Registro públicoModerado
Informe de salud del softwareesquema 0.27.0 · métricas 1.13.0 · 2026-07-28 03:35 UTC
N283T / zsasa
High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings
N283T/zsasa tiene un índice de salud de 63 sobre 100, lo que lo sitúa en la banda Moderado. Su puntuación más alta es Vitality (82/100) y la más baja, Security (42/100). Se actualizó por última vez hoy. Una sola persona concentra la mayor parte del trabajo reciente.
63
global / 100Índice de salud del software
Las métricas se agrupan en categorías ponderadas sobre una escala de 1 a 100. El resultado global parte de su media; cuando la evidencia pública activa la Política de Jurisdicciones de Alto Riesgo, la calificación se ajusta y recibe el límite 49 (En riesgo). Preparación para IA queda fuera.
63
Excelente85-100Ejemplar; cumple prácticamente todos los criterios evaluados
Bueno70-84Saludable; carencias menores
Moderado50-69Aceptable con carencias notables; se recomienda revisión
En riesgo30-49Debilidades significativas; su adopción exige cautela
Crítico1-29Problemas graves (proyecto abandonado, un solo mantenedor, sin higiene)
Perfil de puntuación
Cada eje es una categoría. La forma importa más que la media: un proyecto sano llena toda la figura, mientras que un perfil de picos y cráteres indica que la fortaleza en una dimensión enmascara el riesgo en otra.
Titularidad
N283TCuenta personal
22 seguidores44 repositorios públicosdesde nov 2023
Este repositorio pertenece a una cuenta personal. Un proyecto con un único propietario conlleva más riesgo de continuidad que uno respaldado por una organización.
Ecosistemas de paquetes
| Registro | Paquete | Versión | Descargas / mes | Versiones | Última publicación |
|---|---|---|---|---|---|
| PyPI | zsasa | 0.9.1 | - | 23 | hace 0 días |
Métricas por categoría
Vitalidad
¿Está vivo el proyecto: se escribe código y se publican versiones?
82
Actividad de desarrollo
76Bueno
Cómo se puntúa
| 36/36 | Recencia de push — último push hace 0 días |
| 12.5/36 | Cadencia de commits — 18/52 semanas con commits |
| 18/18 | Volumen de commits — 896 commits en el último año |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
Datos de entrada utilizados
| commits_last_year | 896 |
| human_commit_share | 1 |
| days_since_last_push | 0 |
| active_weeks_last_year | 18 |
Disciplina de publicación
90Excelente
Cómo se puntúa
| 27/27 | Publica versiones — 24 versiones publicadas |
| 36/36 | Recencia de las versiones — última versión hace 0 días |
| 27/27 | Cadencia de publicación — una versión cada ~8 días |
| 0/10 | OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases. |
Datos de entrada utilizados
| releases_count | 24 |
| latest_release_tag | v0.9.1 |
| releases_from_tags | no |
| days_since_latest_release | 0 |
| mean_days_between_releases | 8 |
Comunidad y Adopción
¿Tiene el proyecto usuarios, descargas, atención y unas condiciones acogedoras para quienes contribuyen?
51
Popularidad y adopción
15Crítico
Cómo se puntúa
| 14.6/60 | Estrellas — 9 estrellas |
| 0/25 | Forks — 0 forks |
| 0/15 | Observadores — 1 observadores |
Datos de entrada utilizados
| forks | 0 |
| stars | 9 |
| watchers | 1 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Salud de la comunidad
92Excelente
Cómo se puntúa
| 22.5/22.5 | README |
| 22.5/22.5 | Licencia — licencia reconocida (MIT) |
| 18/18 | Guía CONTRIBUTING |
| 13.5/13.5 | Código de conducta |
| 0/7.2 | Plantilla de issues |
| 6.3/6.3 | Plantilla de PR |
Datos de entrada utilizados
| has_readme | sí |
| has_license | sí |
| has_contributing | sí |
| has_issue_template | no |
| has_code_of_conduct | sí |
| has_pull_request_template | sí |
Sostenibilidad y Gobernanza
¿Sobrevivirá el proyecto a sus personas: factor bus, capacidad de respuesta, quién lo respalda y mantenimiento del paquete?
