Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-09 11:00 UTC

ryannduma / CrystaLyse.AI

Intelligent Scientific Agent for Materials Design

PythonMIT★ 24 stars⑂ 4 forkssince May 2025View on GitHub ↗
KindCommand-line toolLibraryNetwork serviceMCP serverhow this is determined
#agent#ai#ai4science#framework#llm#python

ryannduma/CrystaLyse.AI holds a health index of 67 out of 100, placing it in the Good band. It scores highest on Engineering Quality (96/100) and lowest on Community & Adoption (40/100). It was last updated 8 days ago. A single contributor accounts for most of its recent work.

67
overall / 100
Good

Software 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.

67
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)
VitalityCommunity &AdoptionSustainability &GovernanceEngineeringQualitySecurityAI Readiness

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 61 is calibrated to 67 on the published index scale (record calibration 2026-08-02).

Ownership

Ry NdumaPersonal account
39 followers47 public repossince Aug 2019@Cusp-AI

This repository is owned by a personal account. A single-owner project carries more continuity risk than an organization-backed one.

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIcrystalyse1.0.12371311 days agomaterials-designcrystal-structure-predictionformation-energycomputational-materials-scienceai-agentschemistryinorganic-materialsautonomous-agentsopenai-agentsmcp-serversprovenancecomputational-honesty

Metrics by category

Vitality

Is the project alive — is code being written and are releases shipping?

57Moderate · 21% of overall

Development activity

54Moderate
How it's scored
28.8/36Push recency — last push 8 days ago
6.9/36Commit cadence — 10/52 weeks with commits
18/18Commit volume — 103 commits in the last year
0/10OpenSSF Scorecard: Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
Inputs used
commits_last_year103
human_commit_share0.96
days_since_last_push8
active_weeks_last_year10

Release discipline

62Moderate
How it's scored
27/27Ships releases — 1 releases published
16.2/36Release recency — latest release 279 days ago
12.6/27Release cadence — cadence unknown (single release)
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count1
latest_release_tagv1.0.0
releases_from_tagsno
days_since_latest_release279
mean_days_between_releases—
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?

40Weak · 17% of overall

Popularity & adoption

26At Risk
How it's scored
22.1/60Stars — 24 stars
4/25Forks — 4 forks
0/15Watchers — 1 watchers
Inputs used
forks4
stars24
watchers1
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

57Moderate
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (MIT)
0/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
6.3/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges8
has_contributingno
has_issue_templateno
has_code_of_conductno
readme_badge_servicescodecov.io, github.com, readthedocs.org, shields.io
has_pull_request_templateyes

Ecosystem adoption (downloads)

40Weak
How it's scored
31.7/80Monthly downloads — 237 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packagescrystalyse
dependents—
ecosystemspypi
total_downloads—
monthly_downloads237
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?

54Moderate · 23% of overall

Maintainer resilience (bus factor)

15Critical
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
0.3/22.5Commit distribution — top contributor authored 99% of commits
2.7/13.5Contributor breadth — 2 contributors
3/10OpenSSF Scorecard: Contributors — project has 1 contributing companies or organizations -- score normalized to 3
Inputs used
bus_factor1
contributors_sampled2
top_contributor_share0.988

Issue & PR responsiveness

80Excellent
How it's scored
42/42Issue resolution — 100% of issues closed
25.8/30PR acceptance — 31/36 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
1.5/15OpenSSF Scorecard: Code-Review — Found 1/8 approved changesets -- score normalized to 1
Inputs used
merged_prs31
open_issues0
closed_issues3
prs_merged_7d0
prs_decided_7d0
prs_merged_30d0
prs_decided_30d0
issue_closed_ratio1
closed_unmerged_prs5
first_time_authors_30d0
first_time_prs_merged_30d0
first_time_prs_decided_30d0
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

57Moderate
How it's scored
10/30Ownership backing — personal (user) account
0/20Verified domain — not applicable to user accounts
11.5/25Owner reach — 39 followers of ryannduma
24.2/25Track record — 47 public repos, account ~7 yr old
Inputs used
followers39
owner_typeUser
is_verified—
owner_loginryannduma
public_repos47
account_age_days2,578
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.

Package maintenance

75Good
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
26/35Publish recency — latest publish 311 days ago
4/20Version history — 1 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagescrystalyse
ecosystemspypi
any_deprecatedno
min_days_since_publish311

Engineering Quality

Are baseline engineering and documentation practices in place?

