chore: Bump fgpyo to 1.0

[msto]

No description provided.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.81%. Comparing base (aa21269) to head (03cf842).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #120   +/-   ##
=======================================
  Coverage   96.81%   96.81%           
=======================================
  Files          26       26           
  Lines        1789     1789           
  Branches      215      215           
=======================================
  Hits         1732     1732           
  Misses         31       31           
  Partials       26       26           

☔ View full report in Codecov by Sentry.
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[coderabbitai]

Walkthrough

The change updates the pyproject.toml file of the prymer project by modifying the dependency version for fgpyo from ^0.8.0 to ^1.0.0. No further changes to dependencies or configurations were made.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 9cb2348 and 03cf842.

⛔ Files ignored due to path filters (1)

• poetry.lock is excluded by !**/*.lock

📒 Files selected for processing (1)

• pyproject.toml (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (2)

• GitHub Check: Tests (3.12)
• GitHub Check: Tests (3.11)

🔇 Additional comments (2)

pyproject.toml (2)

40-40: Run comprehensive tests.

Major version bump requires thorough testing.

✅ Verification successful

🏁 Script executed:

#!/bin/bash
# Check test coverage for fgpyo imports
rg -l 'import.*fgpyo|from.*fgpyo' tests/

Length of output: 292

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Tests for fgpyo confirmed across multiple modules.

• Test files in tests/api, tests/offtarget, and tests/primer3 reference fgpyo.
• Ensure full test suite runs successfully before accepting the major version bump.

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40-40: Verify fgpyo 1.0.0 compatibility and security.

Major version bump. Check compatibility and security.

❌ Verification inconclusive

🏁 Script executed:

#!/bin/bash
# Check PyPI for latest versions and release date
curl -s https://pypi.org/pypi/fgpyo/json | jq '.info.version, .releases["1.0.0"].upload_time'

# Check for security advisories
gh api graphql -f query='
{
  securityVulnerabilities(first: 5, ecosystem: PIP, package: "fgpyo") {
    nodes {
      advisory {
        summary
        severity
        publishedAt
      }
      vulnerableVersionRange
    }
  }
}'

Length of output: 458

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🌐 Web query:

What are the breaking changes in fgpyo 1.0.0 compared to 0.8.0?

💡 Result:

The provided search results do not contain specific information about breaking changes in fgpyo 1.0.0 compared to 0.8.0. The available sources ([7][8]) focus on general setup instructions, dependencies (Python 3.9+), and development workflows using Poetry, but they do not document version-specific changes or migrations between these releases.

For detailed release notes or breaking changes in fgpyo, you would need to consult the project’s official changelog, GitHub releases page, or commit history directly—none of which are included in the provided search results.

Citations:

• 1: https://without.boats/blog/failure-1.0/
• 2: https://docs.scipy.org/doc/scipy/release/1.0.0-notes.html
• 3: https://docs.scipy.org/doc/scipy-1.8.0/release.1.1.0.html
• 4: https://www.juliabloggers.com/julia-1-6-what-has-changed-since-julia-1-0/
• 5: https://grafana.com/docs/pyroscope/latest/release-notes/v1-0/
• 6: https://googlecloudplatform.github.io/magic-modules/breaking-changes/breaking-changes/
• 7: https://github.com/fulcrumgenomics/fgpyo
• 8: https://github.com/fulcrumgenomics/fgpyo/issues
• 9: Do not bump to 1.0.0 when issuing a breaking change < 1.0.0 conventional-changelog/conventional-changelog#239
• 10: [FEEDBACK WANTED] Proposal for 1.0.0 breaking changes moment/moment-timezone#1039

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Verify fgpyo 1.0.0 compatibility and security.

• PyPI confirms the latest version is 1.0.0 and no security advisories were found.
• Web searches did not reveal documented breaking changes from 0.8.0 to 1.0.0.
• Given the major version bump, review the official changelog/GitHub releases and conduct comprehensive tests to catch any latent issues.

---

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[msto]

@nh13 if we merge this could it be accompanied by a 3.0.1 release?

I think a patch bump is appropriate based on this comment: semver/semver#148 (comment)