Public recordModerate
Software health reportschema 0.12.0 · metrics 1.13.0 · 2026-07-17 18:15 UTC
pdbeurope / pdbe-mcp-servers
PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.
pdbeurope/pdbe-mcp-servers holds a health index of 67 out of 100, placing it in the Moderate band. It scores highest on Vitality (81/100) and lowest on Community & Adoption (49/100). It was last updated today. A single contributor accounts for most of its recent work.
67
overall / 100Software health index
Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At risk ceiling of 49. AI Readiness sits outside the overall score.
67
Excellent85-100Exemplary; meets essentially all checked criteria
Good70-84Healthy; minor gaps
Moderate50-69Acceptable with notable gaps; review recommended
At risk30-49Significant weaknesses; adoption warrants caution
Critical1-29Severe 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.
Ownership
PDBe EMBL-EBIOrganization
86 followers48 public repossince Sep 2014
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 | pdbe-mcp-server | 1.1.5 | 3,297 | 16 | 2 days ago | automationfetchhttpllmmcpstatelessstreamableweb |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
81
Development activity
69Moderate
How it's scored
| 36/36 | Push recency — last push 0 days ago |
| 10.4/36 | Commit cadence — 15/52 weeks with commits |
| 12.6/18 | Commit volume — 24 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 14 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 24 |
| human_commit_share | — |
| days_since_last_push | 0 |
| active_weeks_last_year | 15 |
Release discipline
100Excellent
How it's scored
| 27/27 | Ships releases — 17 releases published |
| 36/36 | Release recency — latest release 2 days ago |
| 27/27 | Release cadence — a release every ~8.6 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 17 |
| latest_release_tag | v1.1.6 |
| releases_from_tags | no |
| days_since_latest_release | 2 |
| mean_days_between_releases | 8.6 |
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.
Community & Adoption
Does the project have users, downloads, attention, and a welcoming setup for contributors?
49
Popularity & adoption
25Critical
How it's scored
| 25/60 | Stars — 36 stars |
| 0/25 | Forks — 1 forks |
| 0/15 | Watchers — 0 watchers |
Inputs used
| forks | 1 |
| stars | 36 |
| watchers | 0 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
70Good
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (Apache-2.0) |
| 18/18 | CONTRIBUTING guide |
| 0/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 0/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| has_contributing | yes |
| has_issue_template | no |
| has_code_of_conduct | no |
| has_pull_request_template | no |
Ecosystem adoption (downloads)
59Moderate
How it's scored
| 46.9/80 | Monthly downloads — 3,297 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | pdbe-mcp-server |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 3,297 |
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?
61
Maintainer resilience (bus factor)
18Critical
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 0.7/22.5 | Commit distribution — top contributor authored 97% of commits |
| 2.7/13.5 | Contributor breadth — 2 contributors |
| 6/10 | OpenSSF Scorecard: Contributors — project has 2 contributing companies or organizations -- score normalized to 6 |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 2 |
| top_contributor_share | 0.968 |
How it's scored
| 46.8/46.8 | Issue resolution — 100% of issues closed |
| 27.6/38.3 | PR acceptance — 26/36 decided PRs merged |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 0/27 approved changesets -- score normalized to 0 |
Inputs used
| merged_prs | 26 |
| open_issues | 0 |
| closed_issues | 2 |
| issue_closed_ratio | 1 |
| closed_unmerged_prs | 10 |
Ownership & stewardship
68Moderate
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 13.9/25 | Owner reach — 86 followers of PDBeurope |
| 24.3/25 | Track record — 48 public repos, account ~11 yr old |
Inputs used
| followers | 86 |
| owner_type | Organization |
| is_verified | — |
| owner_login | PDBeurope |
| public_repos | 48 |
| account_age_days | 4,321 |
Package maintenance
100Excellent
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 2 days ago |
| 20/20 | Version history — 16 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | pdbe-mcp-server |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 2 |
Engineering Quality
Are baseline engineering and documentation practices in place?
