Public recordExcellent
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-10-19 13:15 UTC
M4i-Imaging-Mass-Spectrometry / thyra
A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.
M4i-Imaging-Mass-Spectrometry/thyra holds a health index of 84 out of 100, placing it in the Excellent band. It scores highest on Engineering Quality (96/100) and lowest on Security (55/100). It was last updated today. A single contributor accounts for most of its recent work.
84
overall / 100Software health index
Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.
84
Exceptional93-100The record's top tier (≈ top 5%); essentially all checked criteria met
Excellent80-92Strong across the board; minor gaps
Good65-79Healthy; gaps are limited and manageable
Moderate50-64Acceptable with notable gaps; review recommended
Weak35-49Material weaknesses across several areas
At Risk20-34Significant weaknesses; adoption warrants caution
Critical1-19Severe problems (abandoned, single-maintainer, no hygiene)
Score profile
Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.
The weighted overall 71 is calibrated to 84 on the published index scale (record calibration 2026-08-02).
Ownership
M4i - Imaging Mass Spectrometry Organization
8 followers4 public repossince Sep 2022
This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.
Package ecosystems
| Registry | Package | Version | Downloads / mo | Versions | Last publish | Tags |
|---|---|---|---|---|---|---|
| PyPI | thyra | 4.5.1 | 3,640 | 109 | 0 days ago | bioinformaticsbrukerdata-conversionimagingimzmlion-mobilitymass-spectrometrymsimsmsomicspasefscientific-computingspatial-omicsspatialdatatimstimstofzarr |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
89
Development activity
88Excellent
How it's scored
| 36/36 | Push recency — last push 0 days ago |
| 24.2/36 | Commit cadence — 35/52 weeks with commits |
| 18/18 | Commit volume — 791 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 30 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 791 |
| human_commit_share | 0.98 |
| days_since_last_push | 0 |
| active_weeks_last_year | 35 |
Release discipline
90Excellent
How it's scored
| 27/27 | Ships releases — 100 releases published |
| 36/36 | Release recency — latest release 0 days ago |
| 27/27 | Release cadence — a release every ~2.3 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases. |
Inputs used
| releases_count | 100 |
| latest_release_tag | v4.5.1 |
| releases_from_tags | no |
| days_since_latest_release | 0 |
| mean_days_between_releases | 2.3 |
Community & Adoption
Does the project have users, downloads, attention, and a welcoming setup for contributors?
56
Popularity & adoption
22At Risk
How it's scored
| 22.4/60 | Stars — 25 stars |
| 0/25 | Forks — 1 forks |
| 0/15 | Watchers — 2 watchers |
Inputs used
| forks | 1 |
| stars | 25 |
| watchers | 2 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
92Excellent
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (MIT) |
| 18/18 | CONTRIBUTING guide |
| 13.5/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 6.3/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| readme_badges | 8 |
| has_contributing | yes |
| has_issue_template | no |
| has_code_of_conduct | yes |
| readme_badge_services | shields.io |
| has_pull_request_template | yes |
Ecosystem adoption (downloads)
59Moderate
How it's scored
| 47.5/80 | Monthly downloads — 3,640 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | thyra |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 3,640 |
| unverified_packages_excluded | — |
Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
56
Maintainer resilience (bus factor)
13Critical
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 0/22.5 | Commit distribution — top contributor authored 100% of commits |
| 1.4/13.5 | Contributor breadth — 1 contributors |
| 3/10 | OpenSSF Scorecard: Contributors — project has 1 contributing companies or organizations -- score normalized to 3 |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 1 |
| top_contributor_share | 1 |
How it's scored
| 38.1/42 | Issue resolution — 91% of issues closed |
| 29/30 | PR acceptance — 322/333 decided PRs merged |
| 0/13 | Newcomer PR acceptance — no first-time contributor's PR decided in 30d |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 0/29 approved changesets -- score normalized to 0 |
Inputs used
| merged_prs | 322 |
| open_issues | 18 |
| closed_issues | 178 |
| prs_merged_7d | 48 |
| prs_decided_7d | 50 |
| prs_merged_30d | 55 |
| prs_decided_30d | 58 |
| issue_closed_ratio | 0.908 |
| closed_unmerged_prs | 11 |
| first_time_authors_30d | 0 |
| first_time_prs_merged_30d | 0 |
| first_time_prs_decided_30d | 0 |
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.
