Öffentliches RegisterMittel
Software-GesundheitsberichtSchema 0.27.0 · Metriken 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 erreicht einen Gesundheitsindex von 63 von 100 und liegt damit im Bereich Mittel. Am stärksten schneidet es bei Vitality (82/100) ab, am schwächsten bei Security (42/100). Zuletzt heute aktualisiert. Ein einzelner Mitwirkender trägt den Großteil der jüngsten Arbeit.
63
gesamt / 100Software-Gesundheitsindex
Metriken werden auf einer Skala von 1–100 in gewichtete Kategorien gruppiert. Der Gesamtwert beginnt als ihr Mittel; sobald öffentliche Evidenz die Richtlinie für Hochrisikojurisdiktionen auslöst, wird die Bewertung angepasst und erhält die Obergrenze 49 (Gefährdet). AI Readiness liegt außerhalb.
63
Exzellent85-100Vorbildlich; erfüllt im Wesentlichen alle geprüften Kriterien
Gut70-84Gesund; geringfügige Lücken
Mittel50-69Akzeptabel mit deutlichen Lücken; Überprüfung empfohlen
Gefährdet30-49Erhebliche Schwächen; eine Übernahme erfordert Vorsicht
Kritisch1-29Schwerwiegende Probleme (aufgegeben, nur ein Maintainer, keine Hygiene)
Bewertungsprofil
Jede Achse ist eine Kategorie. Die Form zählt mehr als der Durchschnitt — ein gesundes Projekt füllt die gesamte Fläche, während ein Profil aus Spitzen und Kratern bedeutet, dass Stärke in einer Dimension Risiken in einer anderen verdeckt.
Eigentümerschaft
N283TPersönliches Konto
22 Follower44 öffentliche Reposseit Nov. 2023
Dieses Repository gehört einem persönlichen Konto. Ein Projekt mit nur einem Eigentümer trägt ein höheres Kontinuitätsrisiko als ein organisationsgetragenes.
Paket-Ökosysteme
| Registry | Paket | Version | Downloads / Monat | Versionen | Zuletzt veröffentlicht |
|---|---|---|---|---|---|
| PyPI | zsasa | 0.9.1 | - | 23 | vor 0 Tagen |
Metriken nach Kategorie
Vitalität
Lebt das Projekt — wird Code geschrieben und werden Releases ausgeliefert?
82
Wie die Bewertung erfolgt
| 36/36 | Push-Aktualität — letzter Push vor 0 Tagen |
| 12.5/36 | Commit-Rhythmus — 18/52 Wochen mit Commits |
| 18/18 | Commit-Volumen — 896 Commits im letzten Jahr |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
Verwendete Eingangsdaten
| commits_last_year | 896 |
| human_commit_share | 1 |
| days_since_last_push | 0 |
| active_weeks_last_year | 18 |
Release-Disziplin
90Exzellent
Wie die Bewertung erfolgt
| 27/27 | Liefert Releases aus — 24 Releases veröffentlicht |
| 36/36 | Release-Aktualität — letztes Release vor 0 Tagen |
| 27/27 | Release-Rhythmus — ein Release etwa alle 8 Tage |
| 0/10 | OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases. |
Verwendete Eingangsdaten
| releases_count | 24 |
| latest_release_tag | v0.9.1 |
| releases_from_tags | nein |
| days_since_latest_release | 0 |
| mean_days_between_releases | 8 |
Community & Verbreitung
Hat das Projekt Nutzer, Downloads, Aufmerksamkeit und ein einladendes Umfeld für Beitragende?
