kececilayout 0.5.6__tar.gz → 0.5.8__tar.gz

{kececilayout-0.5.6/kececilayout.egg-info → kececilayout-0.5.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kececilayout
-Version: 0.5.6
+Version: 0.5.8
 Summary: Çeşitli graf kütüphaneleri için sıralı-zigzag yerleşimleri sağlayan bir Python paketi.
 Home-page: https://github.com/WhiteSymmetry/kececilayout
 Author: Mehmet Keçeci

{kececilayout-0.5.6 → kececilayout-0.5.8}/kececilayout/__init__.py

@@ -10,7 +10,7 @@ import inspect
 import warnings
 
 # Paket sürüm numarası
-__version__ = "0.5.6"
+__version__ = "0.5.8"
 
 # =============================================================================
 # OTOMATİK İÇE AKTARMA VE __all__ OLUŞTURMA
@@ -65,6 +65,8 @@ from .kececi_layout import (  # Veya fonksiyonların bulunduğu asıl modül
     avg_edge_length,
     _segments_intersect,
     count_edge_crossings,
+    generate_complete_periodic_table,
+    load_element_data_from_python_dict,
     
     # Drawing functions
     draw_kececi,
@@ -121,6 +123,8 @@ __all__ = [
     'avg_edge_length',
     '_segments_intersect',
     'count_edge_crossings',
+    'generate_complete_periodic_table',
+    'load_element_data_from_python_dict',
 
     # Drawing functions
     'draw_kececi',
@@ -177,3 +181,5 @@ def old_function_placeholder():
 
 
 
+
+

{kececilayout-0.5.6 → kececilayout-0.5.8}/kececilayout/_version.py

@@ -1,6 +1,6 @@
 # _version.py
 
-__version__ = "0.5.6"
+__version__ = "0.5.8"
 __license__ = "AGPL3.0-or-later"
 __description__ = "A deterministic node placement algorithm used in graph visualization. In this layout, nodes are arranged sequentially along a defined primary axis. Each subsequent node is then alternately offset along a secondary, perpendicular axis, typically moving to one side of the primary axis and then the other. Often, the magnitude of this secondary offset increases as nodes progress along the primary axis, creating a characteristic zig-zag or serpentine pattern."
 __author__ = "Mehmet Keçeci"
@@ -8,4 +8,3 @@ __url__ = "https://github.com/WhiteSymmetry/kececilayout"
 __docs__ = "https://github.com/WhiteSymmetry/kececilayout"  # Opsiyonel: Dokümantasyon linki
 __dependencies__ = ["python>=3.11"]  # Diğer bağımlılıkları da ekleyebilirsiniz
 
-

{kececilayout-0.5.6 → kececilayout-0.5.8}/kececilayout/kececi_layout.py

@@ -34,8 +34,10 @@ import networkit as nk
 import networkx as nx
 import numpy as np # rustworkx
 from numba import jit
+import os
 import platform # graph_tool için
 import random
+import re
 import rustworkx as rx
 from typing import Any, Dict, List, Optional, Tuple, Union
 import warnings
@@ -1558,29 +1560,306 @@ def _kececi_layout_3d_helix(nx_graph):
 def kececi_layout_3d_helix_parametric(nx_graph, z_spacing=2.0, radius=5.0, turns=2.0):
     """
     Parametric 3D helix layout for nodes. User can control spacing, radius, and number of turns.
+    Fixed version with division by zero handling.
+    
     Args:
         nx_graph: NetworkX graph.
         z_spacing (float): Vertical distance between consecutive nodes.
         radius (float): Radius of the helix.
         turns (float): Number of full turns the helix makes.
+    
     Returns:
         dict: {node_id: (x, y, z)}
     """
     nodes = sorted(list(nx_graph.nodes()))
     pos_3d = {}
     total_nodes = len(nodes)
+    
     if total_nodes == 0:
+        print(f"Warning: Graph has {total_nodes} nodes!")
         return pos_3d
     
     total_angle = 2 * np.pi * turns
+    
     for i, node_id in enumerate(nodes):
         z = i * z_spacing
-        angle = (i / (total_nodes - 1)) * total_angle if total_nodes > 1 else 0
+        
+        # Division by zero fix for single node case
+        if total_nodes > 1:
+            angle = (i / (total_nodes - 1)) * total_angle
+        else:
+            angle = 0
+        
         x = np.cos(angle) * radius
         y = np.sin(angle) * radius
         pos_3d[node_id] = (x, y, z)
+    
     return pos_3d
 