Ownership & stewardship
50Moderate
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 6.9/25 | Owner reach — 8 followers of M4i-Imaging-Mass-Spectrometry |
| 13.3/25 | Track record — 4 public repos, account ~4 yr old |
Inputs used
| followers | 8 |
| owner_type | Organization |
| is_verified | no |
| owner_login | M4i-Imaging-Mass-Spectrometry |
| public_repos | 4 |
| account_age_days | 1,496 |
Package maintenance
100Exceptional
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 0 days ago |
| 20/20 | Version history — 109 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | thyra |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 0 |
Engineering Quality
Are baseline engineering and documentation practices in place?
96
Engineering practices
94Exceptional
How it's scored
| 24/24 | CI workflows — 7 workflow(s) |
| 24/24 | Tests present |
| 16/16 | Linter config — .flake8, pyproject.toml ([tool.black], [tool.isort]) |
| 9.6/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 20/20 | OpenSSF Scorecard: CI-Tests — 30 out of 30 merged PRs checked by a CI test -- score normalized to 10 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | yes |
| has_precommit_config | yes |
Documentation
100Exceptional
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://m4i-imaging-mass-spectrometry.github.io/thyra/ |
| 10/10 | Repository description |
| 10/10 | Topics — 17 topics |
| 10/10 | Wiki |
Inputs used
| topics | bioinformatics, bruker, data-conversion, imzml, mass-spectrometry, mass-spectrometry-imaging, msi, omics-data-integration, scientific-computing, spatial-omics, spatialdata, zarr, ecuypers-group, m4i-cuypers-group, ion-mobility, pasef, timstof |
| has_wiki | yes |
| homepage | https://m4i-imaging-mass-spectrometry.github.io/thyra/ |
| docs_site | https://m4i-imaging-mass-spectrometry.github.io/thyra/ |
| has_readme | yes |
| has_docs_dir | yes |
| has_description | yes |
Security
Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?
55
Security posture
44Weak
How it's scored
| 3/7.5 | Binary-Artifacts — binaries present in source code |
| 2.2/7.5 | Branch-Protection — branch protection is not maximal on development and all release branches |
| 2.5/2.5 | CI-Tests — 30 out of 30 merged PRs checked by a CI test -- score normalized to 10 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 0/29 approved changesets -- score normalized to 0 |
| 0.8/2.5 | Contributors — project has 1 contributing companies or organizations -- score normalized to 3 |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | License — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 30 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 1/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 2 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 5/5 | Security-Policy — security policy file detected |
| 0/7.5 | Signed-Releases — Project has not signed or included provenance with any releases. |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 6.8/7.5 | Vulnerabilities — 1 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 18 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 0 |
| scorecard_aggregate | 4.4 |
Dependency advisories
100Exceptional
How it's scored
| 35/35 | Direct dependencies free of known advisories — no direct dependency carries a known advisory |
| 0/25 | Indirect dependencies free of known advisories — transitive set not separable from development and test dependencies in this scope |
| 0/40 | No advisories left outstanding — no advisory carries a publication date |
Inputs used
| source | osv |
| advisories | 2 |
| affected_packages | 1 |
| assessed_packages | 253 |
| unassessed_packages | 0 |
| affected_by_severity | high 1 |
| direct_affected_packages | 0 |
Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 253 resolved dependencies against OSV. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.
AI Readiness
How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.
