Public recordAt risk
Software health reportschema 0.26.0 · metrics 1.13.0 · 2026-07-21 23:48 UTC
chapmanb / bcbb
Incubator for useful bioinformatics code, primarily in Python and R
chapmanb/bcbb holds a health index of 34 out of 100, placing it in the At risk band. It scores highest on Sustainability & Governance (59/100) and lowest on Vitality (10/100). It was last updated 531 days ago. A single contributor accounts for most of its recent work.
34
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.
34
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.
Abandonment Policy applies a 85% multiplier to weighted overall health.
Ownership
Brad ChapmanPersonal account
982 followers121 public repossince Dec 2008Ginkgo Bioworks
This repository is owned by a personal account. A single-owner project carries more continuity risk than an organization-backed one.
Package ecosystems
| Registry | Package | Version | Downloads / mo | Versions | Last publish |
|---|---|---|---|---|---|
| PyPI | bcbio-gff | 0.7.1 | - | 15 | 904 days ago |
| PyPI | bcbio-phyloblastpoints to another repo — not scored | 0.1.2 | - | 3 | 4891 days ago |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
10
Development activity
1Critical
Abandonment alert
Work has arrived and nobody has attended to it
no human commit in 531 daysautomated commits excludedissues left unansweredOpenSSF Scorecard reports it unmaintained
Silence alone is never the finding — a small, finished library may need no commits for years. This alert requires both: no human commit for a long time, and obligations the project is visibly not discharging. Automated commits do not count as maintenance.
How abandonment is assessedHow it's scored
| 0/36 | Push recency — last push 531 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 | 1 |
| days_since_last_push | 531 |
| active_weeks_last_year | 0 |
Release discipline
24Critical
How it's scored
| 16.2/27 | Ships releases — 2 version tags (no GitHub releases) |
| 0/36 | Release recency — latest release 1,749 days ago |
| 5.4/27 | Release cadence — a release every ~3,164.1 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 2 |
| latest_release_tag | v0.6.7 |
| releases_from_tags | yes |
| days_since_latest_release | 1,749 |
| mean_days_between_releases | 3,164.1 |
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?
52
Popularity & adoption
75Good
How it's scored
| 45.6/60 | Stars — 644 stars |
| 19.8/25 | Forks — 241 forks |
| 9.6/15 | Watchers — 55 watchers |
Inputs used
| forks | 241 |
| stars | 644 |
| watchers | 55 |
| growth_state | organic |
| growth_factor_pct | 100 |
Community health
25Critical
How it's scored
| 22.5/22.5 | README |
| 0/22.5 | License — no license file detected |
| 0/18 | 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 | no |
| has_contributing | no |
| has_issue_template | no |
| has_code_of_conduct | no |
| has_pull_request_template | no |
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
59
Maintainer resilience (bus factor)
35At risk
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 2.2/22.5 | Commit distribution — top contributor authored 90% of commits |
| 13.5/13.5 | Contributor breadth — 25 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 25 contributing companies or organizations |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 25 |
| top_contributor_share | 0.904 |
Issue & PR responsiveness
68Moderate
How it's scored
| 36.2/46.8 | Issue resolution — 78% of issues closed |
| 26.3/38.3 | PR acceptance — 46/67 decided PRs merged |
| 6/15 | OpenSSF Scorecard: Code-Review — Found 9/20 approved changesets -- score normalized to 4 |
Inputs used
| merged_prs | 46 |
| open_issues | 18 |
| closed_issues | 62 |
| issue_closed_ratio | 0.775 |
| closed_unmerged_prs | 21 |
Ownership & stewardship
71Good
How it's scored
| 10/30 | Ownership backing — personal (user) account |
| 0/20 | Verified domain — not applicable to user accounts |
| 21.5/25 | Owner reach — 982 followers of chapmanb |
| 25/25 | Track record — 121 public repos, account ~17 yr old |
Inputs used
| followers | 982 |
| owner_type | User |
| is_verified | — |
| owner_login | chapmanb |
| public_repos | 121 |
| account_age_days | 6,433 |
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.
Package maintenance
69Moderate
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 4/35 | Publish recency — latest publish 904 days ago |
| 20/20 | Version history — 15 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | bcbio-gff |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 904 |
Engineering Quality
Are baseline engineering and documentation practices in place?
