autofixes for linting

alphadia/calibration/property.py

@@ -172,7 +172,7 @@ def fit(self, dataframe: pd.DataFrame, plot: bool = False, **kwargs):
             self.function.fit(input_values, target_value)
             self.is_fitted = True
         except Exception as e:
-            logging.error(f"Could not fit estimator {self.name}: {e}")
+            logging.exception(f"Could not fit estimator {self.name}: {e}")
             return
 
         if plot is True:
@@ -200,13 +200,13 @@ def predict(self, dataframe, inplace=True):
             logging.warning(
                 f"{self.name} prediction was skipped as it has not been fitted yet"
             )
-            return
+            return None
 
         if not set(self.input_columns).issubset(dataframe.columns):
             logging.warning(
                 f"{self.name} calibration was skipped as input column {self.input_columns} not found in dataframe"
             )
-            return
+            return None
 
         input_values = dataframe[self.input_columns].values
 

alphadia/data/alpharaw.py

@@ -318,8 +318,6 @@ def filter_spectra(self, **kwargs):
         This function is implemented in the sub-class.
         """
 
-        pass
-
     def jitclass(self):
         return AlphaRawJIT(
             self.cycle,

alphadia/fdrexperimental.py

@@ -8,9 +8,8 @@
 # third party imports
 import numpy as np
 import torch
-import torch.nn as nn
-import torch.optim as optim
 from sklearn import model_selection
+from torch import nn, optim
 from torchmetrics.classification import BinaryAUROC
 from tqdm import tqdm
 
@@ -30,7 +29,6 @@ class Classifier(ABC):
     @abstractmethod
     def fitted(self):
         """Return whether the classifier has been fitted."""
-        pass
 
     @abstractmethod
     def fit(self, x: np.array, y: np.array):
@@ -46,7 +44,6 @@ def fit(self, x: np.array, y: np.array):
             Target values of shape (n_samples,) or (n_samples, n_classes).
 
         """
-        pass
 
     @abstractmethod
     def predict(self, x: np.array):
@@ -65,7 +62,6 @@ def predict(self, x: np.array):
             Predicted class of shape (n_samples,).
 
         """
-        pass
 
     @abstractmethod
     def predict_proba(self, x: np.array):
@@ -84,7 +80,6 @@ def predict_proba(self, x: np.array):
             Predicted class probabilities of shape (n_samples, n_classes).
 
         """
-        pass
 
     @abstractmethod
     def to_state_dict(self):
@@ -97,7 +92,6 @@ def to_state_dict(self):
         state_dict : dict
             State dict of the classifier.
         """
-        pass
 
     @abstractmethod
     def from_state_dict(self, state_dict: dict):
@@ -111,7 +105,6 @@ def from_state_dict(self, state_dict: dict):
             State dict of the classifier.
 
         """
-        pass
 
 
 class BinaryClassifier(Classifier):

alphadia/libtransform.py

@@ -32,7 +32,6 @@ class ProcessingStep:
     def __init__(self) -> None:
         """Base class for processing steps. Each implementation must implement the `validate` and `forward` method.
         Processing steps can be chained together in a ProcessingPipeline."""
-        pass
 
     def __call__(self, *args: typing.Any) -> typing.Any:
         """Run the processing step on the input object."""

alphadia/numba/fft.py

@@ -47,13 +47,13 @@ def rfft2(x: np.array, s: None | tuple = None) -> np.array:
 @overload(rfft2, fastmath=True)
 def _(x, s=None):
     if not isinstance(x, nb.types.Array):
-        return
+        return None
 
     if x.ndim != 2:
-        return
+        return None
 
     if x.dtype != nb.types.float32:
-        return
+        return None
 
     def funcx_impl(x, s=None):
         s, axes = ndshape_and_axes(x, s, (-2, -1))
@@ -98,13 +98,13 @@ def irfft2(x: np.array, s: None | tuple = None) -> np.array:
 @overload(irfft2, fastmath=True)
 def _(x, s=None):
     if not isinstance(x, nb.types.Array):
-        return
+        return None
 
     if x.ndim != 2:
-        return
+        return None
 
     if x.dtype != nb.types.complex64:
-        return
+        return None
 
     def funcx_impl(x, s=None):
         s, axes = ndshape_and_axes(x, s, (-2, -1))
@@ -161,16 +161,16 @@ def convolve_fourier(dense, kernel):
 @overload(convolve_fourier, fastmath=True)
 def _(dense, kernel):
     if not isinstance(dense, nb.types.Array):
-        return
+        return None
 
     if not isinstance(kernel, nb.types.Array):
-        return
+        return None
 
     if kernel.ndim != 2:
-        return
+        return None
 
     if dense.ndim < 2:
-        return
+        return None
 
     if dense.ndim == 2:
 

alphadia/numba/fragments.py

@@ -331,7 +331,9 @@ def get_ion_group_mapping(
 
     score_group_intensity = np.zeros((len(ion_mz)), dtype=np.float32)
 