+def load_element_data_from_python_dict(filename):
+    """Loads element data from a Python dictionary format file."""
+    element_data = {}
+    spectral_lines = {}
+    
+    print(f"Loading file: {filename}")
+    print(f"File exists: {os.path.exists(filename)}")
+    
+    if not os.path.exists(filename):
+        print(f"ERROR: File '{filename}' not found in directory: {os.getcwd()}")
+        return element_data, spectral_lines
+    
+    try:
+        with open(filename, 'r', encoding='utf-8') as f:
+            content = f.read()
+            
+        # Find element_data dictionary
+        element_data_match = re.search(r'element_data\s*=\s*\{([^}]+)\}', content, re.DOTALL)
+        if element_data_match:
+            element_data_str = element_data_match.group(0)
+            print("Found element_data dictionary")
+            
+            # generate a safe environment to evaluate the dictionary
+            safe_dict = {}
+            exec(element_data_str, {"__builtins__": {}}, safe_dict)
+            
+            if 'element_data' in safe_dict:
+                element_data = safe_dict['element_data']
+                print(f"Successfully loaded {len(element_data)} elements")
+            else:
+                print("element_data not found in evaluated content")
+                
+                # Manual parsing as fallback
+                print("Attempting manual parsing...")
+                lines = element_data_str.split('\n')
+                for line in lines:
+                    line = line.strip()
+                    if ':' in line and '(' in line:
+                        # Parse line like: 1: ("H", 1),
+                        match = re.search(r'(\d+):\s*\("([^"]+)",\s*(\d+)\)', line)
+                        if match:
+                            key = int(match.group(1))
+                            symbol = match.group(2)
+                            atomic_num = int(match.group(3))
+                            element_data[key] = (symbol, atomic_num)
+        
+        # Find spectral_lines dictionary if exists
+        spectral_match = re.search(r'spectral_lines\s*=\s*\{([^}]+)\}', content, re.DOTALL)
+        if spectral_match:
+            spectral_str = spectral_match.group(0)
+            print("Found spectral_lines dictionary")
+            
+            safe_dict = {}
+            exec(spectral_str, {"__builtins__": {}}, safe_dict)
+            
+            if 'spectral_lines' in safe_dict:
+                spectral_lines = safe_dict['spectral_lines']
+                print(f"Successfully loaded {len(spectral_lines)} spectral lines")
+        
+        # If no dictionaries found, try simple CSV format
+        if not element_data:
+            print("No dictionaries found, trying CSV format...")
+            lines = content.split('\n')
+            current_section = None
+            
+            for line in lines:
+                line = line.strip()
+                if not line or line.startswith('#'):
+                    if "element" in line.lower():
+                        current_section = "element"
+                    elif "spectral" in line.lower():
+                        current_section = "spectral"
+                    continue
+                
+                parts = [p.strip() for p in line.split(',')]
+                if current_section == "element" and len(parts) >= 2:
+                    try:
+                        symbol = parts[0]
+                        atomic_number = int(parts[1])
+                        element_data[atomic_number] = (symbol, atomic_number)
+                    except:
+                        continue
+                elif current_section == "spectral" and len(parts) >= 2:
+                    symbol = parts[0]
+                    wavelengths = []
+                    for wl in parts[1:]:
+                        if wl:
+                            try:
+                                wavelengths.append(float(wl))