36
Engineering practices
24Critical
How it's scored
| 0/24 | CI workflows |
| 24/24 | Tests present |
| 0/16 | Linter config |
| 0/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 0/20 | OpenSSF Scorecard: CI-Tests — 0 out of 9 merged PRs checked by a CI test -- score normalized to 0 |
Inputs used
| has_ci | no |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | no |
| has_precommit_config | no |
Documentation
55Moderate
How it's scored
| 30/30 | README |
| 0/25 | Documentation directory |
| 15/15 | Documentation / homepage site — http://bcbio.wordpress.com |
| 10/10 | Repository description |
| 0/10 | Topics |
| 0/10 | Wiki |
Inputs used
| topics | — |
| has_wiki | no |
| homepage | http://bcbio.wordpress.com |
| 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?
43
Security posture
29Critical
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — branch protection not enabled on development/release branches |
| 0/2.5 | CI-Tests — 0 out of 9 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 |
| 3/7.5 | Code-Review — Found 9/20 approved changesets -- score normalized to 4 |
| 2.5/2.5 | Contributors — project has 25 contributing companies or organizations |
| 0/10 | Dangerous-Workflow — no data |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 0/2.5 | License — license file not 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 — no data |
| 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 — no data |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 13 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 5 |
| scorecard_aggregate | 2.9 |
Excluded from scoring (no data or not applicable): dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions. Remaining weights renormalized.
Dependency advisories
100Excellent
How it's scored
| 35/35 | Direct dependencies free of known advisories — no direct dependency carries a known advisory |
| 25/25 | Indirect dependencies free of known advisories — no indirect dependency carries a known advisory |
| 0/40 | No advisories left outstanding — no advisory carries a publication date |
Inputs used
| source | osv |
| advisories | 0 |
| affected_packages | 0 |
| assessed_packages | 3 |
| unassessed_packages | 0 |
| affected_by_severity | none |
| direct_affected_packages | 0 |
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:bcbio-gff@0.7.1 runtime dependency closure — what installing the published package pulls in — 3 packages. Reachability is not analyzed.
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.
37
Agent context & guidance
16Critical
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 16/40 | Legible commit history — 30 of 100 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | no |
| legible_history_share | 0.3 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
How it's scored
| 18/18 | One-command bootstrap — abstracts/bosc_2015_bcbio_prioritization/Makefile, abstracts/bosc_2016_bcbio_cwl/Makefile, abstracts/bosc_2017_bcbio_integration/Makefile, abstracts/bosc_2018_bcbio_validation/Makefile, abstracts/hackathon_workshop_2017/Makefile, nextgen/docs/Makefile, papers/bcbio-nextgen/Makefile |
| 22/22 | Automated tests |
| 0/11 | Lint / format config |
| 0/11 | Static type checking |
| 0/10 | Reproducible environment |
| 0/10 | Demonstrated agent practice — no agent-authored commits among the last 100 |
| 0/8 | Automated maintenance — no automated dependency updates observed |
| 0/10 | OpenSSF Scorecard: Pinned-Dependencies — no data |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | — |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | abstracts/bosc_2015_bcbio_prioritization/Makefile, abstracts/bosc_2016_bcbio_cwl/Makefile, abstracts/bosc_2017_bcbio_integration/Makefile, abstracts/bosc_2018_bcbio_validation/Makefile, abstracts/hackathon_workshop_2017/Makefile, nextgen/docs/Makefile, papers/bcbio-nextgen/Makefile |
| has_devcontainer | no |
| has_linter_config | no |
| typecheck_configs | — |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.
Code legibility for models
55Moderate
How it's scored
| 0/45 | Type-checkable code — Python without a type-check config |
| 54.7/55 | Manageable file sizes — 1/186 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 70,319 |
| source_files_sampled | 186 |
| oversized_source_files | 1 |
Machine-readable interfaces
40At risk
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) |
| 0/20 | MCP server |
| 40/40 | Runnable examples — examples, notebooks |
Inputs used
| example_dirs | examples, notebooks |
| has_mcp_signal | no |
| api_schema_files | — |
Key facts
644GitHub stars
25contributors
0commits, last 12 months
531days since last push
2releases
1bus factor
18open issues
PyPIpackage ecosystems
Data collection warnings
- pypi package 'bcbio-phyloblast' points at a different repository (http://bcbio.wordpress.com); excluded from ecosystem scoring
More detail
Star and fork history 644 ★ / 241 ⇿
644Stars
241Forks
2Releases
When each star and fork was added, collected from GitHub and bucketed by day. Cumulative growth sits directly above the daily additions it is made of, so the two read against each other: steady organic accretion looks nothing like an abrupt, short-lived burst. Where that difference is measurable, it is reported as growth authenticity.