78
Engineering practices
90Excellent
How it's scored
| 24/24 | CI workflows — 1 workflow(s) |
| 24/24 | Tests present |
| 16/16 | Linter config — ruff.toml |
| 9.6/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 16/20 | OpenSSF Scorecard: CI-Tests — 23 out of 26 merged PRs checked by a CI test -- score normalized to 8 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | yes |
| has_precommit_config | yes |
Documentation
60Moderate
How it's scored
| 30/30 | README |
| 0/25 | Documentation directory |
| 0/15 | Documentation / homepage site |
| 10/10 | Repository description |
| 10/10 | Topics — 10 topics |
| 10/10 | Wiki |
Inputs used
| topics | ai-integration, api-server, bioinformatics, knowledge-graph, llm-tools, mcp, pdbe, protein-structures, python, structural-biology |
| has_wiki | yes |
| homepage | — |
| has_readme | yes |
| has_docs_dir | no |
| has_description | yes |
Security
Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?
65
Security posture
65Moderate
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — no data |
| 2/2.5 | CI-Tests — 23 out of 26 merged PRs checked by a CI test -- score normalized to 8 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 0/27 approved changesets -- score normalized to 0 |
| 1.5/2.5 | Contributors — project has 2 contributing companies or organizations -- score normalized to 6 |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 7.5/7.5 | Dependency-Update-Tool — update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | License — license file detected |
| 7.5/7.5 | Maintained — 14 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 0/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
| 2/5 | SAST — SAST tool is not run on all commits -- score normalized to 4 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — no data |
| 7.5/7.5 | Token-Permissions — GitHub workflow tokens follow principle of least privilege |
| 5.2/7.5 | Vulnerabilities — 3 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 16 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 2 |
| scorecard_aggregate | 6.5 |
Excluded from scoring (no data or not applicable): branch_protection, signed_releases. Remaining weights renormalized.
AI Readiness
How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score.
51
Agent context & guidance
1Critical
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 0/40 | Legible commit history — no data |
Inputs used
| has_llms_txt | no |
| legible_history_share | — |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.
Verify loop (build / test / typecheck)
88Excellent
How it's scored
| 18/18 | One-command bootstrap — Makefile |
| 22/22 | Automated tests |
| 11/11 | Lint / format config — ruff.toml |
| 11/11 | Static type checking — pdbe_mcp_server/py.typed |
| 10/10 | Reproducible environment — lockfile |
| 0/10 | Demonstrated agent practice — no data |
| 0/8 | Automated maintenance — no data |
| 0/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | uv.lock |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | Makefile |
| has_devcontainer | no |
| has_linter_config | yes |
| typecheck_configs | pdbe_mcp_server/py.typed |
| agent_commit_share | — |
| toolchain_manifests | — |
| dependency_bot_commit_share | — |
Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.
How it's scored
| 27/45 | Type-checkable code — Python with type-check config (pdbe_mcp_server/py.typed) |
| 55/55 | Manageable file sizes — 0/15 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 28,927 |
| source_files_sampled | 15 |
| oversized_source_files | 0 |
Machine-readable interfaces
20Critical
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) |
| 20/20 | MCP server |
| 0/40 | Runnable examples |
Inputs used
| example_dirs | — |
| has_mcp_signal | yes |
| api_schema_files | — |
Key facts
36GitHub stars
2contributors
24commits, last 12 months
0days since last push
17releases
1bus factor
0open issues
PyPIpackage ecosystems
More detail
OpenSSF Scorecard 6.5 / 10
6.5aggregate
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).
| 10 | Binary-Artifacts | no binaries found in the repo |
| n/a | Branch-Protection | 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 |
| 8 | CI-Tests | 23 out of 26 merged PRs checked by a CI test -- score normalized to 8 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 0/27 approved changesets -- score normalized to 0 |
| 6 | Contributors | project has 2 contributing companies or organizations -- score normalized to 6 |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 10 | Dependency-Update-Tool | update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 14 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 0 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 0 |
| 4 | SAST | SAST tool is not run on all commits -- score normalized to 4 |
| 0 | Security-Policy | security policy file not detected |
| n/a | Signed-Releases | no releases found |
| 10 | Token-Permissions | GitHub workflow tokens follow principle of least privilege |
| 7 | Vulnerabilities | 3 existing vulnerabilities detected |
Direct dependencies 10
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | anyio | >=4.5 | pyproject.toml |
| PyPI | click | >=8.1.0 | pyproject.toml |
| PyPI | httpx | >=0.27 | pyproject.toml |
| PyPI | mcp | >=1.23.0 | pyproject.toml |
| PyPI | neo4j | >=5.0 | pyproject.toml |
| PyPI | omegaconf | >=2.3.0 | pyproject.toml |
| PyPI | python-toon | >=0.1.3 | pyproject.toml |
| PyPI | requests | >=2.33.0 | pyproject.toml |
| PyPI | starlette | >=1.0.1 | pyproject.toml |
| PyPI | uvicorn | — | pyproject.toml |
All dependencies 79
Full resolved dependency set from the GitHub dependency graph: 10 direct and 69 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | anyio | 4.9.0 | direct |
| PyPI | click | 8.2.1 | direct |
| PyPI | httpx | 0.28.1 | direct |
| PyPI | mcp | 1.27.2 | direct |
| PyPI | neo4j | 6.1.0 | direct |
| PyPI | omegaconf | 2.3.0 | direct |
| PyPI | python-toon | 0.1.3 | direct |
| PyPI | requests | 2.34.2 | direct |
| PyPI | starlette | 1.3.1 | direct |
| PyPI | uvicorn | 0.34.3 | direct |
| PyPI | annotated-types | 0.7.0 | indirect |
| PyPI | antlr4-python3-runtime | 4.9.3 | indirect |
| PyPI | attrs | 26.1.0 | indirect |
| PyPI | backports-asyncio-runner | 1.2.0 | indirect |
| PyPI | backports-tarfile | 1.2.0 | indirect |
| PyPI | certifi | 2025.4.26 | indirect |
| PyPI | cffi | 2.0.0 | indirect |
| PyPI | charset-normalizer | 3.4.2 | indirect |
| PyPI | colorama | 0.4.6 | indirect |
| PyPI | coverage | 7.11.0 | indirect |
| PyPI | cryptography | 48.0.1 | indirect |
| PyPI | docutils | 0.22.2 | indirect |
| PyPI | exceptiongroup | 1.3.0 | indirect |
| PyPI | h11 | 0.16.0 | indirect |
| PyPI | httpcore | 1.0.9 | indirect |
| PyPI | httpx-sse | 0.4.0 | indirect |
| PyPI | id | 1.5.0 | indirect |
| PyPI | idna | 3.18 | indirect |
| PyPI | importlib-metadata | 8.7.0 | indirect |
| PyPI | iniconfig | 2.1.0 | indirect |
| PyPI | jaraco-classes | 3.4.0 | indirect |
| PyPI | jaraco-context | 6.0.1 | indirect |
| PyPI | jaraco-functools | 4.3.0 | indirect |
| PyPI | jeepney | 0.9.0 | indirect |
| PyPI | jsonschema | 4.26.0 | indirect |
| PyPI | jsonschema-specifications | 2025.9.1 | indirect |
| PyPI | keyring | 25.6.0 | indirect |
| PyPI | markdown-it-py | 4.0.0 | indirect |
| PyPI | mdurl | 0.1.2 | indirect |
| PyPI | more-itertools | 10.8.0 | indirect |
| PyPI | nh3 | 0.3.2 | indirect |
| PyPI | nodeenv | 1.9.1 | indirect |
| PyPI | packaging | 25.0 | indirect |
| PyPI | pdbe-mcp-server | 1.1.4 | indirect |
| PyPI | pluggy | 1.6.0 | indirect |
| PyPI | pycparser | 2.23 | indirect |
| PyPI | pydantic | 2.11.5 | indirect |
| PyPI | pydantic-core | 2.33.2 | indirect |
| PyPI | pydantic-settings | 2.9.1 | indirect |
| PyPI | pygments | 2.20.0 | indirect |
| PyPI | pyjwt | 2.13.0 | indirect |
| PyPI | pyright | 1.1.401 | indirect |
| PyPI | pytest | 9.0.3 | indirect |
| PyPI | pytest-asyncio | 1.4.0 | indirect |
| PyPI | pytest-cov | 7.0.0 | indirect |
| PyPI | pytest-mock | 3.15.1 | indirect |
| PyPI | python-dotenv | 1.2.2 | indirect |
| PyPI | python-multipart | 0.0.32 | indirect |
| PyPI | pytz | 2026.1.post1 | indirect |
| PyPI | pywin32 | 312 | indirect |
| PyPI | pywin32-ctypes | 0.2.3 | indirect |
| PyPI | pyyaml | 6.0.3 | indirect |
| PyPI | readme-renderer | 44.0 | indirect |
| PyPI | referencing | 0.37.0 | indirect |
| PyPI | requests-toolbelt | 1.0.0 | indirect |
| PyPI | rfc3986 | 2.0.0 | indirect |
| PyPI | rich | 14.2.0 | indirect |
