feat: bumped versions

[ryan-gdm]

Related Issues/PRs: #
Solves/Fixes: #

Changes

• Example: Eng: Updated python versions, Feautre: added new pocket constraints

Verification

• Example: CI tests are passing

[github-actions]

Dependency Review

The following issues were found:

• ✅ 0 vulnerable package(s)
• ✅ 0 package(s) with incompatible licenses
• ✅ 0 package(s) with invalid SPDX license definitions
• ⚠️ 4 package(s) with unknown licenses.
• ⚠️ 1 packages with OpenSSF Scorecard issues.

See the Details below.

License Issues

pyproject.toml

Package	Version	License	Issue Type
py3Dmol	>= 2.5.4	Null	Unknown License

uv.lock

Package	Version	License	Issue Type
py3dmol	2.5.4	Null	Unknown License
numpy	2.4.2	Null	Unknown License
tqdm	4.67.3	Null	Unknown License

OpenSSF Scorecard

Scorecard details

Package	Version	Score	Details
pip/py3Dmol	>= 2.5.4	Unknown	Unknown
pip/requests	>= 2.32.5	🟢 8.6	Details Check Score Reason Maintained 🟢 10 15 commit(s) and 2 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Binary-Artifacts 🟢 10 no binaries found in the repo Code-Review 🟢 10 all changesets reviewed Security-Policy 🟢 10 security policy file detected Token-Permissions 🟢 10 GitHub workflow tokens follow principle of least privilege CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Pinned-Dependencies 🟢 7 dependency not pinned by hash detected -- score normalized to 7 Vulnerabilities 🟢 10 0 existing vulnerabilities detected Fuzzing 🟢 10 project is fuzzed License 🟢 10 license file detected Packaging ⚠️ -1 packaging workflow not detected Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md SAST 🟢 10 SAST tool is run on all commits
pip/astroid	4.0.3	🟢 7.9	Details Check Score Reason Binary-Artifacts 🟢 10 no binaries found in the repo Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Security-Policy 🟢 9 security policy file detected Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 30 commit(s) and 14 issue activity found in the last 90 days -- score normalized to 10 Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Fuzzing 🟢 10 project is fuzzed Vulnerabilities 🟢 10 0 existing vulnerabilities detected License 🟢 10 license file detected Signed-Releases 🟢 8 5 out of the last 5 releases have a total of 5 signed artifacts. Branch-Protection 🟢 8 branch protection is not maximal on development and all release branches Packaging 🟢 10 packaging workflow detected SAST 🟢 9 SAST tool detected but not run on all commits
pip/click	8.3.1	🟢 6.3	Details Check Score Reason Maintained 🟢 10 30 commit(s) and 21 issue activity found in the last 90 days -- score normalized to 10 Code-Review 🟢 5 Found 7/13 approved changesets -- score normalized to 5 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Binary-Artifacts 🟢 10 no binaries found in the repo CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Pinned-Dependencies 🟢 8 dependency not pinned by hash detected -- score normalized to 8 Fuzzing 🟢 10 project is fuzzed License 🟢 10 license file detected Packaging 🟢 10 packaging workflow detected Signed-Releases 🟢 4 2 out of the last 5 releases have a total of 2 signed artifacts. Vulnerabilities 🟢 4 6 existing vulnerabilities detected Security-Policy 🟢 9 security policy file detected Branch-Protection 🟢 3 branch protection is not maximal on development and all release branches SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/ipykernel	7.2.0	🟢 5.4	Details Check Score Reason Code-Review 🟢 7 Found 9/12 approved changesets -- score normalized to 7 Maintained 🟢 10 29 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Binary-Artifacts 🟢 10 no binaries found in the repo CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Packaging ⚠️ -1 packaging workflow not detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Vulnerabilities 🟢 10 0 existing vulnerabilities detected Fuzzing 🟢 10 project is fuzzed License 🟢 10 license file detected Security-Policy ⚠️ 0 security policy file not detected Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Branch-Protection 🟢 3 branch protection is