96Exceptional · 19% of overall

Engineering practices

94Exceptional
How it's scored
24/24CI workflows — 1 workflow(s)
24/24Tests present
16/16Linter config — dev/pyproject.toml ([tool.ruff]), pypi-v2/pyproject.toml ([tool.ruff]), pyproject.toml ([tool.ruff])
9.6/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 12 out of 12 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configyes
has_precommit_configyes

Documentation

100Exceptional
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — https://crystalyseai.readthedocs.io/en/latest/
10/10Repository description
10/10Topics — 6 topics
10/10Wiki
Inputs used
topicsagent, ai, ai4science, framework, llm, python
has_wikiyes
homepagehttps://crystalyseai.readthedocs.io/en/latest/
docs_sitehttps://crystalyseai.readthedocs.io/en/latest/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?

54Moderate · 16% of overall

Security posture

42Weak
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — branch protection not enabled on development/release branches
2.5/2.5CI-Tests — 12 out of 12 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0.8/7.5Code-Review — Found 1/8 approved changesets -- score normalized to 1
0.8/2.5Contributors — project has 1 contributing companies or organizations -- score normalized to 3
10/10Dangerous-Workflow — no dangerous workflow patterns detected
7.5/7.5Dependency-Update-Tool — update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — license file detected
0/7.5Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
0/5Packaging — no data
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — no data
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
6.8/7.5Vulnerabilities — 1 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate4.1
Excluded from scoring (no data or not applicable): Packaging, Signed-Releases. Remaining weights renormalized.

Dependency advisories

100Exceptional
How it's scored
35/35Direct dependencies free of known advisories — no direct dependency carries a known advisory
25/25Indirect dependencies free of known advisories — no indirect dependency carries a known advisory
0/40No advisories left outstanding — no advisory carries a publication date
Inputs used
sourceosv
advisories0
affected_packages0
assessed_packages181
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:crystalyse@1.0.1 runtime dependency closure — what installing the published package pulls in — 181 packages. Reachability is not analyzed.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.

69Good · 4% of overall

Agent context & guidance

81Excellent
How it's scored
45/45Agent instructions — docs/concepts/agents.md
0/15Machine-readable docs (llms.txt)
35.6/40Legible commit history — 64 of 96 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share0.667
agent_instruction_filesdocs/concepts/agents.md
agent_instruction_max_bytes12,284

Verify loop (build / test / typecheck)

69Good
How it's scored
18/18One-command bootstrap — Makefile
22/22Automated tests
11/11Lint / format config — dev/pyproject.toml ([tool.ruff]), pypi-v2/pyproject.toml ([tool.ruff]), pyproject.toml ([tool.ruff])
0/11Static type checking
0/10Reproducible environment
10/10Demonstrated agent practice — 13 of the last 100 commits agent-authored or agent-credited
8/8Automated maintenance — 4 of the last 100 commits are automated dependency updates
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfiles—
has_dockerfileno
typed_languageno
bootstrap_filesMakefile
has_devcontainerno
has_linter_configyes
typecheck_configs—
agent_commit_share0.13
toolchain_manifests—
dependency_bot_commit_share0.04

Code legibility for models

54Moderate
How it's scored
0/45Type-checkable code — Python without a type-check config
54.2/55Manageable file sizes — 3/217 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes67,979
source_files_sampled217
oversized_source_files3

Machine-readable interfaces

60Moderate
How it's scored
0/40API schema (OpenAPI/GraphQL/proto)
20/20MCP server
40/40Runnable examples — examples
Inputs used
example_dirsexamples
has_mcp_signalyes
api_schema_files—
interfaces_expected_ofnetwork-service

Key facts

24GitHub stars
2contributors
103commits, last 12 months
8days since last push
1releases
1bus factor
0open issues
PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
  • pypi download statistics for 'crystalyse' unavailable this scan (stats endpoint failed after retries); adoption may be under-evidenced
  • pypi download figures for crystalyse carried forward from the previous scan (stats endpoint unavailable this scan)
  • GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository

More detail

Star and fork history 0 ★ / 4 ⇿
0Stars
4Forks

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.

1223344422026-012026-012026-01
OpenSSF Scorecard 4.1 / 10
4.1aggregate

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).Scorecard v5.5.0 · 2026-09-09 11:00 UTC

