Logging to support catching errors

[jlewi]

Logging to support #7

• Updated logging in Agent.Generate and Executor.Execute so we log the information needed to determine when the human edits the cell

• To properly log protos in structured logging we need to use the zapr proto plugin to generate MarshalLogObject functions for all the protos. We can then use zap.Object to pass the protos as fields to logger

  • We need to enable logr to allow passing zap fields

• Add a logs subcommand and analyzer to process the logs and join the log entries into traces and logs for the blocks

• Log call stack; fix Logs no longer include call stack #53; this was broken when we stopped using the helper functions to build the logs. Now that we explicitly build the logger we need to add the option to log the call stack.

• Altered the SetupLogging method in app/cmd/assets.go to accept a logToFile boolean parameter, allowing conditional logging to files. We only want the serve command to log to files. We don't need the other commands to log to files

Analysis Package (app/pkg/analyze):

• Developed a new package, analyze, responsible for processing and analyzing log files. This includes parsing raw log entries, organizing them into traces and blocks, and producing structured summaries that highlight the execution flow and outcomes.
• Implemented several utility types and methods (LogEntry, Trace, BlockLog, etc.) to facilitate the analysis and organization of logs.

Configuration and Utility Changes:

• Extended the app/pkg/config/config.go to include methods for retrieving both raw and processed log directories, supporting the new logging mechanism.
• Added utility functions in app/pkg/docs/outputs.go to extract specific metadata from logged blocks, such as execution exit codes.

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