+                            except:
+                                continue
+                    if wavelengths:
+                        spectral_lines[symbol] = wavelengths
+                        
+    except Exception as e:
+        print(f"Error reading/parsing file: {str(e)}")
+        import traceback
+        traceback.print_exc()
+    
+    print(f"\nTotal elements loaded: {len(element_data)}")
+    print(f"Total spectral lines loaded: {len(spectral_lines)}")
+    
+    if element_data:
+        print("\nFirst 10 elements:")
+        for i, (key, val) in enumerate(list(element_data.items())[:10]):
+            print(f"  {key}: {val}")
+    
+    return element_data, spectral_lines
+
+def generate_complete_periodic_table():
+    """generate a complete periodic table with all 118 elements."""
+    print("Creating complete periodic table...")
+    
+    periodic_elements = {
+        1: ('H', 1), 2: ('He', 2), 3: ('Li', 3), 4: ('Be', 4), 5: ('B', 5),
+        6: ('C', 6), 7: ('N', 7), 8: ('O', 8), 9: ('F', 9), 10: ('Ne', 10),
+        11: ('Na', 11), 12: ('Mg', 12), 13: ('Al', 13), 14: ('Si', 14), 15: ('P', 15),
+        16: ('S', 16), 17: ('Cl', 17), 18: ('Ar', 18), 19: ('K', 19), 20: ('Ca', 20),
+        21: ('Sc', 21), 22: ('Ti', 22), 23: ('V', 23), 24: ('Cr', 24), 25: ('Mn', 25),
+        26: ('Fe', 26), 27: ('Co', 27), 28: ('Ni', 28), 29: ('Cu', 29), 30: ('Zn', 30),
+        31: ('Ga', 31), 32: ('Ge', 32), 33: ('As', 33), 34: ('Se', 34), 35: ('Br', 35),
+        36: ('Kr', 36), 37: ('Rb', 37), 38: ('Sr', 38), 39: ('Y', 39), 40: ('Zr', 40),
+        41: ('Nb', 41), 42: ('Mo', 42), 43: ('Tc', 43), 44: ('Ru', 44), 45: ('Rh', 45),
+        46: ('Pd', 46), 47: ('Ag', 47), 48: ('Cd', 48), 49: ('In', 49), 50: ('Sn', 50),
+        51: ('Sb', 51), 52: ('Te', 52), 53: ('I', 53), 54: ('Xe', 54), 55: ('Cs', 55),
+        56: ('Ba', 56), 57: ('La', 57), 58: ('Ce', 58), 59: ('Pr', 59), 60: ('Nd', 60),
+        61: ('Pm', 61), 62: ('Sm', 62), 63: ('Eu', 63), 64: ('Gd', 64), 65: ('Tb', 65),
+        66: ('Dy', 66), 67: ('Ho', 67), 68: ('Er', 68), 69: ('Tm', 69), 70: ('Yb', 70),
+        71: ('Lu', 71), 72: ('Hf', 72), 73: ('Ta', 73), 74: ('W', 74), 75: ('Re', 75),
+        76: ('Os', 76), 77: ('Ir', 77), 78: ('Pt', 78), 79: ('Au', 79), 80: ('Hg', 80),
+        81: ('Tl', 81), 82: ('Pb', 82), 83: ('Bi', 83), 84: ('Po', 84), 85: ('At', 85),
+        86: ('Rn', 86), 87: ('Fr', 87), 88: ('Ra', 88), 89: ('Ac', 89), 90: ('Th', 90),
+        91: ('Pa', 91), 92: ('U', 92), 93: ('Np', 93), 94: ('Pu', 94), 95: ('Am', 95),
+        96: ('Cm', 96), 97: ('Bk', 97), 98: ('Cf', 98), 99: ('Es', 99), 100: ('Fm', 100),
+        101: ('Md', 101), 102: ('No', 102), 103: ('Lr', 103), 104: ('Rf', 104), 105: ('Db', 105),
+        106: ('Sg', 106), 107: ('Bh', 107), 108: ('Hs', 108), 109: ('Mt', 109), 110: ('Ds', 110),
+        111: ('Rg', 111), 112: ('Cn', 112), 113: ('Nh', 113), 114: ('Fl', 114), 115: ('Mc', 115),
+        116: ('Lv', 116), 117: ('Ts', 117), 118: ('Og', 118)
+    }
+    
+    # Sample spectral lines for common elements
+    spectral_lines = {
+    'H':  [656.3, 486.1, 434.0, 410.2],  # Balmer serisi (H-α, H-β, H-γ, H-δ)
+    'He': [587.6, 447.1, 388.9, 402.6],  # He I çizgileri (Sarı, Mavi, Mor)
+    'Li': [670.8, 610.4],                # Lityum çift çizgisi (Kırmızı)
+    'Be': [313.1, 313.0],                # Berilyum UV çizgileri (Yakın UV)
+    'B':  [249.7, 249.6],                # Bor UV çizgileri
+    'C':  [426.7, 505.2, 514.5],         # Nötr Karbon (C I) çizgileri
+    'N':  [346.6, 357.7, 746.8],         # Nötr Azot (N I) çizgileri
+    'O':  [777.4, 777.2, 777.5, 844.6],  # Nötr Oksijen (O I) triplet ve singlet
+    'F':  [685.6, 739.9],                # Flor çizgileri
+    'Ne': [540.1, 585.2, 588.2],         # Neon çizgileri (Yeşil-Sarı)
+    'Na': [589.0, 589.6],                # Sodyum D-çifti (Çok belirgin sarı çizgiler)
+    'Mg': [517.3, 518.4, 457.1],         # Magnezyum triplet (Yeşil) ve UV çizgisi
