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Function _hdbscan_candidates has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _hdbscan_candidates(self, points):
        '''
        Use hdbscan clustering to find potential candidates for lattice vectors.

        We rely on the clusterer and its settings to give us tight and well-populated clusters.
Severity: Minor
Found in src/libertem/analysis/fullmatch.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run_tasks has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def run_tasks(
        self,
        tasks: Iterable[TaskProtocol],
        params_handle: Any,
        cancel_id: Any,
Severity: Minor
Found in src/libertem/executor/inline.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function adjust_event_loop_policy has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def adjust_event_loop_policy():
    """
    Set an appropriate event loop policy on Windows. The new one from Python 3.8 doesn't
    work for us by default, so call this as early as possible!
    """
Severity: Minor
Found in src/libertem/common/async_utils.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function decode_r12_swap_2x2 has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def decode_r12_swap_2x2(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
    """
    RAW 12bit format: the pixels need to be re-ordered in groups of 4. `inp`
    should be an uint8 view on padded big endian 12bit data (">u2").
    This is the quad variant.
Severity: Minor
Found in src/libertem/io/dataset/mib.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function decode_r1_swap has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def decode_r1_swap(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
    """
    RAW 1bit format: each pixel is actually saved as a single bit. 64 bits
    need to be unpacked together.
    """
Severity: Minor
Found in src/libertem/io/dataset/mib.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def data(self):
        """
        Get the buffer contents in shape that corresponds to the
        original dataset shape. If a ROI is set, embed the result into a new
        array; unset values have NaN value for floating point types,
Severity: Minor
Found in src/libertem/common/buffers.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _tags_to_nest has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _tags_to_nest(tags: dict[str, Any]):
        tags_nest = {}
        for tag, element in tags.items():
            tag = tag.strip('.')
            _insert_to = tags_nest
Severity: Minor
Found in src/libertem/io/dataset/dm_single.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function numba_ravel_multi_index_multi has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def numba_ravel_multi_index_multi(multi_index, dims):
    # only supports the "multi index" case
    idxs = range(len(dims) - 1, -1, -1)
    res = np.zeros(len(multi_index[0]), dtype=np.intp)
    for i in range(len(res)):
Severity: Minor
Found in src/libertem/common/numba/__init__.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function log_message has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def log_message(message, exception=False):
    log_fn = log.info
    if exception:
        log_fn = log.exception
    if "job" in message:
Severity: Minor
Found in src/libertem/web/base.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _prepare_plots has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _prepare_plots(
        self,
        udfs: list[UDF],
        dataset: DataSet,
        roi: RoiT,
Severity: Minor
Found in src/libertem/api.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function decode_r6_swap_2x2 has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def decode_r6_swap_2x2(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
    """
    RAW 6bit format: the pixels need to be re-ordered in groups of 8. `inp`
    should have dtype uint8. This is the quad variant.
Severity: Minor
Found in src/libertem/io/dataset/mib.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _validate_resources has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _validate_resources(self, workers, resources):
        # This is set in the constructor of DaskJobExecutor
        if self.lt_resources:
            if not self._resources_available(workers, resources):
                raise ResourceError("Requested resources not available in cluster:", resources)
Severity: Minor
Found in src/libertem/executor/dask.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _get_alt_path has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def _get_alt_path(path: str):
    cur_path = Path(path).expanduser()
    try:
        cur_path = cur_path.resolve()
    # Triggered by empty DVD drive or permission denied on Windows
Severity: Minor
Found in src/libertem/io/fs.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function main has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def main():
    BASE_DIR = os.path.abspath(os.path.dirname(__file__))

    with open(os.path.join(BASE_DIR, "../.mypy-checked")) as f:
        files_project = set(f.read().split())
Severity: Minor
Found in scripts/run_mypy.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _setup_device has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def _setup_device(spec: WorkerSpec, pin: bool):
    """
    Set up this worker for its given task - either CPU or GPU comptation,
    and maybe pin CPU workers to a given CPU core.
    """
Severity: Minor
Found in src/libertem/executor/pipelined.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function initialize has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def initialize(self, executor: "JobExecutor") -> "DataSet":
        self._conf = conf = executor.run_function(load_toml, self._path)
        assert conf is not None
        if conf['params']['filetype'].lower() != 'raw_csr':
            raise ValueError(f"Filetype is not CSR, found {conf['params']['filetype']}")
Severity: Minor
Found in src/libertem/io/dataset/raw_csr.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function create_com_analysis has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def create_com_analysis(self, dataset: DataSet, cx: int = None, cy: int = None,
                            mask_radius: float = None, flip_y: bool = False,
                            mask_radius_inner: float = None,
                            scan_rotation: float = 0.0) -> COMAnalysis:
        """
Severity: Minor
Found in src/libertem/api.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _frms6_read_ranges_tile_block has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def _frms6_read_ranges_tile_block(
    slices_arr, fileset_arr, slice_sig_sizes, sig_origins,
    inner_indices_start, inner_indices_stop, frame_indices, sig_size,
    px_to_bytes, bpp, frame_header_bytes, frame_footer_bytes, file_idxs,
    slice_offset, extra, sig_shape,
Severity: Minor
Found in src/libertem/io/dataset/frms6.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _get_norm has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def _get_norm(result, norm_cls=colors.Normalize, vmin=None, vmax=None, damage=None):
    if (vmin is not None) and (vmax is not None):
        return norm_cls(vmin=vmin, vmax=vmax)

    result = result.astype(np.float32)
Severity: Minor
Found in src/libertem/viz/base.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _do_get_results has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def _do_get_results(self) -> Mapping[str, BufferWrapper]:
        results_tmp = self.get_results()
        decl = self.get_result_buffers()

        # include any results that were not explicitly included, but have non-private `use`:
Severity: Minor
Found in src/libertem/udf/base.py - About 25 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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