py2ls 0.2.5.12__py3-none-any.whl → 0.2.5.15__py3-none-any.whl

py2ls/netfinder.py

@@ -1,7 +1,8 @@
-from bs4 import BeautifulSoup
+from bs4 import BeautifulSoup, NavigableString
 import scrapy
 import requests
 import os
+import chardet
 import pandas as pd
 import logging
 import json
@@ -116,8 +117,8 @@ def extract_text_from_content(
 
     def extract_text(element):
         texts = ""
-        if isinstance(element, str) and element.strip():
-            texts += element.strip()
+        if isinstance(element, NavigableString) and element.strip():  
+            texts += element.strip() + " " 
         elif hasattr(element, "children"):
             for child in element.children:
                 texts += extract_text(child)
@@ -172,6 +173,8 @@ def extract_text_from_content(
                 texts = ""
                 for tag in result_set:
                     texts = texts + " " + extract_text(tag) + " \n"
+                    # texts = texts + " " + tag.get_text(" ", strip=True)+ " \n"
+                    
                 text_list = [tx.strip() for tx in texts.split(" \n") if tx.strip()]
                 return text_list
             else:
@@ -816,9 +819,13 @@ def fetch_all(
             )
             if error:
                 return None, None
-                
             content_type = response.headers.get("content-type", "").split(";")[0].lower()
-            content = response.content.decode(response.encoding or 'utf-8', errors='replace')
+            try:
+                detected = chardet.detect(response.content)
+                encoding = detected.get("encoding") or "utf-8"
+                content = response.content.decode(encoding, errors='replace')
+            except:
+                content = response.content.decode(response.encoding or 'utf-8', errors='replace')
             
             return content_type, _parse_content(content, content_type, parser)
             

py2ls/plot.py

@@ -23,6 +23,7 @@ from .ips import (
     get_df_format,
     df_corr,
     df_scaler,
+    df2array,array2df
 )
 import scipy.stats as scipy_stats
 from .stats import *
@@ -1350,7 +1351,7 @@ def catplot(data, *args, **kwargs):
         # # Example usage:
         # custom_order = ['s', 'bx', 'e']
         # full_order = sort_catplot_layers(custom_order)
-
+    data=data.copy()
     ax = kwargs.get("ax", None)
     col = kwargs.get("col", None)
     report = kwargs.get("report", True)
@@ -1363,8 +1364,9 @@ def catplot(data, *args, **kwargs):
             df = data.copy()
             x = kwargs.get("x", None)
             y = kwargs.get("y", None)
-            hue = kwargs.get("hue", None)
+            hue = kwargs.get("hue", None) 
             data = df2array(data=data, x=x, y=y, hue=hue)
+            
             y_max_loc = np.max(data, axis=0)
             xticklabels = []
             if hue is not None:
@@ -1518,7 +1520,11 @@ def catplot(data, *args, **kwargs):
                 display_output(res)
 
             # when the xticklabels are too long, rotate the labels a bit
-            xangle = 30 if max([len(i) for i in xticklabels]) > 50 else 0
+            try:
+                xangle = 30 if max([len(i) for i in xticklabels]) > 50 else 0
+            except:
+                xangle = 0
+
             if kw_figsets is not None:
                 kw_figsets = {
                     "ylabel": y,
@@ -3259,13 +3265,13 @@ def plot_xy(
     x=None,
     y=None,
     ax=None,
-    kind: Union[str, list] = None,  # Specify the kind of plot
+    kind_: Union[str, list] = None,  # Specify the kind of plot
     verbose=False,
     **kwargs,
 ):
     # You can call the original plotxy function if needed
     # or simply replicate the functionality here
-    return plotxy(data, x, y, ax, kind, verbose, **kwargs)
+    return plotxy(data, x=x, y=y, ax=ax, kind_=kind_, verbose=verbose, **kwargs)
 
 
 def plotxy(
@@ -3353,7 +3359,7 @@ def plotxy(
     
     # ============ preprocess data ============
     try:
-        data = df_preprocessing_(data, kind=kind_[0])
+        data = df_preprocessing_(data, kind=kind_[0]) 
         if "variable" in data.columns and "value" in data.columns:
             x, y = "variable", "value"
     except Exception as e:
@@ -3903,7 +3909,7 @@ def df_preprocessing_(data, kind, verbose=False):
         "pointplot",  # Works well with wide format
         "ellipse",
     ]
-
+    print(kind)
     # Wide format (e.g., for heatmap and pairplot)
     if kind in wide_kinds:
         if df_format_ != "wide":

py2ls/stats.py

@@ -8,7 +8,7 @@ import matplotlib.pyplot as plt
 import warnings
 
 warnings.filterwarnings("ignore", category=RuntimeWarning)
-
+from .ips import df2array
 