55
Cómo se puntúa
| 9/54 | Factor bus — la mitad de los commits recae en 1 contribuyente(s) |
| 0/22.5 | Distribución de commits — el principal contribuyente firma el 100% de los commits |
| 1.4/13.5 | Amplitud de contribuyentes — 1 contribuyentes |
| 0/10 | OpenSSF Scorecard: Contributors — project has 0 contributing companies or organizations -- score normalized to 0 |
Datos de entrada utilizados
| bus_factor | 1 |
| contributors_sampled | 1 |
| top_contributor_share | 1 |
Cómo se puntúa
| 44.7/46.8 | Resolución de issues — 96% de issues cerradas |
| 37.6/38.3 | Aceptación de PR — 376/382 PR decididos fusionados |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
Datos de entrada utilizados
| merged_prs | 376 |
| open_issues | 1 |
| closed_issues | 22 |
| issue_closed_ratio | 0,957 |
| closed_unmerged_prs | 6 |
Propiedad y custodia
47En riesgo
Cómo se puntúa
| 10/30 | Respaldo de la propiedad — cuenta personal (usuario) |
| 0/20 | Dominio verificado — no aplicable a cuentas de usuario |
| 9.8/25 | Alcance del propietario — 22 seguidores de N283T |
| 17.5/25 | Trayectoria — 44 repos públicos, cuenta de ~2 años |
Datos de entrada utilizados
| followers | 22 |
| owner_type | User |
| is_verified | — |
| owner_login | N283T |
| public_repos | 44 |
| account_age_days | 995 |
Excluidos de la puntuación (sin datos o no aplicable): Dominio verificado. Los pesos restantes se han renormalizado.
Mantenimiento de paquetes
100Excelente
Cómo se puntúa
| 25/25 | Publicado y resoluble — 1 paquete(s) en pypi |
| 35/35 | Recencia de publicación — última publicación hace 0 días |
| 20/20 | Historial de versiones — 23 versiones en el registro |
| 20/20 | No obsoleto — activo, ni obsoleto ni retirado |
Datos de entrada utilizados
| packages | zsasa |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 0 |
Calidad de Ingeniería
¿Existen unas prácticas mínimas de ingeniería y documentación?
80
Prácticas de ingeniería
66Moderado
Cómo se puntúa
| 24/24 | Flujos de trabajo de CI — 3 flujo(s) de trabajo |
| 24/24 | Pruebas presentes |
| 0/16 | Configuración de linter |
| 0/9.6 | Hooks de pre-commit |
| 0/6.4 | .editorconfig |
| 18/20 | OpenSSF Scorecard: CI-Tests — 27 out of 28 merged PRs checked by a CI test -- score normalized to 9 |
Datos de entrada utilizados
| has_ci | sí |
| has_tests | sí |
| has_editorconfig | no |
| has_linter_config | no |
| has_precommit_config | no |
Documentación
100Excelente
Cómo se puntúa
| 30/30 | README |
| 25/25 | Directorio de documentación |
| 15/15 | Sitio de documentación / página del proyecto — https://n283t.github.io/zsasa/ |
| 10/10 | Descripción del repositorio |
| 10/10 | Topics — 5 topics |
| 10/10 | Wiki |
Datos de entrada utilizados
| topics | bioinformatics, python, sasa, structural-biology, zig |
| has_wiki | sí |
| homepage | https://n283t.github.io/zsasa/ |
| has_readme | sí |
| has_docs_dir | sí |
| has_description | sí |
Seguridad
¿Son sólidas las prácticas visibles de seguridad y de cadena de suministro, sin exposición jurisdiccional de alto riesgo sin resolver?
42
Postura de seguridad
42En riesgo
Cómo se puntúa
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — sin datos |
| 2.2/2.5 | CI-Tests — 27 out of 28 merged PRs checked by a CI test -- score normalized to 9 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
| 0/2.5 | Contributors — project has 0 contributing companies or organizations -- score normalized to 0 |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | Licencia — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 1/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 2 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 5/5 | Security-Policy — security policy file detected |
| 0/7.5 | Signed-Releases — Project has not signed or included provenance with any releases. |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 0/7.5 | Vulnerabilities — 43 existing vulnerabilities detected |
Datos de entrada utilizados
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 4,2 |
Excluidos de la puntuación (sin datos o no aplicable): branch_protection. Los pesos restantes se han renormalizado.
Preparación para IA
¿Hasta qué punto está el repositorio preparado para desarrollarse y mantenerse con agentes de codificación de IA? Es una insignia independiente y experimental — peso 0,0, de modo que se presenta por separado y no afecta a la puntuación de salud global.
