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🟡 Changes recommended
Critical dependency and D1S parsing issues remain, and GitLab connection handling is incomplete.
4 open issues
What changed in this PR
This pull request applies Ruff/isort-style cleanup across the project, updates dependency and documentation configuration, adds CI linting, and includes targeted fixes and regression tests.
Changes:
- Reformats imports, expressions, type annotations, and dataframe handling across source and test modules.
- Adds regression coverage for material headers, D1S irradiation handling, plotting, and tick labels.
- Updates packaging metadata, supported Python versions, documentation installation, and CI workflows.
- Adds Ruff checking and formatting validation to continuous integration.
| File | Summary | Review |
|---|---|---|
tests/run/test_input.py |
Adds material-header and D1S daughter regression tests. | See related issue in src/jade/run/input.py. |
tests/post/test_sim_output.py |
Cleans imports and formatting in simulation-output tests. | No final comment. |
tests/post/test_plotter.py |
Adds plotting and tick-label regression tests. | No final comment. |
tests/post/test_excel_routines.py |
Updates test typing and imports. | No final comment. |
tests/helper/test_openmc.py |
Separates standard-library and third-party imports. | No final comment. |
tests/helper/test_auxiliary_func.py |
Reformats imports and membership checks. | No final comment. |
tests/helper/compatibility_scripts/derive_iter1d_z_coordinates.py |
Adds an ITER coordinate-derivation utility. | No final comment. |
tests/helper/compatibility_scripts/convert_oktavian.py |
Removes an unused import. | No final comment. |
tests/gui/test_post_config_gui.py |
Reformats imports and spacing. | No final comment. |
tests/gui/test_config_gui.py |
Reformats conditional GUI imports. | No final comment. |
tests/config/test_run_config.py |
Removes an unused assignment. | No final comment. |
tests/config/test_raw_config.py |
Reformats imports and removes an unused assignment. | No final comment. |
tests/config/test_excel_config.py |
Simplifies extension matching. | No final comment. |
tests/config/test_atlas_config.py |
Simplifies extension matching. | No final comment. |
tests/app/test_app.py |
Removes an unused import and reformats comments. | No final comment. |
src/jade/run/input.py |
Updates material-header construction and D1S reaction/irradiation handling. | Critical: the specific-reaction path no longer appends the required library suffix before parsing daughter identifiers. |
src/jade/run/benchmark.py |
Removes redundant subprocess work and applies formatting changes. | No final comment. |
src/jade/post/sim_output.py |
Refactors dataframe updates and output handling. | No final comment. |
src/jade/post/raw_processor.py |
Cleans benchmark-selection logic. | No final comment. |
src/jade/post/plotter.py |
Avoids mutating input data and improves tick handling. | No final comment. |
src/jade/post/manipulate_tally.py |
Updates annotations and exception typing. | No final comment. |
src/jade/post/excel_routines.py |
Updates dataframe renaming and MultiIndex handling. | No final comment. |
src/jade/post/atlas.py |
Adds a shared default image-width constant. | No final comment. |
src/jade/helper/openmc.py |
Simplifies dictionary operations and tally processing. | No final comment. |
src/jade/helper/aux_functions.py |
Updates PathLike typing and exception handling. |
No final comment. |
src/jade/helper/__optionals__.py |
Adds import-lint suppressions and reformats logging. | No final comment. |
src/jade/config/status.py |
Simplifies key iteration and boolean returns. | No final comment. |
src/jade/config/run_config.py |
Removes an empty abstract-method body. | No final comment. |
src/jade/config/raw_config.py |
Reorders imports. | No final comment. |
src/jade/config/pp_config.py |
Simplifies YAML extension checks. | No final comment. |
src/jade/config/excel_config.py |
Simplifies mapping membership checks. | No final comment. |
src/jade/config/atlas_config.py |
Simplifies configuration validation. | No final comment. |
src/jade/app/fetch.py |
Adds GitLab timeout and connection handling. | Moderate: connection failures wrapped by python-gitlab can still escape the handler. |
src/jade/app/app.py |
Clarifies variable naming and benchmark iteration. | No final comment. |
pyproject.toml |
Raises the Python minimum, constrains dependencies, and separates optional groups. | Critical: add pydata-sphinx-theme for the configured documentation theme and declare python-docx as a runtime dependency. |
docs/source/usage/installation.rst |
Updates Python support and installation guidance. | No final comment. |
docs/source/requirements.txt |
Removes the standalone documentation requirements file. | No final comment. |
docs/source/conf.py |
Removes an unused import. | No final comment. |
AGENTS.md |
Updates setup, architecture, branching, and CI guidance. | No final comment. |
.readthedocs.yaml |
Installs documentation dependencies from project metadata. | Affected by the missing documentation theme dependency. |
.github/workflows/pytest.yml |
Updates the OS/Python test matrix and coverage configuration. | No final comment. |
.github/workflows/lint.yml |
Adds Ruff checking and formatting validation. | Nit: ruff check does not enable import-sorting rules without selecting I. |
Review effort: Lite
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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