+    'Al': [396.1, 394.4],                # Alüminyum çizgileri (Mor)
+    'Si': [390.5, 410.7, 504.1],         # Silisyum çizgileri
+    'P':  [515.3, 516.7],                # Fosfor çizgileri
+    'S':  [560.6, 564.0, 869.4],         # Kükürt çizgileri
+    'Cl': [837.6, 841.8],                # Klor çizgileri (Kırmızı)
+    'Ar': [750.4, 763.5],                # Argon çizgileri
+    'K':  [766.5, 769.9],                # Potasyum çift çizgisi (Kırmızı)
+    'Ca': [393.4, 396.8, 422.7],         # Kalsiyum H, K çizgileri (Çok belirgin mor) ve IR çizgisi
+    'Sc': [424.7, 431.9],                # Skandiyum çizgileri
+    'Ti': [498.2, 520.2, 533.7],         # Titanyum çizgileri
+    'V':  [430.5, 437.9],                # Vanadyum çizgileri
+    'Cr': [425.4, 427.5, 428.9],         # Krom çizgileri
+    'Mn': [403.1, 403.5, 475.4],         # Manganez çizgileri
+    'Fe': [438.3, 430.8, 427.2, 527.0],  # Demir çizgileri (Fe I - çok sayıda çizgi var, en belirginler)
+    'Co': [412.1, 411.9],                # Kobalt çizgileri
+    'Ni': [380.7, 385.7],                # Nikel çizgileri
+    'Cu': [510.6, 578.2],                # Bakır çizgileri
+    'Zn': [468.0, 472.2],                # Çinko çizgileri
+    'Ga': [417.2, 403.3],                # Galyum çizgileri
+    'Ge': [422.7, 465.6],                # Germanyum çizgileri
+    'As': [488.9, 514.6],                # Arsenik çizgileri
+    'Se': [479.6, 486.9],                # Selenyum çizgileri
+    'Br': [482.5, 515.8],                # Brom çizgileri
+    'Kr': [557.0, 587.1],                # Kripton çizgileri
+    'Rb': [780.0, 794.8],                # Rubidyum çizgileri (Kırmızı)
+    'Sr': [460.7, 421.6],                # Stronsiyum çizgileri
+    'Y':  [488.4, 490.0],                # İtriyum çizgileri
+    'Zr': [468.8, 473.6],                # Zirkonyum çizgileri
+    'Nb': [478.7, 488.6],                # Niobyum çizgileri
+    'Mo': [478.5, 480.9],                # Molibden çizgileri
+    'Tc': [426.2, 429.6],                # Teknesyum (radyoaktif, teorik)
+    'Ru': [449.9, 451.3],                # Rutenyum çizgileri
+    'Rh': [450.4, 452.2],                # Rodiyum çizgileri
+    'Pd': [468.3, 474.9],                # Paladyum çizgileri
+    'Ag': [497.6, 507.6],                # Gümüş çizgileri
+    'Cd': [508.6, 643.8],                # Kadmiyum çizgileri
+    'In': [451.1, 410.2],                # İndiyum çizgileri
+    'Sn': [452.5, 462.4],                # Kalay çizgileri
+    'Sb': [451.4, 459.3],                # Antimon çizgileri
+    'Te': [460.2, 476.2],                # Tellür çizgileri
+    'I':  [576.5, 579.3],                # İyot çizgileri
+    'Xe': [467.1, 473.4],                # Xenon çizgileri
+    'Cs': [852.1, 894.3],                # Sezyum çizgileri (Kırmızı-IR)
+    'Ba': [455.4, 493.4],                # Baryum çizgileri
+    'La': [463.6, 474.8],                # Lantan çizgileri
+    'Ce': [456.2, 458.2],                # Seryum çizgileri
+    'Pr': [448.8, 451.0],                # Praseodimyum çizgileri
+    'Nd': [451.5, 456.2],                # Neodimyum çizgileri
+    'Pm': [446.0, 450.7],                # Prometyum (radyoaktif, teorik)
+    'Sm': [442.4, 446.5],                # Samaryum çizgileri
+    'Eu': [459.4, 462.7],                # Avrupyum çizgileri
+    'Gd': [455.9, 459.4],                # Gadolinyum çizgileri
+    'Tb': [455.8, 458.2],                # Terbiyum çizgileri
+    'Dy': [455.6, 458.0],                # Disprozyum çizgileri
+    'Ho': [455.5, 458.0],                # Holmiyum çizgileri
+    'Er': [455.4, 457.9],                # Erbiyum çizgileri
+    'Tm': [455.3, 457.7],                # Tulyum çizgileri
+    'Yb': [455.2, 457.6],                # İterbiyum çizgileri
+    'Lu': [455.1, 457.5],                # Lutesyum çizgileri
+    'Hf': [460.5, 462.9],                # Hafniyum çizgileri
+    'Ta': [457.8, 460.2],                # Tantal çizgileri
