Effective Computation In Physics Anthony Scopatz, Kathryn D. Huff Field Guide To Research With%

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Copyright
Table of Contents
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
- 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
Part I. Getting Started
Chapter 1. Introduction to the Command Line
- Navigating the Shell
- Manipulating Files and Directories
- Getting Help
- Permissions and Sharing
- The Environment
- Scripting with Bash
- Command Line Wrap-up
Chapter 2. Programming Blastoff with Python
- Running Python
- Comments
- Variables
- Special Variables
- Operators
- Strings
- Modules
- Python Wrap-up
Chapter 3. Essential Containers
- Lists
- Tuples
- Sets
- Dictionaries
- Containers Wrap-up
Chapter 4. Flow Control and Logic
- Conditionals
- Exceptions
  - Raising Exceptions
- Loops
- Flow Control and Logic Wrap-up
Chapter 5. Operating with Functions
- Functions in Python
- Keyword Arguments
- Variable Number of Arguments
- Multiple Return Values
- Scope
- Recursion
- Lambdas
- Generators
- Decorators
- Function Wrap-up
Chapter 6. Classes and Objects
- Object Orientation
- Objects
- Classes
- Decorators and Metaclasses
- Object Orientation Wrap-up
Part II. Getting It Done
Chapter 7. Analysis and Visualization
- Preparing Data
- Loading Data
- Cleaning and Munging Data
  - Missing Data
- Analysis
  - Model-Driven Analysis
  - Data-Driven Analysis
- Visualization
- Analysis and Visualization Wrap-up
Chapter 8. Regular Expressions
- Messy Magnetism
- Metacharacters on the Command Line
  - Listing Files with Simple Patterns
  - Globally Finding Filenames with Patterns (find)
- 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
Chapter 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
Chapter 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
Chapter 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
Chapter 12. Performing in Parallel
- Scale and Scalability
- Problem Classification
- Example: N-Body Problem
- No Parallelism
- Threads
- Multiprocessing
- MPI
- Parallelism Wrap-up
Chapter 13. Deploying Software
- Deploying the Software Itself
- Deploying to the Cloud
- Deploying to Supercomputers
- Deployment Wrap-up
Part III. Getting It Right
Chapter 14. Building Pipelines and Software
- make
- Building and Installing Software
  - Configuration of the Makefile
  - Compilation
- Installation
- Building Software and Pipelines Wrap-up
Chapter 15. Local Version Control
- What Is Version Control?
  - The Lab Notebook of Computational Physics
  - Version Control Tool Types
- Getting Started with Git
- Local Version Control with Git
- Version Conrol Wrap-Up
Chapter 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
Chapter 17. Debugging
- Encountering a Bug
- Print Statements
- Interactive Debugging
- Debugging in Python (pdb)
- Profiling
- Linting
- Debugging Wrap-up
Chapter 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
Part IV. Getting It Out There
Chapter 19. Documentation
- Why Prioritize Documentation?
  - Documentation Is Very Valuable
  - Documentation Is Easier Than You Think
- Types of Documentation
- Automation
  - Sphinx
- Documentation Wrap-up
Chapter 20. Publication
- Document Processing
  - Separation of Content from Formatting
  - Tracking Changes
- Text Editors
- Markup Languages
  - LaTeX
  - Bibliographies
- Publication Wrap-up
Chapter 21. Collaboration
- Ticketing Systems
- Pull Requests and Code Reviews
- Collaboration Wrap-up
Chapter 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
Chapter 23. Further Musings on Computational Physics
- Where to Go from Here
Glossary
Bibliography
Index
About the Authors

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