Effective Computation in Physics

Spis treści książki

• Foreword
• Preface
  • What Is This Book?
  • Who This Book Is For
  • Who This Book Is Not For
  • Case Study on How to Use This Book: Radioactive Decay Constants
    • Accessing Data and Libraries
    • Creating a Simple Program
    • Automating Data Collection
    • Analyzing and Plotting the Data
    • Keeping Track of Changes
    • Testing the Code
    • Documenting the Code
    • Publishing
  • What to Do While Reading This Book
  • Conventions Used in This Book
  • Using Code Examples
  • Installation and Setup
    • Step 1: Download and Install Miniconda (or Anaconda)
    • Step 2: Install the Packages
  • Safari Books Online
  • How to Contact Us
  • Acknowledgments
• I. Getting Started
• 1. Introduction to the Command Line
  • Navigating the Shell
    • The Shell Is a Programming Language
    • Paths and pwd
    • Home Directory (~)
    • Listing the Contents (ls)
    • Changing Directories (cd)
    • File Inspection (head and tail)
  • Manipulating Files and Directories
    • Creating Files (nano, emacs, vi, cat, >, and touch)
      • GUIs for file creation
      • Creating an empty file (touch)
      • The simplest text editor (cat and >)
      • More powerful text editors (nano, emacs, and vim)
    • Copying and Renaming Files (cp and mv)
    • Making Directories (mkdir)
    • Deleting Files and Directories (rm)
    • Flags and Wildcards
  • Getting Help
    • Reading the Manual (man)
      • Arguments, options, and variables
      • Moving around in less
    • Finding the Right Hammer (apropos)
    • Combining Utilities with Redirection and Pipes (>, >>, and |)
  • Permissions and Sharing
    • Seeing Permissions (ls -l)
    • Setting Ownership (chown)
    • Setting Permissions (chmod)
    • Creating Links (ln)
    • Connecting to Other Computers (ssh and scp)
  • The Environment
    • Saving Environment Variables (.bashrc)
    • Running Programs (PATH)
    • Nicknaming Commands (alias)
  • Scripting with Bash
  • Command Line Wrap-up
• 2. Programming Blastoff with Python
  • Running Python
  • Comments
  • Variables
  • Special Variables
    • Boolean Values
    • None Is Not Zero!
    • NotImplemented Is Not None!
  • Operators
  • Strings
    • String Indexing
    • String Concatenation
    • String Literals
    • String Methods
  • Modules
    • Importing Modules
    • Importing Variables from a Module
    • Aliasing Imports
    • Aliasing Variables on Import
    • Packages
    • The Standard Library and the Python Ecosystem
  • Python Wrap-up
• 3. Essential Containers
  • Lists
  • Tuples
  • Sets
  • Dictionaries
  • Containers Wrap-up
• 4. Flow Control and Logic
  • Conditionals
    • if-else Statements
    • if-elif-else Statements
    • if-else Expression
  • Exceptions
    • Raising Exceptions
  • Loops
    • while Loops
    • for Loops
    • Comprehensions
  • Flow Control and Logic Wrap-up
• 5. Operating with Functions
  • Functions in Python
  • Keyword Arguments
  • Variable Number of Arguments
  • Multiple Return Values
  • Scope
  • Recursion
  • Lambdas
  • Generators
  • Decorators
  • Function Wrap-up
• 6. Classes and Objects
  • Object Orientation
  • Objects
  • Classes
    • Class Variables
    • Instance Variables
    • Constructors
    • Methods
    • Static Methods
    • Duck Typing
    • Polymorphism
      • Subclasses
      • Superclasses
      • Multiple inheritance
  • Decorators and Metaclasses
  • Object Orientation Wrap-up
• II. Getting It Done
• 7. Analysis and Visualization
  • Preparing Data
    • Experimental Data
    • Simulation Data
    • Metadata
  • Loading Data
    • NumPy
    • PyTables
    • Pandas
    • Blaze
  • Cleaning and Munging Data
    • Missing Data
  • Analysis
    • Model-Driven Analysis
    • Data-Driven Analysis
  • Visualization
    • Visualization Tools
    • Gnuplot
    • matplotlib
      • The gallery
    • Bokeh
    • Inkscape
  • Analysis and Visualization Wrap-up
• 8. Regular Expressions
  • Messy Magnetism
  • Metacharacters on the Command Line
    • Listing Files with Simple Patterns
      • The wildcard (*)
    • Globally Finding Filenames with Patterns (find)
      • Representing any character (.)
      • Escaping metacharacters (\)
      • Finding either one pattern or another (|)
      • Character sets ([])
  • grep, sed, and awk
  • Finding Patterns in Files (grep)
  • Finding and Replacing Patterns in Files (sed)
    • Finding and Replacing a Complex Pattern
    • sed Extras
  • Manipulating Columns of Data (awk)
  • Python Regular Expressions
  • Regular Expressions Wrap-up
• 9. NumPy: Thinking in Arrays
  • Arrays
  • dtypes
  • Slicing and Views
  • Arithmetic and Broadcasting
  • Fancy Indexing
  • Masking
  • Structured Arrays
  • Universal Functions
  • Other Valuable Functions
  • NumPy Wrap-up
• 10. Storing Data: Files and HDF5
  • Files in Python
  • An Aside About Computer Architecture
  • Big Ideas in HDF5
  • File Manipulations
  • Hierarchy Layout
  • Chunking