| PyPI | rpds-py | 0.30.0 | indirect |
| PyPI | rpds-py | 2026.5.1 | indirect |
| PyPI | ruff | 0.11.12 | indirect |
| PyPI | secretstorage | 3.4.0 | indirect |
| PyPI | sniffio | 1.3.1 | indirect |
| PyPI | sse-starlette | 2.3.6 | indirect |
| PyPI | tomli | 2.2.1 | indirect |
| PyPI | twine | 6.2.0 | indirect |
| PyPI | typing-extensions | 4.14.0 | indirect |
| PyPI | typing-inspection | 0.4.1 | indirect |
| PyPI | urllib3 | 2.7.0 | indirect |
| PyPI | zipp | 3.23.0 | indirect |
Raw JSON report machine-readable
{
"data": {
"repo": {
"topics": [
"ai-integration",
"api-server",
"bioinformatics",
"knowledge-graph",
"llm-tools",
"mcp",
"pdbe",
"protein-structures",
"python",
"structural-biology"
],
"is_fork": false,
"size_kb": 427,
"has_wiki": true,
"homepage": null,
"languages": {
"Python": 157038,
"Makefile": 1825
},
"pushed_at": "2026-07-16T20:55:50Z",
"created_at": "2025-06-08T17:04:48Z",
"owner_type": "Organization",
"updated_at": "2026-07-14T19:03:06Z",
"description": "PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.",
"is_archived": false,
"is_disabled": false,
"license_spdx": "Apache-2.0",
"default_branch": "main",
"primary_language": "Python",
"significant_languages": [
"Python"
]
},
"owner": {
"blog": null,
"name": "PDBe EMBL-EBI",
"type": "Organization",
"login": "PDBeurope",
"company": null,
"location": "United Kingdom",
"followers": 86,
"avatar_url": "https://avatars.githubusercontent.com/u/8808449?v=4",
"created_at": "2014-09-17T14:56:45Z",
"is_verified": null,
"public_repos": 48,
"account_age_days": 4321
},
"activity": {
"releases_count": 17,
"commits_last_year": 24,
"latest_release_at": "2026-07-14T19:04:01Z",
"latest_release_tag": "v1.1.6",
"releases_from_tags": false,
"days_since_last_push": 0,
"active_weeks_last_year": 15,
"days_since_latest_release": 2,
"mean_days_between_releases": 8.6
},
"community": {
"has_readme": true,
"has_license": true,
"has_description": true,
"has_contributing": true,
"health_percentage": 62,
"has_issue_template": false,
"has_code_of_conduct": false,
"has_pull_request_template": false
},
"ecosystem": {
"packages": [
{
"name": "pdbe-mcp-server",
"exists": true,
"license": "Apache-2.0",
"keywords": [
"automation",
"fetch",
"http",
"llm",
"mcp",
"stateless",
"streamable",
"web"
],
"ecosystem": "pypi",
"matches_repo": null,
"registry_url": "https://pypi.org/project/pdbe-mcp-server/",
"is_deprecated": false,
"latest_version": "1.1.5",
"repository_url": null,
"versions_count": 16,
"total_downloads": null,
"dependents_count": null,
"deprecation_note": null,
"maintainers_count": null,
"monthly_downloads": 3297,
"first_published_at": "2025-11-01T15:03:47.912312Z",
"latest_published_at": "2026-07-14T19:05:37.777484Z",
"latest_version_yanked": null,
"days_since_latest_publish": 2
}
]
},
"popularity": {
"forks": 1,
"stars": 36,
"watchers": 0,
"open_issues_and_prs": 2
},
"ai_readiness": {
"has_nix": false,
"example_dirs": [],
"has_llms_txt": false,
"has_dockerfile": false,
"has_mcp_signal": true,
"bootstrap_files": [
"Makefile"
],
"api_schema_files": [],
"has_devcontainer": false,
"typecheck_configs": [
"pdbe_mcp_server/py.typed"
],
"largest_source_bytes": 28927,
"source_files_sampled": 15,
"oversized_source_files": 0,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"dependencies": {
"manifests": [
"pyproject.toml"
],
"ecosystems": [
"pypi"
],
"dependencies": [
{
"name": "anyio",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=4.5"
},
{
"name": "click",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=8.1.0"
},
{
"name": "httpx",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.27"
},
{
"name": "mcp",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=1.23.0"
},
{
"name": "neo4j",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=5.0"
},
{
"name": "omegaconf",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=2.3.0"
},
{
"name": "python-toon",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.1.3"
},
{
"name": "requests",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=2.33.0"
},
{
"name": "starlette",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=1.0.1"
},
{
"name": "uvicorn",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
}
],
"all_dependencies": {
"error": null,
"source": "github-sbom",
"packages": [
{
"name": "anyio",
"direct": true,
"version": "4.9.0",
"ecosystem": "pypi"
},
{
"name": "click",
"direct": true,
"version": "8.2.1",
"ecosystem": "pypi"
},
{
"name": "httpx",
"direct": true,
"version": "0.28.1",