Major 0Minor 1Patch 1
Each point covers 17 days.
OpenSSF Scorecard 2.9 / 10
2.9aggregate
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 |
| 0 | Branch-Protection | branch protection not enabled on development/release branches |
| 0 | CI-Tests | 0 out of 9 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 |
| 4 | Code-Review | Found 9/20 approved changesets -- score normalized to 4 |
| 10 | Contributors | project has 25 contributing companies or organizations |
| n/a | Dangerous-Workflow | no workflows found |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 0 | License | license file not 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 |
| n/a | Pinned-Dependencies | no dependencies found |
| 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 |
| n/a | Token-Permissions | No tokens found |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
All dependencies 3
Full resolved dependency set from the GitHub dependency graph: 0 direct and 3 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | biopython | — | indirect |
| PyPI | pyyaml | — | indirect |
| PyPI | six | — | indirect |
Dependency advisories 0
Installing pypi:bcbio-gff@0.7.1 pulls in 3 packages, direct and transitive: 0 carry known advisories, of which 0 are direct dependencies.
No known advisories affect the assessed dependencies.
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
{
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"homepage": "http://bcbio.wordpress.com",
"languages": {
"R": 14547,
"CSS": 90068,
"TeX": 142313,
"HTML": 248867,
"SCSS": 16872,
"Shell": 2356,
"Python": 850665,
"Clojure": 9818,
"Makefile": 6313,
"JavaScript": 88232,
"Jupyter Notebook": 5429
},
"pushed_at": "2025-02-05T14:20:51Z",
"created_at": "2008-12-09T21:05:22Z",
"owner_type": "User",
"updated_at": "2026-07-09T17:16:49Z",
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"name": "Brad Chapman",
"type": "User",
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"company": "Ginkgo Bioworks",
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"created_at": "2008-12-09T18:45:45Z",
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"public_repos": 121,
"account_age_days": 6433
},
"license": {
"state": "absent",
"spdx_id": null,
"raw_spdx": null,
"file_present": false,
"scorecard_found": false,
"profile_has_license": false
},
"activity": {
"releases": [
{
"tag": "v0.6.7",
"kind": "patch",
"published_at": "2021-10-06T13:26:49Z"
},
{
"tag": "v0.6.0",
"kind": "minor",
"published_at": "2013-02-06T10:19:08Z"
}
],
"recent_commits": [
{
"oid": "320353c64ee0dc938113ca36f19b2e6de6b597be",
"body": "fix: Suppress warning about invalid escape sequence",
"is_bot": false,
"headline": "Merge pull request #147 from phaverty-ginkgo/suppress_regex_warning",
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"headline": "Suppress warning about invalid excape sequence",
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"oid": "9c6d83ee3f0491f647a9ecd5947b13c99b478f26",
"body": null,
"is_bot": false,
"headline": "Version bump: bcbio-gff-v0.7.1",
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"oid": "03e96caa2b91cce22b6d05cf5d5f473cccbb7eb2",
"body": null,
"is_bot": false,
"headline": "Do not smother Biopython deprecation warnings. Fixes #139",
"author_name": "chapmanb",
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{
"oid": "dd0dd8fa6732ff48afc38a7f05aaa32d37010761",
"body": "updates for biopython 1.82",
"is_bot": false,
"headline": "Merge pull request #141 from fubar2/master",
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"body_truncated": false,
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{
"oid": "0db78650b163166337328ea4613ee6a0d9ccc5fa",
"body": "docs: Fix a few typos",
"is_bot": false,
"headline": "Merge pull request #135 from timgates42/bugfix_typos",
"author_name": "Brad Chapman",
"author_login": "chapmanb",
"committed_at": "2024-01-29T13:21:47Z",
"body_truncated": false,
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"oid": "eec72c3faca1e5e9e4e48dbf46d396a9045baa3b",
"body": "fix nofuzzy_start/end deprecation - replaced with start and end\nmove all strands in seqfeatures into simplelocations\nPasses tests !",
"is_bot": false,
"headline": "updates for biopython 1.86",
"author_name": "fubar2",
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"body": "Fix error with biopython 1.81",
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"headline": "Merge pull request #137 from abretaud/unknownseq",
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"headline": "Fix error with biopython 1.81",
"author_name": "Anthony Bretaudeau",
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"body_truncated": false,
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{
"oid": "63224f4b106c49dcfa25cf73406dcaa047a77758",
"body": "There are small typos in:\n- posts/conferences/bosc2018_day1a.md\n- posts/seminars/tumor_heterogeneity_carter.md\n\nFixes:\n- Should read `suppressors` rather than `supressors`.\n- Should read `service` rather than `serivce`.\n\nSigned-off-by: Tim Gates <tim.gates@iress.com>",
"is_bot": false,
