Update

dev/Requirements.txt

@@ -0,0 +1,141 @@
+aiofiles==22.1.0
+aiosqlite==0.19.0
+anyio==3.6.2
+appnope==0.1.3
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+arrow==1.2.3
+asttokens==2.2.1
+attrs==23.1.0
+Babel==2.12.1
+backcall==0.2.0
+beautifulsoup4==4.12.2
+bleach==6.0.0
+blinker==1.4
+certifi==2022.12.7
+cffi==1.15.1
+charset-normalizer==3.1.0
+cmake==3.24.1.1
+cmake-generators==1.0.9
+colorama==0.4.4
+comm==0.1.3
+commonmark==0.9.1
+cycler==0.11.0
+debugpy==1.6.7
+decorator==5.1.1
+defusedxml==0.7.1
+distro==1.7.0
+docutils==0.18.1
+executing==1.2.0
+fastjsonschema==2.16.3
+feedgenerator==2.0.0
+fonttools==4.29.1
+fqdn==1.5.1
+future-fstrings==1.2.0
+gcovr==5.2
+gitdb==4.0.9
+GitPython==3.1.27
+h5py==3.8.0
+idna==3.4
+importlib-metadata==6.6.0
+importlib-resources==5.12.0
+ipykernel==6.22.0
+ipython==8.12.1
+ipython-genutils==0.2.0
+isoduration==20.11.0
+jedi==0.18.2
+Jinja2==3.0.3
+joblib==1.3.1
+json5==0.9.11
+jsonpointer==2.3
+jsonschema==4.17.3
+jupyter-events==0.6.3
+jupyter-ydoc==0.2.4
+jupyter_client==8.2.0
+jupyter_core==5.3.0
+jupyter_server==2.5.0
+jupyter_server_fileid==0.9.0
+jupyter_server_terminals==0.4.4
+jupyter_server_ydoc==0.8.0
+jupyterlab==3.6.3
+jupyterlab-pygments==0.2.2
+jupyterlab_server==2.22.1
+kiwisolver==1.3.2
+lxml==4.9.2
+MarkupSafe==2.0.1
+matplotlib==3.5.1
+matplotlib-inline==0.1.6
+mistune==2.0.5
+mpi4py==3.1.4
+nbclassic==0.5.6
+nbclient==0.7.4
+nbconvert==7.3.1
+nbformat==5.8.0
+nest-asyncio==1.5.6
+networkx==3.1
+ninja==1.10.2.4
+nose==1.3.7
+notebook==6.5.4
+notebook_shim==0.2.3
+numpy==1.22.2
+packaging==21.3
+pandas==1.4.1
+pandocfilters==1.5.0
+parso==0.8.3
+pelican==4.7.2
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==9.0.1
+pkgutil_resolve_name==1.3.10
+platformdirs==3.5.0
+prometheus-client==0.16.0
+prompt-toolkit==3.0.38
+psutil==5.9.5
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pybind11==2.10.0
+pycparser==2.21
+Pygments==2.11.2
+pyparsing==3.0.7
+pyphen==0.13.2
+pyrsistent==0.19.3
+python-dateutil==2.8.2
+python-json-logger==2.0.7
+pytz==2021.3
+PyYAML==6.0
+pyzmq==25.0.2
+requests==2.29.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rich==11.2.0
+rodin @ file:///Users/carlos/Projects/rodin
+scikit-build==0.15.0
+scikit-learn==1.3.0
+scipy==1.9.0
+seaborn==0.12.2
+Send2Trash==1.8.2
+six==1.16.0
+sklearn==0.0.post7
+smmap==5.0.0
+sniffio==1.3.0
+soupsieve==2.4.1
+stack-data==0.6.2
+svn==1.0.1
+termcolor==2.3.0
+terminado==0.17.1
+threadpoolctl==3.2.0
+tinycss2==1.2.1
+tomli==2.0.1
+tornado==6.3.1
+traitlets==5.9.0
+typing_extensions==4.5.0
+Unidecode==1.3.2
+uri-template==1.2.0
+urllib3==1.26.15
+wcwidth==0.2.6
+webcolors==1.13
+webencodings==0.5.1
+websocket-client==1.5.1
+y-py==0.5.9
+ypy-websocket==0.8.2
+zipp==3.15.0

