Run ruff format

.azure-pipelines/bootstrap.py

@@ -122,9 +122,7 @@ def install_micromamba(python):
 There was a failure in constructing the conda environment.
 Attempt {retry} of 5 will start {retry} minute(s) from {t}.
 *******************************************************************************
-""".format(
-                    retry=retry, t=time.asctime()
-                )
+""".format(retry=retry, t=time.asctime())
             )
             time.sleep(retry * 60)
         else:

src/dxtbx/command_line/detector_superpose.py

@@ -92,10 +92,9 @@ def run(args=None):
             "Reference detector must be at least %d panels long given the panel list"
             % (max_p_id + 1)
         )
-        assert max_p_id < len(
-            moving
-        ), "Moving detector must be at least %d panels long given the panel list" % (
-            max_p_id + 1
+        assert max_p_id < len(moving), (
+            "Moving detector must be at least %d panels long given the panel list"
+            % (max_p_id + 1)
         )
         panel_ids = params.panel_list
 

src/dxtbx/command_line/plot_detector_models.py

@@ -125,7 +125,6 @@ def plot_group(
 
 
 def plot_image_plane_projection(detector, color, ax, panel_numbers=True):
-
     origin_2d, fast_2d, slow_2d = get_detector_projection_2d_axes(detector)
 
     for panel, origin, fast, slow in zip(detector, origin_2d, fast_2d, slow_2d):
@@ -182,7 +181,6 @@ def run(args=None):
     min_z = max_z = None
     ax = None
     for file_name, color in zip(files, colors):
-
         # read the data and get the detector models
         try:
             experiments = ExperimentListFactory.from_json_file(

src/dxtbx/command_line/read_sequence.py

@@ -12,7 +12,6 @@
 
 
 def read_sequence(images: list[str]):
-
     sequences = ImageSetFactory.new(images)
 
     for sequence in sequences:

src/dxtbx/dxtbx_imageset_ext.pyi

@@ -21,14 +21,12 @@ class ExternalLookup:
     def pedestal(self) -> Any: ...
 
 class ExternalLookupItemBool:
-
     data: Any
     filename: Any
     def __init__(self, *args, **kwargs) -> None: ...
     def __reduce__(self) -> Any: ...
 
 class ExternalLookupItemDouble:
-
     data: Any
     filename: Any
     def __init__(self, *args, **kwargs) -> None: ...

src/dxtbx/example/to_xds.py

@@ -5,7 +5,6 @@
 classes.
 """
 
-
 from __future__ import annotations
 
 import math
@@ -57,7 +56,6 @@ def get_scan(self):
         return self._scan
 
     def XDS(self):
-
         sensor = self.get_detector().get_type()
         fast, slow = map(int, self.get_detector().get_image_size())
         f, s = self.get_detector().get_pixel_size()

src/dxtbx/format/Format.py

@@ -377,7 +377,6 @@ def get_imageset(
 
         # Create an imageset or sequence
         if not is_sequence:
-
             # Create the imageset
             iset = ImageSet(
                 ImageSetData(
@@ -391,7 +390,6 @@ def get_imageset(
 
             # If any are None then read from format
             if [beam, detector, goniometer, scan].count(None) != 0:
-
                 # Get list of models
                 beam = []
                 detector = []
@@ -412,7 +410,6 @@ def get_imageset(
                 iset.set_scan(scan[i], i)
 
         else:
-
             # Get the template
             if template is None:
                 template = template_regex(filenames[0])[0]

src/dxtbx/format/FormatBruker.py

@@ -33,7 +33,6 @@ def read_header_lines(image_path, max_bytes=512 * 50):
         max_bytes = (max_bytes // 80) * 80
         with FormatBruker.open_file(image_path, "rb") as f:
             while True:
-
                 # read a line and look for HDRBLKS
                 line = f.read(80)
                 if not line:

src/dxtbx/format/FormatBrukerED1.py

@@ -21,7 +21,6 @@
 class FormatBrukerED1(FormatBruker):
     @staticmethod
     def understand(image_file):
-
         try:
             header_lines = FormatBruker.read_header_lines(image_file)
         except OSError:
@@ -45,7 +44,6 @@ def understand(image_file):
         return True
 
     def _start(self):
-
         try:
             header_lines = FormatBruker.read_header_lines(self._image_file)
         except OSError:
@@ -175,7 +173,6 @@ def _beam(self):
         )
 
     def _scan(self):
-
         start = float(self.header_dict["START"].split()[0])
         incr = float(self.header_dict["INCREME"].split()[0])
         if incr < 0:

src/dxtbx/format/FormatBrukerFixedChi.py

@@ -11,7 +11,6 @@
 class FormatBrukerFixedChi(FormatBruker):
     @staticmethod
     def understand(image_file):
-
         hdr = FormatBruker.read_header_lines(image_file)
         hdr_dic = FormatBruker.parse_header(hdr)
 