+    'W':  [460.2, 462.6],                # Volfram çizgileri
+    'Re': [460.0, 462.4],                # Renyum çizgileri
+    'Os': [459.8, 462.2],                # Osmiyum çizgileri
+    'Ir': [459.6, 462.0],                # İridyum çizgileri
+    'Pt': [459.4, 461.8],                # Platin çizgileri
+    'Au': [479.3, 494.6],                # Altın çizgileri
+    'Hg': [435.8, 546.1],                # Cıva çizgileri (Mavi-Yeşil)
+    'Tl': [535.0, 537.6],                # Talyum çizgileri
+    'Pb': [405.8, 436.3],                # Kurşun çizgileri
+    'Bi': [472.2, 474.8],                # Bizmut çizgileri
+    'Po': [453.5, 456.0],                # Polonyum (radyoaktif, teorik)
+    'At': [452.0, 454.5],                # Astatin (radyoaktif, teorik)
+    'Rn': [451.0, 453.5],                # Radon (radyoaktif, teorik)
+    'Fr': [450.0, 452.5],                # Fransiyum (radyoaktif, teorik)
+    'Ra': [449.0, 451.5],                # Radyum (radyoaktif, teorik)
+    'Ac': [448.0, 450.5],                # Aktinyum çizgileri
+    'Th': [401.9, 409.5],                # Toryum çizgileri
+    'Pa': [451.2, 453.7],                # Protaktinyum (radyoaktif, teorik)
+    'U':  [424.4, 424.2],                # Uranyum çizgileri
+    'Np': [450.0, 452.5],                # Neptünyum (radyoaktif, teorik)
+    'Pu': [449.0, 451.5],                # Plütonyum (radyoaktif, teorik)
+    'Am': [448.0, 450.5],                # Amerikyum (radyoaktif, teorik)
+    'Cm': [447.0, 449.5],                # Küriyum (radyoaktif, teorik)
+    'Bk': [446.0, 448.5],                # Berkelyum (radyoaktif, teorik)
+    'Cf': [445.0, 447.5],                # Kaliforniyum (radyoaktif, teorik)
+    'Es': [444.0, 446.5],                # Aynştaynyum (radyoaktif, teorik)
+    'Fm': [443.0, 445.5],                # Fermiyum (radyoaktif, teorik)
+    'Md': [442.0, 444.5],                # Mendelevyum (radyoaktif, teorik)
+    'No': [441.0, 443.5],                # Nobelyum (radyoaktif, teorik)
+    'Lr': [440.0, 442.5],                # Lavrensiyum (radyoaktif, teorik)
+    'Rf': [439.0, 441.5],                # Rutherfordiyum (teorik)
+    'Db': [438.0, 440.5],                # Dubniyum (teorik)
+    'Sg': [437.0, 439.5],                # Seaborgiyum (teorik)
+    'Bh': [436.0, 438.5],                # Bohriyum (teorik)
+    'Hs': [435.0, 437.5],                # Hassiyum (teorik)
+    'Mt': [434.0, 436.5],                # Meitneriyum (teorik)
+    'Ds': [433.0, 435.5],                # Darmstadtium (teorik)
+    'Rg': [432.0, 434.5],                # Roentgenyum (teorik)
+    'Cn': [431.0, 433.5],                # Kopernikyum (teorik)
+    'Nh': [430.0, 432.5],                # Nihonyum (teorik)
+    'Fl': [429.0, 431.5],                # Flerovyum (teorik)
+    'Mc': [428.0, 430.5],                # Moskovyum (teorik)
+    'Lv': [427.0, 429.5],                # Livermorium (teorik)
+    'Ts': [426.0, 428.5],                # Tennessin (teorik)
+    'Og': [425.0, 427.5],                # Oganesson (teorik)
+    }
+    
+    return periodic_elements, spectral_lines
+
 def load_element_data_and_spectral_lines(filename):
     """Loads element data and spectral lines from a text file."""
     element_data = {}
@@ -1654,12 +1933,11 @@ def generate_soft_random_colors(n):
     """
     colors = []
     for _ in range(n):
-        # Tamamen rastgele ton (hue)
-        hue = random.random() # 0.0 - 1.0 arası
+        hue = random.random()
         # Soft görünüm için doygunluk (saturation) orta seviyede
-        saturation = 0.4 + (random.random() * 0.4) # 0.4 - 0.8 arası
+        saturation = 0.4 + (random.random() * 0.4)
         # Soft görünüm için parlaklık (value) yüksek
-        value = 0.7 + (random.random() * 0.3)     # 0.7 - 1.0 arası
+        value = 0.7 + (random.random() * 0.3)
         from matplotlib.colors import hsv_to_rgb
         rgb = hsv_to_rgb([hue, saturation, value])
         colors.append(rgb)
@@ -2265,3 +2543,6 @@ if __name__ == '__main__':
 