61
Agent context & guidance
40Weak
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 40/40 | Legible commit history — 90 of 98 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | no |
| llms_txt_url | — |
| legible_history_share | 0.918 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Verify loop (build / test / typecheck)
56Moderate
How it's scored
| 0/18 | One-command bootstrap |
| 22/22 | Automated tests |
| 11/11 | Lint / format config — .flake8, pyproject.toml ([tool.black], [tool.isort]) |
| 11/11 | Static type checking — thyra/py.typed |
| 10/10 | Reproducible environment — lockfile |
| 0/10 | Demonstrated agent practice — no agent-authored commits among the last 100 |
| 0/8 | Automated maintenance — no automated dependency updates observed |
| 2/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 2 |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | uv.lock |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | — |
| has_devcontainer | no |
| has_linter_config | yes |
| typecheck_configs | thyra/py.typed |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Code legibility for models
80Excellent
How it's scored
| 27/45 | Type-checkable code — Python with type-check config (thyra/py.typed) |
| 53.2/55 | Manageable file sizes — 12/375 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 226,739 |
| source_files_sampled | 375 |
| oversized_source_files | 12 |
Machine-readable interfaces
100Exceptional
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) — not applicable to this kind of software |
| 0/20 | MCP server — not applicable to this kind of software |
| 40/40 | Runnable examples — notebooks |
Inputs used
| example_dirs | notebooks |
| has_mcp_signal | no |
| api_schema_files | — |
| interfaces_expected_of | — |
Excluded from scoring (no data or not applicable): API schema (OpenAPI/GraphQL/proto), MCP server. Remaining weights renormalized.
Key facts
25GitHub stars
1contributors
791commits, last 12 months
0days since last push
100releases
1bus factor
18open issues
PyPIpackage ecosystems
Data collection warnings
- Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
- deps.dev does not index pypi:thyra@4.5.1; advisories assessed against the repository dependency graph instead
More detail
OpenSSF Scorecard 4.4 / 10
4.4aggregate
Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).
| 4 | Binary-Artifacts | binaries present in source code |
| 3 | Branch-Protection | branch protection is not maximal on development and all release branches |
| 10 | CI-Tests | 30 out of 30 merged PRs checked by a CI test -- score normalized to 10 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 0/29 approved changesets -- score normalized to 0 |
| 3 | Contributors | project has 1 contributing companies or organizations -- score normalized to 3 |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 30 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 2 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 2 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 10 | Security-Policy | security policy file detected |
| 0 | Signed-Releases | Project has not signed or included provenance with any releases. |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 9 | Vulnerabilities | 1 existing vulnerabilities detected |