51
Popularität & Verbreitung
15Kritisch
Wie die Bewertung erfolgt
| 14.6/60 | Stars — 9 Stars |
| 0/25 | Forks — 0 Forks |
| 0/15 | Watcher — 1 Watcher |
Verwendete Eingangsdaten
| forks | 0 |
| stars | 9 |
| watchers | 1 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community-Gesundheit
92Exzellent
Wie die Bewertung erfolgt
| 22.5/22.5 | README |
| 22.5/22.5 | Lizenz — anerkannte Lizenz (MIT) |
| 18/18 | CONTRIBUTING-Leitfaden |
| 13.5/13.5 | Verhaltenskodex |
| 0/7.2 | Issue-Vorlage |
| 6.3/6.3 | PR-Vorlage |
Verwendete Eingangsdaten
| has_readme | ja |
| has_license | ja |
| has_contributing | ja |
| has_issue_template | nein |
| has_code_of_conduct | ja |
| has_pull_request_template | ja |
Nachhaltigkeit & Governance
Überdauert das Projekt die Menschen, die es tragen — Bus-Faktor, Reaktionsfähigkeit, Trägerschaft und Paketpflege?
55
Maintainer-Resilienz (Bus-Faktor)
10Kritisch
Wie die Bewertung erfolgt
| 9/54 | Bus-Faktor — 1 Beitragende decken die Hälfte aller Commits ab |
| 0/22.5 | Commit-Verteilung — wichtigste beitragende Person verfasste 100 % der Commits |
| 1.4/13.5 | Breite der Beitragenden — 1 Beitragende |
| 0/10 | OpenSSF Scorecard: Contributors — project has 0 contributing companies or organizations -- score normalized to 0 |
Verwendete Eingangsdaten
| bus_factor | 1 |
| contributors_sampled | 1 |
| top_contributor_share | 1 |
Wie die Bewertung erfolgt
| 44.7/46.8 | Issue-Lösungsquote — 96 % der Issues geschlossen |
| 37.6/38.3 | PR-Annahme — 376/382 entschiedene PRs gemergt |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
Verwendete Eingangsdaten
| merged_prs | 376 |
| open_issues | 1 |
| closed_issues | 22 |
| issue_closed_ratio | 0,957 |
| closed_unmerged_prs | 6 |
Eigentümerschaft & Trägerschaft
47Gefährdet
Wie die Bewertung erfolgt
| 10/30 | Organisatorische Trägerschaft — persönliches (Nutzer-)Konto |
| 0/20 | Verifizierte Domain — für Nutzerkonten nicht anwendbar |
| 9.8/25 | Reichweite des Inhabers — 22 Follower von N283T |
| 17.5/25 | Kontohistorie — 44 öffentliche Repos, Kontoalter ca. 2 Jahre |
Verwendete Eingangsdaten
| followers | 22 |
| owner_type | User |
| is_verified | — |
| owner_login | N283T |
| public_repos | 44 |
| account_age_days | 995 |
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): Verifizierte Domain. Die verbleibenden Gewichte wurden renormalisiert.
Paketpflege
100Exzellent
Wie die Bewertung erfolgt
| 25/25 | Veröffentlicht & auflösbar — 1 Paket(e) auf pypi |
| 35/35 | Veröffentlichungsaktualität — letzte Veröffentlichung vor 0 Tagen |
| 20/20 | Versionshistorie — 23 veröffentlichte Versionen |
| 20/20 | Nicht veraltet — aktiv, nicht veraltet oder zurückgezogen |
Verwendete Eingangsdaten
| packages | zsasa |
| ecosystems | pypi |
| any_deprecated | nein |
| min_days_since_publish | 0 |
Engineering-Qualität
Sind grundlegende Engineering- und Dokumentationspraktiken vorhanden?
80
Engineering-Praktiken
66Mittel
Wie die Bewertung erfolgt
| 24/24 | CI-Workflows — 3 Workflow(s) |
| 24/24 | Tests vorhanden |
| 0/16 | Linter-Konfiguration |
| 0/9.6 | Pre-Commit-Hooks |
| 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 |
Verwendete Eingangsdaten
| has_ci | ja |
| has_tests | ja |
| has_editorconfig | nein |
| has_linter_config | nein |
| has_precommit_config | nein |
Dokumentation
100Exzellent
Wie die Bewertung erfolgt
| 30/30 | README |
| 25/25 | Dokumentationsverzeichnis |
| 15/15 | Dokumentations-/Homepage-Site — https://n283t.github.io/zsasa/ |
| 10/10 | Repository-Beschreibung |
| 10/10 | Topics — 5 Topics |
| 10/10 | Wiki |
Verwendete Eingangsdaten
| topics | bioinformatics, python, sasa, structural-biology, zig |
| has_wiki | ja |
| homepage | https://n283t.github.io/zsasa/ |
| has_readme | ja |
| has_docs_dir | ja |
| has_description | ja |
Sicherheit
Sind die sichtbaren Sicherheits- und Lieferkettenpraktiken belastbar, ohne ungeklärte Exposition gegenüber Hochrisikojurisdiktionen?
