masster 0.3.5__py3-none-any.whl → 0.3.7__py3-none-any.whl

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Files changed (7) hide show
  1. masster/sample/sample.py +13 -2
  2. masster/study/study.py +20 -0
  3. {masster-0.3.5.dist-info → masster-0.3.7.dist-info}/METADATA +1 -1
  4. {masster-0.3.5.dist-info → masster-0.3.7.dist-info}/RECORD +7 -7
  5. {masster-0.3.5.dist-info → masster-0.3.7.dist-info}/WHEEL +0 -0
  6. {masster-0.3.5.dist-info → masster-0.3.7.dist-info}/entry_points.txt +0 -0
  7. {masster-0.3.5.dist-info → masster-0.3.7.dist-info}/licenses/LICENSE +0 -0
masster/sample/sample.py CHANGED
@@ -39,8 +39,13 @@ import sys
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  import polars as pl
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  from masster._version import get_version
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+ from masster.logger import MassterLogger
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  from masster.sample.defaults.sample_def import sample_defaults
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+ from masster.sample.defaults.find_features_def import find_features_defaults
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+ from masster.sample.defaults.find_adducts_def import find_adducts_defaults
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+ from masster.sample.defaults.find_ms2_def import find_ms2_defaults
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+ from masster.sample.defaults.get_spectrum_def import get_spectrum_defaults
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  # Sample-specific imports
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  from masster.sample.h5 import _load_sample5
@@ -67,7 +72,6 @@ from masster.sample.load import chrom_extract
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  from masster.sample.load import index_file
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  from masster.sample.load import load
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  from masster.sample.load import sanitize
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- from masster.logger import MassterLogger
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  from masster.sample.plot import plot_2d
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  from masster.sample.plot import plot_2d_oracle
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  from masster.sample.plot import plot_dda_stats
@@ -157,7 +161,6 @@ class Sample:
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  self.log_sink = params.log_sink
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  # Initialize independent logger
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- from masster.logger import MassterLogger
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  self.logger = MassterLogger(
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  instance_type="sample",
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  level=params.log_level.upper(),
@@ -256,6 +259,14 @@ class Sample:
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  _spec_to_mat = _spec_to_mat
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  _save_featureXML = _save_featureXML
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+ # defaults
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+ sample_defaults = sample_defaults
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+ find_features_defaults = find_features_defaults
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+ merge_defaults = find_features_defaults
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+ find_adducts_defaults = find_adducts_defaults
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+ find_ms2_defaults = find_ms2_defaults
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+ get_spectrum_defaults = get_spectrum_defaults
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+
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  def logger_update(self, level: str | None = None, label: str | None = None, sink: str | None = None):
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  """Update the logging configuration for this Sample instance.
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masster/study/study.py CHANGED
@@ -116,6 +116,15 @@ from masster.study.export import _get_mgf_df
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  from masster.logger import MassterLogger
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  from masster.study.defaults.study_def import study_defaults
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+ from masster.study.defaults.align_def import align_defaults
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+ from masster.study.defaults.export_def import export_mgf_defaults
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+ from masster.study.defaults.fill_chrom_def import fill_chrom_defaults
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+ from masster.study.defaults.fill_def import fill_defaults
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+ from masster.study.defaults.find_consensus_def import find_consensus_defaults
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+ from masster.study.defaults.find_ms2_def import find_ms2_defaults
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+ from masster.study.defaults.integrate_chrom_def import integrate_chrom_defaults
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+ from masster.study.defaults.integrate_def import integrate_defaults
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+ from masster.study.defaults.merge_def import merge_defaults
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  class Study:
@@ -357,6 +366,17 @@ class Study:
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  export_mztab = export_mztab
