masster 0.4.0__tar.gz → 0.4.1__tar.gz

{masster-0.4.0 → masster-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.0
+Version: 0.4.1
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.4.0 → masster-0.4.1}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.4.0"
+version = "0.4.1"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.4.0 → masster-0.4.1}/src/masster/__init__.py

@@ -1,5 +1,5 @@
 """
-master - Mass Spectrometry Analysis Assistant
+masster - Mass Spectrometry Analysis Assistant
 
 A comprehensive Python package for processing and analyzing untargeted metabolomics data,
 supporting both DDA (Data-Dependent Acquisition) and DIA (Data-Independent Acquisition)
@@ -8,14 +8,14 @@ mass spectrometry workflows.
 
 from __future__ import annotations
 
-from master._version import __version__
+from masster._version import __version__
 
-# from master._version import get_version
-from master.chromatogram import Chromatogram
-from master.lib import Lib
-from master.sample.sample import Sample
-from master.spectrum import Spectrum
-from master.study.study import Study
+# from masster._version import get_version
+from masster.chromatogram import Chromatogram
+from masster.lib import Lib
+from masster.sample.sample import Sample
+from masster.spectrum import Spectrum
+from masster.study.study import Study
 
 
 __all__ = [

{masster-0.4.0 → masster-0.4.1}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.4.0"
+__version__ = "0.4.1"
 
 
 def get_version():

{masster-0.4.0 → masster-0.4.1}/src/masster/chromatogram.py

@@ -88,7 +88,7 @@ class Chromatogram:
 
     Example Usage:
         >>> import numpy as np
-        >>> from master import chrom
+        >>> from masster import chrom
         >>> rt = np.linspace(0, 300, 1000)
         >>> intensity = np.random.normal(1000, 100, 1000)
         >>> chromatogram = chrom(rt=rt, inty=intensity, label="EIC m/z 150")
@@ -251,11 +251,7 @@ class Chromatogram:
             inty=self.inty.copy(),
             label=self.label,
             rt_unit=self.rt_unit,
-            **{
-                k: v.copy()
-                for k, v in self.__dict__.items()
-                if isinstance(v, np.ndarray)
-            },
+            **{k: v.copy() for k, v in self.__dict__.items() if isinstance(v, np.ndarray)},
         )
 
     def pandalize(self):
@@ -271,9 +267,7 @@ class Chromatogram:
         find all attributes that are numpy arrays and have the same length as mz
         """
         data = {
-            key: val
-            for key, val in self.__dict__.items()
-            if isinstance(val, np.ndarray) and val.size == self.rt.size
+            key: val for key, val in self.__dict__.items() if isinstance(val, np.ndarray) and val.size == self.rt.size
         }
         return polars.DataFrame(data)
 

{masster-0.4.0 → masster-0.4.1}/src/masster/data/libs/README.md

@@ -1,6 +1,6 @@
 metabolite lib CSVs
 
-This folder contains programmatically generated metabolite lists used as example libs for the master package.
+This folder contains programmatically generated metabolite lists used as example libs for the masster package.
 
 Files (generated by scripts in the repository root):
 - `urine_metabolites.csv` - best-effort list of metabolites reported in human urine (generated by `urine.py`).

