ruff auto fix

Author: Jhsmit

pyhdx/fileIO.py

@@ -24,7 +24,6 @@
 
 import narwhals as nw
 import pyhdx
-from pyhdx.datasets import adapt_for_pyhdx
 
 if TYPE_CHECKING:
     from pyhdx.fitting_torch import TorchFitResult, TorchFitResultSet

pyhdx/models.py

@@ -21,7 +21,7 @@
 from pyhdx.alignment import align_dataframes
 from pyhdx.config import cfg
 from pyhdx.fileIO import dataframe_to_file
-from pyhdx.process import apply_control, correct_d_uptake, parse_temperature, verify_sequence
+from pyhdx.process import correct_d_uptake, parse_temperature, verify_sequence
 from pyhdx.support import dataframe_intersection, reduce_inter
 from pyhdx.datasets import (
     adapt_for_pyhdx,
@@ -31,7 +31,6 @@
     peptides_kwargs,
 )
 from hdxms_datasets.process import merge_peptide_tables, compute_uptake_metrics
-from hdxms_datasets.utils import get_peptides_by_type
 
 
 class Coverage:

pyhdx/web/controller_only.py

@@ -3,10 +3,8 @@
 # %autoreload 2
 
 # %%
-from pyhdx.web.apps import main_app
 from pyhdx.web.controllers import PeptideFileInputControl
-from pyhdx.web.main_controllers import MainController, PyHDXController
-import panel as pn
+from pyhdx.web.main_controllers import PyHDXController
 import logging
 import sys
 

pyhdx/web/controllers.py

@@ -8,7 +8,6 @@
 from dataclasses import dataclass
 from io import BytesIO, StringIO
 from pathlib import Path
-from typing import Any
 
 import colorcet
 import matplotlib
@@ -20,7 +19,7 @@
 import panel as pn
 import param
 from distributed import Client
-from hdxms_datasets import HDXDataSet, apply_filters, compute_uptake_metrics, load_dataset
+from hdxms_datasets import apply_filters, compute_uptake_metrics, load_dataset
 from hdxms_datasets.database import DataBase
 from hdxms_datasets.process import merge_peptide_tables
 from hdxms_datasets.convert import cast_exposure

templates/02_load_from_dataset.py

@@ -6,6 +6,7 @@
 
 from hdxms_datasets import load_dataset
 
+from pyhdx.fitting import fit_d_uptake
 from pyhdx.models import HDXMeasurement, HDXMeasurementSet
 
 # %%
@@ -20,17 +21,30 @@
 dataset.states
 
 
-zip_pth = Path(r"C:\Users\jhsmi\repos\mine\hdxms-datasets\tests\datasets\HDX_3BAE2080.zip")
-dataset = load_dataset(zip_pth)
-dataset
+# %%
+
+# zip_pth = Path(r"C:\Users\jhsmi\repos\mine\hdxms-datasets\tests\datasets\HDX_3BAE2080.zip")
+# dataset = load_dataset(zip_pth)
+# dataset
 
 # %%
 # Load an HDX measurement by state name
 hdxm = HDXMeasurement.from_dataset(dataset.get_state(0))
+hdxm = HDXMeasurement.from_dataset(dataset.get_state("Tetramer"), d_percentage=100.0, drop_first=1)
 print(hdxm)
 print(hdxm.timepoints)
 
 
+# %%
+
+fr = fit_d_uptake(hdxm, r1=0.5, repeats=3, verbose=False)
+fr.output
+
+# %%
+from pyhdx.fileIO import dataframe_to_file
+
+dataframe_to_file(output_dir / "hdxm_data.csv", fr.output)
+
 # %%
 # Load an HDX measurement set from all states in the dataset
 hdxm_set = HDXMeasurementSet.from_dataset(dataset.states)

tests/generate_test_fit_results.py

@@ -21,7 +21,8 @@
     fit_d_uptake,
 )
 from pyhdx.models import HDXMeasurementSet
-from pyhdx.process import apply_control, correct_d_uptake, filter_peptides
+from pyhdx.process import apply_control, correct_d_uptake
+from pyhdx.legacy import filter_peptides
 
 """Run this file to renew the fit results which is used to test against"""
 
@@ -81,8 +82,8 @@
     guess_output = csv_to_dataframe(output_dir / "ecSecB_guess.csv")
 
 # Export protein sequence and intrinsic rate of exchange
-hdxm_apo.coverage.protein.to_file(output_dir / "ecSecB_info.csv")
-hdxm_apo.coverage.protein.to_file(output_dir / "ecSecB_info.txt", fmt="pprint")
+dataframe_to_file(output_dir / "ecSecB_info.csv", hdxm_apo.coverage.protein)
+dataframe_to_file(output_dir / "ecSecB_info.txt", hdxm_apo.coverage.protein, fmt="pprint")
 
 # Save RFU values
 rfu_df = hdxm_apo.rfu_residues

tests/test_fileIO.py

@@ -16,7 +16,6 @@
 
 from pyhdx.models import HDXMeasurement, HDXMeasurementSet
 from pyhdx.fitting import fit_gibbs_global
-from hdxms_datasets.formats import identify_format
 from pyhdx.process import apply_control, correct_d_uptake
 from pyhdx.legacy import filter_peptides
 from pyhdx.fileIO import read_dynamx

tests/test_fitting.py

@@ -5,7 +5,6 @@
 import pandas as pd
 import pytest
 import torch
-import yaml
 from hdxms_datasets import HDXDataSet, load_dataset
 from pandas.testing import assert_frame_equal, assert_series_equal