Sync main to develop

[HarshitSharma14]

Summary of changes

Syncs the develop branch with main. This PR includes the previous 12 commits from main that were missing in develop, along with 1 merge commit to align both branches and ensure that repository safeguards and CI workflows are present in develop.

After review feedback, the CI workflow was also adjusted:

• Updated the linter to only check for missing imports.
• Updated the workflow to install dependencies from Environment_Creation/requirements.txt, as referenced in the project setup documentation.

Related issue(s)

Closes #128

Agent logic / prompts

• I have not modified any agent logic or prompts.
• I have modified agent logic or prompts (please describe in the PR description and discuss with maintainers if needed).

Tests

• I have added or updated tests for my changes.
• This PR does not require new tests / no tests added.

Checklist

• CI checks pass (syntax, imports, lint, tests).
• I have read CONTRIBUTING.md and followed the contribution workflow.

[sarrah-basta]

@HarshitSharma14 please change the linter to only check for missing imports, and not classify unused imports or import * as failures.

[HarshitSharma14]

@HarshitSharma14 please change the linter to only check for missing imports, and not classify unused imports or import * as failures.

Pushed the update to the linter so it now only checks for missing imports. I also switched the workflow to use Environment_Creation/requirements.txt (earlier it was using the smaller requirements.txt), since @quirky-blu has raised a PR proposing removal of the other one and the Environment_Creation/README.md references this file for dependency installation.

If you’d prefer keeping a lighter CI dependency setup instead, we could also introduce a requirements-ci.txt specifically for the workflow. Let me know if you'd like me to change it that way.

[HarshitSharma14]

@sarrah-basta @Orthogonal-Research-Lab

Thanks for the clarification on the linter, I've updated it accordingly.

One remaining point from my earlier comment (#132 (comment)) is the existing python-package.yml workflow, which currently fails because it expects tests. Would you prefer that I adjust it to skip tests, or remove/disable it if it's no longer needed?

[quirky-blu]

@HarshitSharma14

If you’d prefer keeping a lighter CI dependency setup instead, we could also introduce a requirements-ci.txt specifically for the workflow. Let me know if you'd like me to change it that way.

This seems like a superficial fix, it is bypassing actually checking the requirements user is expected to install, so I don't think a new requirements should be introduced just for ci

Also, after going through the changes, i think a 'pip check' should be added after installing the libraries. This should prevent prs with version conflicts.

[HarshitSharma14]

@quirky-blu Fair point about validating the same dependencies users install. I’ve already updated the workflow to use Environment_Creation/requirements.txt. My earlier suggestion about a smaller CI-specific requirements file wasn’t meant as a fix , it’s just something commonly used in many projects to keep CI lighter, so I wanted to check if maintainers preferred that setup.

While testing the installation locally with Environment_Creation/requirements.txt, I noticed some dependency resolution issues (for example around pydantic and ollama). Since you already have a PR addressing the requirements file, it probably makes sense to get that sorted first. After that we can add pip check to CI to catch version conflicts going forward.

Thanks for your input on this.

[quirky-blu]

@HarshitSharma14 yeah I guess we can add pip check on a later pr

[sarrah-basta]

@Orthogonal-Research-Lab could you comment about the earlier python-package.yml?