Public recordModerate
Software health reportschema 0.12.0 · metrics 2.10.0 · 2026-07-17 17:31 UTC
deeprank / deeprank2
An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.
deeprank/deeprank2 holds a health index of 62 out of 100, placing it in the Moderate band. It scores highest on Engineering Quality (78/100) and lowest on Vitality (33/100). It was last updated 127 days ago. A single contributor accounts for most of its recent work.
62
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.
62
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 58 is calibrated to 62 on the published index scale (record calibration 2026-08-02).
Ownership
DeepRankOrganization
25 followers19 public repossince Aug 2017
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 | deeprank2 | 3.1.0 | 335 | 10 | 669 days ago | graph-neural-networkconvolutional-neural-networkprotein-protein-interfacesmissense-variantsdeep-learningpytorch |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
33
Development activity
10Critical
How it's scored
| 9.9/36 | Push recency — last push 127 days ago |
| 0/36 | Commit cadence — 0/52 weeks with commits |
| 0/18 | Commit volume — 0 commits in the last year |
| 0/10 | OpenSSF Scorecard: Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0 |
Inputs used
| commits_last_year | 0 |
| human_commit_share | — |
| days_since_last_push | 127 |
| active_weeks_last_year | 0 |
Release discipline
68Good
How it's scored
| 27/27 | Ships releases — 15 releases published |
| 7.2/36 | Release recency — latest release 669 days ago |
| 27/27 | Release cadence — a release every ~40 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 15 |
| latest_release_tag | v3.1.0 |
| releases_from_tags | no |
| days_since_latest_release | 669 |
| mean_days_between_releases | 40 |
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?
57
Popularity & adoption
43Weak
How it's scored
| 28.6/60 | Stars — 59 stars |
| 9.3/25 | Forks — 14 forks |
| 4.7/15 | Watchers — 8 watchers |
Inputs used
| forks | 14 |
| stars | 59 |
| watchers | 8 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
85Excellent
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (Apache-2.0) |
| 18/18 | CONTRIBUTING guide |
| 13.5/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 0/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| readme_badges | — |
| has_contributing | yes |
| has_issue_template | no |
| has_code_of_conduct | yes |
| readme_badge_services | — |
| has_pull_request_template | no |
How it's scored
| 33.7/80 | Monthly downloads — 335 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | deeprank2 |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 335 |
| 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?
69
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 8.9/22.5 | Commit distribution — top contributor authored 60% of commits |
| 13.5/13.5 | Contributor breadth — 16 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 8 contributing companies or organizations |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 16 |
| top_contributor_share | 0.605 |
Issue & PR responsiveness
87Excellent
How it's scored
| 38.7/42 | Issue resolution — 92% of issues closed |
| 25.4/30 | PR acceptance — 252/298 decided PRs merged |
| 0/13 | Newcomer PR acceptance — no first-time contributor's PR decided in 30d |
| 12/15 | OpenSSF Scorecard: Code-Review — Found 6/7 approved changesets -- score normalized to 8 |
Inputs used
| merged_prs | 252 |
| open_issues | 27 |
| closed_issues | 315 |
| prs_merged_7d | — |
| prs_decided_7d | — |
| prs_merged_30d | — |
| prs_decided_30d | — |
| issue_closed_ratio | 0.921 |
| closed_unmerged_prs | 46 |
| first_time_authors_30d | — |
| first_time_prs_merged_30d | — |
| first_time_prs_decided_30d | — |
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.
Ownership & stewardship
77Good
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain — verified-domain status not read for this organization |
| 10.2/25 | Owner reach — 25 followers of DeepRank |
| 21.5/25 | Track record — 19 public repos, account ~8 yr old |
Inputs used
| followers | 25 |
| owner_type | Organization |
| is_verified | — |
| owner_login | DeepRank |
| public_repos | 19 |
| account_age_days | 3,245 |
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.
Package maintenance
79Good
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 14/35 | Publish recency — latest publish 669 days ago |
| 20/20 | Version history — 10 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | deeprank2 |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 669 |
Engineering Quality
Are baseline engineering and documentation practices in place?
78
Engineering practices
64Moderate
How it's scored
| 24/24 | CI workflows — 15 workflow(s) |
| 24/24 | Tests present |
| 16/16 | Linter config — .ruff.toml |
| 0/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 0/20 | OpenSSF Scorecard: CI-Tests — 0 out of 7 merged PRs checked by a CI test -- score normalized to 0 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | yes |
| has_precommit_config | no |
Documentation
100Exceptional
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://deeprank2.readthedocs.io/en/latest/?badge=latest |
| 10/10 | Repository description |
| 10/10 | Topics — 7 topics |
| 10/10 | Wiki |
Inputs used
| topics | convolutional-neural-networks, deep-learning, graph-neural-networks, pytorch, structural-biology, protein-protein-interfaces, single-residue-variants |
| has_wiki | yes |
| homepage | https://deeprank2.readthedocs.io/en/latest/?badge=latest |
| docs_site | https://deeprank2.readthedocs.io/en/latest/?badge=latest |
| 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?
