Bump ipython from 7.34.0 to 8.10.0

.github/workflows/ci.yml

@@ -14,62 +14,98 @@ jobs:
         python-version: ["3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Install uv and Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          version: "0.11.32"
+          enable-cache: true
 
       - name: Install dependencies
-        run: poetry install --without compass
+        run: uv sync --locked
 
       - name: Run tests
-        run: poetry run pytest
+        run: uv run pytest
 
   lint:
     runs-on: ubuntu-latest
     needs: test
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv and Python
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
         with:
           python-version: "3.11"
+          version: "0.11.32"
+          enable-cache: true
 
-      - name: Install ruff
-        run: pip install ruff
+      - name: Install dependencies
+        run: uv sync --locked
 
       - name: Run ruff
-        run: ruff check pleque/ tests/
+        run: uv run ruff check pleque/ tests/
 
   typecheck:
     runs-on: ubuntu-latest
     needs: test
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv and Python
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
         with:
           python-version: "3.11"
-
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          version: "0.11.32"
+          enable-cache: true
 
       - name: Install dependencies
-        run: poetry install --without compass
+        run: uv sync --locked
 
       - name: Run ty
-        run: poetry run ty check pleque/
+        run: uv run ty check pleque/
         continue-on-error: true  # ty is new; don't fail CI until annotations are complete
+
+  build:
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: Install uv and Python
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          python-version: "3.11"
+          version: "0.11.32"
+          enable-cache: true
+
+      - name: Build distributions
+        run: uv build
+
+  docs:
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: Install uv and Python
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          python-version: "3.11"
+          version: "0.11.32"
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --locked
+
+      - name: Install Pandoc
+        run: sudo apt-get update && sudo apt-get install --yes --no-install-recommends pandoc
+
+      - name: Build documentation
+        run: uv run make -C docs html

.github/workflows/tests.yml

@@ -2,9 +2,9 @@ name: Tests
 
 on:
   push:
-    branches: [master, main]
+    branches: [master, main, develop]
   pull_request:
-    branches: [master, main]
+    branches: [master, main, develop]
 
 jobs:
   test:
@@ -15,31 +15,24 @@ jobs:
       pull-requests: write
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
 
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
-
-      - name: Cache Poetry dependencies
-        uses: actions/cache@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
         with:
-          path: ~/.cache/pypoetry
-          key: ${{ runner.os }}-poetry-${{ hashFiles('poetry.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-poetry-
+          version: "0.11.32"
+          enable-cache: true
 
       - name: Install dependencies
-        run: poetry install --without compass
+        run: uv sync --locked
 
       - name: Run tests
-        run: poetry run pytest --junitxml=report.xml --cov=pleque --cov-report=xml:coverage.xml --cov-report=term-missing
+        run: uv run pytest --junitxml=report.xml --cov=pleque --cov-report=xml:coverage.xml --cov-report=term-missing
 
       - name: Upload test results artifact
         uses: actions/upload-artifact@v4

.gitignore

@@ -42,5 +42,7 @@ docs/_static/
 docs/source/_build/
 
 venv/
+.venv/
+.uv-cache/
 /local/gfile_vs_spline.ipynb
 /local/

.gitlab-ci.yml

@@ -1,24 +1,17 @@
-#image: python:3.9
 image: python:3.10
 
 variables:
-  POETRY_HOME: "$CI_PROJECT_DIR/.poetry"
-  POETRY_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pypoetry"
+  UV_CACHE_DIR: "/tmp/.uv-cache"
+  UV_LINK_MODE: copy
 