{masster-0.4.0 → masster-0.4.1}/src/masster/data/libs/ccm.csv

@@ -1,120 +1,120 @@
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-N-acetylglucosamine,C8H14NO,CC(O)=N[C@@H](C=O)[C@@H](O)[C@H](O)[C@H](O)CO,MBLBDJOUHNCFQT-LXGUWJNJSA-N
-Choline,C5H13NO,[H]OC([H])([H])C([H])([H])N(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H],OEYIOHPDSNJKLS-UHFFFAOYSA-N
-Betaine,C5H10NO,[H]OC(=O)C([H])([H])N(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H],KWIUHFFTVRNATP-UHFFFAOYSA-N
-Carnitine,C7H14NO,[H]OC(=O)C([H])([H])C([H])(O[H])C([H])([H])N(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H],PHIQHXFUZVPYII-UHFFFAOYSA-N
-Phosphocholine,C5H14NO4P,[H]OP(=O)(O[H])OC([H])([H])C([H])([H])N(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H],YHHSONZFOIEMCP-UHFFFAOYSA-O
-Glycerol,C3H7O,OCC(O)CO,PEDCQBHIVMGVHV-UHFFFAOYSA-N
-Sorbitol,C6H13O,OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO,FBPFZTCFMRRESA-JGWLITMVSA-N
-Inositol,C6H11O,OC1C(O)C(O)C(O)C(O)C1O,CDAISMWEOUEBRE-UHFFFAOYSA-N
-Cholesterol,C27H46O,CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C,HVYWMOMLDIMFJA-DPAQBDIFSA-N
-Pantothenate,C9H21NO,CC(C)(CO)C(O)C(O)=NCCC(=O)O,GHOKWGTUZJEAQD-UHFFFAOYSA-M
+Name,Formula,SMILES,InChIKey,db_id,db
+Glucose,C6H11O,OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O,WQZGKKKJIJFFOK-GASJEMHNSA-N,CID:5793,pubchem
+Glucose-6-phosphate,C6H13O9P,O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O,VFRROHXSMXFLSN-SLPGGIOYSA-N,CID:439958,pubchem
+Fructose-6-phosphate,C6H13O9P,O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O,GSXOAOHZAIYLCY-HSUXUTPPSA-N,CID:69507,pubchem
+"Fructose-1,6-bisphosphate",C6H13O12P,O=P(O)(O)OC[C@H]1O[C@](O)(COP(=O)(O)O)[C@@H](O)[C@@H]1O,RNBGYGVWRKECFJ-ARQDHWQXSA-N,CID:10267,pubchem
+Glyceraldehyde-3-phosphate,C3H7O6P,O=C[C@H](O)COP(=O)(O)O,LXJXRIRHZLFYRP-VKHMYHEASA-N,CID:439168,pubchem
+Dihydroxyacetone phosphate,C3H7O6P,O=C(CO)COP(=O)(O)O,GNGACRATGGDKBX-UHFFFAOYSA-N,CID:668,pubchem
+3-Phosphoglycerate,C3H7O7P,O=C(O)C(O)COP(=O)(O)O,OSJPPGNTCRNQQC-UHFFFAOYSA-N,CID:724,pubchem
+2-Phosphoglycerate,C3H7O7P,O=C(O)C(CO)OP(=O)(O)O,GXIURPTVHJPJLF-UHFFFAOYSA-N,CID:59,pubchem
+Phosphoenolpyruvate,C3H5O6P,C=C(OP(=O)(O)O)C(=O)O,DTBNBXWJWCWCIK-UHFFFAOYSA-N,CID:1005,pubchem
+Pyruvate,C3H6O,CC(=O)C(=O)O,LCTONWCANYUPML-UHFFFAOYSA-M,CID:107735,pubchem
+Lactate,C3H8O,CC(O)C(=O)O,JVTAAEKCZFNVCJ-UHFFFAOYSA-M,CID:91435,pubchem
+Acetyl-CoA,C23H38N7O17P3S,CC(=O)SCCN=C(O)CCN=C(O)[C@H](O)C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)(O)O,ZSLZBFCDCINBPY-ZSJPKINUSA-N,CID:444493,pubchem
+Citric acid,C6H7O,O=C(O)CC(O)(CC(=O)O)C(=O)O,KRKNYBCHXYNGOX-UHFFFAOYSA-N,CID:311,pubchem
+Isocitrate,C6H7O,O=C(O)CC(C(=O)O)C(O)C(=O)O,ODBLHEXUDAPZAU-UHFFFAOYSA-N,CID:1198,pubchem
+Alpha-ketoglutaric acid,C5H5O,O=C(O)CCC(=O)C(=O)O,KPGXRSRHYNQIFN-UHFFFAOYSA-N,CID:51,pubchem