not maximal on development and all release branches SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/jupyter-client	8.8.0	🟢 5.2	Details Check Score Reason Code-Review 🟢 5 Found 16/30 approved changesets -- score normalized to 5 Security-Policy 🟢 9 security policy file detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Packaging ⚠️ -1 packaging workflow not detected Maintained 🟢 10 17 commit(s) and 3 issue activity found in the last 90 days -- score normalized to 10 Binary-Artifacts 🟢 10 no binaries found in the repo Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Vulnerabilities 🟢 10 0 existing vulnerabilities detected Fuzzing ⚠️ 0 project is not fuzzed License 🟢 10 license file detected Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Branch-Protection 🟢 3 branch protection is not maximal on development and all release branches SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/matplotlib	3.10.8	🟢 8.3	Details Check Score Reason Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 30 commit(s) and 17 issue activity found in the last 90 days -- score normalized to 10 Security-Policy 🟢 10 security policy file detected Packaging ⚠️ -1 packaging workflow not detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions License 🟢 9 license file detected Signed-Releases ⚠️ -1 no releases found Binary-Artifacts 🟢 10 no binaries found in the repo Branch-Protection 🟢 8 branch protection is not maximal on development and all release branches Fuzzing 🟢 10 project is fuzzed Vulnerabilities 🟢 10 0 existing vulnerabilities detected Pinned-Dependencies 🟢 6 dependency not pinned by hash detected -- score normalized to 6 SAST 🟢 10 SAST tool is run on all commits
pip/ml-dtypes	0.5.4	Unknown	Unknown
pip/numpy	2.4.2	🟢 7.2	Details Check Score Reason Dependency-Update-Tool 🟢 10 update tool detected Maintained 🟢 10 30 commit(s) and 27 issue activity found in the last 90 days -- score normalized to 10 Code-Review 🟢 10 all changesets reviewed Packaging ⚠️ -1 packaging workflow not detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions 🟢 10 GitHub workflow tokens follow principle of least privilege Binary-Artifacts 🟢 10 no binaries found in the repo CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Pinned-Dependencies 🟢 3 dependency not pinned by hash detected -- score normalized to 3 Vulnerabilities ⚠️ 0 24 existing vulnerabilities detected SAST 🟢 9 SAST tool detected but not run on all commits License 🟢 9 license file detected Fuzzing 🟢 10 project is fuzzed Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Branch-Protection 🟢 3 branch protection is not maximal on development and all release branches Security-Policy 🟢 9 security policy file detected CI-Tests 🟢 10 20 out of 20 merged PRs checked by a CI test -- score normalized to 10 Contributors 🟢 10 project has 100 contributing companies or organizations
pip/onnx	1.20.1	🟢 6.8	Details Check Score Reason Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 30 commit(s) and 16 issue activity found in the last 90 days -- score normalized to 10 Security-Policy 🟢 10 security policy file detected Dependency-Update-Tool 🟢 10 update tool detected Dangerous-Workflow ⚠️ 0 dangerous workflow patterns detected Token-Permissions 🟢 9 detected GitHub workflow tokens with excessive permissions CII-Best-Practices 🟢 5 badge detected: Passing Binary-Artifacts 🟢 10 no binaries found in the repo Pinned-Dependencies 🟢 3 dependency not pinned by hash detected -- score normalized to 3 Fuzzing ⚠️ 0 project is not fuzzed Signed-Releases ⚠️ -1 no releases found Vulnerabilities ⚠️ 0 75 existing vulnerabilities detected SAST 🟢 9 SAST tool detected but not run on all commits License 🟢 10 license file detected Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md Packaging 🟢 10 packaging workflow detected CI-Tests 🟢 10 30 out of 30 merged PRs checked by a CI test -- score normalized to 10 Contributors 🟢 10 project has 31 contributing companies or organizations