Direct dependencies 20
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | dask | >=2026.3.0, <2026.8 | pyproject.toml |
| PyPI | click | >=8.1, <9 | pyproject.toml |
| PyPI | defusedxml | >=0.7.1 | pyproject.toml |
| PyPI | geopandas | >=0.9.0 | pyproject.toml |
| PyPI | numpy | >=2.0.0, <3 | pyproject.toml |
| PyPI | pandas | >=2.0.0, <4 | pyproject.toml |
| PyPI | pyimzML | >=1.4.0 | pyproject.toml |
| PyPI | scipy | >=1.7.0 | pyproject.toml |
| PyPI | Shapely | >=2.0.0 | pyproject.toml |
| PyPI | spatialdata | >=0.8.0, <0.9 | pyproject.toml |
| PyPI | ome-zarr | >=0.16.0, <0.19 | pyproject.toml |
| PyPI | tqdm | >=4.50.0 | pyproject.toml |
| PyPI | zarr | >=3.4.0, <3.5 | pyproject.toml |
| PyPI | imagecodecs | >=2024.1.1 | pyproject.toml |
| PyPI | anndata | >=0.13.2, <0.14 | pyproject.toml |
| PyPI | psutil | >=5.0.0 | pyproject.toml |
| PyPI | pydantic | >=2.7, <3 | pyproject.toml |
| PyPI | tifffile | >=2026.5.2 | pyproject.toml |
| PyPI | xarray | >=2024.10.0 | pyproject.toml |
| PyPI | pillow | >=10.1 | pyproject.toml |
All dependencies 253
Full resolved dependency set from the GitHub dependency graph: 20 direct and 233 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | anndata | 0.13.2 | direct |
| PyPI | click | 8.4.2 | direct |
| PyPI | dask | 2026.7.1 | direct |
| PyPI | defusedxml | 0.7.1 | direct |
| PyPI | geopandas | 1.1.4 | direct |
| PyPI | imagecodecs | 2026.8.16 | direct |
| PyPI | numpy | 2.5.2 | direct |
| PyPI | ome-zarr | 0.18.0 | direct |
| PyPI | pandas | 3.0.5 | direct |
| PyPI | pillow | 12.3.0 | direct |
| PyPI | psutil | 7.2.2 | direct |
| PyPI | pydantic | 2.12.5 | direct |
| PyPI | pyimzml | 1.5.5 | direct |
| PyPI | scipy | 1.18.1 | direct |
| PyPI | shapely | 2.1.2 | direct |
| PyPI | spatialdata | 0.8.0 | direct |
| PyPI | tifffile | 2026.8.23 | direct |
| PyPI | tqdm | 4.70.0 | direct |
| PyPI | xarray | 2026.7.0 | direct |
| PyPI | zarr | 3.4.0 | direct |
| PyPI | aiobotocore | 3.9.0 | indirect |
| PyPI | aiohappyeyeballs | 2.7.1 | indirect |
| PyPI | aiohttp | 3.14.3 | indirect |
| PyPI | aioitertools | 0.13.0 | indirect |
| PyPI | aiosignal | 1.4.0 | indirect |
| PyPI | annotated-types | 0.8.0 | indirect |
| PyPI | annsel | 0.1.3 | indirect |
| PyPI | anyio | 4.14.2 | indirect |
| PyPI | appnope | 1.0.0 | indirect |
| PyPI | argon2-cffi | 25.1.0 | indirect |
| PyPI | argon2-cffi-bindings | 26.1.0 | indirect |
| PyPI | array-api-compat | 1.15.0 | indirect |
| PyPI | arrow | 1.4.0 | indirect |
| PyPI | ast-serialize | 0.8.0 | indirect |
| PyPI | asttokens | 3.0.2 | indirect |
| PyPI | async-lru | 2.3.0 | indirect |
| PyPI | attrs | 26.1.0 | indirect |
| PyPI | babel | 2.18.0 | indirect |
| PyPI | backrefs | 8.0 | indirect |
| PyPI | bandit | 1.9.4 | indirect |
| PyPI | beautifulsoup4 | 4.15.0 | indirect |
| PyPI | black | 26.5.1 | indirect |
| PyPI | bleach | 6.4.0 | indirect |
| PyPI | botocore | 1.43.56 | indirect |
| PyPI | certifi | 2026.7.22 | indirect |
| PyPI | cffi | 2.1.1 | indirect |
| PyPI | cfgv | 3.5.0 | indirect |
| PyPI | charset-normalizer | 3.5.1 | indirect |
