Lint (#352)

* ruff fix all auto

* fix: incorrect import

* lint: add param import

* switch linting workflow to ruff

* workflow name

* fix: update ruff check cmd

* restore missing import, add __all__

.github/workflows/lint.yml

@@ -1,14 +1,13 @@
-name: Linting
-on: [push]
+name: Lint
+on: [push, pull_request]
 
 jobs:
-  lint:
+  format:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: "3.9"
-      - run: python -m pip install black[jupyter]
-      - run: |
-          black . --check
+      - run: python -m pip install ruff
+      - run: ruff check .

pyhdx/__init__.py

@@ -1,16 +1,28 @@
+from pyhdx.__version__ import __version__
+from pyhdx.datasets import read_dynamx
+from pyhdx.fitting_torch import TorchFitResult, TorchFitResultSet
 from pyhdx.models import (
-    HDXTimepoint,
-    HDXMeasurement,
     Coverage,
+    HDXMeasurement,
     HDXMeasurementSet,
+    HDXTimepoint,
 )
-from pyhdx.datasets import read_dynamx
-from pyhdx.fitting_torch import TorchFitResult, TorchFitResultSet
-from pyhdx.__version__ import __version__
 
 VERSION_STRING = f"PyHDX {__version__}"
 
 try:
     from pyhdx.output import FitReport
 except ModuleNotFoundError:
     pass
+
+
+__all__ = [
+    "HDXTimepoint",
+    "HDXMeasurement",
+    "Coverage",
+    "HDXMeasurementSet",
+    "read_dynamx",
+    "TorchFitResult",
+    "TorchFitResultSet",
+    "FitReport",
+]

pyhdx/config.py

@@ -3,7 +3,7 @@
 from contextlib import contextmanager
 from os import PathLike
 from pathlib import Path
-from typing import Union, Dict, Any, Optional, Generator
+from typing import Union, Any, Optional, Generator
 
 import torch
 from omegaconf import OmegaConf, DictConfig, DictKeyType

pyhdx/web/constructor.py

@@ -1,16 +1,17 @@
 import collections
 
+import param
 from distributed import Client
 
 from pyhdx.support import gen_subclasses
+from pyhdx.web.cache import Cache
 from pyhdx.web.controllers import *
 from pyhdx.web.main_controllers import MainController
 from pyhdx.web.opts import OptsBase
 from pyhdx.web.sources import *
 from pyhdx.web.tools import supported_tools
 from pyhdx.web.transforms import *
 from pyhdx.web.views import View
-from pyhdx.web.cache import Cache
 
 element_count = 0
 

pyhdx/web/tools.py

@@ -1,6 +1,5 @@
 from bokeh.models.tools import *
 
-
 supported_tools = {
     "pan": PanTool,
     "wheel_pan": WheelPanTool,

templates/01_load_secb_data.py

@@ -4,8 +4,9 @@
 
 import numpy as np
 
-from pyhdx import HDXMeasurement, read_dynamx
 from pyhdx.datasets import filter_peptides
+from pyhdx.fileIO import read_dynamx
+from pyhdx.models import HDXMeasurement
 from pyhdx.process import apply_control, correct_d_uptake
 
 # %%