fix: update packages with detected vulnerabilities

[jselig-rigetti]

From https://github.com/rigetti/pyquil/actions/runs/17415859364/job/49444091708?pr=1833

 +-------------------------------------+------+-----------+--------------+---------+-------------+
| OSV URL                             | CVSS | ECOSYSTEM | PACKAGE      | VERSION | SOURCE      |
+-------------------------------------+------+-----------+--------------+---------+-------------+
| https://osv.dev/GHSA-33p9-3p43-82vq | 7.3  | PyPI      | jupyter-core | 5.7.2   | poetry.lock |
| https://osv.dev/GHSA-9hjg-9r4m-mvj7 | 5.3  | PyPI      | requests     | 2.32.3  | poetry.lock |
| https://osv.dev/PYSEC-2025-49       | 8.8  | PyPI      | setuptools   | 70.3.0  | poetry.lock |
| https://osv.dev/GHSA-5rjg-fvgr-3xxf |      |           |              |         |             |
| https://osv.dev/GHSA-7cx3-6m66-7c5m | 7.5  | PyPI      | tornado      | 6.4.2   | poetry.lock |
| https://osv.dev/GHSA-48p4-8xcf-vxj5 | 5.3  | PyPI      | urllib3      | 2.3.0   | poetry.lock |
| https://osv.dev/GHSA-pq67-6m6q-mj2v | 5.3  | PyPI      | urllib3      | 2.3.0   | poetry.lock |
+-------------------------------------+------+-----------+--------------+---------+-------------+

[windsurf-bot]

1 file skipped due to size limits:

• poetry.lock

Looks good to me 🤙

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[github-actions]

Bencher Report

Branch	jselig/fix-dep-vulns
Testbed	ci-runner-linux

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Benchmark	Latency	seconds (s)
test/benchmarks/test_program.py::test_copy_everything_except_instructions	📈 view plot ⚠️ NO THRESHOLD	10.49 s
test/benchmarks/test_program.py::test_instructions	📈 view plot ⚠️ NO THRESHOLD	4.08 s
test/benchmarks/test_program.py::test_iteration	📈 view plot ⚠️ NO THRESHOLD	4.12 s

🐰 View full continuous benchmarking report in Bencher

[github-actions]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
7268	6384	88%	87%	🟢

New Files

No new covered files...

Modified Files

File	Coverage	Status
pyquil/latex/_ipython.py	29%	🟢
pyquil/quilatom.py	83%	🟢
pyquil/quilbase.py	94%	🟢
TOTAL	69%	🟢

updated for commit: e7d5d62 by action🐍

[asaites]

It's not something that needs to be fixed here, but I think the $pyquil_version is meant to be passed as a build-arg from the Makefile for the docker target.

[jselig-rigetti]

It's not something that needs to be fixed here, but I think the $pyquil_version is meant to be passed as a build-arg from the Makefile for the docker target.

@asaites created #1835 to follow up