From a12aaaa4f59affb9619e0c2034b4eb3f66e1973b Mon Sep 17 00:00:00 2001
From: Jochem Smit <jhsmit@gmail.com>
Date: Tue, 8 Aug 2023 15:58:40 +0200
Subject: [PATCH] cleaning

---
 examples/load_from_yaml.py  | 10 +++-------
 hdxms_datasets/__init__.py  |  7 ++++++-
 hdxms_datasets/datasets.py  |  4 +++-
 hdxms_datasets/datavault.py |  2 +-
 hdxms_datasets/process.py   |  5 +----
 5 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/examples/load_from_yaml.py b/examples/load_from_yaml.py
index 909e25b..ecfeed0 100644
--- a/examples/load_from_yaml.py
+++ b/examples/load_from_yaml.py
@@ -6,17 +6,13 @@
 
 test_pth = Path("../tests").resolve()
 data_pth = test_pth / "datasets"
-data_id = '20221007_1530_SecA_Krishnamurthy'
+data_id = "20221007_1530_SecA_Krishnamurthy"
 
 hdx_spec = yaml.safe_load((data_pth / data_id / "hdx_spec.yaml").read_text())
 metadata = yaml.safe_load((data_pth / data_id / "metadata.yaml").read_text())
 
 #%%
 
-dataset = HDXDataSet.from_spec(
-    hdx_spec,
-    data_dir=data_pth / data_id,
-    metadata=metadata
-)
+dataset = HDXDataSet.from_spec(hdx_spec, data_dir=data_pth / data_id, metadata=metadata)
 
-print(dataset.describe())
\ No newline at end of file
+print(dataset.describe())
diff --git a/hdxms_datasets/__init__.py b/hdxms_datasets/__init__.py
index d998233..cdc14a4 100644
--- a/hdxms_datasets/__init__.py
+++ b/hdxms_datasets/__init__.py
@@ -4,5 +4,10 @@
 from hdxms_datasets.config import cfg
 from hdxms_datasets.datasets import HDXDataSet, DataFile
 from hdxms_datasets.datavault import DataVault
-from hdxms_datasets.process import convert_temperature, convert_time, filter_peptides, parse_data_files
+from hdxms_datasets.process import (
+    convert_temperature,
+    convert_time,
+    filter_peptides,
+    parse_data_files,
+)
 from hdxms_datasets.reader import read_dynamx
diff --git a/hdxms_datasets/datasets.py b/hdxms_datasets/datasets.py
index cf72f65..8d4605a 100644
--- a/hdxms_datasets/datasets.py
+++ b/hdxms_datasets/datasets.py
@@ -57,7 +57,9 @@ class HDXDataSet(object):
     _cache: dict[tuple[str, str], pd.DataFrame] = field(init=False, default_factory=dict)
 
     @classmethod
-    def from_spec(cls, hdx_spec: dict, data_dir: Path, data_id = Optional[str], metadata: Optional[dict] = None):
+    def from_spec(
+        cls, hdx_spec: dict, data_dir: Path, data_id=Optional[str], metadata: Optional[dict] = None
+    ):
         metadata = metadata or {}
         data_id = data_id or uuid.uuid4().hex
         data_files = parse_data_files(hdx_spec["data_files"], data_dir)
diff --git a/hdxms_datasets/datavault.py b/hdxms_datasets/datavault.py
index b7f0693..a24b739 100644
--- a/hdxms_datasets/datavault.py
+++ b/hdxms_datasets/datavault.py
@@ -146,5 +146,5 @@ def load_dataset(self, data_id: str) -> HDXDataSet:
             hdx_spec=hdx_spec,
             data_dir=self.cache_dir / data_id,
             data_id=data_id,
-            metadata=dataset_metadata
+            metadata=dataset_metadata,
         )
diff --git a/hdxms_datasets/process.py b/hdxms_datasets/process.py
index 453ac67..8c173f4 100644
--- a/hdxms_datasets/process.py
+++ b/hdxms_datasets/process.py
@@ -1,9 +1,8 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import Literal, Optional, Union, TypeVar, TYPE_CHECKING
+from typing import Literal, Optional, Union, TYPE_CHECKING
 
-import numpy.typing as npt
 import pandas as pd
 
 from hdxms_datasets.config import cfg
@@ -15,8 +14,6 @@
 TIME_FACTORS = {"s": 1, "m": 60.0, "min": 60.0, "h": 3600, "d": 86400}
 TEMPERATURE_OFFSETS = {"c": 273.15, "celsius": 273.15, "k": 0.0, "kelvin": 0.0}
 
-A = TypeVar("A", npt.ArrayLike, pd.Series, pd.DataFrame)
-
 
 def convert_temperature(
     temperature_dict: dict, target_unit: str = "c"