Development

[gjbex]

Summary by Sourcery

Improve robustness of hands-on notebooks and extend examples around environment variables and Hydra logging configuration.

New Features:

• Add on-demand installation of the sh module and conditional download of the Julia source file in the Julia hands-on notebook.
• Introduce dotenv-based environment variable demo with supporting README, sample env file, and gitignore.
• Configure Hydra-based custom logging via a new job_logging configuration file and document how to control log levels.
• Add shell command and environment setup cells to the shell interaction notebook to illustrate direct shell usage and importing os.

Enhancements:

• Update notebook metadata to target a modern Python ipykernel and recent Python version.
• Clarify documentation for environment variable examples and Hydra usage, including how logging is configured through Hydra.

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[sourcery-ai]

Reviewer's Guide

Makes the Julia and shell interaction notebooks more robust and self-contained, updates environment-variable and Hydra documentation, introduces a dotenv-based environment variable demo, and configures Hydra to use a custom logging setup.

Sequence diagram for dotenv_demo environment variable loading

sequenceDiagram
    actor User
    participant dotenv_demo
    participant os_env
    participant dotenv
    participant env_file
    participant Console

    User->>dotenv_demo: run dotenv_demo.py
    dotenv_demo->>os_env: check MY_SECRET in environ
    alt MY_SECRET present
        os_env-->>dotenv_demo: MY_SECRET found
        dotenv_demo->>Console: print "MY_SECRET is already set in the environment."
    else MY_SECRET absent
        os_env-->>dotenv_demo: MY_SECRET not found
        dotenv_demo->>Console: print "Loading environment variables from .env file..."
        dotenv_demo->>dotenv: load_dotenv()
        dotenv->>env_file: read .env
        env_file-->>dotenv: key value pairs
        dotenv-->>os_env: update environment
    end

    dotenv_demo->>os_env: getenv MY_SECRET
    os_env-->>dotenv_demo: secret_key
    alt secret_key present
        dotenv_demo->>Console: print "MY_SECRET_KEY: {secret_key}"
    else secret_key absent
        dotenv_demo->>Console: print "MY_SECRET not found in environment variables."
    end

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File-Level Changes

Change	Details	Files
Make the Julia hands-on notebook self-contained and idempotent for sh installation and source download, and update kernel metadata.	Replace explicit pip-install code cell for sh with conditional import-and-install logic in the main import cell. Guard the download of the Fortran source file so it only runs if the file is missing, and switch to the updated GitHub URL and repository path. Clarify markdown instructions to explain conditional installation and download behavior. Update notebook kernel metadata (display name, Python version, nbformat minor version).	hands-on/julia.ipynb
Enhance the shell interaction notebook with explicit shell and environment examples.	Add a code cell that runs a bare !ls -l shell command to complement the sh.ls example. Insert an explicit import os cell before environment-variable examples to make the notebook self-contained.	hands-on/shell_interaction.ipynb
Document and demonstrate using dotenv for loading environment variables from a .env file.	Extend the environment-variables README to mention the dotenv package and its role. Add a dotenv demo script that conditionally loads environment variables from a .env file and prints MY_SECRET. Introduce a dotenv-focused README describing usage, inputs, and purpose. Add supporting files for dotenv usage, including a template dot_env file and a .gitignore entry to ignore the real .env file.	source-code/enviroment-variables/README.md source-code/enviroment-variables/dotenv/dotenv_demo.py source-code/enviroment-variables/dotenv/README.md source-code/enviroment-variables/dotenv/.gitignore source-code/enviroment-variables/dotenv/dot_env
Configure Hydra-based example to use a custom logging configuration and document how to control logging via configuration.	Add a custom Hydra job_logging configuration that defines a simple console handler and INFO root level. Update the main Hydra config defaults to include the custom job_logging override. Extend the Hydra README with documentation and an example command showing how to change the log level via Hydra configuration.	source-code/hydra/README.md source-code/hydra/conf/config.yaml source-code/hydra/conf/hydra/job_logging/custom.yaml

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[sourcery-ai]

Hey - I've found 1 issue, and left some high level feedback:

• In dotenv_demo.py the printed label MY_SECRET_KEY does not match the environment variable name MY_SECRET, which is likely to confuse users; align the message with the actual variable name (e.g. print MY_SECRET).

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- In `dotenv_demo.py` the printed label `MY_SECRET_KEY` does not match the environment variable name `MY_SECRET`, which is likely to confuse users; align the message with the actual variable name (e.g. print `MY_SECRET`).

## Individual Comments

### Comment 1
<location path="source-code/enviroment-variables/dotenv/dotenv_demo.py" line_range="17-20" />
<code_context>
+        load_dotenv()
+
+    # Access an environment variable
+    secret_key = os.getenv('MY_SECRET')
+
+    if secret_key:
+        print(f'MY_SECRET_KEY: {secret_key}')
+    else:
+        print('MY_SECRET not found in environment variables.')
</code_context>
<issue_to_address>
**issue:** Inconsistent naming between the environment variable (`MY_SECRET`) and the printed label (`MY_SECRET_KEY`).

The code reads `MY_SECRET` from the environment but prints it as `MY_SECRET_KEY`, which can mislead users about which variable to configure. Please use a consistent name for both the environment lookup and the printed label (e.g., `MY_SECRET`).
</issue_to_address>

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