Use pyproject.toml for isort and black

Author: LaurentRDC

dev-requirements.txt

@@ -7,4 +7,5 @@ sphinx_rtd_theme >= 0.4
 pytest >= 6,<8
 flaky >= 3,<4
 black
+isort
 wheel

docs/conf.py

@@ -16,22 +16,24 @@
 #
 import os
 import sys
+
 import matplotlib
 
 matplotlib.use("agg")  # required for Readthedocs
 
 currentpath = os.path.dirname(__file__)
 sys.path.append(os.path.join(currentpath, ".."))
 
-import iris
-
-# -- General configuration ------------------------------------------------
-
 # If your documentation needs a minimal Sphinx version, state it here.
 #
 # needs_sphinx = '1.5'
 from datetime import datetime
+
 import alabaster
+import iris
+
+# -- General configuration ------------------------------------------------
+
 
 year = datetime.now().year
 

example_plugins/example1.py

@@ -4,8 +4,8 @@
 ==============
 """
 
-from iris import AbstractRawDataset, ExperimentalParameter
 import numpy as np
+from iris import AbstractRawDataset, ExperimentalParameter
 
 
 class MinimalRawDataset(AbstractRawDataset):
@@ -33,9 +33,7 @@ def __init__(self, source=None, metadata=dict()):
         # Metadata can be filled as a dictionary before
         # initialization. # Attributes which are not
         # ExperimentalParameters are ignored.
-        metadata.update(
-            {"temperature": 100, "exposure": 1, "this_will_be_ignored": True}
-        )
+        metadata.update({"temperature": 100, "exposure": 1, "this_will_be_ignored": True})
         super().__init__(source, metadata)
 
         # Metadata can also be changed attribute by attribute

installer/build.py

@@ -5,15 +5,15 @@
 Inspired from the Spyder installer script:
 https://github.com/spyder-ide/spyder/tree/master/installers/Windows
 """
-from pathlib import Path
-import sys
-import subprocess
-from functools import wraps
-import logging
-import tempfile
+import argparse
 import importlib.util as iutil
+import logging
 import shutil
-import argparse
+import subprocess
+import sys
+import tempfile
+from functools import wraps
+from pathlib import Path
 
 logging.basicConfig(encoding="utf-8", level=logging.INFO)
 
@@ -45,9 +45,7 @@
 directory=build/nsis/
 """
 
-parser = argparse.ArgumentParser(
-    prog="build.py", description="Iris Windows installer build script."
-)
+parser = argparse.ArgumentParser(prog="build.py", description="Iris Windows installer build script.")
 parser.add_argument(
     "exe_name",
     metavar="TARGET",
@@ -108,22 +106,14 @@ def generate_pynsist_config(python_exe, filename, exe_name):
     freeze = check_output(f"{python_exe} -m pip freeze --all").decode("latin1")
     # PyQt5/PyQt5-sip requirements are baked in the template string
     requirements = [
-        line
-        for line in freeze.splitlines()
-        if package_name(line) not in {"iris-ued", "PyQt5", "PyQt5-sip"}
+        line for line in freeze.splitlines() if package_name(line) not in {"iris-ued", "PyQt5", "PyQt5-sip"}
     ]
     packages = [package_name(p) for p in requirements]
 
-    python_version = (
-        check_output(f"{env_python} --version").decode("latin1").split(" ")[-1].strip()
-    )
+    python_version = check_output(f"{env_python} --version").decode("latin1").split(" ")[-1].strip()
 
-    iris_version = check_output(
-        f'{python_exe} -c "import iris; print(iris.__version__)"'
-    ).decode("latin1")
-    iris_authors = check_output(
-        f'{python_exe} -c "import iris; print(iris.__author__)"'
-    ).decode("latin1")
+    iris_version = check_output(f'{python_exe} -c "import iris; print(iris.__version__)"').decode("latin1")
+    iris_authors = check_output(f'{python_exe} -c "import iris; print(iris.__author__)"').decode("latin1")
 
     pynsist_cfg_payload = PYNSIST_CFG_TEMPLATE.format(
         version=iris_version,
@@ -153,14 +143,10 @@ def generate_pynsist_config(python_exe, filename, exe_name):
         # Generating configuration file BEFORE installing pynsist ensures that
         # we bundle the requirements for iris
         cfg_path = work_dir / "pynsist.cfg"
-        generate_pynsist_config(
-            python_exe=env_python, filename=cfg_path, exe_name=exe_name
-        )
+        generate_pynsist_config(python_exe=env_python, filename=cfg_path, exe_name=exe_name)
         print(open(cfg_path, "rt").read())
 