-cache:
-  paths:
-    - .poetry
-    - .cache/pypoetry
-
-before_script:
-  - curl -sSL https://install.python-poetry.org | python3 -
-  - export PATH="$POETRY_HOME/bin:$PATH"
-  - poetry config virtualenvs.create false
-  - poetry install --without compass # --with omas # omas is temporarily skipped due to the complicated dependencies
+default:
+  before_script:
+    - python -m pip install --disable-pip-version-check "uv==0.11.32"
+    - uv sync --locked
 
 test:pytest:
   script:
-    - pytest --junitxml=report.xml --cov=pleque --cov-report=xml:coverage.xml --cov-report=term-missing
+    - uv run pytest --junitxml=report.xml --cov=pleque --cov-report=xml:coverage.xml --cov-report=term-missing
   artifacts:
     when: always
     reports:
@@ -30,19 +23,27 @@ test:pytest:
       - report.xml
       - coverage.xml
     expire_in: 1 week
-    - pytest
 
 lint:ruff:
-  stage: test
   script:
-    - pip install ruff
-    - ruff check pleque/ tests/
+    - uv run ruff check pleque/ tests/
   needs: ["test:pytest"]
 
 typecheck:ty:
-  stage: test
   script:
-    - pip install ty
-    - ty check pleque/
+    - uv run ty check pleque/
   needs: ["test:pytest"]
-  allow_failure: true  # ty is new; don't block pipeline until annotations are complete
+  allow_failure: true
+
+build:package:
+  script:
+    - uv build
+
+docs:html:
+  before_script:
+    # nbsphinx converts the example notebooks with pandoc
+    - apt-get update
+    - apt-get install --yes --no-install-recommends pandoc
+    - !reference [default, before_script]
+  script:
+    - uv run make -C docs html

AGENTS.md

@@ -0,0 +1,28 @@
+# Repository Guidelines
+
+## Project Structure & Module Organization
+
+`pleque/` contains the installable Python package. Core equilibrium and coordinate behavior lives in `pleque/core/`; format readers and writers are in `pleque/io/`; shared numerical and plotting helpers are in `pleque/utils/`; spatial transformations are in `pleque/spatran/`. Keep bundled sample equilibria in `pleque/resources/`. The main test suite is under `tests/`, with reusable package-side test helpers in `pleque/tests/`. User-facing demonstrations belong in `examples/` or `notebooks/`, while Sphinx sources live in `docs/source/`.
+
+## Build, Test, and Development Commands
+
+- `uv sync` creates the locked development environment from `pyproject.toml` and `uv.lock`.
+- `uv sync --group compass` additionally installs the optional COMPASS/CDB integration.
+- `uv run pytest` runs the complete test suite configured by `pytest.ini`.
+- `uv run pytest tests/test_gfile.py -q` runs a focused module while developing.
+- `uv run ruff check pleque tests` checks Python style and common correctness issues.
+- `uv run ty check pleque` runs the advisory type checker used by CI.
+- `uv build` creates source and wheel distributions through Hatchling.
+- `uv run make -C docs html` builds the Sphinx documentation into `docs/build/html/`.
+
+## Coding Style & Naming Conventions
+
+Use four-space indentation and follow the existing scientific Python style. Name modules, functions, and variables with `snake_case`; classes use `PascalCase`; constants use `UPPER_SNAKE_CASE`. Preserve established domain notation such as `R`, `Z`, `psi_n`, and `COCOS` where it improves correspondence with equations and file formats. Keep public APIs documented with concise docstrings, and avoid mixing unrelated formatting changes into functional patches. Use Ruff for linting and `uv run ruff format pleque tests` for automatic formatting.
+
+## Testing Guidelines
+
+Tests use Pytest and NumPy assertion helpers. Add tests close to the affected behavior, normally as `tests/test_<topic>.py` with functions named `test_<behavior>`. Reuse fixtures from `tests/conftest.py` and sample data from `pleque/resources/` instead of adding large generated artifacts. Cover numerical results with explicit tolerances and include regression cases for bug fixes. Run focused tests first, then the full suite before submitting.
+
+## Commit & Pull Request Guidelines
+
+Recent history favors short, imperative or descriptive subjects such as `Add reference publication to README.md` and `Update dependencies`. Keep each commit scoped to one logical change; use `Bump version to X.Y.Z` for release-only version commits. Pull requests should explain the user-visible or numerical impact, list verification commands, and link relevant issues. Include plots or screenshots when visualization output changes, and call out compatibility, dependency, or equilibrium-data changes explicitly.