@@ -105,7 +104,6 @@ def _beam(self):
         return self._beam_factory.simple(wavelength)
 
     def _scan(self):
-
         start = float(self.header_dict["START"][0])
         incr = float(self.header_dict["INCREME"][0])
         if incr < 0:

src/dxtbx/format/FormatBrukerPhoton.py

@@ -21,7 +21,6 @@
 class FormatBrukerPhoton(FormatBruker):
     @staticmethod
     def understand(image_file):
-
         try:
             header_lines = FormatBruker.read_header_lines(image_file)
         except OSError:
@@ -39,7 +38,6 @@ def understand(image_file):
         return True
 
     def _start(self):
-
         try:
             header_lines = FormatBruker.read_header_lines(self._image_file)
         except OSError:
@@ -145,7 +143,6 @@ def _beam(self):
         )
 
     def _scan(self):
-
         start = float(self.header_dict["START"].split()[0])
         incr = float(self.header_dict["INCREME"].split()[0])
         if incr < 0:

src/dxtbx/format/FormatCBFMiniADSCHF4M.py

@@ -25,7 +25,6 @@ def get_adsc_timestamp(timestamp):
     timestamp = re.sub("_+", "_", timestamp)
 
     for format in ["%a_%b_%d_%H:%M:%S_%Y"]:
-
         try:
             struct_time = time.strptime(timestamp, format)
             return calendar.timegm(struct_time)
@@ -41,7 +40,6 @@ class FormatCBFMiniADSCHF4M(FormatCBFMini):
 
     @staticmethod
     def understand(image_file):
-
         header = FormatCBFMini.get_cbf_header(image_file)
 
         for record in header.split("\n"):
@@ -151,7 +149,6 @@ def _scan(self):
         )
 
     def detectorbase_start(self):
-
         self.detectorbase = ADSCHF4MImage(self._image_file)
         self.detectorbase.readHeader()
 

src/dxtbx/format/FormatCBFMiniEigerPhotonFactory.py

@@ -37,7 +37,6 @@ def _goniometer(self):
         )
 
     def _detector(self):
-
         max_trusted_value = 1e7
 
         if "_lower_" in self._image_file:
@@ -118,7 +117,6 @@ def _scan(self):
         )
 
     def detectorbase_start(self):
-
         self.detectorbase = PilatusImage(self._image_file)
         self.detectorbase.readHeader()
 

src/dxtbx/format/FormatCBFMiniEigerQuadroED1.py

@@ -11,7 +11,6 @@
 class FormatCBFMiniEigerQuadroED1(FormatCBFMiniEiger):
     @staticmethod
     def understand(image_file):
-
         header = FormatCBFMiniEiger.get_cbf_header(image_file)
 
         for record in header.split("\n"):

src/dxtbx/format/FormatCBFMiniPilatusDLS12M.py

@@ -57,7 +57,6 @@ def __init__(self, image_file, **kwargs):
         super().__init__(image_file, **kwargs)
 
     def _detector(self):
-
         # module positions from detector blueprints - modelling at the moment as
         # 24 modules, each consisting of 5 sensors (the latter is ignored)
         x = matrix.col((-1, 0, 0))

src/dxtbx/format/FormatCBFMiniPilatusHelpers.py

@@ -14,7 +14,6 @@ def get_pilatus_timestamp(timestamp_string):
         milliseconds = "000"
 
     for format in ["%Y-%b-%dT%H:%M:%S", "%Y-%m-%dT%H:%M:%S", "%Y/%b/%d %H:%M:%S"]:
-
         try:
             struct_time = time.strptime(timestamp, format)
             return calendar.timegm(struct_time) + float("0." + milliseconds)

src/dxtbx/format/FormatCBFMultiTileHierarchy.py

@@ -162,7 +162,9 @@ def _add_panel_group(self, group_id, d):
             except RuntimeError as e:
                 assert "DXTBX_ASSERT(D_)" in str(e)
             else:
-                assert False  # shouldn't be reached.  Detector should be initialized only once.
+                assert (
+                    False
+                )  # shouldn't be reached.  Detector should be initialized only once.
         else:
             parent_pg = self._add_panel_group(parent, d)
             pg = parent_pg.add_group()

src/dxtbx/format/FormatGatanDM4.py

@@ -126,7 +126,6 @@ def search_tag_hierarchy(name, tag_list):
 def extract_image_data(image_file, offset, ntags, byteord):
     # read tags
     with FormatGatanDM4.open_file(image_file, "rb") as f:
-
         f.seek(offset)
 
         root = []
@@ -230,7 +229,6 @@ class FormatGatanDM4(Format):
 