"headline": "docs: Fix a few typos",
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{
"oid": "dbfb52711f0bfcc1d26c5a5b53c9ff4f50dc0027",
"body": null,
"is_bot": false,
"headline": "v0.6.9: fix ID matching when no rec.id fixes #134",
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{
"oid": "438f4242063b29f507282bc507ca67fddcfa64ed",
"body": "NCBI PGAP can produce fastas with NCBI headers (`lcl|1`) and GFFs\nwith plain IDs (`1`). This avoids creating duplicate records by\nmatching these and using a consistent contig ID when combining sequences\nand GFF files.\n\nThe contig ID used in the final output SeqRecords is the first one\nencountered. So if you use an external FASTA it's the IDs in the FASTA\nand if you use a GFF embedded FASTA it's the IDs in the GFF.",
"is_bot": false,
"headline": "v0.6.8: match records between fasta and GFF with NCBI style headers",
"author_name": "chapmanb",
"author_login": "chapmanb",
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},
{
"oid": "599c64c5d5f5a53ec35c6c3f3619614fa92e3a3c",
"body": null,
"is_bot": false,
"headline": "v0.6.7: handle problem sequence-region directives without contigs",
"author_name": "chapmanb",
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"committed_at": "2021-10-06T13:26:49Z",
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},
{
"oid": "d3c51a22ac961584cca1689c7261b1c8ebe1830a",
"body": null,
"is_bot": false,
"headline": "GFF to Genbank: support latest biopython without alphabets",
"author_name": "chapmanb",
"author_login": "chapmanb",
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"body_truncated": false,
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},
{
"oid": "74502a06d56afa9e1d60bffcb21725f078d8d83f",
"body": "Support zero length reads in FakeHandle",
"is_bot": false,
"headline": "Merge pull request #133 from peterjc/patch-1",
"author_name": "Brad Chapman",
"author_login": "chapmanb",
"committed_at": "2021-06-08T09:17:29Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f980be9bcdddfae96c605694e90465bc6f428c5d",
"body": "Biopython now uses this to detect file mode (text/unicode versus binary/bytes).\r\n\r\nhttps://github.com/biopython/biopython/issues/3575",
"is_bot": false,
"headline": "Support zero length reads in FakeHandle",
"author_name": "Peter Cock",
"author_login": "peterjc",
"committed_at": "2021-06-03T16:46:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3ba0ec42120065cca136fd496948948f57081039",
"body": "Add license to setup.py",
"is_bot": false,
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"status": "partial",
"details": [
{
"code": "decided_prs_merged",
"params": {
"merged": 46,
"decided": 67
}
}
],
"max_points": 38.25
},
{
"key": "openssf_scorecard_code_review",
"name": "OpenSSF Scorecard: Code-Review",
"detail": "Found 9/20 approved changesets -- score normalized to 4",
"points": 6,
"status": "partial",
"details": [],
"max_points": 15
}
]
},
{
"key": "stewardship",
"band": "good",
"name": "Ownership & stewardship",
"note": "Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"verified_domain"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 71,
"inputs": {
"followers": 982,
"owner_type": "User",
"is_verified": null,
"owner_login": "chapmanb",
"public_repos": 121,
"account_age_days": 6433
},
"components": [
{
"key": "ownership_backing",
"name": "Ownership backing",
"detail": "personal (user) account",
"points": 10,
"status": "partial",
"details": [
{
"code": "owner_personal",
"params": {}
}
],
"max_points": 30
},
{
"key": "verified_domain",
"name": "Verified domain",
"detail": "not applicable to user accounts",
"points": 0,
"status": "excluded",
"details": [
{
"code": "not_applicable_to_user_accounts",
"params": {}
}
],
"max_points": 20
},
{
"key": "owner_reach",
"name": "Owner reach",
"detail": "982 followers of chapmanb",
"points": 21.5,
"status": "partial",
"details": [
{
"code": "owner_followers",
"params": {
"count": 982,
"login": "chapmanb"
}
}
],
"max_points": 25
},
{
"key": "track_record",
"name": "Track record",
"detail": "121 public repos, account ~17 yr old",
"points": 25,
"status": "met",
"details": [
{
"code": "public_repos",
"params": {
"count": 121
}
},
{
"code": "account_age_years",
"params": {
"years": 17
}
}
],
"max_points": 25
}
]
},
{
"key": "package_maintenance",
"band": "moderate",
"name": "Package maintenance",
"note": null,
"notes": [],
"value": 69,
"inputs": {
"packages": [
"bcbio-gff"
],
"ecosystems": "pypi",
"any_deprecated": false,
"min_days_since_publish": 904
},
"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"
}
}
],
"max_points": 25
},
{
"key": "publish_recency",
"name": "Publish recency",
"detail": "latest publish 904 days ago",
"points": 4,
"status": "partial",
"details": [
{
"code": "publish_recency",
"params": {
"days": 904
}
}
],
"max_points": 35
},
{
"key": "version_history",
"name": "Version history",
"detail": "15 published versions",
"points": 20,
"status": "met",
"details": [
{
"code": "published_versions",
"params": {
"count": 15
}
}
],
"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": "at_risk",
"name": "Engineering Quality",
