Bump pytest from 7.4.4 to 9.0.3

.env

@@ -0,0 +1,2 @@
+PWD=/home/kripner/Projects/pleque
+OLDPWD=/home/kripner

.github/workflows/ci.yml

@@ -0,0 +1,75 @@
+name: CI
+
+on:
+  push:
+    branches: ["master", "develop", "claude/**"]
+  pull_request:
+    branches: ["master", "develop"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: poetry install --without compass
+
+      - name: Run tests
+        run: poetry run pytest
+
+  lint:
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install ruff
+        run: pip install ruff
+
+      - name: Run ruff
+        run: ruff check pleque/ tests/
+
+  typecheck:
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: poetry install --without compass
+
+      - name: Run ty
+        run: poetry run ty check pleque/
+        continue-on-error: true  # ty is new; don't fail CI until annotations are complete

.github/workflows/tests.yml

@@ -0,0 +1,75 @@
+name: Tests
+
+on:
+  push:
+    branches: [master, main]
+  pull_request:
+    branches: [master, main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    permissions:
+      checks: write
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        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
+        with:
+          path: ~/.cache/pypoetry
+          key: ${{ runner.os }}-poetry-${{ hashFiles('poetry.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-poetry-
+
+      - name: Install dependencies
+        run: poetry install --without compass
+
+      - name: Run tests
+        run: poetry 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
+        if: always()
+        with:
+          name: test-results
+          path: |
+            report.xml
+            coverage.xml
+
+      - name: Publish test results
+        uses: dorny/test-reporter@v1
+        if: always()
+        with:
+          name: pytest results
+          path: report.xml
+          reporter: java-junit
+
+      - name: Publish coverage summary
+        uses: irongut/CodeCoverageSummary@v1.3.0
+        if: always()
+        with:
+          filename: coverage.xml
+          badge: true
+          format: markdown
+          output: both
+
+      - name: Add coverage comment to PR
+        uses: marocchino/sticky-pull-request-comment@v2
+        if: github.event_name == 'pull_request'
+        with:
+          recreate: true
+          path: code-coverage-results.md

.gitlab-ci.yml

@@ -18,4 +18,31 @@ before_script:
 
 test:pytest:
   script:
+    - pytest --junitxml=report.xml --cov=pleque --cov-report=xml:coverage.xml --cov-report=term-missing
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+    paths:
+      - report.xml
+      - coverage.xml
+    expire_in: 1 week
     - pytest
+
+lint:ruff:
+  stage: test
+  script:
+    - pip install ruff
+    - ruff check pleque/ tests/
+  needs: ["test:pytest"]
+
+typecheck:ty:
+  stage: test
+  script:
+    - pip install ty
+    - ty check pleque/
+  needs: ["test:pytest"]
+  allow_failure: true  # ty is new; don't block pipeline until annotations are complete

CLAUDE.md

@@ -0,0 +1,100 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Overview
+
+PLEQUE (**PL**asma **EQU**ilibrium **E**njoyment module) is a Python library for visualisation and
+manipulation of tokamak plasma equilibria. Its central abstraction is the `Equilibrium` class,
+typically constructed by reading an equilibrium file (e.g. G-EQDSK) via `pleque.io.readers`.
+
+## 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:
+
+```bash
+poetry install --without compass     # install dependencies (this is what CI does)
+
+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
+
+ruff check pleque/ tests/            # lint (CI runs exactly this)
+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)
+```
+
+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`.
+
+## Branches and releases
+
+- `develop` is the main development branch; `master` holds releases.
+- CI (`.github/workflows/ci.yml`) runs tests on Python 3.10 and 3.11 for pushes to `master`,
+  `develop`, and `claude/**` branches, then lint (ruff) and type check (ty).
+- The version string lives in `pleque/__init__.py` (`__version__`), with the minor version also
+  in `docs/source/conf.py`. The release process is documented in `how_to_publish_release.md`.
+
+## Architecture
+
+### Core (`pleque/core/`)
+
+- `equilibrium.py` — `Equilibrium`, the heart of the package (~2000 lines). Wraps an
+  `xarray.Dataset` of poloidal flux on an (R, Z) grid plus 1D profiles, builds 2D/1D splines
+  (`RectBivariateSpline` / `UnivariateSpline`), finds the magnetic axis, X-points, LCFS and
+  strike points, and exposes evaluation methods (`B_R`, `B_Z`, `B_tor`, `B_abs`, `psi`, `q`, ...),
+  flux-surface generation, mapping, and plotting helpers.
+- `coordinates.py` — `Coordinates`, the universal coordinate container. Nearly every public
+  `Equilibrium` method accepts flexible coordinate input (1D `psi_n`, 2D `(R, Z)`, 3D
+  `(R, Z, phi)`, arrays, grids, other `Coordinates`) and normalises it through this class.
+- `fluxsurface.py` — `Surface` / `FluxSurface` (closed/open contours, built on `shapely`),
+  with geometry properties (area, volume, geometric averages).
+- `fluxfunctions.py` / `surfacefunctions.py` — containers for 1D profile functions attached to
+  an equilibrium.
+- `cocos.py` — COCOS (tokamak COordinate COnventionS, Sauter & Medvedev) coefficient handling.
+  Readers take a `cocos` argument; `Coordinates` carries cocos through transformations.
+
+**Import-order caveat:** `pleque/core/__init__.py` has a load-order-dependent import sequence
+due to circular imports (`Equilibrium` must be imported last). Ruff `I001`/`F401` are suppressed
+for it in `pyproject.toml` — do not let an auto-formatter reorder those imports.
+
+### IO (`pleque/io/`)
+
+- `readers.py` — high-level entry points (`read_geqdsk`, ...) that return `Equilibrium` instances.
+- `geqdsk.py` is the public G-EQDSK read/write API; `_geqdsk.py` contains the low-level format
+  routines (vendored from FreeGS, LGPL — keep its license header intact).
+- Per-source readers: `compass.py` (CDB / FIESTA / EFIT HDF5), `omas.py` (OMAS/IMAS),
+  `metis.py`, `jet/`. Optional heavy dependencies are imported inside functions so the package
+  works without them.
+- `io/__init__.py` files re-export the public API (`F401` suppressed for them).
+
+### Supporting packages
+
+- `pleque/utils/` — numerics behind `Equilibrium`: `surfaces.py` (contour finding, boundary
+  tracking), `field_line_tracers.py`, `flux_expansions.py`, `equi_tools.py`, `plotting.py`, and
+  `decorators.py` (see array convention below).
+- `pleque/config/settings.py` — `pydantic-settings` based `Settings`; access via the
+  `lru_cache`d `get_settings()`, so settings are effectively process-global.
+- `pleque/spatran/` — affine transformations and reference frames for spatial transforms.
+- `pleque/resources/` — bundled test equilibria (eqdsk/gfile/netCDF files).
+- `pleque/tests/utils.py` — loads the bundled equilibria (`load_testing_equilibrium(case)`);
+  used by `tests/conftest.py`, whose module-scoped `equilibrium` fixture parametrizes most tests
+  over six bundled test cases.
+
+### Array convention (important for any new evaluation function)
+
+Public evaluation functions follow a component-first convention, enforced via decorators in
+`pleque/utils/decorators.py` (`scalar_function`, `vector_function`,
+`ordered_path_scalar_function`):
+
+- Scalars at paired points return `[n_elements]`; on a grid (`grid=True`) return `[n_z, n_r]`,
+  matching `np.meshgrid(R, Z)`.
+- Vectors return `[n_dim, ...]` (e.g. `[n_dim, n_z, n_r]` for grids).
+- SciPy's `RectBivariateSpline` returns grids as `(n_R, n_Z)`;
+  `Equilibrium._shape_spline_result` transposes to the public `(n_Z, n_R)` layout — use it when
+  adding spline-backed methods.