"ecosystem": "pypi"
},
{
"name": "mcp",
"direct": true,
"version": "1.27.2",
"ecosystem": "pypi"
},
{
"name": "neo4j",
"direct": true,
"version": "6.1.0",
"ecosystem": "pypi"
},
{
"name": "omegaconf",
"direct": true,
"version": "2.3.0",
"ecosystem": "pypi"
},
{
"name": "python-toon",
"direct": true,
"version": "0.1.3",
"ecosystem": "pypi"
},
{
"name": "requests",
"direct": true,
"version": "2.34.2",
"ecosystem": "pypi"
},
{
"name": "starlette",
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"name": "License",
"detail": "recognized license (Apache-2.0)",
"points": 22.5,
"status": "met",
"details": [
{
"code": "license_standard",
"params": {}
},
{
"code": "license_spdx",
"params": {
"spdx": "Apache-2.0"
}
}
],
"max_points": 22.5
},
{
"key": "contributing_guide",
"name": "CONTRIBUTING guide",
"detail": null,
"points": 18,
"status": "met",
"details": [],
"max_points": 18
},
{
"key": "code_of_conduct",
"name": "Code of conduct",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 13.5
},
{
"key": "issue_template",
"name": "Issue template",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.2
},
{
"key": "pr_template",
"name": "PR template",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 6.3
}
]
},
{
"key": "ecosystem_adoption",
"band": "moderate",
"name": "Ecosystem adoption (downloads)",
"note": "Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"registry_dependents"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 59,
"inputs": {
"packages": [
"pdbe-mcp-server"
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"dependents": null,
"ecosystems": "pypi",
"total_downloads": null,
"monthly_downloads": 3297
},
"components": [
{
"key": "monthly_downloads",
"name": "Monthly downloads",
"detail": "3,297 downloads/month across pypi",
"points": 46.9,
"status": "partial",
"details": [
{
"code": "downloads_monthly",
"params": {
"count": 3297,
"ecosystems": "pypi"
}
}
],
"max_points": 80
},
{
"key": "registry_dependents",
"name": "Registry dependents",
"detail": "not reported by this ecosystem",
"points": 0,
"status": "excluded",
"details": [
{
"code": "not_reported_by_this_ecosystem",
"params": {}
}
],
"max_points": 20
}
]
}
],
"description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
},
{
"key": "governance",
"band": "moderate",
"name": "Sustainability & Governance",
"value": 61,
"weight": 0.24,
"metrics": [
{
"key": "maintainer_resilience",
"band": "critical",
"name": "Maintainer resilience (bus factor)",
"note": null,
"notes": [],
"value": 18,
"inputs": {
"bus_factor": 1,
"contributors_sampled": 2,
"top_contributor_share": 0.968
},
"components": [
{
"key": "bus_factor",
"name": "Bus factor",
"detail": "1 contributor(s) cover half of all commits",
"points": 9,
"status": "partial",
"details": [
{
"code": "bus_factor",
"params": {
"count": 1
}
}
],
"max_points": 54
},
{
"key": "commit_distribution",
"name": "Commit distribution",
"detail": "top contributor authored 97% of commits",
"points": 0.7,
"status": "partial",
"details": [
{
"code": "top_contributor_share",
"params": {
"share": 97
}
}
],
"max_points": 22.5
},
{
"key": "contributor_breadth",
"name": "Contributor breadth",
"detail": "2 contributors",
"points": 2.7,
"status": "partial",
"details": [
{
"code": "contributors_sampled",
"params": {
"count": 2
}
}
],
"max_points": 13.5
},
{
"key": "openssf_scorecard_contributors",
"name": "OpenSSF Scorecard: Contributors",
"detail": "project has 2 contributing companies or organizations -- score normalized to 6",
"points": 6,
"status": "partial",
"details": [],
"max_points": 10
}
]
},
{
"key": "responsiveness",
"band": "good",
"name": "Issue & PR responsiveness",
"note": null,
"notes": [],
"value": 74,
"inputs": {
"merged_prs": 26,
"open_issues": 0,
"closed_issues": 2,
"issue_closed_ratio": 1,
"closed_unmerged_prs": 10
},
"components": [
{
"key": "issue_resolution",
"name": "Issue resolution",
"detail": "100% of issues closed",
"points": 46.8,
"status": "met",
"details": [
{
"code": "issues_closed_share",
"params": {
"share": 100
}
}
],
"max_points": 46.75
},
{
"key": "pr_acceptance",
"name": "PR acceptance",
"detail": "26/36 decided PRs merged",
"points": 27.6,
"status": "partial",
"details": [
{
"code": "decided_prs_merged",
"params": {
"merged": 26,
"decided": 36
}
}
],
"max_points": 38.25
},
{
"key": "openssf_scorecard_code_review",
"name": "OpenSSF Scorecard: Code-Review",
"detail": "Found 0/27 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