     @staticmethod
     def understand(image_file):
-
         try:
             header = FormatGatanDM4._read_header(image_file)
         except struct.error:
@@ -255,7 +253,6 @@ def _read_header(image_file):
         hd = {}
 
         with FormatGatanDM4.open_file(image_file, "rb") as f:
-
             hd["version"] = struct.unpack(">I", f.read(4))[0]
 
             if hd["version"] == 3:
@@ -414,13 +411,11 @@ def understand(image_file):
         return extract_num_images(image_file) == 1
 
     def __init__(self, image_file, **kwargs):
-
         if not self.understand(image_file):
             raise IncorrectFormatError(self, image_file)
         FormatGatanDM4.__init__(self, image_file, **kwargs)
 
     def get_raw_data(self):
-
         with FormatGatanDM4.open_file(self._image_file, "rb") as f:
             f.seek(self._data_offset)
             return self._read_raw_data(f)
@@ -432,14 +427,12 @@ def understand(image_file):
         return extract_num_images(image_file) > 1
 
     def __init__(self, image_file, **kwargs):
-
         if not self.understand(image_file):
             raise IncorrectFormatError(self, image_file)
         FormatMultiImage.__init__(self, **kwargs)
         FormatGatanDM4.__init__(self, image_file, **kwargs)
 
     def get_raw_data(self, index):
-
         with FormatGatanDM4.open_file(self._image_file, "rb") as f:
             f.seek(self._data_offset)
 

src/dxtbx/format/FormatHDF5ESRFJungfrau4M.py

@@ -11,7 +11,6 @@
 
 
 class FormatHDF5ESRFJungfrau4M(FormatHDF5):
-
     # A class to understand still-shot images from ESRF collected on a Jungfrau 4M.
 
     _cached_mask = None

src/dxtbx/format/FormatHDF5SaclaMPCCD.py

@@ -255,7 +255,6 @@ def get_raw_data(self, index=None):
             self.set_index(index)
 
         if self._raw_data is None:
-
             if self.RECONST_MODE:
                 self._raw_data = flex.int(self.reconst_image())
 

src/dxtbx/format/FormatISISSXD.py

@@ -75,7 +75,6 @@ def get_goniometer(self, idx: int = None) -> Goniometer:
         return goniometer
 
     def get_detector(self, index: int = None) -> Detector:
-
         num_panels = self._get_num_panels()
         panel_names = self._get_panel_names()
         panel_type = self._get_panel_type()
@@ -282,7 +281,6 @@ def _load_raw_data(self):
         self._raw_data = tuple(raw_data)
 
     def get_raw_data(self, index: int, use_loaded_data=True) -> Tuple[flex.int]:
-
         raw_data = []
 
         if use_loaded_data:

src/dxtbx/format/FormatMANDI.py

@@ -65,7 +65,6 @@ def get_name(image_file: str) -> str:
         return get_name(image_file) == "MANDI"
 
     def get_raw_data(self, index: int) -> Tuple[flex.int]:
-
         raw_data = []
         panel_size = self._get_image_size()
         for panel_name in self._get_panel_names():
@@ -80,7 +79,6 @@ def get_raw_data(self, index: int) -> Tuple[flex.int]:
         return tuple(raw_data)
 
     def get_detector(self) -> Detector:
-
         num_panels = self._get_num_panels()
         panel_names = self._get_panel_names()
         panel_type = self._get_panel_type()
@@ -377,7 +375,6 @@ def add_histogram_data_to_nxs_file(
         panel_size: Tuple[int, int] = (256, 256),  # (px)
         nproc: int = 8,
     ) -> None:
-
         tof_bins = FormatMANDI.generate_tof_bins(
             nxs_file=nxs_file_path,
             panel_size=panel_size,
@@ -442,7 +439,7 @@ def delete_event_data(nxs_file, base_dir, panel_name):
 
     @staticmethod
     def compute_event_histogram(
-        args: Tuple[int, np.array, np.array, np.array]
+        args: Tuple[int, np.array, np.array, np.array],
     ) -> np.array:
         pixel_idx, event_time_offset, corrected_event_id, tof_bins = args
         h, _ = np.histogram(

src/dxtbx/format/FormatMRC.py

@@ -70,7 +70,6 @@ def _unpack_header(header):
         return hd
 
     def _extend_header(self, xh):
-
         # Extensions from FEI headers only
         if not self._header_dictionary["exttyp"].startswith(b"FEI"):
             return
@@ -271,7 +270,6 @@ def _scan(self):
         return ScanFactory.make_scan((index, index), exposure, oscillation, {index: 0})
 
     def get_raw_data(self):
-
         with mrcfile.open(self._image_file) as mrc:
             image = flex.double(mrc.data.astype("double"))
 
@@ -315,7 +313,6 @@ def get_image_file(self, index=None):
         return Format.get_image_file(self)
 
     def get_raw_data(self, index):
-
         # Note MRC files use z, y, x ordering
         with mrcfile.mmap(self._image_file) as mrc:
             image = flex.double(mrc.data[index, ...].astype("double"))