42
Sicherheitslage
42Gefährdet
Wie die Bewertung erfolgt
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — keine Daten |
| 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 | Lizenz — 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 |
Verwendete Eingangsdaten
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 4,2 |
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): branch_protection. Die verbleibenden Gewichte wurden renormalisiert.
AI Readiness
Wie gut ist das Repository dafür ausgestattet, mit KI-Coding-Agenten entwickelt und gepflegt zu werden? Ein unabhängiges, experimentelles Badge — Gewicht 0,0, es wird eigenständig ausgewiesen und verändert den Gesamt-Gesundheitswert nicht.
69
AI-Agentenkontext & Leitlinien
85Exzellent
Wie die Bewertung erfolgt
| 45/45 | Agentenanweisungen — AGENTS.md |
| 0/15 | Maschinenlesbare Doku (llms.txt) |
| 40/40 | Lesbare Commit-Historie — 99 von 100 menschlichen Commits benennen ihre Absicht (strukturierter Betreff oder erläuternder Text) |
Verwendete Eingangsdaten
| has_llms_txt | nein |
| legible_history_share | 0,99 |
| agent_instruction_files | AGENTS.md |
| agent_instruction_max_bytes | 6.650 |
Wie die Bewertung erfolgt
| 18/18 | Bootstrap mit einem Befehl — benchmarks/external/freesasa_batch/Makefile |
| 22/22 | Automatisierte Tests |
| 0/11 | Lint-/Format-Konfiguration |
| 11/11 | Statische Typprüfung — website/tsconfig.json |
| 10/10 | Reproduzierbare Umgebung — Dockerfile, Nix, lockfile |
| 0/10 | Belegte Agentenpraxis — keine von Agenten verfassten Commits unter den letzten 100 |
| 0/8 | Automatisierte Wartung — keine automatisierten Abhängigkeits-Updates beobachtet |
| 2/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 2 |
Verwendete Eingangsdaten
| has_nix | ja |
| has_tests | ja |
| lockfiles | package-lock.json, uv.lock |
| has_dockerfile | ja |
| typed_language | nein |
| bootstrap_files | benchmarks/external/freesasa_batch/Makefile |
| has_devcontainer | nein |
| has_linter_config | nein |
| typecheck_configs | website/tsconfig.json |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Wie die Bewertung erfolgt
| 27/45 | Typprüfbarer Code — Zig mit Typprüfungs-Konfiguration (website/tsconfig.json) |
| 55/55 | Handhabbare Dateigrößen — 0/70 Quelldateien über 60 KB |
Verwendete Eingangsdaten
| primary_language | Zig |
| largest_source_bytes | 37.433 |
| source_files_sampled | 70 |
| oversized_source_files | 0 |
Maschinenlesbare AI-Schnittstellen
40Gefährdet
Wie die Bewertung erfolgt
| 0/40 | API-Schema (OpenAPI/GraphQL/proto) |
| 0/20 | MCP-Server |
| 40/40 | Lauffähige Beispiele — examples |
Verwendete Eingangsdaten
| example_dirs | examples |
| has_mcp_signal | nein |
| api_schema_files | — |
Eckdaten
9GitHub-Sterne
1Mitwirkende
896Commits, letzte 12 Monate
0Tage seit letztem Push
24Releases
1Bus-Faktor
1offene Issues
npm, PyPIPaket-Ökosysteme
Warnungen zur Datenerhebung
- 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
Weitere Details
OpenSSF Scorecard 4.2 / 10
4.2Gesamtwert
Unabhängige, werkzeugneutrale Sicherheitsbewertung durch das quelloffene OpenSSF Scorecard. Jede Prüfung honoriert eine Sicherheits-Praxis, nicht das Werkzeug eines bestimmten Anbieters. Prüfungen, die Scorecard nicht ermitteln konnte, sind mit k. A. markiert und vom Sicherheitswert ausgeschlossen (nie als null gezählt).