+Succinyl-CoA,C25H40N7O19P3S,CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)(O)O)[C@@H](O)C(O)=NCCC(O)=NCCSC(=O)CCC(=O)O,VNOYUJKHFWYWIR-ITIYDSSPSA-N,CID:92133,pubchem
+Succinic acid,C4H5O,O=C(O)CCC(=O)O,KDYFGRWQOYBRFD-UHFFFAOYSA-N,CID:1110,pubchem
+Fumaric acid,C4H3O,O=C(O)/C=C/C(=O)O,VZCYOOQTPOCHFL-OWOJBTEDSA-N,CID:444972,pubchem
+Malic acid,C4H5O,O=C(O)CC(O)C(=O)O,BJEPYKJPYRNKOW-UHFFFAOYSA-N,CID:525,pubchem
+Oxaloacetic acid,C4H3O,O=C(O)CC(=O)C(=O)O,KHPXUQMNIQBQEV-UHFFFAOYSA-N,CID:970,pubchem
+Ribose-5-phosphate,C5H11O8P,O=C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O,PPQRONHOSHZGFQ-LMVFSUKVSA-N,CID:77982,pubchem
+Ribulose-5-phosphate,C5H11O8P,O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O,FNZLKVNUWIIPSJ-UHNVWZDZSA-N,CID:439184,pubchem
+Sedoheptulose-7-phosphate,C7H15O10P,O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O,JDTUMPKOJBQPKX-GBNDHIKLSA-N,CID:165007,pubchem
+Erythrose-4-phosphate,C4H9O7P,O=C[C@H](O)[C@H](O)COP(=O)(O)O,NGHMDNPXVRFFGS-IUYQGCFVSA-N,CID:122357,pubchem
+"Sedoheptulose-1,7-bisphosphate",C7H15O13P,O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O,OKHXOUGRECCASI-SHUUEZRQSA-N,CID:164735,pubchem
+Glycerol-3-phosphate,C3H9O6P,O=P(O)(O)OCC(O)CO,AWUCVROLDVIAJX-UHFFFAOYSA-N,CID:754,pubchem
+Glycerate,C3H9O,O=C(O)C(O)CO,RBNPOMFGQQGHHO-UHFFFAOYSA-M,CID:4643312,pubchem
+Pentose,C5H9O,OC1COC(O)C(O)C1O,SRBFZHDQGSBBOR-UHFFFAOYSA-N,CID:229,pubchem
+Acetaldehyde,C2H4O,CC=O,IKHGUXGNUITLKF-UHFFFAOYSA-N,CID:177,pubchem
+Acetic acid,C2H3O,CC(=O)O,QTBSBXVTEAMEQO-UHFFFAOYSA-N,CID:176,pubchem
+Alanine,C3H6NO,C[C@H](N)C(=O)O,QNAYBMKLOCPYGJ-REOHCLBHSA-N,CID:5950,pubchem
+Arginine,C6H13N4O,N=C(N)NCCC[C@H](N)C(=O)O,ODKSFYDXXFIFQN-BYPYZUCNSA-N,CID:6322,pubchem
+Asparagine,C4H7N2O,N=C(O)C[C@H](N)C(=O)O,DCXYFEDJOCDNAF-REOHCLBHSA-N,CID:6267,pubchem
+Aspartic acid,C4H6NO,N[C@@H](CC(=O)O)C(=O)O,CKLJMWTZIZZHCS-REOHCLBHSA-N,CID:5960,pubchem
+Cysteine,C3H7NO2S,N[C@@H](CS)C(=O)O,XUJNEKJLAYXESH-REOHCLBHSA-N,CID:5862,pubchem
+Glutamic acid,C5H8NO,N[C@@H](CCC(=O)O)C(=O)O,WHUUTDBJXJRKMK-VKHMYHEASA-N,CID:33032,pubchem
+Glutamine,C5H9N2O,N=C(O)CC[C@H](N)C(=O)O,ZDXPYRJPNDTMRX-VKHMYHEASA-N,CID:5961,pubchem
+Glycine,C2H4NO,NCC(=O)O,DHMQDGOQFOQNFH-UHFFFAOYSA-N,CID:750,pubchem
+Histidine,C6H8N3O,N[C@@H](Cc1cnc[nH]1)C(=O)O,HNDVDQJCIGZPNO-YFKPBYRVSA-N,CID:6274,pubchem
+Isoleucine,C6H12NO,CC[C@H](C)[C@H](N)C(=O)O,AGPKZVBTJJNPAG-WHFBIAKZSA-N,CID:6306,pubchem
+Leucine,C6H12NO,CC(C)C[C@H](N)C(=O)O,ROHFNLRQFUQHCH-YFKPBYRVSA-N,CID:6106,pubchem
+Lysine,C6H13N2O,NCCCC[C@H](N)C(=O)O,KDXKERNSBIXSRK-YFKPBYRVSA-N,CID:5962,pubchem
+Methionine,C5H11NO2S,CSCC[C@H](N)C(=O)O,FFEARJCKVFRZRR-BYPYZUCNSA-N,CID:6137,pubchem
+Phenylalanine,C9H10NO,N[C@@H](Cc1ccccc1)C(=O)O,COLNVLDHVKWLRT-QMMMGPOBSA-N,CID:6140,pubchem
+Proline,C5H8NO,O=C(O)[C@@H]1CCCN1,ONIBWKKTOPOVIA-BYPYZUCNSA-N,CID:145742,pubchem
