Renamed root package for consistency

README.md

@@ -23,11 +23,6 @@ For development, run:
 pip install --editable .
 ```
 
-Or from the root of this repository:
-```sh
-pip install --editable implementations/python
-```
-
 Test with
 ```
 pytest

bench/nist_msp_ftp_test.py

@@ -5,8 +5,8 @@
 
 from urllib.request import urlopen
 
-from mzlib.backends import msp
-from mzlib import annotation
+from mzspeclib.backends import msp
+from mzspeclib import annotation
 
 
 urls = [

examples/draw_entry.py

@@ -4,8 +4,8 @@
 
 from matplotlib import pyplot as plt
 
-from mzlib.spectrum_library import SpectrumLibrary
-from mzlib.draw import draw_spectrum
+from mzspeclib.spectrum_library import SpectrumLibrary
+from mzspeclib.draw import draw_spectrum
 
 
 def main(path, spectrum_key):

examples/first_n_entries.py

@@ -1,10 +1,10 @@
 import click
 
-from mzlib import SpectrumLibrary
-from mzlib.backends import SpectralLibraryBackendBase, FormatInferenceFailure, TextSpectralLibraryWriter
-from mzlib.cluster import SpectrumCluster
-from mzlib.index import MemoryIndex, SQLIndex
-from mzlib.spectrum import Spectrum
+from mzspeclib import SpectrumLibrary
+from mzspeclib.backends import SpectralLibraryBackendBase, FormatInferenceFailure, TextSpectralLibraryWriter
+from mzspeclib.cluster import SpectrumCluster
+from mzspeclib.index import MemoryIndex, SQLIndex
+from mzspeclib.spectrum import Spectrum
 
 @click.command('first_n_entries')
 @click.argument('inpath', type=click.Path(exists=True))

makefile

@@ -1,5 +1,5 @@
 test:
-	pytest -r a -v tests --cov mzlib --cov-report=html --cov-report term
+	pytest -r a -v tests --cov mzspeclib --cov-report=html --cov-report term
 
 retest:
 	py.test -v tests --lf --pdb

mzspeclib/__init__.py

@@ -0,0 +1,11 @@
+"""HUPO-PSI Spectral library format."""
+
+from mzspeclib.spectrum import Spectrum
+from mzspeclib.analyte import Analyte, Interpretation
+
+from mzspeclib.index import MemoryIndex, SQLIndex
+
+from mzspeclib.spectrum_library import SpectrumLibrary
+from mzspeclib.spectrum_library_index import SpectrumLibraryIndex
+from mzspeclib.spectrum_library_collection import SpectrumLibraryCollection
+from mzspeclib.universal_spectrum_identifier import UniversalSpectrumIdentifier

mzlib/analyte.py → mzspeclib/analyte.py

@@ -4,7 +4,7 @@
 
 from pyteomics import proforma
 
-from mzlib.attributes import AttributedEntity, IdentifiedAttributeManager, AttributeManagedProperty, AttributeProxy, AttributeGroupFacet
+from mzspeclib.attributes import AttributedEntity, IdentifiedAttributeManager, AttributeManagedProperty, AttributeProxy, AttributeGroupFacet
 
 
 FIRST_ANALYTE_KEY = '1'

mzlib/backends/base.py → mzspeclib/backends/base.py

@@ -12,13 +12,13 @@
 from psims.controlled_vocabulary import Entity
 from psims.controlled_vocabulary.controlled_vocabulary import (
     load_uo, load_unimod, load_psims)
-from mzlib.cluster import SpectrumCluster
+from mzspeclib.cluster import SpectrumCluster
 
-from mzlib.index import MemoryIndex, SQLIndex, IndexBase
-from mzlib.spectrum import LIBRARY_SPECTRUM_INDEX, LIBRARY_SPECTRUM_KEY, Spectrum
-from mzlib.analyte import Analyte, Interpretation, InterpretationMember, ANALYTE_MIXTURE_TERM
-from mzlib.attributes import Attributed, AttributedEntity, AttributeSet, AttributeManagedProperty
-from mzlib.ontology import _VocabularyResolverMixin
+from mzspeclib.index import MemoryIndex, SQLIndex, IndexBase
+from mzspeclib.spectrum import LIBRARY_SPECTRUM_INDEX, LIBRARY_SPECTRUM_KEY, Spectrum
+from mzspeclib.analyte import Analyte, Interpretation, InterpretationMember, ANALYTE_MIXTURE_TERM
+from mzspeclib.attributes import Attributed, AttributedEntity, AttributeSet, AttributeManagedProperty
+from mzspeclib.ontology import _VocabularyResolverMixin
 
