From ad8666bff952068381f6811f5ed8112355a071fd Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 30 May 2026 22:40:24 +0200 Subject: [PATCH] docs(readme): add a checklist of not-yet-implemented functionality Convert the trailing 'what's still open' sentence in the Status section into a tick-box list (visualization, metabolomics-based (f)tINIT scoring, binary and KEGG artefact release publishing), and note that the MetaCyc / dynamic-FBA omissions are out of scope rather than pending. --- README.md | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 14febac..028e93b 100644 --- a/README.md +++ b/README.md @@ -48,8 +48,22 @@ omissions: it ([`dfba`](https://pypi.org/project/dfba/), [`reframed`](https://pypi.org/project/reframed/), [`mewpy`](https://pypi.org/project/mewpy/)). -What's still open is catalogued in **[docs/todo.md](docs/reference/todo.md)** (visualisation / Phase -6 is the main item). +### Not yet implemented + +Planned or partial functionality still on the books (full detail in +**[docs/todo.md](docs/reference/todo.md)**): + +- [ ] **Visualization (`plotting/`)** — pathway maps (Escher), omics-overlay and + flux-distribution plots. *The main open item.* +- [ ] **Metabolomics-based scoring in tINIT / ftINIT** — passing a non-empty `metabolomics` + argument currently raises `NotImplementedError`. +- [ ] **Published binary release ZIPs** (BLAST / DIAMOND / HMMER) — the resolver in + `binaries.py` is ready; the registry is empty until the ZIPs are published as release assets. +- [ ] **Published KEGG data-artefact releases** — the build pipeline exists; the artefact + bundle is not published yet. + +The two principled omissions above (MetaCyc reconstruction, dynamic FBA) are **not** on this +list — they are deliberately out of scope, not pending work. ## Installation (development)