69
Contexto y guía para agentes
85Excelente
Cómo se puntúa
| 45/45 | Instrucciones para agentes — AGENTS.md |
| 0/15 | Documentación legible por máquinas (llms.txt) |
| 40/40 | Historial de commits legible — 99 de 100 commits humanos declaran su intención (asunto estructurado o cuerpo explicativo) |
Datos de entrada utilizados
| has_llms_txt | no |
| legible_history_share | 0,99 |
| agent_instruction_files | AGENTS.md |
| agent_instruction_max_bytes | 6650 |
Cómo se puntúa
| 18/18 | Arranque con un solo comando — benchmarks/external/freesasa_batch/Makefile |
| 22/22 | Pruebas automatizadas |
| 0/11 | Configuración de lint / formato |
| 11/11 | Verificación estática de tipos — website/tsconfig.json |
| 10/10 | Entorno reproducible — Dockerfile, Nix, lockfile |
| 0/10 | Práctica demostrada con agentes — ningún commit con autoría de agente entre los últimos 100 |
| 0/8 | Mantenimiento automatizado — no se observan actualizaciones automáticas de dependencias |
| 2/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 2 |
Datos de entrada utilizados
| has_nix | sí |
| has_tests | sí |
| lockfiles | package-lock.json, uv.lock |
| has_dockerfile | sí |
| typed_language | no |
| bootstrap_files | benchmarks/external/freesasa_batch/Makefile |
| has_devcontainer | no |
| has_linter_config | no |
| typecheck_configs | website/tsconfig.json |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Cómo se puntúa
| 27/45 | Código verificable por tipos — Zig con configuración de verificación de tipos (website/tsconfig.json) |
| 55/55 | Tamaños de archivo manejables — 0/70 archivos fuente de más de 60 KB |
Datos de entrada utilizados
| primary_language | Zig |
| largest_source_bytes | 37.433 |
| source_files_sampled | 70 |
| oversized_source_files | 0 |
Interfaces legibles por máquina
40En riesgo
Cómo se puntúa
| 0/40 | Esquema de API (OpenAPI/GraphQL/proto) |
| 0/20 | Servidor MCP |
| 40/40 | Ejemplos ejecutables — examples |
Datos de entrada utilizados
| example_dirs | examples |
| has_mcp_signal | no |
| api_schema_files | — |
Datos clave
9estrellas de GitHub
1contribuidores
896commits en los últimos 12 meses
0días desde el último push
24versiones publicadas
1factor bus
1issues abiertas
npm, PyPIecosistemas de paquetes
Advertencias de recopilación de datos
- Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
- GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository
- deps.dev does not index pypi:zsasa@0.9.1; advisories assessed against the repository dependency graph instead
Más detalle
OpenSSF Scorecard 4.2 / 10
4.2agregado
Evaluación de seguridad independiente y agnóstica en cuanto a herramientas, procedente del proyecto de código abierto OpenSSF Scorecard. Cada comprobación premia una práctica de seguridad, no la herramienta de un proveedor concreto. Las comprobaciones que Scorecard no pudo determinar se marcan como n/d y se excluyen de la puntuación de seguridad (nunca se cuentan como cero).
| 10 | Binary-Artifacts | no binaries found in the repo |
| n/d | 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 |
| 9 | CI-Tests | 27 out of 28 merged PRs checked by a CI test -- score normalized to 9 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 0/30 approved changesets -- score normalized to 0 |
| 0 | Contributors | project has 0 contributing companies or organizations -- score normalized to 0 |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 2 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 2 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 10 | Security-Policy | security policy file detected |
| 0 | Signed-Releases | Project has not signed or included provenance with any releases. |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 0 | Vulnerabilities | 43 existing vulnerabilities detected |
Dependencias directas 7
| Registro | Paquete | Restricción de versión | Manifiesto |
|---|---|---|---|
| PyPI | numpy | >=1.24 | python/pyproject.toml |
| PyPI | cffi | >=1.15 | python/pyproject.toml |
| npm | @docusaurus/core | ^3.7 | website/package.json |
| npm | @docusaurus/preset-classic | ^3.7 | website/package.json |
| npm | prism-react-renderer | ^2.4 | website/package.json |
| npm | react | ^19.0 | website/package.json |
| npm | react-dom | ^19.0 | website/package.json |
Todas las dependencias no recopilado
No fue posible recopilar el conjunto de dependencias resuelto para este informe: GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository
Informe JSON sin procesar legible por máquina
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"headline": "fix: gate inline CCD parsing (#392)",
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"headline": "fix: optimize multichain workflow parsing (#385)",
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"headline": "feat: allow batch thread overcommit (#384)",
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"headline": "docs: refresh benchmark website (#381)",
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"headline": "docs: recommend pyztraj for Python trajectory I/O (#379)",
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"headline": "feat: reuse parsed inputs across workflow jobs (#374)",
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"headline": "fix: use inline CCD from BinaryCIF (#373)",
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"is_bot": false,
"headline": "Add BinaryCIF input support (#372)",
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"headline": "feat: add adaptive bitmask batch mode (#371)",