  • In-Core and Out-of-Core Operations
    • In-Core
    • Out-of-Core
  • Querying
  • Compression
  • HDF5 Utilities
  • Storing Data Wrap-up
• 11. Important Data Structures in Physics
  • Hash Tables
    • Resizing
    • Collisions
  • Data Frames
    • Series
    • The Data Frame Structure
  • B-Trees
  • K-D Trees
  • Data Structures Wrap-up
• 12. Performing in Parallel
  • Scale and Scalability
  • Problem Classification
  • Example: N-Body Problem
  • No Parallelism
  • Threads
  • Multiprocessing
  • MPI
  • Parallelism Wrap-up
• 13. Deploying Software
  • Deploying the Software Itself
    • pip
    • Conda
    • Virtual Machines
    • Docker
  • Deploying to the Cloud
  • Deploying to Supercomputers
  • Deployment Wrap-up
• III. Getting It Right
• 14. Building Pipelines and Software
  • make
    • Running make
    • Makefiles
    • Targets
    • Special Targets
  • Building and Installing Software
    • Configuration of the Makefile
      • Platform configuration
      • System and user configuration
      • Dependency configuration
    • Compilation
  • Installation
  • Building Software and Pipelines Wrap-up
• 15. Local Version Control
  • What Is Version Control?
    • The Lab Notebook of Computational Physics
    • Version Control Tool Types
  • Getting Started with Git
    • Installing Git
    • Getting Help (git --help)
    • Control the Behavior of Git (git config)
  • Local Version Control with Git
    • Creating a Local Repository (git init)
    • Staging Files (git add)
    • Checking the Status of Your Local Copy (git status)
    • Saving a Snapshot (git commit)
    • git log: Viewing the History
    • Viewing the Differences (git diff)
    • Unstaging or Reverting a File (git reset)
    • Discard Revisions (git revert)
    • Listing, Creating, and Deleting Branches (git branch)
    • Switching Between Branches (git checkout)
    • Merging Branches (git merge)
    • Dealing with Conflicts
  • Version Conrol Wrap-Up
• 16. Remote Version Control
  • Repository Hosting (github.com)
  • Creating a Repository on GitHub
  • Declaring a Remote (git remote)
  • Sending Commits to Remote Repositories (git push)
  • Downloading a Repository (git clone)
  • Fetching the Contents of a Remote (git fetch)
  • Merging the Contents of a Remote (git merge)
  • Pull = Fetch and Merge (git pull)
  • Conflicts
  • Resolving Conflicts
  • Remote Version Control Wrap-up
• 17. Debugging
  • Encountering a Bug
  • Print Statements
  • Interactive Debugging
  • Debugging in Python (pdb)
    • Setting the Trace
    • Stepping Forward
    • Querying Variables
    • Setting the State
    • Running Functions and Methods
    • Continuing the Execution
    • Breakpoints
  • Profiling
    • Viewing the Profile with pstats
    • Viewing the Profile Graphically
    • Line Profiling with Kernprof
  • Linting
  • Debugging Wrap-up
• 18. Testing
  • Why Do We Test?
  • When Should We Test?
  • Where Should We Write Tests?
  • What and How to Test?
  • Running Tests
  • Edge Cases
    • Corner Cases
  • Unit Tests
  • Integration Tests
  • Regression Tests
  • Test Generators
  • Test Coverage
  • Test-Driven Development
  • Testing Wrap-up
• IV. Getting It Out There
• 19. Documentation
  • Why Prioritize Documentation?
    • Documentation Is Very Valuable
    • Documentation Is Easier Than You Think
  • Types of Documentation
    • Theory Manuals
    • User and Developer Guides
    • Readme Files
    • Comments
    • Self-Documenting Code
      • Naming
      • Simple functions
      • Consistent style
    • Docstrings
  • Automation
    • Sphinx
      • Getting started
      • Comment style
  • Documentation Wrap-up
• 20. Publication
  • Document Processing
    • Separation of Content from Formatting
    • Tracking Changes
  • Text Editors
  • Markup Languages
    • LaTeX
      • LaTeX document class
      • LaTeX environments
      • Building the document
      • LaTeX metadata
      • Document structure
      • Typesetting mathematical formulae
      • Tables and figures
      • Internal references
    • Bibliographies
      • Reference management
  • Publication Wrap-up
• 21. Collaboration
  • Ticketing Systems
    • Workflow Overview
    • Creating an Issue
      • Core features of an issue
      • Issue metadata
    • Assigning an Issue
    • Discussing an Issue
    • Closing an Issue
  • Pull Requests and Code Reviews
    • Submitting a Pull Request
    • Reviewing a Pull Request
    • Merging a Pull Request
  • Collaboration Wrap-up
• 22. Licenses, Ownership, and Copyright
  • What Is Copyrightable?
  • Right of First Publication
  • What Is the Public Domain?
  • Choosing a Software License
  • Berkeley Software Distribution (BSD) License
  • GNU General Public License (GPL)
  • Creative Commons (CC)
  • Other Licenses
  • Changing the License
  • Copyright Is Not Everything
  • Licensing Wrap-up
• 23. Further Musings on Computational Physics
  • Where to Go from Here
• Glossary
• Bibliography
• Index

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