-        run(
-            f"{env_python} -m pip install -r {INSTALLER_REQUIREMENTS_FILE} --no-warn-script-location"
-        )
+        run(f"{env_python} -m pip install -r {INSTALLER_REQUIREMENTS_FILE} --no-warn-script-location")
 
         run(f"{env_python} -m nsist {cfg_path}")
 

iris/__init__.py

@@ -4,10 +4,9 @@
 __license__ = "GPLv3"
 __version__ = "5.3.5"
 
-from .raw import AbstractRawDataset, check_raw_bounds, open_raw
-from .dataset import DiffractionDataset, MigrationWarning, MigrationError
-from .powder import PowderDiffractionDataset
+from . import plugins
+from .dataset import DiffractionDataset, MigrationError, MigrationWarning
 from .meta import ExperimentalParameter
 from .plugins import install_plugin, load_plugin
-
-from . import plugins
+from .powder import PowderDiffractionDataset
+from .raw import AbstractRawDataset, check_raw_bounds, open_raw

iris/__main__.py

@@ -3,8 +3,8 @@
 import argparse
 import sys
 import webbrowser
-from pathlib import Path
 from multiprocessing import freeze_support
+from pathlib import Path
 
 from iris import __version__
 from iris.gui import run
@@ -24,17 +24,13 @@
 parser = argparse.ArgumentParser(prog="iris", description=DESCRIPTION, epilog=EPILOG)
 parser.add_argument("-v", "--version", action="version", version=__version__)
 
-subparsers = parser.add_subparsers(
-    title="Subcommands", help="Available sub-commands", dest="subcmd"
-)
+subparsers = parser.add_subparsers(title="Subcommands", help="Available sub-commands", dest="subcmd")
 
 # Parser to open a path
 # To facilitate format determination, we need flags specifying whether the
 # path points to a raw, compact, or reduced dataset
 open_parser = subparsers.add_parser("open", help=OPEN_HELP)
-open_parser.add_argument(
-    "path", help="Path to the dataset", type=Path, nargs="?", default=None
-)
+open_parser.add_argument("path", help="Path to the dataset", type=Path, nargs="?", default=None)
 dset_modes = open_parser.add_mutually_exclusive_group(required=True)
 dset_modes.add_argument(
     "--raw",

iris/dataset.py

@@ -7,17 +7,10 @@
 from warnings import warn
 
 import h5py
+import npstreams as ns
 import numpy as np
 from scipy.ndimage import gaussian_filter
-
-import npstreams as ns
-from skued import (
-    __version__,
-    nfold,
-    autocenter,
-    ArbitrarySelection,
-    Selection,
-)
+from skued import ArbitrarySelection, Selection, __version__, autocenter, nfold
 
 from .meta import HDF5ExperimentalParameter, MetaHDF5Dataset
 
@@ -44,9 +37,7 @@ def write_access_needed(f):
     @wraps(f)
     def newf(self, *args, **kwargs):
         if self.mode != "r+":
-            raise PermissionError(
-                f"The dataset {self.filename} has not been opened with write access."
-            )
+            raise PermissionError(f"The dataset {self.filename} has not been opened with write access.")
         return f(self, *args, **kwargs)
 
     return newf
@@ -91,26 +82,14 @@ class DiffractionDataset(h5py.File, metaclass=MetaHDF5Dataset):
         "acquisition_date", str, default=""
     )  # Acquisition date, no specific format
     energy = HDF5ExperimentalParameter("energy", float, default=90)  # keV
-    pump_wavelength = HDF5ExperimentalParameter(
-        "pump_wavelength", int, default=800
-    )  # nanometers
-    fluence = HDF5ExperimentalParameter(
-        "fluence", float, default=0
-    )  # milliJoules / centimeters ^ 2
-    time_zero_shift = HDF5ExperimentalParameter(
-        "time_zero_shift", float, default=0
-    )  # picoseconds
-    temperature = HDF5ExperimentalParameter(
-        "temperature", float, default=293
-    )  # kelvins
+    pump_wavelength = HDF5ExperimentalParameter("pump_wavelength", int, default=800)  # nanometers
+    fluence = HDF5ExperimentalParameter("fluence", float, default=0)  # milliJoules / centimeters ^ 2
+    time_zero_shift = HDF5ExperimentalParameter("time_zero_shift", float, default=0)  # picoseconds
+    temperature = HDF5ExperimentalParameter("temperature", float, default=293)  # kelvins
     exposure = HDF5ExperimentalParameter("exposure", float, default=1)  # seconds
     scans = HDF5ExperimentalParameter("scans", tuple, default=(1,))
-    camera_length = HDF5ExperimentalParameter(
-        "camera_length", float, default=0.23
-    )  # meters
-    pixel_width = HDF5ExperimentalParameter(
-        "pixel_width", float, default=14e-6
-    )  # meters
+    camera_length = HDF5ExperimentalParameter("camera_length", float, default=0.23)  # meters
+    pixel_width = HDF5ExperimentalParameter("pixel_width", float, default=14e-6)  # meters
     aligned = HDF5ExperimentalParameter("aligned", bool, default=False)
     normalized = HDF5ExperimentalParameter("normalized", bool, default=False)
     notes = HDF5ExperimentalParameter("notes", str, default="")
@@ -234,9 +213,7 @@ def from_collection(
 
