Close 9 open CodeQL/Dependabot alerts (workflow permissions + torch in test fixtures)

[ackizilkale]

Closes the 9 remaining open security alerts on master:

• 5× medium actions/missing-workflow-permissions (Bugs in client / example #3, Make client pip installable #4, Use setuptools so the client can be pip-installed. #5, Import gives ApiError, ApiThrottledError, ApiBadRequestError #6, Update __init__.py #7)
• 4× medium/low torch CVEs in test runner fixtures (Setup.py refers to nonexistent scripts dir #35, Model training failing with error code 21111 #37, Has concepts list a limit length? (Python 3.5, clarifai 2.0.17)  #45, expired token #46)

Commits

1. fd198a4 — Add explicit GITHUB_TOKEN permissions to workflows

File	Scopes	Why
publish.yml	workflow: contents: read publish-github-release job: contents: write	PyPI upload uses TWINE_USERNAME/PASSWORD (independent of GITHUB_TOKEN). The release-creation job needs contents: write for softprops/action-gh-release.
run_tests.yml	contents: read pull-requests: write	Coverage step uses marocchino/sticky-pull-request-comment which posts on PRs.
run_tests_staging.yml / run_tests_prod.yml	contents: read	Cron callers; the PR-comment step has if: github.event_name == 'pull_request' so it never fires here.

2. 8f5714d — Bump torch to 2.8.0 in test runner fixtures

Test fixtures only — not shipped SDK code:

• tests/runners/dummy_vllm_models/requirements.txt: torch==2.6.0 → 2.8.0
• tests/runners/hf_mbart_model/requirements.txt: torch==2.6.0 → 2.8.0

Covers both CVEs:

• CVE-2025-2953 (GHSA-3749-ghw9-m3mg, low) — patched in 2.7.1-rc1
• CVE-2025-3730 (GHSA-887c-mr87-cxwp, medium) — patched in 2.8.0

Test plan

• yaml.safe_load round-trip parses all 4 workflow files cleanly.
• CI green on this branch (workflow changes don't affect existing test logic; they only narrow the auto-provisioned token).
• CodeQL re-run closes alerts Bugs in client / example #3, Make client pip installable #4, Use setuptools so the client can be pip-installed. #5, Import gives ApiError, ApiThrottledError, ApiBadRequestError #6, Update __init__.py #7.
• Dependabot re-evaluation closes alerts Setup.py refers to nonexistent scripts dir #35, Model training failing with error code 21111 #37, Has concepts list a limit length? (Python 3.5, clarifai 2.0.17)  #45, expired token #46.

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR addresses remaining CodeQL and Dependabot security alerts by tightening default GITHUB_TOKEN permissions across GitHub Actions workflows and updating the pinned torch version used only in test runner fixtures.

Changes:

• Add explicit permissions blocks to workflows to avoid overly broad default GITHUB_TOKEN scopes.
• Grant job-scoped contents: write only where GitHub Releases are created.
• Bump torch from 2.6.0 to 2.8.0 in test runner fixture requirements to pick up CVE fixes.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
.github/workflows/publish.yml	Adds explicit workflow token permissions and scopes contents: write to the release job only.
.github/workflows/run_tests.yml	Adds explicit token permissions for checkout and PR coverage commenting.
.github/workflows/run_tests_staging.yml	Adds explicit contents: read permissions for scheduled staging test invocations.
.github/workflows/run_tests_prod.yml	Adds explicit contents: read permissions for scheduled prod test invocations.
tests/runners/dummy_vllm_models/requirements.txt	Updates test-fixture torch pin to 2.8.0.
tests/runners/hf_mbart_model/requirements.txt	Updates test-fixture torch pin to 2.8.0.

[sanjaychelliah]

@copilot apply changes based on this feedback

[Copilot]

Done in commit 3e11ae6. Workflow-level permissions are now contents: read only. pull-requests: write has been moved to a new dedicated coverage-comment job that has if: github.event_name == 'pull_request' at the job level, so it never runs on push to master. The build job uploads code-coverage-results.md as an artifact (for Linux + Python 3.11 only), which the new job downloads before posting the PR comment.

[github-actions]

Package	Line Rate	Health
clarifai	45%	❌
clarifai.cli	62%	➖
clarifai.cli.templates	67%	➖
clarifai.cli.templates.toolkits	100%	✔
clarifai.client	64%	➖
clarifai.client.auth	67%	➖
clarifai.constants	100%	✔
clarifai.datasets	100%	✔
clarifai.datasets.export	69%	➖
clarifai.datasets.upload	75%	➖
clarifai.datasets.upload.loaders	37%	❌
clarifai.models	100%	✔
clarifai.rag	0%	❌
clarifai.runners	52%	➖
clarifai.runners.models	61%	➖
clarifai.runners.pipeline_steps	45%	❌
clarifai.runners.pipelines	77%	➖
clarifai.runners.utils	61%	➖
clarifai.runners.utils.data_types	72%	➖
clarifai.schema	100%	✔
clarifai.urls	56%	➖
clarifai.utils	62%	➖
clarifai.utils.evaluation	16%	❌
clarifai.workflows	95%	✔
examples	64%	➖
Summary	61% (12536 / 20612)	➖

Minimum allowed line rate is 50%