README.md

@@ -14,7 +14,7 @@ For more information see the documentation at https://pleque.readthedocs.io.
 The following packages are required to install `pleque`:
 
 ```
-python>=3.5
+python>=3.11
 numpy
 scipy
 shapely
@@ -59,12 +59,13 @@ pip install --user .
 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.
 
 ```python
+from importlib import resources
+
 from pleque.io import readers
-import pkg_resources
 import matplotlib as plt
 
 #Locate a test equilibrium
-filepath = pkg_resources.resource_filename('pleque', 'resources/baseline_eqdsk')
+filepath = resources.files('pleque').joinpath('resources', 'baseline_eqdsk')
 ```
 The heart of `pleque` is its `Equilibrium` class, which contains all the equilibrium information (and much more). Typically its instances are called `eq`.
 
@@ -89,9 +90,35 @@ B = eq.B_abs(R, Z)
 
 Equilibria may be visualised in many different ways; they may be used for mapping or field line tracing; the possibilities are virtually endless. If there's a caveat you find missing from `pleque`, write to us! Further examples can be found as notebooks in the `notebooks` folder or in the `examples` directory. 
 
-## Version
+## Array convention
+
+Public evaluation functions use a component-first convention for vector quantities and
+the same spatial shape as the requested coordinates for scalar quantities.
+
+* Scalar functions evaluated at paired points return `[n_elements]`.
+* Scalar functions evaluated on a grid return `[n_z, n_r]`, matching `np.meshgrid(R, Z)`.
+* Vector functions return `[n_dim, ...]`, for example `[n_dim, n_elements]` for paired points
+  and `[n_dim, n_z, n_r]` for grids.
+* Passing mesh-shaped `R` and `Z` arrays with `grid=False` is treated as elementwise evaluation
+  and preserves the mesh shape.
+
+## Configuration
+
+All tunable algorithm parameters (grid resolutions, solver tolerances, search heuristics, ...)
+have built-in defaults that can be overridden by a `pleque.toml` file — in the working
+directory, in the user config directory (`~/.config/pleque/` or `%APPDATA%\pleque\`), or as a
+`[tool.pleque]` table in `pyproject.toml` — or by `PLEQUE_`-prefixed environment variables:
+
+```toml
+[flux_surfaces]
+n_psi = 300
+
+[lcfs]
+search_grid_nr = 1000
+```
 
-0.0.9
+See the [configuration documentation](https://pleque.readthedocs.io/en/latest/configuration.html)
+for the file lookup order and the full settings reference.
 
 ## Authors
 
@@ -116,6 +143,7 @@ Although the systematic development of the project was intended, it endup bit or
 
 * 0.0.8 - Tagged master branch with the last change from 19-08-2024.
 * 0.0.9 - Tagged develop branch with maintained back compatibility with 0.0.8. 
+* 0.0.10 All the phd-related work merged the master + update of array ordering. This version may thus introduce breaking changes! 
 
 
 ## Related projects

docs/source/conf.py

@@ -138,6 +138,12 @@
      'Lukas Kripner', 'manual'),
 ]
 
+# DEBUG temporal fix
+
+from logging import getLogger
+getLogger('nbsphinx').warning("nbsphinx allow errors enabled in conf.py")
+nbsphinx_allow_errors = True
+
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples