style: sort __all__ and change linter configuration

kmnhan · Apr 10, 2024 · c07262e · c07262e
1 parent b0d2d01
commit c07262e
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diff --git a/docs/source/user-guide/io.ipynb b/docs/source/user-guide/io.ipynb
@@ -167,7 +167,7 @@
     "file path or a sequence number:\n",
     "\n",
     ".. image:: ../images/flowchart_single.pdf\n",
-    "   :align9: center\n",
+    "   :align: center\n",
     "\n",
     "However, there are some setups where data for a single scan is saved over\n",
     "multiple files. In this case, the files will look like ``file_0001_0001.h5``,\n",

diff --git a/pyproject.toml b/pyproject.toml
@@ -191,12 +191,20 @@ select = [
     "FA",
     "ICN",
     "PIE",
+    "PT",
+    "Q",
     "RSE",
+    "TID",
     "TCH",
+    # "PTH",
+    # "FIX",
+    "TRY",
+    "FLY",
     "NPY",
+    "PERF",
     "RUF",
 ]
-ignore = ["B905", "ICN001", "RUF001", "RUF002", "RUF003", "RUF012"]
+ignore = ["B905", "ICN001", "TRY003", "RUF001", "RUF002", "RUF003", "RUF012"]
 extend-select = [
     "UP", # pyupgrade
 ]
@@ -213,4 +221,6 @@ docstring-code-line-length = "dynamic"
 profile = "black"
 
 [tool.pytest.ini_options]
+addopts = ["--import-mode=importlib"]
+pythonpath = "src"
 testpaths = "tests"
diff --git a/src/erlab/accessors.py b/src/erlab/accessors.py
@@ -8,11 +8,11 @@
 """
 
 __all__ = [
-    "PlotAccessor",
     "ImageToolAccessor",
-    "SelectionAccessor",
     "MomentumAccessor",
     "OffsetView",
+    "PlotAccessor",
+    "SelectionAccessor",
 ]
 
 import functools

diff --git a/src/erlab/analysis/__init__.py b/src/erlab/analysis/__init__.py
@@ -22,13 +22,13 @@
 """
 
 __all__ = [
+    "correct_with_edge",
+    "mask_with_hex_bz",
     "mask_with_polygon",
     "polygon_mask",
     "polygon_mask_points",
-    "mask_with_hex_bz",
     "rotateinplane",
     "rotatestackinplane",
-    "correct_with_edge",
 ]
 
 from erlab.analysis import correlation, fit, gold, interpolate, kspace  # noqa: F401

diff --git a/src/erlab/analysis/correlation.py b/src/erlab/analysis/correlation.py
@@ -1,6 +1,6 @@
 """Macros for correlation analysis."""
 
-__all__ = ["acf2stack", "acf2", "match_dims", "xcorr1d"]
+__all__ = ["acf2", "acf2stack", "match_dims", "xcorr1d"]
 
 
 import itertools

diff --git a/src/erlab/analysis/fit/__init__.py b/src/erlab/analysis/fit/__init__.py
@@ -17,10 +17,10 @@
 
 __all__ = [
     "ExtendedAffineBroadenedFD",
-    "PolynomialModel",
-    "MultiPeakModel",
     "LeastSq",
     "Minuit",
+    "MultiPeakModel",
+    "PolynomialModel",
 ]
 
 from erlab.analysis.fit.minuit import LeastSq, Minuit

diff --git a/src/erlab/analysis/fit/functions/__init__.py b/src/erlab/analysis/fit/functions/__init__.py
@@ -15,18 +15,18 @@
 