 # FuncStars --v 0.1.1
 def FuncStars(
@@ -902,148 +902,5 @@ def df_wide_long(df):
         return "Long"
 
 
-def sort_rows_move_nan(arr, sort=False):
-    # Handle edge cases where all values are NaN
-    if np.all(np.isnan(arr)):
-        return arr  # Return unchanged if the entire array is NaN
-
-    if sort:
-        # Replace NaNs with a temporary large value for sorting
-        temp_value = (
-            np.nanmax(arr[np.isfinite(arr)]) + 1 if np.any(np.isfinite(arr)) else np.inf
-        )
-        arr_no_nan = np.where(np.isnan(arr), temp_value, arr)
-
-        # Sort each row
-        sorted_arr = np.sort(arr_no_nan, axis=1)
-
-        # Move NaNs to the end
-        result_arr = np.where(sorted_arr == temp_value, np.nan, sorted_arr)
-    else:
-        result_rows = []
-        for row in arr:
-            # Separate non-NaN and NaN values
-            non_nan_values = row[~np.isnan(row)]
-            nan_count = np.isnan(row).sum()
-            # Create a new row with non-NaN values followed by NaNs
-            new_row = np.concatenate([non_nan_values, [np.nan] * nan_count])
-            result_rows.append(new_row)
-        # Convert the list of rows back into a 2D NumPy array
-        result_arr = np.array(result_rows)
-
-    # Remove rows/columns that contain only NaNs
-    clean_arr = result_arr[~np.isnan(result_arr).all(axis=1)]
-    clean_arr_ = clean_arr[:, ~np.isnan(clean_arr).all(axis=0)]
-
-    return clean_arr_
-
-
-def df2array(data: pd.DataFrame, x=None, y=None, hue=None, sort=False):
-    if hue is None:
-        a = []
-        if sort:
-            cat_x = np.sort(data[x].unique().tolist()).tolist()
-        else:
-            cat_x = data[x].unique().tolist()
-        for i, x_ in enumerate(cat_x):
-            new_ = data.loc[data[x] == x_, y].to_list()
-            a = padcat(a, new_, axis=0)
-        return sort_rows_move_nan(a).T
-    else:
-        a = []
-        if sort:
-            cat_x = np.sort(data[x].unique().tolist()).tolist()
-            cat_hue = np.sort(data[hue].unique().tolist()).tolist()
-        else:
-            cat_x = data[x].unique().tolist()
-            cat_hue = data[hue].unique().tolist()
-        for i, x_ in enumerate(cat_x):
-            for j, hue_ in enumerate(cat_hue):
-                new_ = data.loc[(data[x] == x_) & (data[hue] == hue_), y].to_list()
-                a = padcat(a, new_, axis=0)
-        return sort_rows_move_nan(a).T
-
-
-def array2df(data: np.ndarray):
-    df = pd.DataFrame()
-    df["group"] = (
-        np.tile(
-            ["group" + str(i) for i in range(1, data.shape[1] + 1)], [data.shape[0], 1]
-        )
-        .reshape(-1, 1, order="F")[:, 0]
-        .tolist()
-    )
-    df["value"] = data.reshape(-1, 1, order="F")
-    return df
-
-
-def padcat(*args, fill_value=np.nan, axis=1, order="row"):
-    """
-    Concatenate vectors with padding.
-
-    Parameters:
-    *args : variable number of list or 1D arrays
-        Input arrays to concatenate.
-    fill_value : scalar, optional
-        The value to use for padding the shorter lists (default is np.nan).
-    axis : int, optional
-        The axis along which to concatenate (0 for rows, 1 for columns, default is 1).
-    order : str, optional
-        The order for flattening when required: "row" or "column" (default is "row").
-
-    Returns:
-    np.ndarray
-        A 2D array with the input arrays concatenated along the specified axis,
-        padded with fill_value where necessary.
-    """
-    # Set the order for processing
-    if "ro" in order.lower():
-        order = "C"  # row-major order
-    else:
-        order = "F"  # column-major order
-
-    # Process input arrays based on their dimensions
-    processed_arrays = []
-    for arg in args:
-        arr = np.asarray(arg)
-        if arr.ndim == 1:
-            processed_arrays.append(arr)  # Keep 1D arrays as is
-        elif arr.ndim == 2:
-            if axis == 0:
-                # If concatenating along rows, split 2D arrays into 1D arrays row-wise
-                processed_arrays.extend(arr)
-            elif axis == 1:
-                # If concatenating along columns, split 2D arrays into 1D arrays column-wise
-                processed_arrays.extend(arr.T)
-            else:
-                raise ValueError("axis must be 0 or 1")
-        else:
-            raise ValueError("Input arrays must be 1D or 2D")
-
-    if axis == 0:
-        # Concatenate along rows
-        max_len = max(arr.size for arr in processed_arrays)
-        result = np.full((len(processed_arrays), max_len), fill_value)
-        for i, arr in enumerate(processed_arrays):
-            result[i, : arr.size] = arr
-    elif axis == 1:
-        # Concatenate along columns
-        max_len = max(arr.size for arr in processed_arrays)
-        result = np.full((max_len, len(processed_arrays)), fill_value)
-        for i, arr in enumerate(processed_arrays):
-            result[: arr.size, i] = arr
-    else:
-        raise ValueError("axis must be 0 or 1")
-
-    return result
 
 
-# # Example usage:
-# a = [1, np.nan]
-# b = [1, 3, 4, np.nan, 2, np.nan]
-# c = [1, 2, 3, 4, 5, 6, 7, 8, 10]
-# d = padcat(a, b)
-# result1 = padcat(d, c)
-# result2 = padcat(a, b, c)
-# print("Result of padcat(d, c):\n", result1)
-# print("Result of padcat(a, b, c):\n", result2)

{py2ls-0.2.5.12.dist-info → py2ls-0.2.5.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.5.12
+Version: 0.2.5.15
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com
@@ -14,239 +14,92 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Provides-Extra: full
+Provides-Extra: light
 Provides-Extra: ml
 Provides-Extra: neuroscience
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 Description-Content-Type: text/markdown
 
 # Install
@@ -255,6 +108,10 @@ Description-Content-Type: text/markdown
 pip install py2ls
 ```
 
+- Minimal version: pip install py2ls
+- Light version: pip install py2ls[light]
+- Full version: pip install py2ls[full]
+- Or any combination like pip install py2ls[full,ml]
 
 
 # ips