}
]
},
{
"key": "stewardship",
"band": "moderate",
"name": "Ownership & stewardship",
"note": null,
"notes": [],
"value": 68,
"inputs": {
"followers": 86,
"owner_type": "Organization",
"is_verified": null,
"owner_login": "PDBeurope",
"public_repos": 48,
"account_age_days": 4321
},
"components": [
{
"key": "ownership_backing",
"name": "Ownership backing",
"detail": "organization-owned",
"points": 30,
"status": "met",
"details": [
{
"code": "owner_organization",
"params": {}
}
],
"max_points": 30
},
{
"key": "verified_domain",
"name": "Verified domain",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "owner_reach",
"name": "Owner reach",
"detail": "86 followers of PDBeurope",
"points": 13.9,
"status": "partial",
"details": [
{
"code": "owner_followers",
"params": {
"count": 86,
"login": "PDBeurope"
}
}
],
"max_points": 25
},
{
"key": "track_record",
"name": "Track record",
"detail": "48 public repos, account ~11 yr old",
"points": 24.3,
"status": "partial",
"details": [
{
"code": "public_repos",
"params": {
"count": 48
}
},
{
"code": "account_age_years",
"params": {
"years": 11
}
}
],
"max_points": 25
}
]
},
{
"key": "package_maintenance",
"band": "excellent",
"name": "Package maintenance",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"packages": [
"pdbe-mcp-server"
],
"ecosystems": "pypi",
"any_deprecated": false,
"min_days_since_publish": 2
},
"components": [
{
"key": "published_resolvable",
"name": "Published & resolvable",
"detail": "1 package(s) on pypi",
"points": 25,
"status": "met",
"details": [
{
"code": "packages_published",
"params": {
"count": 1,
"ecosystems": "pypi"
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}
],
"max_points": 25
},
{
"key": "publish_recency",
"name": "Publish recency",
"detail": "latest publish 2 days ago",
"points": 35,
"status": "met",
"details": [
{
"code": "publish_recency",
"params": {
"days": 2
}
}
],
"max_points": 35
},
{
"key": "version_history",
"name": "Version history",
"detail": "16 published versions",
"points": 20,
"status": "met",
"details": [
{
"code": "published_versions",
"params": {
"count": 16
}
}
],
"max_points": 20
},
{
"key": "not_deprecated",
"name": "Not deprecated",
"detail": "active, not deprecated or yanked",
"points": 20,
"status": "met",
"details": [
{
"code": "package_not_deprecated",
"params": {}
}
],
"max_points": 20
}
]
}
],
"description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
},
{
"key": "engineering",
"band": "good",
"name": "Engineering Quality",
"value": 78,
"weight": 0.2,
"metrics": [
{
"key": "engineering_practices",
"band": "excellent",
"name": "Engineering practices",
"note": null,
"notes": [],
"value": 90,
"inputs": {
"has_ci": true,
"has_tests": true,
"has_editorconfig": false,
"has_linter_config": true,
"has_precommit_config": true
},
"components": [
{
"key": "ci_workflows",
"name": "CI workflows",
"detail": "1 workflow(s)",
"points": 24,
"status": "met",
"details": [
{
"code": "ci_workflows",
"params": {
"count": 1
}
}
],
"max_points": 24
},
{
"key": "tests_present",
"name": "Tests present",
"detail": null,
"points": 24,
"status": "met",
"details": [],
"max_points": 24
},
{
"key": "linter_config",
"name": "Linter config",
"detail": "ruff.toml",
"points": 16,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "ruff.toml"
}
}
],
"max_points": 16
},
{
"key": "pre_commit_hooks",
"name": "Pre-commit hooks",
"detail": null,
"points": 9.6,
"status": "met",
"details": [],
"max_points": 9.6
},
{
"key": "editorconfig",
"name": ".editorconfig",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 6.4
},
{
"key": "openssf_scorecard_ci_tests",
"name": "OpenSSF Scorecard: CI-Tests",
"detail": "23 out of 26 merged PRs checked by a CI test -- score normalized to 8",
"points": 16,
"status": "partial",
"details": [],
"max_points": 20
}
]
},
{
"key": "documentation",
"band": "moderate",
"name": "Documentation",
"note": null,
"notes": [],
"value": 60,
"inputs": {
"topics": [
"ai-integration",
"api-server",
"bioinformatics",
"knowledge-graph",
"llm-tools",
"mcp",
"pdbe",
"protein-structures",
"python",
"structural-biology"
],
"has_wiki": true,
"homepage": null,
"has_readme": true,
"has_docs_dir": false,
"has_description": true
},
"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 30,
"status": "met",
"details": [],
"max_points": 30
},
{
"key": "documentation_directory",
"name": "Documentation directory",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 25
},
{
"key": "documentation_homepage_site",