dev/py/include_dependencies.py

@@ -0,0 +1,241 @@
+import os
+import re
+import numpy as np
+import matplotlib.pyplot as plt
+import argparse
+import networkx as nx
+from pathlib import Path
+from shutil import which
+from termcolor import colored
+from networkx.drawing.nx_agraph import write_dot
+
+PT_TO_INCH = (1.0 / 72)
+
+MIN_NODE_SIZE = 2.0
+MAX_NODE_SIZE = 7.0
+
+MIN_FONT_SIZE = 6
+MAX_FONT_SIZE = 42
+
+
+COMMON_CPP_EXTENSIONS = ['.h', '.hpp', '.hxx']
+
+COLORSCHEME = 'spectral9'
+NUMBER_OF_COLORS = 9
+
+RODIN_TOP_LEVEL_INCLUDES = {
+    'Rodin.h',
+    'Rodin/Alert.h',
+    'Rodin/Variational.h',
+    'Rodin/Geometry.h',
+    'RodinExternal.h',
+    'RodinExternal/MMG.h',
+}
+
+RODIN_TOP_LEVEL_INCLUDES_COLOR_MAP = {
+    'Alert.h': 'red',
+    'Variational.h': 'green',
+    'Geometry.h': 'blue'
+}
+
+
+class GraphvizNotFoundError(Exception):
+    pass
+
+
+def merge_matching_paths(path1, path2):
+    parts1 = Path(path1).parts
+    parts2 = Path(path2).parts
+    if parts2[:len(parts1)] == parts1:
+        merged_parts = parts1 + parts2[len(parts1):]
+        merged_path = Path(*merged_parts)
+        return str(merged_path)
+    else:
+        joined_path = Path(path1) / path2
+        return str(joined_path)
+
+
+def extract_includes(file_path, context_path):
+    includes = []
+    with open(file_path, 'r') as file:
+        for line in file:
+            # system_include_match = re.match(r'#include\s*[<](.*)[>]', line)
+            user_include_match = re.match(r'#include\s*["](.*)["]', line)
+            if user_include_match:
+                include = user_include_match.group(1)
+                if include == 'ForwardDecls.h':
+                    continue
+                include_path = os.path.dirname(include)
+                if include_path:
+                    if not include_path.startswith('Rodin'):
+                        include = merge_matching_paths(context_path, include)
+                else:
+                    include = os.path.join(context_path, include)
+                includes.append(include)
+    return includes
+
+
+def generate_dependency_graph(root_path, extensions):
+    G = nx.DiGraph()
+    for root, _, files in os.walk(root_path):
+        for file in files:
+            if any(file.endswith(ext) for ext in extensions):
+                source_path = os.path.join(root, file)
+                relative_path = os.path.relpath(source_path, root_path)
+                context_path = os.path.dirname(relative_path)
+                includes = extract_includes(source_path, context_path)
+                G.add_node(relative_path)
+                for include in includes:
+                    G.add_edge(relative_path, include)
+    return G
+
+def get_predecessors_map(graph):
+    sinks = set()
+    node_to_set = {}
+    for node in graph.nodes():
+        node_to_set[node] = set()
+        if graph.out_degree(node) == 0:
+            sinks.add(node)
+    for sink in sinks:
+        visited = set()
+        q = { sink }
+        while len(q) > 0:
+            node = q.pop()
+            visited.add(node)
+            for n in graph.predecessors(node):
+                node_to_set[n].add(node)
+                node_to_set[n] |= node_to_set[node]
+                if n not in visited:
+                    q.add(n)
+    return node_to_set
+
+def get_accumulated_map(graph):
+    predecessors_map = get_predecessors_map(graph)
+    node_to_accumulated = {}
+    for node, predecessors in predecessors_map.items():
+        node_to_accumulated[node] = len(predecessors)
+    return node_to_accumulated
+
+def get_flow_map(graph):
+    node_to_flow = {}
+    for node in graph.nodes():
+        out_degree = graph.out_degree(node)
+        in_degree = graph.in_degree(node)
+        node_to_flow[node] = in_degree - out_degree
+    return node_to_flow
+
+def get_laplacian_map(graph):
+    laplacian_matrix = nx.directed_laplacian_matrix(graph)
+    node_to_laplacian = {}
+    for node_idx, node in enumerate(graph.nodes()):
+        laplacian_value = laplacian_matrix[node_idx, node_idx]
+        node_to_laplacian[node] = laplacian_value
+    return node_to_laplacian
+
+def get_pagerank_map(graph):
+    pagerank_scores = nx.pagerank(graph, alpha=0.85)
+    return pagerank_scores
+
+def get_color_map(m):
+    max_v = max(m.values())
+    min_v = min(m.values())
