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Update the dependencies and fix security issues - #1037
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Sergiy Matusevych (motus) merged 10 commits intoOct 14, 2026
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Bound pandas, SQLAlchemy, Matplotlib, and pandas type stubs to compatible versions. Declare pytz explicitly and escape database URLs for Alembic configuration, with regression coverage. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Copilot-Session: f69bfcb1-e2f8-4cbe-8b6d-ba01db29587a
Sergiy Matusevych (motus)
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🟢 Approval recommended
Functional changes are coherent and action SHAs match their documented releases; remaining feedback is non-blocking cleanup.
2 open findings
What changed in this PR
Updates dependency compatibility, fixes Alembic URL interpolation, and incorporates #1036’s CI supply-chain hardening.
Changes:
- Adds dependency upper bounds and declares
pytzdirectly. - Escapes percent signs in Alembic URLs with regression coverage.
- Pins GitHub Actions to verified SHAs and adds a Dependabot cooldown.
| File | Description |
|---|---|
mlos_viz/setup.py |
Caps Matplotlib below 3.11. |
mlos_core/setup.py |
Caps pandas below 3. |
mlos_bench/setup.py |
Caps SQLAlchemy and adds pytz. |
mlos_bench/mlos_bench/tests/storage/schema_test.py |
Tests Alembic URL round trips. |
mlos_bench/mlos_bench/storage/sql/schema.py |
Escapes URL percent signs. |
conda-envs/mlos.yml |
Caps pandas stubs. |
conda-envs/mlos-windows.yml |
Caps Windows pandas stubs. |
conda-envs/mlos-3.13.yml |
Caps Python 3.13 pandas stubs. |
conda-envs/mlos-3.12.yml |
Caps Python 3.12 pandas stubs. |
conda-envs/mlos-3.11.yml |
Caps Python 3.11 pandas stubs. |
conda-envs/mlos-3.10.yml |
Caps Python 3.10 pandas stubs. |
.github/workflows/windows.yml |
Pins Windows workflow actions. |
.github/workflows/markdown-link-check.yml |
Pins link-check actions. |
.github/workflows/macos.yml |
Pins macOS workflow actions. |
.github/workflows/linux.yml |
Pins Linux workflow actions. |
.github/workflows/devcontainer.yml |
Pins build and deployment actions. |
.github/workflows/codeql.yml |
Pins CodeQL actions. |
.github/dependabot.yml |
Adds a seven-day Actions cooldown. |
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Keep the existing hooks compatible with pre-commit.ci, whose default Python 3.14 cannot build untokenize and breaks the pinned pyupgrade. Add the missing newline in the Dependabot config detected by the full hook run. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Copilot-Session: f69bfcb1-e2f8-4cbe-8b6d-ba01db29587a
Sergiy Matusevych (motus)
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Sergiy Matusevych (motus)
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Johannes Freischuetz (@jsfreischuetz) can you approve the PR, when you have a minute? You're the only MLOS maintainer left ))
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closing and opening again to trigger the CI |
Add an explicit Linux Python 3.14 matrix entry and matching Conda environment. Update floating-version assertions to Python 3.14. Keep base Python 3.12 available for pinned pre-commit hooks and restore Conda channel acceptance after replacing the ToS plugin. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Copilot-Session: f69bfcb1-e2f8-4cbe-8b6d-ba01db29587a
Use compatible pandas type stubs and align Conda runtime bounds with pip. Correct Windows environment-cache hashing and verify imported dependency versions. Expose Python 3.12 for container hooks after Conda activation. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Copilot-Session: f69bfcb1-e2f8-4cbe-8b6d-ba01db29587a
Sergiy Matusevych (motus)
enabled auto-merge (squash)
October 13, 2026 01:04
Sergiy Matusevych (motus)
disabled auto-merge
October 13, 2026 22:28
Move the three CodeQL steps to the verified stable v4 release without changing workflow configuration. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Copilot-Session: f69bfcb1-e2f8-4cbe-8b6d-ba01db29587a
Eu Jing Chua (eujing)
approved these changes
Oct 13, 2026
Update documentation dependencies, development tools, FLAML, and SHA-pinned workflow actions. Make three minimal typing adjustments for newer checkers. Retain NumPy 1 because NumPy 2 fails the SMAC run-history regression. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Copilot-Session: f69bfcb1-e2f8-4cbe-8b6d-ba01db29587a
This was referenced Oct 13, 2026
This was referenced Oct 13, 2026
Increase the minimization fixture to 30 trials while retaining its original score target and categorical configuration checks. Accept only equal-or-better latency rather than a sampler-version-specific exact point. Verified with Optuna 2.8 and 3.6.1, including Python 3.12 and 3.14. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Copilot-Session: f69bfcb1-e2f8-4cbe-8b6d-ba01db29587a
Sergiy Matusevych (motus)
enabled auto-merge (squash)
October 13, 2026 23:29
This was referenced Oct 13, 2026
Closed
Sergiy Matusevych (motus)
changed the title
Sergiy Matusevych (motus)
merged commit Oct 14, 2026
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29 of 33 checks passed
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This PR also includes #1036