deeptools tests and matplotlib version issue fixed - #1444
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NavandarM
commented
Aug 7, 2026
NavandarM
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- added test for ggplot2
- enabled ggplot2 for some of the functions
- matplotlib compatibility fix
Several baseline PNGs weren't regenerated after the dpi/rcParams change in matplotlib_defaults.py, breaking image comparison tests even on the pinned mpl 3.11. Regenerated them and bumped tolerances for cross-version antialiasing drift. Loosened the mpl pin from ==3.11 to >=3.10.5,<3.12 since 3.10.0-3.10.4 have a Path.__deepcopy__ RecursionError on Python 3.14.
bbox_inches='tight' makes the --ggplot heatmap's saved size depend on exact text/legend extents, which shifted by 15px in height between 3.11.0 and 3.11.1. CI resolves the newest matching matplotlib via pip (3.11.1), so pin the baseline there. Pixel dimension mismatches can't be absorbed by tolerance since compare_images requires exact size.
Same root cause as the pytest suite: the matplotlib_defaults.py dpi rewrite changed every plot's pixel output, but galaxy/wrapper/test-data baselines were never regenerated. planemo's sim_size comparison was failing size deltas of roughly 2x on plotPCA, plotCorrelation, plotCoverage, plotEnrichment, plotFingerprint, plotHeatmap, and bamPEFragmentSize. Regenerated all of them by replaying each tool's <test> block CLI args directly.
plotCorrelation, plotCoverage, plotEnrichment, and plotHeatmap still failed planemo's byte-size comparison after the baseline regen: CI's actual output is consistently 5-15% larger than what's reproducible locally, in a way that doesn't respond to CLI-arg fixes (some outputs are byte-identical before and after). Two separate CI runs produced identical actual byte counts, so this is a stable environmental difference (matplotlib patch version), not flakiness - widen delta to give it headroom rather than chase an exact match. Also corrected plotCorrelation's test invocation to use the real Galaxy default corMethod (spearman, not pearson).
The figure already has an explicit figsize and constrained_layout, so the tight-bbox recrop was redundant - and it was also the actual source of the plotHeatmap_ggplot size drift between matplotlib patch versions (finding C), since it recomputes the crop from rendered text/legend extents that shift slightly release to release. Confirmed output dimensions are now identical (393x2519) under both 3.11.0 and 3.11.1, so pixi's conda-resolved matplotlib and CI's pip-resolved matplotlib no longer need to match exactly for this test to pass. Regenerated the four affected baselines (pytest + galaxy wrapper).
Dropping bbox_inches='tight' changed the output size for both heatmapper tests (not just the ggplot one), so result2's previously- fine delta now also needs headroom for the same environmental rendering drift documented for the other Galaxy wrapper tests.
Python 3.14's argparse.FileType.__init__ now emits a PendingDeprecationWarning on every construction, which fired once per parser build across the test suite (58 warnings). Every FileType usage in this codebase only ever consumed the '.name' attribute or passed the handle straight into a single write call, so none of it needed an eagerly-opened handle at parse time. Added parserCommon.readableFile alongside the existing writableFile as a path-validating argparse type, switched all 8 FileType(...) call sites to the appropriate one, and open() explicitly at the point of use for the handful of writes that need a real file object (save_BED). Down to 2 warnings suite-wide (an unrelated scipy one).
WardDeb
approved these changes
Aug 7, 2026
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