renamed module to simplify rebase

imspy/imspy/data/__init__.py

@@ -0,0 +1,4 @@
+from imspy.data.frame import TimsFrame
+from imspy.data.spectrum import TimsSpectrum, MzSpectrum
+from imspy.data.handle import TimsDataset, TimsDatasetDDA, TimsDatasetDIA
+from imspy.data.slice import TimsSlice

pyims/pyims/data/frame.py → imspy/imspy/data/frame.py

@@ -6,10 +6,10 @@
 from tensorflow import sparse as sp
 
 import numpy as np
-import pyims_connector as pims
-from pyims.data.spectrum import MzSpectrum, TimsSpectrum
+import imspy_connector as pims
+from imspy.data.spectrum import MzSpectrum, TimsSpectrum
 
-from pyims.utilities import re_index_indices
+from imspy.utilities import re_index_indices
 
 
 class TimsFrame:

pyims/pyims/data/handle.py → imspy/imspy/data/handle.py

@@ -5,13 +5,13 @@
 import sqlite3
 from numpy.typing import NDArray
 
-import pyims_connector as pims
+import imspy_connector as pims
 import opentims_bruker_bridge as obb
 
 from abc import ABC
 
-from pyims.data.frame import TimsFrame
-from pyims.data.slice import TimsSlice
+from imspy.data.frame import TimsFrame
+from imspy.data.slice import TimsSlice
 
 
 

pyims/pyims/data/slice.py → imspy/imspy/data/slice.py

@@ -4,11 +4,11 @@
 
 from tensorflow import sparse as sp
 
-from pyims.utilities import re_index_indices
+from imspy.utilities import re_index_indices
 
-import pyims_connector as pims
-from pyims.data.frame import TimsFrame, TimsFrameVectorized
-from pyims.data.spectrum import MzSpectrum
+import imspy_connector as pims
+from imspy.data.frame import TimsFrame, TimsFrameVectorized
+from imspy.data.spectrum import MzSpectrum
 
 
 class TimsSlice:

pyims/pyims/data/spectrum.py → imspy/imspy/data/spectrum.py

@@ -5,7 +5,7 @@
 import pandas as pd
 from numpy.typing import NDArray
 
-import pyims_connector as pims
+import imspy_connector as pims
 
 
 class MzSpectrum:

pyims/pyims/feature.py → imspy/imspy/feature.py

@@ -4,9 +4,9 @@
 
 import json
 
-from pyims.data import TimsSlice, TimsFrame
-from pyims.utility import gaussian, exp_gaussian
-from pyims.isotopes import IsotopePatternGenerator, create_initial_feature_distribution
+from imspy.data import TimsSlice, TimsFrame
+from imspy.utility import gaussian, exp_gaussian
+from imspy.isotopes import IsotopePatternGenerator, create_initial_feature_distribution
 from abc import ABC, abstractmethod
 from typing import Optional, Dict
 class Profile:

pyims/pyims/isotopes.py → imspy/imspy/isotopes.py

@@ -6,12 +6,12 @@
 from abc import ABC, abstractmethod
 
 from scipy.signal import argrelextrema
-from pyims.data import MzSpectrum
-from pyims.utility import gaussian, exp_gaussian, normal_pdf
+from imspy.data import MzSpectrum
+from imspy.utility import gaussian, exp_gaussian, normal_pdf
 import numba
 import pyopenms
 
-from pyims.noise import detection_noise
+from imspy.noise import detection_noise
 
 MASS_PROTON = 1.007276466621
 MASS_NEUTRON = 1.00866491595

pyims/pyims/noise.py → imspy/imspy/noise.py

@@ -5,8 +5,8 @@
 import numba
 from typing import Callable, Optional, Tuple
 from numpy.typing import ArrayLike
-from pyims.data import MzSpectrum
-from pyims.utility import normal_pdf
+from imspy.data import MzSpectrum
+from imspy.utility import normal_pdf
 
 @numba.jit(nopython=True)
 def mu_function_normal_default(intensity: ArrayLike) -> ArrayLike:

pyims/pyims/proteome.py → imspy/imspy/proteome.py

@@ -5,11 +5,11 @@
 from numpy.typing import ArrayLike
 import pandas as pd
 import sqlite3
-from pyims.data import MzSpectrum
-from pyims.chemistry import get_mono_isotopic_weight, MASS_PROTON
+from imspy.data import MzSpectrum
+from imspy.chemistry import get_mono_isotopic_weight, MASS_PROTON
 
