Add --debug-log logs for internal model state

[Copilot]

Adds a new CLI option to emit per-timestep debug logs for SIPNET internal state. When enabled, the run produces structured envi, fluxes, and trackers logs with headers derived from the current global state structs.

• CLI and output lifecycle

  • Adds --debug-log <prefix> to configure debug log output with an arbitrary prefix/path.
  • Opens and closes:
    • <prefix>_envi.log
    • <prefix>_fluxes.log
    • <prefix>_trackers.log
  • Keeps existing output behavior unchanged when the option is unset.

• Per-timestep debug logging

  • Extends model output flow to write one row per timestep to each debug file.
  • All debug logs begin with year day time, matching sipnet.out.

• Structured field coverage

  • *_envi.log: one column per envi field, using the field name directly.
  • *_fluxes.log: one column per fluxes field, using the field name directly.
  • *_trackers.log: one column per trackers field with t. prefix, plus phenologyTrackers fields with pt. prefix.

• Config and documentation

  • Registers the new option in context/config handling and CLI help text.
  • Documents the new debug-output behavior in the user guide.

• Focused coverage

  • Adds an infrastructure test that runs SIPNET with --debug-output, verifies all three files are created, checks representative headers, and confirms row counts match sipnet.out.

Example:

./sipnet -i sipnet.in --debug-log debug/run1

Outputs:

debug/run1_envi.log
debug/run1_fluxes.log
debug/run1_trackers.log

[Alomir]

@copilot:

• Please refactor as much new output code as makes sense into two new files, debug_log.h and debug_log.c

[Copilot]

@copilot:

• Please refactor as much new output code as makes sense into two new files, debug_log.h and debug_log.c

Addressed in 92f1533.

[Alomir]

@copilot Please remove the shouldSkipConfigEntry check and always print DEBUG_OUTPUT_PREFIX in the config dump

[Copilot]

@copilot Please remove the shouldSkipConfigEntry check and always print DEBUG_OUTPUT_PREFIX in the config dump

Addressed in 97befcd.

[Alomir]

@copilot please rename --debug-output to --debug-log

[Copilot]

@copilot please rename --debug-output to --debug-log

Addressed in ce63d03.

[Alomir]

@copilot Please change all new names such as debugOutput and DEBUG_OUTPUT to line up with previous rename of --debug-output to --debug-log. Don't forget the name of the new test file.

[Copilot]

@copilot Please change all new names such as debugOutput and DEBUG_OUTPUT to line up with previous rename of --debug-output to --debug-log. Don't forget the name of the new test file.

Addressed in ef3a6b6.

[Alomir]

@copilot:

• debugOutputPrefix never made it into the codebase - don't worry about it for backwards compatibility in src/common/context.c
• Please add debug_log.c and the new test file to CMakeLists.txt

[Copilot]

@copilot:

• debugOutputPrefix never made it into the codebase - don't worry about it for backwards compatibility in src/common/context.c
• Please add debug_log.c and the new test file to `CMakeL...

Addressed in 546171e.

[Copilot]

Pull request overview

Adds an optional per-timestep “debug state” logging facility to SIPNET, wiring a new CLI flag through context handling and the model loop to emit additional structured outputs for internal state.

Changes:

• Adds --debug-log <prefix> CLI support plus DEBUG_LOG_PREFIX context/config plumbing.
• Introduces src/sipnet/debug_log.{c,h} and integrates header/state row emission into runModelOutput().
• Adds an infrastructure test and updates smoke expected config dumps/docs to reflect the new context key.

Reviewed changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/smoke/russell_3/sipnet.config	Updates expected config dump to include DEBUG_LOG_PREFIX.
tests/smoke/russell_2/sipnet.config	Updates expected config dump to include DEBUG_LOG_PREFIX.
tests/smoke/russell_1/sipnet.config	Updates expected config dump to include DEBUG_LOG_PREFIX.
tests/smoke/niwot/sipnet.config	Updates expected config dump to include DEBUG_LOG_PREFIX.
tests/sipnet/test_sipnet_infrastructure/testDebugLogFiles.c	Adds infrastructure test verifying debug log creation/headers/row counts.
tests/sipnet/test_sipnet_infrastructure/Makefile	Registers the new infrastructure test and cleans its artifacts.
src/sipnet/sipnet.h	Extends runModelOutput() API to accept debug log file handles.
src/sipnet/sipnet.c	Emits debug headers/rows and initializes/frees debug field arrays.
src/sipnet/frontend.c	Initializes/opens/closes debug log files and passes them into the model run.
src/sipnet/debug_log.h	Declares debug logging API and DebugLogFiles handles.
src/sipnet/debug_log.c	Implements debug logging (headers + per-timestep rows).
src/sipnet/cli.c	Adds --debug-log argument parsing and help text.
src/common/context.h	Adds debugLogPrefix to the global context struct.
src/common/context.c	Registers DEBUG_LOG_PREFIX in context initialization.
Makefile	Adds debug_log.c to the build.
docs/user-guide/running-sipnet.md	Documents the new debug log feature (but needs key-name correction).
docs/user-guide/model-inputs.md	Documents the new option (but had inconsistent formatting).
CMakeLists.txt	Adds debug_log.c and the new test to the CLion/IDE build config.

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[Alomir]

Note: copilot review comments above are valid, will fix tomorrow

[Alomir]

👍