| PyPI | cloudpickle | 3.1.2 | indirect |
| PyPI | colorama | 0.4.6 | indirect |
| PyPI | colorcet | 3.2.1 | indirect |
| PyPI | comm | 0.2.3 | indirect |
| PyPI | contourpy | 1.3.3 | indirect |
| PyPI | coverage | 7.15.4 | indirect |
| PyPI | cycler | 0.12.1 | indirect |
| PyPI | dask-image | 2026.5.0 | indirect |
| PyPI | datashader | 0.19.1 | indirect |
| PyPI | debugpy | 1.8.21 | indirect |
| PyPI | deprecated | 1.3.1 | indirect |
| PyPI | distlib | 0.4.3 | indirect |
| PyPI | distributed | 2026.7.1 | indirect |
| PyPI | docformatter | 1.7.8 | indirect |
| PyPI | donfig | 0.8.1.post1 | indirect |
| PyPI | executing | 2.2.1 | indirect |
| PyPI | fastjsonschema | 2.22.2 | indirect |
| PyPI | filelock | 3.32.4 | indirect |
| PyPI | flake8 | 7.3.0 | indirect |
| PyPI | fonttools | 4.63.0 | indirect |
| PyPI | fqdn | 1.5.1 | indirect |
| PyPI | frozenlist | 1.8.0 | indirect |
| PyPI | fsspec | 2026.7.0 | indirect |
| PyPI | ghp-import | 2.1.0 | indirect |
| PyPI | google-crc32c | 1.8.0 | indirect |
| PyPI | griffelib | 2.2.0 | indirect |
| PyPI | h11 | 0.16.0 | indirect |
| PyPI | h5py | 3.16.0 | indirect |
| PyPI | httpcore | 1.0.9 | indirect |
| PyPI | httpx | 0.28.1 | indirect |
| PyPI | identify | 2.6.19 | indirect |
| PyPI | idna | 3.19 | indirect |
| PyPI | imageio | 2.37.4 | indirect |
| PyPI | iniconfig | 2.3.0 | indirect |
| PyPI | ipykernel | 6.31.0 | indirect |
| PyPI | ipython | 9.16.1 | indirect |
| PyPI | ipython-pygments-lexers | 1.1.1 | indirect |
| PyPI | ipywidgets | 8.1.9 | indirect |
| PyPI | isoduration | 20.11.0 | indirect |
| PyPI | isort | 8.0.1 | indirect |
| PyPI | jedi | 0.20.0 | indirect |
| PyPI | jinja2 | 3.1.6 | indirect |
| PyPI | jmespath | 1.1.0 | indirect |
| PyPI | json5 | 0.15.0 | indirect |
| PyPI | jsonpointer | 3.1.1 | indirect |
| PyPI | jsonschema | 4.26.0 | indirect |
| PyPI | jsonschema-specifications | 2025.9.1 | indirect |
| PyPI | jupyter | 1.1.1 | indirect |
| PyPI | jupyter-builder | 1.2.2 | indirect |
| PyPI | jupyter-client | 8.9.1 | indirect |
| PyPI | jupyter-console | 6.6.3 | indirect |
| PyPI | jupyter-core | 5.9.1 | indirect |
| PyPI | jupyter-events | 0.12.1 | indirect |
| PyPI | jupyter-lsp | 2.3.1 | indirect |
| PyPI | jupyter-server | 2.20.0 | indirect |
| PyPI | jupyter-server-terminals | 0.5.4 | indirect |
| PyPI | jupyterlab | 4.6.4 | indirect |
| PyPI | jupyterlab-pygments | 0.3.0 | indirect |
| PyPI | jupyterlab-server | 2.28.0 | indirect |
| PyPI | jupyterlab-widgets | 3.0.17 | indirect |
| PyPI | jupytext | 1.19.5 | indirect |
| PyPI | kiwisolver | 1.5.0 | indirect |
| PyPI | lark | 1.3.1 | indirect |
| PyPI | lazy-loader | 0.5 | indirect |
| PyPI | legacy-api-wrap | 1.5 | indirect |
| PyPI | librt | 0.15.0 | indirect |
| PyPI | llvmlite | 0.49.0 | indirect |
| PyPI | locket | 1.0.0 | indirect |
| PyPI | markdown | 3.10.3 | indirect |
| PyPI | markdown-it-py | 4.2.0 | indirect |
| PyPI | markupsafe | 3.0.3 | indirect |
| PyPI | matplotlib | 3.11.1 | indirect |
| PyPI | matplotlib-inline | 0.2.2 | indirect |
| PyPI | mccabe | 0.7.0 | indirect |
| PyPI | mdit-py-plugins | 0.6.1 | indirect |
| PyPI | mdurl | 0.1.2 | indirect |
| PyPI | mergedeep | 1.3.4 | indirect |
| PyPI | mistune | 3.3.4 | indirect |
