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fix: Update dependencies and fix submatrix_to_pandas behavior#230

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totonga merged 8 commits intomainfrom
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Mar 19, 2026
Merged

fix: Update dependencies and fix submatrix_to_pandas behavior#230
totonga merged 8 commits intomainfrom
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@totonga totonga commented Mar 19, 2026

Update various dependencies to their latest versions and restore the previous behavior of the submatrix_to_pandas function by ensuring it does not set the independent column as the index by default. Additionally, update the development container configuration and fix the GitHub Copilot Chat extension usage.

dependabot Bot and others added 8 commits February 22, 2026 08:48
Bumps [pylint](https://github.com/pylint-dev/pylint) from 4.0.4 to 4.0.5.
- [Release notes](https://github.com/pylint-dev/pylint/releases)
- [Commits](pylint-dev/pylint@v4.0.4...v4.0.5)

---
updated-dependencies:
- dependency-name: pylint
  dependency-version: 4.0.5
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…0.0 (#224)

Updates the requirements on [protobuf](https://github.com/protocolbuffers/protobuf) to permit the latest version.
- [Release notes](https://github.com/protocolbuffers/protobuf/releases)
- [Commits](https://github.com/protocolbuffers/protobuf/commits)

---
updated-dependencies:
- dependency-name: protobuf
  dependency-version: 7.34.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [bandit[toml]](https://github.com/PyCQA/bandit) from 1.9.3 to 1.9.4.
- [Release notes](https://github.com/PyCQA/bandit/releases)
- [Commits](PyCQA/bandit@1.9.3...1.9.4)

---
updated-dependencies:
- dependency-name: bandit[toml]
  dependency-version: 1.9.4
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [black](https://github.com/psf/black) from 26.1.0 to 26.3.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@26.1.0...26.3.1)

---
updated-dependencies:
- dependency-name: black
  dependency-version: 26.3.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
#229)

The behavior of submatrix_to_pandas has been different in the past.
Set back to last behavior and make sure by test it won't break again.
@totonga totonga merged commit f038fd3 into main Mar 19, 2026
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