Add files

Author: sunqm

README.md

@@ -0,0 +1,11 @@
+# Python for Quantum Chemistry: A Full Stack Programming Guide
+
+Welcome to the repository for the book *Python for Quantum Chemistry: A Full Stack Programming Guide*. This repository contains all the code examples and supplementary materials in the book.
+
+To run the code examples, make sure to install the required libraries:
+```
+pip install -r requirements.txt
+```
+Please note that some chapters may have specific dependencies. You can install these dependencies by using the provided `requirements.txt` file in each chapter.
+
+We welcome your feedback and encourage you to use the issue board to post comments, ask questions, or report any issues you encounter in the book.

code-examples/__init__.py

@@ -0,0 +1,4 @@
+from . import module_b
+
+def factory():
+    return module_b.B()

code-examples/chap01/circular-dep/mypkg/module_a.py

@@ -0,0 +1,4 @@
+from . import module_a
+
+def inspect():
+    return dir(module_a)

code-examples/chap01/circular-dep/mypkg/module_b.py

@@ -0,0 +1,7 @@
+from . import module_b
+
+class A:
+    pass
+
+def factory():
+    return module_b.B()

code-examples/chap01/circular-dep/mypkg_cd/module_a.py

@@ -0,0 +1,4 @@
+from . import module_a
+
+class B(module_a.A):
+    pass

code-examples/chap01/circular-dep/mypkg_cd/module_b.py

@@ -0,0 +1 @@
+Tool for inspecting Python pacakge dependencies

code-examples/chap01/pyldd/README.md

@@ -0,0 +1,16 @@
+package:
+  name: pyldd
+  version: 0.1.0
+
+source:
+  path: ..
+
+build:
+  script: pip install --no-deps .
+
+requirements:
+  host:
+    - python
+  run:
+    - python
+    - click

code-examples/chap01/pyldd/conda-recipe/meta.yaml

@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+'''
+Find and print all dependent libraries required by a package.
+'''
+
+import os
+import importlib
+import ast
+import argparse
+import pathlib
+
+def get_all_imports(path):
+    raw_imports = set()
+    for root, dirs, files in os.walk(path):
+        for file_name in files:
+            if os.path.splitext(file_name)[1] != ".py":
+                continue
+            file_name = os.path.join(root, file_name)
+            with open(file_name, 'r') as f:
+                contents = f.read()
+            try:
+                tree = ast.parse(contents)
+                for node in ast.walk(tree):
+                    if isinstance(node, ast.Import):
+                        for subnode in node.names:
+                            raw_imports.add(subnode.name)
+                    elif isinstance(node, ast.ImportFrom):
+                        raw_imports.add(node.module)
+            except Exception as exc:
+                print(f'Failed to parse file: {file_name}')
+    return list(raw_imports)
+
+def main():
+    parser = argparse.ArgumentParser(prog='pyldd', description=__doc__)
+    parser.add_argument('path', type=pathlib.Path)
+    parser.add_argument('--depth', type=int, default=0, help='The maximum depth of sub-packages to inspect')
+    args = parser.parse_args()
+
+    imports = get_all_imports(args.path)
+    imports = [imp for imp in imports if imp.count('.') <= args.depth]
+    for name in set(imports):
+        try:
+            mod = importlib.import_module(name)
+            print(mod)
+        except Exception:
+            print(f'Module {name} not found')
+
+
+if __name__ == '__main__':
+    main()

code-examples/chap01/pyldd/pyldd/__init__.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+from os.path import dirname
+from typing import List
+import importlib
+import click
+from pipreqs import pipreqs
+
+def dep_modules(path: str) -> List[str]:
+    imports = pipreqs.get_all_imports(path)
+    modules = {}
+    for name in imports:
+        try:
+            mod = importlib.import_module(name)
+            modules[name] = mod
+        except Exception as e:
+            print(repr(e))
+    return modules
+
+@click.command(name='pyldd')
+@click.option('--depth', default=1, type=int, help="Recursively solve dependencies")
+@click.option('--with-version', is_flag=True, help="Also print version of each library")
+@click.argument('path', type=click.Path(exists=True, dir_okay=True))
+def main(path, depth=1, with_version=False):
+    '''
+    Find and print all dependent libraries reuired by a package.
+    '''
+    imports = pipreqs.get_all_imports(path)
+    paths = [path]
+    sub_paths = []
+    modules = {}
+    for _ in range(depth):
+        deps = {}
+        for path in paths:
+            deps.update(dep_modules(path))
+        paths = [dirname(v.__file__) for v in deps.values()]
+        modules.update(deps)
+
+    for name, mod in modules.items():
+        if with_version:
+            try:
+                print(f'{mod} version={mod.__version__}')
+            except AttributeError:
+                print(mod)
+        else:
+            print(mod)
+
+if __name__ == '__main__':
+    main()