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"headline": "docs: restructure website docs (#370)",
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"headline": "chore: add agent instructions and ignore local docs (#367)",
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"body": "* docs: design workflow manifest\n\n* docs: plan workflow manifest implementation\n\n* feat: add workflow manifest parser\n\n* fix: reject duplicate workflow manifest keys\n\n* fix: detect empty duplicate workflow sections\n\n* feat: require TOML custom classifiers\n\n* fix: tighten legacy classifier config rej\n[…]\nkflow classifier docs\n\n* fix: include workflow manifest read errors\n\n* test: add workflow smoke fixtures\n\n* fix: create calc workflow output directories\n\n* fix: honor calc classifier workflow override",
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"headline": "[codex] add workflow manifest support (#366)",
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"body": "* docs: specify batch JSONL residue map\n\n* feat: add JSONL residue map serialization\n\n* feat: parse batch residue map option\n\n* feat: validate residue map JSONL format\n\n* feat: stream residue map JSONL rows\n\n* feat: build residue maps for batch results\n\n* docs: document batch residue map output\n\n* refactor: rename batch JSONL row helper",
"is_bot": false,
"headline": "[codex] Add batch JSONL residue map output (#364)",
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"headline": "release: v0.3.1 (#362)",
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"body": "* docs: design batch manifest\n\n* docs: plan batch manifest implementation\n\n* feat: parse manifest TOML values\n\n* fix: clean up TOML parser allocations\n\n* fix: clean up inline TOML values\n\n* feat: parse batch manifests\n\n* feat: parse batch manifest options\n\n* feat: filter batch inputs by chain\n\n* feat: run batch manifests\n\n* fix: validate batch manifest numeric options\n\n* fix: preserve CLI auth-chain override\n\n* docs: document batch manifests\n\n* docs: clarify batch manifest usage",
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"body": "## [0.3.0] - 2026-05-17\n\n### Added\n\n- **Zstandard decompression for structure inputs**: `.json.zst`, `.pdb.zst`, `.cif.zst`, `.mmcif.zst`, `.ent.zst`, `.sdf.zst`, and `.mol.zst` are now detected and transparently decompressed via native `std.compress.zstd`. (#357)\n\n### Changed\n\n- **CLI progress bars\n[…]\n` and `traj`, reducing custom rendering logic while preserving progress reporting. (#358)\n- **Project branding documentation**: add the project logo to README and refresh logo SVG assets. (#355, #356)",
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"body": "* docs: add CLI progress bars design\n\n* feat: use std progress for CLI progress bars\n\n* fix: let quiet mode override progress display",
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"headline": "[codex] use std progress for CLI progress bars (#358)",
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"oid": "a85e52fc2f9e36182fa5fca352e1ad9bd922cd56",
"body": "* feat: add zstd compressed input support\n\n* fix: allow exact decompression size limit",
"is_bot": false,
"headline": "[codex] add zstd compressed input support (#357)",
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"body": "docs: update logo SVG assets",
"is_bot": false,
"headline": "Merge pull request #356 from N283T/codex/update-logo-svg",
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"committed_at": "2026-05-04T15:43:45Z",
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"is_bot": false,
"headline": "docs: update logo svg assets",
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"oid": "2ec53d9efeabfffb5894970d079cb426e4ed4472",
"body": "docs: add project logo",
"is_bot": false,
"headline": "Merge pull request #355 from N283T/codex/add-logo-readme",
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"headline": "docs: add project logo",
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"committed_at": "2026-05-04T15:29:29Z",
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"oid": "63a9241e965e3f0a9f79519cc9b10a8e431a5eaf",
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"headline": "release: v0.2.11 (#354)",
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"committed_at": "2026-04-26T12:43:16Z",
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{
"oid": "e02b8cd68cc7d3bbb4ef42c0eb596d235f36d1a3",
"body": "The Build & Publish workflow has been silently broken since v0.2.9 because\nPR1 missed several Zig version pins outside build.zig.zon / flake.nix /\n.github/workflows/. v0.2.10's wheel/Docker publish surfaced these plus\ntwo follow-on issues.\n\nChanges:\n\n- **Bump Zig 0.15.2 → 0.16.0 in 9 files** missed \n[…]\neamTooLong errors on benign reads (broke\n the Windows wheel test for examples/1ubq.cif). For trusted local input\n files .unlimited is acceptable; mmapFile callers already trust the path.\n\nRefs: #342",
"is_bot": false,
"headline": "fix: clean up Zig 0.15.2 pins and Windows mmap reader regression (#353)",
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"committed_at": "2026-04-26T12:36:54Z",
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{
"oid": "01a96229a483c444e3f005aec25a46f1d4e5ab85",
"body": "- Bump version in build.zig, build.zig.zon, python/pyproject.toml, python/uv.lock\n- Bump flake.nix derivation version from 0.2.4 → 0.2.10 (catches up the stale Nix derivation field that previous releases missed)\n- CHANGELOG entry for the gzip → native std.compress.flate revert (#351)\n\nRefs: #342",
"is_bot": false,
"headline": "release: v0.2.10 (#352)",
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"committed_at": "2026-04-26T12:17:47Z",
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"oid": "3691a63be747ada9d816816e8803fce10f4a3725",
"body": "* fix: revert gzip to native std.compress.flate\n\nThe upstream panic (ziglang/zig#25035) that prompted #320's C-zlib workaround\nis fixed in Zig 0.16. Restore the native flate decompressor while preserving\nthe 4 GB decompression-bomb cap and the public API (readGzip / readGzipLimited\n/ DEFAULT_MAX_SIZ\n[…]\ns without\n.link_libc; on Linux the explicit flag is mandatory and removing it\nbroke the Linux jobs in CI for #351.\n\nThe CLI executable does not need libc — it uses GeneralPurposeAllocator.\n\nRefs: #342",
"is_bot": false,
"headline": "fix: revert gzip to native std.compress.flate (#351)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T12:06:16Z",
"body_truncated": true,
"is_coding_agent": false
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{
"oid": "c323fd4a82fb379d981f73bd365a7518eb1c5290",
"body": "Implementation plan for reverting the C-zlib gzip workaround introduced\nin #320 back to native std.compress.flate. Covers the 3-commit sequence\nfrom the migration spec (rewrite gzip.zig, drop zlib from build.zig,\ndrop zlib from build.zig.zon) plus full verification matrix including\nthe 2oxd.cif.gz headline check.\n\nRefs: #342",
"is_bot": false,
"headline": "docs: add Zig 0.16 migration PR2 plan (#350)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T11:26:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "aaa726c6f5dfce4e27823ae6c0b0c27154bd86f5",
"body": null,
"is_bot": false,
"headline": "release: v0.2.9 (#349)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T11:04:00Z",
"body_truncated": false,
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},
{
"oid": "9bb95928ac4d27f9564b8fa25c7e3a7c71f22038",
"body": "* chore: bump toolchain to Zig 0.16.0\n\n* refactor: introduce Io.Threaded in main and thread io through subcommands\n\nConstruct one std.Io.Threaded (.init_single_threaded) in main() and\nthread std.Io through to calc.run, batch.run, traj.run, and\ncompile_dict.run. Subcommand handlers accept io as a stu\n[…]\nexpand wrapper comment to explain why zlib_wrapper.h exists\n (addTranslateC requires b.path(), not a dependency lazy path)\n- src/c/zlib_wrapper.h: add one-line rationale comment referencing build.zig",
"is_bot": false,
"headline": "chore: migrate to Zig 0.16 (#345)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T10:53:45Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "27729b29732ec5b4dd4f714330f3d663d61df617",
"body": "* docs: add Zig 0.16 migration design spec\n\nTwo-PR plan to migrate zsasa from Zig 0.15.2 to 0.16.0 (issue #342):\n- PR1: toolchain bump + 0.16 API migration\n- PR2: revert gzip C-zlib workaround to native std.compress.flate\n\nEach PR ships independently as a patch release.\n\n* docs: add Zig 0.16 migrati\n[…]\nontainer conversion, @cImport relocation, float-to-int audit,\nand verification (build/test/smoke matrix/python bindings).\n\nRefs #342, spec docs/superpowers/specs/2026-04-26-zig-016-migration-design.md",
"is_bot": false,
"headline": "docs: add Zig 0.16 migration spec and PR1 plan (#344)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T06:11:07Z",
"body_truncated": true,
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},
{
"oid": "8e52d97019d39f4c888d34a28b7e8882b97ad077",
"body": "fix: bump python/pyproject.toml to 0.2.8",
"is_bot": false,
"headline": "Merge pull request #341 from N283T/fix/release-version-sync",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T12:58:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "db0f334e19827abb877e26d38e2fb9bcba5a2053",
"body": "Was missed in the v0.2.8 release, causing PyPI publish to fail\n(wheels were built as 0.2.7, which already exists on PyPI).",
"is_bot": false,
"headline": "fix: bump python/pyproject.toml version to 0.2.8",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T12:55:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ebe977d31458eef1dc6d29ac8b0f99d295dd98da",
"body": "release: v0.2.8",
"is_bot": false,
"headline": "Merge pull request #340 from N283T/release/v0.2.8",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T05:28:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ac84e00aeb1284204d6f5f788f94214cced16828",
"body": "- SDF/MOL file support (V2000/V3000)\n- --sdf option for CCD-unregistered compounds\n- --mol option for molecule selection\n- Batch SDF expansion (per-molecule SASA)\n- ProtOr as CCD alias, Python CCD default\n- Memory safety fixes",
"is_bot": false,
"headline": "release: v0.2.8",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:59:33Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d23483be880239efbe98fc32e125088df16a3459",
"body": "fix: process SDF molecules independently",
"is_bot": false,
"headline": "Merge pull request #339 from N283T/fix/sdf-per-molecule",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:54:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9588f651a82ebb089e4fc1dfac9bde1cad0cc95e",
"body": "- C1: Log warnings on SDF read/parse failures in buildWorkItems\n- I1+I2: Log warnings for toStoredComponent and dict allocation failures\n in processOneSdfMolecule instead of silently discarding errors\n- I3: Initialize result slot on double alloc failure in parallelWorker\n- I4: Free display_name str\n[…]\nlecules in selectMolecule\n- M3: Move doc comment to correct function (runBatchSequential)\n- M4: Warn when display name fallback to filename occurs\n- M5: Mention 1-based indexing in --mol error message",
