refactor: rename plotting subpackage to visualization

.github/workflows/ci.yml

@@ -43,10 +43,10 @@ jobs:
           cache: pip
           cache-dependency-path: pyproject.toml
       - run: pip install --upgrade pip
-      # ``-e .[dev,plotting,excel]`` so every optional extra is exercised.
+      # ``-e .[dev,visualization,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,plotting,excel]"
+      - run: pip install -e ".[dev,visualization,excel]"
       - run: pytest -q --maxfail=5 --durations=20
 
   docs:
@@ -61,7 +61,7 @@ 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,plotting]" -r docs/requirements.txt
+      - run: pip install -e ".[excel,visualization]" -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 +21,7 @@ python:
       path: .
       extra_requirements:
         - excel
-        - plotting
+        - visualization
     - requirements: docs/requirements.txt
 
 formats:

CHANGELOG.md

@@ -43,7 +43,7 @@ RAVEN-style I/O formats (YAML / SIF / Excel). Validated against MATLAB RAVEN on
 
 * **Licensing:** released under the **MIT** license (previously GPL-3.0-or-later).
 * **Docs:** Sphinx + MyST documentation site (sources under `docs/`).
-* Not yet implemented: visualization (`plotting/`), metabolomics-based (f)tINIT scoring,
+* Not yet implemented: visualization (`visualization/`), metabolomics-based (f)tINIT scoring,
   and published binary / KEGG-artefact release bundles. See the README and
   [docs/todo.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/todo.md).
 

README.md

@@ -53,7 +53,7 @@ omissions:
 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
+- [ ] **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`.

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

docs/reference/api/index.md

@@ -25,6 +25,6 @@ resolvers
 ```
 
 :::{note}
-The `plotting` subpackage is a stub — pathway-map and omics-overlay visualisation
+The `visualization` subpackage is a stub — pathway-map and omics-overlay visualisation
 (Phase 6) is not yet implemented.
 :::

docs/reference/todo.md

@@ -6,7 +6,7 @@ catalogue of raven-python improvements that should also be back-ported into MATL
 
 ## Major
 
-### Visualization (`plotting/`)
+### Visualization (`visualization/`)
 
 Not started. RAVEN has limited plotting (`drawMap` etc., MATLAB-bound). For raven-python the most
 useful targets are:

pyproject.toml

@@ -54,7 +54,7 @@ dev = [
 excel = [
     "openpyxl>=3.1",
 ]
-plotting = [
+visualization = [
     "matplotlib>=3.5",
 ]