 __all__ = [
     "TINY",
+    "FermiEdge2dFunction",
+    "MultiPeakFunction",
+    "PolynomialFunction",
     "do_convolve",
     "do_convolve_y",
-    "gaussian_wh",
-    "lorentzian_wh",
     "fermi_dirac",
     "fermi_dirac_linbkg",
     "fermi_dirac_linbkg_broad",
-    "step_linbkg_broad",
+    "gaussian_wh",
+    "lorentzian_wh",
     "step_broad",
-    "PolynomialFunction",
-    "MultiPeakFunction",
-    "FermiEdge2dFunction",
+    "step_linbkg_broad",
 ]
 
 from erlab.analysis.fit.functions.dynamic import (

diff --git a/src/erlab/analysis/fit/functions/dynamic.py b/src/erlab/analysis/fit/functions/dynamic.py
@@ -5,11 +5,11 @@
 """
 
 __all__ = [
-    "get_args_kwargs",
     "DynamicFunction",
-    "PolynomialFunction",
-    "MultiPeakFunction",
     "FermiEdge2dFunction",
+    "MultiPeakFunction",
+    "PolynomialFunction",
+    "get_args_kwargs",
 ]
 import functools
 import inspect

diff --git a/src/erlab/analysis/fit/functions/general.py b/src/erlab/analysis/fit/functions/general.py
@@ -7,13 +7,13 @@
     "TINY",
     "do_convolve",
     "do_convolve_y",
-    "gaussian_wh",
-    "lorentzian_wh",
     "fermi_dirac",
     "fermi_dirac_linbkg",
     "fermi_dirac_linbkg_broad",
-    "step_linbkg_broad",
+    "gaussian_wh",
+    "lorentzian_wh",
     "step_broad",
+    "step_linbkg_broad",
 ]
 
 from collections.abc import Callable

diff --git a/src/erlab/analysis/fit/models.py b/src/erlab/analysis/fit/models.py
@@ -2,10 +2,10 @@
 
 __all__ = [
     "ExtendedAffineBroadenedFD",
-    "StepEdgeModel",
-    "PolynomialModel",
-    "MultiPeakModel",
     "FermiEdge2dModel",
+    "MultiPeakModel",
+    "PolynomialModel",
+    "StepEdgeModel",
 ]
 
 import lmfit
@@ -161,7 +161,11 @@ def guess(self, data, x, **kwargs):
 class StepEdgeModel(lmfit.Model):
     def __init__(self, independent_vars=("x",), prefix="", missing="raise", **kwargs):
         kwargs.update(
-            {"prefix": prefix, "missing": missing, "independent_vars": independent_vars}
+            {
+                "prefix": prefix,
+                "missing": missing,
+                "independent_vars": independent_vars,
+            }
         )
         super().__init__(step_linbkg_broad, **kwargs)
         self.set_param_hint("sigma", min=0.0)

diff --git a/src/erlab/analysis/gold.py b/src/erlab/analysis/gold.py
@@ -4,9 +4,9 @@
     "edge",
     "poly",
     "poly_from_edge",
-    "spline_from_edge",
     "resolution",
     "resolution_roi",
+    "spline_from_edge",
 ]
 
 from collections.abc import Sequence

diff --git a/src/erlab/analysis/image.py b/src/erlab/analysis/image.py
@@ -100,7 +100,7 @@ def gaussian_filter(
 
     """
     if np.isscalar(sigma):
-        sigma = {d: sigma for d in darr.dims}
+        sigma = dict.fromkeys(darr.dims, sigma)
     elif not isinstance(sigma, dict):
         sigma = dict(zip(darr.dims, sigma))
 
@@ -117,7 +117,7 @@ def gaussian_filter(
             raise ValueError("`radius` does not match dimensions of `sigma`")
 
         if np.isscalar(radius):
-            radius = {d: radius for d in sigma.keys()}
+            radius = dict.fromkeys(sigma.keys(), radius)
         elif not isinstance(radius, dict):
             radius = dict(zip(sigma.keys(), radius))
 
