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

Welcome?0.1The Big Picture?0.2 Intended Audience?0.3 What You Will Learn0.4 Using this Book0.5 Contributing and Re-Use?0.6 Acknowledgments? 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? 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? 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 Summary3.8 Exercises?3.9 Key Points? Going Further with the Unix Shell4.1 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? Building Command-Line Tools with Python 5.1 Programs and Modules5.2 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 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 Files6.10 Summary6.11 Exercises?6.12 Key Points? 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 Workflow7.8 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? Working in Teams?8.1 What is a Project??8.2 Include Everyone?8.3 Establish a Code of Conduct8.4 Include a License8.5 Planning8.6 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 Exercises8.15 Key Points Automating Analyses with Make9.1 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 Analyses9.10 Summary?9.11 Exercises?9.12 Key PointsConfiguring Programs10.1 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 Exercises10.9 Key Points? Testing Software11.1 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 Integration11.9 When to Write Tests?11.10 Summary?11.11 Exercises11.12 Key Points? Handling Errors?12.1 Exceptions?12.2 Writing Useful Error Messages12.3 Testing Error Handling?12.4 Reporting Errors?12.5 Summary?12.6 Exercises?12.7 Key Points? Tracking Provenance?13.1 Data Provenance?13.2 Code Provenance?13.3 Summary?13.4 Exercises?13.5 Key Points? Creating Packages with Python?14.1 Creating a Python Package?14.2 Virtual Environments?14.3 Installing a Development Package?14.4 What Installation Does14.5 Distributing Packages?14.6 Documenting Packages?14.7 Software Journals?14.8 Summary?14.9 Exercises?14.10 Key Points? Finale?15.1 Why We Wrote This Book? Appendix?A Solutions?B Learning Objectives?C Key Points?D Project Tree?E Working Remotely?F Writing Readable Code?G Documenting Programs?H YAMLI Anaconda?J Glossary?K References?Index?