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

def parse_index_file(filename):
    index = []
    for line in open(filename):
        index.append(int(line.strip()))
    return index
Severity: Major
Found in julia/datasets-gcn-to-npz.py and 1 other location - About 1 hr to fix
gae/input_data.py on lines 7..11

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 41.

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

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

def parse_index_file(filename):
    index = []
    for line in open(filename):
        index.append(int(line.strip()))
    return index
Severity: Major
Found in gae/input_data.py and 1 other location - About 1 hr to fix
julia/datasets-gcn-to-npz.py on lines 20..24

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 41.

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

Function mask_test_edges has 30 lines of code (exceeds 25 allowed). Consider refactoring.
Open

def mask_test_edges(adj):
    # Function to build test set with 10% positive links
    # NOTE: Splits are randomized and results might slightly deviate from reported numbers in the paper.
    # TODO: Clean up.
Severity: Minor
Found in gae/preprocessing.py - About 1 hr to fix

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

            with tf.variable_scope(self.name + '_vars'):
            self.vars['weights'] = weight_variable_glorot(input_dim, output_dim, name="weights")
    Severity: Major
    Found in gae/layers.py and 1 other location - About 1 hr to fix
    gae/layers.py on lines 71..72

    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 40.

    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

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

            with tf.variable_scope(self.name + '_vars'):
            self.vars['weights'] = weight_variable_glorot(input_dim, output_dim, name="weights")
    Severity: Major
    Found in gae/layers.py and 1 other location - About 1 hr to fix
    gae/layers.py on lines 90..91

    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 40.

    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

    Function build_user_features_lcc has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

    def build_user_features_lcc(uid2orig, orig2lcc, uid2tweets, word2cluster):
    """Build the COO matrix of user features, for users in
    the mutual mention largest connected component."""

    logging.info("Build user feature matrix from word/hashtag clustering")
    Severity: Minor
    Found in projects/twitter/csv_to_npz.py - About 1 hr 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 __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(self, input_dim, output_dim, adj, features_nonzero, dropout=0., act=tf.nn.relu, **kwargs):
    Severity: Major
    Found in gae/layers.py - About 50 mins to fix

      Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, input_dim, output_dim, adj, dropout=0., act=tf.nn.relu, **kwargs):
      Severity: Minor
      Found in gae/layers.py - About 45 mins to fix

        Avoid deeply nested control flow statements.
        Open

                        for model_type in tqdm([MODEL_OVERLAP, MODEL_NOOVERLAP]):
                    if model_type == MODEL_OVERLAP:
                        dim_ξ_adj = dim_ξ_ov_adj
                        dim_ξ_v = dim_ξ_ov_v
                        q_overlap = ov
        Severity: Major
        Found in projects/behaviour/scenarios-exploration-asymmetric-n_nodes=1000.py - About 45 mins to fix

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

                  self.reconstructions = InnerProductDecoder(input_dim=FLAGS.hidden2,
                                      act=lambda x: x,
                                      logging=self.logging)(self.embeddings)
          Severity: Minor
          Found in gae/model.py and 1 other location - About 45 mins to fix
          gae/model.py on lines 114..116

          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 35.

          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

          Function make_train_vae has 6 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def make_train_vae(dims, q_overlap, p_ξ_slices, skey, with_progress=True):
          Severity: Minor
          Found in projects/behaviour/scenarios-exploration-asymmetric-n_nodes=1000.py - About 45 mins to fix

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

                    self.cost = norm * tf.reduce_mean(tf.nn.weighted_cross_entropy_with_logits(logits=preds_sub, targets=labels_sub, pos_weight=pos_weight))
            Severity: Minor
            Found in gae/optimizer.py and 1 other location - About 45 mins to fix
            gae/optimizer.py on lines 28..28

            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 35.

            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

            Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def __init__(self, preds, labels, model, num_nodes, pos_weight, norm):
            Severity: Minor
            Found in gae/optimizer.py - About 45 mins to fix

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

                      self.cost = norm * tf.reduce_mean(tf.nn.weighted_cross_entropy_with_logits(logits=preds_sub, targets=labels_sub, pos_weight=pos_weight))
              Severity: Minor
              Found in gae/optimizer.py and 1 other location - About 45 mins to fix
              gae/optimizer.py on lines 12..12

              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 35.

              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

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

                      self.reconstructions = InnerProductDecoder(input_dim=FLAGS.hidden2,
                                      act=lambda x: x,
                                      logging=self.logging)(self.z)
              Severity: Minor
              Found in gae/model.py and 1 other location - About 45 mins to fix
              gae/model.py on lines 72..74

              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 35.

              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

              Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(self, placeholders, num_features, num_nodes, features_nonzero, **kwargs):
              Severity: Minor
              Found in gae/model.py - About 35 mins to fix

                Function make_vae has 5 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                def make_vae(n_nodes, dims, q_overlap, p_ξ_slices):
                Severity: Minor
                Found in projects/behaviour/scenarios-exploration-asymmetric-n_nodes=1000.py - About 35 mins to fix

                  Function train has 5 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                  def train(model, A, labels, features, with_progress=True):
                  Severity: Minor
                  Found in projects/behaviour/scenarios-exploration-asymmetric-n_nodes=1000.py - About 35 mins to fix

                    Function csv_to_adj has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                    Open

                    def csv_to_adj(filepath):
    """Read a `weight,src,dst` csv file into a COO adjacency matrix.

    Return the adjacency matrix in COO format, and the map of node ids in
    the file to ids in the matrix.
                    Severity: Minor
                    Found in projects/twitter/csv_to_npz.py - About 35 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

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

                    pos_weight = float(adj.shape[0] * adj.shape[0] - adj.sum()) / adj.sum()
                    Severity: Minor
                    Found in gae/train.py and 1 other location - About 35 mins to fix
                    gae/train.py on lines 78..78

                    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 33.

                    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

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