def extract_bower_zipfile(self, zip_file, dest, expected_version=None):
        bower_json = None
        root = None
        deps_installed = []
        for info in zip_file.infolist():
            if PurePath(info.filename).name == "bower.json":
                with zip_file.open(info) as f:
                    bower_json = json.load(f)
                    root = str(PurePath(info.filename).parent)
                break
        version = bower_json["version"]
        if expected_version is not None:
            expected_version = Bower.clean_semver(expected_version)
            if not semver.match(version, expected_version):
                click.secho("error: versions do not match ({} =/= {})".format(
                    version, expected_version))
                raise InvalidPackageError
        if "dependencies" in bower_json:
            for package, version in bower_json["dependencies"].items():
                url = Bower.get_package_url(package)
                deps_installed.extend(self.get_bower_package(
                    url, dest=dest, version=version))
        ignore_patterns = [GitIgnorePattern(ig) for ig in bower_json["ignore"]]
        path_spec = PathSpec(ignore_patterns)
        namelist = [path for path in zip_file.namelist()
                    if PurePath(path).parts[0] == root]
        ignored = list(path_spec.match_files(namelist))
        for path in namelist:
            dest_path = PurePath(
                bower_json["name"],
                *PurePath(path).parts[1:])

            if path in ignored:
                continue

            for path in ignored:
                for parent in PurePath(path):
                    if parent in ignored:
                        continue

            if path.endswith("/"):
                if list(path_spec.match_files([str(dest_path)])):
                    ignored.append(PurePath(path))
                elif not (dest / dest_path).is_dir():
                    (dest / dest_path).mkdir(parents=True)
            else:
                target_path = dest / dest_path.parent / dest_path.name
                source = zip_file.open(path)
                target = target_path.open("wb")
                with source, target:
                    shutil.copyfileobj(source, target)
        deps_installed.append((bower_json["name"], bower_json["version"]))
        return deps_installed
def apply_svm(K, y, n_folds=5, iterations=10000, subjects=False, verbose=True,
              random_state=None):
    """
    Compute the balanced accuracy, its null distribution and the p-value.

    Parameters:
    ----------
    K: array-like
        Kernel matrix
    y: array_like
        class labels
    cv: Number of folds in the stratified cross-validation
    verbose: bool
        Verbosity

    Returns:
    -------
    acc: float
        Average balanced accuracy.
    acc_null: array
        Null distribution of the balanced accuracy.
    p_value: float
         p-value
    """
    # Computing the accuracy
    param_grid = [{'C': np.logspace(-5, 5, 20)}]
    if subjects:
        acc = compute_svm_subjects(K, y, n_folds)
    else:
        acc = compute_svm_score_nestedCV(K, y, n_folds, param_grid=param_grid,
                                         random_state=random_state)
    if verbose:
        print("Mean balanced accuracy = %s" % (acc))
        print("Computing the null-distribution.")

    # Computing the null-distribution

    # acc_null = np.zeros(iterations)
    # for i in range(iterations):
    #     if verbose and (i % 1000) == 0:
    #         print(i),
    #         stdout.flush()

    #     y_perm = np.random.permutation(y)
    #     acc_null[i] = compute_svm_score_nestedCV(K, y_perm, n_folds,
    #                                              param_grid=param_grid)

    # if verbose:
    #     print ''

    # Computing the null-distribution
    if subjects:
        yis = [permutation_subjects(y) for i in range(iterations)]
        acc_null = Parallel(n_jobs=-1)(delayed(compute_svm_subjects)(K, yis[i], n_folds) for i in range(iterations))
    else:
        yis = [np.random.permutation(y) for i in range(iterations)]
        acc_null = Parallel(n_jobs=-1)(delayed(compute_svm_score_nestedCV)(K, yis[i], n_folds, scoring=balanced_accuracy_scoring, param_grid=param_grid) for i in range(iterations))
    # acc_null = Parallel(n_jobs=-1)(delayed(compute_svm_cv)(K, yis[i], C=100., n_folds=n_folds) for i in range(iterations))

    p_value = max(1.0 / iterations, (acc_null > acc).sum()
                  / float(iterations))
    if verbose:
        print("p-value ~= %s \t (resolution : %s)" % (p_value, 1.0/iterations))

    return acc, acc_null, p_value