"is_bot": false,
"headline": "fix: address review issues for SDF per-molecule processing",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:44:46Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "d2edf1c32fd9063be95bf081a61a0d14d65cb44c",
"body": "Multi-molecule SDF files previously combined all molecules into a single\nAtomInput (as chains A, B, C...), causing inter-molecule SASA interference.\n\ncalc: add --mol=NAME|N option to select a specific molecule; default to\nfirst molecule with a warning when multiple exist.\n\nbatch: expand each SDF fil\n[…]\n every molecule\ngets its own independent SASA calculation. Output files use stem_molname\nformat (e.g., two_molecules_water.json).\n\nsdf_parser: add test for single-molecule slice usage via toAtomInput.",
"is_bot": false,
"headline": "fix: process SDF molecules independently instead of as one structure",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:28:45Z",
"body_truncated": true,
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},
{
"oid": "6b1d6ba44144f7750b93e72e1a4ae593545a31a5",
"body": "feat: add SDF/MOL file support",
"is_bot": false,
"headline": "Merge pull request #338 from N283T/feature/sdf-support",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T04:05:57Z",
"body_truncated": false,
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{
"oid": "b23a55467f5b76da73dbddb566a5afaf006a5825",
"body": "PR #337 changed the default classifier from NACCESS to CCD in\nPython bindings, but tests were not updated. Fix:\n- Update expected radii to CCD values (ALA:O 1.42, not 1.40)\n- Add explicit NACCESS classifier to NACCESS-specific tests\n- Add CCD-specific test for unknown residue behavior (returns None)",
"is_bot": false,
"headline": "fix: update Python classifier tests for CCD default",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T03:59:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "11d53880291291a721a146960d05315a5977b1b9",
"body": "- C1: Fix toAtomInput over-allocation when >26 molecules by computing\n max_chains before the first-pass atom count\n- C2: Free StoredComponent on components.put failure in all locations\n- C3: Check for duplicate molecule names before inserting to avoid\n silent replacement and StoredComponent leak\n-\n[…]\nting double-free bug in parseSingleMolecule V3000 error\n path (errdefer freed name that parseV3000Body already owns)\n- Add tests: >26 molecules chain limit, V3000 bad bond index, bond\n order mapping",
"is_bot": false,
"headline": "fix: address critical and important issues from SDF PR review",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T03:52:20Z",
"body_truncated": true,
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},
{
"oid": "b077f976930c0009d3084356029cd27969203405",
"body": null,
"is_bot": false,
"headline": "docs: add SDF/MOL to supported input formats in README",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:40:11Z",
"body_truncated": false,
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{
"oid": "63bc9b270d14b3548aa3c154098158f50e958a29",
"body": "…traj\n\nAdd .sdf case to readInputFile in calc.zig and batch.zig, enabling\ndirect SDF file input with auto-format detection. Add --sdf=PATH CLI\noption to all three subcommands for loading external SDF bond topology\ninto the CCD classifier. SDF components from input files are\nauto-registered as CCD components (Task 9). The --sdf option can be\nspecified multiple times (up to 16 paths) and takes priority order:\nexplicit --sdf > auto-detected SDF > inline mmCIF > external CCD.",
"is_bot": false,
"headline": "feat: add SDF input support and --sdf CLI option to calc, batch, and …",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:36:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b6fc27254eded38ecdb02c94de2153aacb7ce9b7",
"body": "Add SDF and MOL file extensions to format detection so the system\ncan recognize .sdf, .sdf.gz, .mol, .mol.gz files (and uppercase\nvariants) and map them to the new `sdf` InputFormat variant.",
"is_bot": false,
"headline": "feat: add SDF/MOL format detection",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:27:18Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "16d66e8da766133ead440746d98b2bb3d653ca37",
"body": "Add two conversion functions to bridge SDF molecules with the CCD\nclassifier and SASA calculation pipeline:\n\n- toStoredComponent: converts SdfMolecule bond topology into a\n StoredComponent that the CCD classifier can use for hybridization\n analysis. Generates atom names as element+counter (C1, C2,\n[…]\nO1...).\n\n- toAtomInput: converts SDF molecules into AtomInput for SASA\n calculation. Each molecule maps to a separate chain (A-Z), with\n element VdW radii as defaults and optional hydrogen skipping.",
"is_bot": false,
"headline": "feat: add toStoredComponent and toAtomInput for SDF parser",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:25:53Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "9072e04c8ec3241cfc499a76ca39981346c854d2",
"body": "Replace the V3000 stub with a working parser that handles\nM V30 CTAB blocks including COUNTS, ATOM, and BOND sections.\nBond indices are converted from 1-based to 0-based with validation.",
"is_bot": false,