10Binary-Artifactsno binaries found in the repo
0Branch-Protectionbranch protection not enabled on development/release branches
10CI-Tests12 out of 12 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
1Code-ReviewFound 1/8 approved changesets -- score normalized to 1
3Contributorsproject has 1 contributing companies or organizations -- score normalized to 3
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
0Maintained0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
n/aPackagingpackaging workflow not detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
9Vulnerabilities1 existing vulnerabilities detected
Direct dependencies 64
RegistryPackageVersion constraintManifest
PyPIopenai>=1.0.0dev/pyproject.toml
PyPIopenai-agents>=0.13.6,<0.14dev/pyproject.toml
PyPIpymatgen>=2024.1.0dev/pyproject.toml
PyPIase>=3.22.0dev/pyproject.toml
PyPInumpy>=1.24.0,<3.0.0dev/pyproject.toml
PyPIpandas>=2.0.0dev/pyproject.toml
PyPItyping-extensions>=4.5.0dev/pyproject.toml
PyPIpydantic>=2.0.0dev/pyproject.toml
PyPIasyncio>=3.4.3dev/pyproject.toml
PyPIrich>=13.0.0dev/pyproject.toml
PyPIclick>=8.1.0dev/pyproject.toml
PyPIprompt-toolkit>=3.0.0dev/pyproject.toml
PyPItyper>=0.12.0dev/pyproject.toml
PyPIchemeleon-dng@ git+https://github.com/hspark1212/chemeleon-dng.git@v0.1.2dev/pyproject.toml
PyPItorch>=2.1.0,<2.11dev/pyproject.toml
PyPIsmact>=2.7.0dev/pyproject.toml
PyPImace-torch>=0.3.0dev/pyproject.toml
PyPIopenai>=1.0.0pypi-v2/pyproject.toml
PyPIopenai-agents>=0.13.6,<0.14pypi-v2/pyproject.toml
PyPIpymatgen>=2024.1.0pypi-v2/pyproject.toml
PyPIase>=3.22.0pypi-v2/pyproject.toml
PyPIsmact>=3.0.0pypi-v2/pyproject.toml
PyPItorch>=2.1.0,<2.11pypi-v2/pyproject.toml
PyPImace-torch>=0.3.0pypi-v2/pyproject.toml
PyPIchemeleon-dng>=0.1.2pypi-v2/pyproject.toml
PyPIfastmcp>=0.5.0pypi-v2/pyproject.toml
PyPIpython-mcp>=1.0.0pypi-v2/pyproject.toml
PyPIfastapi>=0.104.0pypi-v2/pyproject.toml
PyPIuvicorn>=0.23.0pypi-v2/pyproject.toml
PyPIstarlette>=0.27.0pypi-v2/pyproject.toml
PyPInumpy>=1.24.0,<2.0.0pypi-v2/pyproject.toml
PyPIpandas>=2.0.0pypi-v2/pyproject.toml
PyPIscipy>=1.11.0pypi-v2/pyproject.toml
PyPItyping-extensions>=4.5.0pypi-v2/pyproject.toml
PyPIpydantic>=2.0.0pypi-v2/pyproject.toml
PyPIclick>=8.1.0pypi-v2/pyproject.toml
PyPItyper>=0.12.0pypi-v2/pyproject.toml
PyPIrich>=13.0.0pypi-v2/pyproject.toml
PyPIprompt-toolkit>=3.0.0pypi-v2/pyproject.toml
PyPIasyncio>=3.4.3pypi-v2/pyproject.toml
PyPIhttpx>=0.24.0pypi-v2/pyproject.toml
PyPIwebsockets>=11.0.0pypi-v2/pyproject.toml
PyPIrequests>=2.31.0pypi-v2/pyproject.toml
PyPItqdm>=4.66.0pypi-v2/pyproject.toml
PyPIPyYAML>=6.0.0pypi-v2/pyproject.toml
PyPItoml>=0.10.0pypi-v2/pyproject.toml
PyPIpython-dotenv>=1.0.0pypi-v2/pyproject.toml
PyPIopenai>=1.0.0pyproject.toml
PyPIopenai-agents>=0.13.6,<0.14pyproject.toml
PyPIpymatgen>=2024.1.0pyproject.toml
PyPIase>=3.22.0pyproject.toml
PyPInumpy>=1.24.0pyproject.toml
PyPIpandas>=2.0.0pyproject.toml
PyPItyping-extensions>=4.5.0pyproject.toml
PyPIpydantic>=2.0.0pyproject.toml
PyPIasyncio>=3.4.3pyproject.toml
PyPIrich>=13.0.0pyproject.toml
PyPIclick>=8.1.0pyproject.toml
PyPIprompt-toolkit>=3.0.0pyproject.toml
PyPItyper>=0.12.0pyproject.toml
PyPIchemeleon-dng@ git+https://github.com/hspark1212/chemeleon-dng.git@v0.1.2pyproject.toml
PyPItorch>=2.1.0,<2.11pyproject.toml
PyPIsmact>=2.7.0pyproject.toml
PyPImace-torch>=0.3.0pyproject.toml
All dependencies not collected

The resolved dependency set could not be collected for this report: GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository

Dependency advisories 0

Installing pypi:crystalyse@1.0.1 pulls in 181 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

Feedback

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Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.

Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v2.10.0, schema v0.34.0 — full methodology · metrics wiki.

How one result sits in the wider record: aggregate statistics — PyPI.