-    for precursor, mz, intensity in zip(ion_precursor, ion_mz, ion_intensity):  # noqa: B905 ('strict' not supported by numba yet
+    for precursor, mz, intensity in zip(
+        ion_precursor, ion_mz, ion_intensity
+    ):  # ('strict' not supported by numba yet
         # score_group_idx = precursor_group[precursor]
 
         if len(grouped_mz) == 0 or np.abs(grouped_mz[-1] - mz) > EPSILON:

alphadia/outputtransform.py

@@ -116,7 +116,7 @@ def accumulate_frag_df(
         raw_name, df = next(df_iterable, (None, None))
         if df is None:
             logger.warning(f"no frag file found for {raw_name}")
-            return
+            return None
 
         df = prepare_df(df, self.psm_df, column=self.column)
 
@@ -886,7 +886,7 @@ def build_library(
 
         if len(psm_df) == 0:
             logger.warning("No precursors found, skipping library building")
-            return
+            return None
 
         libbuilder = libtransform.MbrLibraryBuilder(
             fdr=0.01,

alphadia/peakgroup/kernel.py

@@ -177,7 +177,6 @@ def get_dense_matrix(self, verbose: bool = True):
         mobility_resolution = np.mean(np.diff(self.dia_data.mobility_values[::-1]))
 
         if verbose:
-            pass
             logger.info(
                 f"Duty cycle consists of {rt_datapoints} frames, {rt_resolution:.2f} seconds cycle time"
             )
@@ -189,7 +188,6 @@ def get_dense_matrix(self, verbose: bool = True):
         mobility_sigma = self.determine_mobility_sigma(mobility_resolution)
 
         if verbose:
-            pass
             logger.info(
                 f"FWHM in RT is {self.fwhm_rt:.2f} seconds, sigma is {rt_sigma:.2f}"
             )

alphadia/peakgroup/search.py

@@ -688,7 +688,7 @@ def build_candidates(
     cycle_limits_list = np.zeros((peak_cycle_list.shape[0], 2), dtype="int32")
 
     for candidate_rank, (scan_relative, cycle_relative) in enumerate(
-        zip(peak_scan_list, peak_cycle_list)  # noqa: B905 ('strict' not supported by numba yet)
+        zip(peak_scan_list, peak_cycle_list)  # ('strict' not supported by numba yet)
     ):
         scan_limits_relative, cycle_limits_relative = numeric.symetric_limits_2d(
             score,
@@ -738,7 +738,7 @@ def build_candidates(
         peak_score_list,
         scan_limits_list,
         cycle_limits_list,
-    ):  # noqa: B905 ('strict' not supported by numba yet)
+    ):  # ('strict' not supported by numba yet)
         # does not work anymore
 
         scan_limits_absolute = numeric.wrap1(

alphadia/peakgroup/utils.py

@@ -18,16 +18,16 @@ def assemble_isotope_mz(mono_mz, charge, isotope_intensity):
 @overload(assemble_isotope_mz)
 def _(mono_mz, charge, isotope_intensity):
     if not isinstance(mono_mz, nb.types.Float):
-        return
+        return None
 
     if not isinstance(charge, nb.types.Integer):
-        return
+        return None
 
     if not isinstance(isotope_intensity, nb.types.Array):
-        return
+        return None
 
     if isotope_intensity.ndim != 1:
-        return
+        return None
 
     def funcx_impl(mono_mz, charge, isotope_intensity):
         offset = np.arange(len(isotope_intensity)) * 1.0033548350700006 / charge

alphadia/planning.py

@@ -70,9 +70,9 @@ def __init__(
         reporting.init_logging(self.output_folder)
 
         logger.progress("          _      _         ___ ___   _   ")
-        logger.progress("     __ _| |_ __| |_  __ _|   \_ _| /_\  ")
-        logger.progress("    / _` | | '_ \ ' \\/ _` | |) | | / _ \ ")
-        logger.progress("    \__,_|_| .__/_||_\__,_|___/___/_/ \_\\")
+        logger.progress(r"     __ _| |_ __| |_  __ _|   \_ _| /_\  ")
+        logger.progress("    / _` | | '_ \\ ' \\/ _` | |) | | / _ \\ ")
+        logger.progress("    \\__,_|_| .__/_||_\\__,_|___/___/_/ \\_\\")
         logger.progress("           |_|                           ")
         logger.progress("")
 

alphadia/transferlearning/train.py

@@ -994,7 +994,7 @@ def finetune_ccs(self, psm_df: pd.DataFrame) -> pd.DataFrame:
             logger.error(
                 "Failed to finetune CCS model. PSM dataframe does not contain mobility or ccs columns."
             )
-            return
+            return None
         if "ccs" not in psm_df.columns:
             psm_df["ccs"] = mobility_to_ccs_for_df(psm_df, "mobility")
         elif "mobility" not in psm_df.columns:

alphadia/utils.py

@@ -8,13 +8,13 @@
 # alpha family imports
 import alphatims.bruker
 import alphatims.utils
-import matplotlib.patches as patches
 import numba as nb
 import numpy as np
 