"value": 36,
"weight": 0.2,
"metrics": [
{
"key": "engineering_practices",
"band": "critical",
"name": "Engineering practices",
"note": null,
"notes": [],
"value": 24,
"inputs": {
"has_ci": false,
"has_tests": true,
"has_editorconfig": false,
"has_linter_config": false,
"has_precommit_config": false
},
"components": [
{
"key": "ci_workflows",
"name": "CI workflows",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 24
},
{
"key": "tests_present",
"name": "Tests present",
"detail": null,
"points": 24,
"status": "met",
"details": [],
"max_points": 24
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{
"key": "linter_config",
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"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 16
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{
"key": "pre_commit_hooks",
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"detail": null,
"points": 0,
"status": "missed",
"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",
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"points": 0,
"status": "missed",
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"max_points": 20
}
]
},
{
"key": "documentation",
"band": "moderate",
"name": "Documentation",
"note": null,
"notes": [],
"value": 55,
"inputs": {
"topics": [],
"has_wiki": false,
"homepage": "http://bcbio.wordpress.com",
"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": "http://bcbio.wordpress.com",
"points": 15,
"status": "met",
"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": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "wiki",
"name": "Wiki",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
}
],
"description": "Are baseline engineering and documentation practices in place?"
},
{
"key": "security",
"band": "at_risk",
"name": "Security",
"value": 43,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "critical",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): Dangerous-Workflow, Packaging, Pinned-Dependencies, Signed-Releases, Token-Permissions. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
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"packaging",
"pinned_dependencies",
"signed_releases",
"token_permissions"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 29,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 13,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 5,
"scorecard_aggregate": 2.9
},
"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": "branch protection not enabled on development/release branches",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "0 out of 9 merged PRs checked by a CI test -- score normalized to 0",
"points": 0,
"status": "missed",
"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 9/20 approved changesets -- score normalized to 4",
"points": 3,
"status": "partial",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 25 contributing companies or organizations",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "dangerous_workflow",
"name": "Dangerous-Workflow",
"detail": "no workflows found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "no update tool detected",
"points": 0,
"status": "missed",
"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 not detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
"name": "Packaging",
"detail": "packaging workflow not detected",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "sast",
"name": "SAST",
"detail": "SAST tool is not run on all commits -- score normalized to 0",
"points": 0,
"status": "missed",
"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": "No tokens found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "0 existing vulnerabilities detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
}
]
},
{
"key": "dependency_advisories",
"band": "excellent",
"name": "Dependency advisories",
"note": "Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:bcbio-gff@0.7.1 runtime dependency closure — what installing the published package pulls in — 3 packages. Reachability is not analyzed.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
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]
}
},
{
"code": "weights_renormalized",
"params": {}
},
{
"code": "advisories_scope_published",
"params": {
"package": "pypi:bcbio-gff@0.7.1",
"assessed": 3
}
},
{
"code": "advisories_reachability",
"params": {}
}
],
"value": 100,
"inputs": {
"source": "osv",
"advisories": 0,
"affected_packages": 0,
"assessed_packages": 3,
"unassessed_packages": 0,
"affected_by_severity": "none",
"direct_affected_packages": 0
},
"components": [
{
"key": "direct_dependencies_free_of_known_advisories",
"name": "Direct dependencies free of known advisories",
"detail": "no direct dependency carries a known advisory",
"points": 35,
"status": "met",
"details": [
{
"code": "no_direct_advisories",
"params": {}
}
],
"max_points": 35
},
{
"key": "indirect_dependencies_free_of_known_advisories",
"name": "Indirect dependencies free of known advisories",
"detail": "no indirect dependency carries a known advisory",
"points": 25,
"status": "met",
"details": [
{
"code": "no_indirect_advisories",