pip/pandas	3.0.0	🟢 6.4	Details Check Score Reason Binary-Artifacts 🟢 10 no binaries found in the repo Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration CI-Tests 🟢 10 30 out of 30 merged PRs checked by a CI test -- score normalized to 10 CII-Best-Practices ⚠️ 0 no badge detected Code-Review 🟢 8 25 out of last 30 changesets reviewed before merge -- score normalized to 8 Contributors 🟢 10 47 different organizations found -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Dependency-Update-Tool ⚠️ 0 no update tool detected Fuzzing 🟢 10 project is fuzzed with [OSSFuzz] License 🟢 10 license file detected Maintained 🟢 10 30 commit(s) out of 30 and 21 issue activity out of 30 found in the last 90 days -- score normalized to 10 Packaging ⚠️ -1 no published package detected Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 SAST 🟢 7 SAST tool detected but not run on all commmits Security-Policy 🟢 10 security policy file detected Signed-Releases ⚠️ 0 0 out of 5 artifacts are signed or have provenance Token-Permissions ⚠️ 0 non read-only tokens detected in GitHub workflows Vulnerabilities 🟢 10 no vulnerabilities detected
pip/pandas-stubs	3.0.0.260204	⚠️ 2.6	Details Check Score Reason Dangerous-Workflow ⚠️ -1 no workflows found Packaging ⚠️ -1 packaging workflow not detected Maintained ⚠️ 0 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0 Token-Permissions ⚠️ -1 No tokens found Code-Review ⚠️ 0 Found 2/28 approved changesets -- score normalized to 0 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Pinned-Dependencies ⚠️ -1 no dependencies found Binary-Artifacts 🟢 10 no binaries found in the repo Security-Policy ⚠️ 0 security policy file not detected Fuzzing ⚠️ 0 project is not fuzzed License 🟢 10 license file detected Signed-Releases ⚠️ -1 no releases found Vulnerabilities 🟢 4 6 existing vulnerabilities detected Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/pre-commit	4.5.1	🟢 5	Details Check Score Reason Code-Review ⚠️ 0 Found 1/12 approved changesets -- score normalized to 0 Maintained 🟢 10 30 commit(s) and 28 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Packaging ⚠️ -1 packaging workflow not detected Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Binary-Artifacts 🟢 10 no binaries found in the repo CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Vulnerabilities 🟢 10 0 existing vulnerabilities detected Fuzzing ⚠️ 0 project is not fuzzed License 🟢 10 license file detected Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md Security-Policy 🟢 10 security policy file detected SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/py3dmol	2.5.4	Unknown	Unknown
pip/pydantic	2.12.5	🟢 6.6	Details Check Score Reason Code-Review 🟢 10 all changesets reviewed Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Maintained 🟢 10 30 commit(s) and 11 issue activity found in the last 90 days -- score normalized to 10 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected License 🟢 10 license file detected Binary-Artifacts 🟢 10 no binaries found in the repo Token-Permissions ⚠️ 0 detected GitHub workflow tokens with excessive permissions Signed-Releases ⚠️ -1 no releases found Fuzzing 🟢 10 project is fuzzed Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Security-Policy 🟢 10 security policy file detected Branch-Protection ⚠️ 1 branch protection is not maximal on development and all release branches Packaging 🟢 10 packaging workflow detected Vulnerabilities 🟢 7 3 existing vulnerabilities detected SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/pydantic-core	2.41.5	Unknown	Unknown
pip/pydantic-settings	2.12.0	Unknown	Unknown
pip/pylint	4.0.4	🟢 8.2	Details Check Score Reason Maintained 🟢 10 30 commit(s) and 8 issue activity found in the last 90 days -- score normalized to 10 Code-Review 🟢 10 all changesets reviewed Security-Policy 🟢 9 security policy file detected CII-Best-Practices 🟢 5 badge detected: Passing Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions 🟢 9 detected GitHub workflow tokens with excessive permissions License 🟢 10 license file detected Signed-Releases 🟢 8 5 out of the last 5 releases have a total of 5 signed artifacts. Branch-Protection 🟢 8 branch protection is not maximal on development and all release branches Fuzzing ⚠️ 0 project is not fuzzed Binary-Artifacts 🟢 10 no binaries found in the repo Packaging 🟢 10 packaging workflow detected Vulnerabilities 🟢 9 1 existing vulnerabilities detected Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 SAST 🟢 10 SAST tool is run on all commits
