Bump pytest from 7.4.4 to 9.0.3#67
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Merge phd-thesis work to the master See merge request kripner/pleque!141
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Bump version to 0.0.10 and update release documentation See merge request kripner/pleque!142
- Remove four redundant in-method `mu_0` imports; module-level import covers them - Remove commented-out old __init__ signature left over from a prior refactor - Remove commented-out matplotlib debug code from arg_longest_monotonic_subsequence - Wire critical-point search grid (700×1200) to pleque.config.settings so users can override nr_grid/nz_grid via environment variables - Extract triplicated psi_xysq_func closure in equi_tools.py to a single _make_psi_grad_sq factory, eliminating the duplication across find_extremes, recognize_mg_axis, and recognize_x_points https://claude.ai/code/session_01FS9C1xD1y9tceTjGBvcyhn
- Remove three deprecated mis-named methods from Coordinates: incidence_angle_cos, impact_angle_cos, pol_projection_impact_angle_cos. All were wrappers around the correctly-named sin variants and had no callers anywhere in the codebase. - Delete pleque/io/_test_gfile_loader.py: dead code with no callers, superseded by the proper geqdsk.read() path, and contained Equilibrium monkey-patching. - Populate pleque/io/__init__.py with top-level re-exports (read_geqdsk, write_geqdsk, read_efithdf5, read_fiesta_equilibrium) so users can import directly from pleque.io. https://claude.ai/code/session_01FS9C1xD1y9tceTjGBvcyhn
…oup 5) __init__ is now a ~30-line orchestration that delegates to five private methods: - _load_spatial_data: loads psi grid, first wall, and spatial metadata from dataset - _load_profiles: loads 1D profile arrays (F, FFprime, pressure, pprime) - _setup_psi_spline: builds the 2D RectBivariateSpline for psi(R, Z) - _find_critical_points: finds x-points/o-points and recognizes plasma type - _setup_plasma_boundary: finds LCFS contour and strike points - _setup_1d_profiles: builds all UnivariateSpline profile interpolants No behavior change; all tests pass. Also included in this commit: - Remove three deprecated cos-misnamed methods from Coordinates that had no callers (incidence_angle_cos, impact_angle_cos, pol_projection_impact_angle_cos) https://claude.ai/code/session_01FS9C1xD1y9tceTjGBvcyhn
…2203 Refactor: clean up code structure (Groups 1 & 2)
- Replace flake8 and pylint with ruff + ty in pyproject.toml - Configure ruff with rules E,W,F,I,B,UP,RUF at 120-char line limit - Ignore N802/N803/N806: physics variable naming (R, Z, X, Y) is intentional and forms part of the public API - Add GitLab CI lint:ruff job after test:pytest - Add GitHub Actions CI with separate test, lint, and typecheck jobs (ty runs with continue-on-error until annotations are more complete) - Fix auto-fixable issues: unused imports, invalid escape sequences, import ordering, f-string modernisation, UP04x pyupgrade fixes - Fix bare except → except Exception in omas.py and plotting.py - Fix E741 ambiguous variable l → lis_len/arc_length in tools/fluxsurface - Fix B008 mutable default args: np.array/np.eye moved into function bodies - Fix B007 unused loop variable i → _i in tools.py arglis - Fix affine.py bug: np.zeros_like(transform) → np.zeros_like(self.transformation) - Change star import in fluxsurface.py to explicit import of deprecated - Use explicit re-export (X as X) in pleque/core/__init__.py - Add E402 noqa suppression in test_cdb.py (importorskip must come first) Memo – issues not fixed (would break public API or need larger refactor): - N802/N803/N806: physics coordinate names (R, Z, X, Y, B_tor, …) - C901/PLR0913/PLR0915: physics algorithms are inherently complex - E501 (18 remaining at 120 chars): all in long docstring prose - F841/RUF059: some unpacked variables are intentional - ANN*: type annotations largely absent; tracked separately https://claude.ai/code/session_01NoBcY348U4MKRmAgQHCx1w
Equilibrium must be imported last since equilibrium.py depends on Coordinates, FluxFunctions, Surface and SurfaceFunctions already being registered on the pleque.core module object. https://claude.ai/code/session_01NoBcY348U4MKRmAgQHCx1w
…-dependent Equilibrium must be imported last to avoid circular imports; isort cannot reorder these freely. https://claude.ai/code/session_01NoBcY348U4MKRmAgQHCx1w