         if ckwargs is None:
             ckwargs = {"compression": "lzf", "shuffle": True, "fletcher32": True}
-        ckwargs[
-            "chunks"
-        ] = True  # For some reason, if no chunking, writing to disk is SLOW
+        ckwargs["chunks"] = True  # For some reason, if no chunking, writing to disk is SLOW
 
         first, patterns = ns.peek(patterns)
         if dtype is None:
@@ -498,16 +475,12 @@ def mask_apply(self, func):
         if r.dtype != bool:
             raise TypeError(f"Diffraction pattern masks must be boolean, not {r.dtype}")
         if r.shape != old_mask.shape:
-            raise ValueError(
-                f"Expected diffraction pattern mask with shape {old_mask.shape}, but got {r.shape}"
-            )
+            raise ValueError(f"Expected diffraction pattern mask with shape {old_mask.shape}, but got {r.shape}")
         self.experimental_parameters_group["valid_mask"][:] = func(self.valid_mask)
 
     @write_access_needed
     @update_equilibrium_pattern
-    def symmetrize(
-        self, mod, center=None, kernel_size=None, callback=None, processes=1
-    ):
+    def symmetrize(self, mod, center=None, kernel_size=None, callback=None, processes=1):
         """
         Symmetrize diffraction images based on n-fold rotational symmetry.
 
@@ -610,9 +583,7 @@ def shift_time_zero(self, shift):
         """
         differential = shift - self.time_zero_shift
         self.time_zero_shift = shift
-        self.experimental_parameters_group["time_points"][:] = (
-            self.time_points + differential
-        )
+        self.experimental_parameters_group["time_points"][:] = self.time_points + differential
 
     def _get_time_index(self, timedelay):
         """
@@ -632,9 +603,7 @@ def _get_time_index(self, timedelay):
         time_index = np.argmin(np.abs(self.time_points - timedelay))
         actual_timedelay = self.time_points[time_index]
         if actual_timedelay != timedelay:
-            warn(
-                f"Time-delay {timedelay}ps not available. Using closest-timedelay {actual_timedelay}ps instead"
-            )
+            warn(f"Time-delay {timedelay}ps not available. Using closest-timedelay {actual_timedelay}ps instead")
         return time_index
 
     def diff_eq(self):
@@ -691,9 +660,7 @@ def _recompute_diff_eq(self):
         else:
             diff_eq = ns.average((intensity[:, :, i] for i in range(t0_index)), axis=2)
 
-        eq_dset = self.diffraction_group.require_dataset(
-            name="equilibrium", shape=diff_eq.shape, dtype=float
-        )
+        eq_dset = self.diffraction_group.require_dataset(name="equilibrium", shape=diff_eq.shape, dtype=float)
         eq_dset[:] = diff_eq
 
     def diff_data(self, timedelay, relative=False, out=None):
@@ -866,7 +833,7 @@ def _autocenter(self):
         # diffraction center rather than fail the autocenter routine.
         # See #26.
         if np.allclose(image * self.valid_mask, 0):
-            r, c = image.shape[0]//2, image.shape[1]//2
+            r, c = image.shape[0] // 2, image.shape[1] // 2
         else:
             r, c = autocenter(im=image, mask=self.valid_mask)
 

iris/gui/__init__.py

@@ -12,10 +12,10 @@
 
 import pyqtgraph as pg
 from PyQt5 import QtGui, QtWidgets
+from qdarkstyle import load_stylesheet_pyqt5
 
 from ..raw import open_raw
-from .gui import Iris, IMAGE_FOLDER
-from qdarkstyle import load_stylesheet_pyqt5
+from .gui import IMAGE_FOLDER, Iris
 
 
 @contextmanager
@@ -29,9 +29,7 @@ def gui_environment():
     Note that interactions with the screen (e.g. mask creation) assumes that the image-axis order is
     row-major.
     """
-    old_qt_lib = os.environ.get(
-        "PYQTGRAPH_QT_LIB", "PyQt5"
-    )  # environment variable might not exist
+    old_qt_lib = os.environ.get("PYQTGRAPH_QT_LIB", "PyQt5")  # environment variable might not exist
     os.environ["PYQTGRAPH_QT_LIB"] = "PyQt5"
 
     old_image_axis_order = pg.getConfigOption("imageAxisOrder")