"headline": "feat: add SDF V3000 parser support",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:22:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0eb3203a1f18b13d68ebbe742c378de4f0f112f2",
"body": "- Free name allocation on premature EOF return-null paths to prevent leaks\n- Separate toOwnedSlice calls with errdefer to prevent atoms leak if bonds fail\n- Use idiomatic try+orelse instead of catch-return for parseSingleMolecule\n- Extract sdfBondOrder helper for reuse in future V3000 parser",
"is_bot": false,
"headline": "fix: resolve memory safety issues in SDF parser",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:19:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "53070e608ba5a5e204706c73629c92525ada89b2",
"body": "Implements core SDF parser (sdf_parser.zig) with:\n- V2000 atom block parsing (coordinates + element symbols)\n- V2000 bond block parsing (1-based to 0-based index conversion)\n- Multi-molecule SDF support (separated by $$$$)\n- MOL file compatibility (single molecule without $$$$)\n- CRLF line ending handling\n- V3000 detection stub (returns error.InvalidV3000)\n- Comprehensive error handling and 7 embedded tests",
"is_bot": false,
"headline": "feat: add SDF/MOL parser with V2000 support",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:13:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "beff839dbd074a0d0c1c0ace526299bb042a9e08",
"body": "…rmats",
"is_bot": false,
"headline": "test: add SDF test data files for V2000, V3000, and multi-molecule fo…",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:13:09Z",
"body_truncated": false,
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},
{
"oid": "4bbd6993f1fc1c8c5479a76ea86c0b57b64c80b1",
"body": "11-task plan covering:\n- SDF V2000/V3000 parser\n- Format detection\n- calc/batch/traj --sdf option\n- Auto CCD component registration for SDF input\n- Integration tests",
"is_bot": false,
"headline": "docs: add SDF support implementation plan",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T02:06:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c576e2df933922a93e152483d553aa9f03d211c6",
"body": "Design for two use cases:\n1. SDF as direct input file for SASA calculation\n2. --sdf option to provide bond topology for CCD-unregistered compounds",
"is_bot": false,
"headline": "docs: add SDF file support design spec",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:57:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "afd056a77780cbbff933adeaa504f4cca8446599",
"body": "feat: warn when --include-hydrogens used with CCD classifier",
"is_bot": false,
"headline": "Merge pull request #337 from N283T/feature/ccd-skip-hydrogens",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:39:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a9cdb555f84b22aa658becd20b6bcdcae39e7c7e",
"body": "MD trajectories typically contain explicit hydrogen atoms. CCD/ProtOr\nuse united-atom radii (implicit H), which causes double-counting with\nexplicit H. NACCESS handles explicit H via element fallback (H=1.10A).\n\n- Change traj default classifier from null to NACCESS\n- Update traj help text to explain the default\n- Update docs: Quick Recommendation shows per-command defaults\n- Simplify united-atom radii warning to recommend zsasa traj for MD",
"is_bot": false,
"headline": "feat: default traj classifier to NACCESS for MD trajectories",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:37:52Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fcdc1d518cf2c7dab57ff3eea67ce386107d7281",
"body": "CCD uses united-atom radii where heavy atom radii already account for\nimplicit hydrogens. Including explicit H atoms causes double-counting.\n\n- Add warning in calc.zig, batch.zig, traj.zig when CCD/ProtOr +\n --include-hydrogens is detected\n- Add docs warning about united-atom radii and explicit hydrogens\n- Document workarounds for MD trajectories with explicit H",
"is_bot": false,
"headline": "feat: warn when --include-hydrogens used with CCD classifier",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:34:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "621db008a8a835ca6f0e68cb63407cdb1c74fbc0",
"body": "docs: update classifier docs for ProtOr-CCD alias",
"is_bot": false,
"headline": "Merge pull request #336 from N283T/docs/protor-ccd-alias-update",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:34:25Z",
"body_truncated": false,
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},
{
"oid": "51b81e13b7fa7cdc9d8915c971a34ba92d79fd1a",
"body": "- CCD is now documented as default (not ProtOr)\n- ProtOr listed as alias for backward compatibility\n- Merge ProtOr/CCD Key Differences columns into single \"CCD (= ProtOr)\"\n- Update all code examples to use ClassifierType.CCD\n- Simplify CCD section intro (no longer contrasts with ProtOr)",
"is_bot": false,
"headline": "docs: update classifier docs to reflect ProtOr-CCD alias",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:27:24Z",
"body_truncated": false,
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},
{
"oid": "5b03d9e376d5593b9fd6f7b23e729c1826e8ab43",
"body": "refactor: make ProtOr an alias for CCD classifier",
"is_bot": false,
"headline": "Merge pull request #335 from N283T/refactor/protor-ccd-alias",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:25:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c648ddabe53b55ac0eeb54b24e85dec154b4a64b",
"body": "- Fix traj.zig parseClassifierType to use ClassifierType.fromString()\n (was hand-rolled parser that didn't accept \"ccd\")\n- Unify Python defaults to CCD across all modules:\n batch.py, biotite.py, biopython.py, gemmi.py\n- Fix calc.zig error message classifier ordering\n- Update c_api.zig constant comments (PROTOR = alias, CCD = default)",