Resolve conflicts with the develop refactor (PR #69 split of Equilibrium.__init__ into helpers and dead-code removal): - equilibrium.py: take develop's _setup_plasma_boundary() extraction; the inline boundary block my branch only lint-touched now lives in the dedicated helper. Re-applied the UP032 f-string fix there. - equi_tools.py: take develop's _make_psi_grad_sq() helper that replaces the duplicated nested psi_xysq_func. - _test_gfile_loader.py: accept develop's deletion (dead code, no references); my branch had only lint-touched it. - io/__init__.py: develop added public-API re-exports; sorted imports and added the module to ruff F401 per-file-ignores. ruff passes; full test suite green (775 passed, 37 skipped). https://claude.ai/code/session_01NoBcY348U4MKRmAgQHCx1w
Add ruff and ty linting; replace flake8/pylint; add CI workflows
- GitLab CI: run pytest with --junitxml and expose report.xml via artifacts.reports.junit so results appear in the GitLab test report UI - GitHub Actions: new workflow that installs Poetry, runs pytest with --junitxml, uploads report.xml via actions/upload-artifact, and publishes a check-run summary via dorny/test-reporter https://claude.ai/code/session_01SCWaAYTAKQdf4DpfiuczAM
Add pytest-cov to dev dependencies and run pytest with --cov=pleque --cov-report=xml:coverage.xml in both pipelines. - GitLab CI: exposes coverage.xml via artifacts.reports.coverage_report (Cobertura format) so GitLab renders line-level coverage diffs in MRs - GitHub Actions: uploads coverage.xml as artifact, publishes a coverage summary badge+table via irongut/CodeCoverageSummary, and posts a sticky comment on PRs with the coverage breakdown https://claude.ai/code/session_01SCWaAYTAKQdf4DpfiuczAM
…-ayr3rk ci: store pytest results as artifacts in GitLab and GitHub CI
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…loading Extract magic numbers (grid resolutions, solver tolerances, search heuristics, spline parameters, plotting and IO writer defaults) from equilibrium.py, equi_tools.py, surfaces.py, field_line_tracers.py, plotting.py, geqdsk.py and omas.py into pleque.config.Settings, organized into per-topic sections (grid, splines, critical_points, lcfs, field_line_tracing, flux_surfaces, plotting, io). Function arguments still override settings per call; settings are now read at use time instead of being captured at import time. Settings load from the first existing of: $PLEQUE_CONFIG_FILE, ./pleque.toml, the per-user config dir (%APPDATA%\pleque on Windows, $XDG_CONFIG_HOME/pleque elsewhere), or a [tool.pleque] table in the nearest pyproject.toml, with PLEQUE_-prefixed environment variables taking precedence over files. The winning file is recorded on the settings object (config_source, config_files_consulted) and reload_settings() re-reads the configuration at runtime. The old flat fields moved into sections: npsi_grid -> flux_surfaces.n_psi, psin0 -> flux_surfaces.psi_n_min, nr_grid/nz_grid -> lcfs.search_grid_nr/nz (the None sentinel is gone; defaults are 700/1200 directly). Also fix lcfs_field_line ignoring its vect_no and xp_shift arguments (they were hardcoded in the track_plasma_boundary call). Add tests for defaults, precedence, source tracking, env vars and reload; document the feature in docs/source/configuration.rst (kept in sync by a test) and README. pydantic-settings gains the toml extra for Python 3.10 support. https://claude.ai/code/session_01HRFoBXP3uhqR5cZuURzdhS
…magic-numbers-7rq85x Centralize algorithm parameters in grouped Settings with config-file loading
Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.4 to 9.0.3. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@7.4.4...9.0.3) --- updated-dependencies: - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com>
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Bumps pytest from 7.4.4 to 9.0.3.
Release notes
Sourced from pytest's releases.
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a7d58d7Prepare release version 9.0.3089d981Merge pull request #14366 from bluetech/revert-14193-backport8127eafRevert "Fix: assertrepr_compare respects dict insertion order (#14050) (#14193)"99a7e60Merge pull request #14363 from pytest-dev/patchback/backports/9.0.x/95d8423bd...ddee02aMerge pull request #14343 from bluetech/cve-2025-71176-simple74eac69doc: Update training info (#14298) (#14301)f92dee7Merge pull request #14267 from pytest-dev/patchback/backports/9.0.x/d6fa26c62...7ee58acMerge pull request #12378 from Pierre-Sassoulas/fix-implicit-str-concat-and-d...37da870Merge pull request #14259 from mitre88/patch-4 (#14268)c34bfa3Add explanation for string context diffs (#14257) (#14266)