diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cdfbe0c..60d534c 100644 --- a/.github/workflows/ci.yml +++ b/.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 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 996ad6b..35b2d10 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -21,7 +21,7 @@ python: path: . extra_requirements: - excel - - plotting + - visualization - requirements: docs/requirements.txt formats: diff --git a/CHANGELOG.md b/CHANGELOG.md index 44f3149..2bd72aa 100644 --- a/CHANGELOG.md +++ b/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). diff --git a/README.md b/README.md index 9908222..039f861 100644 --- a/README.md +++ b/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`. diff --git a/docs/README.md b/docs/README.md index 2ccac8e..d3ac917 100644 --- a/docs/README.md +++ b/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 diff --git a/docs/installation.md b/docs/installation.md index 6be617a..f09afe6 100644 --- a/docs/installation.md +++ b/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 diff --git a/docs/reference/api/index.md b/docs/reference/api/index.md index b3945b0..93224e9 100644 --- a/docs/reference/api/index.md +++ b/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. ::: diff --git a/docs/reference/todo.md b/docs/reference/todo.md index 8c24129..ac40abc 100644 --- a/docs/reference/todo.md +++ b/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: diff --git a/pyproject.toml b/pyproject.toml index 376a961..b53443c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ dev = [ excel = [ "openpyxl>=3.1", ] -plotting = [ +visualization = [ "matplotlib>=3.5", ] diff --git a/src/raven_python/plotting/__init__.py b/src/raven_python/visualization/__init__.py similarity index 100% rename from src/raven_python/plotting/__init__.py rename to src/raven_python/visualization/__init__.py