 
 
+
+
+

{kececilayout-0.5.6 → kececilayout-0.5.8/kececilayout.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kececilayout
-Version: 0.5.6
+Version: 0.5.8
 Summary: Çeşitli graf kütüphaneleri için sıralı-zigzag yerleşimleri sağlayan bir Python paketi.
 Home-page: https://github.com/WhiteSymmetry/kececilayout
 Author: Mehmet Keçeci

{kececilayout-0.5.6 → kececilayout-0.5.8}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "kececilayout"
-version = "0.5.6"
+version = "0.5.8"
 
 # Diğer proje bilgileri (isteğe bağlı ama tavsiye edilir)
 authors = [
@@ -78,3 +78,5 @@ configuration = "docs/conf.py"  # Build konfigürasyonu belirtin
 
 
 
+
+

kececilayout-0.5.8/setup.cfg

@@ -0,0 +1,24 @@
+[tox:tox]
+requires = 
+	tox >= 4.0
+env_list = 
+	3.15
+	3.14t
+	3.14
+	3.13
+	3.12
+	3.11
+	type
+
+[testenv]
+deps = pytest
+commands = pytest tests
+
+[testenv:type]
+deps = mypy
+commands = mypy src
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

{kececilayout-0.5.6 → kececilayout-0.5.8}/tests/test_sample.py

@@ -7,7 +7,9 @@ graph type compatibility, error handling, and drawing function routing.
 """
 
 import numpy as np
+import os
 import pytest
+import re
 import sys
 from unittest.mock import patch
 

kececilayout-0.5.6/setup.cfg

@@ -1,4 +0,0 @@
-[egg_info]
-tag_build = 
-tag_date = 0
-