Research Software Engineering with Python: Building software that makes research possible

Cover
Title Page
Copyright Page
Dedication
Contents
Welcome
   0.1 The Big Picture
   0.2 Intended Audience
   0.3 What You Will Learn
   0.4 Using this Book
   0.5 Contributing and Re-Use
   0.6 Acknowledgments
1 Getting Started
   1.1 Project Structure
   1.2 Downloading the Data
   1.3 Installing the Software
   1.4 Summary
   1.5 Exercises
   1.6 Key Points
2 The Basics of the Unix Shell
   2.1 Exploring Files and Directories
   2.2 Moving Around
   2.3 Creating New Files and Directories
   2.4 Moving Files and Directories
   2.5 Copying Files and Directories
   2.6 Deleting Files and Directories
   2.7 Wildcards
   2.8 Reading the Manual
   2.9 Summary
   2.10 Exercises
   2.11 Key Points
3 Building Tools with the Unix Shell
   3.1 Combining Commands
   3.2 How Pipes Work
   3.3 Repeating Commands on Many Files
   3.4 Variable Names
   3.5 Redoing Things
   3.6 Creating New Filenames Automatically
   3.7 Summary
   3.8 Exercises
   3.9 Key Points
4 Going Further with the Unix Shell
   4.1 Creating New Commands
   4.2 Making Scripts More Versatile
   4.3 Turning Interactive Work into a Script
   4.4 Finding Things in Files
   4.5 Finding Files
   4.6 Configuring the Shell
   4.7 Summary
   4.8 Exercises
   4.9 Key Points
5 Building Command-Line Tools with Python
   5.1 Programs and Modules
   5.2 Handling Command-Line Options
   5.3 Documentation
   5.4 Counting Words
   5.5 Pipelining
   5.6 Positional and Optional Arguments
   5.7 Collating Results
   5.8 Writing Our Own Modules
   5.9 Plotting
   5.10 Summary
   5.11 Exercises
   5.12 Key Points
6 Using Git at the Command Line
   6.1 Setting Up
   6.2 Creating a New Repository
   6.3 Adding Existing Work
   6.4 Describing Commits
   6.5 Saving and Tracking Changes
   6.6 Synchronizing with Other Repositories
   6.7 Exploring History
   6.8 Restoring Old Versions of Files
   6.9 Ignoring Files
   6.10 Summary
   6.11 Exercises
   6.12 Key Points
7 Going Further with Git
   7.1 What\'s a Branch?
   7.2 Creating a Branch
   7.3 What Curve Should We Fit?
   7.4 Verifying Zipf\'s Law
   7.5 Merging
   7.6 Handling Conflicts
   7.7 A Branch-Based Workflow
   7.8 Using Other People\'s Work
   7.9 Pull Requests
   7.10 Handling Conflicts in Pull Requests
   7.11 Summary
   7.12 Exercises
   7.13 Key Points
8 Working in Teams
   8.1 What Is a Project?
   8.2 Include Everyone
   8.3 Establish a Code of Conduct
   8.4 Include a License
   8.5 Planning
   8.6 Bug Reports
   8.7 Labeling Issues
   8.8 Prioritizing
   8.9 Meetings
   8.10 Making Decisions
   8.11 Make All This Obvious to Newcomers
   8.12 Handling Conflict
   8.13 Summary
   8.14 Exercises
   8.15 Key Points
9 Automating Analyses with Make
   9.1 Updating a Single File
   9.2 Managing Multiple Files
   9.3 Updating Files When Programs Change
   9.4 Reducing Repetition in a Makefile
   9.5 Automatic Variables
   9.6 Generic Rules
   9.7 Defining Sets of Files
   9.8 Documenting a Makefile
   9.9 Automating Entire Analyses
   9.10 Summary
   9.11 Exercises
   9.12 Key Points
10 Configuring Programs
   10.1 Configuration File Formats
   10.2 Matplotlib Configuration
   10.3 The Global Configuration File
   10.4 The User Configuration File
   10.5 Adding Command-Line Options
   10.6 A Job Control File
   10.7 Summary
   10.8 Exercises
   10.9 Key Points
11 Testing Software
   11.1 Assertions
   11.2 Unit Testing
   11.3 Testing Frameworks
   11.4 Testing Floating-Point Values
   11.5 Integration Testing
   11.6 Regression Testing
   11.7 Test Coverage
   11.8 Continuous Integration
   11.9 When to Write Tests
   11.10 Summary
   11.11 Exercises
   11.12 Key Points
12 Handling Errors
   12.1 Exceptions
   12.2 Writing Useful Error Messages
   12.3 Testing Error Handling
   12.4 Reporting Errors
   12.5 Summary
   12.6 Exercises
   12.7 Key Points
13 Tracking Provenance
   13.1 Data Provenance
   13.2 Code Provenance
   13.3 Summary
   13.4 Exercises
   13.5 Key Points
14 Creating Packages with Python
   14.1 Creating a Python Package
   14.2 Virtual Environments
   14.3 Installing a Development Package
   14.4 What Installation Does
   14.5 Distributing Packages
   14.6 Documenting Packages
   14.7 Software Journals
   14.8 Summary
   14.9 Exercises
   14.10 Key Points
15 Finale
   15.1 Why We Wrote This Book
Appendix
   A Solutions
   B Learning Objectives
      B.1 Getting Started
      B.2 The Basics of the Unix Shell
      B.3 Building Tools with the Unix Shell
      B.4 Going Further with the Unix Shell
      B.5 Building Command-Line Tools with Python
      B.6 Using Git at the Command Line
      B.7 Going Further with Git
      B.8 Working in Teams
      B.9 Automating Analyses with Make
      B.10 Configuring Programs
      B.11 Testing Software
      B.12 Handling Errors
      B.13 Tracking Provenance
      B.14 Creating Packages with Python
   C Key Points
      C.1 Getting Started
      C.2 The Basics of the Unix Shell
      C.3 Building Tools with the Unix Shell
      C.4 Going Further with the Unix Shell
      C.5 Building Command-Line Programs in Python
      C.6 Using Git at the Command Line
      C.7 Going Further with Git
      C.8 Working in Teams
      C.9 Automating Analyses with Make
      C.10 Configuring Programs
      C.11 Testing Software
      C.12 Handling Errors
      C.13 Tracking Provenance
      C.14 Creating Packages with Python
   D Project Tree
   E Working Remotely
      E.1 Logging In
      E.2 Copying Files
      E.3 Running Commands
      E.4 Creating Keys
      E.5 Dependencies
   F Writing Readable Code
      F.1 Python Style
      F.2 Order
      F.3 Checking Style
      F.4 Refactoring
      F.5 Code Reviews
      F.6 Python Features
      F.7 Summary
   G Documenting Programs
      G.1 Writing Good Docstrings
      G.2 Defining Your Audience
      G.3 Creating an FAQ
   H YAML
   I Anaconda
      I.1 Package Management with conda
      I.2 Environment Management with conda
   J Glossary
   K References
Index