@@ -196,7 +196,7 @@ def gaussian_laplace(
         filter.
     """
     if np.isscalar(sigma):
-        sigma = {d: sigma for d in darr.dims}
+        sigma = dict.fromkeys(darr.dims, sigma)
     elif not isinstance(sigma, dict):
         sigma = dict(zip(darr.dims, sigma))
 

diff --git a/src/erlab/analysis/mask/__init__.py b/src/erlab/analysis/mask/__init__.py
@@ -17,11 +17,11 @@
 """
 
 __all__ = [
+    "hex_bz_mask_points",
+    "mask_with_hex_bz",
     "mask_with_polygon",
     "polygon_mask",
     "polygon_mask_points",
-    "mask_with_hex_bz",
-    "hex_bz_mask_points",
 ]
 
 import numba

diff --git a/src/erlab/analysis/utilities.py b/src/erlab/analysis/utilities.py
@@ -1,4 +1,4 @@
-__all__ = ["shift", "correct_with_edge"]
+__all__ = ["correct_with_edge", "shift"]
 
 import itertools
 from collections.abc import Callable

diff --git a/src/erlab/interactive/bzplot.py b/src/erlab/interactive/bzplot.py
@@ -302,12 +302,12 @@ def set_latt(self, a, b, c, alpha, beta, gamma):
 
     def set_avec(self, avec):
         self.params_avec.set_values(
-            **{f"a{i+1}{('x', 'y', 'z')[j]}": v for (i, j), v in np.ndenumerate(avec)}
+            **{f"a{i + 1}{('x', 'y', 'z')[j]}": v for (i, j), v in np.ndenumerate(avec)}
         )
 
     def set_bvec(self, bvec):
         self.params_bvec.set_values(
-            **{f"b{i+1}{('x', 'y', 'z')[j]}": v for (i, j), v in np.ndenumerate(bvec)}
+            **{f"b{i + 1}{('x', 'y', 'z')[j]}": v for (i, j), v in np.ndenumerate(bvec)}
         )
 
     @property
@@ -368,11 +368,11 @@ def __init__(self, bvec):
         # plot reciprocal lattice vectors
         self._bvecs = []
         for i, b in enumerate(bvec):
-            p = self.ax.plot(*[(0, bi) for bi in b], "-", c=f"C{i+1}", clip_on=False)
+            p = self.ax.plot(*[(0, bi) for bi in b], "-", c=f"C{i + 1}", clip_on=False)
             t = self.ax.text(
                 *(b + 0.15 * b / np.linalg.norm(b)),
-                f"$b_{i+1}$",
-                c=f"C{i+1}",
+                f"$b_{i + 1}$",
+                c=f"C{i + 1}",
                 ha="center",
                 va="center_baseline",
             )

diff --git a/src/erlab/interactive/colors.py b/src/erlab/interactive/colors.py
@@ -3,13 +3,13 @@
 from __future__ import annotations
 
 __all__ = [
+    "BetterColorBarItem",
+    "BetterImageItem",
     "ColorMapComboBox",
     "ColorMapGammaWidget",
-    "BetterImageItem",
-    "BetterColorBarItem",
     "color_to_QColor",
-    "pg_colormap_names",
     "pg_colormap_from_name",
+    "pg_colormap_names",
     "pg_colormap_powernorm",
     "pg_colormap_to_QPixmap",
 ]

diff --git a/src/erlab/interactive/derivative.py b/src/erlab/interactive/derivative.py
@@ -245,17 +245,19 @@ def copy_code(self):
             }
             lines.append(f"_processed = {data_name}.copy()")
             data_name = "_processed"
-            lines.append(f"for _ in range({self.sn_spin.value()}):")
-            lines.append(
-                "\t"
-                + gen_function_code(
-                    copy=False,
-                    **{
-                        "_processed = era.image.gaussian_filter": [
-                            f"|{data_name}|",
-                            arg_dict,
-                        ]
-                    },
+            lines.extend(
+                (
+                    f"for _ in range({self.sn_spin.value()}):",
+                    "\t"
+                    + gen_function_code(
+                        copy=False,
+                        **{
+                            "_processed = era.image.gaussian_filter": [
+                                f"|{data_name}|",
+                                arg_dict,
+                            ]
+                        },
+                    ),
                 )
             )
             data_name = "_processed"