+Serine,C3H6NO,N[C@@H](CO)C(=O)O,MTCFGRXMJLQNBG-REOHCLBHSA-N,CID:5951,pubchem
+Threonine,C4H8NO,C[C@@H](O)[C@H](N)C(=O)O,AYFVYJQAPQTCCC-GBXIJSLDSA-N,CID:6288,pubchem
+Tryptophan,C11H11N2O,N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O,QIVBCDIJIAJPQS-VIFPVBQESA-N,CID:6305,pubchem
+Tyrosine,C9H10NO,N[C@@H](Cc1ccc(O)cc1)C(=O)O,OUYCCCASQSFEME-QMMMGPOBSA-N,CID:6057,pubchem
+Valine,C5H10NO,CC(C)[C@H](N)C(=O)O,KZSNJWFQEVHDMF-BYPYZUCNSA-N,CID:6287,pubchem
+Ornithine,C5H11N2O,NCCC[C@H](N)C(=O)O,AHLPHDHHMVZTML-BYPYZUCNSA-N,CID:6262,pubchem
+Citrulline,C6H12N3O,N=C(O)NCCC[C@H](N)C(=O)O,RHGKLRLOHDJJDR-BYPYZUCNSA-N,CID:9750,pubchem
+Homocysteine,C4H9NO2S,N[C@@H](CCS)C(=O)O,FFFHZYDWPBMWHY-VKHMYHEASA-N,CID:91552,pubchem
+S-adenosylmethionine,C15H22N6O5S,C[S](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O,MEFKEPWMEQBLKI-AIRLBKTGSA-N,CID:34755,pubchem
+S-adenosylhomocysteine,C14H20N6O5S,Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)[C@@H](O)[C@H]1O,ZJUKTBDSGOFHSH-WFMPWKQPSA-N,CID:439155,pubchem
+Formic acid,CHO,O=CO,BDAGIHXWWSANSR-UHFFFAOYSA-N,CID:284,pubchem
+Propionic acid,C3H5O,CCC(=O)O,XBDQKXXYIPTUBI-UHFFFAOYSA-N,CID:1032,pubchem
+Butyric acid,C4H7O,CCCC(=O)O,FERIUCNNQQJTOY-UHFFFAOYSA-N,CID:264,pubchem
+Malonic acid,C3H3O,O=C(O)CC(=O)O,OFOBLEOULBTSOW-UHFFFAOYSA-N,CID:867,pubchem
+2-Hydroxyglutarate,C5H7O,O=C(O)CCC(O)C(=O)O,HWXBTNAVRSUOJR-UHFFFAOYSA-N,CID:43,pubchem
+3-Hydroxybutyrate,C4H10O,CC(O)CC(=O)O,WHBMMWSBFZVSSR-UHFFFAOYSA-M,CID:3541112,pubchem
+Acetoacetate,C4H8O,CC(=O)CC(=O)O,WDJHALXBUFZDSR-UHFFFAOYSA-M,CID:6971017,pubchem
+Beta-hydroxybutyrate,C4H7O,CC(O)CC(=O)O,WHBMMWSBFZVSSR-UHFFFAOYSA-N,CID:441,pubchem
+Pyruvic acid,C3H3O,CC(=O)C(=O)O,LCTONWCANYUPML-UHFFFAOYSA-N,CID:1060,pubchem
+Lactic acid,C3H5O,CC(O)C(=O)O,JVTAAEKCZFNVCJ-UHFFFAOYSA-N,CID:612,pubchem
+Myristic acid,C14H27O,CCCCCCCCCCCCCC(=O)O,TUNFSRHWOTWDNC-UHFFFAOYSA-N,CID:11005,pubchem
+Palmitic acid,C16H31O,CCCCCCCCCCCCCCCC(=O)O,IPCSVZSSVZVIGE-UHFFFAOYSA-N,CID:985,pubchem
+Stearic acid,C18H35O,CCCCCCCCCCCCCCCCCC(=O)O,QIQXTHQIDYTFRH-UHFFFAOYSA-N,CID:5281,pubchem
+Palmitoleic acid,C16H29O,CCCCCC/C=C\CCCCCCCC(=O)O,SECPZKHBENQXJG-FPLPWBNLSA-N,CID:445638,pubchem
+Oleic acid,C18H33O,CCCCCCCC/C=C\CCCCCCCC(=O)O,ZQPPMHVWECSIRJ-KTKRTIGZSA-N,CID:445639,pubchem
+Linoleic acid,C18H31O,CCCCC/C=C\C/C=C\CCCCCCCC(=O)O,OYHQOLUKZRVURQ-HZJYTTRNSA-N,CID:5280450,pubchem
+Alpha-linolenic acid,C18H29O,CC/C=C\C/C=C\C/C=C\CCCCCCCC(=O)O,DTOSIQBPPRVQHS-PDBXOOCHSA-N,CID:5280934,pubchem
+Arachidonic acid,C20H31O,CCCCC/C=C\C/C=C\C/C=C\C/C=C\CCCC(=O)O,YZXBAPSDXZZRGB-DOFZRALJSA-N,CID:444899,pubchem
+Adenine,C5H4N,Nc1nc[nH]c2ncnc1-2,GFFGJBXGBJISGV-UHFFFAOYSA-N,CID:190,pubchem
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+Cytosine,C4H5N3O,N=c1ccnc(O)[nH]1,OPTASPLRGRRNAP-UHFFFAOYSA-N,CID:597,pubchem
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