"name": "Documentation / homepage site",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "repository_description",
"name": "Repository description",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "topics",
"name": "Topics",
"detail": "10 topics",
"points": 10,
"status": "met",
"details": [
{
"code": "topics_count",
"params": {
"count": 10
}
}
],
"max_points": 10
},
{
"key": "wiki",
"name": "Wiki",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
}
],
"description": "Are baseline engineering and documentation practices in place?"
},
{
"key": "security",
"band": "moderate",
"name": "Security",
"value": 65,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "moderate",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"branch_protection",
"signed_releases"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 65,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 16,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 2,
"scorecard_aggregate": 6.5
},
"components": [
{
"key": "binary_artifacts",
"name": "Binary-Artifacts",
"detail": "no binaries found in the repo",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "branch_protection",
"name": "Branch-Protection",
"detail": "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",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "23 out of 26 merged PRs checked by a CI test -- score normalized to 8",
"points": 2,
"status": "partial",
"details": [],
"max_points": 2.5
},
{
"key": "cii_best_practices",
"name": "CII-Best-Practices",
"detail": "no effort to earn an OpenSSF best practices badge detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 2.5
},
{
"key": "code_review",
"name": "Code-Review",
"detail": "Found 0/27 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 2 contributing companies or organizations -- score normalized to 6",
"points": 1.5,
"status": "partial",
"details": [],
"max_points": 2.5
},
{
"key": "dangerous_workflow",
"name": "Dangerous-Workflow",
"detail": "no dangerous workflow patterns detected",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "update tool detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "license",
"name": "License",
"detail": "license file detected",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "14 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
"name": "Packaging",
"detail": "packaging workflow detected",
"points": 5,
"status": "met",
"details": [],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "sast",
"name": "SAST",
"detail": "SAST tool is not run on all commits -- score normalized to 4",
"points": 2,
"status": "partial",
"details": [],
"max_points": 5
},
{
"key": "security_policy",
"name": "Security-Policy",
"detail": "security policy file not detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "signed_releases",
"name": "Signed-Releases",
"detail": "no releases found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "token_permissions",
"name": "Token-Permissions",
"detail": "GitHub workflow tokens follow principle of least privilege",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "3 existing vulnerabilities detected",
"points": 5.2,
"status": "partial",
"details": [],
"max_points": 7.5
}
]
},
{
"key": "high_risk_jurisdiction_exposure",
"band": "excellent",
"name": "High-Risk Jurisdiction Exposure",
"note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
"notes": [
{
"code": "jurisdiction_evidence_limits",
"params": {}
}
],
"value": 100,
"inputs": {
"meaning": "self-published location evidence; not nationality or citizenship",
"red_flag": false,
"exposures": [],
"policy_countries": [
"Russia",
"Iran",
"North Korea"
],
"review_only_matches": 0,
"assessed_self_published_locations": 2
},
"components": [
{
"key": "policy_exposure_multiplier",
"name": "Policy exposure multiplier",
"detail": "no confirmed policy-scope location match",
"points": 100,
"status": "met",
"details": [
{
"code": "jurisdiction_no_match",
"params": {}
}
],
"max_points": 100
}
]
}
],
"description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
},
{
"key": "ai_readiness",
"band": "moderate",
"name": "AI Readiness",
"value": 51,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "critical",
"name": "Agent context & guidance",
"note": "Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"legible_commit_history"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 1,
"inputs": {
"has_llms_txt": false,