| PyPI | mkdocs | 1.6.1 | indirect |
| PyPI | mkdocs-autorefs | 1.4.4 | indirect |
| PyPI | mkdocs-get-deps | 0.2.2 | indirect |
| PyPI | mkdocs-jupyter | 0.26.3 | indirect |
| PyPI | mkdocs-material | 9.7.7 | indirect |
| PyPI | mkdocs-material-extensions | 1.3.1 | indirect |
| PyPI | mkdocstrings | 1.0.6 | indirect |
| PyPI | mkdocstrings-python | 2.0.7 | indirect |
| PyPI | mock | 5.2.0 | indirect |
| PyPI | more-itertools | 11.1.0 | indirect |
| PyPI | msgpack | 1.2.1 | indirect |
| PyPI | msgspec | 0.21.1 | indirect |
| PyPI | multidict | 6.9.1 | indirect |
| PyPI | multipledispatch | 1.0.0 | indirect |
| PyPI | multiscale-spatial-image | 2.0.3 | indirect |
| PyPI | mypy | 2.3.1 | indirect |
| PyPI | mypy-extensions | 1.1.0 | indirect |
| PyPI | narwhals | 2.25.0 | indirect |
| PyPI | natsort | 8.4.0 | indirect |
| PyPI | nbclient | 0.11.0 | indirect |
| PyPI | nbconvert | 7.17.1 | indirect |
| PyPI | nbformat | 5.11.1 | indirect |
| PyPI | nest-asyncio | 1.6.0 | indirect |
| PyPI | networkx | 3.6.1 | indirect |
| PyPI | nodeenv | 1.10.0 | indirect |
| PyPI | notebook | 7.6.3 | indirect |
| PyPI | notebook-shim | 0.2.4 | indirect |
| PyPI | numba | 0.67.0 | indirect |
| PyPI | numcodecs | 0.16.5 | indirect |
| PyPI | ome-zarr-models | 1.7 | indirect |
| PyPI | packaging | 26.3 | indirect |
| PyPI | paginate | 0.5.7 | indirect |
| PyPI | pandocfilters | 1.5.1 | indirect |
| PyPI | param | 2.4.1 | indirect |
| PyPI | parso | 0.8.7 | indirect |
| PyPI | partd | 1.4.2 | indirect |
| PyPI | pathlib-abc | 0.5.2 | indirect |
| PyPI | pathspec | 1.1.1 | indirect |
| PyPI | pexpect | 4.9.0 | indirect |
| PyPI | pims | 0.7 | indirect |
| PyPI | platformdirs | 4.11.4 | indirect |
| PyPI | pluggy | 1.6.0 | indirect |
| PyPI | pooch | 1.9.0 | indirect |
| PyPI | pre-commit | 4.6.2 | indirect |
| PyPI | prometheus-client | 0.26.0 | indirect |
| PyPI | prompt-toolkit | 3.0.53 | indirect |
| PyPI | propcache | 0.5.2 | indirect |
| PyPI | ptitprince | 0.3.1 | indirect |
| PyPI | ptyprocess | 0.7.0 | indirect |
| PyPI | pure-eval | 0.2.3 | indirect |
| PyPI | pyarrow | 25.0.1 | indirect |
| PyPI | pycodestyle | 2.14.0 | indirect |
| PyPI | pycparser | 3.0 | indirect |
| PyPI | pyct | 0.6.0 | indirect |
| PyPI | pydantic-core | 2.41.5 | indirect |
| PyPI | pydantic-settings | 2.15.0 | indirect |
| PyPI | pydantic-zarr | 0.10.0 | indirect |
| PyPI | pydocstyle | 6.3.0 | indirect |
| PyPI | pyflakes | 3.4.0 | indirect |
| PyPI | pygments | 2.21.0 | indirect |
| PyPI | pymdown-extensions | 11.0.2 | indirect |
| PyPI | pyogrio | 0.13.0 | indirect |
| PyPI | pyparsing | 3.3.2 | indirect |
| PyPI | pyproj | 3.7.2 | indirect |
| PyPI | pytest | 9.1.1 | indirect |
| PyPI | pytest-cov | 7.1.0 | indirect |
| PyPI | python-dateutil | 2.9.0.post0 | indirect |
| PyPI | python-discovery | 1.6.2 | indirect |
| PyPI | python-dotenv | 1.2.3 | indirect |
| PyPI | python-json-logger | 4.2.0 | indirect |
| PyPI | pytokens | 0.4.1 | indirect |
| PyPI | pywinpty | 3.0.5 | indirect |
| PyPI | pyyaml | 6.0.3 | indirect |
| PyPI | pyyaml-env-tag | 1.1 | indirect |
| PyPI | pyzmq | 27.2.0 | indirect |
| PyPI | rangehttpserver | 1.4.0 | indirect |