 from .utils import open_stream, _LineBuffer
 

mzlib/backends/bibliospec.py → mzspeclib/backends/bibliospec.py

@@ -13,14 +13,14 @@
 
 from pyteomics import proforma
 
-from mzlib import annotation
-from mzlib.analyte import FIRST_ANALYTE_KEY, FIRST_INTERPRETATION_KEY, Analyte
-from mzlib.spectrum import Spectrum, SPECTRUM_NAME, CHARGE_STATE
-from mzlib.attributes import AttributeManager, Attributed
+from mzspeclib import annotation
+from mzspeclib.analyte import FIRST_ANALYTE_KEY, FIRST_INTERPRETATION_KEY, Analyte
+from mzspeclib.spectrum import Spectrum, SPECTRUM_NAME, CHARGE_STATE
+from mzspeclib.attributes import AttributeManager, Attributed
 
-from mzlib.backends.base import SpectralLibraryBackendBase, FORMAT_VERSION_TERM, DEFAULT_VERSION
+from mzspeclib.backends.base import SpectralLibraryBackendBase, FORMAT_VERSION_TERM, DEFAULT_VERSION
 
-from mzlib.index.base import IndexBase
+from mzspeclib.index.base import IndexBase
 
 
 class BibliospecBase:

mzlib/backends/diann.py → mzspeclib/backends/diann.py

@@ -10,10 +10,10 @@
 
 from pyteomics import proforma
 
-from mzlib import annotation
-from mzlib.backends.base import DEFAULT_VERSION, FORMAT_VERSION_TERM, LIBRARY_NAME_TERM, _CSVSpectralLibraryBackendBase
-from mzlib.backends.utils import open_stream, urlify
-from mzlib.spectrum import Spectrum, SPECTRUM_NAME
+from mzspeclib import annotation
+from mzspeclib.backends.base import DEFAULT_VERSION, FORMAT_VERSION_TERM, LIBRARY_NAME_TERM, _CSVSpectralLibraryBackendBase
+from mzspeclib.backends.utils import open_stream, urlify
+from mzspeclib.spectrum import Spectrum, SPECTRUM_NAME
 
 
 def _rewrite_unimod_peptide_as_proforma(sequence: str) -> str:

mzlib/backends/encyclopedia.py → mzspeclib/backends/encyclopedia.py

@@ -13,14 +13,14 @@
 
 from pyteomics import proforma
 
-from mzlib import annotation
-from mzlib.analyte import FIRST_ANALYTE_KEY, FIRST_INTERPRETATION_KEY, Analyte, ProteinDescription
-from mzlib.spectrum import Spectrum, SPECTRUM_NAME, CHARGE_STATE
-from mzlib.attributes import AttributeManager, Attributed, Attribute
+from mzspeclib import annotation
+from mzspeclib.analyte import FIRST_ANALYTE_KEY, FIRST_INTERPRETATION_KEY, Analyte, ProteinDescription
+from mzspeclib.spectrum import Spectrum, SPECTRUM_NAME, CHARGE_STATE
+from mzspeclib.attributes import AttributeManager, Attributed, Attribute
 
-from mzlib.backends.base import SpectralLibraryBackendBase, FORMAT_VERSION_TERM, DEFAULT_VERSION
+from mzspeclib.backends.base import SpectralLibraryBackendBase, FORMAT_VERSION_TERM, DEFAULT_VERSION
 
-from mzlib.index.base import IndexBase
+from mzspeclib.index.base import IndexBase
 
 
 DECOY_SPECTRUM = "MS:1003192|decoy spectrum"

mzlib/backends/json.py → mzspeclib/backends/json.py

@@ -7,13 +7,13 @@
 from typing import Any, Iterable, List, Dict, Mapping, Union
 
 from pathlib import Path
-from mzlib.cluster import SpectrumCluster
+from mzspeclib.cluster import SpectrumCluster
 
-from mzlib.index import MemoryIndex
-from mzlib.attributes import AttributeManager, Attributed, AttributeSet
-from mzlib.annotation import parse_annotation, IonAnnotationBase
-from mzlib.analyte import Analyte, Interpretation, FIRST_INTERPRETATION_KEY
-from mzlib.spectrum import Spectrum
+from mzspeclib.index import MemoryIndex
+from mzspeclib.attributes import AttributeManager, Attributed, AttributeSet
+from mzspeclib.annotation import parse_annotation, IonAnnotationBase
+from mzspeclib.analyte import Analyte, Interpretation, FIRST_INTERPRETATION_KEY
+from mzspeclib.spectrum import Spectrum
 
 from .base import SpectralLibraryBackendBase, SpectralLibraryWriterBase, FORMAT_VERSION_TERM, AttributeSetTypes
 from .utils import open_stream