v0.6.10-beta

v0.6.10-beta - Zenodo Relation Metadata Fix

This beta release focuses on resolving Zenodo metadata validation issues related to relation types in .zenodo.json.

Highlights

• Replaced unsupported isRelatedTo relation values with Zenodo-safe references
• Updated release metadata for v0.6.10-beta
• Kept CITATION.cff in a minimal Zenodo-safe format
• Continued alignment between:
  • Git tag
  • GitHub release
  • .zenodo.json
  • CITATION.cff

Metadata Fixes

This release addresses another Zenodo schema validation issue identified in earlier beta releases.

.zenodo.json

• updated version to 0.6.10-beta
• replaced invalid relation values with safer Zenodo-compatible relation types
• retained a simplified metadata structure to reduce schema risk

CITATION.cff

• updated version to v0.6.10-beta
• retained minimal citation metadata for Zenodo compatibility

Goal

The goal of this release is to resolve the Zenodo ingestion error caused by unsupported isRelatedTo relation values and move the repository closer to a successful published archival record.

Context

Recent beta releases exposed several Zenodo validation constraints involving:

• unsupported contributor types
• unsupported funding relation types
• unsupported related identifier relation values
• overly complex citation metadata

This release specifically addresses the related identifier relation issue.

Notes

• This is a beta release
• The focus is metadata compatibility and archival infrastructure
• No intentional breaking changes were introduced to the core pipeline functionality

v0.6.9-beta

v0.6.9-beta - Zenodo Metadata Cleanup

This beta release focuses on simplifying and correcting repository metadata to improve Zenodo compatibility.

Highlights

• Simplified CITATION.cff for Zenodo-safe citation handling
• Removed unsupported or problematic metadata patterns from .zenodo.json
• Removed grant-related metadata that was causing validation issues
• Reduced metadata complexity to improve archival portability and DOI generation

Metadata Fixes

This release consolidates several metadata-related corrections introduced across recent commits, including:

• correction of contributor metadata
• correction of relation metadata
• simplification of citation metadata
• removal of grant metadata
• alignment of release metadata for v0.6.9-beta

Goal

The goal of this release is to provide a cleaner Zenodo ingestion target after repeated failures in earlier beta releases caused by strict metadata validation.

Context

Earlier beta releases exposed Zenodo validation constraints involving:

• unsupported contributor types
• unsupported relation values
• unsupported or risky metadata fields
• overly complex citation metadata

This release is intended to minimize that risk and provide a stable metadata checkpoint.

Notes

• This is a beta release
• The focus is metadata compatibility and archival infrastructure
• No intentional breaking changes were introduced to the core pipeline functionality

v0.6.8-beta

v0.6.8-beta - Zenodo Metadata Simplification

This beta release focuses on simplifying and aligning release metadata for Zenodo compatibility.

Highlights

• Simplified archival metadata for Zenodo ingestion
• Aligned release versioning across:
  • Git tag
  • GitHub release
  • .zenodo.json
  • CITATION.cff
• Retained core repository citation and authorship information
• Reduced metadata complexity to improve release portability and DOI generation

Metadata Changes

This release prepares the repository for cleaner Zenodo processing by using a more conservative metadata profile.

.zenodo.json

• updated version to 0.6.8-beta
• retained core descriptive metadata
• retained creator and contributor attribution
• retained safe related repository links
• reduced schema risk by avoiding previously problematic metadata patterns

CITATION.cff

• updated version to v0.6.8-beta
• aligned citation metadata with the release tag
• kept citation information focused on the core software record

Goal

The goal of this release is to provide a stable metadata checkpoint for Zenodo archival after multiple earlier beta releases exposed schema and validation constraints.

Context

Previous releases revealed Zenodo validation issues related to:

• unsupported contributor types
• unsupported relation values
• overly complex citation and archival metadata

This release is intended to minimize that risk and restore successful Zenodo processing.

Notes

• This is a beta release
• The focus is metadata compatibility and release infrastructure
• No intentional breaking changes were introduced to the core pipeline functionality

v0.6.7-beta

v0.6.7-beta - Zenodo Metadata Compatibility Fixes

This beta release focuses on resolving Zenodo ingestion and metadata compatibility issues identified in previous beta releases.

Highlights

• Simplified CITATION.cff to a minimal Zenodo-safe format
• Corrected unsupported Zenodo contributor metadata
• Replaced invalid relation types in .zenodo.json
• Improved alignment between GitHub release metadata, citation metadata, and Zenodo archival metadata

Metadata Fixes

This release addresses issues that affected previous Zenodo ingestions, including:

• unsupported contributor type values
• unsupported related identifier relation values
• overly complex citation metadata for Zenodo parsing

Context

Earlier beta releases exposed several Zenodo schema and validation constraints. This release is intended to provide a clean metadata checkpoint for archival and DOI generation.

Repository Status

• Python dependencies were previously stabilized
• requirements.txt now installs successfully in .venv
• pip check passes
• the number of actionable dependency vulnerabilities was significantly reduced before this release

Goal

The goal of v0.6.7-beta is to restore successful Zenodo processing and DOI generation for the data-pipeline repository.

Notes

• This is a beta release
• The focus is metadata compatibility and release infrastructure
• No intentional breaking changes were introduced to the core pipeline functionality

v0.6.6-beta

v0.6.6-beta - Zenodo Metadata Fix

This beta release fixes Zenodo metadata compatibility issues.