+    color_map = {}
+    for node, v in m.items():
+        std = float(v - min_v) / float(max_v - min_v)
+        color_map[node] = int(NUMBER_OF_COLORS - std * (NUMBER_OF_COLORS - 1))
+    return color_map
+
+def get_nodesize_map(m):
+    max_v = max(m.values())
+    min_v = min(m.values())
+    size_map = {}
+    for node, v in m.items():
+        std = float(v - min_v) / float(max_v - min_v)
+        size_map[node] = int((MAX_NODE_SIZE - MIN_NODE_SIZE) * std + MIN_NODE_SIZE)
+    return size_map
+
+def get_fontsize_map(m):
+    max_v = max(m.values())
+    min_v = min(m.values())
+    fontsize_map = {}
+    for node, v in m.items():
+        std = float(v - min_v) / float(max_v - min_v)
+        fontsize_map[node] = int((MAX_FONT_SIZE - MIN_FONT_SIZE) * std + MIN_FONT_SIZE)
+    return fontsize_map
+
+
+def check_graphviz_command(command):
+    dot_command = which(command)
+    if not dot_command:
+        raise GraphvizNotFoundError(
+            "Graphviz %s command not found. Please install Graphviz to generate graphical output." % command)
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        description='Generates #include dependency graph.')
+    parser.add_argument('root_path', help='Root path of the codebase.')
+    parser.add_argument('--layout_engine',
+                        default='dot',
+                        help='Layout engine.')
+    parser.add_argument('--dot',
+                        help='Output DOT file path.')
+    parser.add_argument('--png',
+                        help='Output PNG file path.')
+    parser.add_argument('--svg',
+                        help='Output SVG file path.')
+    parser.add_argument('--extensions', nargs='+',
+                        default=COMMON_CPP_EXTENSIONS,
+                        help='List of file extensions to consider.')
+    args = parser.parse_args()
+
+    root_path = args.root_path
+    folder_name = os.path.basename(os.path.normpath(root_path))
+
+    dot_filename = args.dot if args.dot else f'{folder_name}_include_dependency_graph.dot'
+
+    try:
+        check_graphviz_command(args.layout_engine)
+    except GraphvizNotFoundError as e:
+        print(colored(e, 'red'))
+        exit(1)
+
+    root_path = args.root_path
+    dependency_graph = generate_dependency_graph(root_path, args.extensions)
+    weight_map = get_accumulated_map(dependency_graph)
+    color_map = get_color_map(weight_map)
+    fontsize_map = get_fontsize_map(weight_map)
+    nodesize_map = get_nodesize_map(weight_map)
+
+    nx.set_node_attributes(dependency_graph, 'filled', name='style')
+    nx.set_node_attributes(dependency_graph, 'circle', name='shape')
+    nx.set_node_attributes(dependency_graph, 'true', name='fixedsize')
+    nx.set_node_attributes(dependency_graph, COLORSCHEME, name='colorscheme')
+    nx.set_node_attributes(dependency_graph, color_map, name='fillcolor')
+    nx.set_node_attributes(dependency_graph, weight_map, name='weight')
+    nx.set_node_attributes(dependency_graph, nodesize_map, name='width')
+    nx.set_node_attributes(dependency_graph, nodesize_map, name='height')
+    nx.set_node_attributes(dependency_graph, fontsize_map, name='fontsize')
+
+    write_dot(dependency_graph, dot_filename)
+    print(colored(f'DOT output generated: {dot_filename}', 'green'))
+
+    layout_engine = args.layout_engine
+    print(colored(f'Using layout engine {layout_engine}', 'blue'))
+    command_line = f'{layout_engine} '
+    command_line += '-Goverlap=prism -Gbeautify=true -Gsmoothing=true'
+    if args.png:
+        png_filename = args.png
+        command_line += " -Tpng -o %s " % png_filename
+
+    if args.svg:
+        svg_filename = args.svg
+        command_line += " -Tsvg -o %s " % svg_filename
+
+    command_line += dot_filename
+    os.system(command_line)
+
+    if args.png:
+        print(colored(f'PNG output generated: {png_filename}', 'green'))
+    if args.svg:
+        print(colored(f'SVG output generated: {svg_filename}', 'green'))
+

examples/Misc/RS2023/Domain.cpp

@@ -18,7 +18,7 @@ static constexpr Attribute interior = 1;
 static constexpr Attribute exterior = 2;
 static constexpr Attribute ball = 3;
 
-static constexpr Scalar hmax = 0.005;
+static constexpr Scalar hmax = 0.01;
 static constexpr Scalar hmin = 0.01 * hmax;
 
 static const Math::Vector x0{{0.5, 0.5}}; // Center of domain