Lint: add codespell#303
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Captures decisions on UV adoption, hatchling build backend, ruff/basedpyright tooling, and three-tier test strategy (unit/contract/e2e). Sequences the work as 17 small PRs ending with a mass reformat. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Per-task implementation plan for the first PR of the modernisation effort. Covers pyproject.toml updates, uv.lock generation, CI/RTD switch to uv, deletion of requirements*.txt / tox.ini / setup.cfg, and developer-doc updates to drop the PYTHONPATH=. pattern. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- Add SPEASY_CORE_HTTP_REWRITE_RULES env to PRs.yml non-3.10 pytest step (previously only on push/scheduled tests.yml — would have hit a non-existent server on PR builds for non-3.10 matrix entries). - Add --with wheel to PRs.yml build step for parity with tests.yml. - Scope flake8 to 'speasy tests' in both workflows (matches Makefile lint target). Avoids silently broadening lint to docs/conf.py and removes the .venv exclusion workaround that was needed when flake8 ran from repo root.
Without UV_PROJECT_ENVIRONMENT, uv creates .venv/ inside the project and RTD's sphinx step (which calls $READTHEDOCS_VIRTUALENV_PATH/bin/python directly) fails with 'python: not found'. Point uv at RTD's venv so the install lands where the runner looks for it.
Classified via devtools/apply_test_markers.py: - 12 files marked unit (pure-logic, no network) - 19 files marked contract (real-server, will be migrated to cassettes in PRs 4-9) Reclassifications during manual review: - test_cache.py: contract -> unit (pure cache-logic, no network or speasy provider use) - test_file_access.py: unit -> contract (uses HTTP via any_loc_open against live servers) test_wasm.py was manually adjusted to place pytestmark at module level (the file's body lives inside a try/except ImportError block, so the script's naive insertion landed at wrong indentation).
…le path and sample across the inventory The flat_inventories.generic_archive lookup uses module attribute access on an instance, not a submodule import. Also, the first N parameters in the flat inventory are clustered by mission, so a fixed time range can miss all of them; sample across the full list instead.
- test_e2e_smoke.test_generic_archive: fail loudly if every candidate raises (was silently skipping, defeating the e2e tier's purpose). - pyproject.toml: drop dead --ignore=setup.py from addopts and document the -m unit override semantics so future contributors don't trip on 'pytest tests/test_amda.py' silently collecting nothing. - contract.yml / e2e.yml: add concurrency groups so a manual run can't overlap with a cron run hammering the same upstream servers. - CONTRIBUTING.rst: add a short note explaining the three test tiers and how to invoke each from local dev.
CI failure (blocking): - unit.yml: 'make doctest' was using system Python (no sphinx in scope). Prefix with 'uv run' so make uses the project venv. Reviewer findings: - wasm_tests.yml: pytest tests/test_wasm.py without -m collected 0 tests under the new addopts default (test_wasm.py is contract-marked). Add -m '' to override. - CLAUDE.md: examples like 'uv run pytest tests/test_amda.py' silently collected 0 tests under -m unit default. Replaced with tier-aware examples and added -m '' for the all-tests case. - unit.yml: only sync --group docs on the coverage runner that needs it, not on every matrix entry.
nbsphinx requires the system pandoc binary (not the Python pandoc wrapper that's in the docs dependency group). PR 1's tests.yml had 'sudo apt install -y texlive pandoc' before make doctest; my unit.yml rewrite in PR 2 dropped that line, so the doctest job failed with 'nbsphinx.NotebookError: PandocMissing in examples/AMDA.ipynb'. Restored as a separate apt step on the coverage runner.
The doctest step's examples reference all data providers (cdpp3dview included) and live inventories. The job-level SPEASY_CORE_DISABLED_PROVIDERS='cdpp3dview' makes the inventory tree's cdpp3dview attribute missing during doctest, surfacing as 'types.SimpleNamespace object has no attribute cdpp3dview' and a chain of NameErrors for variables defined in earlier doctest blocks. Original tests.yml overrode SPEASY_CORE_DISABLED_PROVIDERS="" on the combined pytest+doctest step, plus set HTTP_REWRITE_RULES (re-routes the placeholder URL used in some examples to LPP's mirror) and USER_AGENT. My PR 2 rewrite dropped the env block; restoring it on the doctest step.
Pandas now prints its public name in type() repr ('pandas.DataFrame')
rather than the internal module path ('pandas.core.frame.DataFrame').
The user/numpy.rst doctest was written against the old form.
Surfaced now that uv.lock pins a recent pandas; pip-installed envs
were getting older pandas where the old form still applied.
Automatic fixes from codespell -w plus one manual fix for 'Cant'' → 'Can't' in speasy/products/variable.py (codespell's auto-write skips apostrophe-adjacent corrections). Affects 9 files: HISTORY.rst, docstrings in speasy/core/proxy, speasy/core/impex, speasy/core/hapi, speasy/data_providers/amda, speasy/products/catalog, speasy/products/variable, and a test assertion message in tests/test_hapi_codecs.
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| def version_to_str(v: Union[Version, datetime.datetime]) -> str: | ||
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #303 +/- ##
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- Coverage 85.10% 74.65% -10.46%
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Files 69 82 +13
Lines 4834 5077 +243
Branches 668 693 +25
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- Hits 4114 3790 -324
- Misses 479 1046 +567
Partials 241 241
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Summary
Twelfth PR of the modernisation effort. Adds codespell — a mature spellchecker for English misspellings in source/comments/docs — and wires it into CI alongside ruff.
Plan:
docs/superpowers/plans/2026-05-15-pr12-codespell.md.Stacked on PR #302 (ruff config).
What this PR does
pyproject.toml: adds[tool.codespell]withskipglobs (binary cassettes/CDFs, lockfiles, generated docs, virtualenv, planning artifacts) andignore-words-list = "tha,thb,thc,thd,nd"(THEMIS satellite identifiers and "N-D" for N-dimensional).HISTORY.rst:maping → mapping,cleanned → cleaned,improvments → improvementsminimun → minimum,begining → beginning,unkown → unknown,goup → group,identic → identical,connexion → connection(English standard)speasy/products/variable.py:Cant' → Can't(manual fix; codespell auto-write skips apostrophe-adjacent corrections)tests/test_hapi_codecs.py:writen → writtenlint.yml(after the ruff step),Makefilelinttarget, and theCLAUDE.mdCommon Commands.What this PR does NOT do
pytest-sugarwas already added in PR 3's dev group (mentioned in the spec under PR 12 grouping; no work needed here).Test plan
lint.ymlgreen (ruff + codespell)unit.ymlgreen (no test behavior changes — typo fixes are doc/error-message text only)make lintexits 0