CLAUDE.md

@@ -1,6 +1,7 @@
 # CLAUDE.md
 
 This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+Shared contributor instructions are defined in `AGENTS.md`; this file adds Claude-specific project context.
 
 ## Overview
 
@@ -10,27 +11,28 @@ typically constructed by reading an equilibrium file (e.g. G-EQDSK) via `pleque.
 
 ## Commands
 
-The project uses Poetry. The `compass` dependency group pulls `pycdb-compass` from an internal
-IPP git repository that is not reachable outside the COMPASS network — always exclude it:
+The project uses uv. The `compass` dependency group pulls `pycdb-compass` from an internal
+IPP git repository that is not reachable outside the COMPASS network, so install it only when needed:
 
 ```bash
-poetry install --without compass     # install dependencies (this is what CI does)
+uv sync                                      # install locked default and development dependencies
+uv sync --group compass                      # additionally install the COMPASS integration
 
-poetry run pytest                            # run the whole test suite
-poetry run pytest tests/test_equilibria.py   # run one test file
-poetry run pytest tests/test_equilibria.py::test_name   # run a single test
+uv run pytest                                # run the whole test suite
+uv run pytest tests/test_equilibria.py       # run one test file
+uv run pytest tests/test_equilibria.py::test_name       # run a single test
 
-ruff check pleque/ tests/            # lint (CI runs exactly this)
-ruff format pleque/ tests/           # format (line-length 120, double quotes)
+uv run ruff check pleque/ tests/              # lint (CI runs exactly this)
+uv run ruff format pleque/ tests/             # format (line-length 120, double quotes)
 
-poetry run ty check pleque/          # type check (advisory: CI runs it with continue-on-error
-                                     # because the legacy codebase is largely un-annotated)
+uv run ty check pleque/                       # type check (advisory: CI runs it with continue-on-error
+                                              # because the legacy codebase is largely un-annotated)
 ```
 
 Tests that need unavailable optional dependencies (e.g. `pyCDB` in `tests/test_cdb.py`) skip
 themselves via `pytest.importorskip` — they are not failures.
 
-Docs are Sphinx-based in `docs/` (built on Read the Docs): `make -C docs html`.
+Docs are Sphinx-based in `docs/` (built on Read the Docs): `uv run make -C docs html`.
 
 ## Branches and releases
 

README.md

@@ -54,6 +54,27 @@ pip install --user .
 ```
  Congratulations, you have just installed `pleque`!
 
+### Development with uv
+
+For a development checkout, install the locked runtime and development
+dependencies with [uv](https://docs.astral.sh/uv/):
+
+```bash
+uv sync
+```
+
+Run tests through the managed environment:
+
+```bash
+uv run pytest
+```
+
+The optional COMPASS integration can be installed with:
+
+```bash
+uv sync --group compass
+```
+
 ## Examples
 
 The following example shows how to load an equilibrium saved in the `eqdsk` format. The equilibrium used here comes from a FIESTA simulation of the COMPASS-Upgrade tokamak.

docs/Makefile

@@ -2,7 +2,9 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+# -W turns Sphinx warnings into errors so the build stays warning-free;
+# override with e.g. `make html SPHINXOPTS=` while iterating on the docs.
+SPHINXOPTS    = -W
 SPHINXBUILD   = python -msphinx
 SPHINXPROJ    = Pleque
 SOURCEDIR     = source

docs/source/conf.py

@@ -73,7 +73,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -164,8 +164,10 @@
      'Miscellaneous'),
 ]
 
-#Give each notebook cell 3 minutes to execute
-nbsphinx_timeout=180
+# Render committed notebook outputs during documentation builds. Executing the
+# example notebooks is a separate maintenance task and is not reproducible in
+# the minimal documentation environment.
+nbsphinx_execute = 'never'
 
 
 def skip(app, what, name, obj, would_skip, options):