release: prepare v1.1.1

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

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

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)

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

VERSION

@@ -1 +1 @@
-1.1.0
+1.1.1

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)
 

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.

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