code-examples/chap01/pyldd/pyldd/pyldd-argparse.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+'''
+Find and print all dependent libraries required by a package.
+'''
+
+import os
+import importlib
+import ast
+import click
+
+def get_all_imports(path):
+    raw_imports = set()
+    for root, dirs, files in os.walk(path):
+        for file_name in files:
+            if os.path.splitext(file_name)[1] != ".py":
+                continue
+            file_name = os.path.join(root, file_name)
+            with open(file_name, 'r') as f:
+                contents = f.read()
+            try:
+                tree = ast.parse(contents)
+                for node in ast.walk(tree):
+                    if isinstance(node, ast.Import):
+                        for subnode in node.names:
+                            raw_imports.add(subnode.name)
+                    elif isinstance(node, ast.ImportFrom):
+                        raw_imports.add(node.module)
+            except Exception as exc:
+                print(f'Failed to parse file: {file_name}')
+    return list(raw_imports)
+
+@click.command(name='pyldd', help=__doc__)
+@click.option('--depth', type=int, default=0, help='The maximum depth of sub-packages to inspect')
+@click.argument('path', type=click.Path(exists=True, dir_okay=True))
+def main(path, depth):
+    imports = get_all_imports(path)
+    imports = [imp for imp in imports if imp.count('.') <= depth]
+    for name in set(imports):
+        try:
+            mod = importlib.import_module(name)
+            print(mod)
+        except Exception:
+            print(f'Module {name} not found')
+
+
+if __name__ == '__main__':
+    main()

code-examples/chap01/pyldd/pyldd/pyldd-recursive.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+
+import importlib
+import click
+from pipreqs import pipreqs
+
+@click.command(name='pyldd')
+@click.option('--with-version', is_flag=True, help="Also print version of each library")
+@click.argument('path', type=click.Path(exists=True, dir_okay=True))
+def main(path, with_version=False):
+    '''
+    Find and print all dependent libraries reuired by a package.
+    '''
+    imports = pipreqs.get_all_imports(path)
+    for name in imports:
+        try:
+            mod = importlib.import_module(name)
+        except Exception:
+            print(f'Failed to inspect module {name}')
+        if with_version:
+            try:
+                print(f'{mod} version={mod.__version__}')
+            except AttributeError:
+                print(mod)
+        else:
+            print(mod)
+
+
+if __name__ == '__main__':
+    main()

code-examples/chap01/pyldd/pyldd/pyldd-sub-package.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+
+import importlib
+import click
+from pipreqs import pipreqs
+
+@click.command(name='pyldd')
+@click.option('--with-version', is_flag=True, help="Also print version of each library")
+@click.argument('path', type=click.Path(exists=True, dir_okay=True))
+def main(path, with_version=False):
+    '''
+    Find and print all dependent libraries reuired by a package.
+    '''
+    imports = pipreqs.get_all_imports(path)
+    for name in imports:
+        mod = importlib.import_module(name)
+        if with_version:
+            try:
+                print(f'{mod} version={mod.__version__}')
+            except AttributeError:
+                print(mod)
+        else:
+            print(mod)
+
+if __name__ == '__main__':
+    main()

code-examples/chap01/pyldd/pyldd/pyldd-sub-version.py

@@ -0,0 +1,12 @@
+[project]
+name = "pyldd"
+version = "0.1.0"
+description = "Tool for inspecting Python pacakge dependencies"
+readme = "README.md"
+dependencies = [
+  "pipreqs>=0.4",
+  "click"
+]
+
+[project.scripts]
+pyldd = "pyldd.pyldd:main"

code-examples/chap01/pyldd/pyldd/pyldd.py

@@ -0,0 +1,11 @@
+from setuptools import setup, find_packages
+
+setup(
+    name='pyldd',
+    packages=find_packages(),
+    entry_points={
+        "console_scripts": [
+            'pyldd = pyldd.cli:main'
+        ]
+    }
+)

code-examples/chap01/pyldd/pyproject.toml

@@ -0,0 +1,12 @@
+from setuptools import setup, Extension
+
+ext1 = Extension(
+    'example.simple_cpp',
+    sources=['example_A.cpp', 'example_B.cpp'],
+    language='c++',
+    libraries=[':libblas.so.3.9.0'],
+    #/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
+    library_dirs=['/usr/lib/x86_64-linux-gnu/blas/'],
+)
+setup(ext_modules=[ext1])
+

code-examples/chap01/pyldd/setup.py

@@ -0,0 +1,35 @@
+import numpy as np
+import mpmath as mp
+mp.mp.dps = 30
+
+def mpfftfreq(n):
+    if n % 2 == 0:
+        p1 = mp.arange(0, n//2)
+        p2 = mp.arange(-n//2, 0)
+    else:
+        p1 = mp.arange(0, (n+1)//2)
+        p2 = mp.arange(-(n-1)//2, 0)
+    return np.append(p1, p2) / n
+
+mpexp = np.vectorize(mp.exp)
+
+def mpfft(a):
+    n = a.shape[-1]
+    kx = 2j*mp.pi * mpfftfreq(n)
+    fac = mpexp(-np.arange(n)[:,None] * kx)
+    return a.dot(fac)
+
+def mpifft(a):
+    n = a.shape[-1]
+    kx = 2j*mp.pi * mpfftfreq(n)
+    fac = mpexp(np.arange(n)[:,None] * kx)
+    return a.dot(fac) / n
+
+if __name__ == '__main__':
+    a = np.random.rand(7)
+    print(abs(np.fft.fft(a) - mpfft(a)).max())
+    print(abs(a - mpifft(mpfft(a))).max())
+
+    a = np.random.rand(3,6)
+    print(abs(np.fft.fft(a) - mpfft(a)).max())
+    print(abs(a - mpifft(mpfft(a))).max())