"legible_history_share": null,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"components": [
{
"key": "agent_instructions",
"name": "Agent instructions",
"detail": "no CLAUDE.md / AGENTS.md / editor rules",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_instructions",
"params": {}
}
],
"max_points": 45
},
{
"key": "machine_readable_docs_llms_txt",
"name": "Machine-readable docs (llms.txt)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "legible_commit_history",
"name": "Legible commit history",
"detail": "no data",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "excellent",
"name": "Verify loop (build / test / typecheck)",
"note": "Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"demonstrated_agent_practice",
"automated_maintenance"
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}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 88,
"inputs": {
"has_nix": false,
"has_tests": true,
"lockfiles": [
"uv.lock"
],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [
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"has_devcontainer": false,
"has_linter_config": true,
"typecheck_configs": [
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"toolchain_manifests": [],
"dependency_bot_commit_share": null
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": "Makefile",
"points": 18,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "Makefile"
}
}
],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 22,
"status": "met",
"details": [],
"max_points": 22
},
{
"key": "lint_format_config",
"name": "Lint / format config",
"detail": "ruff.toml",
"points": 11,
"status": "met",
"details": [
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"code": "file_list",
"params": {
"files": "ruff.toml"
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}
],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": "pdbe_mcp_server/py.typed",
"points": 11,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "pdbe_mcp_server/py.typed"
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}
],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": "lockfile",
"points": 10,
"status": "met",
"details": [
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"code": "file_list",
"params": {
"files": "lockfile"
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}
],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no data",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "no data",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "good",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 82,
"inputs": {
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"largest_source_bytes": 28927,
"source_files_sampled": 15,
"oversized_source_files": 0
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Python with type-check config (pdbe_mcp_server/py.typed)",
"points": 27,
"status": "partial",
"details": [
{
"code": "typecheck_config_language",
"params": {
"files": "pdbe_mcp_server/py.typed",
"language": "Python"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "0/15 source files over 60KB",
"points": 55,
"status": "met",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 15,
"oversized": 0
}
}
],
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}
]
},
{
"key": "ai_interfaces",
"band": "critical",
"name": "Machine-readable interfaces",
"note": null,
"notes": [],
"value": 20,
"inputs": {
"example_dirs": [],
"has_mcp_signal": true,
"api_schema_files": []
},
"components": [
{
"key": "api_schema_openapi_graphql_proto",
"name": "API schema (OpenAPI/GraphQL/proto)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 40
},
{
"key": "mcp_server",
"name": "MCP server",
"detail": null,
"points": 20,
"status": "met",
"details": [],
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},
{
"key": "runnable_examples",
"name": "Runnable examples",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
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}
]
}
],
"description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
}
],
"metrics_version": "1.13.0"
},
"warnings": [],
"report_type": "repository",
"generated_at": "2026-07-17T18:15:21.262144Z",
"schema_version": "0.12.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/p/pdbeurope/pdbe-mcp-servers.svg",
"full_name": "pdbeurope/pdbe-mcp-servers",
"license_state": "standard",
"license_spdx": "Apache-2.0"
}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 v1.13.0, schema v0.12.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.