Changes

• Updated release metadata to v0.6.6-beta
• Corrected Zenodo contributor type handling
• Kept CITATION.cff in a minimal Zenodo-safe format
• Aligned repository archival metadata for GitHub and Zenodo ingestion

Goal

This release is intended to resolve the Zenodo ingestion failures seen in:

• v0.6.2-beta
• v0.6.3-beta
• v0.6.4-beta
• v0.6.5-beta

Notes

• This is a beta release
• The change is focused on metadata compatibility, not core pipeline functionality

v0.6.5-beta

v0.6.5-beta - Zenodo Metadata Compatibility Fix

This beta release simplifies citation metadata to improve Zenodo compatibility.

Changes

• Simplified CITATION.cff to a minimal, Zenodo-safe structure
• Updated citation metadata for v0.6.5-beta
• Kept core release metadata aligned with the upcoming beta tag

Goal

This release is intended to resolve Zenodo ingestion failures seen in:

• v0.6.2-beta
• v0.6.3-beta
• v0.6.4-beta

Notes

• This is a beta release
• The change is focused on metadata compatibility, not core pipeline functionality

v0.6.4-beta

v0.6.4-beta - Dependency Stabilization and Citation Metadata Update

This beta release focuses on dependency stabilization, environment consistency, and release metadata improvements.

Highlights

• Stabilized the Python dependency environment
• Fixed multiple resolver conflicts in requirements.txt
• Verified clean installation with:
  • pip install -r requirements.txt
  • pip check
• Reduced the active security remediation scope to 3 remaining actionable items:
  • protobuf
  • pyasn1
  • torch

Dependency Improvements

Updated and stabilized several packages, including:

• cryptography
• cffi
• filelock
• future
• Jinja2
• pillow
• pydicom
• PyJWT
• requests
• urllib3
• typing_extensions

Also resolved compatibility issues involving:

• sympy and torch
• torch, torchaudio, and torchvision
• cryptography and cffi
• pyasn1 and pyasn1-modules
• typing_extensions and the pydantic stack

Validation

The environment was validated successfully with:

• pip install -r requirements.txt
• pip check → no broken requirements found
• python -m safety scan

Security Status

At this stage, the remaining actionable dependency updates are:

• protobuf==4.25.8
• pyasn1==0.5.1
• torch==2.7.1

These will be handled carefully in future releases due to their compatibility impact on the Google and PyTorch dependency stacks.

Metadata and Citation

• Updated CITATION.cff for v0.6.4-beta
• Improved citation metadata for release and archival workflows
• Repository is better prepared for release tracking and Zenodo integration

Notes

• This is a beta release
• The environment is now significantly more stable and reproducible
• No intentional breaking changes were introduced to the core pipeline workflow

v0.6.3-beta

v0.6.3-beta - Dependency Stabilization

This release focuses on stabilizing the Python environment, improving dependency consistency, and addressing multiple security vulnerabilities identified during development.

Key Improvements

• Resolved multiple dependency conflicts across the pipeline, including issues involving PyTorch, cryptography, and authentication-related packages.
• Updated core libraries to more recent and secure versions, including:
  • cryptography
  • requests
  • urllib3
  • Jinja2
  • pydicom
  • PyJWT
  • pillow
  • future
• Fixed compatibility issues between cffi and cryptography.
• Restored compatibility within the pyasn1 ecosystem to ensure stable integration with Google authentication libraries.
• Upgraded typing_extensions to align with the current pydantic stack.

Environment Stability

• The project environment is now fully installable using:
  pip install -r requirements.txt
• Dependency consistency verified with:
  pip check (no broken requirements found)

Security

• Reduced the number of actionable vulnerabilities identified by Safety.
• Remaining items (to be addressed in future releases):
  • protobuf
  • pyasn1 (pending coordinated upgrade with pyasn1-modules)
  • torch (requires coordinated update with torchaudio and torchvision)

Reproducibility and Research Integration

• Added .zenodo.json for Zenodo integration and DOI-based archival.
• Added CITATION.cff to support standardized software citation.

Notes

• This is a beta release intended to stabilize the development environment.
• No breaking changes to core pipeline functionality are expected.
• Further dependency upgrades will be handled incrementally in future releases.

v0.6.2-beta

v0.6.2-beta - Zenodo and Citation Metadata

This pre-release improves repository metadata and citation readiness.

Added

• .zenodo.json for Zenodo integration and DOI-ready metadata
• CITATION.cff for citation support

Metadata Improvements

• Added creator and contributor attribution
• Added ORCID support
• Added project and funding references
• Linked related ecosystem repositories:
  • MIMBCD-UI
  • MIDA
  • BreastScreening
  • BreastScreeningAI

Notes

• This is a beta release
• The repository remains under active development
• Intended to improve reproducibility, citation, and archival readiness

v0.6.1-beta

v0.6.1-beta - Robust BIRADS Parsing and Multimodal Analysis

This pre-release improves robustness and correctness of BIRADS parsing across multimodal imaging pipelines (MG, US, MRI).

Improvements

• Fixed parsing of float values (e.g., "5.0")
• Fixed handling of multiple annotations per cell ("," and ";" separators)
• Correct extraction of maximum BIRADS per patient
• Improved handling of empty and malformed values
• Stable generation of:
  • MG frequency plots (CCL, CCR, MLOL, MLOR)
  • US side-by-side plots (USL vs USR with image counts)
  • MRI side-by-side plots (MRIL vs MRIR)

Technical Fixes

• Eliminated errors:
  • "invalid literal for int()"
  • "max() arg is an empty sequence"
  • duplicate index issues in pandas
• Improved regex-based parsing
• Added safer numeric extraction logic

Notes

• MRI data may remain sparse depending on dataset completeness
• This is a beta release and not production-ready

Ecosystem

• https://github.com/MIMBCD-UI
• https://github.com/mida-project
• https://github.com/BreastScreening
• https://github.com/BreastScreeningAI

Next Steps

• Zenodo DOI integration
• JSON metadata standardization
• Unit testing for parsing edge cases