ms_comparison", "get_rt_range")
+__all__ = ("round_rt", "get_truncated_normal", "ms_comparison", "get_rt_range", "create_alignment")
 
 
 def round_rt(rt: Union[str, float, Decimal]) -> Decimal:
@@ -150,7 +152,7 @@ def get_rt_range(project: "Project") -> Tuple[float, float]:
 
 	:rtype:
 
-	,, versionadded:: 0.7.0
+	.. versionadded:: 0.7.0
 	"""
 
 	# Get RT extremes from intensity matrix
@@ -166,3 +168,25 @@ def get_rt_range(project: "Project") -> Tuple[float, float]:
 	max_rt = max(max_rts) / 60
 
 	return min_rt, max_rt
+
+
+def create_alignment(peakpos: Sequence[Sequence[Peak]], expr_code: List[str], similarity: float = 0) -> Alignment:
+	"""
+	Create a new :class:`pyms.DPA.Alignment.Alignment` object.
+
+	:param peakpos: Nested list of aligned peaks. Top level list contains lists of peaks for each experiment in ``expr_code``.
+	:param expr_code: Experiment names. Order must match ``peakpos``.
+	:param similarity:
+
+	:rtype:
+
+	.. versionadded:: 0.8.0
+	"""
+
+	alignment = Alignment(None)
+	alignment.peakpos = peakpos
+	alignment.peakalgt = numpy.transpose(alignment.peakpos).tolist()
+	alignment.expr_code = expr_code
+	alignment.similarity = similarity
+
+	return alignment

{libgunshotmatch-0.7.3 → libgunshotmatch-0.8.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "whey"
 
 [project]
 name = "libgunshotmatch"
-version = "0.7.3"
+version = "0.8.0"
 description = "Base library for GunShotMatch."
 readme = "README.rst"
 keywords = []
@@ -124,6 +124,7 @@ extensions = [
     "enum_tools.autoenum",
     "attr_utils.autoattrs",
     "remove_factory_defaults",
+    "sphinx_toolbox.more_autosummary.column_widths",
 ]
 sphinxemoji_style = "twemoji"
 gitstamp_fmt = "%d %b %Y"