| PyPI | referencing | 0.37.0 | indirect |
| PyPI | requests | 2.34.2 | indirect |
| PyPI | rfc3339-validator | 0.1.4 | indirect |
| PyPI | rfc3986-validator | 0.1.1 | indirect |
| PyPI | rfc3987-syntax | 1.1.0 | indirect |
| PyPI | rich | 14.3.4 | indirect |
| PyPI | rpds-py | 2026.6.3 | indirect |
| PyPI | s3fs | 2026.7.0 | indirect |
| PyPI | scikit-image | 0.26.0 | indirect |
| PyPI | scverse-misc | 0.1.3 | indirect |
| PyPI | seaborn | 0.13.2 | indirect |
| PyPI | send2trash | 2.1.0 | indirect |
| PyPI | session-info2 | 0.4.2 | indirect |
| PyPI | setuptools | 84.0.0 | indirect |
| PyPI | six | 1.17.0 | indirect |
| PyPI | slicerator | 1.1.0 | indirect |
| PyPI | snowballstemmer | 3.1.1 | indirect |
| PyPI | sortedcontainers | 2.4.0 | indirect |
| PyPI | soupsieve | 2.9.2 | indirect |
| PyPI | spatial-image | 1.2.3 | indirect |
| PyPI | stack-data | 0.6.3 | indirect |
| PyPI | stevedore | 5.9.1 | indirect |
| PyPI | tblib | 3.2.2 | indirect |
| PyPI | terminado | 0.18.1 | indirect |
| PyPI | thyra | 4.5.1 | indirect |
| PyPI | tinycss2 | 1.5.1 | indirect |
| PyPI | toolz | 1.1.0 | indirect |
| PyPI | tornado | 6.5.10 | indirect |
| PyPI | traitlets | 5.16.1 | indirect |
| PyPI | types-pyyaml | 6.0.12.20260815 | indirect |
| PyPI | types-requests | 2.33.0.20260712 | indirect |
| PyPI | typing-extensions | 4.16.0 | indirect |
| PyPI | typing-inspection | 0.4.4 | indirect |
| PyPI | tzdata | 2026.3 | indirect |
| PyPI | universal-pathlib | 0.3.10 | indirect |
| PyPI | uri-template | 1.3.0 | indirect |
| PyPI | urllib3 | 2.8.0 | indirect |
| PyPI | virtualenv | 21.14.7 | indirect |
| PyPI | watchdog | 6.0.0 | indirect |
| PyPI | wcwidth | 0.8.2 | indirect |
| PyPI | webcolors | 25.10.0 | indirect |
| PyPI | webencodings | 0.6.1 | indirect |
| PyPI | websocket-client | 1.9.0 | indirect |
| PyPI | wheezy-template | 3.2.5 | indirect |
| PyPI | widgetsnbextension | 4.0.16 | indirect |
| PyPI | wrapt | 2.3.0 | indirect |
| PyPI | xarray-dataclass | 3.0.0 | indirect |
| PyPI | xarray-spatial | 0.10.17 | indirect |
| PyPI | yarl | 1.24.5 | indirect |
| PyPI | zict | 3.0.0 | indirect |
| PyPI | zstandard | 0.25.0 | indirect |
Dependency advisories 1
This repository publishes no package the index resolves, so its own dependency graph was assessed — 253 packages, which also include development and test pins that never ship: 1 carry known advisories, of which 0 are direct.
| Package | Version | Relation | Severity | Advisories | Fixed in |
|---|---|---|---|---|---|
| jupyter-server | 2.20.0 | indirect | high | 2 | 2.21.0 |
An advisory means the version recorded in the dependency graph falls inside an advisory’s affected range. Reachability is not analysed, and the graph includes development and test pins — a finding may concern tooling rather than shipped software.
Raw JSON report machine-readable
Feedback
Spotted something off in this report, or have thoughts to share? Wrong measurements, missed tooling, ideas, questions — anything is welcome. Every message is read and gets a response.
Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.
Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v2.10.0, schema v0.34.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.