Remove the visualization stub and [visualization] extra

.github/workflows/ci.yml

@@ -59,10 +59,10 @@ jobs:
           cache: pip
           cache-dependency-path: pyproject.toml
       - run: pip install --upgrade pip
-      # ``-e .[dev,visualization,excel]`` so every optional extra is exercised.
+      # ``-e .[dev,excel]`` so every optional extra is exercised.
       # Gurobi is not installable on free runners; the relevant tests
       # skip themselves when ``optlang.gurobi_interface`` cannot import.
-      - run: pip install -e ".[dev,visualization,excel]"
+      - run: pip install -e ".[dev,excel]"
       - run: pytest -q --maxfail=5 --durations=20
 
   docs:
@@ -77,7 +77,7 @@ jobs:
           cache-dependency-path: pyproject.toml
       - run: pip install --upgrade pip
       # The package (with autodoc's import-time extras) plus the docs toolchain.
-      - run: pip install -e ".[excel,visualization]" -r docs/requirements.txt
+      - run: pip install -e ".[excel]" -r docs/requirements.txt
       # ``-W --keep-going`` keeps the docs build warning-clean; mirrors the
       # ReadTheDocs build (docs/conf.py + .readthedocs.yaml).
       - run: sphinx-build -b html -W --keep-going docs docs/_build/html

.readthedocs.yaml

@@ -21,7 +21,6 @@ python:
       path: .
       extra_requirements:
         - excel
-        - visualization
     - requirements: docs/requirements.txt
 
 formats:

CHANGELOG.md

@@ -4,6 +4,12 @@ Milestones in the raven-python port. For function-level status see
 [docs/raven_migration.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/migration.md); for open work see
 [docs/todo.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/todo.md).
 
+## Unreleased
+
+* **Removed the `visualization` stub and `[visualization]` extra**, mirroring MATLAB
+  RAVEN dropping its pathway-map / omics-overlay plotting functions (`drawMap`,
+  `colorPathway`, etc.) as obsolete. cobrapy + Escher cover this externally.
+
 ## 0.1.0 — 2026-06-10
 
 First release with **published, downloadable KEGG artefacts**, plus a cobra-aligned

README.md

@@ -53,8 +53,6 @@ omissions:
 Planned or partial functionality still on the books (full detail in
 **[docs/todo.md](docs/reference/todo.md)**):
 
-- [ ] **Visualization (`visualization/`)** — 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

docs/README.md

@@ -6,7 +6,7 @@ The rendered documentation is built with **Sphinx** (MyST Markdown) and hosted o
 Build it locally:
 
 ```bash
-pip install -e ".[excel,visualization]"
+pip install -e ".[excel]"
 pip install -r docs/requirements.txt
 sphinx-build -b html docs docs/_build/html
 # open docs/_build/html/index.html

docs/installation.md

@@ -18,11 +18,10 @@ Some features need extra packages, exposed as optional extras:
 | Extra | Pulls in | Needed for |
 | --- | --- | --- |
 | `excel` | `openpyxl` | {func}`raven_python.io.excel.export_to_excel` |
-| `visualization` | `matplotlib` | visualisation (Phase 6, in progress) |
 | `dev` | `pytest`, `pytest-cov`, `ruff` | running the test-suite / linting |
 
 ```bash
-pip install -e ".[excel,visualization,dev]"
+pip install -e ".[excel,dev]"
 ```
 
 ## Solvers

docs/reference/api/index.md

@@ -23,8 +23,3 @@ analysis
 comparison
 resolvers
 ```
-
-:::{note}
-The `visualization` subpackage is a stub — pathway-map and omics-overlay visualisation
-(Phase 6) is not yet implemented.
-:::

docs/reference/todo.md

@@ -6,17 +6,6 @@ catalogue of raven-python improvements that should also be back-ported into MATL
 
 ## Major
 
-### Visualization (`visualization/`)
-
-Not started. RAVEN has limited plotting (`drawMap` etc., MATLAB-bound). For raven-python the most
-useful targets are:
-
-* Pathway maps / Escher integration for context-specific models.
-* Omics overlay (gene-score / expression heatmaps on the reaction set).
-* Flux distribution overlays.
-
-cobrapy + Escher already covers a lot here — likely a thin integration layer rather than a port.
-
 ### Metabolomics-based scoring in ftINIT
 
 The metabolomics-detected metabolite production-reward block in [`init.ftinit`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/init/ftinit.py)

pyproject.toml

@@ -55,9 +55,6 @@ dev = [
 excel = [
     "openpyxl>=3.1",
 ]
-visualization = [
-    "matplotlib>=3.5",
-]
 
 [project.urls]
 Homepage = "https://github.com/SysBioChalmers/raven-python"