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File cli.py has 710 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""Definitions for command-line (Click) commands for invoking Annif
operations and printing the results to console."""

import collections
import importlib
Severity: Major
Found in annif/cli.py - About 1 day to fix

    File mllm.py has 292 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """MLLM (Maui-like Lexical Matchin) model for Annif"""

from __future__ import annotations

import collections
    Severity: Minor
    Found in annif/lexical/mllm.py - About 3 hrs to fix

      File hfh_util.py has 288 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      """Utility functions for interactions with Hugging Face Hub."""

import binascii
import configparser
import importlib
      Severity: Minor
      Found in annif/hfh_util.py - About 2 hrs to fix

        File project.py has 280 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        """Project management functionality for Annif"""

from __future__ import annotations

import enum
        Severity: Minor
        Found in annif/project.py - About 2 hrs to fix

          AnnifProject has 24 functions (exceeds 20 allowed). Consider refactoring.
          Open

          class AnnifProject(DatadirMixin):
    """Class representing the configuration of a single Annif project."""

    # defaults for uninitialized instances
    _transform = None
          Severity: Minor
          Found in annif/project.py - About 2 hrs to fix

            Cyclomatic complexity is too high in function run_eval. (10)
            Open

            @cli.command("eval")
@cli_util.project_id
@click.argument("paths", type=click.Path(exists=True), nargs=-1)
@click.option("--limit", "-l", default=10, help="Maximum number of subjects")
@click.option("--threshold", "-t", default=0.0, help="Minimum score threshold")
            Severity: Minor
            Found in annif/cli.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in method _suggest. (9)
            Open

                def _suggest(self, text: str, params: dict[str, Any]) -> list[SubjectSuggestion]:
        data = {"text": text}
        if "project" in params:
            data["project"] = params["project"]
        if "limit" in params:
            Severity: Minor
            Found in annif/backend/http.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in function run_optimize. (8)
            Open

            @cli.command("optimize")
@cli_util.project_id
@click.argument("paths", type=click.Path(exists=True), nargs=-1)
@click.option(
    "--jobs", "-j", default=1, help="Number of parallel jobs (0 means all CPUs)"
            Severity: Minor
            Found in annif/cli.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in function _documents_to_corpus. (8)
            Open

            def _documents_to_corpus(
    documents: list[dict[str, Any]],
    subject_index: SubjectIndex | None,
) -> annif.corpus.document.DocumentList:
    if subject_index is not None:
            Severity: Minor
            Found in annif/rest.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

            def get_project(project_id: str, min_access: Access = Access.private) -> AnnifProject:
    """return the definition of a single Project by project_id"""

    projects = get_projects(min_access)
    try:
            Severity: Major
            Found in annif/registry.py and 1 other location - About 2 hrs to fix
            annif/registry.py on lines 155..162

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 58.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Cyclomatic complexity is too high in method save. (7)
            Open

                def save(self, path: str) -> None:
        """Save this subject index into a file with the given path name."""

        fieldnames = ["uri", "notation"] + [f"label_{lang}" for lang in self._languages]
            Severity: Minor
            Found in annif/corpus/subject.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in function filter_suggestion. (7)
            Open

            def filter_suggestion(
    preds: csr_array,
    limit: int | None = None,
    threshold: float = 0.0,
) -> csr_array:
            Severity: Minor
            Found in annif/suggestion.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in method tokenize_words. (7)
            Open

                def tokenize_words(self, text: str, filter: bool = True) -> list[str]:
        lemmas = [
            lemma
            for lemma in (token.lemma_ for token in self.nlp(text.strip()))
            if (not filter or self.is_valid_token(lemma))
            Severity: Minor
            Found in annif/analyzer/spacy.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in function run_upload. (7)
            Open

            @cli.command("upload")
@click.argument("project_ids_pattern", shell_complete=cli_util.complete_param)
@click.argument("repo_id")
@click.option(
    "--token",
            Severity: Minor
            Found in annif/cli.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

            def get_vocab(vocab_id: str, min_access: Access = Access.private) -> AnnifVocabulary:
    """return a single AnnifVocabulary by vocabulary id"""

    vocabs = get_vocabs(min_access)
    try:
            Severity: Major
            Found in annif/registry.py and 1 other location - About 2 hrs to fix
            annif/registry.py on lines 130..137

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 58.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Cyclomatic complexity is too high in method _create_train_file. (7)
            Open

                def _create_train_file(self, veccorpus: csr_matrix, corpus: DocumentCorpus) -> None:
        self.info("creating train file")
        path = os.path.join(self.datadir, self.TRAIN_FILE)
        with open(path, "w", encoding="utf-8") as trainfile:
            # Extreme Classification Repository format header line
            Severity: Minor
            Found in annif/backend/omikuji.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in function run_suggest. (7)
            Open

            @cli.command("suggest")
@cli_util.project_id
@click.argument(
    "paths", type=click.Path(dir_okay=False, exists=True, allow_dash=True), nargs=-1
)
            Severity: Minor
            Found in annif/cli.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in function run_index. (7)
            Open

            @cli.command("index")
@cli_util.project_id
@click.argument("directory", type=click.Path(exists=True, file_okay=False))
@click.option(
    "--suffix", "-s", default=".annif", help="File name suffix for result files"
            Severity: Minor
            Found in annif/cli.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in method _write_train_file. (6)
            Open

                def _write_train_file(self, corpus: DocumentCorpus, filename: str) -> None:
        with open(filename, "w", encoding="utf-8") as trainfile:
            for doc in corpus.documents:
                text = self._normalize_text(doc.text)
                if text == "":
            Severity: Minor
            Found in annif/backend/fasttext.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Cyclomatic complexity is too high in method _generate_subjects_from_documents. (6)
            Open

                def _generate_subjects_from_documents(
        self, corpus: DocumentCorpus
    ) -> Iterator[str]:
        with tempfile.TemporaryDirectory() as tempdir:
            subject_buffer = {}
            Severity: Minor
            Found in annif/backend/tfidf.py by radon

            Cyclomatic Complexity

            Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

            Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

            Construct Effect on CC Reasoning
            if +1 An if statement is a single decision.
            elif +1 The elif statement adds another decision.
            else +0 The else statement does not cause a new decision. The decision is at the if.
            for +1 There is a decision at the start of the loop.
            while +1 There is a decision at the while statement.
            except +1 Each except branch adds a new conditional path of execution.
            finally +0 The finally block is unconditionally executed.
            with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
            assert +1 The assert statement internally roughly equals a conditional statement.
            Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
            Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

            Source: http://radon.readthedocs.org/en/latest/intro.html

            Severity
            Category
            Status
            Source
            Language