 # third party imports
 import pandas as pd
 import torch
+from matplotlib import patches
 
 logger = logging.getLogger()
 

alphadia/workflow/optimization.py

@@ -57,12 +57,9 @@ def step(self, precursors_df: pd.DataFrame, fragments_df: pd.DataFrame):
 
         """
 
-        pass
-
     @abstractmethod
     def skip(self):
         """Record skipping of optimization. Can be overwritten with an empty method if there is no need to record skips."""
-        pass
 
     def proceed_with_insufficient_precursors(self, precursors_df, fragments_df):
         self.workflow.reporter.log_string(
@@ -80,7 +77,6 @@ def proceed_with_insufficient_precursors(self, precursors_df, fragments_df):
     @abstractmethod
     def plot(self):
         """Plots the progress of the optimization. Can be overwritten with an empty method if there is no need to plot the progress."""
-        pass
 
     @abstractmethod
     def _update_workflow():
@@ -92,7 +88,6 @@ def _update_workflow():
         and FWHM_mobility
 
         """
-        pass
 
     @abstractmethod
     def _update_history():
@@ -107,7 +102,6 @@ def _update_history():
             The filtered fragment dataframe for the search.
 
         """
-        pass
 
 
 class AutomaticOptimizer(BaseOptimizer):
@@ -503,7 +497,6 @@ def _get_feature_value(
 
 
         """
-        pass
 
 
 class TargetedOptimizer(BaseOptimizer):
@@ -611,11 +604,9 @@ def step(
 
     def skip(self):
         """See base class."""
-        pass
 
     def plot(self):
         """See base class"""
-        pass
 
     def _update_workflow(self):
         pass

pyproject.toml

@@ -60,7 +60,7 @@ version = {attr = "alphadia.__version__"}
 alphadia = "alphadia.cli:run"
 
 [tool.ruff]
-extend-exclude = ["misc/.bumpversion.cfg"]
+extend-exclude = ["misc/.bumpversion.cfg", "tests"]
 
 [tool.ruff.lint]
 select =  [
@@ -76,10 +76,39 @@ select =  [
     "SIM",
     # isort
     "I",
+    #"ALL"
 ]
 
 ignore = [
+    "D",
+    "ANN",
+    "SLF001", # Private member accessed TODO this needs to be fixed in alphabase
+
     "E501",  # Line too long  (ruff wraps code, but not docstrings)
     "B028",  #  No explicit `stacklevel` keyword argument found (for warnings)
-    "B905"  # This causes problems in numba code: `zip()` without an explicit `strict=` parameter
+    "B905",  # This causes problems in numba code: `zip()` without an explicit `strict=` parameter
+    "COM812", #may cause conflicts when used with the formatter
+    "ISC001", #may cause conflicts when used with the formatter
+    "D211", # no-blank-line-before-class
+    "D213", # multi-line-summary-second-line
+    "S101", # Use of `assert` detected
+    "INP001", # implicit namespace package.
+    "ERA001", # Found commented-out code
+    "D203", # 1 blank line required before class docstring
+    "TD002", "TD003", "FIX002",  # things around TO-DO
+    "PT011", #pytest.raises(ValueError) is too broad
+    "G004", "EM102", # Logging statement uses f-string
+    "TRY003", # Avoid specifying long messages outside the exception class
+    "ANN101", # Missing type annotation for `self` in method
+    "ANN102", # Missing type annotation for `cls` in classmethod
+    "ANN002", # Missing type annotation for `*args`
+    "ANN003", # Missing type annotation for `**kwargs
+    "FA102", # Missing `from __future__ import annotations
+    "EM101", # Exception must not use a string literal, assign to variable first
+    "D104", # Missing docstring in public package
+    "ANN204", # Missing return type annotation for special method `__init__`
+    "D401", # First line of docstring should be in imperative mood
+    "B023", # Function definition does not bind loop variable
+    "PD901", # Avoid using the generic variable name `df` for DataFrames"
+    "TCH003", # Move standard library import into a type-checking block
 ]

tests/performance_tests/1_brunner_2022_1ng_all.py

@@ -22,7 +22,7 @@
     try:
         test_dir = os.environ["TEST_DATA_DIR"]
     except KeyError:
-        logging.error("TEST_DATA_DIR environtment variable not set")
+        logging.exception("TEST_DATA_DIR environtment variable not set")
         raise KeyError from None
 
     logging.info(f"Test data directory: {test_dir}")