pip/pytest	9.0.2	🟢 6.4	Details Check Score Reason Code-Review 🟢 10 all changesets reviewed Maintained 🟢 10 30 commit(s) and 16 issue activity found in the last 90 days -- score normalized to 10 CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions 🟢 9 detected GitHub workflow tokens with excessive permissions Binary-Artifacts 🟢 10 no binaries found in the repo Security-Policy ⚠️ 0 security policy file not detected Pinned-Dependencies 🟢 4 dependency not pinned by hash detected -- score normalized to 4 Fuzzing ⚠️ 0 project is not fuzzed License 🟢 10 license file detected Vulnerabilities 🟢 10 0 existing vulnerabilities detected Signed-Releases ⚠️ 0 Project has not signed or included provenance with any releases. Packaging 🟢 10 packaging workflow detected Branch-Protection 🟢 4 branch protection is not maximal on development and all release branches SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/ruff	0.15.0	Unknown	Unknown
pip/scikit-learn	1.8.0	🟢 9.5	Details Check Score Reason Maintained 🟢 10 30 commit(s) and 22 issue activity found in the last 90 days -- score normalized to 10 Dangerous-Workflow ⚠️ -1 no workflows found Packaging ⚠️ -1 packaging workflow not detected Token-Permissions ⚠️ -1 No tokens found Code-Review 🟢 10 all changesets reviewed Security-Policy 🟢 10 security policy file detected CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Binary-Artifacts 🟢 10 no binaries found in the repo License 🟢 10 license file detected Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md Vulnerabilities 🟢 10 0 existing vulnerabilities detected Signed-Releases ⚠️ -1 no releases found Pinned-Dependencies ⚠️ -1 no dependencies found Fuzzing 🟢 10 project is fuzzed SAST 🟢 10 SAST tool is run on all commits
pip/tqdm	4.67.3	🟢 7	Details Check Score Reason Dangerous-Workflow ⚠️ -1 no workflows found Maintained 🟢 10 16 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 Code-Review 🟢 4 Found 2/5 approved changesets -- score normalized to 4 Packaging ⚠️ -1 packaging workflow not detected Token-Permissions ⚠️ -1 No tokens found Binary-Artifacts 🟢 10 no binaries found in the repo Pinned-Dependencies ⚠️ -1 no dependencies found CII-Best-Practices 🟢 5 badge detected: Passing Security-Policy ⚠️ 0 security policy file not detected Vulnerabilities 🟢 10 0 existing vulnerabilities detected Fuzzing 🟢 10 project is fuzzed License 🟢 9 license file detected Signed-Releases 🟢 8 5 out of the last 5 releases have a total of 5 signed artifacts. Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/typing-extensions	4.15.0	🟢 7.4	Details Check Score Reason Maintained 🟢 10 16 commit(s) and 15 issue activity found in the last 90 days -- score normalized to 10 Packaging ⚠️ -1 packaging workflow not detected Code-Review 🟢 9 Found 28/29 approved changesets -- score normalized to 9 Dangerous-Workflow 🟢 10 no dangerous workflow patterns detected Token-Permissions 🟢 10 GitHub workflow tokens follow principle of least privilege CII-Best-Practices ⚠️ 0 no effort to earn an OpenSSF best practices badge detected Binary-Artifacts 🟢 10 no binaries found in the repo Pinned-Dependencies ⚠️ 0 dependency not pinned by hash detected -- score normalized to 0 Vulnerabilities 🟢 10 0 existing vulnerabilities detected Fuzzing ⚠️ 0 project is not fuzzed License 🟢 9 license file detected Signed-Releases ⚠️ -1 no releases found Security-Policy 🟢 10 security policy file detected Branch-Protection ⚠️ -1 internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md SAST ⚠️ 0 SAST tool is not run on all commits -- score normalized to 0
pip/typing-inspection	0.4.2	Unknown	Unknown

Scanned Files

• pyproject.toml
• uv.lock