52
Security posture
52Moderate
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 4.5/7.5 | Branch-Protection — branch protection is not maximal on development and all release branches |
| 0/2.5 | CI-Tests — 0 out of 7 merged PRs checked by a CI test -- score normalized to 0 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 6/7.5 | Code-Review — Found 6/7 approved changesets -- score normalized to 8 |
| 2.5/2.5 | Contributors — project has 8 contributing companies or organizations |
| 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 |
| 0/7.5 | Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0 |
| 0/5 | Packaging — no data |
| 0/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — no data |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 16 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 2 |
| scorecard_aggregate | 5.2 |
Excluded from scoring (no data or not applicable): Packaging, Signed-Releases. Remaining weights renormalized.
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.
53
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 |
| llms_txt_url | — |
| legible_history_share | — |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.
How it's scored
| 18/18 | One-command bootstrap — docs/Makefile |
| 22/22 | Automated tests |
| 11/11 | Lint / format config — .ruff.toml |
| 0/11 | Static type checking |
| 10/10 | Reproducible environment — Dockerfile |
| 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 | — |
| has_dockerfile | yes |
| typed_language | no |
| bootstrap_files | docs/Makefile |
| has_devcontainer | no |
| has_linter_config | yes |
| typecheck_configs | — |
| 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.
Code legibility for models
55Moderate
How it's scored
| 0/45 | Type-checkable code — Python without a type-check config |
| 55/55 | Manageable file sizes — 0/87 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 56,395 |
| source_files_sampled | 87 |
| oversized_source_files | 0 |
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
59GitHub stars
16contributors
0commits, last 12 months
127days since last push
15releases
1bus factor
27open issues
PyPIpackage ecosystems
More detail
OpenSSF Scorecard 5.2 / 10
5.2aggregate
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 |
| 6 | Branch-Protection | branch protection is not maximal on development and all release branches |
| 0 | CI-Tests | 0 out of 7 merged PRs checked by a CI test -- score normalized to 0 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 8 | Code-Review | Found 6/7 approved changesets -- score normalized to 8 |
| 10 | Contributors | project has 8 contributing companies or organizations |
| 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 |
| 0 | Maintained | 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0 |
| n/a | Packaging | packaging workflow not detected |
| 0 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 0 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 0 | Security-Policy | security policy file not detected |
| n/a | Signed-Releases | no releases found |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 19
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | notebook | >= 7.2.1, < 8.0 | pyproject.toml |
| PyPI | markov-clustering | >= 0.0.6.dev0, < 1.0 | pyproject.toml |
| PyPI | tensorboard | >= 0.9.0, < 3.0 | pyproject.toml |
| PyPI | protobuf | >= 3.20.1, < 6.0 | pyproject.toml |
| PyPI | dill | >= 0.3.8, < 1.0 | pyproject.toml |
| PyPI | pyarrow | >= 16.1.0, < 17.0 | pyproject.toml |
| PyPI | tables | >= 3.9.2, < 4.0 | pyproject.toml |
| PyPI | numpy | >= 1.25, < 2.0 | pyproject.toml |
| PyPI | scipy | >= 1.13.1, < 2.0 | pyproject.toml |
| PyPI | h5py | >= 3.11.0, < 4.0 | pyproject.toml |
| PyPI | networkx | >= 3.1, < 4.0 | pyproject.toml |
| PyPI | matplotlib | >= 3.9.0, < 4.0 | pyproject.toml |
| PyPI | scikit-learn | >= 1.5.0, < 2.0 | pyproject.toml |
| PyPI | chart-studio | >= 1.1.0, < 2.0 | pyproject.toml |
| PyPI | pdb2sql | >= 0.5.3, < 1.0 | pyproject.toml |
| PyPI | python-louvain | >= 0.16, < 1.0 | pyproject.toml |
| PyPI | tqdm | >= 4.66.4, < 5.0 | pyproject.toml |
| PyPI | freesasa | >= 2.1.1, < 3.0 | pyproject.toml |
| PyPI | biopython | >= 1.83, < 2.0 | pyproject.toml |
All dependencies 25
Full resolved dependency set from the GitHub dependency graph: 19 direct and 6 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | biopython | — | direct |
| PyPI | chart-studio | — | direct |
| PyPI | dill | — | direct |
| PyPI | freesasa | — | direct |
| PyPI | h5py | — | direct |
| PyPI | markov-clustering | — | direct |
| PyPI | matplotlib | — | direct |
| PyPI | networkx | — | direct |
| PyPI | notebook | — | direct |
| PyPI | numpy | — | direct |
| PyPI | pdb2sql | — | direct |
| PyPI | protobuf | — | direct |
| PyPI | pyarrow | — | direct |
| PyPI | python-louvain | — | direct |
| PyPI | scikit-learn | — | direct |
| PyPI | scipy | — | direct |
| PyPI | tables | — | direct |
| PyPI | tensorboard | — | direct |
| PyPI | tqdm | — | direct |
| PyPI | myst-parser | — | indirect |
| PyPI | readthedocs-sphinx-search | 0.3.2 | indirect |
| PyPI | sphinx | 5.3.0 | indirect |
| PyPI | sphinx-rtd-theme | 1.1.1 | indirect |
| PyPI | toml | — | indirect |
| PyPI | typing-extensions | — | indirect |
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 v0.12.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.