From e5a028d1e4792d79ca128215599bf29796f60495 Mon Sep 17 00:00:00 2001 From: MikeLippincott <1michaell2017@gmail.com> Date: Thu, 11 Jun 2026 18:27:49 -0600 Subject: [PATCH 1/2] add new roadmap --- ROADMAP.md | 116 ++++------------------------------------------------- 1 file changed, 7 insertions(+), 109 deletions(-) diff --git a/ROADMAP.md b/ROADMAP.md index f6864d3..d72e29d 100644 --- a/ROADMAP.md +++ b/ROADMAP.md @@ -4,115 +4,13 @@ This file is for planning of new modules, features, and PRs that are needed the The roadmap is organized into phases, with each phase containing a set of PRs that build upon each other. The roadmap is intended to be a living document and may be updated as needed. -## Scope for current release +## Future Plans -### In scope - -- [ ] Handcrafted featurization modules: - - [ ] volumesizeshape - - [ ] Colocalization - - [ ] Intensity - - [ ] Granularity - - [ ] Neighbors - - [ ] Texture -- [ ] Featurization helper utilities needed by the modules -- [ ] Full test suite with coverage gate (>=85%) -- [ ] Sphinx documentation -- [ ] Example notebooks for module usage -- [ ] Our [RFC2119-specification](./docs/src/Feature_Naming_Convention.md) driven feature naming policy - -## Architecture and Product Decisions - -- [ ] Linux-first, CPU-only, low RAM usage for the current release. -- [ ] File-format agnostic APIs operating on NumPy arrays. -- [ ] Input contracts: - - [ ] Single-channel arrays: (z, y, x) - - [ ] Multi-channel arrays: (c, z, y, x) -- [ ] Modules are intentionally small and composable for external parallel orchestration. - -## PR Plan - -### Phase 1: Foundation (PR 1-3) - -1. PR 1: Packaging and environment baseline - -- [x] Python package scaffold, uv dependency management, version metadata 0.0.1, lint/test tooling, CI skeleton. -- [x] Linux support and CPU-only scope statements in metadata and docs. - -2. PR 2: Core data model and API contracts - -- [x] Canonical input contracts, loader interfaces, common error types. -- [x] Return schema contract (required keys, types, deterministic ordering). - -3. PR 3: RFC2119 naming specification and validators - -- [x] Port and adapt naming conventions into this repository. -- [x] Add runtime and CI naming validation helpers and conformance tests. - -### Phase 2: Feature modules and tests (PR 4-9) - -4. PR 4: volumesizeshape module and tests - - - [x] Implement module - -1. PR 5: Colocalization module and tests - - - [x] Implement module - -1. PR 6: Intensity module and tests - - - [x] Implement module - -1. PR 7: Granularity module and tests - - - [x] Implement module - -1. PR 8: Neighbors module and tests - - - [x] Implement module - -1. PR 9: Texture module and tests - - - [x] Implement module - -### Phase 3: Integration, docs, release (PR 10-13) - -10. PR 10: Integration matrix and parallelization guidance - -- [x] Cross-module integration tests and explicit non-goal docs for internal parallelization. - -11. PR 11: Example notebooks and public dataset references - -- [ ] One notebook per module plus one end-to-end chaining notebook. - -12. PR 12: Sphinx docs, logo, API docs - -- [ ] API pages, architecture and scope pages, docs build checks in CI. - -13. PR 13: Release v0.0.1 and publish workflow - -- [ ] Changelog, semantic tag, PyPI publish automation, README install updates. - -### Phase 4: Post-release improvements (PR 14+) - -14. Add the ability for loading of images from array instead of file - file paths for increased flexibility in data sources and testing. - -## Verification Gates - -- [x] Run full unit and integration tests on Linux with coverage >=85%. -- [x] Run naming validation tests for all emitted feature names. -- [ ] Build Sphinx docs in CI with warnings treated as errors. -- [ ] Execute example notebooks in a clean environment. -- [ ] Validate install/import from both wheel and sdist. -- [ ] Perform release dry-run before publishing. - -## v0.0.2 Backlog (Planned) - -- [ ] Nucleocentric featurization. - [ ] Optional mask output mode. - [ ] Expanded benchmark strategy. - -## v0.0.3 Backlog (Planned) - -- [ ] Potential Arrow Flight handoff experiments. +- [ ] Cytomining V2 support. +- [ ] Support for additional image formats (e.g., TIFF, JPEG, OME-arrow). +- [ ] Integration with cloud storage solutions (e.g., AWS S3, Google Cloud Storage). +- [ ] Support with DeepProfiler image handoff (thin arrow flight, but simplified for the use case of image handoff). +- [ ] Support for additional feature extraction methods (e.g., mesh, graph-based features, point-clouds, polygons). +- [ ] Feature-extraction time estimation and optimization. From 39b3e2d4e1df378de62ba86f1b7b2b8530e10ad9 Mon Sep 17 00:00:00 2001 From: MikeLippincott <1michaell2017@gmail.com> Date: Thu, 11 Jun 2026 18:30:53 -0600 Subject: [PATCH 2/2] udpate list --- ROADMAP.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/ROADMAP.md b/ROADMAP.md index d72e29d..395848b 100644 --- a/ROADMAP.md +++ b/ROADMAP.md @@ -6,10 +6,13 @@ The roadmap is intended to be a living document and may be updated as needed. ## Future Plans +- [ ] Pick between pandas and polars for dataframe handling. - [ ] Optional mask output mode. - [ ] Expanded benchmark strategy. - [ ] Cytomining V2 support. - [ ] Support for additional image formats (e.g., TIFF, JPEG, OME-arrow). +- [ ] Support multi-channel image loading (lazily). +- [ ] Support loading of shapes, vectors, outlines, and contours. - [ ] Integration with cloud storage solutions (e.g., AWS S3, Google Cloud Storage). - [ ] Support with DeepProfiler image handoff (thin arrow flight, but simplified for the use case of image handoff). - [ ] Support for additional feature extraction methods (e.g., mesh, graph-based features, point-clouds, polygons).