| 10 | Binary-Artifacts | no binaries found in the repo |
| k. A. | Branch-Protection | internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md |
| 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 |
Direkte Abhängigkeiten 7
| Registry | Paket | Versionsvorgabe | Manifest |
|---|---|---|---|
| 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 |
Alle Abhängigkeiten nicht erhoben
Der aufgelöste Abhängigkeitssatz konnte für diesen Bericht nicht erhoben werden: GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository
JSON-Rohbericht maschinenlesbar
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"headline": "feat: add safe AlphaFold batch fast path (#399)",
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"headline": "fix: gate inline CCD parsing (#392)",
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"headline": "feat: add trajectory bitmask LUT modes (#387)",
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"headline": "fix: optimize multichain workflow parsing (#385)",
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"body": "* docs: plan batch chunked io experiments\n\n* feat: add experimental batch chunk flags\n\n* feat: validate batch chunk options\n\n* feat: add chunked batch range scheduler\n\n* feat: buffer batch jsonl writes by chunk\n\n* docs: document experimental batch chunk options\n\n* fix: harden batch chunk range arith\n[…]\nro shards\n\n* docs: document experimental batch shard option\n\n* feat: add batch macro-batch experiments\n\n* refactor: narrow batch io experiment scope\n\n* fix: join spawned batch workers on spawn failure",
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"headline": "feat: allow batch thread overcommit (#384)",
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"body": "* docs: design paper benchmark website refresh\n\n* docs: plan paper benchmark website refresh\n\n* docs: refresh benchmark website from paper results\n\n* docs: improve benchmark figures and navigation\n\n* docs: restore benchmark-script figures\n\n* docs: use clickable benchmark figure grids\n\n* docs: expand\n[…]\nand validation\n\n* docs: keep validation scatter grids collapsed\n\n* docs: add representative validation scatters\n\n* docs: clarify validation interpretation\n\n* docs: lead benchmark sections with figures",
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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": "test: cover batch jsonl and ffi concurrency (#376)",
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"body": "* docs: design file-first workflow batch\n\n* docs: plan file-first workflow batch\n\n* test: add workflow chain selection helper\n\n* refactor: reuse prepared batch SASA calculation\n\n* feat: process workflow batch files once\n\n* fix: preserve workflow auth-chain fallback\n\n* fix: honor workflow thread coun\n[…]\nkflow file-first outputs\n\n* test: exercise workflow file-first output layout\n\n* docs: note workflow job reuse\n\n* docs: clarify workflow reuse eligibility\n\n* fix: preserve long chain workflow filtering",
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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": "ci: ignore gitignore-only changes (#368)",
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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",
"is_bot": false,
"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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"oid": "36f3d9e8ed76cfa72470497820f4a8f56b796ac3",
"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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"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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"committed_at": "2026-05-15T10:10:56Z",
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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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"author_login": "N283T",
"committed_at": "2026-05-04T15:29:57Z",
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"headline": "docs: add project logo",
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"committed_at": "2026-05-04T15:29:29Z",
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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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"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)",
"author_name": "N283T",
"author_login": "N283T",
"committed_at": "2026-04-26T12:17:47Z",
"body_truncated": false,
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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,
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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,
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{
"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",
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{
"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",
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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,
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},
{
"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,
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},
{
"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,
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{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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,
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},
{
"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",
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"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"
}Bewertungen sind Signale, keine Garantien. Sie spiegeln öffentlich sichtbare Praxis auf GitHub wider — kein Code-Audit und keine Sicherheitsgarantie.
Fehlende Daten werden ausgeschlossen und die Gewichte neu normiert, nie als null bewertet. Die Methodik ist versioniert und offen: Metriken v1.13.0, Schema v0.27.0 — vollständige Methodik · Metriken-Wiki.
Wie ein einzelnes Ergebnis im Gesamtregister steht: aggregierte Statistiken — PyPI.