Conversation
Tests: add spec-guided TDD support conftest Add tests/conftest.py from the spec-guided-tdd skill, formatted to ProteoPy's black/flake8 standards. It only affects test modules marked `pytestmark = pytest.mark.spec_guided` (e.g. tests/pl/test_upset.py); all other tests run unchanged. - `pytest` (default, CI) runs the holdout and randomized tests and deselects the `_IMP` mirrors - `pytest --implementer` runs the `_IMP` and randomized tests with obscured failure output, for implementation sessions - `--seed N` reproduces randomized inputs (seed printed in the header) - provides the `rng` and `report_input` fixtures - checks test naming and holdout/_IMP pairing
Tests: pl.var_detected_by_cat_upset() Add a spec-guided test suite for var_detected_by_cat_upset() (module marked `spec_guided`, run by tests/conftest.py): - TestVarDetectedByCatUpset: 75 holdout tests plus 9 randomized property and metamorphic tests - TestVarDetectedByCatUpsetIMP: 75 _IMP mirrors on different inputs, run only with `pytest --implementer` Coverage: intersection counts and thresholds (min_count / min_fraction, inclusivity, per-category denominators, empty categories, float edge cases), zero/NaN detection, category order and str coercion, sparse input, non-mutation (incl. views), UpSet construction and rendered axes, print_stats tables (incl. column-name collisions), verbose output, save/show, and argument validation. UpSet calls are observed through spies on the upsetplot class; randomized tests use the seeded rng fixture (reproduce with `--seed N`).
Feature: pl.var_detected_by_cat_upset() Add an UpSet plot of which features (.var) are detected in which categories of an .obs column, e.g. which proteins are found in which tissues. - A feature is a member of a category when it is detected (non-NaN in .X; with zero_to_na=True also non-zero) in enough of that category's observations: min_count (default 1) or min_fraction, inclusive, per category. Setting both raises ValueError. - Features that are members of no category form a "No category" set, always included, also with a count of 0. - Categories follow the default pl order: category order for a Categorical column (unused categories kept), else lexicographic order of the str-coerced values. Values colliding after str coercion raise ValueError. - print_stats prints global, per-intersection and per-category tables; verbose reports the input matrix, threshold and sizes. - Sparse .X is densified with a UserWarning; adata is never modified. - Returns the axes dict of upsetplot's UpSet.plot(). Add upsetplot>=0.9.0,<0.10 as a core dependency. upsetplot 0.9.0 is broken on pandas 3 / numpy >= 2.4, so proteopy.pl.upset patches it on import (dot style defaults, single-category aggregation, count-label positions, all-empty totals warning). The upper bound keeps these patches from hitting an untested upsetplot release. Export via pr.pl, list it under Quality Control in the plotting API docs, and add a HISTORY.md entry.
Docs: plotting tutorial Add a protein-level plotting tutorial on the Karayel et al. (2020) erythropoiesis data, walking through the pr.pl quality-control and exploration plots, each framed by the question it answers: - conventions: ordering samples and groups via ordered Categoricals, missing values vs measured zeros, working with a supplied or returned Axes - coverage and completeness: n_samples_per_category, n_cat1_per_cat2_hist, n_proteins_per_sample, completeness_per_sample, completeness_per_var, var_detected_by_cat_upset (default and min_fraction=1.0 thresholds) - abundance: intensity_hist, intensity_box_per_sample, abundance_rank, box, cv_by_group - structure: sample_correlation_matrix, binary_heatmap, hclustv_profiles_heatmap The notebook ends by checking that the raw intensities are unchanged by the plotting calls. The peptide-level section is a placeholder for a later installment. Outputs are stored in the notebook, as Sphinx does not execute notebooks (nbsphinx_execute = 'never'). The notebook lives in docs/tutorials/ and is linked into the Sphinx source by a symlink; it is listed in tutorials/index.rst.
Documentation build overview
7 files changed ·
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
upset_test_spec.md
upset_function_spec.md