🎨 Format Python code with Black

Author: ruiqwy

BiFuncLib/AuxFunc.py

@@ -6,23 +6,27 @@
 
 
 class AuxFunc:
-    def __init__(self, n, m = None, x = None, V = None):
+    def __init__(self, n, m=None, x=None, V=None):
         self.n = n
         self.m = m if m is not None else None
         self.x = np.array(x) if x is not None else None
         self.V = np.array(V) if V is not None else None
 
     # Generate break sequence in spline expansion
     def knots_eq(self):
-        return np.r_[self.x.min(), np.linspace(self.x.min(), self.x.max(), self.m+2)[1:-1], self.x.max()]
+        return np.r_[
+            self.x.min(),
+            np.linspace(self.x.min(), self.x.max(), self.m + 2)[1:-1],
+            self.x.max(),
+        ]
 
     # Construct the adjacency matrix
-    def create_adjacency(self, plot = True):
+    def create_adjacency(self, plot=True):
         differences = np.linalg.norm(self.V, axis=0)
         connected_ix = np.where(differences == 0)[0]
         index = pd.DataFrame(itertools.combinations(range(self.n), 2))
-        i = index.iloc[list(connected_ix),0]
-        j = index.iloc[list(connected_ix),1]
+        i = index.iloc[list(connected_ix), 0]
+        j = index.iloc[list(connected_ix), 1]
         A = lil_matrix((self.n, self.n))
         A[i, j] = 1
         if plot == True:
@@ -31,4 +35,3 @@ def create_adjacency(self, plot = True):
             plt.show()
         A_array = A.toarray()
         return A_array
-

BiFuncLib/BiclustResult.py

@@ -9,4 +9,4 @@ def __init__(self, params, RowxNumber, NumberxCol, Number, info):
         self.Number = Number
         self.info = info
         self.cluster_row_sizes = np.sum(RowxNumber, axis=0)
-        self.cluster_col_sizes = np.sum(NumberxCol, axis=0)
+        self.cluster_col_sizes = np.sum(NumberxCol, axis=0)

BiFuncLib/BsplineFunc.py

@@ -1,16 +1,39 @@
-from .simulation_data import pf_sim_data,local_sim_data,cc_sim_data,lbm_sim_data
-from .simulation_data import sas_sim_data,sparse_sim_data,cvx_sim_data,ssvd_sim_data
+from .simulation_data import (
+    pf_sim_data,
+    local_sim_data,
+    cc_sim_data,
+    lbm_sim_data,
+)
+from .simulation_data import (
+    sas_sim_data,
+    sparse_sim_data,
+    cvx_sim_data,
+    ssvd_sim_data,
+)
 from .BsplineFunc import BsplineFunc
 from .BiclustResult import BiclustResult
 from .bcheatmap import bcheatmap
 from .fem_bifunc import fem_bifunc
-from .sparse_main_func import FKMSparseClustering_permute, FKMSparseClustering, cer
+from .sparse_main_func import (
+    FKMSparseClustering_permute,
+    FKMSparseClustering,
+    cer,
+)
 from .fem_main_func import fem_main_func
 from .AuxFunc import AuxFunc
 from .pf_main_func import inv_uty_cal, beta_ini_cal, biclustr_admm
-from .cvx_main_func import gkn_weights, cobra_validate, cobra_pod, biclust_smooth
+from .cvx_main_func import (
+    gkn_weights,
+    cobra_validate,
+    cobra_pod,
+    biclust_smooth,
+)
 from .ssvd_main_func import ssvd_bc, s4vd, jaccardmat
-from .cc_main_func import template_evaluation, medoid_evaluation, warping_function_plot
+from .cc_main_func import (
+    template_evaluation,
+    medoid_evaluation,
+    warping_function_plot,
+)
 from .bimax_biclus import bimax_biclus
 from .cc_main_func import bigcc_fun, evaluate_mat_dist, ccscore_fun
 from .sas_main_func import sasfclust_init, loglik, get_msdrule, get_zero
@@ -19,12 +42,50 @@
 from .lbm_main_func import lbm_main_func
 
 
-__all__ = ['pf_sim_data', 'local_sim_data', 'cc_sim_data', 'lbm_sim_data', 'sas_sim_data',
-           'sparse_sim_data', 'cvx_sim_data', 'ssvd_sim_data', 'BsplineFunc', 'fem_bifunc',
-           'FKMSparseClustering_permute', 'FKMSparseClustering', 'cer', 'fem_main_func',
-           'AuxFunc', 'inv_uty_cal', 'beta_ini_cal', 'biclustr_admm', 'gkn_weights',
-           'cobra_validate', 'cobra_pod', 'biclust_smooth', 'ssvd_bc', 's4vd', 'bcheatmap',
-           'jaccardmat', 'template_evaluation', 'medoid_evaluation', 'warping_function_plot',
-           'bimax_biclus', 'bigcc_fun', 'evaluate_mat_dist', 'ccscore_fun', 'sasfclust_init',
-           'loglik', 'get_msdrule', 'get_zero', 'sasfclust_Mstep', 'sasfclust_Estep', 'classify',
-           'calculate_gcv', 'calculate_bic', 'local_admm', 'lbm_main_func', 'BiclustResult']
+__all__ = [
+    "pf_sim_data",
+    "local_sim_data",
+    "cc_sim_data",
+    "lbm_sim_data",
+    "sas_sim_data",
+    "sparse_sim_data",
+    "cvx_sim_data",
+    "ssvd_sim_data",
+    "BsplineFunc",
+    "fem_bifunc",
+    "FKMSparseClustering_permute",
+    "FKMSparseClustering",
+    "cer",
+    "fem_main_func",
+    "AuxFunc",
+    "inv_uty_cal",
+    "beta_ini_cal",
+    "biclustr_admm",
+    "gkn_weights",
+    "cobra_validate",
+    "cobra_pod",
+    "biclust_smooth",
+    "ssvd_bc",
+    "s4vd",
+    "bcheatmap",
+    "jaccardmat",
+    "template_evaluation",
+    "medoid_evaluation",
+    "warping_function_plot",
+    "bimax_biclus",
+    "bigcc_fun",
+    "evaluate_mat_dist",
+    "ccscore_fun",
+    "sasfclust_init",
+    "loglik",
+    "get_msdrule",
+    "get_zero",
+    "sasfclust_Mstep",
+    "sasfclust_Estep",
+    "classify",
+    "calculate_gcv",
+    "calculate_bic",
+    "local_admm",
+    "lbm_main_func",
+    "BiclustResult",
+]