Note: Cover -- Half Title -- 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.