"params": {}
}
],
"max_points": 25
},
{
"key": "no_advisories_left_outstanding",
"name": "No advisories left outstanding",
"detail": "no advisory carries a publication date",
"points": 0,
"status": "excluded",
"details": [
{
"code": "advisories_no_publication_date",
"params": {}
}
],
"max_points": 40
}
]
},
{
"key": "malicious_dependencies",
"band": "excellent",
"name": "Malicious dependencies",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"source": "osv",
"meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
"packages": [],
"red_flag": false,
"assessed_packages": 3,
"malicious_packages": 0,
"direct_malicious_packages": 0,
"withdrawn_malicious_packages": 0,
"installable_malicious_packages": 0
},
"components": [
{
"key": "no_dependency_reported_as_a_malicious_package",
"name": "No dependency reported as a malicious package",
"detail": "no dependency is reported as a malicious package",
"points": 100,
"status": "met",
"details": [
{
"code": "no_malicious_dependencies",
"params": {}
}
],
"max_points": 100
}
]
},
{
"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": 19
},
"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": "at_risk",
"name": "AI Readiness",
"value": 37,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "critical",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 16,
"inputs": {
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"legible_history_share": 0.3,
"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": "30 of 100 human commits state their intent (structured subject or explanatory body)",
"points": 16,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 30,
"sampled": 100
}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
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"note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
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}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 44,
"inputs": {
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"has_tests": true,
"lockfiles": [],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [
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"abstracts/bosc_2017_bcbio_integration/Makefile",
"abstracts/bosc_2018_bcbio_validation/Makefile",
"abstracts/hackathon_workshop_2017/Makefile",
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"typecheck_configs": [],
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"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": "abstracts/bosc_2015_bcbio_prioritization/Makefile, abstracts/bosc_2016_bcbio_cwl/Makefile, abstracts/bosc_2017_bcbio_integration/Makefile, abstracts/bosc_2018_bcbio_validation/Makefile, abstracts/hackathon_workshop_2017/Makefile, nextgen/docs/Makefile, papers/bcbio-nextgen/Makefile",
"points": 18,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
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}
],
"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": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no agent-authored commits among the last 100",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_authored_commits",
"params": {
"sampled": 100
}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "no automated dependency updates observed",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_dependency_automation",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "moderate",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 55,
"inputs": {
"primary_language": "Python",
"largest_source_bytes": 70319,
"source_files_sampled": 186,
"oversized_source_files": 1
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Python without a type-check config",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_typecheck_config_language",
"params": {
"language": "Python"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "1/186 source files over 60KB",
"points": 54.7,
"status": "partial",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 186,
"oversized": 1
}
}
],
"max_points": 55
}
]
},
{
"key": "ai_interfaces",
"band": "at_risk",
"name": "Machine-readable interfaces",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"example_dirs": [
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"notebooks"
],
"has_mcp_signal": false,
"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": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "runnable_examples",
"name": "Runnable examples",
"detail": "examples, notebooks",
"points": 40,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "examples, notebooks"
}
}
],
"max_points": 40
}
]
}
],
"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": [
"pypi package 'bcbio-phyloblast' points at a different repository (http://bcbio.wordpress.com); excluded from ecosystem scoring"
],
"report_type": "repository",
"generated_at": "2026-07-21T23:48:23.672955Z",
"schema_version": "0.26.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/c/chapmanb/bcbb.svg",
"full_name": "chapmanb/bcbb",
"license_state": "absent",
"license_spdx": null
}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 v0.26.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.