diff --git a/CHANGELOG.md b/CHANGELOG.md index 0900dcf..12e17a4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,46 @@ CancerPPIr follows Semantic Versioning. ## [Unreleased] +## [1.1.1] - 2026-08-17 + +### Added + +- Added validated optional pseudonymous case identifiers for privacy-safe output + folders and provenance. +- Added eight-stage elapsed-time progress reporting and CLI version output. +- Added a central public schema registry, autonomous test bootstrap, and unified + `fast` and `full` quality commands. + +### Fixed + +- Corrected local enrichment query and background sizes to use proteins present + in the local STRING term map. +- Made STRING cache validation fail closed on malformed headers, schemas, and + incomplete newly downloaded gzip resources. +- Prevented implicit reuse or overwriting of existing result folders and Excel + reports; successful runs are published atomically from staging directories. +- Removed original input filenames from newly generated output manifests. + +### Changed + +- Advanced the output-manifest schema from `1.0.0` to `2.1.0` for filename + privacy and optional pseudonymous case identity. Validators retain support for + manifest schemas `1.0.0` and `2.0.0`. +- Added early input, cache, case-ID, and output-target preflight checks. +- Preserved legacy input-basename output behavior when `case_id` is omitted, + while emitting an explicit privacy reminder. + +### Compatibility + +- CancerPPIr product version advances from `1.1.0` to `1.1.1`. +- STRING mapping, network construction, candidate scoring, Louvain membership, + and canonical biological interpretation are not intentionally changed. +- Inputs containing proteins absent from the local STRING annotation map can + receive corrected enrichment universe sizes. +- Impact audits found no enrichment-universe changes in the seven qualified + regression cases. + + ## [1.1.0] - 2026-08-16 ### Added diff --git a/CITATION.cff b/CITATION.cff index be586ec..05ce03f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -5,8 +5,8 @@ type: software authors: - family-names: "Silin" given-names: "Danil V." -version: "1.1.0" -date-released: 2026-08-16 +version: "1.1.1" +date-released: 2026-08-17 repository-code: "https://github.com/Danil-V-Silin/CancerPPIr" url: "https://github.com/Danil-V-Silin/CancerPPIr" license: MIT diff --git a/README.md b/README.md index 19f58a2..4d5889c 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![R tests](https://github.com/Danil-V-Silin/CancerPPIr/actions/workflows/r-tests.yml/badge.svg)](https://github.com/Danil-V-Silin/CancerPPIr/actions/workflows/r-tests.yml) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE) -![Version](https://img.shields.io/badge/version-1.1.0-blue) +![Version](https://img.shields.io/badge/version-1.1.1-blue) CancerPPIr is an R workflow for patient-specific protein-protein interaction (PPI) subnetwork profiling from bulk RNA-seq-derived gene tables. It maps gene @@ -237,7 +237,7 @@ release used in the analysis and the associated article when available. ## Development and governance -Current stable version: `1.1.0`. +Current stable version: `1.1.1`. - [Quick start](docs/user-guide/quick-start.md) - [Contributing](CONTRIBUTING.md) diff --git a/SECURITY.md b/SECURITY.md index a8a49e0..a344595 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -2,7 +2,7 @@ ## Supported versions -`1.1.0` is the current supported stable release. Security fixes are provided +`1.1.1` is the current supported stable release. Security fixes are provided for the latest supported release line. ## Reporting a vulnerability diff --git a/VERSION b/VERSION index 9084fa2..524cb55 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.1.0 +1.1.1 diff --git a/docs/README.md b/docs/README.md index ab6f483..cbba5e8 100644 --- a/docs/README.md +++ b/docs/README.md @@ -34,7 +34,7 @@ tree; released states remain available through Git history and immutable tags. - [Repository governance](development/repository-governance.md) - [Repository quality policy](development/repository-quality-policy.md) - [Publication-readiness checklist](development/publication-readiness-checklist.md) -- [Stable release notes](development/release-notes-v1.1.0.md) +- [Stable release notes](development/release-notes-v1.1.1.md) - [Output-quality specification](development/specifications/output-quality-and-biological-interpretation.md) - [Workbook-duplication review](development/workbook-duplication-review-v1.0.0.md) diff --git a/docs/development/release-notes-v1.1.1.md b/docs/development/release-notes-v1.1.1.md new file mode 100644 index 0000000..2975135 --- /dev/null +++ b/docs/development/release-notes-v1.1.1.md @@ -0,0 +1,59 @@ +# CancerPPIr 1.1.1 + +Release date: 2026-08-17. + +CancerPPIr 1.1.1 is a patch release focused on scientific correctness, cache +integrity, output safety, privacy, command-line usability, and maintainability. + +## Scientific correctness + +Local enrichment now calculates query and background sizes only from proteins +represented in the local STRING term map. Impact audits confirmed that this +correction does not change the qualified seven-case regression set. + +## Cache integrity + +STRING v12 cache resources are validated against role-specific headers and +schemas. Newly downloaded gzip files receive complete validation before +publication, and malformed enrichment resources fail explicitly. + +## Output safety and privacy + +CancerPPIr refuses existing case-output targets and existing Excel reports. +Completed runs are published atomically from sibling staging directories. +Original input filenames are excluded from new manifests. + +Manifest schema `2.1.0` records a validated pseudonymous case ID when explicitly +provided. Manifest schemas `1.0.0` and `2.0.0` remain readable for validation of +existing results. + +## Usability + +The CLI supports `--case-id` and `--version`, performs early path preflight, +and reports eight numbered stages with elapsed run time. Omitting `case_id` +retains legacy basename behavior with a privacy reminder. + +## Maintainability + +Public schema versions are defined in one central registry. Tests bootstrap the +supported modules automatically, and maintainers can use one documented quality +runner in `fast` or `full` mode. + +## Compatibility + +The product version advances from `1.1.0` to `1.1.1`. STRING mapping, network +construction, candidate scoring, deterministic Louvain membership, and canonical +biological interpretation are not intentionally changed. Analyses containing +proteins absent from the local STRING annotation map can receive corrected +enrichment universe sizes. + +## Release qualification + +Publication requires the complete seven-case qualification on the exact final +`main` commit. Clinical inputs, input fingerprints, case-level summaries, and +patient-level outputs are excluded from the public release evidence archive. + +## Responsible use + +CancerPPIr remains a hypothesis-generation workflow and is not a clinical +decision-support system. diff --git a/docs/development/repository-governance.md b/docs/development/repository-governance.md index 91adac4..52bec13 100644 --- a/docs/development/repository-governance.md +++ b/docs/development/repository-governance.md @@ -31,6 +31,7 @@ v1.0.0-rc.1 v1.0.0 v1.0.1 v1.1.0 +v1.1.1 ``` Release tags are annotated and immutable. Superseded pre-release tags may be