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  _get_mgf_df = _get_mgf_df # New function for MGF data extraction
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+ # defaults
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+ study_defaults = study_defaults
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+ align_defaults = align_defaults
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+ export_mgf_defaults = export_mgf_defaults
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+ fill_chrom_defaults = fill_chrom_defaults
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+ fill_defaults = fill_defaults
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+ find_consensus_defaults = find_consensus_defaults
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+ find_ms2_defaults = find_ms2_defaults
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+ integrate_chrom_defaults = integrate_chrom_defaults
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+ integrate_defaults = integrate_defaults
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+ merge_defaults = merge_defaults
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  def _reload(self):
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  """
{masster-0.3.5.dist-info → masster-0.3.7.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: masster
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- Version: 0.3.5
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+ Version: 0.3.7
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  Summary: Mass spectrometry data analysis package
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  Project-URL: homepage, https://github.com/zamboni-lab/masster
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  Project-URL: repository, https://github.com/zamboni-lab/masster
{masster-0.3.5.dist-info → masster-0.3.7.dist-info}/RECORD RENAMED
@@ -19,7 +19,7 @@ masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,
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  masster/sample/plot.py,sha256=uUJAd2qxhVG6Ev2hLuU406zFA2TDkkBz2MG12P9fLik,71449
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  masster/sample/processing.py,sha256=NjNLt47Fy0UF3Xs35NBhADg57qTC6Lfa4Xz8Y30v83A,58250
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  masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
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- masster/sample/sample.py,sha256=bsCieIitztHiys7xyyfkKAkyHQRTo9uc0MLq10tsEn0,16178
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+ masster/sample/sample.py,sha256=ekS-qBfzx3_Lb2KLMu-s90owRlk3lK4616mmiAiiHTc,16726
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  masster/sample/sample5_schema.json,sha256=3SPFQZH4SooLYUt_lW-PCOE9rHnl56Vhc2XG-r1nyEQ,3586
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  masster/sample/save.py,sha256=o9eFSqqr7KYwvCD3gOJt_nZ4h3pkflWqs0n0oSLM-sU,31970
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  masster/sample/sciex.py,sha256=q6PdcjCtV2PWnJiXuvfISu09zjkaTR_fvHvWN9OvOcM,46870
@@ -39,7 +39,7 @@ masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3
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  masster/study/plot.py,sha256=NW31XdM9Bf5wNvIAs-56AIoPA8VLTqBzr6qJInfZmhc,25159
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  masster/study/processing.py,sha256=BQuSBO7O8iTlCjXenECyg0_PAsPF1NNiUllypuemPZI,46101
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  masster/study/save.py,sha256=bcRADWTvhTER9WRkT9zNU5mDUPQZkZB2cuJwpRsYmrM,6589
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- masster/study/study.py,sha256=5TZgG7tr7mzqHh1tm48V8SEcvRcWiFYG9iDqz0U9ACc,27073
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+ masster/study/study.py,sha256=5cgJaSOSrGnM3rqXAe3YdNkbWoT1ze6KGt-83nTq-AM,28144
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  masster/study/study5_schema.json,sha256=A_xDPzB97xt2EFeQsX9j8Ut7yC4_DS7BZ24ucotOXIw,5103
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  masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
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  masster/study/defaults/align_def.py,sha256=9aM7kY4_ecgG8QC6v57AASiRRkPxwG77r3-PlQ2BkHk,9139
@@ -52,8 +52,8 @@ masster/study/defaults/integrate_chrom_def.py,sha256=Rih3-vat7fHGVfIvRitjNJJI3zL
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  masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
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  masster/study/defaults/merge_def.py,sha256=EBsKE3hsAkTEzN9dpdRD5W3_suTKy_WZ_96rwS0uBuE,8572
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  masster/study/defaults/study_def.py,sha256=hj8bYtEPwzdowC95yfyoCFt6fZkQePLjpJtmpNz9Z5M,9533
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- masster-0.3.5.dist-info/METADATA,sha256=1ftc3kQLG0JgPN0ys1DFGWb1xE2IpXiUQlUmE9C1yII,44292
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- masster-0.3.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- masster-0.3.5.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
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- masster-0.3.5.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
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- masster-0.3.5.dist-info/RECORD,,
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+ masster-0.3.7.dist-info/METADATA,sha256=O5N1DYy-vg2mHR5HVrW7bhjfk9ckdQC0SuaFRKAiXjo,44292
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+ masster-0.3.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ masster-0.3.7.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
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+ masster-0.3.7.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
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+ masster-0.3.7.dist-info/RECORD,,