"is_bot": false,
"headline": "fix: address review findings — traj parser, defaults, comments",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:24:51Z",
"body_truncated": false,
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},
{
"oid": "d4ea2fa4d513a94881f3aba39377c99232efd941",
"body": "ProtOr and CCD use identical radii for standard residues. CCD is a\nstrict superset that additionally handles non-standard residues via\nbond topology analysis. This removes the redundant classifier_protor.zig\nand routes all ProtOr lookups through CcdClassifier.\n\nChanges:\n- Delete src/classifier_proto\n[…]\nfrom protor to ccd\n- Update Python bindings default from NACCESS to CCD\n- HETATM auto-include remains ccd-only (no behavior change for protor users)\n- Update CLI help text and classifier documentation",
"is_bot": false,
"headline": "refactor: make ProtOr an alias for CCD classifier",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:17:51Z",
"body_truncated": true,
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},
{
"oid": "6460ee260163cbeee27c4baa0dd85bcef36c2d1c",
"body": "docs: rewrite CCD classifier section with accurate architecture",
"is_bot": false,
"headline": "Merge pull request #334 from N283T/docs/ccd-classifier-details",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:08:31Z",
"body_truncated": false,
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},
{
"oid": "34f9f2c6f680709e2835d6fe200f0794dd2e5000",
"body": "\"most comprehensive\" → \"unique to zsasa\" to convey that the CCD\nclassifier is an original feature not found in other SASA tools.",
"is_bot": false,
"headline": "docs: clarify CCD classifier as unique to zsasa",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:08:10Z",
"body_truncated": false,
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},
{
"oid": "e401d98ba5d554080961122365bd162ae927f1c8",
"body": "- Fix \"zsasa's original classifier\" → \"most comprehensive\" (CCD is newest)\n- Fix residue count 37 → 45 with accurate grouping (selenoamino acids,\n PTMs, modified nucleotide PSU)\n- Split OONS C sp2 row: carbonyl (1.55, polar) vs aromatic (1.75, apolar)\n- Fix hybridization examples to match actual de\n[…]\nr uses element fallback for non-standard residues, CCD does not)\n- Add per-classifier residue support breakdown\n- Add PSU to nucleic acids section\n- Add rationale for CCD recommended vs ProtOr default",
"is_bot": false,
"headline": "docs: fix review findings — radii table, residue count, examples",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T01:05:59Z",
"body_truncated": true,
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},
{
"oid": "fba5fe2d4be665348fc17cf3322cd62a7eb71f97",
"body": "- Fix misleading \"NACCESS: compatible with FreeSASA\" — FreeSASA defaults\n to ProtOr, not NACCESS\n- Fix code examples showing NACCESS as recommended/default\n- Replace simple radii table with detailed hybridization-based reference\n table covering C (sp2/sp3), N, O (sp2/sp3), S, Se, P\n- Merge ProtOr/CCD columns since they produce identical radii for\n standard residues\n- Add info box explaining ProtOr/CCD equivalence\n- Expand polarity warning to include Se and P (not just S)",
"is_bot": false,
"headline": "docs: fix NACCESS description, expand radii reference table",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-13T00:56:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c167aa9d7688392d84ed45f7135e4eff1a331202",
"body": "- Fix incorrect \"Inline CCD\" description (was \"~35,000 components embedded\n in the binary at compile time\", should be \"_chem_comp_atom/_chem_comp_bond\n loops from mmCIF files\")\n- Correct 4-level to 3-level lookup (hardcoded table → runtime CCD\n analysis → element fallback)\n- Add \"Why Use CCD?\" mo\n[…]\n)\n- Add PDB + external CCD usage examples\n- Document hybridization analysis process\n- Add RCSB Ligand Expo download links for component CIFs\n- Expand supported residues list with all hardcoded entries",
"is_bot": false,
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{
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{
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{
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{
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{
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{
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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": [
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"GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository",
"deps.dev does not index pypi:zsasa@0.9.1; advisories assessed against the repository dependency graph instead"
],
"report_type": "repository",
"generated_at": "2026-07-28T03:35:26.781985Z",
"schema_version": "0.27.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/n/N283T/zsasa.svg",
"full_name": "N283T/zsasa",
"license_state": "standard",
"license_spdx": "MIT"
}Las puntuaciones son señales, no garantías. Reflejan prácticas públicamente visibles en GitHub; no son una auditoría de código ni una garantía de seguridad.
Los datos ausentes se excluyen y los pesos se renormalizan; nunca se puntúan como cero. La metodología es versionada y abierta: métricas v1.13.0, esquema v0.27.0 — metodología completa · wiki de métricas.
Cómo se sitúa un resultado dentro del registro general: estadísticas agregadas — PyPI.