diff --git a/src/erlab/interactive/imagetool/__init__.py b/src/erlab/interactive/imagetool/__init__.py
@@ -17,7 +17,7 @@
 
 from __future__ import annotations
 
-__all__ = ["itool", "ImageTool"]
+__all__ = ["ImageTool", "itool"]
 
 import gc
 import sys

diff --git a/src/erlab/interactive/imagetool/_deprecated/imagetool_old.py b/src/erlab/interactive/imagetool/_deprecated/imagetool_old.py
@@ -1845,7 +1845,7 @@ def onMouseDrag(self, evt):
         for i in range(self.data_ndim):
             if D[i]:
                 ind = self.get_index_of_value(i, V[i])
-                if self.snap and (ind == self._last_ind[i]) or self.axis_locked[i]:
+                if (self.snap and (ind == self._last_ind[i])) or self.axis_locked[i]:
                     D[i] = False
                 else:
                     self._last_ind[i] = ind

diff --git a/src/erlab/interactive/imagetool/controls.py b/src/erlab/interactive/imagetool/controls.py
@@ -1,10 +1,10 @@
 from __future__ import annotations
 
 __all__ = [
-    "ItoolCrosshairControls",
     "ColorControls",
-    "ItoolColormapControls",
     "ItoolBinningControls",
+    "ItoolColormapControls",
+    "ItoolCrosshairControls",
 ]
 
 from typing import TYPE_CHECKING

diff --git a/src/erlab/interactive/kspace.py b/src/erlab/interactive/kspace.py
@@ -286,11 +286,13 @@ def copy_code(self):
                 f"{input_name}.kspace.inner_potential"
                 f" = {self._offset_spins['V0'].value()}"
             )
-        out_lines.append(f"{input_name}.kspace.offsets = {self.offset_dict}")
-        out_lines.append(
-            gen_function_code(
-                copy=False,
-                **{f"{input_name}_kconv = {input_name}.kspace.convert": [arg_dict]},
+        out_lines.extend(
+            (
+                f"{input_name}.kspace.offsets = {self.offset_dict}",
+                gen_function_code(
+                    copy=False,
+                    **{f"{input_name}_kconv = {input_name}.kspace.convert": [arg_dict]},
+                ),
             )
         )
 
@@ -397,7 +399,10 @@ def get_bz_lines(
 
             if rot != 0.0:
                 rotmat = np.array(
-                    [[np.cos(rot), -np.sin(rot)], [np.sin(rot), np.cos(rot)]]
+                    [
+                        [np.cos(rot), -np.sin(rot)],
+                        [np.sin(rot), np.cos(rot)],
+                    ]
                 )
                 lines = (rotmat @ lines.transpose(1, 2, 0)).transpose(2, 0, 1)
                 vertices = (rotmat @ vertices.T).T

diff --git a/src/erlab/interactive/utilities.py b/src/erlab/interactive/utilities.py
@@ -18,17 +18,17 @@
 from erlab.interactive.colors import BetterImageItem, pg_colormap_powernorm
 
 __all__ = [
-    "parse_data",
-    "copy_to_clipboard",
-    "gen_single_function_code",
-    "gen_function_code",
-    "BetterSpinBox",
-    "BetterAxisItem",
-    "xImageItem",
-    "ParameterGroup",
     "AnalysisWidgetBase",
     "AnalysisWindow",
+    "BetterAxisItem",
+    "BetterSpinBox",
     "DictMenuBar",
+    "ParameterGroup",
+    "copy_to_clipboard",
+    "gen_function_code",
+    "gen_single_function_code",
+    "parse_data",
+    "xImageItem",
 ]