Automatic Computational Research Notebook

ACORN automates the decoration and logging of computational research in a smart way that makes it easy to keep “lab notebooks” for computational scientists. This API focuses on the python backend that handles all the package decoration functions needed to implement smart logging.

Note

the ipython notebook interface provides logging of commands typed into the notebook. In that way, it is possible to keep a log of everything that was done. However, the log is not as useful as acorn because it is just text. We treat variables and methods individually and expose ways to analyze and document results automatically.

The backend is made up a few key pieces:

1. Decorator logic that can handle any kind of package, including the C-extension modules that optimize numerical operations.
2. Descriptors that use configuration files to decide how best to describe variables/objects in the database.
3. A database module that saves method calls, object instantiations and the objects and variables used in those calls.
4. Automated importer so that new packages (including those created by users) can be decorated without modifying acorn.
5. Ipython extension module that allows classes and functions defined in an ipython notebook to be automatically decorated and included in the database.
6. Special sub-classing modules for optimized packages that cannot be handled by the default decoration machinery (e.g., numpy.ndarray).
7. An analysis module that analyzes the results of certain function calls (based on the FQDN of the function) to expose additional features that are interesting to the user in the context of a notebook. For example, when a ML model is fit, the scores can be configured to automatically be extracted whenever *.predict is called on the model.

Each of these building blocks is described below in a separate documentation file. Each file also includes the API documentation for the code. Additionally, the syntax for configuring which parts of packages are included is described in the Global and Package Configuration in ACORN section.

Contents:

• Automatic Decoration of Packages
• ACORN Object Descriptor Interface
• Notebook Database Documentation
• Acorn Automated Package Decoration on Import
• Ipython Extension Module
• Special Sub-classes in ACORN
• Method Call Analysis
• Global and Package Configuration in ACORN

Indices and tables

• Index
• Module Index
• Search Page