-from pyims.feature import RTProfile, ScanProfile, ChargeProfile
-from pyims.utility import tokenize_proforma_sequence, TokenSequence, get_aa_num_proforma_sequence
+from imspy.feature import RTProfile, ScanProfile, ChargeProfile
+from imspy.utility import tokenize_proforma_sequence, TokenSequence, get_aa_num_proforma_sequence
 from enum import Enum
 from abc import ABC, abstractmethod
 

pyims/pyims/simulation/experiment.py → imspy/imspy/simulation/experiment.py

@@ -8,10 +8,10 @@
 import pyarrow as pa
 import pyarrow.parquet as pq
 from tqdm import tqdm
-from pyims.data import MzSpectrum, TimsFrame
-from pyims.proteome import PeptideDigest, ProteomicsExperimentSampleSlice, ProteomicsExperimentDatabaseHandle
-from pyims.isotopes import AveragineGenerator
-import pyims.simulation.hardware_models as hardware
+from imspy.data import MzSpectrum, TimsFrame
+from imspy.proteome import PeptideDigest, ProteomicsExperimentSampleSlice, ProteomicsExperimentDatabaseHandle
+from imspy.isotopes import AveragineGenerator
+import imspy.simulation.hardware_models as hardware
 
 class ProteomicsExperiment(ABC):
     def __init__(self, path: str):

pyims/pyims/simulation/hardware_models.py → imspy/imspy/simulation/hardware_models.py

@@ -9,11 +9,11 @@
 import pandas as pd
 from scipy.stats import exponnorm, norm, binom, gamma
 
-from pyims.chemistry import  STANDARD_TEMPERATURE, STANDARD_PRESSURE, CCS_K0_CONVERSION_CONSTANT, BufferGas, get_num_protonizable_sites
-from pyims.proteome import ProteomicsExperimentSampleSlice
-from pyims.feature import RTProfile, ScanProfile, ChargeProfile
-from pyims.isotopes import AveragineGenerator
-from pyims.utility import tokenizer_from_json
+from imspy.chemistry import  STANDARD_TEMPERATURE, STANDARD_PRESSURE, CCS_K0_CONVERSION_CONSTANT, BufferGas, get_num_protonizable_sites
+from imspy.proteome import ProteomicsExperimentSampleSlice
+from imspy.feature import RTProfile, ScanProfile, ChargeProfile
+from imspy.isotopes import AveragineGenerator
+from imspy.utility import tokenizer_from_json
 
 class Device(ABC):
     def __init__(self, name:str):

pyims/pyims/utility.py → imspy/imspy/utility.py

@@ -10,8 +10,8 @@
 import pandas as pd
 
 from tqdm import tqdm
-from pyims.data import MzSpectrum
-# TODO bring to pyims
+from imspy.data import MzSpectrum
+# TODO bring to imspy
 #from proteolizardalgo.hashing import ReferencePattern
 
 

pyims/pyproject.toml → imspy/pyproject.toml

@@ -1,5 +1,5 @@
 [tool.poetry]
-name = "pyims"
+name = "imspy"
 version = "0.1.0"
 description = ""
 authors = ["theGreatHerrLebert <davidteschner@googlemail.com>"]

pyims_connector/Cargo.toml

@@ -1,11 +1,11 @@
 [package]
-name = "pyims_connector"
+name = "imspy_connector"
 version = "0.1.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
-name = "pyims_connector"
+name = "imspy_connector"
 crate-type = ["cdylib"]
 
 [dependencies]

pyims_connector/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["maturin>=1.2,<2.0"]
 build-backend = "maturin"
 
 [project]
-name = "pyims_connector"
+name = "imspy_connector"
 dependencies = [
     "opentims-bruker-bridge>=1.1.0",
 ]

pyims_connector/src/lib.rs

@@ -10,7 +10,7 @@ use crate::py_tims_frame::{PyTimsFrame, PyTimsFrameVectorized};
 use crate::py_tims_slice::{PyTimsPlane, PyTimsSlice, PyTimsSliceVectorized};
 
 #[pymodule]
-fn pyims_connector(_py: Python, m: &PyModule) -> PyResult<()> {
+fn imspy_connector(_py: Python, m: &PyModule) -> PyResult<()> {
     m.add_class::<PyTimsDataHandle>()?;
     m.add_class::<PyMzSpectrum>()?;
     m.add_class::<PyMzSpectrumVectorized>()?;