Research task (Technical Documentation):
Look at this public Github repository "clever-rockies" by user suzytamang. <https://github.com/suzytamang/clever-rockies>

The folders include "res", "src", and "tests". Go to the README, read it carefully to see what the point of the code is. Then, I have three requests.

First, walk me through exactly what each step does. Do it at a high level first, and then break it down to chunks of actual code. You should start with generating some sample data based on the code and the context, at least several rows of it, and tell me how the data changes after each step.

Second, walk me through exactly what I'd need to do to run this code on my computer, including how I'd need to organize my input and output files at each stage. 

Finally, suggest improvements to the code. First output the code that's written there, and then mark exactly what you'd change and why, then give a final version and tell me how the logic would change.

Evaluation rubric:
criterion: The response begins with an introductory high-level overview of the repository "clever-rockies" before diving into other details.
weight: 5
axis: Explicit Criteria

criterion: The response provides a clearly labeled section (or sections) that breaks the repository workflow down into finer-grained code chunks (such as per module or function) after the high-level introduction.
weight: 5
axis: Explicit Criteria

criterion: The response includes at least one formatted directory tree that lists the key top-level folders (i.e., envs, res, src, and tests).
weight: 2
axis: Implicit Criteria

criterion: The response explicitly and correctly identifies the key sub-folders and files of the main folders as follows:
- 'envs' includes 'README.md'.
- 'res' includes the 'dicts' subfolder and 5 individual files: 'assessment_terms.txt', 'headers.txt', 'na_trigs.json', 'neg_trigs.json', and 'other_terms_to_drop.txt'.
- 'src' includes subfolders 'step2', 'step3', 'step4', 'step5' and files 'grabtargets.py', 'make_one_out.py', and 'run_all_steps.py'.
- 'tests' includes the subfolder 'test_notes' and the file 'test.README.md'.
weight: 3
axis: Implicit Criteria

criterion: The response uses verbatim quotes from README.md to describe the project's purpose, which is to run the Clinical Event Recognizer (CLEVER) from the Program Evaluation Resource Center via Python 3.
weight: 4
axis: Explicit Criteria

criterion: The response generates sample input data containing >= 3 rows and shows that data in a fixed-width code block or table.
weight: 5
axis: Explicit Criteria

criterion: The response shows a ‘before’ and ‘after’ view of the sample data (either as tables or code blocks) for every processing step described.
weight: 3
axis: Explicit Criteria

criterion: The response mentions using the 'git clone' command to clone the repository to run locally, such as `git clone https://github.com/suzytamang/clever-rockies.git`.
weight: 5
axis: Implicit Criteria

criterion: The response refers users to the instructions in the README.md file in the envs folder to create the appropriate Conda virtual environment to run the repository (i.e., `conda create -n clever_env python=3.12 pandas` followed by `conda activate clever_env`).
weight: 5
axis: Explicit Criteria

criterion: The response explains how input and output files will be placed using theoretical folder names or paths relative to the organization in the repository.
weight: 5
axis: Explicit Criteria

criterion: The response provides an annotated diff or clearly marked comments that identify every proposed code change (e.g., "# CHANGE:" or unified diff with +/- lines).
weight: 3
axis: Explicit Criteria

criterion: The response mentions or uses any file, function, class, or object (case-sensitive) that is not present in the repository. 
weight: -5
axis: Explicit Criteria

criterion: The response provides a justification for each suggested change to the code, such as improvement of code quality, performance, readability or error handling.
weight: 3
axis: Implicit Criteria

criterion: The response explains how the overall program logic or outputs would change as a result of the suggested improvements.
weight: 4
axis: Explicit Criteria

criterion: The response gives any claims or messages saying that the repository or its parts are inaccessible.
weight: -5
axis: Explicit Criteria

criterion: The response cautions the users to pay attention to relative file paths when running the files in this repository.
weight: 3
axis: Implicit Criteria

criterion: The response mentions 'Step 1' of the repository without referencing the fact that it is not used, as stated in the main README.md.
weight: -3
axis: Explicit Criteria

criterion: The response fails to mention the purpose of any key file from the src or res folders in its discussion (e.g., skips explaining what grabtargets.py does or how neg_trigs.json is used).
weight: -2
axis: Communication Quality

criterion: The response provides the full, revised code (final version) in code blocks after applying all proposed changes.
weight: 4
axis: Explicit Criteria

criterion: The response uses the instructions in the main README.md file to walk users through how to use the repository, including those under 'General Targets', 'Testing Functionality', and 'Main Steps'.
weight: 5
axis: Explicit Criteria